Background: The aim of this study was to determine the frequency of alterations in BRAF and other RAS/RAF genes, as well as other targetable pathways in malignant peripheral nerve sheath tumors (MPNSTs). Patients and Methods: Pathology specimens were available for 2 cohorts: (1) patients with MPNST at Swedish Cancer Institute (n=17) from 2004 through 2016, and (2) patients with MPNST evaluated for >300 genomic alterations at Foundation Medicine from 2014 through 2016 (n=186; including 2 Swedish patients with BRAF-mutated MPNST). Results: Of 201 MPNSTs, 13 (6.5%) demonstrated BRAF alterations. In the Foundation Medicine cohort, 10 of 84 tumors (11.9%) with no NF1 alterations had BRAF mutations (5 were V600E, 5 other), as did 3 of 102 (2.9%) tumors with NF1 alterations (1 V600E, 2 other). In the Foundation Medicine cohort, 47% of patients had an alteration in at least one other gene in the RAS/RAF pathway (not including NF1 or BRAF); 46% had alterations in the PI3 pathway, with 70% having alterations in at least 1 of the 2 pathways; 57% had a CDKN2A alteration (80% in BRAF-mutated and 71% in NF1-altered patients); and 70% had an alteration in DNA repair genes. MPNST, both NF1 wild-type and NF1-mutated, often harbor alterations in the RAS/RAF pathway as well as changes related to DNA repair and CDKN2A/B. V600E and other mutations occur in BRAF, suggesting the need for second-generation activating BRAF inhibitors. The concurrence of BRAF and/or NF1 alterations with CDKN2A/B mutations, in particular, may be significant in the transformation of neurologic tumors from benign to malignant. Conclusions: All MPNSTs would benefit from a comprehensive genomic analysis. Treatments targeted to RAS/RAF, DNA repair, and CDKN2A/B pathways should be used and/or developed to treat this uncommon tumor.
Henry G. Kaplan, Steven Rostad, Jeffrey S. Ross, Siraj M. Ali and Sherri Z. Millis
Stuart L. Cramer, Rong Li, Siraj Ali, Julie A. Bradley, Hee K. Kim and Joseph G. Pressey
Primitive myxoid mesenchymal tumor of infancy (PMMTI) is a rare tumor with <20 cases reported to date. Recently PMMTI tumors have been found to harbor BCOR internal tandem duplication (ITD), the same genetic alteration detected in clear cell sarcoma of the kidney (CCSK). Complete surgical resection of PMMTI is often curative, but no standard of care has been established for unresectable tumors. We describe a female patient who presented at 13 months of age with a paraspinal mass and spinal cord compression. Histology was consistent with PMMTI, and the tumor was found to harbor BCOR ITD. The patient experienced disease recurrences after multiple surgical resections. After failing to respond to vincristine and actinomycin therapy, the patient demonstrated a nearly complete response to a doxorubicin-containing chemotherapy regimen. The patient's therapy was consolidated with proton beam radiotherapy, and she has remained in remission for >12 months after the conclusion of therapy. This case confirms BCOR ITD as a key finding in PMMTI. The therapeutic approach described here is similar to that used for CCSK and provides a model for the treatment of PMMTI not amenable to complete surgical resection.
Saranya Chumsri, Jodi Weidler, Siraj Ali, Sohail Balasubramanian, Gerald Wallweber, Lisa DeFazio-Eli, Ahmed Chenna, Weidong Huang, Angela DeRidder, Lindsay Goicocheal and Edith A. Perez
In the current genomic era, increasing evidence demonstrates that approximately 2% of HER2-negative breast cancers, by current standard testings, harbor activating mutations of ERBB2. However, whether patients with HER2-negative breast cancer with activating mutations of ERBB2 also experience response to anti-HER2 therapies remains unclear. This case report describes a patient with HER2-nonamplified heavily pretreated breast cancer who experienced prolonged response to trastuzumab in combination with pertuzumab and fulvestrant. Further molecular analysis demonstrated that her tumors had an elevated HER2 dimerization that corresponded to ERBB2 S310F mutation. Located in the extracellular domain of the HER2 protein, this mutation was reported to promote noncovalent dimerization that results in the activation of the downstream signaling pathways. This case highlights the fact that HER2-targeted therapy may be valuable in patients harboring an ERBB2 S310F mutation.
Vinod Ravi, Eric M. Sanford, Wei-Lien Wang, Jeffrey S. Ross, Naveen Ramesh, Andrew Futreal, Shreyaskumar Patel, Phillip J. Stephens, Vincent A. Miller and Siraj M. Ali
Background: Angiosarcoma is a malignant neoplastic disease originating from or differentiating toward vascular endothelium, for which systemic pharmacologic treatment has limited durability. The molecular oncogenesis of angiosarcoma is often linked to inappropriate activations of vascular endothelial growth factor receptor (VEGFR) family members, which presents an opportunity for the use of therapy that selectively targets the machinery of vascular signaling. Methods: Hybridization capture of 3,320 exons of 182 cancer-related genes and the introns of 14 genes frequently rearranged in cancer was applied to more than 50 ng of DNA extracted from a formalin-fixed, paraffin-embedded biopsy of recurrent angiosarcoma and was sequenced to high, uniform coverage of 939x. Results: The angiosarcoma harbored amplifications of VEGFR2 (KDR) of 8 copies and VEGFR3 (FLT4) of 16 copies. The patient was initially treated with sorafenib, an inhibitor of VEGFR2, and developed progressive disease. The patient then received pazopanib, an inhibitor of VEGFR2 and VEGFR3 and experienced a potent antitumor response resulting in clinically stable disease for 6 months. Conclusions: This exceptional response to pazopanib treatment suggests that a subset of patients with angiosarcoma with genomic alterations in vascular signaling genes may respond well to pazopanib.
Aatur D. Singhi, Siraj M. Ali, Jill Lacy, Andrew Hendifar, Khanh Nguyen, Jamie Koo, Jon H. Chung, Joel Greenbowe, Jeffrey S. Ross, Marina N. Nikiforova, Herbert J. Zeh, Inderpal S. Sarkaria, Anil Dasyam and Nathan Bahary
Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal cancers, with a 5-year survival of 8%. Current therapeutic regimens are largely ineffective and underscore the need for novel treatment strategies. Chromosomal rearrangements involving the anaplastic lymphoma kinase (ALK) gene have been identified in several neoplasms. In addition, ALK protein inhibitors have proven efficacy in patients with ALK-rearranged tumors. However, ALK translocations in PDAC have not been described. Through comprehensive genomic profiling of 3,170 PDACs, we identified 5 cases (0.16%) that harbored an ALK fusion gene: an exon 6 EML4–exon 20 ALK translocation (n=3), an exon 13 EML4–exon 20 ALK translocation (n=1), and an exon 3 STRN–exon 20 ALK translocation (n=1). Among the most prevalent PDAC-related genes, activating KRAS mutations were absent in all 5 cases, who were <50 years of age. Among patients aged <50 years in our study cohort, ALK translocations constituted 1.3% of PDACs. Four of 5 patients were treated with an ALK inhibitor, and 3 of these patients demonstrated stable disease, radiographic response, and/or normalization of serum CA 19-9. Although rare, ALK fusions occur in PDAC, and screening for ALK rearrangements should be considered in young patients with PDAC.
Silviya K. Meletath, Dean Pavlick, Tim Brennan, Roy Hamilton, Juliann Chmielecki, Julia A. Elvin, Norma Palma, Jeffrey S. Ross, Vincent A. Miller, Philip J. Stephens, George Snipes, Veena Rajaram, Siraj M. Ali and Isaac Melguizo-Gavilanes
Background: Gangliogliomas are slow-growing, low-grade central nervous system tumors affecting children and young adults. However, some patients will experience tumor recurrence and/or malignant progression. This article reports on the clinical history, molecular findings, and treatment response in a patient with BRAF V600–mutated high-grade glioma arising from ganglioglioma. Methods: Hematoxylin-eosin staining and comprehensive genomic profiling via Foundation One were performed on the tumor sample from a male patient undergoing treatment at the Department of Neuro-Oncology at Baylor University Medical Center. Results: The patient was eligible for participation in a clinical trial (ClinicalTrials.gov identifier: NCT00916409) of a tumor treatment fields (TTFields) device, NovoTTF-100A, with concurrent radiation and chemotherapy (CCRT). His disease relapsed 4 months after completion of his CCRT, with MRI showing areas of enhancement. Temozolomide was discontinued and he was offered dabrafenib, an oral selective inhibitor of BRAF V600E, with continued use of NovoTTF. At the time of this report, after 2 years of treatment with dabrafenib and TTFields, the patient shows a durable complete response in all areas with no active lesions or new areas of enhancement. Conclusions: This report suggests that TTFields delivered in combination with targeted therapy dabrafenib yielded a remarkable clinical and radiologic response in this recurrent high-grade glioma. Targeted therapy matched to genomic alterations combined with TTFields treatment could provide clinical benefit and should be prospectively explored in the near future.