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Das S, Idate R, Lana SE, Regan DP, Duval DL. Integrated analysis of canine soft tissue sarcomas identifies recurrent mutations in TP53, KMT genes and PDGFB fusions. Sci Rep 2023; 13:10422. [PMID: 37369741 DOI: 10.1038/s41598-023-37266-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 06/19/2023] [Indexed: 06/29/2023] Open
Abstract
Soft tissue sarcomas (STS) are a heterogenous group of mesenchymal tumors representing over 50 distinct types with overlapping histological features and non-specific anatomical locations. Currently, localized sarcomas are treated with surgery + / - radiation in both humans and dogs with few molecularly targeted therapeutic options. However, to improve precision-based cancer therapy through trials in pet dogs with naturally occurring STS tumors, knowledge of genomic profiling and molecular drivers in both species is essential. To this purpose, we sought to characterize the transcriptomic and genomic mutation profiles of canine STS subtypes (fibrosarcoma, undifferentiated pleomorphic sarcoma, and peripheral nerve sheath tumors), by leveraging RNAseq, whole exome sequencing, immunohistochemistry, and drug assays. The most common driver mutations were in cell cycle/DNA repair (31%, TP53-21%) and chromatin organization/binding (41%, KMT2D-21%) genes. Similar to a subset of human sarcomas, we identified fusion transcripts of platelet derived growth factor B and collagen genes that predict sensitivity to PDGFR inhibitors. Transcriptomic profiling grouped these canine STS tumors into 4 clusters, one PNST group (H1), and 3 FSA groups selectively enriched for extracellular matrix interactions and PDFGB fusions (H2), homeobox transcription factors (H3), and elevated T-cell infiltration (H4). This multi-omics approach provides insights into canine STS sub-types at a molecular level for comparison to their human counterparts, to improve diagnosis, and may provide additional targets for chemo- and immuno-therapy.
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Affiliation(s)
- Sunetra Das
- Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA
- Flint Animal Cancer Center, Colorado State University, Fort Collins, CO, 80523, USA
| | - Rupa Idate
- Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA
- Flint Animal Cancer Center, Colorado State University, Fort Collins, CO, 80523, USA
| | - Susan E Lana
- Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA
- Flint Animal Cancer Center, Colorado State University, Fort Collins, CO, 80523, USA
| | - Daniel P Regan
- Flint Animal Cancer Center, Colorado State University, Fort Collins, CO, 80523, USA
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Dawn L Duval
- Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA.
- Flint Animal Cancer Center, Colorado State University, Fort Collins, CO, 80523, USA.
- University of Colorado Cancer Center, Anschutz Medical Campus, Aurora, CO, 80045, USA.
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Das S, Idate R, Regan DP, Lana SE, Duval DL. Molecular landscape of canine soft tissue sarcoma. FASEB J 2022. [DOI: 10.1096/fasebj.2022.36.s1.r4711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Sunetra Das
- Clinical SciencesColorado State UniversityFort CollinsCO
| | - Rupa Idate
- Clinical SciencesColorado State UniversityFort CollinsCO
| | | | - Susan E. Lana
- Clinical SciencesColorado State UniversityFort CollinsCO
| | - Dawn L. Duval
- Clinical SciencesColorado State UniversityFort CollinsCO
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Duval DL, Idate R, Das S, Ackart D, Gustafson DL, Cronise K. Characterizing a Canine Urothelial Carcinoma Model of Acquired MEK1/2 Inhibitor Resistance. FASEB J 2022. [DOI: 10.1096/fasebj.2022.36.s1.r5565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Dawn L. Duval
- Clinical SciencesColorado State UniversityFort CollinsCO
| | - Rupa Idate
- Clinical SciencesColorado State UniversityFort CollinsCO
| | - Sunetra Das
- Clinical SciencesColorado State UniversityFort CollinsCO
| | - David Ackart
- Microbiology, Immunology, and PathologyColorado State UniversityFort CollinsCO
| | | | - Kathryn Cronise
- Microbiology, Immunology, and PathologyColorado State UniversityFort CollinsCO
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Das S, Idate R, Regan DP, Fowles JS, Lana SE, Thamm DH, Gustafson DL, Duval DL. Immune pathways and TP53 missense mutations are associated with longer survival in canine osteosarcoma. Commun Biol 2021; 4:1178. [PMID: 34635775 PMCID: PMC8505454 DOI: 10.1038/s42003-021-02683-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 09/15/2021] [Indexed: 12/20/2022] Open
Abstract
Osteosarcoma affects about 2.8% of dogs with cancer, with a one-year survival rate of approximately 45%. The purpose of this study was to characterize mutation and expression profiles of osteosarcoma and its association with outcome in dogs. The number of somatic variants identified across 26 samples ranged from 145 to 2,697 with top recurrent mutations observed in TP53 and SETD2. Additionally, 47 cancer genes were identified with copy number variations. Missense TP53 mutation status and low pre-treatment blood monocyte counts were associated with a longer disease-free interval (DFI). Patients with longer DFI also showed increased transcript levels of anti-tumor immune response genes. Although, T-cell and myeloid cell quantifications were not significantly associated with outcome; immune related genes, PDL-1 and CD160, were correlated with T-cell abundance. Overall, the association of gene expression and mutation profiles to outcome provides insights into pathogenesis and therapeutic interventions in osteosarcoma patients.
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Affiliation(s)
- Sunetra Das
- Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA.
- Flint Animal Cancer Center, Colorado State University, Fort Collins, CO, 80523, USA.
| | - Rupa Idate
- Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA
- Flint Animal Cancer Center, Colorado State University, Fort Collins, CO, 80523, USA
| | - Daniel P Regan
- Flint Animal Cancer Center, Colorado State University, Fort Collins, CO, 80523, USA
- Department of Microbiology, Immunology, & Pathology, Colorado State University, Fort Collins, CO, 80523, USA
- University of Colorado Cancer Center, Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Jared S Fowles
- Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA
- Flint Animal Cancer Center, Colorado State University, Fort Collins, CO, 80523, USA
- Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, CO, 80523, USA
| | - Susan E Lana
- Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA
- Flint Animal Cancer Center, Colorado State University, Fort Collins, CO, 80523, USA
| | - Douglas H Thamm
- Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA
- Flint Animal Cancer Center, Colorado State University, Fort Collins, CO, 80523, USA
- University of Colorado Cancer Center, Anschutz Medical Campus, Aurora, CO, 80045, USA
- Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, CO, 80523, USA
| | - Daniel L Gustafson
- Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA
- Flint Animal Cancer Center, Colorado State University, Fort Collins, CO, 80523, USA
- University of Colorado Cancer Center, Anschutz Medical Campus, Aurora, CO, 80045, USA
- Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, CO, 80523, USA
| | - Dawn L Duval
- Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA.
- Flint Animal Cancer Center, Colorado State University, Fort Collins, CO, 80523, USA.
- University of Colorado Cancer Center, Anschutz Medical Campus, Aurora, CO, 80045, USA.
- Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, CO, 80523, USA.
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Das S, Idate R, Fowles JS, Lana SE, Regan DP, Gustafson DL, Duval DL. Molecular Landscape of Canine Osteosarcoma. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.05364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Das S, Idate R, Cronise KE, Gustafson DL, Duval DL. Identifying Candidate Druggable Targets in Canine Cancer Cell Lines Using Whole-Exome Sequencing. Mol Cancer Ther 2019; 18:1460-1471. [PMID: 31175136 DOI: 10.1158/1535-7163.mct-18-1346] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 03/15/2019] [Accepted: 05/24/2019] [Indexed: 12/15/2022]
Abstract
Cancer cell culture has been a backbone in cancer research, in which analysis of human cell line mutational profiles often correlates with oncogene addiction and drug sensitivity. We have conducted whole-exome sequence analyses on 33 canine cancer cell lines from 10 cancer types to identify somatic variants that contribute to pathogenesis and therapeutic sensitivity. A total of 66,344 somatic variants were identified. Mutational load ranged from 15.79 to 129.37 per Mb, and 13.2% of variants were located in protein-coding regions (PCR) of 5,085 genes. PCR somatic variants were identified in 232 genes listed in the Cancer Gene Census (COSMIC). Cross-referencing variants with human driving mutations on cBioPortal identified 61 variants as candidate cancer drivers in 30 cell lines. The most frequently mutated cancer driver was TP53 (15 mutations in 12 cell lines). No drivers were identified in three cell lines. We identified 501 non-COSMIC genes with PCR variants that functionally annotate with COSMIC genes. These genes frequently mapped to the KEGG MAPK and PI3K-AKT pathways. We evaluated the cell lines for ERK1/2 and AKT(S473) phosphorylation and sensitivity to the MEK1/2 inhibitor, trametinib. Twelve of the 33 cell lines were trametinib-sensitive (IC50 < 32 nmol/L), all 12 exhibited constitutive or serum-activated ERK1/2 phosphorylation, and 8 carried MAPK pathway cancer driver variants: NF1(2), BRAF(3), N/KRAS(3). This functionally annotated database of canine cell line variants will inform hypothesis-driven preclinical research to support the use of companion animals in clinical trials to test novel combination therapies.
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Affiliation(s)
- Sunetra Das
- Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado. .,Flint Animal Cancer Center, Colorado State University, Fort Collins, Colorado
| | - Rupa Idate
- Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado.,Flint Animal Cancer Center, Colorado State University, Fort Collins, Colorado
| | - Kathryn E Cronise
- Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado.,Flint Animal Cancer Center, Colorado State University, Fort Collins, Colorado.,Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, Colorado
| | - Daniel L Gustafson
- Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado.,Flint Animal Cancer Center, Colorado State University, Fort Collins, Colorado.,University of Colorado Cancer Center, Anschutz Medical Campus, Aurora, Colorado
| | - Dawn L Duval
- Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado.,Flint Animal Cancer Center, Colorado State University, Fort Collins, Colorado.,University of Colorado Cancer Center, Anschutz Medical Campus, Aurora, Colorado
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Sishc BJ, Nelson CB, McKenna MJ, Battaglia CLR, Herndon A, Idate R, Liber HL, Bailey SM. Telomeres and Telomerase in the Radiation Response: Implications for Instability, Reprograming, and Carcinogenesis. Front Oncol 2015; 5:257. [PMID: 26636039 PMCID: PMC4656829 DOI: 10.3389/fonc.2015.00257] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 11/06/2015] [Indexed: 01/06/2023] Open
Abstract
Telomeres are nucleoprotein complexes comprised of tandem arrays of repetitive DNA sequence that serve to protect chromosomal termini from inappropriate degradation, as well as to prevent these natural DNA ends from being recognized as broken DNA (double-strand breaks) and triggering of inappropriate DNA damage responses. Preservation of telomere length requires telomerase, the specialized reverse transcriptase capable of maintaining telomere length via template-mediated addition of telomeric repeats onto the ends of newly synthesized chromosomes. Loss of either end-capping function or telomere length maintenance has been associated with genomic instability or senescence in a variety of settings; therefore, telomeres and telomerase have well-established connections to cancer and aging. It has long been recognized that oxidative stress promotes shortening of telomeres, and that telomerase activity is a radiation-inducible function. However, the effects of ionizing radiation (IR) exposure on telomeres per se are much less well understood and appreciated. To gain a deeper understanding of the roles, telomeres and telomerase play in the response of human cells to IRs of different qualities, we tracked changes in telomeric end-capping function, telomere length, and telomerase activity in panels of mammary epithelial and hematopoietic cell lines exposed to low linear energy transfer (LET) gamma(γ)-rays or high LET, high charge, high energy (HZE) particles, delivered either acutely or at low dose rates. In addition to demonstrating that dysfunctional telomeres contribute to IR-induced mutation frequencies and genome instability, we reveal non-canonical roles for telomerase, in that telomerase activity was required for IR-induced enrichment of mammary epithelial putative stem/progenitor cell populations, a finding also suggestive of cellular reprograming. Taken together, the results reported here establish the critical importance of telomeres and telomerase in the radiation response and, as such, have compelling implications not only for accelerated tumor repopulation following radiation therapy but also for carcinogenic potential following low dose exposures as well, including those of relevance to spaceflight-associated galactic cosmic radiations.
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Affiliation(s)
- Brock J Sishc
- Division of Molecular Radiation Oncology, Department of Radiation Oncology, University of Texas Southwestern Medical Center Dallas , Dallas, TX , USA ; Department of Environmental and Radiological Health Sciences, Colorado State University , Fort Collins, CO , USA
| | - Christopher B Nelson
- Department of Environmental and Radiological Health Sciences, Colorado State University , Fort Collins, CO , USA
| | - Miles J McKenna
- Department of Environmental and Radiological Health Sciences, Colorado State University , Fort Collins, CO , USA
| | - Christine L R Battaglia
- Department of Environmental and Radiological Health Sciences, Colorado State University , Fort Collins, CO , USA
| | - Andrea Herndon
- Department of Environmental and Radiological Health Sciences, Colorado State University , Fort Collins, CO , USA
| | - Rupa Idate
- Department of Environmental and Radiological Health Sciences, Colorado State University , Fort Collins, CO , USA
| | - Howard L Liber
- Department of Environmental and Radiological Health Sciences, Colorado State University , Fort Collins, CO , USA
| | - Susan M Bailey
- Department of Environmental and Radiological Health Sciences, Colorado State University , Fort Collins, CO , USA
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Parplys AC, Zhao W, Sharma N, Groesser T, Liang F, Maranon DG, Leung SG, Grundt K, Dray E, Idate R, Østvold AC, Schild D, Sung P, Wiese C. NUCKS1 is a novel RAD51AP1 paralog important for homologous recombination and genome stability. Nucleic Acids Res 2015; 43:9817-34. [PMID: 26323318 PMCID: PMC4787752 DOI: 10.1093/nar/gkv859] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 08/17/2015] [Indexed: 01/20/2023] Open
Abstract
NUCKS1 (nuclear casein kinase and cyclin-dependent kinase substrate 1) is a 27 kD chromosomal, vertebrate-specific protein, for which limited functional data exist. Here, we demonstrate that NUCKS1 shares extensive sequence homology with RAD51AP1 (RAD51 associated protein 1), suggesting that these two proteins are paralogs. Similar to the phenotypic effects of RAD51AP1 knockdown, we find that depletion of NUCKS1 in human cells impairs DNA repair by homologous recombination (HR) and chromosome stability. Depletion of NUCKS1 also results in greatly increased cellular sensitivity to mitomycin C (MMC), and in increased levels of spontaneous and MMC-induced chromatid breaks. NUCKS1 is critical to maintaining wild type HR capacity, and, as observed for a number of proteins involved in the HR pathway, functional loss of NUCKS1 leads to a slow down in DNA replication fork progression with a concomitant increase in the utilization of new replication origins. Interestingly, recombinant NUCKS1 shares the same DNA binding preference as RAD51AP1, but binds to DNA with reduced affinity when compared to RAD51AP1. Our results show that NUCKS1 is a chromatin-associated protein with a role in the DNA damage response and in HR, a DNA repair pathway critical for tumor suppression.
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Affiliation(s)
- Ann C Parplys
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Weixing Zhao
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Neelam Sharma
- Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Torsten Groesser
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Fengshan Liang
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - David G Maranon
- Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Stanley G Leung
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kirsten Grundt
- Department of Molecular Medicine, Institute of Basic Medical Science, University of Oslo, 0317 Oslo, Norway
| | - Eloïse Dray
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Rupa Idate
- Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Anne Carine Østvold
- Department of Molecular Medicine, Institute of Basic Medical Science, University of Oslo, 0317 Oslo, Norway
| | - David Schild
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Claudia Wiese
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523, USA
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Abstract
An interesting problem associated with studying the effects of low doses of high atomic number and energy (HZE) particles, as found in space, is that not all cells will necessarily be similarly traversed during exposure, a scenario that greatly complicates the measurement of end points that require time to develop, gene-locus mutation being a perfect example. The standard protocol for measuring mutations at the heterozygous thymidine kinase locus in human lymphoblastoid cells involves waiting three days after treatment for newly induced mutants to fully express, at which time cells are then plated in the presence of the selective agent, and mutants are counted three weeks later. This approach is acceptable as long as all cells are uniformly affected, as is the case with low-linear energy transfer (LET) ionizing radiation. However, for HZE particles some fraction of cells may not be traversed or perhaps would receive fewer than the average number of "hits", and they would continue to grow at or closer to the normal rate, thus outpacing cells that received more damage. As a result, at three days post-treatment, more heavily damaged cells will have been "diluted" by the less damaged ones, and thus the measured mutant frequency (MF) will underestimate actual mutant frequency. We therefore developed a modified approach for measuring mutation that eliminates this problem and demonstrates that the mutagenicity of 1 GeV/n Fe ions are underestimated by a factor of two when using the standard MF protocol. Furthermore, we determined the mutagenic effects of a variety of heavy ions, all of which induced mutations in a linear fashion. We found that the maximal yield of mutations (i.e., highest relative biological efficiency) was about 7.5 times higher at an LET of 70 keV/μ (400 MeV/n Si) than for gamma rays. Nontargeted mutagenicity after treatment with ionizing radiation was also investigated. For each particular ion/energy examined and in agreement with many previous studies, there was no clear evidence of a dose response for bystander mutagenesis, i.e., the MF plateaued. Interestingly, the magnitudes of the bystander MFs induced by different ion/energy combinations did vary, with bystander MFs ranging from 0.8 to 2.2× higher than the background. Furthermore, the nontargeted MFs appeared to reflect a mirror image of that for direct mutagenesis.
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Affiliation(s)
- Howard L Liber
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado 80525
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