A SNaPshot of potentially personalized care: Molecular diagnostics in gynecologic cancer

BACKGROUND

Genetic abnormalities underlie the development and progression of cancer, and represent potential opportunities for personalized cancer therapy in Gyn malignancies.

METHODS

We identified Gyn oncology patients at the MGH Cancer Center with tumors genotyped for a panel of mutations by SNaPshot, a CLIA approved assay, validated in lung cancer, that uses SNP genotyping in degraded DNA from FFPE tissue to identify 160 described mutations across 15 cancer genes (AKT1, APC, BRAF, CTNNB1, EGFR, ERBB2, IDH1, KIT, KRAS, MAP2KI, NOTCH1, NRAS, PIK3CA, PTEN, TP53).

RESULTS

Between 5/17/10 and 8/8/13, 249 pts consented to SNaPshot analysis. Median age 60 (29-84) yrs. Tumors were ovarian 123 (49%), uterine 74(30%), cervical 14(6%), fallopian 9(4%), primary peritoneal 13(5%), or rare 16(6%) with the incidence of testing high grade serous ovarian cancer (HGSOC) halving over time. SNaPshot was positive in 75 (30%), with 18 of these (24%) having 2 or 3 (n=5) mutations identified. TP53 mutations are most common in high-grade serous cancers yet a low detection rate (17%) was likely related to the assay. However, 4 of the 7 purely endometrioid ovarian tumors (57%) harbored a p53 mutation. Of the 38 endometrioid uterine tumors, 18 mutations (47%) in the PI3Kinase pathway were identified. Only 9 of 122 purely serous (7%) tumors across all tumor types harbored a 'drugable' mutation, compared with 20 of 45 (44%) of endometrioid tumors (p<0.0001). 17 pts subsequently enrolled on a clinical trial; all but 4 of whom had PIK3CA pathway mutations. Eight of 14 (47%) cervical tumors harbored a 'drugable' mutation.

CONCLUSION

Although SNaPshot can identify potentially important therapeutic targets, the incidence of 'drugable' targets in ovarian cancer is low. In this cohort, only 7% of subjects eventually were treated on a relevant clinical trial. Geneotyping should be used judiciously and reflect histologic subtype and available platform.

A comparative study of automatic thresholding approaches for 3D x-ray microtomography of trabecular bone

PURPOSE

This paper presents a comparative study of automatic thresholding algorithms for segmenting trabecular bone volume in x-ray microtomography (μCT).

METHODS

First, a preprocessing stage was established, which considered noise reduction by applying anisotropic diffusion filtering and contrast enhancement by using morphological top-hats. Next, four automatic thresholding algorithms were implemented: clustering, maximum entropy, moment preservation, and concavity-based. These approaches analyze the preprocessed 3D μCT image histogram to optimize some parameters to find the best gray-level threshold. Thirty-eight vertebra bone samples were acquired from 19 normal Wistar rats, specifically the L3 and L4 vertebrae. The μCT images were acquired with a microfocus x-ray device at 100 slices/sample. Next, three human operators segmented the entire 3D μCT images manually to establish ground-truth segmentations so as to associate the segmentation problem with perceptual grouping. The normalized probabilistic Rand index (NPRI) was used to quantify the agreement between each computerized segmentation and the corresponding set of three ground-truth segmentations. Hence, the NPRI value should tend toward unity for an acceptable performance. Finally, a statistical analysis was done to determine which thresholding approach achieved the best performance. Besides, 3D morphometric indices were also measured.

RESULTS

The Games-Howell test (α = 0.05) was used to compare the equality of means from the NPRI results considering the four thresholding algorithms (multiple comparisons). This statistical analysis indicated that the clustering and moment preservation techniques performed similarly, with NPRI values of 0.594 ± 0.126 and 0.607 ± 0.127, respectively.

CONCLUSIONS

The main advantage of computerized segmentation is that it is fully automatic; that is, no interaction with the user is required. Thus, the method could be considered objective. Besides, the proposed preprocessing stage plays an important role in enhancing the μCT image quality to achieve better separation between the background volume and the trabecular bone volume.

P1-07-13: Efficiency of a Laboratory Developed HER2 FISH Test on Circulating Tumor Cells

INTRODUCTION: Most circulating tumor cell (CTC) platforms rely on EpCAM for capture and cytokeratin (CK) for detection. However, an important population of cells that are CK-negative (i.e. cells with epithelial-mesenchymal transition (EMT) phenotype) will be missed. We report a new strategy to efficiently isolate a more heterogeneous population of CTCs using an antibody cocktail.

METHODS: In the first prospective study, blood (20 mL) was collected from 89 patients diagnosed with various late stage metastatic/recurrent cancers (breast, CRC, lung, prostate) following IRB approval. PBMCs were incubated with either EpCAM alone or a mixture of 10 capture antibodies to target both epithelial and mesenchymal cells. CTCs were subsequently captured in the OncoCEE™ channels and detected with cytokeratin (CK) and CD45. A second prospective IRB approved study involving 54 patients diagnosed with late stage metastatic/recurrent breast cancer was performed using similar detection strategies (CK cocktail mixture and anti-CD45) with the addition of HER2 FISH to determine amplification status among captured CK+/CD45- and CK-/CD45-cells.

RESULTS: In the first study, overall detection of CK+ cells was 83% with EpCAM alone and 93% with antibody cocktail. In addition, a median of 0.4 CK+ cells/mL and 1.0 CK+ cells/mL was observed using EpCAM and antibody cocktail, respectively. In the second study, CK+/CD45- cells were detected in 43 of 54 cases (80%). Among the 43 cases in which CK+/CD45- cells were detected, high concordance (93%) in HER2 status between primary tumor and CTCs was observed with HER2 amplification noted in both CK+/CD45- (50%) and CK-/CD45- (50%) cells.

CONCLUSIONS: We have developed a novel and robust method for CTC enumeration that utilizes a cocktail of antibodies for the detection of a heterogeneous (CK+ and CK-) population of CTCs. Our findings suggest an important population of CK- cells is being missed by current stain criteria in breast cancer patients. Data also demonstrate that recovery of CTCs from peripheral blood using the OncoCEE™ platform is efficient and suitable for FISH-based laboratory testing.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P1-07-13.

Cryopreservation of Digitalis obscura selected genotypes by encapsulation-dehydration

Shoot-tips from several genotypes of the cardenolide-producing perennial shrub Digitalis obscura L. were successfully cryopreserved using the encapsulation-dehydration technique. Precultivation on MS medium containing 0.5 M sucrose, followed by 2.5 h dehydration (final weight 30 %) induced shoot regrowth in 42 % of cryopreserved shoot-tips. Cold-hardening of the in vitro cultures before sucrose treatment dramatically increased shoot recovery up to 86 %. The optimized cryopreservation protocol was then employed using different shoot cultures from five D. obscura genotypes. Responses to cryopreservation depended mainly on the genotype, best results being obtained when shoot tips from HU3 and LL11 were used. Prolonged subcultures reduced proliferation rates in both control and cryopreserved HU3 shoot-tips, whereas long-term storage in LN did not affect the shoot recovery rate of the genotype. RAPD markers were employed to evaluate possible somaclonal variation occurring in shoots regenerated through successive subcultures and after cryopreservation. The band patterns revealed differences between the original parent plant and the shoots grown in vitro, especially after a prolonged subculture (84.9 % of matches for HU3 after 16 subcultures vs. 93.4 % for AY3 after 2 subcultures). Nevertheless, match percentages were higher (98.6 % to 99.5 %) when band patterns from subcultured shoots were compared to those obtained from their respective control or frozen progenies indicating that cryopreservation ensure genetic stability of selected Digitalis obscura genotypes.

Population genetic study in the Balearic endemic plant species Digitalis minor (Scrophulariaceae) using RAPD markers

Digitalis minor (Scrophulariaceae) is a cardenolide-producing plant endemic to the eastern Balearic Islands (Mallorca, Menorca, and Cabrera) that occurs in two morphologically distinct varieties: D. minor var. minor (pubescent) and D. minor var. palaui (glabrous). Levels and patterns of genetic diversity in 162 individuals from 17 D. minor populations across the entire geographic range were assessed using random amplified polymorphic DNA (RAPD) markers. Comigrating RAPD fragments tested were found to be homologous by Southern hybridization in both var. minor and var. palaui. To avoid bias in parameter estimation, analyses of population genetic structure were restricted to those RAPD bands that fulfilled the 3/N criterion (observed frequencies were less than 1 - [3/N] in each population) either among or within each island. Analyses of molecular variance (AMOVAs) with distances among individuals corrected for the dominant nature of RAPD (genotypic analysis) showed low values (1.57-17.55%) of between-population variability, indicating a relatively restricted population differentiation as expected for an outcrossing species such as D. minor. Nested AMOVAs demonstrated, however, a not significant partitioning of genetic diversity among Mallorca, Menorca, and Cabrera islands. Estimates of the Wright, Weir, and Cockerham and the Lynch and Milligan F(ST) from null allele frequencies corroborated AMOVA partitioning and provided evidence for population differentiation in D. minor. Our RAPD data did not show significant differences between pubescent and glabrous populations of D. minor, suggesting a failure to find a correlation between the RAPD loci and this morphological trait.