Identification by NGS of a Diagnostic and Theranostic Mutation in a High-Grade Sarcoma of the Humerus

reprinted from january 2019

pathology ◆ laboratory medicine ◆ laboratory management Identification by NGS of a diagnostic and theranostic mutation in a high-grade sarcoma of the humerus

CAP TODAY and the Association for Mo- measuring approximately 7.5 cm that SOX9, SOX10, BRAF-V600E, S100 lecular Pathology have teamed up to bring disrupted the posteromedial cortex protein, pankeratin, and GATA3 (not molecular case reports to CAP TODAY of the humerus and extended into the shown). The Ki-67 proliferative index readers. AMP members write the reports soft tissues. The superior aspect of the was approximately 90 percent. The tumor showed septal enhancement, presence of osteoid with SATB2 and suggestive of enchondroma, while p53 positivity raised the possibility of the distal aspect of the lesion showed osteosarcoma, either as a primary disorganized, heterogeneous en- diagnosis or as the dedifferentiated hancement and a large soft tissue component of chondrosarcoma. Since case report mass extending from the medullary preoperative chemotherapy is usu- cavity. These imaging findings were ally given in cases of osteosarcoma or using clinical cases from their own prac- suggestive of dedifferentiated undifferentiated sarcoma and not tices that show molecular testing’s impor- chondrosarcoma. Prominent axillary routinely in cases of dedifferentiated tant role in diagnosis, prognosis, and lymph nodes were observed; how- chondrosarcoma, the distinction was treatment. The following report comes ever, no distant metastases were clinically important. from the University of Texas MD Ander- identified. An initial preliminary diagnosis of son Cancer Center. If you would like to The patient was referred to our high-grade malignant neoplasm, pos- submit a case report, please send an email institution for further management, sibly dedifferentiated chondrosarco- to the AMP at [email protected]. For more infor- where an x-ray followed by an ultra- ma, was rendered and FFPE tissue mation about the AMP and all previously sound-guided core-needle biopsy was sent to the molecular diagnostics published case reports, visit www.amp.org. (Figs. 1B and 1C) were performed laboratory for DNA extraction and Roberto Ruiz-Cordero, MD prior to receipt of the outside MRI targeted next-generation sequencing. Jeanne M. Meis, MD studies. The histologic sections We performed mutational analysis on Russell R. Broaddus, MD, PhD showed sheets of large epithelioid the Ion Torrent semiconductor-based A 75-year-old woman with history of cells with well-defined cytoplasmic sequencer (Thermo Fisher Scientific) melanoma localized to the right fore- margins with osteoid deposition and using a 50 cancer-related gene custom arm and status post excision six years a minute fragment of atypical carti- panel. Mutations in the IDH2 prior presented with a two-month lage. The initial morphologic differ- (NM_002168.2(IDH2):c.516G>T history of continuous left shoulder ential diagnosis included metastatic p.R172S) and TP53 (NM_000546.5 pain. She was managed initially with melanoma, metastatic breast carci- (TP53):c.535C>A p.H179N) genes physical therapy and hydrocodone noma, and high-grade sarcoma in- were identified Figs.( 1G and 1H). No with no effect. Initial workup at an cluding dedifferentiated chondro mutations in the BRAF gene were outside institution included an x-ray sarcoma. Immunohistochemistry detected. The presence of the IDH2 of the left shoulder (Fig. 1A, page 2) analysis performed on formalin- mutation confirmed the initial radio- that showed a destructive lytic lesion fixed, paraffin-embedded tissue sec- logic, morphologic, and immunophe- involving the proximal aspect of the tions showed that the tumor cells notypic findings of dedifferentiated left humerus associated with a patho- were positive for SATB2 (Fig. 1C, chondrosarcoma; thus the patient logic fracture. A subsequent MRI (Fig. middle panel) and p53 (Fig. 1C, bot- was eligible to participate in a pan- 1D) showed a dichotomous tumor tom panel) and negative for MART-1, IDH inhibitor clinical trial. 2 | CAP TODAY

Fig. 1 low-up and died four months after surgery. Mutations in the genes encoding the isocitrate dehydrogenase (IDH) 1/2 enzyme have been found in several tumors, including gliomas, some acute leukemias, cartilaginous tumors, thyroid carcinomas, cholangio- carcinoma, prostate cancer, paragan- glioma, colorectal carcinoma, and melanoma.1 IDH2 catalyzes in the mitochondria the conversion of isocitrate to α-ketoglutarate, also known as 2-oxoglutarate (2OG), as part of the transformation of pyruvate into glu- tamate in the Krebs cycle,2 thereby playing a major role in cellular me- tabolism and energy production. En- zymes including histone methylases and other hydroxylases depend on 2OG to function properly.1 While somatic mutations of IDH1/2 were first described in gliomas,3 specific mutations in the arginine 172 residue of IDH2 have been reported in giant cell tumors of bone and cartilaginous tumors.4 Mutated IDH2 proteins ac- quire unique enzymatic activities that facilitate the production of oncometabolite D-2-hydroxyglutarate that inhibits 2OG-dependent enzymes.1 IDH2-R172S mutation has been found in 87 percent of enchondromas and 70 percent of spindle cell heman- giomas in association with Ollier disease and Maffucci syndrome5; however, IDH1/2 mutations can also be found in up to 87 percent of dedifferentiated chondrosarcomas and 30 percent of conventional chondrosarcomas.6 Moreover, IDH1/2 mutations in codons 132 or 172 are useful to discriminate between dedifferentiated chondrosarcoma and undifferentiated pleomorphic sarcoma of bone.6 The The patient underwent radical tic features, including large and bi- dedifferentiation process is complex resection of the tumor (Fig. 1E) with zarre nuclei with pseudoinclusions, and incompletely understood. Early endoprosthetic reconstruction of the irregular nuclear contours, variable reports identified similar genetic al- left proximal humerus. Microscopic chromatin distribution, and eosino- terations in both components includ- examination of the surgical specimen philic cytoplasm (Fig. 1I, inset). The ing loss of chromosome 13 and over- showed minor areas of conventional patient received the first cycle of IDH- expression of p53, with the anaplastic chondrosarcoma (Fig. 1F); however, inhibitor treatment, and radiation component also showing severe an- the majority of the tumor was dedif- therapy was recommended. Unfor- euploidy, loss of heterozygosity at ferentiated with high-grade anaplas- tunately, the patient was lost to fol- additional loci, and amplification and CAP TODAY | 3 deletion of several other chromo- 4. Liu X, Ogasawara S, Kaneko MK, et al. somes.7 The TP53 missense mutation A novel monoclonal antibody SMab-2 rec- Test yourself found in our case (H179N) has been ognizes endogenous IDH2-R172S of chon- Here are three questions taken from the reported in the Catalogue of Somatic drosarcoma. Biochem Biophys Res Comm. 2015;459(4):636–642. case report. Answers are online now at Mutations in Cancer database as 5. Pansuriya TC, van Eijk R, d’Adamo P, et www.amp.org/casereports and will be pub- pathogenic in at least 27 different al. Somatic mosaic IDH1 and IDH2 mu- lished next month in CAP TODAY. samples including primarily carcino- tations are associated with enchondroma 1. Mutations in which of the following and spindle cell hemangioma in Ollier dis- mas of the gastrointestinal tract and genes can help distinguish between ease and Maffucci syndrome. Nat Genet. one case of soft tissue sarcoma. Stud- dedifferentiated chondrosarcoma and 2011;43(12):1256–1261. ies have shown that p53 mutant pro- undifferentiated pleomorphic sarcoma teins have a longer half-life resulting 6. Chen S, Fritchie K, Wei S, et al. Diagnostic of bone? utility of IDH1/2 mutations to distinguish a. MDM2 in p53 IHC positivity in the majority dedifferentiated chondrosarcoma from un- of cases, as in our case, thereby mak- b. TP53 differentiated pleomorphic sarcoma of bone. c. IDH2 ing p53 IHC a good surrogate for Hum Pathol. 2017;65:239–246. d. PIK3CA TP53 mutation status.8 7. Bovée JV, Cleton-Jansen AM, Rosenberg C, Limited sample size or quality can Taminiau AH, Cornelisse CJ, Hogendoorn PC. 2. What molecule is isocitrate converted result in an equivocal microscopic Molecular genetic characterization of both to by IDH1/2 enzymes? diagnosis, and thus the identification components of a dedifferentiated chondrosar- a. D-2-hydroxyglutarate coma, with implications for its histogenesis. J b. 2-oxyglutarate, also known as α-ketoglutarate by NGS of specific mutation(s) can Pathol. 1999;189(4):454–462. c. Isocitrate aid in the final diagnosis and in man- 8. Murnyák B, Hortobágyi T. Immunohis- d. Citrate aging the disease. In summary, this tochemical correlates of TP53 somatic mu- e. Succinyl Co-A case demonstrates how the integra- tations in cancer. Oncotarget. 2016;7(40): 64910–64920. 3. What is the key oncometabolite pro- tion of clinical, radiological, patho- duced as a result of gain of function of logical, and molecular data can help Dr. Ruiz-Cordero is currently an assis- IDH2 due to mutations in the Arg140 or pathologists achieve the correct diag- Arg172 residues? tant professor, Department of Pathology, nosis, which is crucial for subsequent a. D-2-hydroxyglutarate University of California, San Francis- personalized therapy. b. 2-oxyglutarate, also known as α-ketoglutarate co. However, the content of this report c. Isocitrate 1. Yang H, Ye D, Guan KL, Xiong Y. IDH1 and comes from, and the report was written d. Citrate IDH2 mutations in tumorigenesis: mecha- at, the University of Texas MD Anderson e. Succinyl Co-A nistic insights and clinical perspectives. Clin Cancer Center, Houston, while he was Cancer Res. 2012;18(20):5562–5571. a hematopathology fellow (and former 2. Losman JA, Kaelin WG Jr. What a differ- molecular genetics pathology and cyto- ence a hydroxyl makes: mutant IDH, (R)-2- pathology fellow). Dr. Meis is a professor hydroxyglutarate, and cancer. Genes Dev. 2013; of bone and soft tissue pathology, and Dr. 27(8):836–852. Broaddus is a professor of gynecologic and 3. Yan H, Parsons DW, Jin G, et al. IDH1 and molecular pathology—both in the Depart- IDH2 mutations in gliomas. N Engl J Med. ment of Pathology, University of Texas 2009;360(8):765–773. MD Anderson Cancer Center.