Genes, Chromosomes and Cancer

Vaňková, Bohuslava; Vaněček, Tomáš; Ptáková, Nikola; Hájková, Veronika; Dušek, Martin; Michal, Michael; Švajdler, Peter; Daum, Ondřej; Daumová, Magdaléna; Michal, Michal; Mezencev, Roman; Švajdler, Marián

doi: 10.1002/gcc.22861pmid: 32427409

Oncogenic gene fusions represent attractive targets for therapy of cancer. However, the frequency of actionable genomic rearrangements in colorectal cancer (CRC) is very low, and universal screening for these alterations seems to be impractical and costly. To address this problem, several large scale studies retrospectivelly showed that CRC with gene fusions are highly enriched in groups of tumors defined by MLH1 DNA mismatch repair protein deficiency (MLH1d), and hypermethylation of MLH1 promoter (MLH1ph), and/or the presence of microsatellite instability, and BRAF/KRAS wild‐type status (BRAFwt/KRASwt). In this study, we used targeted next generation sequencing (NGS) to explore the occurence of potentially therapeutically targetable gene fusions in an unselected series of BRAFwt/KRASwt CRC cases that displayed MLH1d/MLH1ph. From the initially identified group of 173 MLH1d CRC cases, 141 cases (81.5%) displayed MLH1ph. BRAFwt/RASwt genotype was confirmed in 23 of 141 (~16%) of MLH1d/MLH1ph cases. Targeted NGS of these 23 cases identified oncogenic gene fusions in nine patients (39.1%; CI95: 20.5%‐61.2%). Detected fusions involved NTRK (four cases), ALK (two cases), and BRAF genes (three cases). As a secondary outcome of NGS testing, we identified PIK3K‐AKT‐mTOR pathway alterations in two CRC cases, which displayed PIK3CA mutation. Altogether, 11 of 23 (~48%) MLH1d/MLH1ph/BRAFwt/RASwt tumors showed genetic alterations that could induce resistance to anti‐EGFR therapy. Our study confirms that targeted NGS of MLH1d/MLH1ph and BRAFwt/RASwt CRCs could be a cost‐effective strategy in detecting patients with potentially druggable oncogenic kinase fusions.

Smith, Scott C.; Althof, Pamela A.; Dave, Bhavana J.; Sanmann, Jennifer N.

doi: 10.1002/gcc.22874pmid: 32447782

Multiple myeloma is a clonal malignancy of plasma cells in the bone marrow. Risk stratification is partly based on cytogenetic findings that include abnormalities of the IGH locus as determined by fluorescence in situ hybridization (FISH), such as rearrangements that result in either standard‐risk or high‐risk gene fusions. IGH deletions have been evaluated as a group in multiple myeloma patients with respect to cumulative outcomes but have provided limited guidance. Whether these deletions have the potential to result in gene fusions and thus further stratify patients is unknown. We identified 229 IGH deletions in patients referred for plasma cell dyscrasia genetic testing over 5.5 years. Follow‐up was conducted on 208 of the deletions with dual fusion FISH probes for standard‐risk (IGH‐CCND1) and high‐risk IGH gene fusions (IGH‐FGFR3, IGH‐MAF, IGH‐MAFB). Of all deletions identified with follow‐up, 44 (21%) resulted in a gene fusion as detected by FISH, 15 (7%) of which were fusion partners associated with high‐risk multiple myeloma. All fusion‐positive 3′‐IGH deletions (6 fusions) resulted in high‐risk IGH‐FGFR3 fusions. Of the 15 high‐risk fusion‐positive cases, eight were without other high‐risk cytogenetic findings. This study is the first to evaluate the presence of IGH gene fusions upon identification of IGH deletions and to characterize the deletion locus. Importantly, these findings indicate that follow‐up FISH studies with dual fusion probes should be standard of care when IGH deletions are identified in multiple myeloma.

Kao, Yu‐Chien; Suurmeijer, Albert J. H.; Argani, Pedram; Dickson, Brendan C.; Zhang, Lei; Sung, Yun‐Shao; Agaram, Narasimhan P; Fletcher, Christopher D. M.; Antonescu, Cristina R.

doi: 10.1002/gcc.22877pmid: 32506523

Gene fusions resulting in oncogenic activation of various receptor tyrosine kinases, including NTRK1‐3, ALK, and RET, have been increasingly recognized in soft tissue tumors (STTs), displaying a wide morphologic spectrum and therefore diagnostically challenging. A subset of STT with NTRK1 rearrangements were recently defined as lipofibromatosis‐like neural tumors (LPFNTs), being characterized by mildly atypical spindle cells with a highly infiltrative growth in the subcutis and expression of S100 and CD34 immunostains. Other emerging morphologic phenotypes associated with kinase fusions include infantile/adult fibrosarcoma and malignant peripheral nerve sheath tumor‐like patterns. In this study, a large cohort of 73 STT positive for various kinase fusions, including 44 previously published cases, was investigated for the presence of an LPFNT phenotype, to better define the incidence of this distinctive morphologic pattern and its relationship with various gene fusions. Surprisingly, half (36/73) of STT with kinase fusions showed at least a focal LPFNT component defined as >10%. Most of the tumors occurred in the subcutaneous tissues of the extremities (n = 25) and trunk (n = 9) of children or young adults (<30 years old) of both genders. Two‐thirds (24/36) of these cases showed hybrid morphologies with alternating LPFNT and solid areas of monomorphic spindle to ovoid tumor cells with fascicular or haphazard arrangement, while one‐third (12/36) had pure LPFNT morphology. Other common histologic findings included lymphocytic infiltrates, staghorn‐like vessels, and perivascular or stromal hyalinization, especially in hybrid cases. Mitotic activity was generally low (<4/10 high power fields in 81% cases), being increased only in a minority of cases. Immunoreactivity for CD34 (92% in hybrid cases, 89% in pure cases) and S100 (89% in hybrid cases, 64% in pure cases) were commonly present. The gene rearrangements most commonly involved NTRK1 (75%), followed by RET (8%) and less commonly NTRK2, NTRK3, ROS1, ALK, and MET.

Polski, Ashley; Xu, Liya; Prabakar, Rishvanth K.; Gai, Xiaowu; Kim, Jonathan W.; Shah, Rachana; Jubran, Rima; Kuhn, Peter; Cobrinik, David; Hicks, James; Berry, Jesse L.

doi: 10.1002/gcc.22859pmid: 32390242

Retinoblastoma (RB) is a childhood intraocular cancer initiated by biallelic inactivation of the RB tumor suppressor gene (RB1−/−). RB can be hereditary (germline RB1 pathogenic allele is present) or non‐hereditary. Somatic copy number alterations (SCNAs) contribute to subsequent tumorigenesis. Previous studies of only enucleated RB eyes have reported associations between heritability status and the prevalence of SCNAs. Herein, we use an aqueous humor (AH) liquid biopsy to investigate RB genomic profiles in the context of germline RB1 status, age, and International Intraocular Retinoblastoma Classification (IIRC) clinical grouping for both enucleated and salvaged eyes. Between 2014 and 2019, AH was sampled from a total of 54 eyes of 50 patients. Germline RB1 status was determined from clinical blood testing, and cell‐free DNA from AH was analyzed for SCNAs. Of the 50 patients, 23 (46.0%; 27 eyes) had hereditary RB, and 27 (54.0%, 27 eyes) had non‐hereditary RB. Median age at diagnosis was comparable between hereditary (13 ± 10 months) and non‐hereditary (13 ± 8 months) eyes (P = 0.818). There was no significant difference in the prevalence or number of SCNAs based on (1) hereditary status (P > 0.56) or (2) IIRC grouping (P > 0.47). There was, however, a significant correlation between patient age at diagnosis, and (1) number of total SCNAs (r[52] = 0.672, P < 0.00001) and (2) number of highly‐recurrent RB SCNAs (r[52] = 0.616, P < 0.00001). This evidence does not support the theory that specific molecular or genomic subtypes exist between hereditary and non‐hereditary RB; rather, the prevalence of genomic alterations in RB eyes is strongly related to patient age at diagnosis.

Williamson, Sean R.; Cardili, Leonardo; Whiteley, Lisa J.; Sanchez, Jessica; Kis, Olena

doi: 10.1002/gcc.22860pmid: 32418252

The tuberous sclerosis genes and MTOR are increasingly being found to have important roles in novel subtypes of renal cancer, particularly emerging entities eosinophilic solid and cystic renal cell carcinoma (RCC) and high‐grade oncocytic renal tumor (HOT)/RCC with eosinophilic and vacuolated cytoplasm. We report a unique renal neoplasm in a 66‐year‐old woman that initially mimicked MITF family translocation RCC due to mixed clear and eosinophilic cells, extensive stromal hyalinization, and psammoma bodies, yet which was negative for TFE3 and TFEB fluorescence in situ hybridization and a next generation sequencing (NGS) gene fusion assay. Cytoplasmic stippling triggered consideration of TSC‐associated neoplasms, and a targeted NGS assay revealed a variant in exon 21 of TSC1 resulting in c.2626G>T p.(Glu876*) truncating mutation. This report adds to the morphologic spectrum of TSC‐related renal neoplasms, including prominent stromal hyalinization as a potentially deceptive pattern. Due to the overlap in cytoplasmic stippling between eosinophilic solid and cystic RCC and HOT/RCC with eosinophilic and vacuolated cytoplasm, it is debatable which category this example would best fit. Further understanding of these entities and other renal neoplasms with alterations in the TSC genes will elucidate whether they should be considered a family of tumors.

Sheng, Shao‐Jie; Li, Ju‐Ming; Zou, Yue‐Fen; Peng, Xiao‐Jing; Wang, Qian‐Yu; Fang, Hai‐Sheng; Li, Xiao; Ding, Ying; Fan, Qin‐He; Zhang, Zhi‐Hong; Wei, Yong‐Zhong; Gong, Qi‐Xing

doi: 10.1002/gcc.22875pmid: 32447786

Recently, a novel group of spindle cell tumors defined by S100 and CD34 co‐expression harboring recurrent fusions involving RET, RAF1, BRAF, and NTRK1/2 gene has been identified. Morphologically, they are characterized by monomorphic neoplasm cells, “patternless” growth pattern, stromal, and perivascular hyalinization, lacked necrosis. We reported a 52‐year‐old Chinese female patient with a S100 and CD34 co‐expression sarcoma presenting in the right proximal forearm. The forearm mass initially emerged 19 months ago when it was misdiagnosed as a solitary fibrous tumor and was surgically removed without further treatment. Microscopically, the primary and the recurred tumors share the same features, resembling the morphology of the recently characterized group. Nevertheless, some distinct features, such as predominantly epithelioid tumor cells and focally staghorn vessels, were also present in our case. Genomic profiling with clinical next‐generation sequencing was performed and revealed CDC42SE2‐BRAF gene fusion, MET amplification, and CDKN2A/B deletion. Both FISH and nested RT‐PCR were performed to confirm the gene fusion. The patient was treated with crizotinib for two cycles but showed no obvious benefit. The presented case adds to the spectrum of the novel, characterized solid tumors, and provides suggestions for emerging therapeutic strategies for precision medicine involving targeted kinase inhibitors.

Heilig, Christoph E.; Horak, Peter; Lipka, Daniel B.; Mock, Andreas; Uhrig, Sebastian; Kreutzfeldt, Simon; Richter, Susan; Gieldon, Laura; Fröhlich, Martina; Hutter, Barbara; Hübschmann, Daniel; Teleanu, Veronica; Schmier, Johann‐Wilhelm; Philipzen, Johannes; Beuthien‐Baumann, Bettina; Schröck, Evelin; Deimling, Andreas; Bauer, Sebastian; Heining, Christoph; Mechtersheimer, Gunhild; Stenzinger, Albrecht; Brors, Benedikt; Wardelmann, Eva; Glimm, Hanno; Hartmann, Wolfgang; Fröhling, Stefan

doi: 10.1002/gcc.22876pmid: 32501622

Gastrointestinal stromal tumors (GISTs) are the most frequent mesenchymal tumors of the gastrointestinal tract. Inactivating mutations or epigenetic deregulation of succinate dehydrogenase complex (SDH) genes are considered defining features of a subset of GIST occurring in the stomach. Based on comprehensive molecular profiling and biochemical analysis within a precision oncology program, we identified hallmarks of SDH deficiency (germline SDHB‐inactivating mutation accompanied by somatic loss of heterozygosity, lack of SDHB expression, global DNA hypermethylation, and elevated succinate/fumarate ratio) in a 40‐year‐old woman with undifferentiated gastric spindle cell sarcoma that did not meet the diagnostic criteria for other mesenchymal tumors of the stomach, including GIST. These data reveal that the loss of SDH function can be involved in the pathogenesis of non‐GIST sarcoma of the gastrointestinal tract.