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Ludwig M, Birkeland A, Smith J, Gensterblum-Miller E, Zhai JI, Kulkarni A, Jiang H, Brenner C. A Genome Wide CRISPR Pro filing Approach Identi fies Mechanisms of Cisplatin Resistance in Head and Neck Squamous Cell Carcinoma. RESEARCH SQUARE 2024:rs.3.rs-3922565. [PMID: 38464196 PMCID: PMC10925415 DOI: 10.21203/rs.3.rs-3922565/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Background Head and neck squamous cell carcinoma (HNSCC) is a lethal disease with poor survival rates, especially for cancers arising in the oral cavity or larynx. Cisplatin is a key chemotherapeutic for HNSCC; however poor survival rates may be partially due to cisplatin resistance observed in some HNSCCs. Here, we examined the utility of genome-wide CRISPR knockout profiling for nominating pivotal mechanisms of cisplatin resistance in HNSCC models. Methods We characterized the cisplatin sensitivity of 18 HNSCC cell lines. Next, we used a genome-wide CRISPR/Cas9 library to identify genes involved in cisplatin resistance. We next performed validation assays in the UM-SCC-49 cell line model. Results Our data prioritized 207 genes as pivotal for cisplatin resistance in HNSCC, including novel genes VGLL3, CIRHA1, NCOR1, SPANXA1, MAP2K7, ULK1, and CDK16. Gene set enrichment analysis identified several NOTCH family genes comprising the top pathway driving cisplatin resistance, which we then validated using a targeted NOTCH1 knockout model. Interestingly, we noted that HNSCC models with natural NOTCH pathway alterations including single allele mutations and/or frameshift alterations had diverse responses to cisplatin treatment suggesting that complex and multi-faceted mechanisms contribute to cisplatin resistance in HNSCC. Conclusions Collectively, our study validates a genome-wide CRISPR/Cas9 approach for the discovery of resistance mechanisms in HNSCC, adds to the growing evidence that NOTCH1 status should be evaluated as a biomarker of cisplatin response and provides a framework for future work aimed at overcoming cisplatin resistance.
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Heft Neal ME, Birkeland AC, Bhangale AD, Zhai J, Kulkarni A, Foltin SK, Jewell BM, Ludwig ML, Pinatti L, Jiang H, McHugh JB, Marentette L, McKean EL, Brenner JC. Genetic analysis of sinonasal undifferentiated carcinoma discovers recurrent SWI/SNF alterations and a novel PGAP3-SRPK1 fusion gene. BMC Cancer 2021; 21:636. [PMID: 34051734 PMCID: PMC8164750 DOI: 10.1186/s12885-021-08370-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 05/12/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Sinonasal Undifferentiated Carcinoma (SNUC) is a rare and aggressive skull base tumor with poor survival and limited treatment options. To date, targeted sequencing studies have identified IDH2 and SMARCB1 as potential driver alterations, but the molecular alterations found in SMARCB1 wild type tumors are unknown. METHODS We evaluated survival outcomes in a cohort of 46 SNUC patients treated at an NCI designated cancer center and identify clinical and disease variables associated with survival on Kaplan-Meier and Cox multivariate survival analysis. We performed exome sequencing to characterize a series of SNUC tumors (n = 5) and cell line (MDA8788-6) to identify high confidence mutations, copy number alterations, microsatellite instability, and fusions. Knockdown studies using siRNA were utilized for validation of a novel PGAP3-SRPK1 gene fusion. RESULTS Overall survival analysis revealed no significant difference in outcomes between patients treated with surgery +/- CRT and CRT alone. Tobacco use was the only significant predictor of survival. We also confirmed previously published findings on IDH and SMARC family mutations and identified novel recurrent aberrations in the JAK/STAT and PI3K pathways. We also validated a novel PGAP3-SRPK1 gene fusion in the SNUC cell line, and show that knockdown of the fusion is negatively associated with EGFR, E2F and MYC signaling. CONCLUSION Collectively, these data demonstrate recurrent alterations in the SWI/SNF family as well as IDH, JAK/STAT, and PI3K pathways and discover a novel fusion gene (PGAP3-SRPK1). These data aim to improve understanding of possible driver mutations and guide future therapeutic strategies for this disease.
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Affiliation(s)
- Molly E Heft Neal
- Department of Otolaryngology - Head and Neck Surgery, University of Michigan, 1150 E. Medical Center Dr., 9301B MSRB3, Ann Arbor, MI, 48109-0602, USA
| | - Andrew C Birkeland
- Department of Otolaryngology - Head and Neck Surgery, University of Michigan, 1150 E. Medical Center Dr., 9301B MSRB3, Ann Arbor, MI, 48109-0602, USA
| | - Apurva D Bhangale
- Department of Otolaryngology - Head and Neck Surgery, University of Michigan, 1150 E. Medical Center Dr., 9301B MSRB3, Ann Arbor, MI, 48109-0602, USA
| | - Jingyi Zhai
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Aditi Kulkarni
- Department of Otolaryngology - Head and Neck Surgery, University of Michigan, 1150 E. Medical Center Dr., 9301B MSRB3, Ann Arbor, MI, 48109-0602, USA
| | - Susan K Foltin
- Department of Otolaryngology - Head and Neck Surgery, University of Michigan, 1150 E. Medical Center Dr., 9301B MSRB3, Ann Arbor, MI, 48109-0602, USA
| | - Brittany M Jewell
- Department of Otolaryngology - Head and Neck Surgery, University of Michigan, 1150 E. Medical Center Dr., 9301B MSRB3, Ann Arbor, MI, 48109-0602, USA
| | - Megan L Ludwig
- Department of Otolaryngology - Head and Neck Surgery, University of Michigan, 1150 E. Medical Center Dr., 9301B MSRB3, Ann Arbor, MI, 48109-0602, USA.,Program in Cellular and Molecular Biology, University of Michigan, 1150 E. Medical Center Dr., 9301B MSRB3, Ann Arbor, MI, 48109-0602, USA
| | - Lisa Pinatti
- Department of Otolaryngology - Head and Neck Surgery, University of Michigan, 1150 E. Medical Center Dr., 9301B MSRB3, Ann Arbor, MI, 48109-0602, USA.,Program in Cancer Biology, University of Michigan, Ann Arbor, MI, USA
| | - Hui Jiang
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA.,Rogel Cancer Center, University of Michigan Medical School, 1150 E. Medical Center Dr., 9301B MSRB3, Ann Arbor, MI, 48109-0602, USA
| | - Jonathan B McHugh
- Rogel Cancer Center, University of Michigan Medical School, 1150 E. Medical Center Dr., 9301B MSRB3, Ann Arbor, MI, 48109-0602, USA.,Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Lawence Marentette
- Department of Otolaryngology - Head and Neck Surgery, University of Michigan, 1150 E. Medical Center Dr., 9301B MSRB3, Ann Arbor, MI, 48109-0602, USA.,Rogel Cancer Center, University of Michigan Medical School, 1150 E. Medical Center Dr., 9301B MSRB3, Ann Arbor, MI, 48109-0602, USA
| | - Erin L McKean
- Department of Otolaryngology - Head and Neck Surgery, University of Michigan, 1150 E. Medical Center Dr., 9301B MSRB3, Ann Arbor, MI, 48109-0602, USA.,Rogel Cancer Center, University of Michigan Medical School, 1150 E. Medical Center Dr., 9301B MSRB3, Ann Arbor, MI, 48109-0602, USA
| | - J Chad Brenner
- Department of Otolaryngology - Head and Neck Surgery, University of Michigan, 1150 E. Medical Center Dr., 9301B MSRB3, Ann Arbor, MI, 48109-0602, USA. .,Program in Cellular and Molecular Biology, University of Michigan, 1150 E. Medical Center Dr., 9301B MSRB3, Ann Arbor, MI, 48109-0602, USA. .,Rogel Cancer Center, University of Michigan Medical School, 1150 E. Medical Center Dr., 9301B MSRB3, Ann Arbor, MI, 48109-0602, USA. .,Department of Pharmacology, University of Michigan, 1150 E. Medical Center Dr., 9301B MSRB3, Ann Arbor, MI, 48109-0602, USA.
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Heft Neal ME, Gensterblum-Miller E, Bhangale AD, Kulkarni A, Zhai J, Smith J, Brummel C, Foltin SK, Thomas D, Jiang H, McHugh JB, Brenner JC. Integrative sequencing discovers an ATF1-motif enriched molecular signature that differentiates hyalinizing clear cell carcinoma from mucoepidemoid carcinoma. Oral Oncol 2021; 117:105270. [PMID: 33827033 DOI: 10.1016/j.oraloncology.2021.105270] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 03/16/2021] [Accepted: 03/20/2021] [Indexed: 12/27/2022]
Abstract
OBJECTIVES Salivary gland tumors are comprised of a diverse group of malignancies with widely varying prognoses. These cancers can be difficult to differentiate, especially in cases with limited potential for immunohistochemistry (IHC)-based characterization. Here, we sought to define the molecular profile of a rare salivary gland cancer called hyalinizing clear cell carcinoma (HCCC), and identify a molecular gene signature capable of distinguishing between HCCC and the histopathologically similar disease, mucoepidermoid carcinoma (MEC). MATERIALS AND METHODS We performed the first integrated full characterization of five independent HCCC cases. RESULTS We discovered insulin-like growth factor alterations and aberrant IGF2 and/or IGF1R expression in HCCC tumors, suggesting a potential dependence on this pathway. Further, we identified a 354 gene signature that differentiated HCCC from MEC, and was significantly enriched for genes with an ATF1 binding motif in their promoters, supporting a transcriptional pathogenic mechanism of the characteristic EWSR1-ATF1 fusion found in these tumors. Of the differentially expressed genes, IGF1R, SGK1 and SGK3 were found to be elevated in the HCCCs relative to MECs. Finally, analysis of immune checkpoints and subsequent IHC demonstrated that CXCR4 protein was elevated in several of the HCCC cases. CONCLUSION Collectively, our data identify an ATF1-motif enriched gene signature that may have clinical utility for molecular differentiation of HCCCs from other salivary gland tumors and discover potential actionable alterations that may benefit the clinical care of recurrent HCCC patients.
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Affiliation(s)
- M E Heft Neal
- Department of Otolaryngology - Head and Neck Surgery, University of Michigan Medical School, Ann Arbor, MI, United States
| | - E Gensterblum-Miller
- Department of Otolaryngology - Head and Neck Surgery, University of Michigan Medical School, Ann Arbor, MI, United States
| | - A D Bhangale
- Department of Otolaryngology - Head and Neck Surgery, University of Michigan Medical School, Ann Arbor, MI, United States
| | - A Kulkarni
- Department of Otolaryngology - Head and Neck Surgery, University of Michigan Medical School, Ann Arbor, MI, United States
| | - J Zhai
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - J Smith
- Department of Otolaryngology - Head and Neck Surgery, University of Michigan Medical School, Ann Arbor, MI, United States
| | - C Brummel
- Department of Otolaryngology - Head and Neck Surgery, University of Michigan Medical School, Ann Arbor, MI, United States
| | - S K Foltin
- Department of Otolaryngology - Head and Neck Surgery, University of Michigan Medical School, Ann Arbor, MI, United States
| | - D Thomas
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, United States
| | - H Jiang
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, United States; Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, United States
| | - J B McHugh
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, United States
| | - J C Brenner
- Department of Otolaryngology - Head and Neck Surgery, University of Michigan Medical School, Ann Arbor, MI, United States; Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, United States; Department of Pharmacology, University of Michigan Medical School, Ann Arbor, MI, United States.
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Swiecicki PL, Durm G, Bellile E, Bhangale A, Brenner JC, Worden FP. A multi-center phase II trial evaluating the efficacy of palbociclib in combination with carboplatin for the treatment of unresectable recurrent or metastatic head and neck squamous cell carcinoma. Invest New Drugs 2020; 38:1550-1558. [PMID: 31981071 DOI: 10.1007/s10637-020-00898-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Accepted: 01/15/2020] [Indexed: 02/06/2023]
Abstract
Background Palbociclib is a selective inhibitor of CDK4/6 approved in metastatic breast cancer as well as evidence of activity in malignancies with CDK4-amplifications. Extensive preclinical evidence has demonstrated synergy of CDK4/6 inhibitors with platinum chemotherapy suggesting a potential role for clinical synthetic lethality. Given the sensitivity to platinum therapy as well as the landscape of genomic alterations, concurrent treatment with platinum chemotherapy and palbociclib is of significant interest as a novel treatment approach. Patients and Methods Patients with unresectable, recurrent, or metastatic head and neck cancer (R/M HNC) were enrolled. Eligible patients were required to have no previous treatment with cytotoxic chemotherapy in the recurrent/metastatic setting. This was a multicenter phase II trial in which patients were administered carboplatin in addition to concurrent palbociclib. The primary endpoint of this trial was 12-week disease control rate (DCR). Results Twenty-one patients were enrolled and 18 were evaluable for response. Grade 3/4 treatment related toxicities were seen in 79% of patients of which the most common were related to myelosuppression. 12-week DCR was 33% (5 patients with stable disease, 1 with a partial response). Median progression free survival was 2.9 months (range: 1.2-13.3) and overall survival was 4.6 months (range: 1.4-14.8). Conclusion The combination of carboplatin and palbociclib is associated with significant treatment related toxicity and insufficient anti-tumor activity.
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Affiliation(s)
- Paul L Swiecicki
- Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan Medical School, 300 N Ingalls St, SPC 5419, Ann Arbor, MI, 48109, USA. .,Department of Internal Medicine, Division of Hematology/Oncology, Ann Arbor Veterans Affairs Medical Center, Ann Arbor, MI, USA. .,Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA.
| | - Greg Durm
- Department of Internal Medicine, Division of Hematology/Oncology, Indiana University, Indianapolis, IN, USA
| | - Emily Bellile
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Apurva Bhangale
- Department of Otolaryngology-Head and Neck Surgery, University of Michigan Medical School, University of Michigan Health System, Ann Arbor, MI, USA
| | - J Chad Brenner
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA.,Department of Otolaryngology-Head and Neck Surgery, University of Michigan Medical School, University of Michigan Health System, Ann Arbor, MI, USA.,Department of Pharmacology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Francis P Worden
- Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan Medical School, 300 N Ingalls St, SPC 5419, Ann Arbor, MI, 48109, USA.,Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA
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