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Anjanappa M, Hao Y, Simpson ER, Bhat-Nakshatri P, Nelson JB, Tersey SA, Mirmira RG, Cohen-Gadol AA, Saadatzadeh MR, Li L, Fang F, Nephew KP, Miller KD, Liu Y, Nakshatri H. A system for detecting high impact-low frequency mutations in primary tumors and metastases. Oncogene 2017; 37:185-196. [PMID: 28892047 DOI: 10.1038/onc.2017.322] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 08/01/2017] [Accepted: 08/02/2017] [Indexed: 12/14/2022]
Abstract
Tumor complexity and intratumor heterogeneity contribute to subclonal diversity. Despite advances in next-generation sequencing (NGS) and bioinformatics, detecting rare mutations in primary tumors and metastases contributing to subclonal diversity is a challenge for precision genomics. Here, in order to identify rare mutations, we adapted a recently described epithelial reprograming assay for short-term propagation of epithelial cells from primary and metastatic tumors. Using this approach, we expanded minor clones and obtained epithelial cell-specific DNA/RNA for quantitative NGS analysis. Comparative Ampliseq Comprehensive Cancer Panel sequence analyses were performed on DNA from unprocessed breast tumor and tumor cells propagated from the same tumor. We identified previously uncharacterized mutations present only in the cultured tumor cells, a subset of which has been reported in brain metastatic but not primary breast tumors. In addition, whole-genome sequencing identified mutations enriched in liver metastases of various cancers, including Notch pathway mutations/chromosomal inversions in 5/5 liver metastases, irrespective of cancer types. Mutations/rearrangements in FHIT, involved in purine metabolism, were detected in 4/5 liver metastases, and the same four liver metastases shared mutations in 32 genes, including mutations of different HLA-DR family members affecting OX40 signaling pathway, which could impact the immune response to metastatic cells. Pathway analyses of all mutated genes in liver metastases showed aberrant tumor necrosis factor and transforming growth factor signaling in metastatic cells. Epigenetic regulators including KMT2C/MLL3 and ARID1B, which are mutated in >50% of hepatocellular carcinomas, were also mutated in liver metastases. Thus, irrespective of cancer types, organ-specific metastases may share common genomic aberrations. Since recent studies show independent evolution of primary tumors and metastases and in most cases mutation burden is higher in metastases than primary tumors, the method described here may allow early detection of subclonal somatic alterations associated with metastatic progression and potentially identify therapeutically actionable, metastasis-specific genomic aberrations.
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Affiliation(s)
- M Anjanappa
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Y Hao
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, IN, USA
| | - E R Simpson
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, IN, USA
| | - P Bhat-Nakshatri
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
| | - J B Nelson
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - S A Tersey
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - R G Mirmira
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - A A Cohen-Gadol
- Department of Neurosurgery, Indiana University School of Medicine, Indianapolis, IN, USA
| | - M R Saadatzadeh
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - L Li
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, IN, USA.,Department of Medical and Molecular Genetics, Indiana University School of Medicine, IN, USA
| | - F Fang
- Medical Science Program, Indiana University, Bloomington, IN, USA
| | - K P Nephew
- Medical Science Program, Indiana University, Bloomington, IN, USA
| | - K D Miller
- Division of Hematology/Oncology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Y Liu
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, IN, USA.,Department of Medical and Molecular Genetics, Indiana University School of Medicine, IN, USA
| | - H Nakshatri
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, USA.,Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA.,Roudebush VA Medical Center, Indianapolis, IN, USA
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Cabrera SM, Colvin SC, Tersey SA, Maier B, Nadler JL, Mirmira RG. Effects of combination therapy with dipeptidyl peptidase-IV and histone deacetylase inhibitors in the non-obese diabetic mouse model of type 1 diabetes. Clin Exp Immunol 2013; 172:375-82. [PMID: 23600825 DOI: 10.1111/cei.12068] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/10/2013] [Indexed: 12/24/2022] Open
Abstract
Type 1 diabetes (T1D) results from T helper type 1 (Th1)-mediated autoimmune destruction of insulin-producing β cells. Novel experimental therapies for T1D target immunomodulation, β cell survival and inflammation. We examined combination therapy with the dipeptidyl peptidase-IV inhibitor MK-626 and the histone deacetylase inhibitor vorinostat in the non-obese diabetic (NOD) mouse model of T1D. We hypothesized that combination therapy would ameliorate T1D by providing protection from β cell inflammatory destruction while simultaneously shifting the immune response towards immune-tolerizing regulatory T cells (T(regs)). Although neither mono- nor combination therapies with MK-626 and vorinostat caused disease remission in diabetic NOD mice, the combination of MK-626 and vorinostat increased β cell area and reduced the mean insulitis score compared to diabetic control mice. In prediabetic NOD mice, MK-626 monotherapy resulted in improved glucose tolerance, a reduction in mean insulitis score and an increase in pancreatic lymph node T(reg) percentage, and combination therapy with MK-626 and vorinostat increased pancreatic lymph node T(reg) percentage. We conclude that neither single nor combination therapies using MK-626 and vorinostat induce diabetes remission in NOD mice, but combination therapy appears to have beneficial effects on β cell area, insulitis and T(reg) populations. Combinations of vorinostat and MK-626 may serve as beneficial adjunctive therapy in clinical trials for T1D prevention or remission.
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Affiliation(s)
- S M Cabrera
- Department of Pediatrics and the Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
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