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Macias SL, Palmer O, Simonovich JA, Clark RA, Hudalla GA, Keselowsky BG. Immunometabolic Approaches Mitigating Foreign Body Response and Transcriptome Characterization of the Foreign Body Capsule. Adv Healthc Mater 2024:e2400602. [PMID: 39148172 DOI: 10.1002/adhm.202400602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 07/08/2024] [Indexed: 08/17/2024]
Abstract
Directing immunometabolism presents new opportunities to modulate key cell types associated with the formation of foreign body response (FBR) capsule. Contrasting approaches directing immunometabolism are investigated to mitigate FBR: a broadly suppressive metabolic inhibitor (MI) cocktail comprised of 2-deoxyglucose (2-DG), metformin, and 6-diazo-5-oxo-l-norleucine (DON) with daily systemic dosing regimen, and local weekly injection of the more narrowly focused tryptophan catabolizing IDO-Gal3 fusion protein. Treatments significantly decrease FBR capsule formed around subcutaneously implanted cellulose disks. MI cocktail results in a substantially thinner FBR capsule (40% of control), while weekly local injection of IDO-Gal3 also results in a thinner FBR capsule (69% of control). RNA-sequencing capsule transcripts reveal MI cocktail promotes quiescence, with decreased antigen processing and presentation, T helper subset differentiation, and cytokine-cytokine receptor pathway. IDO-Gal3 promotes pro-regenerative, alternatively activated M2-like macrophages and T helper 2 cells, with increased expression of type 2 response-associated genes (Il4, Il13, Arg1, Mrc1, Chil3, Gata3). IDO-Gal3 decreases pro-inflammatory innate sensing pathways, and C-type lectin receptor, NOD-like receptor, RIG-I-like receptor, and Toll-like receptor signaling. This work helps define key gene targets and pathways concomitantly regulated in the FBR capsule during immunometabolic modulation compared to control FBR capsule.
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Affiliation(s)
- Sabrina L Macias
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL, 32611, USA
| | - Olivia Palmer
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL, 32611, USA
| | - Jennifer A Simonovich
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL, 32611, USA
| | - Ryan A Clark
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL, 32611, USA
| | - Gregory A Hudalla
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL, 32611, USA
| | - Benjamin G Keselowsky
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL, 32611, USA
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
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2
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Harada-Kagitani S, Kouchi Y, Shinomiya Y, Kodama M, Ohira G, Matsubara H, Ikeda JI, Kishimoto T. Keratin 6A Is Expressed at the Invasive Front and Enhances the Progression of Colorectal Cancer. J Transl Med 2024; 104:102075. [PMID: 38729352 DOI: 10.1016/j.labinv.2024.102075] [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: 11/30/2023] [Revised: 04/25/2024] [Accepted: 05/01/2024] [Indexed: 05/12/2024] Open
Abstract
Keratins (KRTs) are intermediate filament proteins in epithelial cells, and they are important for cytoskeletal organization. KRT6A, classified as a type II KRT, is normally expressed in stratified squamous epithelium and squamous cell carcinomas. Little is known about the expression and role of KRT6A in adenocarcinomas. We investigated the clinicopathologic and molecular biological significance of KRT6A in colorectal adenocarcinoma. Immunostaining of colorectal adenocarcinoma cases treated at our institution demonstrated that KRT6A showed significantly stronger expression at the invasive front than that at the tumor center (P < .0001). The high KRT6A-expression cases (n = 47) tended to have a high budding grade associated with significantly worse prognoses. A multivariate analysis revealed that the KRT6A expression status was an independent prognostic factor for overall survival (P = .0004), disease-specific survival (P = .0097), and progression-free survival (P = .0033). The correlation between KRT6A and patient prognoses was also validated in an external cohort from a published data set. To determine the function of KRT6A in vitro, KRT6A was overexpressed in 3 colon cancer cell lines: DLD-1, SW620, and HCT 116. KRT6A overexpression increased migration and invasion in DLD-1 but did not in SW620 and HCT116. In 3-dimensional sphere-forming culture, KRT6A expression enhanced the irregular protrusion around the spheroid in DLD-1. Our findings in this study indicated that KRT6A expression is a valuable prognostic marker of colorectal cancer and KRT6A may be involved the molecular mechanism in the progression of invasive areas of colorectal cancer.
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Affiliation(s)
- Sakurako Harada-Kagitani
- Department of Molecular Pathology, Chiba University Graduate School of Medicine, Chiba, Japan; Department of Pathology, Chiba University Hospital, Chiba, Japan
| | - Yusuke Kouchi
- Department of Molecular Pathology, Chiba University Graduate School of Medicine, Chiba, Japan; Department of Pathology, Chiba University Hospital, Chiba, Japan
| | - Yoshiki Shinomiya
- Department of Molecular Pathology, Chiba University Graduate School of Medicine, Chiba, Japan; Department of Pathology, Chiba University Hospital, Chiba, Japan
| | - Makoto Kodama
- Department of Pathology, Tokyo Yamate Medical Center, Tokyo, Japan
| | - Gaku Ohira
- Department of Frontier Surgery, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Hisahiro Matsubara
- Department of Frontier Surgery, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Jun-Ichiro Ikeda
- Department of Pathology, Chiba University Hospital, Chiba, Japan; Department of Diagnostic Pathology, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Takashi Kishimoto
- Department of Molecular Pathology, Chiba University Graduate School of Medicine, Chiba, Japan.
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3
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Du W, Xia X, Gou Q, Xie Y, Gao L. Comprehensive review regarding the association of E2Fs with the prognosis and immune infiltrates in human head and neck squamous cell carcinoma. Asian J Surg 2024; 47:2106-2121. [PMID: 38320907 DOI: 10.1016/j.asjsur.2024.01.130] [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: 06/01/2023] [Revised: 12/14/2023] [Accepted: 01/19/2024] [Indexed: 02/08/2024] Open
Abstract
E2F transcription factors (E2Fs) are a group of genes that encode a family of transcription factors. They have been identified as being involved in the tumor progression of various cancer types. However, little is known about the expression level, genetic variation, molecular mechanism, and prognostic value and immune infiltration of different E2Fs in HNSCC.In this study, we utilized multiple databases to investigate the mRNA expression level, genetic alteration, and biological function of E2Fs in HNSCC patients. Then, the relationship between E2Fs expression and its association with the occurrence, progress, prognosis, and immune cell infiltration in patients with HNSCC was evaluated. We found that all eight E2Fs were higher expressed in HNSCC tissues than in normal tissues, and the expression levels of E2F1/2/3/4/5/6/8 were also associated with the stage and grade of HNSCC. The abnormal expression of E2F1/2/4/8 in HNSCC patients is related to the clinical outcome. The expression of E2Fs was statistically correlated with the immune cell infiltration in HNSCC and the infiltration of B cells and CD8+ T cells were positively associated with better OS in HNSCC patients. Furthermore, we verified the E2F2 at the tissue level in the validation experiment. Our study may provide novel insights into the choice of immunotherapy targets and potential prognostic biomarkers in HNSCC patients.
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Affiliation(s)
- Wei Du
- Department of Targetting Therapy & Immunology, Cancer Cencer, West China Hospital, Sichuan University, Chengdu, China
| | - Xueming Xia
- Division of Head & Neck Tumor Multimodaligy Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Qiheng Gou
- Division of Head & Neck Tumor Multimodaligy Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yuxin Xie
- Division of Head & Neck Tumor Multimodaligy Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Lanyang Gao
- Academician (Expert) Workstation of Sichuan Province, Metabolic Hepatobiliary and Pancreatic Diseases Key Laboratory of Luzhou City, The Affiliated Hospital of Southwest Medical University, Sichuan, China.
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Maggisano V, Capriglione F, Mio C, Bulotta S, Damante G, Russo D, Celano M. RNA Profile of Cell Bodies and Exosomes Released by Tumorigenic and Non-Tumorigenic Thyroid Cells. Int J Mol Sci 2024; 25:1407. [PMID: 38338696 PMCID: PMC10855121 DOI: 10.3390/ijms25031407] [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: 12/22/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
Tumor cells release exosomes, extracellular vesicle containing various bioactive molecules such as protein, DNA and RNA. The analysis of RNA molecules packaged in exosomes may provide new potential diagnostic or prognostic tumor biomarkers. The treatment of radioiodine-refractory aggressive thyroid cancer is still an unresolved clinical challenge, and the search for biomarkers that are detectable in early phase of the disease has become a fundamental goal for thyroid cancer research. By using transcriptome analysis, this study aimed to analyze the gene expression profiles of exosomes secreted by a non-tumorigenic thyroid cell line (Nthy-ori 3.1-exo) and a papillary thyroid cancer (TPC-1-exo) cell line, comparing them with those of cell bodies (Nthy-ori 3.1-cells and TPC-1-cells). A total of 9107 transcripts were identified as differentially expressed when comparing TPC-1-exo with TPC-1-cells and 5861 when comparing Nthy-ori 3.1-exo with Nthy-ori 3.1-cells. Among them, Sialic acid-binding immunoglobulin-like lectins 10 and 11 (SIGLEC10, SIGLEC11) and Keratin-associated protein 5 (KRTAP5-3) transcripts, genes known to be involved in cancer progression, turned out to be up-regulated only in TPC-1-exo. Gene ontology analysis revealed significantly enriched pathways, and only in TPC-1-exo were the differential expressed genes associated with an up-regulation in epigenetic processes. These findings provide a proof of concept that some mRNA species are specifically packaged in tumor-cell-derived exosomes and may constitute a starting point for the identification of new biomarkers for thyroid tumors.
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Affiliation(s)
- Valentina Maggisano
- Department of Health Sciences, University "Magna Graecia" of Catanzaro, 88100 Catanzaro, Italy
| | - Francesca Capriglione
- Department of Health Sciences, University "Magna Graecia" of Catanzaro, 88100 Catanzaro, Italy
| | - Catia Mio
- Department of Medical and Biological Sciences, University of Udine, 33100 Udine, Italy
| | - Stefania Bulotta
- Department of Health Sciences, University "Magna Graecia" of Catanzaro, 88100 Catanzaro, Italy
| | - Giuseppe Damante
- Department of Medical and Biological Sciences, University of Udine, 33100 Udine, Italy
| | - Diego Russo
- Department of Health Sciences, University "Magna Graecia" of Catanzaro, 88100 Catanzaro, Italy
| | - Marilena Celano
- Department of Health Sciences, University "Magna Graecia" of Catanzaro, 88100 Catanzaro, Italy
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Guo L, Liu Y, Yang T, Wang G, Liu J, Li S, Liu B, Cai J. CAV1 and KRT5 are potential targets for prostate cancer. Medicine (Baltimore) 2023; 102:e36473. [PMID: 38065913 PMCID: PMC10713156 DOI: 10.1097/md.0000000000036473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 11/14/2023] [Indexed: 12/18/2023] Open
Abstract
Prostate cancer is the most common malignant tumor of male urogenital system that occurs in prostate epithelium. However, relationship between CAV1 and KRT5 and prostate cancer remains unclear. The prostate cancer datasets GSE114740 and GSE200879 were downloaded from Gene Expression Omnibus generated by GPL11154 and GPL32170. De-batch processing was performed, differentially expressed genes (DEGs) were screened, and weighted gene co-expression network analysis. The construction and analysis of protein-protein interaction network, functional enrichment analysis, gene set enrichment analysis. Gene expression heat map was drawn and immune infiltration analysis was performed. Comparative toxicogenomics database analysis were performed to find the disease most related to core gene. In addition, the cell experiment was performed to verify the role of CAV1 and KRT5 by western blot. Divided into 4 groups: control, prostate cancer, prostate cancer-over expression, and prostate cancer- knock out. TargetScan screened miRNAs that regulated central DEGs; 770 DEGs were identified. According to Gene Ontology analysis, they were mainly concentrated in actin binding and G protein coupled receptor binding. In Kyoto Encyclopedia of Gene and Genome analysis, they were mainly concentrated in PI3K-Akt signal pathway, MAPK signal pathway, and ErbB signal pathway. The intersection of enrichment terms of differentially expressed genes and GOKEGG enrichment terms was mainly concentrated in ErbB signaling pathway and MAPK signaling pathway. Three important modules were generated. The protein-protein interaction network obtained 8 core genes (CAV1, BDNF, TGFB3, FGFR1, PRKCA, DLG4, SNAI2, KRT5). Heat map of gene expression showed that core genes (CAV1, TGFB3, FGFR1, SNAI2, KRT5) are highly expressed in prostate cancer tissues and low in normal tissues. Comparative toxicogenomics database analysis showed that core genes (CAV1, TGFB3, FGFR1, SNAI2, KRT5) were associated with prostate tumor, cancer, tumor metastasis, necrosis, and inflammation. CAV1 and KRT5 are up-regulated in prostate cancer. CAV1 and KRT5 are highly expressed in prostate cancer. The higher expression of CAV1 and KRT5, the worse prognosis.
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Affiliation(s)
- Liuxiong Guo
- Department of Graduate School, Hebei Medical University, Shijiazhuang, China
- Department of Surgery and Urology, Hebei General Hospital, Shijiazhuang, China
| | - Yixuan Liu
- Department of Rheumatology and Immunology, Hebei General Hospital, Shijiazhuang, China
| | - Tao Yang
- Department of Surgery and Urology, Hebei General Hospital, Shijiazhuang, China
| | - Gang Wang
- Department of Surgery and Urology, Hebei General Hospital, Shijiazhuang, China
| | - Junjiang Liu
- Department of Surgery and Urology, Hebei General Hospital, Shijiazhuang, China
| | - Suwei Li
- YETEM Biotechnology Hebei Corporation, Ltd., Zhengding Area of Hebei Free Trade Zone, Shijiazhuang, China
| | - Bin Liu
- Department of Urology Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang City, Hebei, China
| | - Jianhui Cai
- Department of Graduate School, Hebei Medical University, Shijiazhuang, China
- YETEM Biotechnology Hebei Corporation, Ltd., Zhengding Area of Hebei Free Trade Zone, Shijiazhuang, China
- Department of Surgery, Department of Oncology & Immunotherapy, Hebei General Hospital, Shijiazhuang, China
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6
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Litman T, Stein WD. Ancient lineages of the keratin-associated protein (KRTAP) genes and their co-option in the evolution of the hair follicle. BMC Ecol Evol 2023; 23:7. [PMID: 36941546 PMCID: PMC10029157 DOI: 10.1186/s12862-023-02107-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 02/23/2023] [Indexed: 03/23/2023] Open
Abstract
BLAST searches against the human genome showed that of the 93 keratin-associated proteins (KRTAPs) of Homo sapiens, 53 can be linked by sequence similarity to an H. sapiens metallothionein and 16 others can be linked similarly to occludin, while the remaining KRTAPs can themselves be linked to one or other of those 69 directly-linked proteins. The metallothionein-linked KRTAPs comprise the high-sulphur and ultrahigh-sulphur KRTAPs and are larger than the occludin-linked set, which includes the tyrosine- and glycine-containing KRTAPs. KRTAPs linked to metallothionein appeared in increasing numbers as evolution advanced from the deuterostomia, where KRTAP-like proteins with strong sequence similarity to their mammalian congeners were found in a sea anemone and a starfish. Those linked to occludins arose only with the later-evolved mollusca, where a KRTAP homologous with its mammalian congener was found in snails. The presence of antecedents of the mammalian KRTAPs in a starfish, a sea anemone, snails, fish, amphibia, reptiles and birds, all of them animals that lack hair, suggests that some KRTAPs may have a physiological role beyond that of determining the characteristics of hair fibres. We suggest that homologues of these KRTAPs found in non-hairy animals were co-opted by placodes, formed by the ectodysplasin pathway, to produce the first hair-producing cells, the trichocytes of the hair follicles.
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Affiliation(s)
- Thomas Litman
- Department of Immunology and Microbiology, University of Copenhagen, Mærsk Tower 07-12-70 Nørre Allé 14, 2200, Copenhagen N, Denmark
| | - Wilfred D Stein
- Silberman Institute of Life Sciences, Hebrew University, 91904, Jerusalem, Israel.
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7
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Ährlund-Richter A, Holzhauser S, Dalianis T, Näsman A, Mints M. Whole-Exome Sequencing of HPV Positive Tonsillar and Base of Tongue Squamous Cell Carcinomas Reveals a Global Mutational Pattern along with Relapse-Specific Somatic Variants. Cancers (Basel) 2021; 14:cancers14010077. [PMID: 35008243 PMCID: PMC8750256 DOI: 10.3390/cancers14010077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 02/06/2023] Open
Abstract
Simple Summary To better prevent/combat recurrence and identify predictive/targetable markers upon diagnosis, we performed whole-exome sequencing (WES) of primary tumours and relapses of human papillomavirus positive (HPV+) tonsillar and base of tongue cancer (TSCC/BOTSCC) on patients treated with curative intent, with and without relapse. A specific deletion in the CDC27 gene was observed only in the primaries of 5/17 patients that recurred but in none of the 18 patients without recurrence. Furthermore, three specific variants and 26 mutated genes enriched in mucins were identified in at least 30% of all primaries irrespective of recurrence. To conclude, a specific CDC27 deletion could be specific for recurrent HPV+ TSCC/BOTSCC, while BCLAF1, AQP7 and other globally mutated genes could be of significance for further investigation. Abstract To identify predictive/targetable markers in human papillomavirus positive (HPV+) tonsillar and base of tongue cancer (TSCC/BOTSCC), whole-exome sequencing (WES) of tumours of patients with/without recurrence was performed. Forty primary tumours and adjacent normal tissue were separated by micro-dissection from formalin-fixed paraffin-embedded tissue from patients treated with curative intent 2000–2014 at Karolinska University Hospital. Successful sequencing was obtained in primary tumours of 18 patients without and primaries of 17 with local or distant recurrence, as well as in 10 corresponding recurrences (i.e., five local relapses and five distant metastases) from these 17 patients. One variant—a high-impact deletion in the CDC27 gene—was observed only in primaries of 5/17 patients that had a recurrence after full treatment but in none of those without recurrence. In addition, 3 variants and 26 mutated genes, including CDC27, BCLAF1 and AQP7, were present in at least 30% of all primary tumours independent of prognosis. To conclude, a CDC27 deletion was specific and found in ~30% of samples from patients with a local relapse/distant metastasis and could, therefore, potentially be a prospective marker to predict prognosis. Commonly mutated genes, such as BCLAF1, should be further studied in the context of targeted therapy.
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Affiliation(s)
- Andreas Ährlund-Richter
- Department of Oncology-Pathology, Karolinska Institutet, Karolinska University Hospital, 171 64 Stockholm, Sweden; (A.Ä.-R.); (S.H.); (T.D.)
| | - Stefan Holzhauser
- Department of Oncology-Pathology, Karolinska Institutet, Karolinska University Hospital, 171 64 Stockholm, Sweden; (A.Ä.-R.); (S.H.); (T.D.)
| | - Tina Dalianis
- Department of Oncology-Pathology, Karolinska Institutet, Karolinska University Hospital, 171 64 Stockholm, Sweden; (A.Ä.-R.); (S.H.); (T.D.)
| | - Anders Näsman
- Department of Oncology-Pathology, Karolinska Institutet, Karolinska University Hospital, 171 64 Stockholm, Sweden; (A.Ä.-R.); (S.H.); (T.D.)
- Department of Clinical Pathology, CCK R8:02, Karolinska University Hospital, 171 64 Stockholm, Sweden
- Correspondence: (A.N.); (M.M.)
| | - Michael Mints
- Department of Oncology-Pathology, Karolinska Institutet, Karolinska University Hospital, 171 64 Stockholm, Sweden; (A.Ä.-R.); (S.H.); (T.D.)
- Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, 171 64 Stockholm, Sweden
- Department of Surgical and Perioperative Science, Urology and Andrology, Umeå University, 907 36 Umeå, Sweden
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
- Correspondence: (A.N.); (M.M.)
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8
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Ye R, Liu D, Guan H, AiErken N, Fang Z, Shi Y, Zhang Y, Wang S. AHNAK2 promotes thyroid carcinoma progression by activating the NF-κB pathway. Life Sci 2021; 286:120032. [PMID: 34627772 DOI: 10.1016/j.lfs.2021.120032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 10/03/2021] [Accepted: 10/03/2021] [Indexed: 02/06/2023]
Abstract
Thyroid carcinoma metastasis is the main reason for treatment failure; therefore, understanding the regulatory mechanisms of thyroid carcinoma metastasis is critical to treat patients with thyroid carcinoma. The present study aimed to investigate the role of AHNAK Nucleoprotein 2 (AHNAK2) in thyroid carcinoma metastasis. AHNAK2 was found to be upregulated in thyroid carcinoma tissues, especially in metastatic thyroid carcinoma tissues. Patients with high AHNAK2 expression had poor prognosis. AHNAK2 knockdown inhibited thyroid carcinoma migration, invasion, and metastasis. Mechanistic analysis showed that AHNAK2 knockdown reduced thyroid carcinoma progression by inhibiting nuclear factor kappa B (NF-κB) pathway activity. The results identified a novel target to treat metastatic thyroid carcinoma.
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Affiliation(s)
- Runyi Ye
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Dongwei Liu
- Department of General Practice,The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Hongyu Guan
- Department of Endocrinology and Diabetes Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - NiJiati AiErken
- Department of Breast and Thyroid Surgery, The Seventh Affiliated Hospital, Sun Yat-sen University, ShenZhen 518107, China
| | - Zeng Fang
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yawei Shi
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yunjian Zhang
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China.
| | - Shenming Wang
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China.
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9
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Cancer Cell Invasion and Metastasis in Zebrafish Models (Danio rerio). Methods Mol Biol 2021; 2294:3-16. [PMID: 33742390 DOI: 10.1007/978-1-0716-1350-4_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Cancer cell vascular invasion and extravasation at metastatic sites are hallmarks of malignant progression of cancer and associated with poor disease outcome. Here we describe an in vivo approach to study the invasive ability of cancer cells into the vasculature and their hematogenous metastatic seeding in zebrafish (Danio rerio). In one approach, extravasation of fluorescently labeled cancer cells is monitored in zebrafish embryos whose vasculature is marked by a contrasting fluorescent reporter. After injection into the precardiac sinus of 2-day-old embryos, cancer cells can extravasate from the vasculature into tissues over the next few days. Extravasated cancer cells are identified and counted in live embryos via fluorescence microscopy. In a second approach, intravasation of cancer cells can be evaluated by changing their injection site to the yolk sac of zebrafish embryos. In addition to monitoring the impact of drivers of malignant progression, candidate inhibitors can be studied in this in vivo model system for their efficacy as well as their toxicity for the host.
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10
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Sharif GM, Campbell MJ, Nasir A, Sengupta S, Graham GT, Kushner MH, Kietzman WB, Schmidt MO, Pearson GW, Loudig O, Fineberg S, Wellstein A, Riegel AT. An AIB1 Isoform Alters Enhancer Access and Enables Progression of Early-Stage Triple-Negative Breast Cancer. Cancer Res 2021; 81:4230-4241. [PMID: 34135000 DOI: 10.1158/0008-5472.can-20-3625] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 04/23/2021] [Accepted: 06/08/2021] [Indexed: 02/06/2023]
Abstract
AIB1Δ4 is an N-terminally truncated isoform of the oncogene amplified in breast cancer 1 (AIB1) with increased expression in high-grade human ductal carcinoma in situ (DCIS). However, the role of AIB1Δ4 in DCIS malignant progression has not been defined. Here we CRISPR-engineered RNA splice junctions to produce normal and early-stage DCIS breast epithelial cells that expressed only AIB1Δ4. These cells showed enhanced motility and invasion in 3D cell culture. In zebrafish, AIB1Δ4-expressing cells enabled invasion of parental cells when present in a mixed population. In mouse xenografts, a subpopulation of AIB1Δ4 cells mixed with parental cells enhanced tumor growth, recurrence, and lung metastasis. AIB1Δ4 chromatin immunoprecipitation sequencing revealed enhanced binding to regions including peroxisome proliferator-activated receptor (PPAR) and glucocorticoid receptor (GR) genomic recognition sites. H3K27ac and H3K4me1 genomic engagement patterns revealed selective activation of breast cancer-specific enhancer sites by AIB1Δ4. AIB1Δ4 cells displayed upregulated inflammatory response genes and downregulated PPAR signaling gene expression patterns. In the presence of AIB1Δ4 enabler cells, parental cells increased NF-κB and WNT signaling. Cellular cross-talk was inhibited by the PPARγ agonist efatutazone but was enhanced by treatment with the GR agonist dexamethasone. In conclusion, expression of the AIB1Δ4-selective cistrome in a small subpopulation of cells triggers an "enabler" phenotype hallmarked by an invasive transcriptional program and collective malignant progression in a heterogeneous tumor population. SIGNIFICANCE: A minor subset of early-stage breast cancer cells expressing AIB1Δ4 enables bulk tumor cells to become invasive, suggesting that selective eradication of this population could impair breast cancer metastasis.
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Affiliation(s)
- Ghada M Sharif
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, District of Columbia
| | - Moray J Campbell
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, Ohio
| | - Apsra Nasir
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, District of Columbia
| | - Surojeet Sengupta
- The Hormel Institute, University of Minnesota, Medical Research Center, Austin, Minnesota
| | - Garrett T Graham
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, District of Columbia
| | - Max H Kushner
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, District of Columbia
| | - William B Kietzman
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, District of Columbia
| | - Marcel O Schmidt
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, District of Columbia
| | - Gray W Pearson
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, District of Columbia
| | - Olivier Loudig
- Hackensack Meridian Health Center for Discovery and Innovation, Nutley, New Jersey
| | - Susan Fineberg
- Department of Pathology, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York
| | - Anton Wellstein
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, District of Columbia
| | - Anna T Riegel
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, District of Columbia.
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11
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Mishra YG, Manavathi B. Focal adhesion dynamics in cellular function and disease. Cell Signal 2021; 85:110046. [PMID: 34004332 DOI: 10.1016/j.cellsig.2021.110046] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 05/13/2021] [Indexed: 02/06/2023]
Abstract
Acting as a bridge between the cytoskeleton of the cell and the extra cellular matrix (ECM), the cell-ECM adhesions with integrins at their core, play a major role in cell signalling to direct mechanotransduction, cell migration, cell cycle progression, proliferation, differentiation, growth and repair. Biochemically, these adhesions are composed of diverse, yet an organised group of structural proteins, receptors, adaptors, various enzymes including protein kinases, phosphatases, GTPases, proteases, etc. as well as scaffolding molecules. The major integrin adhesion complexes (IACs) characterised are focal adhesions (FAs), invadosomes (podosomes and invadopodia), hemidesmosomes (HDs) and reticular adhesions (RAs). The varied composition and regulation of the IACs and their signalling, apart from being an integral part of normal cell survival, has been shown to be of paramount importance in various developmental and pathological processes. This review per-illustrates the recent advancements in the research of IACs, their crucial roles in normal as well as diseased states. We have also touched on few of the various methods that have been developed over the years to visualise IACs, measure the forces they exert and study their signalling and molecular composition. Having such pertinent roles in the context of various pathologies, these IACs need to be understood and studied to develop therapeutical targets. We have given an update to the studies done in recent years and described various techniques which have been applied to study these structures, thereby, providing context in furthering research with respect to IAC targeted therapeutics.
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Affiliation(s)
- Yasaswi Gayatri Mishra
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - Bramanandam Manavathi
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India.
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12
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Ramroach S, John M, Joshi A. Lung cancer type classification using differentiator genes. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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13
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Xiao J, Glasgow E, Agarwal S. Zebrafish Xenografts for Drug Discovery and Personalized Medicine. Trends Cancer 2020; 6:569-579. [PMID: 32312681 DOI: 10.1016/j.trecan.2020.03.012] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/18/2020] [Accepted: 03/24/2020] [Indexed: 02/06/2023]
Abstract
Cancer is the second leading cause of death in the world. Given that cancer is a highly individualized disease, predicting the best chemotherapeutic treatment for individual patients can be difficult. Ex vivo models such as mouse patient-derived xenografts (PDX) and organoids are being developed to predict patient-specific chemosensitivity profiles before treatment in the clinic. Although promising, these models have significant disadvantages including long growth times that introduce genetic and epigenetic changes to the tumor. The zebrafish xenograft assay is ideal for personalized medicine. Imaging of the small, transparent fry is unparalleled among vertebrate organisms. In addition, the speed (5-7 days) and small patient tissue requirements (100-200 cells per animal) are unique features of the zebrafish xenograft model that enable patient-specific chemosensitivity analyses.
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Affiliation(s)
- Jerry Xiao
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Eric Glasgow
- Department of Oncology, Georgetown University Medical Center, Washington, DC 20057, USA.
| | - Seema Agarwal
- Department of Pathology, Center for Cell Reprogramming, Georgetown University Medical Center, Washington, DC 20007, USA.
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14
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Dayama G, Priya S, Niccum DE, Khoruts A, Blekhman R. Interactions between the gut microbiome and host gene regulation in cystic fibrosis. Genome Med 2020; 12:12. [PMID: 31992345 PMCID: PMC6988342 DOI: 10.1186/s13073-020-0710-2] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 01/05/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Cystic fibrosis is the most common autosomal recessive genetic disease in Caucasians. It is caused by mutations in the CFTR gene, leading to poor hydration of mucus and impairment of the respiratory, digestive, and reproductive organ functions. Advancements in medical care have led to markedly increased longevity of patients with cystic fibrosis, but new complications have emerged, such as early onset of colorectal cancer. Although the pathogenesis of colorectal cancer in cystic fibrosis remains unclear, altered host-microbe interactions might play a critical role. To investigate this, we characterized changes in the microbiome and host gene expression in the colonic mucosa of cystic fibrosis patients relative to healthy controls, and identified host gene-microbiome interactions in the colon of cystic fibrosis patients. METHODS We performed RNA-seq on colonic mucosa samples from cystic fibrosis patients and healthy controls to determine differentially expressed host genes. We also performed 16S rRNA sequencing to characterize the colonic mucosal microbiome and identify gut microbes that are differentially abundant between patients and healthy controls. Lastly, we modeled associations between relative abundances of specific bacterial taxa in the gut mucosa and host gene expression. RESULTS We find that 1543 genes, including CFTR, show differential expression in the colon of cystic fibrosis patients compared to healthy controls. These genes are enriched with functions related to gastrointestinal and colorectal cancer, such as metastasis of colorectal cancer, tumor suppression, p53, and mTOR signaling pathways. In addition, patients with cystic fibrosis show decreased gut microbial diversity, decreased abundance of butyrate producing bacteria, such as Ruminococcaceae and Butyricimonas, and increased abundance of other taxa, such as Actinobacteria and Clostridium. An integrative analysis identified colorectal cancer-related genes, including LCN2 and DUOX2, for which gene expression is correlated with the abundance of colorectal cancer-associated bacteria, such as Ruminococcaceae and Veillonella. CONCLUSIONS In addition to characterizing host gene expression and mucosal microbiome in cystic fibrosis patients, our study explored the potential role of host-microbe interactions in the etiology of colorectal cancer in cystic fibrosis. Our results provide biomarkers that may potentially serve as targets for stratifying risk of colorectal cancer in patients with cystic fibrosis.
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Affiliation(s)
- Gargi Dayama
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Sambhawa Priya
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - David E Niccum
- Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Alexander Khoruts
- Department of Medicine, University of Minnesota, Minneapolis, MN, USA.
- Center for Immunology, BioTechnology Institute, University of Minnesota, Minneapolis, MN, USA.
| | - Ran Blekhman
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA.
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, MN, USA.
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15
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Du H, Wang X, Dong R, Hu D, Xiong Y. miR-601 inhibits proliferation, migration and invasion of prostate cancer stem cells by targeting KRT5 to inactivate the Wnt signaling pathway. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2019; 12:4361-4379. [PMID: 31933840 PMCID: PMC6949885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 11/26/2019] [Indexed: 06/10/2023]
Abstract
OBJECTIVE This study aimed to verify the hypothesis that downregulation of miR-601 inhibits the proliferation, migration, and invasion of prostate cancer stem cells (PCSCs) by the Wnt signaling pathway through targeting keratin 5 (KRT5). METHODS Bioinformatic tools were applied to predict miRNAs and genes potentially associated with prostate cancer, then miR-601 and KRT5 were selected. Subsequently, PCSCs were investigated with respect to miR-601 overexpression or inhibition, KRT5 overexpression, or treatment with a Wnt pathway inhibitor. A series of experiments including western blotting, RT-qPCR, wound healing experiment, transwell assay, MTT assay, annexin V-FITC/PI flow cytometric analysis, nude mice assay and immunohistochemistry were then carried out. RESULTS Compared with negative control group, migration, invasion, and proliferation of PCSCs and Wnt-1 expression were all enhanced, but apoptosis was attenuated in the miR-601 mimic group. Furthermore, results identified in the other groups (KRT5, miR-601 inhibitor, miR-601 inhibitor + KRT5, Wnt signaling pathway inhibitor, PRI-724/PRI-724 + KRT5) were opposite to those identified with the miR-601 mimic group (all P<0.05). Compared with the miR-601 inhibitor + KRT5 group, migration, invasion, and proliferation of PCSCs and Wnt-1 expression were all increased, whereas apoptosis was suppressed in KRT5 or miR-601 inhibitor groups (all P<0.05). Compared with the PRI-724 + KRT5 group, migration, invasion, and proliferation of PCSCs and Wnt-1 expression were also enhanced, whereas apoptosis was inhibited in PRI-724 or KRT5 groups (all P<0.05). CONCLUSION Results obtained from the present study have demonstrated that downregulation of miR-601 is able to inhibit the proliferation, migration, and invasion of PCSCs by activating KRT5, and subsequently inhibiting the Wnt pathway.
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Affiliation(s)
- Hongbing Du
- Department of Urology, Zhongnan Hospital of Wuhan University Wuhan 430071, Hubei, P.R. China
| | - Xinghuan Wang
- Department of Urology, Zhongnan Hospital of Wuhan University Wuhan 430071, Hubei, P.R. China
| | - Rui Dong
- Department of Urology, Zhongnan Hospital of Wuhan University Wuhan 430071, Hubei, P.R. China
| | - Dongliang Hu
- Department of Urology, Zhongnan Hospital of Wuhan University Wuhan 430071, Hubei, P.R. China
| | - Yaoyi Xiong
- Department of Urology, Zhongnan Hospital of Wuhan University Wuhan 430071, Hubei, P.R. China
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16
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Kietzman WB, Graham GT, Ory V, Sharif GM, Kushner MH, Gallanis GT, Kallakury B, Wellstein A, Riegel AT. Short- and Long-Term Effects of CDK4/6 Inhibition on Early-Stage Breast Cancer. Mol Cancer Ther 2019; 18:2220-2232. [PMID: 31451564 PMCID: PMC6891167 DOI: 10.1158/1535-7163.mct-19-0231] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 06/05/2019] [Accepted: 08/14/2019] [Indexed: 02/06/2023]
Abstract
CDK4/6 inhibitors are used in the treatment of advanced estrogen receptor (ER)(+) breast cancer. Their efficacy in ER(-) and early-stage breast cancer is currently under investigation. Here, we show that palbociclib, a CDK4/6 inhibitor, can inhibit both progression of ductal carcinoma in situ (DCIS) and growth of invasive disease in both an ER(-) basal breast cancer model (MCFDCIS) and an ER(+) luminal model (MCF7 intraductal injection). In MCFDCIS cells, palbociclib repressed cell-cycle gene expression, inhibited proliferation, induced senescence, and normalized tumorspheres formed in Matrigel while the formation of acini by normal mammary epithelial cells (MCF10A) was not affected. Palbociclib treatment of mice with MCFDCIS tumors inhibited their malignant progression and reduced proliferation of invasive lesions. Transcriptomic analysis of the tumor and stromal cell compartments showed that cell cycle and senescence genes, and MUC16, an ovarian cancer biomarker gene, were repressed during treatment. Knockdown of MUC16 in MCFDCIS cells inhibited proliferation of invasive lesions but not progression of DCIS. After cessation of palbociclib treatment genes associated with differentiation, for example, P63, inflammation, IFNγ response, and antigen processing and presentation remained suppressed in the tumor and surrounding stroma. We conclude that palbociclib can prevent progression of DCIS and is antiproliferative in ER(-) invasive disease mediated in part via MUC16. Lasting effects of CDK4/6 inhibition after drug withdrawal on differentiation and the immune response could impact the approach to treatment of early-stage ER(-) breast cancer.
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Affiliation(s)
- William B Kietzman
- Department of Oncology, Georgetown University, Washington, District of Columbia
| | - Garrett T Graham
- Department of Oncology, Georgetown University, Washington, District of Columbia
| | - Virginie Ory
- Department of Oncology, Georgetown University, Washington, District of Columbia
| | - Ghada M Sharif
- Department of Oncology, Georgetown University, Washington, District of Columbia
| | - Max H Kushner
- Department of Oncology, Georgetown University, Washington, District of Columbia
| | - Gregory T Gallanis
- Department of Oncology, Georgetown University, Washington, District of Columbia
| | - Bhaskar Kallakury
- Department of Pathology, Georgetown University, Washington, District of Columbia
- The Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia
| | - Anton Wellstein
- Department of Oncology, Georgetown University, Washington, District of Columbia
- The Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia
| | - Anna T Riegel
- Department of Oncology, Georgetown University, Washington, District of Columbia.
- The Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia
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17
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GWAS for Meat and Carcass Traits Using Imputed Sequence Level Genotypes in Pooled F2-Designs in Pigs. G3-GENES GENOMES GENETICS 2019; 9:2823-2834. [PMID: 31296617 PMCID: PMC6723123 DOI: 10.1534/g3.119.400452] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In order to gain insight into the genetic architecture of economically important traits in pigs and to derive suitable genetic markers to improve these traits in breeding programs, many studies have been conducted to map quantitative trait loci. Shortcomings of these studies were low mapping resolution, large confidence intervals for quantitative trait loci-positions and large linkage disequilibrium blocks. Here, we overcome these shortcomings by pooling four large F2 designs to produce smaller linkage disequilibrium blocks and by resequencing the founder generation at high coverage and the F1 generation at low coverage for subsequent imputation of the F2 generation to whole genome sequencing marker density. This lead to the discovery of more than 32 million variants, 8 million of which have not been previously reported. The pooling of the four F2 designs enabled us to perform a joint genome-wide association study, which lead to the identification of numerous significantly associated variant clusters on chromosomes 1, 2, 4, 7, 17 and 18 for the growth and carcass traits average daily gain, back fat thickness, meat fat ratio, and carcass length. We could not only confirm previously reported, but also discovered new quantitative trait loci. As a result, several new candidate genes are discussed, among them BMP2 (bone morphogenetic protein 2), which we recently discovered in a related study. Variant effect prediction revealed that 15 high impact variants for the traits back fat thickness, meat fat ratio and carcass length were among the statistically significantly associated variants.
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18
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Pawar S, Stanam A. A Six-Gene-Based Prognostic Model Predicts Survival in Head and Neck Squamous Cell Carcinoma Patients. J Maxillofac Oral Surg 2019; 18:320-327. [PMID: 30996559 DOI: 10.1007/s12663-019-01187-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Accepted: 01/14/2019] [Indexed: 02/06/2023] Open
Abstract
Background and Objective Head and neck cancer is a malignant tumor that begins in the head and neck region, and has the sixth highest incidence worldwide. Previous studies have indicated several prognostic markers for head and neck squamous cell carcinoma (HNSCC), but due to poor accuracy and sensitivity of these clinical characteristic markers attention has been gradually switched to molecular biomarkers. This study aimed to sort out the mRNAs correlated with patient survival time to establish an mRNA combination prognostic biomarker model for HNSCC patient risk stratification, providing optimal therapeutic regimens and improving patient prognosis. Methods Clinical data and transcriptome sequencing data of HNSCC were retrieved from TCGA database and were allocated into training and validation datasets. The prognostic model was established using the mRNAs, which were sorted out from training dataset by a significant correlation with survival time. Eventually, the prediction property of the model was evaluated by Kaplan-Meier survival analysis and receiver operating characteristic (ROC) curve. Results An optimal prognostic model by the combination of six mRNAs was established. Kaplan-Meier survival analysis revealed effective risk stratification by this model for patients in the two datasets. The area under ROC curve (AUC) was > 0.65 for training and validation datasets, indicating good sensitivity and specificity of this model. Moreover, prominent superiority of this model to investigate prognostic biomarkers was demonstrated. Conclusion Our model provided effective prognostication in terms of death risk stratification and evaluation in HNSCC patients. Combination of this prognostic model with current treatment measures is expected to greatly improve the patients' prognosis.
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Affiliation(s)
- Shrikant Pawar
- 1Department of Computer Science, Georgia State University, 34 Peachtree Street, Atlanta, GA 30303 USA
- 2Department of Biology, Georgia State University, 34 Peachtree Street, Atlanta, GA 30303 USA
| | - Aditya Stanam
- 3Department of Pathology, The University of Iowa, 500 Newton Road, #ML 1132, Iowa City, IA 52242-5000 USA
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19
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Lin SH, Raju GS, Huff C, Ye Y, Gu J, Chen JS, Hildebrandt MAT, Liang H, Menter DG, Morris J, Hawk E, Stroehlein JR, Futreal A, Kopetz S, Mishra L, Wu X. The somatic mutation landscape of premalignant colorectal adenoma. Gut 2018; 67:1299-1305. [PMID: 28607096 PMCID: PMC6031265 DOI: 10.1136/gutjnl-2016-313573] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 05/02/2017] [Accepted: 05/04/2017] [Indexed: 02/06/2023]
Abstract
OBJECTIVE There are few studies which characterised the molecular alterations in premalignant colorectal adenomas. Our major goal was to establish colorectal adenoma genome atlas and identify molecular markers of progression from colorectal adenoma to adenocarcinoma. DESIGN Whole-exome sequencing and targeted sequencing were carried out in 149 adenoma samples and paired blood from patients with conventional adenoma or sessile serrated adenoma to characterise the somatic mutation landscape for premalignant colorectal lesions. The identified somatic mutations were compared with those in colorectal cancer (CRC) samples from The Cancer Genome Atlas. A supervised random forest model was employed to identify gene panels differentiating adenoma from CRC. RESULTS Similar somatic mutation frequencies, but distinctive driver mutations, were observed in sessile serrated adenomas and conventional adenomas. The final model included 20 genes and was able to separate the somatic mutation profile of colorectal adenoma and adenocarcinoma with an area under the curve of 0.941. CONCLUSION The findings of this project hold potential to better identify patients with adenoma who may be candidates for targeted surveillance programmes and preventive interventions to reduce the incidence of CRC.
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Affiliation(s)
- Shu-Hong Lin
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA,The University of Texas Graduate School of Biomedical Sciences at Houston and MD Anderson Cancer Center, Houston, Texas, USA
| | - Gottumukkala S Raju
- Department of Gastroenterology, Hepatology and Nutrition, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Chad Huff
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Yuanqing Ye
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jian Gu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jiun-Sheng Chen
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA,The University of Texas Graduate School of Biomedical Sciences at Houston and MD Anderson Cancer Center, Houston, Texas, USA
| | - Michelle A T Hildebrandt
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Han Liang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - David G Menter
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jeffery Morris
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ernest Hawk
- Division of Cancer Prevention and Population Science, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - John R Stroehlein
- Department of Gastroenterology, Hepatology and Nutrition, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Lopa Mishra
- Department of Gastroenterology, Hepatology and Nutrition, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Xifeng Wu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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Ory V, Kietzman WB, Boeckelman J, Kallakury BV, Wellstein A, Furth PA, Riegel AT. The PPARγ agonist efatutazone delays invasive progression and induces differentiation of ductal carcinoma in situ. Breast Cancer Res Treat 2018; 169:47-57. [PMID: 29350308 DOI: 10.1007/s10549-017-4649-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 12/26/2017] [Indexed: 02/06/2023]
Abstract
PURPOSE Ductal carcinoma in situ (DCIS) is a pre-invasive lesion of the breast considered a precursor of invasive ductal carcinoma. This study aimed to determine whether activated PPARγ acts as a tumor suppressor in human DCIS progression. METHODS We utilized the high-affinity PPARγ agonist, efatutazone, to activate endogenous PPARγ in a well-defined model for the progression of basal (triple negative) DCIS, MCFDCIS cells, cultured under 2D and 3D conditions. We studied the effects of activated PPARγ on DCIS progression in MCFDCIS xenograft and C3(1)/Tag transgenic mice treated with 30 mg/kg of efatutazone. RESULTS In vitro, efatutazone did not alter the MCFDCIS cell proliferation but induced phenotypic and gene expression changes, indicating that activated PPARγ is able to differentiate MCFDCIS cells into more luminal and lactational-like cells. In addition, MCFDCIS tumorsphere formation in 3D was reduced by PPARγ activation. In vivo, efatutazone-treated MCFDCIS tumors exhibited fat deposition along with upregulation of PPARγ responsive genes in both epithelial and stromal compartments, suggesting features of milk-producing mammary epithelial cell differentiation. The efatutazone-treated lesions were less invasive with fewer CD44+/p63+ basal progenitor cells. PPARγ activation downregulated Akt phosphorylation in these tumors, although the ERK pathway remained unchanged. Similar trends in gene expression changes consistent with lactational and luminal cell differentiation were observed in the C3(1)/Tag mouse model after efatutazone treatment. CONCLUSIONS Our data suggest that activation of the PPARγ pathway differentiates DCIS lesions and may be a useful approach to delay DCIS progression.
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Affiliation(s)
- Virginie Ory
- Department of Oncology, Georgetown University, Washington, DC, USA.
| | | | - Jacob Boeckelman
- Department of Oncology, Georgetown University, Washington, DC, USA
| | - Bhaskar V Kallakury
- Department of Pathology, Georgetown University, Washington, DC, USA.,The Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Anton Wellstein
- Department of Oncology, Georgetown University, Washington, DC, USA.,The Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Priscilla A Furth
- Department of Oncology, Georgetown University, Washington, DC, USA.,Department of Medicine, Georgetown University, Washington, DC, USA.,The Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Anna T Riegel
- Department of Oncology, Georgetown University, Washington, DC, USA.,The Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
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21
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Qu LW, Zhou B, Wang GZ, Chen Y, Zhou GB. Genomic variations in paired normal controls for lung adenocarcinomas. Oncotarget 2017; 8:104113-104122. [PMID: 29262625 PMCID: PMC5732791 DOI: 10.18632/oncotarget.22020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 09/23/2017] [Indexed: 02/06/2023] Open
Abstract
Somatic genomic mutations in lung adenocarcinomas (LUADs) have been extensively dissected, but whether the counterpart normal lung tissues that are exposed to ambient air or tobacco smoke as the tumor tissues do, harbor genomic variations, remains unclear. Here, the genome of normal lung tissues and paired tumors of 11 patients with LUAD were sequenced, the genome sequences of counterpart normal controls (CNCs) and tumor tissues of 513 patients were downloaded from TCGA database and analyzed. In the initial screening, genomic alterations were identified in the "normal" lung tissues and verified by Sanger capillary sequencing. In CNCs of TCGA datasets, a mean of 0.2721 exonic variations/Mb and 5.2885 altered genes per sample were uncovered. The C:G→T:A transitions, a signature of tobacco carcinogen N-methyl-N-nitro-N-nitrosoguanidine, were the predominant nucleotide changes in CNCs. 16 genes had a variant rate of more than 2%, and CNC variations in MUC5B, ZXDB, PLIN4, CCDC144NL, CNTNAP3B, and CCDC180 were associated with poor prognosis whereas alterations in CHD3 and KRTAP5-5 were associated with favorable clinical outcome of the patients. This study identified the genomic alterations in CNC samples of LUADs, and further highlighted the DNA damage effect of tobacco on lung epithelial cells.
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Affiliation(s)
- Li-Wei Qu
- Division of Molecular Carcinogenesis and Targeted Therapy for Cancer, State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Bo Zhou
- Division of Molecular Carcinogenesis and Targeted Therapy for Cancer, State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Gui-Zhen Wang
- Division of Molecular Carcinogenesis and Targeted Therapy for Cancer, State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ying Chen
- Division of Molecular Carcinogenesis and Targeted Therapy for Cancer, State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Guang-Biao Zhou
- Division of Molecular Carcinogenesis and Targeted Therapy for Cancer, State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
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22
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Shuptrine CW, Ajina R, Fertig EJ, Jablonski SA, Kim Lyerly H, Hartman ZC, Weiner LM. An unbiased in vivo functional genomics screening approach in mice identifies novel tumor cell-based regulators of immune rejection. Cancer Immunol Immunother 2017; 66:1529-1544. [PMID: 28770278 DOI: 10.1007/s00262-017-2047-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 07/26/2017] [Indexed: 02/06/2023]
Abstract
The clinical successes of immune checkpoint therapies for cancer make it important to identify mechanisms of resistance to anti-tumor immune responses. Numerous resistance mechanisms have been identified employing studies of single genes or pathways, thereby parsing the tumor microenvironment complexity into tractable pieces. However, this limits the potential for novel gene discovery to in vivo immune attack. To address this challenge, we developed an unbiased in vivo genome-wide RNAi screening platform that leverages host immune selection in strains of immune-competent and immunodeficient mice to select for tumor cell-based genes that regulate in vivo sensitivity to immune attack. Utilizing this approach in a syngeneic triple-negative breast cancer (TNBC) model, we identified 709 genes that selectively regulated adaptive anti-tumor immunity and focused on five genes (CD47, TGFβ1, Sgpl1, Tex9 and Pex14) with the greatest impact. We validated the mechanisms that underlie the immune-related effects of expression of these genes in different TNBC lines, as well as tandem synergistic interactions. Furthermore, we demonstrate the impact of different genes with previously unknown immune functions (Tex9 and Pex14) on anti-tumor immunity. Thus, this innovative approach has utility in identifying unknown tumor-specific regulators of immune recognition in multiple settings to reveal novel targets for future immunotherapies.
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Affiliation(s)
- Casey W Shuptrine
- Department of Oncology and Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, 3970 Reservoir Road NW, Washington DC, 20057, USA.,Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - Reham Ajina
- Department of Oncology and Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, 3970 Reservoir Road NW, Washington DC, 20057, USA
| | - Elana J Fertig
- Department of Oncology, Division of Biostatistics, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Sandra A Jablonski
- Department of Oncology and Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, 3970 Reservoir Road NW, Washington DC, 20057, USA
| | - H Kim Lyerly
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - Zachary C Hartman
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - Louis M Weiner
- Department of Oncology and Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, 3970 Reservoir Road NW, Washington DC, 20057, USA.
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Juul M, Bertl J, Guo Q, Nielsen MM, Świtnicki M, Hornshøj H, Madsen T, Hobolth A, Pedersen JS. Non-coding cancer driver candidates identified with a sample- and position-specific model of the somatic mutation rate. eLife 2017; 6. [PMID: 28362259 PMCID: PMC5440169 DOI: 10.7554/elife.21778] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Accepted: 03/14/2017] [Indexed: 02/06/2023] Open
Abstract
Non-coding mutations may drive cancer development. Statistical detection of non-coding driver regions is challenged by a varying mutation rate and uncertainty of functional impact. Here, we develop a statistically founded non-coding driver-detection method, ncdDetect, which includes sample-specific mutational signatures, long-range mutation rate variation, and position-specific impact measures. Using ncdDetect, we screened non-coding regulatory regions of protein-coding genes across a pan-cancer set of whole-genomes (n = 505), which top-ranked known drivers and identified new candidates. For individual candidates, presence of non-coding mutations associates with altered expression or decreased patient survival across an independent pan-cancer sample set (n = 5454). This includes an antigen-presenting gene (CD1A), where 5'UTR mutations correlate significantly with decreased survival in melanoma. Additionally, mutations in a base-excision-repair gene (SMUG1) correlate with a C-to-T mutational-signature. Overall, we find that a rich model of mutational heterogeneity facilitates non-coding driver identification and integrative analysis points to candidates of potential clinical relevance.
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Affiliation(s)
- Malene Juul
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark
| | - Johanna Bertl
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark
| | - Qianyun Guo
- Bioinformatics Research Centre (BiRC), Aarhus University, Aarhus, Denmark
| | - Morten Muhlig Nielsen
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark
| | - Michał Świtnicki
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark
| | - Henrik Hornshøj
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark
| | - Tobias Madsen
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark
| | - Asger Hobolth
- Bioinformatics Research Centre (BiRC), Aarhus University, Aarhus, Denmark
| | - Jakob Skou Pedersen
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark.,Bioinformatics Research Centre (BiRC), Aarhus University, Aarhus, Denmark
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Berens EB, Sharif GM, Wellstein A, Glasgow E. Testing the Vascular Invasive Ability of Cancer Cells in Zebrafish (Danio Rerio). J Vis Exp 2016:55007. [PMID: 27842376 PMCID: PMC5226185 DOI: 10.3791/55007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Cancer cell vascular invasion and extravasation is a hallmark of metastatic progression. Traditional in vitro models of cancer cell invasion of endothelia typically lack the fluid dynamics that invading cells are otherwise exposed to in vivo. However, in vivo systems such as mouse models, though more physiologically relevant, require longer experimental timescales and present unique challenges associated with monitoring and data analysis. Here we describe a zebrafish assay that seeks to bridge this technical gap by allowing for the rapid assessment of cancer cell vascular invasion and extravasation. The approach involves injecting fluorescent cancer cells into the precardiac sinus of transparent 2-day old zebrafish embryos whose vasculature is marked by a contrasting fluorescent reporter. Following injection, the cancer cells must survive in circulation and subsequently extravasate from vessels into tissues in the caudal region of the embryo. Extravasated cancer cells are efficiently identified and scored in live embryos via fluorescence imaging at a fixed timepoint. This technique can be modified to study intravasation and/or competition amongst a heterogeneous mixture of cancer cells by changing the injection site to the yolk sac. Together, these methods can evaluate a hallmark behavior of cancer cells and help uncover mechanisms indicative of malignant progression to the metastatic phenotype.
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Affiliation(s)
- Eric B Berens
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University
| | - Ghada M Sharif
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University
| | - Anton Wellstein
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University;
| | - Eric Glasgow
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University;
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