Bioinformatic Analysis of Recurrent Genomic Alterations and Corresponding Pathway Alterations in Ewing Sarcoma

Ewing Sarcoma (ES) is an aggressive, mesenchymal malignancy associated with a poor prognosis in the recurrent or metastatic setting with an estimated overall survival (OS) of <30% at 5 years. ES is characterized by a balanced, reciprocal chromosomal translocation involving the EWSR1 RNA-binding protein and ETS transcription factor gene (EWS-FLI being the most common). Interestingly, murine ES models have failed to produce tumors phenotypically representative of ES. Genomic alterations (GA) in ES are infrequent and may work synergistically with EWS-ETS translocations to promote oncogenesis. Aberrations in fibroblast growth factor receptor (FGFR4), a receptor tyrosine kinase (RTK) have been shown to contribute to carcinogenesis. Mouse embryonic fibroblasts (MEFs) derived from knock-in strain of homologous Fgfr4G385R mice display a transformed phenotype with enhanced TGF-induced mammary carcinogenesis. The association between the FGFRG388R SNV in high-grade soft tissue sarcomas has previously been demonstrated conferring a statistically significant association with poorer OS. How the FGFR4G388R SNV specifically relates to ES has not previously been delineated. To further define the genomic landscape and corresponding pathway alterations in ES, comprehensive genomic profiling (CGP) was performed on the tumors of 189 ES patients. The FGFR4G388R SNV was identified in a significant proportion of the evaluable cases (n = 97, 51%). In line with previous analyses, TP53 (n = 36, 19%), CDK2NA/B (n = 33, 17%), and STAG2 (n = 22, 11.6%) represented the most frequent alterations in our cohort. Co-occurrence of CDK2NA and STAG2 alterations was observed (n = 5, 3%). Notably, we identified a higher proportion of TP53 mutations than previously observed. The most frequent pathway alterations affected MAPK (n = 89, 24% of pathological samples), HRR (n = 75, 25%), Notch1 (n = 69, 23%), Histone/Chromatin remodeling (n = 57, 24%), and PI3K (n = 64, 20%). These findings help to further elucidate the genomic landscape of ES with a novel investigation of the FGFR4G388R SNV revealing frequent aberration.

Clinical, pathological, and genomic features of EWSR1-PATZ1 fusion sarcoma

Molecular diagnostics of sarcoma subtypes commonly involve the identification of characteristic oncogenic fusions. EWSR1-PATZ1 is a rare fusion partnering in sarcoma, with few cases reported in the literature. In the current study, a series of 11 cases of EWSR1-PATZ1 fusion positive malignancies are described. EWSR1-PATZ1-related sarcomas occur across a wide age range and have a strong predilection for chest wall primary site. Secondary driver mutations in cell-cycle genes, and in particular CDKN2A (71%), are common in EWSR1-PATZ1 sarcomas in this series. In a subset of cases, an extended clinical and histopathological review was performed, as was confirmation and characterization of the fusion breakpoint revealing a novel intronic pseudoexon sequence insertion. Unified by a shared gene fusion, EWSR1-PATZ1 sarcomas otherwise appear to exhibit divergent morphology, a polyphenotypic immunoprofile, and variable clinical behavior posing challenges for precise classification.

Genomic Features for Therapeutic Insights of Chemotherapy-Resistant, Primary Mediastinal Nonseminomatous Germ Cell Tumors and Comparison with Gonadal Counterpart

Primary mediastinal nonseminomatous germ cell tumors (PMNSGCT) frequently become refractory to chemotherapy, and no effective salvage therapy exists. We performed genomic profiling on a series of 44 PMNSGCT and compared the results with those from chemorefractory, metastatic pure seminomatous (Sem, n = 22) and nonseminomatous (NS, n = 86) testicular germ cell tumors. Archival tissues were sequenced by a hybrid capture-based technology (FoundationONE; Foundation Medicine, Inc., Cambridge, MA). Microsatellite instability (MSI) and tumor mutational burden (TMB, mutations [mut]/Mb) were determined.Statistically significant differences in genomic alterations (GA) of PMNSGCT versus NS included higher TP53 pathway GA (p < .0001), PIK3CA pathway GA (p < .0001), and lower cell-cycle pathway GA (p = .0004). There were no MSI-high PMNSGCT cases. Mean TMB was similar between the groups, but there were more ≥10 mut/Mb in the PMNSGCT group versus NS (11.4% vs. 4.6%).The GA identified in PMNSGCT were similar to the findings from NS, with differential opportunities for targeted therapies and immunotherapies. Further study of precision treatments appears warranted.

Abstract P2-12-01: Comprehensive genomic profiling of 34 cases of breast angiosarcoma

Background: Angiosarcoma of the breast (BAS) is a rare but lethal neoplasia, either arising de novo or secondary to radiation therapy, with incidence of the latter disease increasing. We queried a database of more than 70,000 advanced cancer patients assayed with comprehensive genomic profiling (CGP) in the course of clinical care to uncover the frequency, type and associated genomic alterations (GA) in BAS and to highlight possible routes to benefit from targeted therapy.

Methods: CGP was performed for 34 BAS cases using a hybrid-capture, adaptor ligation based next generation sequencing assay of up to 315 genes to a mean coverage depth of &gt;500X. The results were analyzed for base substitutions, short insertions and deletions, selected rearrangements, and copy number changes. RNA sequencing for 265 genes was also performed for 24 cases. Limited clinical histories from submitted pathology reports were reviewed under IRB permission.

Results: Clinical specimens from 34 BAS patients, all females, were assayed. The cases harbored 87 total GA for a mean of 2.59 per case, 25% of which were copy number amplifications. The most commonly altered genes were MYC (41%, 14/34), PIK3CA (26%, 9/34), and KDR (26%, 9/34). All MYC alterations were amplifications with a mean copy number of 39, and alterations in other MYC family members (MYCN and MYCL1) were not observed. KDR was recurrently altered as T771R (7/9) and T771K (1/9) and amplified in one case (1/9).

MYC and KDR alterations were mutually exclusive (p&lt;0.0001). 6/14 MYC amplified cases had prior histories of breast carcinoma, with 3/6 noted as being treated with radiation therapy. For the remainder of MYC amplified cases (8/14), no relevant clinical history was available.

Two cases harboring gene fusions were identified including CIC-MEGF8 and NTRK1-PEAR1. Two rearrangements of potential functional significance including CIC-DEDD2 and HT-ALK (exon1 HT - exon5-29 ALK including kinase domain) were also observed. The case harboring HT-ALK also had MYC amplification and known prior radiation therapy. Two other MYC amplified cases also harbored targetable kinase alterations, including FLT4 amplification (described as targetable in Ravi et al JNCCN 2016) and FGFR3 S249C, a known activating mutation.

Conclusions: MYC amplification defines over 40% (14/34) of advanced BAS cases. Of MYC amplified cases, 28% (4/14) harbored targetable alterations of tyrosine kinases including a potential novel ALK fusion. FLT4 amplification only co-occurred with MYC amplification, but this result was not statistically significant in this small series. KDR and MYC alteration were mutually exclusive, and 45% of non-MYC altered cases (9/20) harbored KDR alterations, which were predominantly mutations of T771. Further clinico-pathologic correlation, particularly history of radiation therapy, will be explored in this series, as well defining BAS that harbor neither MYC nor KDR alterations.

Citation Format: Ravi V, Madison R, Schrock AB, Cote G, Millis S, Alvarez R, Choy E, Katz D, Chung J, Gay L, Miller VA, Ross JS, Ali SM, Schnitt S. Comprehensive genomic profiling of 34 cases of breast angiosarcoma [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P2-12-01.

Psychometric Analysis of the Visual Form Discrimination Test

The Visual Form Discrimination Test is a matching-to-sample test involving visual discrimination. Although normative information has been presented, limited psychometric data have been available. The current study estimated the internal consistency and additional psychometric properties of the test in a sample of 66 persons with acute traumatic brain injury. Internal consistency as measured by alpha was .66. A homogeneous sample and a restricted range of scores likely attenuated this estimate. Using the standard cutoff score, only 32% of the sample showed impaired performance. Visual form discrimination as measured by this test may be affected less by traumatic brain injury than other cognitive processes such as attention and memory.

Integrating molecular profiling into cancer treatment decision making: Experience with over 35,000 cases

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Background: Molecular profiling of both common and rare cancer types provides for the identification of actionable targets for chemotherapy with many unexpected associations. Methods: Caris Life Sciences database of >35,000 profiled cancers was reviewed for well-established driver gene mutations and copy number alterations, and protein expression patterns that are relevant for selection of targeted therapy. Based on the published literature, these tumor characteristics were then associated with potential benefit or no benefit to the specific therapeutic agents. All relevant published studies were evaluated using the USPSTF grading scheme for study design and validity. Assay methodologies included sequencing (Sanger, pyrosequencing), PCR, FISH, CISH, and immunohistochemistry. Results: All common malignancies (10 most common cancer types in men and women) and 10 rare cancer types were well represented (minimum of 100 cases in each individual cancer type). Well established driver mutations and protein expression in common cancers were all identified with expected frequencies (e.g. HER2 amplification in breast, PIK3CA mutations in ER+ breast cancer, EGFR mutations in NSCLC, etc.). Importantly, unexpected new and potentially actionable targets were identified in common (e.g., 6.7% HER2 amplification in NSCLC, 1.6% KRAS mutation in prostatic adenocarcinoma) and rare cancers (e.g., 8.3% ALK alteration in soft tissue sarcomas, 10.5% c-MET and 26.4% EGFR gene amplification in melanomas, 16.3% KRAS mutation in cholangiocarcinomas, 10% AR expression in STS), as well in cancers of unknown primary site (approximately 4% of all tested cases). Conclusions: This review of the large referral cancer profiling database provided an unparalleled insight in the distribution of common and rare genetic and protein alterations with direct and potential treatment implications. Numerous targets were discovered that had a potential to be treated by the conventional chemotherapy as well as targeted therapy not usually considered for the cancer type. Comparison between an individual patient tumor profile and database for the matched cancer type provides additional level of support for targeted treatment choices.

Neuropsychological outcome and community re-integration following traumatic brain injury: The impact of frontal and non-frontal lesions

PRIMARY OBJECTIVE

To examine the relationship between cortical lesion location and brain injury outcome. It was hypothesized that focal frontal lesions after traumatic brain injury (TBI) would result in decreased executive and memory functioning and poor community participation outcome.

RESEARCH DESIGN

Three quasi-experimental, prospective studies employed a total of 643 patients with focal frontal, fronto-temporal, non-frontal or no lesions in CT scans.

METHODS AND PROCEDURES

CT scan analysis, neuropsychological assessment, the Neurobehavioural Functioning Inventory (NFI), the Community Integration Questionnaire (CIQ).

MAIN RESULTS

In study 1, frontal and fronto-temporal groups performed worse in executive functioning and better in constructional ability. Study 2 found no differences in neuropsychological and community re-integration measures at 1-year follow-up. Study 3 found comparable neuropsychological test score improvement across groups over 1 year.

CONCLUSIONS

Results are consistent with previous findings and document the potential for test score improvement with rehabilitation and suggest that lesion location needs to be considered when individual rehabilitation plans are being implemented in the post-acute stage of TBI.

Electrodiagnostic changes of the lower limbs in subjects with chronic complete cervical spinal cord injury

OBJECTIVE

To assess the electrodiagnostic changes in the lower limbs as measured by nerve conduction studies (NCSs) and electromyography in individuals with chronic complete tetraplegia.

DESIGN

Prospective testing of NCS and electromyography.

SETTING

Model spinal cord injury rehabilitation center.

PARTICIPANTS

Twenty-five individuals with chronic complete tetraplegia without risk factors for peripheral neuropathy or other lower motoneuron disorders.

INTERVENTIONS

Nerve conduction parameters recorded from the peroneal, tibial, and sural nerves, and compared with normal values. The presence of spontaneous activity (SA), including fibrillation and positive sharp waves, recorded in 5 muscle groups-2 proximal (vastus medialis, iliopsoas), 2 distal (tibialis anterior, medial gastrocnemius), and L4 lumbar paraspinals. Analysis to see if the presence of SA correlated with the distance of the muscle from the spinal cord or with spasticity (measured by the modified Ashworth scale).

MAIN OUTCOME MEASURES

Nerve conduction latencies and velocities; motor and sensory conduction latencies; compound muscle action potential (CMAP) and sensory nerve action potential amplitudes; spontaneous potentials: fibrillation and positive sharp waves; and spasticity.

RESULTS

NCS responses were obtained at a decreased frequency relative to able-bodied subjects. Statistically significant results in comparison to normal means included a diminished sural amplitude, and diminished peroneal and tibial CMAP and nerve conduction velocity (p <.0001). SA was recorded in at least 1 of the muscles tested in 92% of subjects, with 72% having SA in more than 1 of the muscles tested affected. A significant difference was seen for SA in the medial gastrocnemius as compared with the iliopsoas (p =.039). No correlation was noted in terms of SA with degree of spasticity.

CONCLUSION

A statistically significant difference in NCS responses in the lower limbs in chronic tetraplegia was found relative to normal control values. However, only the frequency of responses elicited and the decreased CMAP of the peroneal nerve are clinically significant. SA was present in many of the lower extremity muscles in the subjects. Predominantly axonal changes were evident in individuals with chronic complete tetraplegia.

Functional independence measure prediction: an initial evaluation of residents' skills

The purpose of this preliminary study was to assess the ability of first-year PM&R residents to accurately predict functional outcome in an acute rehabilitation setting. Although statistically significant, the accuracy and precision of the residents' predictive skills were rather modest. A future focus on innovative methods to evaluate and develop these clinical skills appears warranted.

Sitting balance following brain injury: does it predict outcome?

Balance dysfunction is commonly observed following traumatic brain injury. There are many proposed predictors of functional outcome in the traumatic brain injury population. It was hypothesized that the degree of balance dysfunction on admission to rehabilitation would be a significant predictor of the need for assistance at discharge, as measured by the Functional Independence Measure (FIM). This study involved 237 cases of traumatic brain injury patients admitted to a rehabilitation unit between November 1989 and September 1996. Using a multiple regression model, controlling for age, initial Glasgow Coma Score (GCS), rehabilitation admission strength, sitting balance and standing balance, it was found that the degree of impairment in sitting balance at admission to rehabilitation was a significant predictor of Discharge FIM-Total (FIM-T) score (p < 0.0001) and also of selected elements from the Discharge FIM-Motor (FIM-M) score (p < 0.0005). The combination of age, initial admission GCS, rehabilitation admission strength, standing balance and sitting balance accounted for 29% of the variance in the Discharge Total FIM score. Among these, sitting balance was the second most powerful predictor of both selected elements of the Discharge FIM motor score and discharge FIM-T. Sitting balance predictive capacity was exceeded in power only by age. Impairments in sitting balance appear to have a significant impact on functional outcome. Emphasis on unique rehabilitation techniques to treat balance dysfunction in the adult TBI population is warranted.