Fumarate Hydratase-Deficient Leiomyoma of the Uterine Corpus: Comparative Morphologic Analysis of Protein-Deficient Tumors With and Without Pathogenic Germline Fumarate Hydratase Gene Mutations

Deficiency of fumarate hydratase (FH) protein expression in uterine corpus leiomyomas may be attributable to either germline or somatic mutations of the FH gene, the former being definitional for the hereditary leiomyomatosis and renal cell cancer syndrome. The authors assess whether, using previously reported FH-associated morphologic features, FH protein-deficient uterine corpus leiomyomas associated with a pathogenic germline mutations of the FH gene (group 1) are distinguishable from FH protein-deficient uterine corpus leiomyomas without such mutations (and whose FH protein loss is presumed to be attributable to somatic/epigenetic inactivation or other unknown phenomena: group 2). Groups 1 and 2 were compared regarding a variety of clinicopathologic features, including 7 core "FH-associated" tumoral morphologic features: staghorn vasculature; alveolar-type edema; bizarre nuclei; chain-like tumor nuclei; hyaline cytoplasmic globules; prominent nucleoli, intranuclear inclusions, and perinucleolar halos; and prominent eosinophilic/fibrillary cytoplasm. Among 2418 patients diagnosed with uterine corpus leiomyoma during the study period, FH-associated morphologic features were reported in 1.5% (37 patients), and FH immunohistochemistry was performed in 29 (1.19%). Fourteen (48.27%) of the 29 patients showed FH protein deficiency by immunohistochemistry. Twelve patients underwent germline testing, of which 8 (66.7%) were classified as group 1 and 4 (33.3%) as group 2. FH protein-deficient tumors were larger (10.44 vs 4.08 cm, P  =  0.01) and associated with younger patients (42.05 vs 47.97, P  =  0.004) than 370 randomly selected uterine leiomyoma controls. Groups 1 and 2 showed no significant differences in patient age and tumor size. In group 1 tumors, the FH-associated morphologic features were generally present diffusely; all group 1 tumors displayed ≥5 FH-associated features, whereas all group 2 tumors displayed <5 FH-associated features (means 6.5  ±  0.53 vs 3.5  ±  1.00, P < 0.001). Notably, eosinophilic/fibrillary cytoplasm and alveolar-type edema were each significantly more prevalent in group 1 tumors than group 2 tumors (P  =  0.018 for both). No single morphologic feature was found to be completely sensitive and specific in making the distinction between group 1 and 2 tumors. Our findings suggest that groups 1 and 2 are unlikely to be morphologically distinguishable by individual morphologic features. Whether there is a combination of features that can reliably make this distinction is unclear and will require additional studies with larger cohorts.

B3 thymoma mimicking poorly differentiated thyroid carcinoma: Diagnostic pitfalls of anterior mediastinal mass fine needle aspiration

B3 thymoma is a rare malignant type of thymic epithelial neoplasm found in the anterior mediastinum. Diagnosis of thymoma from fine needle aspiration (FNA) can be challenging due to the infrequency of sampling and its morphologic overlap with other entities such as squamous cell carcinoma, lymphoma or thyroid carcinoma. We report a case of B3 thymoma mimicking poorly differentiated thyroid carcinoma. We present its diagnostic pitfalls on cytology specimens, especially where it concerns identifying the correct location of the lesion, discuss the differential diagnosis, and correlation with the corresponding surgical resection specimen. A neck computed tomography angiogram (CTA) revealed a partially calcified 2.1 cm mass inferior to the left thyroid lobe in a 51 yr old woman being evaluated for stroke/TIA symptoms. She was referred for evaluation of the lesion. On the initial FNA and core needle biopsy, the lesion showed high-grade epithelioid cells with abundant lymphocytic infiltration and occasional necrosis, and was diagnosed as a high-grade carcinoma, favored to represent a poorly differentiated thyroid carcinoma considering the location on imaging. The patient subsequently underwent total thyroidectomy, central neck dissection, and thymectomy. Final surgical pathologic diagnosis indicated a type B3 thymoma. Due to the infrequency of sampling, thymoma poses a diagnostic challenge on preoperative FNA or core needle biopsy. Herein, we present a case of B3 thymoma with a preoperative cytologic specimen that consisted of hyperchromatic sheets of epithelioid tumor cells with a background of lymphocytes without definitive follicular cells or colloid. The core needle biopsy and cell block material showed abundant necrosis, intermixed lymphocytes and neoplastic epithelial cells with strong positive staining for pan-keratin and p40. The cytology and core needle biopsy material were interpreted as representing a probable thyroid neoplasm and raised a broad differential including anaplastic thyroid carcinoma, poorly differentiated thyroid carcinoma with squamous features, metastatic squamous carcinoma, and metastatic carcinoma to a lymph node. The final surgical resection specimen showed a B3 type-thymoma.

Accurate genome-wide genotyping from archival tissue to explore the contribution of common genetic variants to pre-cancer outcomes

PURPOSE

The contribution of common genetic variants to pre-cancer progression is understudied due to long follow-up time, rarity of poor outcomes and lack of available germline DNA collection. Alternatively, DNA from diagnostic archival tissue is available, but its somatic nature, limited quantity and suboptimal quality would require an accurate cost-effective genome-wide germline genotyping methodology.

EXPERIMENTAL DESIGN

Blood and tissue DNA from 10 individuals were used to benchmark the accuracy of Single Nucleotide Polymorphisms (SNP) genotypes, Polygenic Risk Scores (PRS) or HLA haplotypes using low-coverage whole-genome sequencing (lc-WGS) and genotype imputation. Tissue-derived PRS were further evaluated for 36 breast cancer patients (11.7 years median follow-up time) diagnosed with DCIS and used to model the risk of Breast Cancer Subsequent Events (BCSE).

RESULTS

Tissue-derived germline DNA profiling resulted in accurate genotypes at common SNPs (blood correlation r2 > 0.94) and across 22 disease-related polygenic risk scores (PRS, mean correlation r = 0.93). Imputed Class I and II HLA haplotypes were 96.7% and 82.5% concordant with clinical-grade blood HLA haplotypes, respectively. In DCIS patients, tissue-derived PRS was significantly associated with BCSE (HR = 2, 95% CI 1.2-3.8). The top and bottom decile patients had an estimated 28% and 5% chance of BCSE at 10 years, respectively.

CONCLUSIONS

Archival tissue DNA germline profiling using lc-WGS and imputation, represents a cost and resource-effective alternative in the retrospective design of long-term disease genetic studies. Initial results in breast cancer suggest that common risk variants contribute to pre-cancer progression.

PTEN Loss and ARID1A Mutation in an HPV-positive Metastatic Adenocarcinoma Diagnosed Almost 18 yr After an Intact Cone Excision for Endocervical Adenocarcinoma In Situ

There have been previous reports of neoplasms with the morphology of endocervical adenocarcinoma in situ (AIS) that secondarily involve the ovaries, presumably through transtubal spread, with a smaller subset metastasizing to distant sites. These ovarian metastases have been discovered up to 7 yr postexcision of the endocervical lesion, consistent with the known potential for overtly invasive cervical carcinomas to recur late after primary curative management. Herein, we present a case of a premenopausal woman with a pelvic mass classified as metastatic human papillomavirus (HPV)-associated endocervical adenocarcinoma (p16-block immunoreactive, high-risk HPV positive by in situ hybridization with PTEN loss, ARID1A, and PBRM1 mutations detected by qualitative next-generation sequencing), identified 17.7 yr (212 mo) after a fertility-sparing cone excision with negative margins for endocervical AIS [HPV-associated, p16-block immunoreactive; PTEN, and BAF250a (ARID1a) expression retained]. Our case highlights: (1) the potential for a subset of lesions with the morphology of AIS to metastasize, and the extraordinarily long timeframe (almost 18 y, the longest reported to date) during which metastases may still be identified; (2) alterations in PTEN and ARID1A may play a role in the progression of a subset of endocervical carcinomas; and (3) the need for studies to evaluate the utility of incorporating ovarian/pelvic imaging into surveillance protocols following fertility-sparing excisions or ovarian-preserving hysterectomies, during the management of endocervical adenocarcinomas, as well as the need to counsel patients about the small but real risk of delayed discovery of ovarian metastases following fertility-preserving surgeries for AIS.

Using computer-assisted content analysis to advance anal dysplasia natural history research

OBJECTIVE

Our study aim was to validate the use of computer-aided narrative content analysis in the extraction of standard diagnostic categories using an archived cytology database that included individually overread reference classification.

DESIGN

A retrospective analysis of narrative anal cytology results collected on HIV-infected patients at the University of California, San Diego between January and December 2001.

METHODS

We used computer-assisted content analysis extraction methodology using Wordstat 8.0 (Provalis Research) that operated using a classification dictionary that we developed for the following diagnostic categories: NAMC, ASCUS, LSIL, HSIL. We compared its accuracy to a physician overread manually extracted method: that classified each report into the most severe diagnostic category referenced in the narrative report. Agreement between content analysis mapped diagnostic categories and the reference category was evaluated using kappa agreement.

RESULTS

During 2001, 901 patients underwent 997 anal cytological examinations as routine screening. By reference diagnostic category: 54 (5.4%) were unsatisfactory, 460 (46.1%) were NAMC, 291 (29.2%) were ASCUS, 131 (13.1%) were LSIL, and 61 (6.1%) were HSIL. Computer-aided content analysis extracted a single diagnosis from each report in 963 (96.2%) cases and two diagnoses in 38 (3.8%) cases. The Kappa agreement was 0.96 (0.019 s.e.). There were 29 cases classified ASCUS by reference category but LSIL by adjudicated content analysis. A focused review indicated that the over reader assigned reference category was in error.

CONCLUSION

Computer-aided narrative content analysis of anal cytology results yielded accurate and time-efficient classification into meaningful diagnostic categories that can be used to evaluate screening programs and modeling natural history.

Abstract P5-06-02: A gene expression meta-analysis identifies microenvironment differences in cellular composition and cell-cell interactions associated with breast cancer invasion

Background: The invasion of malignant cells into surrounding stroma is the histological hallmark differentiating invasive ductal carcinoma (IDC) from ductal carcinoma in situ (DCIS). The associated variations in the cellular composition and interactions in the tumor microenvironment, and how those mediate invasion are poorly understood. Systematic analyses of gene expression differences between DCIS and IDC are rare, confounded by cellular heterogeneity, and limited to few cases unable to distinguish stromal from epithelial contributions or compare pure DCIS from those synchronous with IDC. To address these problems we have assembled multiple datasets from publicly available gene expression studies of microdissected DCIS and IDC samples. Methods: The transcriptome from 192 regions microdissected from 140 cases was assembled from 5 published studies and included DCIS (83 epithelial, 22 stromal) and IDC (67 epithelial, 20 stromal) cases. Differences in infiltration of 10 immune cell types were measured using expression signatures. Expression subtypes were determined from the PAM50 signatures of epithelial regions using the genefu package. Gene Set Enrichment Analysis (GSEA) was performed using the gene sets in the Hallmark and Reactome collections. Cell-cell interactions between stromal and epithelial regions were measured using the co-expression of 1175 curated pairs of ligand-receptor genes and compared between DCIS and IDC using a permutation test. The corresponding interacting cell types were identified using RNA sequencing of 5444 single nuclei extracted from fine needle aspirates of two excised DCIS specimens. Results: Of the measured immune cell types, B cells showed a progressive depletion from normal to DCIS to IDC stroma. Pure IDC regions were significantly less likely to be the Luminal A subtype compared to synchronous IDC/DCIS and pure DCIS (p=0.0008). IFN signaling was higher in IDC epithelium suggesting possible differences in immune visibility between these two diseases. Higher calcium and glutamate signaling is observed in the DCIS stroma compared to IDC, calcium signaling has been implicated as both essential to normal breast function and as a positive effector of IDC proliferation. The expression-based measurement of stromal-epithelial interactions identified 99 and 115 ligand-receptor interactions enriched in DCIS and IDC, respectively (FDR&lt;0.1). To precisely identify the corresponding interacting cell types, the expression profile of cells within the DCIS microenvironment was determined using single-nucleus RNA sequencing from two DCIS patients. The analysis identified 9 cell types, including luminal, basal, macrophage, adipocyte and endothelial, and 54% of the candidate cell-cell interactions could be mapped to at least one cell type pair. Based on these cell type mappings, interactions between luminal cells and fibroblasts were gained in IDC while those involving the vascular endothelium were lost, including interactions between CD24 and P-selectin, an interaction involved in leukocyte recruitment. Increased macrophage autocrine interactions were identified in both IDC stroma and epithelium through urokinase-urokinase receptor gene co-expression, an interaction previously associated with a transition to the M2 phenotype. Conclusions: The meta-analysis combined with novel computational methods, improves our ability to characterize the micro-environment of DCIS specimens, typically hard to study. Changes in cellular dynamics involving both immune and non-immune cell types suggest that mechanisms other than direct immune escape accompany progression.

Citation Format: Adam Officer, Andre Dempsey, Farnaz Hasteh, Michal Slyper, Asa Segerstolpe, Joanna Klughammer, Judit Jane-Valbuena, Orit Rozenblatt-Rosen, Lyndsay Murrow, Zev Gartner, Aviv Regev, Christina Yau, Pablo Tamayo, Olivier Harismendy. A gene expression meta-analysis identifies microenvironment differences in cellular composition and cell-cell interactions associated with breast cancer invasion [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P5-06-02.

The breast pre-cancer atlas illustrates the molecular and micro-environmental diversity of ductal carcinoma in situ

Microenvironmental and molecular factors mediating the progression of Breast Ductal Carcinoma In Situ (DCIS) are not well understood, impeding the development of prevention strategies and the safe testing of treatment de-escalation. We addressed methodological barriers and characterized the mutational, transcriptional, histological, and microenvironmental landscape across 85 multiple microdissected regions from 39 cases. Most somatic alterations, including whole-genome duplications, were clonal, but genetic divergence increased with physical distance. Phenotypic and subtype heterogeneity was frequently associated with underlying genetic heterogeneity and regions with low-risk features preceded those with high-risk features according to the inferred phylogeny. B- and T-lymphocytes spatial analysis identified three immune states, including an epithelial excluded state located preferentially at DCIS regions, and characterized by histological and molecular features of immune escape, independently from molecular subtypes. Such breast pre-cancer atlas with uniquely integrated observations will help scope future expansion studies and build finer models of outcomes and progression risk.

Rectal endometriosis mimicking primary rectal adenocarcinoma

Endometriosis is a benign entity defined as the presence of endometrium tissue outside of uterine cavity. It is a common disease involving peritoneum, pelvic organs, gastrointestinal tract, and so on. Diagnosis based on cytology specimen can be challenge when we encounter increased cytological atypia in the glandular epithelium, with abundant inflammatory cells and debris in the background. We presented a case of deep rectal endometriosis mimicking rectal adenocarcinoma on cytology specimen and on MRI imaging studies. The combination of endometrial glands, cellular Mullerian stroma, hemorrhage, and hemosiderin-laden macrophages are the characteristic features on cytologic specimens.

Abstract 131: Remodeling of stromal-epithelial interactions in breast cancer progression as inferred from regional and single-cell gene expression analysis

Background: The transition from ductal carcinoma in situ (DCIS) to invasive ductal carcinoma (IDC) is defined by the invasion of malignant cells into surrounding tissues, but associated changes in the cellular composition and interactions in the tumor microenvironment are poorly understood. Systematic analysis of gene expression differences between DCIS and IDC are confounded by cellular heterogeneity and few studies have separated stromal and epithelial contributions or distinguished pure DCIS from those synchronous with IDC.

Methods: The gene expression of 192 microdissected regions from 140 cases was assembled from 5 studies and included DCIS (83 epithelial, 22 stromal) and IDC (67 epithelial, 20 stromal) cases. Differences in infiltration of 10 immune cell types were measured using expression signatures. Cell-cell interactions between stromal and epithelial regions were measured using the co-expression of 1175 curated pairs of ligand-receptor genes and compared between DCIS and IDC using a permutation test. The corresponding interacting cell types were identified using RNA sequencing of 5444 single nuclei extracted from fine needle aspirates of two excised DCIS specimens.

Results: Stromal regions of Her2+ cases had the highest level of immune infiltration compared to IDC and Her2- cases. Of the measured immune cell types, B cells showed a progressive depletion from normal to DCIS to IDC. The expression-based measurement of stromal-epithelial interactions identified 99 and 115 ligand-receptor interactions stronger in DCIS and IDC, respectively (FDR&lt;0.1). To precisely identify the corresponding interacting cell types, the expression profile of cells within the DCIS microenvironment was determined using single-nucleus RNA sequencing from two DCIS patients. The analysis identified 9 cell types, including luminal, basal, macrophage, adipocyte and endothelial, and 54% of the candidate cell-cell interactions could be mapped to at least one cell type pair. Based on these cell type mappings, interactions between luminal cells and fibroblasts were gained in IDC while those involving the vascular endothelium were lost, including interactions between CD24 and SELP, an interaction involved in leukocyte recruitment. Increased macrophage autocrine interactions were identified in both IDC stroma and epithelium through PLAU-PLAUR co-expression, an interaction previously associated with a transition to the M2 phenotype.

Conclusion: The analysis of published gene expression studies with novel computational methods, augmented with a single-cell landscape representative of the disease, can help compensate for the difficulty in studying pure DCIS specimens. The microenvironment changes in cellular dynamics involved both immune and non-immune cell types suggesting mechanisms other than direct immune escape contribute to progression.

Citation Format: Adam Officer, Andre Dempsey, Farnaz Hasteh, Michal Slyper, Asa Segerstolpe, Joanna Klughammer, Judit Jane-Valbuena, Orit Rozenblatt-Rosen, Aviv Regev, Christina Yau, Olivier Harismendy. Remodeling of stromal-epithelial interactions in breast cancer progression as inferred from regional and single-cell gene expression analysis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 131.

Abstract 2176: Mutational profiling of premalignant breast microbiopsies

Ductal carcinoma in situ (DCIS) comprises ~20% of all breast cancer diagnoses in the United States. Nearly all DCIS are treated to prevent progression to potentially lethal invasive cancer, yet it is estimated about half of DCIS progress within 10 years making the systematic treatment controversial. This highlights an urgent need for reliable molecular markers to stratify patients by risk. Small, degraded biopsies have made molecular profiling historically challenging; furthermore, a single biopsy can have several regions varying in nuclear grade, hormone receptor status, and histological architecture requiring laser-capture microdissection. Recent advances in whole-exome sequencing now enable mutational profiling from limited quantities (&lt;10ng) of damaged, formalin-fixed, paraffin-embedded (FFPE) DNA, and present an opportunity to sequence individual regions and relate the phenotypic heterogeneity with genetic alterations. Here, we apply these advances to obtain mutational profiles from pure DCIS microbiopsies, enabling a comprehensive molecular profile of pure DCIS, direct measurement of genetic heterogeneity, and associations between molecular and histopathological features.

Whole-exome sequencing was performed on 59 regions across 31 pure DCIS cases varying in nuclear grade (including 19% low-grade), and histological architecture (52% cribriform, 39% solid). Driver analysis revealed breast cancer-like driver alterations in 30/31 cases, and evidence for multiple putative drivers in 26/31, even in low-grade DCIS. The most frequently mutated genes across patients were common breast cancer driver genes: PIK3CA (37%), TP53 (22%), and GATA3 (11%). Phylogenetic trees constructed on multi-region biopsies revealed that regions of the same biopsy shared 12-336 alterations, and all pathogenic driver point mutations. Nevertheless, 1-22 region-specific alterations were found in each biopsy, some of which were likely driver CNA. We identified several histological associations with genetic alterations including high grade (p=2x10-4) and solid DCIS (p=3x10-4) associated with high copy number burden, and a non-significant increase in GATA3 (13% vs 0%) and PIK3CA (50% vs 28%) pathogenic mutations in cribriform vs solid architecture. Lastly, the most genetically diverse DCIS were HER2+/ER- (p=0.07) and those displaying necrosis (p=0.006). Overall, using novel methodology we performed detailed multi-region mutational profiling on difficult to sequence precancer lesions, revealing varying genetic diversity within a biopsy and novel associations between histology and underlying genetic landscape. We illustrate multiple driver genetic alterations and diversity present even in low-grade, pure DCIS lesions, providing key insight into early breast carcinogenesis and representing a critical step towards the development of prognostic markers of progression.

Citation Format: Daniela Nachmanson, Mark F. Evans, Joseph Steward, Adam Officer, Huazhen Yao, Thomas J. O'Keefe, Farnaz Hasteh, Gary S. Stein, Kristen Jepsen, Donald L. Weaver, Gillian L. Hirst, Brian L. Sprague, Laura J. Esserman, Alexander Borowsky, Janet L. Stein, Olivier Harismendy. Mutational profiling of premalignant breast microbiopsies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2176.

Nonmass enhancement lesions of the breast on core needle biopsy: outcomes, frequency of malignancy, and pathologic findings

Nonmass enhancement (NME) on breast magnetic resonance imaging (MRI) is defined as an area whose internal enhancement characteristics can be distinguished from the normal surrounding breast parenchyma, without an associated mass in the Breast Imaging Reporting and Data System lexicon. In this study, we evaluated the pathologic correlates of NME lesions of the breast identified on MRI at our institution, including the frequency of atypical or malignant lesions in the core needle biopsies (CNBs), performed after such a radiologic finding. A retrospective study was performed on all CNBs performed for NME on breast MRI between 2010 and 2019. A total of 443 biopsies from 411 patients were identified, comprising 5.5% of all CNBs over the study period. The pathologic diagnoses were benign in the majority of the biopsies (68.0%), whereas 11.5% and 20.5% of the cases were atypical and malignant lesions, respectively. Of the malignant cases, 69.2% were ductal carcinoma in situ (DCIS) and 30.8% were invasive carcinomas. The most common invasive cancer was invasive ductal carcinoma (50%), followed by invasive lobular carcinoma (39.3%). NME identified on breast MRI carried a significant (32%) risk of atypia and malignancy in our cohort, which confirms that biopsy evaluation of these lesions is warranted. DCIS was the most commonly identified malignancy. Notably, among invasive cancers, invasive lobular carcinoma was identified at a substantially higher frequency that would be expected for that histotype.

Abstract GS2-01: The breast pre-cancer atlas illustrates the molecular and micro-environmental diversity of ductal carcinoma in situ

Background: With the implementation of widespread breast cancer screening, the diagnosis of Ductal Carcinoma In Situ (DCIS) has increased 5 fold. Most cases are treated with combinations of surgery, radiation and endocrine therapy, reducing the risk of second events, including ipsilateral invasive cancer. Without standard markers to confidently identify the most indolent lesions, a subset of cases are likely over-treated. The mutational landscapes of DCIS and invasive ductal carcinoma (IDC) are similar and not sufficient to identify higher risk lesions with recent studies suggesting that clonal selection plays a limited role in progression. Histological analysis highlighted the role of the extracellular matrix and immune-surveillance to maintain duct integrity and limit progression. Due to the small size, limited availability and quality of research specimens, few biomarker studies investigated pure DCIS with adequate follow-up or genome-wide methods, let alone integrated more than one type of biomarker. Unlike breast cancer, there is no comprehensive, systematic, multi-modal atlas of DCIS, limiting the ability to test broad and novel hypotheses and characterize processes maintaining breast tissue homeostasis.

Methods: Through sequential sectioning of pure DCIS archived specimens, a total of 70 histological regions from 40 cases were annotated and profiled using up to 3 platforms: multiplex immuno-histochemistry (mIHC), RNA-seq, and whole-exome sequencing. Stromal and epithelial spatial distribution of immune cells and states were quantified using mIHC. The epithelial compartments were microdissected and profiled using genome-wide gene expression, DNA mutations and copy number alterations.

Results: Epithelial regions were classified according to expression subtypes consistent with histological markers, highlighting associations with the lesion architecture and grade. Compared to solid pattern, cribriform pattern DCIS has induced EMT processes and repressed proliferation processes, a trend reminiscent of low-recurrence-risk expression signatures measured in IDC. The DNA copy number burden increased with grade and the mutational burden was the highest in solid DCIS. Both were higher in Her2+ cases. The clustering of mutations at chromosome 17p - attributed to the APOBEC-driven Kataegis phenomenon - was observed in a subset of regions, suggesting this event can occur in pre-invasive lesions. All DCIS had somatic alterations of at least one known driver gene with some associated with grade (TP53) or expression subtype (ERBB2). Multi-region profiling available in a subset of samples revealed genetic heterogeneity of likely-driver events between proximal regions of similar histological characteristics. The density and proliferative states of selected immune cells - including T-cells, B-cells and Macrophages - highlights the diversity of the tumor immune environment with the highest densities observed in Her2+ ducts and stroma, minimal ductal infiltration in other lesions, fewer dividing B- and T-cells around the more proliferative areas and a small number of regions depleted from any adaptive immune cells.

Conclusion: This first multi-modal profiling of pure DCIS reveals an unsuspected diversity of molecular and microenvironmental states and presents their association with progression risk factors. The observations support the need for stronger integration of molecular and clinicopathology features, especially at sub-histological levels, to ensure the findings can be interpreted in the correct clinical and phenotypic context. The compatibility of the approach with archived specimens supports the expansion to larger retrospective DCIS collections with outcomes.

Citation Format: Olivier Harismendy, Daniela Nachmanson, Mark F. Evans, Hidetoshi Mori, Adam Officer, Christina Yau, Joseph Steward, Huazhen Yao, Thomas O'Keefe, Farnaz Hasteh, Gary S. Stein, Kristen Jepsen, Michael Campbell, Donald L. Weaver, Gillian L. Hirst, Brian L. Sprague, Laura J. Esserman, Jonathan A. Gordon, Alexander Borowsky, Janet L. Stein. The breast pre-cancer atlas illustrates the molecular and micro-environmental diversity of ductal carcinoma in situ [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr GS2-01.

Mutational profiling of micro-dissected pre-malignant lesions from archived specimens

BACKGROUND

Systematic cancer screening has led to the increased detection of pre-malignant lesions (PMLs). The absence of reliable prognostic markers has led mostly to over treatment resulting in potentially unnecessary stress, or insufficient treatment and avoidable progression. Importantly, most mutational profiling studies have relied on PML synchronous to invasive cancer, or performed in patients without outcome information, hence limiting their utility for biomarker discovery. The limitations in comprehensive mutational profiling of PMLs are in large part due to the significant technical and methodological challenges: most PML specimens are small, fixed in formalin and paraffin embedded (FFPE) and lack matching normal DNA.

METHODS

Using test DNA from a highly degraded FFPE specimen, multiple targeted sequencing approaches were evaluated, varying DNA input amount (3-200 ng), library preparation strategy (BE: Blunt-End, SS: Single-Strand, AT: A-Tailing) and target size (whole exome vs. cancer gene panel). Variants in high-input DNA from FFPE and mirrored frozen specimens were used for PML-specific variant calling training and testing, respectively. The resulting approach was applied to profile and compare multiple regions micro-dissected (mean area 5 mm²) from 3 breast ductal carcinoma in situ (DCIS).

RESULTS

Using low-input FFPE DNA, BE and SS libraries resulted in 4.9 and 3.7 increase over AT libraries in the fraction of whole exome covered at 20x (BE:87%, SS:63%, AT:17%). Compared to high-confidence somatic mutations from frozen specimens, PML-specific variant filtering increased recall (BE:85%, SS:80%, AT:75%) and precision (BE:93%, SS:91%, AT:84%) to levels expected from sampling variation. Copy number alterations were consistent across all tested approaches and only impacted by the design of the capture probe-set. Applied to DNA extracted from 9 micro-dissected regions (8 PML, 1 normal epithelium), the approach achieved comparable performance, illustrated the data adequacy to identify candidate driver events (GATA3 mutations, ERBB2 or FGFR1 gains, TP53 loss) and measure intra-lesion genetic heterogeneity.

CONCLUSION

Alternate experimental and analytical strategies increased the accuracy of DNA sequencing from archived micro-dissected PML regions, supporting the deeper molecular characterization of early cancer lesions and achieving a critical milestone in the development of biology-informed prognostic markers and precision chemo-prevention strategies.

Abstract 2499: Genomic spatial profiling of archived pre-malignant lesions of the breast epithelium

The widespread adoption of breast cancer screening has increased the detection of pre-malignant lesions such as ductal carcinoma in situ (DCIS) but there are currently no reliable biomarkers to stratify DCIS and avoid over-treatment. Importantly, the identification of novel biomarkers in DCIS is notoriously difficult. The rare and late recurrence to subsequent breast cancer (10% at 10 years) poses challenges in experimental design that only a few established, retrospective studies can solve. Most tissue specimens in the associated registries are small, fixed and archived in paraffin (FFPE), precluding their characterization via standard genomic assays. Besides, pure DCIS often present multi-focal heterogenous histology of unclear mutational make-up. Here, we present an approach combining laser capture microdissection with state-of-the-art genomic library preparation methods to enable molecular profiling from minute amounts of damaged nucleic acids and demonstrate its validity for the spatial molecular characterization of DCIS specimen.

Targeted DNA sequencing was performed on limited dilutions of a test DNA from archived breast tissue. Three library preparation strategies were evaluated, included adaptation of classic A-tailing (AT), alternate single-strand (SS) or blunt-end (BE) adapter ligations. The use of an AT protocol resulted less than 10% of targeted base pairs covered at more than 20x (Cov20) from lower than 50ng of DNA and suggested the adapter ligation as initial bottleneck. In contrast, SS or BE adapter ligation from 3ng of DNA reduced the fraction of duplicate reads, increasing the Cov20 to 49% and 100% respectively. Artifactual C to T substitutions, a signature of formalin damage, were restricted to variants of low allelic fraction (&lt;5%). As a result, the use of ensemble variant calling and heuristic filtering to eliminate artifacts and germline variants, led to exome-wide mutational profile of 89% precision and 88% recall from 3ng input, comparable to replicate deep sequencing from a mirrored fresh frozen specimen. The presence of an ERBB2 amplification was validated in all tested conditions. The BE approach for whole exomes was validated on DCIS regions (N=8) and normal epithelium (N=1) dissected from 3 FFPE DCIS blocks. The normal epithelium was unaltered and copy number alterations both consistent and inconsistent within specimen were identified, including FGFR1 and ERBB2 gains or TP53 loss restricted to high-grade lesions. Short variants and indels were rare (~123 per region), mostly shared within each specimen and unlikely to represent driver mutations. The proposed approach can support the spatial mutational profiling of pre-malignant lesions. Compatible with a limited quantity of tissue from archived specimens, the approach sets a new paradigm for the retrospective molecular characterization of specimen with longitudinal follow-up and associated long-term outcome.

Citation Format: Daniela Nachmanson, Joseph Steward, Taeyong Kim, Huazhen Yao, Eliza Jeong, Thomas O'Keefe, Gillian L. Hirst, Laura Esserman, Alexander Borowsky, Farnaz Hasteh, Kristen Jepsen, Olivier Harismendy. Genomic spatial profiling of archived pre-malignant lesions of the breast epithelium [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2499.

Abstract P4-05-05: A high-sensitivity molecular profiling approach to spatially characterize archived pre-cancer lesions

Background: The widespread adoption of breast cancer screening has increased the detection of pre-malignant lesions such as ductal carcinoma in situ (DCIS) but has not translated into increased survival rates. There are currently no reliable biomarkers to stratify DCIS into those which would not develop into an aggressive invasive cancer from those that do, and avoid over-treatment. The interaction with the DCIS microenvironment has likely been under-appreciated or not studied in the adequate clinical context. Importantly, the identification of novel biomarkers in DCIS is notoriously difficult. The rare and late recurrence to subsequent breast cancer (10% at 10 years) poses challenges in experimental design that only a few established, retrospective studies can solve. Most tissue specimens in the associated registries are small, fixed and archived in paraffin (FFPE), precluding their characterization via standard genomic assays. Here, we present an approach combining laser capture microdissection (LCM) with state-of-the-art genomic library preparation methods to enable molecular profiling from minute amounts of damaged nucleic acids and demonstrate its validity for the spatial molecular characterization of DCIS specimen. Methods: Targeted DNA sequencing (whole exome and cancer gene panel) was performed on limited dilutions (200, 50, 10,3 ng) of a test DNA from archived breast tissue, or validation DNA from 10 LCM regions from 3 DCIS specimens. Three library preparation strategies were evaluated, included adaptation of classic A-tailing (AT), or alternate single-strand (SS) or blunt-end (BE) adapter ligations. The expression profiling was performed using SMART-3SEQ protocol on 15 LCM regions from 8 DCIS specimen.

Results: The use of an FFPE-optimized hybrid-capture AT protocol resulted in poor coverage performance (7% of targeted base pairs covered at ≥20x) from test DNA inputs lower than 50 ng and suggested the ligation of the sequencing adapter as the initial bottleneck. Alternatively steps using SS or BE adapter ligation from 3 ng of test DNA (~500 cells) increased the library complexity, reducing the fraction of duplicate reads and increasing the fraction of targeted base pairs covered at 20x to 49% and 100% respectively. Artifactual cytosine to tyrosine substitutions, a signature of formalin damage, were restricted to variants of low allelic fraction (&lt;5%). As a result, the use of molecular barcodes, ensemble variant calling and heuristic variant filtering, resulted in 98% precision and 96% recall in variant calling accuracy from 3ng input, when compared to 200 ng input from a fresh frozen mirrored specimen. Similarly, the presence of an ERBB2 amplification was validated in all tested conditions. The validation of the BE approach on 10 LCM regions from 3 DCIS showed decreasing levels of clonal relationships when comparing regions from adjacent sections, then from matching distinct regions, then from distinct specimen. The heterogeneity of TP53 loss of heterozygosity within a specimen was consistent with high-grade. Furthermore, gene expression profiling of 15 regions from 8 archived DCIS specimen differentiated expression profiles of stromal and epithelial regions, within and between specimen, highlighting sets of genes associated with DCIS subtype and the immune make-up of the micro-environment. Conclusion: The proposed approach - from coordinated specimen preparation to mutational and expression profiling - was therefore validated to support the spatial characterization of pre-cancerous lesions and the microenvironment in which they evolve. Compatible with a limited quantity of tissue from archived specimens, the approach sets a new paradigm for the retrospective molecular characterization of specimen with longitudinal follow-up and associated long-term outcome.

Citation Format: Daniela Nachamanson, Joseph Steward, Taeyong Kim, Huazhen Yao, Eliza Jeong, Thomas O'Keefe, Gillian L. Hirst, Farnaz Hasteh, Kristen Jepsen, Laura J. Esserman, Alexander Borowsky, Olivier Harismendy. A high-sensitivity molecular profiling approach to spatially characterize archived pre-cancer lesions [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P4-05-05.

Normal human lymph node T follicular helper cells and germinal center B cells accessed via fine needle aspirations

Germinal centers (GC) are critically important for maturation of the antibody response and generation of memory B cells, processes that form the basis for long-term protection from pathogens. GCs only occur in lymphoid tissue, such as lymph nodes, and are not present in blood. Therefore, GC B cells and GC T follicular helper (T_FH) cells are not well-studied in humans under normal healthy conditions, due to the limited availability of healthy lymph node samples. We used a minimally invasive, routine clinical procedure, lymph node fine needle aspirations (LN FNAs), to obtain LN cells from healthy human subjects. This study of 73 LNs demonstrates that human LN FNAs are a safe and feasible technique for immunological research, and suggests benchmarks for human GC biology under noninflammatory conditions. The findings indicate that assessment of the GC response via LN FNAs will have application to the study of human vaccination, allergy, and autoimmune disease.

Intranodal palisaded myofibroblastoma of para-esophageal lymph node: Case report with cytologic and histologic findings

Intranodal palisaded myofibroblastoma is a rare lymph node mesenchymal neoplasm that most commonly arises in inguinal lymph nodes. There is limited data about cytologic features of this tumor and its diagnostic pitfalls. The combination of bland appearing spindle cells, fibrillary matrix, and hemosiderin pigments are the characteristic features of this neoplasm in cytologic specimens.

Intratumor Heterogeneity of the Estrogen Receptor and the Long-term Risk of Fatal Breast Cancer

Background

Breast cancer patients with estrogen receptor (ER)–positive disease have a continuous long-term risk for fatal breast cancer, but the biological factors influencing this risk are unknown. We aimed to determine whether high intratumor heterogeneity of ER predicts an increased long-term risk (25 years) of fatal breast cancer.

Methods

The STO-3 trial enrolled 1780 postmenopausal lymph node–negative breast cancer patients randomly assigned to receive adjuvant tamoxifen vs not. The fraction of cancer cells for each ER intensity level was scored by breast cancer pathologists, and intratumor heterogeneity of ER was calculated using Rao’s quadratic entropy and categorized into high and low heterogeneity using a predefined cutoff at the second tertile (67%). Long-term breast cancer-specific survival analyses by intra-tumor heterogeneity of ER were performed using Kaplan-Meier and multivariable Cox proportional hazard modeling adjusting for patient and tumor characteristics.

Results

A statistically significant difference in long-term survival by high vs low intratumor heterogeneity of ER was seen for all ER-positive patients (P < .001) and for patients with luminal A subtype tumors (P = .01). In multivariable analyses, patients with high intratumor heterogeneity of ER had a twofold increased long-term risk as compared with patients with low intratumor heterogeneity (ER-positive: hazard ratio [HR] = 1.98, 95% confidence interval [CI] = 1.31 to 3.00; luminal A subtype tumors: HR = 2.43, 95% CI = 1.18 to 4.99).

Conclusions

Patients with high intratumor heterogeneity of ER had an increased long-term risk of fatal breast cancer. Interestingly, a similar long-term risk increase was seen in patients with luminal A subtype tumors. Our findings suggest that intratumor heterogeneity of ER is an independent long-term prognosticator with potential to change clinical management, especially for patients with luminal A tumors.

A Single Institutional Experience With the Paris System for Reporting Urinary Cytology: Correlation of Cytology and Histology in 194 Cases

OBJECTIVES

The Paris System for Reporting Urinary Cytology (TPS) is designed to standardize the criteria and terminology used in urinary tract cytology reporting. The aim of this study was to evaluate the impact of implementing TPS and to analyze the correlation with follow-up biopsies in order to assess its reproducibility.

METHODS

Urinary tract cytology specimens with follow-up biopsies over a 2-year period were reviewed and reclassified according to TPS criteria. Surgical follow-up diagnoses were correlated with the initial cytology diagnoses and TPS interpretations, and the results were compared.

RESULTS

Applying TPS in comparison to our previous reporting system resulted in fewer cases in the atypia category (11.8% vs 24.2%) and higher specificity, accuracy, and predictive value. We observed acceptable interobserver agreement in diagnostic categories of this reporting system.

CONCLUSIONS

TPS improves the overall performance of urinary tract cytology by standardizing the criteria and terminology.

Her2/neu Status Determination in Breast Cancer: A Single Institutional Experience Using a Dual-Testing Approach With Immunohistochemistry and Fluorescence In Situ Hybridization

OBJECTIVES

According to current guidelines, either immunohistochemistry (IHC) or in situ hybridization (ISH) can be used to determine human epidermal growth factor receptor 2 (Her2/neu) status in breast carcinoma. While the guidelines explicitly delineate result interpretation, there is no consensus on the most appropriate testing algorithm.

METHODS

The Her2/neu statuses of 369 consecutive cases of invasive breast cancer (from 351 patients) were assessed in a dual-testing algorithm that uses both IHC and fluorescence ISH (FISH). FISH was performed using dual-color HER2/ chromosome enumeration probe 17 ( CEP17 ) probes, and if equivocal results were obtained, reflex testing using HER2/lissencephaly gene 1 ( LIS1 ) probes was used. Results from both modalities were scored and reported using American Society of Clinical Oncology/College of American Pathologists 2013 criteria.

RESULTS

Sixty-one (16.5%) of the 369 tumors were found to be Her2/neu positive by at least one modality. The overall concordance between IHC and FISH results was 97.6%. Six of the 369 tumors were reclassified as Her2/neu positive after a negative IHC result. FISH was also able to identify significantly more Her2/neu-positive cases than IHC.

CONCLUSIONS

The commonly used reflex strategy based on IHC results may deny potentially beneficial targeted therapy for a small cohort of patients, which should be considered as testing guidelines are formulated and the cost-benefit analyses of various testing algorithms are assessed.

Abstract P3-07-49: Residual cancer burden (RCB) with veliparib/carboplatin in the I-SPY2 trial

Background: I-SPY2 is a multicenter phase 2 trial in high risk stage II/III breast cancer (BC) using adaptive randomization within biomarker subtypes to evaluate novel agents added to standard neoadjuvant chemotherapy. The first regimen to graduate based on the predicted probability of a higher pCR rate within predefined subsets was veliparib/carboplatin + paclitaxel (VC+T→AC vs T→AC) in triple negative BC (TNBC). In TNBC the residual cancer burden (RCB) is prognostic, whether as a continuous index or grouped into classes, with pCR (RCB-0) and RCB-I classes having identical survival. Therefore, we evaluated the use of RCB to further discriminate between investigational and control arms.

Methods: Site pathologists reported RCB for 99% of subjects in the primary efficacy analysis based on pCR (n=114/115). We compared the distribution of RCB reported as a continuous index in each treatment-subset combination to matched concurrently randomized controls using the Wilcoxon rank sum test for RCB index, and Fisher's Exact test for RCB classes (RCB-0/I vs RCB-II/III). The statistics are descriptive rather than inferential, and given the small sample size have no claim on generalizability. We modified the Bayesian model used to compute the estimated probability of success in a future, randomized, phase 3 trial of 300 subjects, if response were defined by either pCR or RCB-I (RCB0/I), or separately if it were defined by pCR alone.

Results: VC+T→AC led to a significantly lower RCB index than T→AC in TNBC (p=0.0021), with a near-significant trend when those with pCR were excluded (p=0.06). There was no significant difference in RCB distributions in the other breast cancer subtypes treated. In TNBC, the odds ratio (OR) for achieving RCB-0/I in the VC+T→AC arm vs control was 8.2 (95% confidence interval (CI): 2.1–35), whereas the OR for achieving pCR was 4.56 (95% CI: 1.25–19.53). The simulations using response information from I-SPY2 to predict the probability of success for VC+T→AC for TNBC in a future phase 3 trial estimated this probability to be 0.99 if modeled using RCB-0/I as the response endpoint, and 0.90 if modeled using pCR as the response endpoint.

Conclusions: Use of RCB index and classes provided additional insight into the effect of adding VC to T, appearing to magnify the improved treatment response that had been observed with pCR rates in TNBC. It will be important to test in randomized trials whether a decrease in the RCB index relative to controls, and/or increased rates of RCB-0/I class, are predictive of survival benefit in TNBC.

Citation Format: Liu MC, Symmans WF, Yau C, Chen Y-Y, Rugo HS, Olopade OF, Datnow B, Chen B, Feldman M, Kallakury B, Hasteh F, Tickman R, Ritter J, Troxel M, Mhawech-Fauceglia P, Duan X, Berry D, Esserman L, DeMichele A. Residual cancer burden (RCB) with veliparib/carboplatin in the I-SPY2 trial. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P3-07-49.

Mutational Profiling Can Establish Clonal or Independent Origin in Synchronous Bilateral Breast and Other Tumors

Background

Synchronous tumors can be independent primary tumors or a primary-metastatic (clonal) pair, which may have clinical implications. Mutational profiling of tumor DNA is increasingly common in the clinic. We investigated whether mutational profiling can distinguish independent from clonal tumors in breast and other cancers, using a carefully defined test based on the Clonal Likelihood Score (CLS = 100 x # shared high confidence (HC) mutations/ # total HC mutations).

Methods

Statistical properties of a formal test using the CLS were investigated. A high CLS is evidence in favor of clonality; the test is implemented as a one-sided binomial test of proportions. Test parameters were empirically determined using 16,422 independent breast tumor pairs and 15 primary-metastatic tumor pairs from 10 cancer types using The Cancer Genome Atlas.

Results

We validated performance of the test with its established parameters, using five published data sets comprising 15,758 known independent tumor pairs (maximum CLS = 4.1%, minimum p-value = 0.48) and 283 known tumor clonal pairs (minimum CLS 13%, maximum p-value <0.01), across renal cell, testicular, and colorectal cancer. The CLS test correctly classified all validation samples but one, which it appears may have been incorrectly classified in the published data. As proof-of-concept we then applied the CLS test to two new cases of invasive synchronous bilateral breast cancer at our institution, each with one hormone receptor positive (ER+/PR+/HER2-) lobular and one triple negative ductal carcinoma. High confidence mutations were identified by exome sequencing and results were validated using deep targeted sequencing. The first tumor pair had CLS of 81% (p-value < 10–15), supporting clonality. In the second pair, no common mutations of 184 variants were validated (p-value >0.99), supporting independence. A plausible molecular mechanism for the shift from hormone receptor positive to triple negative was identified in the clonal pair.

Conclusion

We have developed the statistical properties of a carefully defined Clonal Likelihood Score test from mutational profiling of tumor DNA. Under identified conditions, the test appears to reliably distinguish between synchronous tumors of clonal and of independent origin in several cancer types. This approach may have scientific and clinical utility.

"Score the Core" Web-based pathologist training tool improves the accuracy of breast cancer IHC4 scoring

Hormone receptor status is an integral component of decision-making in breast cancer management. IHC4 score is an algorithm that combines hormone receptor, HER2, and Ki-67 status to provide a semiquantitative prognostic score for breast cancer. High accuracy and low interobserver variance are important to ensure the score is accurately calculated; however, few previous efforts have been made to measure or decrease interobserver variance. We developed a Web-based training tool, called "Score the Core" (STC) using tissue microarrays to train pathologists to visually score estrogen receptor (using the 300-point H score), progesterone receptor (percent positive), and Ki-67 (percent positive). STC used a reference score calculated from a reproducible manual counting method. Pathologists in the Athena Breast Health Network and pathology residents at associated institutions completed the exercise. By using STC, pathologists improved their estrogen receptor H score and progesterone receptor and Ki-67 proportion assessment and demonstrated a good correlation between pathologist and reference scores. In addition, we collected information about pathologist performance that allowed us to compare individual pathologists and measures of agreement. Pathologists' assessment of the proportion of positive cells was closer to the reference than their assessment of the relative intensity of positive cells. Careful training and assessment should be used to ensure the accuracy of breast biomarkers. This is particularly important as breast cancer diagnostics become increasingly quantitative and reproducible. Our training tool is a novel approach for pathologist training that can serve as an important component of ongoing quality assessment and can improve the accuracy of breast cancer prognostic biomarkers.

Malignant cell contamination may lead to false-positive findings at endosonographic fine needle aspiration for tumor staging

BACKGROUND AND STUDY AIMS

Endoscopic ultrasound-guided fine needle aspiration (EUS-FNA) of lymph nodes is used for staging of gastrointestinal malignancies. False-positive rates of 5 % - 7 % are not well understood. Elements of EUS examinations that contribute to false-positive cytological findings were investigated.

PATIENTS AND METHODS

13 patients undergoing EUS staging of gastrointestinal luminal malignancy were consecutively enrolled together with 3 patients with extraluminal tumors (pancreas, lung) defined as controls. After EUS, cellular debris and fluid were collected from the FNA needle catheter, instrument channel, and endoscope tip for cytologic and histologic investigation.

RESULTS

6 of 13 patients (46 %) had malignant cells contaminating the FNA needle catheter, instrument channel, or endoscope tip. Malignant cells were present in the instrument channel in 5 cases (38 %), exterior tip of echoendoscope in 4 (31 %) and needle catheter in 2 (15 %).

CONCLUSIONS

Echoendoscopes used for FNA in patients with luminal tumors are at risk for malignant cell contamination of the instrument channel, FNA needle catheter, and echoendoscope tip. FNA needle contamination can contribute to false-positive findings.

A single institution experience with the new bethesda system for reporting thyroid cytopathology: correlation with existing cytologic, clinical, and histological data

Our goal was to evaluate the Bethesda system (TBS) in comparison to the previously used system at our institution. One hundred consecutive thyroid fine needle aspirations (FNAs) and 45 consecutive indeterminate FNAs were reviewed by two cytopathology-boarded pathologists, diagnosed based on TBS and correlated with management and follow-up. Re-evaluation led to a diagnosis change in 48% of cases. Thirty-nine percent of benign cases were unsatisfactory under TBS. For malignant diagnoses the positive predictive value (PPV) was unchanged, while the negative predictive value (NPV) was slightly improved using TBS. Both the PPV and NPV were improved for actionable diagnoses. Inter-observer variability across all categories was in moderate agreement. Clinical management of both follicular lesion (FL) and indeterminate cases ranged from none to immediate surgery. Repeat FNA resolved the diagnosis in 50% of indeterminate cases. Indeterminate cases had an overall malignancy rate of 27%; higher in pre- (46%) than post-TBS cases (8%). Inter-observer variability between the reviewing pathologists and the original pathologists for indeterminate cases was fair, and between the two reviewing pathologists was moderate. Using TBS criteria increased the unsatisfactory rate and led to improved prediction of malignancy and actionable diagnoses. The pre-Bethesda diagnosis of FL at our institution led to inconsistent clinical management. Clinical management of patients with indeterminate diagnoses was essentially unchanged following adoption of TBS. The moderate inter-observer agreement between the reviewing pathologists may be related to level of cytology experience, strict adherence to TBS, and the exclusive use of cytomorphology for diagnosis.

Evaluation of ultra-deep targeted sequencing for personalized breast cancer care

INTRODUCTION

The increasing number of targeted therapies, together with a deeper understanding of cancer genetics and drug response, have prompted major healthcare centers to implement personalized treatment approaches relying on high-throughput tumor DNA sequencing. However, the optimal way to implement this transformative methodology is not yet clear. Current assays may miss important clinical information such as the mutation allelic fraction, the presence of sub-clones or chromosomal rearrangements, or the distinction between inherited variants and somatic mutations. Here, we present the evaluation of ultra-deep targeted sequencing (UDT-Seq) to generate and interpret the molecular profile of 38 breast cancer patients from two academic medical centers.

METHODS

We sequenced 47 genes in matched germline and tumor DNA samples from 38 breast cancer patients. The selected genes, or the pathways they belong to, can be targeted by drugs or are important in familial cancer risk or drug metabolism.

RESULTS

Relying on the added value of sequencing matched tumor and germline DNA and using a dedicated analysis, UDT-Seq has a high sensitivity to identify mutations in tumors with low malignant cell content. Applying UDT-Seq to matched tumor and germline specimens from the 38 patients resulted in a proposal for at least one targeted therapy for 22 patients, the identification of tumor sub-clones in 3 patients, the suggestion of potential adverse drug effects in 3 patients and a recommendation for genetic counseling for 2 patients.

CONCLUSION

Overall our study highlights the additional benefits of a sequencing strategy, which includes germline DNA and is optimized for heterogeneous tumor tissues.

Examination of sources of diagnostic error leading to cervical cone biopsies with no evidence of dysplasia

At our institution, 17% of cervical conization specimens are reported as negative for dysplasia or malignancy. To identify sources of error, we reviewed 53 negative conization specimens and their prior and follow-up cytology, biopsy, and endocervical curettage specimens. Examination of deeper-level sections and p16 immunostaining were performed on all conization specimens and selected biopsy specimens. Dysplasia was detected in 26% (14/53) of conization specimens. Twenty-eight percent (15/53) of cones were truly negative, and the presurgical material had been overcalled as high-grade squamous intraepithelial lesions (HSIL). Forty-five percent (24/53) of cones were truly negative and HSIL was confirmed in the presurgical material. Of these, 11% (6/53) showed subsequent evidence of residual dysplasia and 26% (14/53) were negative on further follow-up. Deeper-level sections, p16 immunostains, and consensus review may help identify squamous dysplasia in conization specimens and may prevent the overdiagnosis of HSIL on cervical biopsies.

Abstract P2-06-01: Breast-to-breast metastasis can cause hormone-receptor positive/triple negative bilateral synchronous tumors

Background: Prior work suggests that synchronous bilateral breast cancers may be clonal, with one tumor a metastasis, although prior techniques lacked resolution to prove this relationship. We used deep whole exome and shallow whole genome sequencing to compare bilateral tumors in two cases. In both cases, tumors were invasive and node negative with one tumor ER+/PR+/HER2− (HR+) lobular and the other triple negative (TN) ductal. Case 1 is a 75-year-old African American woman and Case 2 a 70-year-old white woman. With 44 and 12 months of follow up, respectively, neither patient has recurred.

Methods: Agilent SureSelect All Exon 50Mb Target Enrichment Kits were used for exome capture. Paired-end sequencing was performed with 200 base pair reads on the Illumina HiSeq 2000. Sequencing depth was targeted to cover 80% of the genome at 100x for three tumors with 70% cellularity, 200x for one tumor with 40% cellularity and 30x for germline. Tumor and germline exome results were compared to identify high confidence somatic single nucleotide variants (HC SNV). HC SNV's were called using GATK and stringent custom filtering to avoid false positives resulting from unrecognized germline single nucleotide polymorphisms. For each tumor pair, we define a clonality likelihood score (CLS) as the ratio of the number of HC SNV called at the same site and with the same alternate base in both tumors, to the total number of sites with an HC SNV called in either tumor. For comparison we analyzed the called SNV data from The Cancer Genome Atlas (TCGA) for exome sequenced HR+ or TN breast cancers.

Results: In Case 1, of 102 HC SNVs called in either tumor, 82 were shared, for a CLS of 80.3%. Additionally, 11 shared SNVs were synonymous, consistent with clonality. Lastly the non-shared HC SNVs were asymmetrically found in the TN tumor, consistent with clonal evolution during metastasis. Copy number analysis (CNA) showed Case 1 to have a deletion in 6q, including the ESR1 gene, unique to the TN tumor.

To assess significance of the CLS, we found three primary/metastatic clonal pairs in the TCGA to serve as positive controls. To serve as negative controls, from 357 ER+ and 46 TN primary TCGA tumors, we formed a total of 16,422 independent ER+/TN pairs. For the 3 clonal TCGA pairs, the CLS values were 39.3%, 58.5% and 60.0%. Most of the independent TCGA pairs had a CLS of zero (98.5%), with a maximum CLS of 2.8%. As the CLS for Case 1 lies above maximum observed CLS among 16,422 independent tumor pairs, we reject the hypothesis that this tumor pair is independent, at p &lt; 0.0001. For Case 2, of 222 HC SNV sites, 5 were shared for a CLS of 2.3%, consistent with independence.

Conclusion: Somatic single nucleotide mutations identified by exome sequencing found that the two tumors in Case 1 share &gt;80% of SNVs, consistent with clonal evolution of metastasis. The two tumors from Case 2 have few shared SNVs, consistent with independent origin. CNA results were consistent. This is the first clonality analysis reported from deep sequencing of phenotypically discordant synchronous bilateral breast cancers, and demonstrates that next-generation sequencing can distinguish clonal from independent tumor pairs with high confidence.

Funding: The Breast Cancer Research Foundation

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P2-06-01.

Raising the bar: Breast cancer biomarkers IHC4 harmonization from University of California-Athena pathology collaboration

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Background: Breast cancer treatment depends on the accurate analysis of immunohistochemical biomarkers (IHC4): estrogen and progesterone receptors, Ki-67, HER2. The Athena Harmonization project was undertaken to reduce technical and scoring variances between different laboratories and different pathologists. Methods: Initial assessment: Five breast cancer samples were sectioned and distributed to 5 UC campuses, where IHC4 and HER2 FISH tests were done per usual methods. Samples were selected to cover the range of negative, positive, and moderate for each antigen. Stained slides were circulated to 10 pathologists for scoring. Digital whole slide images (WSI) were made and scored. Technical variance reduction: A Delphi voting process identified an ideal histology slide for each IHC4 antigen. Laboratories adjusted techniques to match the appearance of the ideal slides, followed by pathologist and quantitative image analysis (QIA) validation. Scoring variance reduction: A digital pathology training tool was created where pathologists scored breast cancer tissue microarrays with known scores for the IHC4 antigens. Results: Scoring variance did not exceed clinical thresholds, although there were significant technical and scoring variances between laboratories that could affect research outcomes. The mean values and variance were similar for WSI and glass slides, except for HER2 (higher scores on WSI but without benefit of workstation calibration). Each laboratory adjusted technical parameters to more closely match the ideal IHC4. Early QIA data indicate reduced variance between adjusted and ideal histology slides. Conclusions: Considerable and significant technical and interpretational variances between five University of California laboratories can be overcome by harmonizing protocols, setting new inter-institutional standards for pathology and histology best practices. Quantitative image analysis and whole slide imaging were instrumental. Subsequent harmonization will include cases near thresholds for clinical treatment guidelines.

The clinical significance of "squamous intraepithelial lesion of indeterminate grade" as a distinct cytologic category

The histologic and/or cytologic follow-up of 127 cases of cervical lesions termed "squamous intraepithelial lesion of indeterminate grade" (SIL) on Papanicolaou (Pap) smears by the 2001 Bethesda System was compared with 150 control cases of low-grade SIL (LSIL), high-grade SIL (HSIL), and atypical squamous cells, cannot exclude HSIL (ASC-H). A follow-up diagnosis of cervical intraepithelial neoplasia (CIN) 2 or higher was identified in 22.8% of SIL cases, which was 2.6 times higher than LSIL, 3 times lower than HSIL, and 1.5 times lower than ASC-H. A follow-up diagnosis of CIN 1 was identified in 31.5% of SIL cases, which was 2 times lower than the LSIL group, 1.5 times higher than the ASC-H cases, and 1.8 times higher than the HSIL group. We found that 22.0% of cases diagnosed as SIL were followed up by Pap smears rather than colposcopy and biopsy, compared with about 1% of LSIL and HSIL cases. Because SIL cases have a significant risk of harboring CIN 2 or greater, we recommend follow-up by colposcopy and biopsy.

Thyroid cyst wall atypia in a patient with a history of malignant melanoma: a pitfall in fine-needle aspiration cytology

We present an interesting case report from a patient with a history of desmoplastic malignant melanoma (MM), who presented with a thyroid nodule. The patient's clinical diagnosis included a benign thyroid nodule versus a primary thyroid malignancy or metastatic MM. Fine-needle aspiration biopsy showed highly atypical spindle cells suspicious for metastatic MM. The acellular cell block prevented further studies such as immunohistochemical analysis. The patient underwent surgical excision of the mass, which showed a benign cystic thyroid nodule with an atypical cyst lining. Here, we report the presence of atypical cyst-lining cells in a patient with diagnosis of MM. The atypical cytology of the cyst-lining cells has been reported in the English literature; however, presence of significant cytological atypia, especially in a patient with a history of another malignancy, can be problematic. The cytopathologist should be aware of this entity and its diagnostic pitfalls.

1-hexyl n-cyanoacrylate compound (Neucrylate™ AN), a new berry aneurysm treatment. II. Rabbit implant studies: technique and histology

INTRODUCTION

Following satisfactory benchtop testing of a new liquid embolic agent, animal implant studies were performed.

MATERIALS AND METHOD

Elastase aneurysms were created in the right common carotid artery of New Zealand rabbits under approved institutional guidelines. Using direct fluoroscopic control and commercially available microcatheters, the device was introduced into the aneurysms. At 2 months, 12 months and 24 months, follow-up angiography was performed and analyzed. The animals were sacrificed, the brachiocephalic arteries were explanted and fixed, and the histologic appearance of the treated aneurysms was evaluated.

RESULTS

The Neucrylate polymerized into an open pore elastic sponge. The open pores permitted fibrous tissue ingrowth. By 2 months, all of the aneurysm necks had been covered by fibrous tissue and a neointima. Two of the aneurysms originally inadequately filled allowed opportunity for retreatment. The reactive change within the aneurysms demonstrated fibroblastic proliferation, collagen and some giant cells but no vascular necrosis. Results at 2 months, 12 months and 24 months were for all practical purposes similar.

CONCLUSION

The lack of necrosis, the mild inflammatory response and the permanence of the implant are interesting in a cyanoacrylate based embolic agent, especially in light of the experience with lower chain homologs and other liquid embolic agents.

OT2-04-02: Metformin for Breast Cancer Prevention: A Pilot Study

Background

There is a body of accumulating evidence connecting metformin, a biguanide derivative which reduces hepatic gluconeogensis and improves skeletal muscle insulin sensitivity, to reduced breast cancer risk. This, in addition to a well established drug safety record among diabetics and non-diabetics, has provoked an interest in further study of metformin's effects on breast cancer risk indicators. In our study, we examine the effects of metformin on breast density and proliferative cell marker Ki67, both indicators of breast cancer risk. This is a small observational pilot study to determine the feasibility of subject recruitment, data collection through fine-needle aspiration, and breast density measurement.

Trial Design: Recruitment of 10 breast surgery patients with high risk histology to: 1. Undergo peri-areolar fine needle aspiration (RPFNA) used to collect breast cells for analysis of proliferative marker Ki67. 2. Breast density assessment by a) mammography (the standard method) and b) whole-breast ultrasound (an innovative method recently developed at UCSD).

Each subject will undergo a single view mammogram, whole-breast ultrasound, and intra-operative RPFNA. No drug or therapeutic intervention will take place in this pilot study.

Eligibility: Female undergoing excisional high risk breast surgery.

Specific Aims: Aim 1. To determine the feasibility of recruiting high risk breast surgery patients to an observational study involving RPFNA, mammography, and whole-breast ultrasound.

Aim 2. a) To compare mammography and whole-breast ultrasound for measurement of breast density. b) To examine potential for detecting biomarkers of cell proliferation through RPFNA.

Statistical Method: Breast density will be determined by the ratio of fibroglandular tissue to fat measured on mammogram and WBU. Cell proliferation will be assessed by the percentage of positivity for biomarker Ki67 in breast ductal cells.

Accrual and target accrual: Five of ten breast excisional high risk breast surgery subjects have been accrued at this time.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr OT2-04-02.

Reliability of Her2/neu, estrogen receptor, and progesterone receptor testing by immunohistochemistry on cell block of FNA and serous effusions from patients with primary and metastatic breast carcinoma

The prognostic and predictive value of Her2/neu and the hormone receptors in patient with primary or metastatic breast cancer is essential for a favorable outcome of treatment. We have been experiencing increasing requests to test cytologic specimens for these markers in patients with metastatic breast carcinoma. A recent study threw some doubts on the validity of such testing using cell blocks. In this study we compared our immunohistochemical Her2/neu, ER and PR testing performed on 42 formalin-fixed, paraffin-embedded cell blocks from 27 fine needle aspirations (FNA) and 15 serous effusions of 42 patients with metastatic (n = 38) and primary (n = 4) breast carcinoma to the test results obtained on tissue sections. In seven cases the Her2/neu immunohistochemistry (IHC) results on cell blocks were also compared with Her2/neu fluorescence in situ hybridization (FISH) on tissue or cell block. The study revealed 100% correlation for positive and negative Her2/neu results. For ER testing the results showed 85.7% sensitivity, 100% specificity, 100% positive predictive value (PPV), and 85.7% negative predictive value (NPV). For PR testing the results showed 80% sensitivity, 100% specificity, 100% PPV, and 88.8% NPV respectively. In conclusion, IHC for Her2/neu, ER and PR performed on formalin-fixed, paraffin-embedded cell blocks prepared from fresh FNA and serous fluid is reliable in predicting the expression of these markers when correlated with IHC and FISH performed on the corresponding tumor tissue.

Oncocytic variant of papillary thyroid carcinoma associated with Hashimoto's thyroiditis: a case report and review of the literature

Identification of Hürthle cells on fine-needle aspiration (FNA) of the thyroid leads to a wide differential diagnosis including benignand malignant entities. We report the cytological and histological findings of a patient with an oncocytic variant of papillary thyroid carcinoma (PTC) with concurrent Hashimoto's thyroiditis. FNA revealed a lymphoplasmacytic infiltrate with Hürthle cells demonstrating abnormal chromatin patterns, nuclear enlargement, pleomorphism, intranuclear cytoplasmic invaginations, and foci of papillary aggregates. Because of the degree of nuclear atypia and suspicion for concurrent papillary thyroid carcinoma, a total thyroidectomy was performed revealing a papillary arrangement of Hürthle cells with classic PTC nuclear changes and associated Hashimoto's thyroiditis. This report discusses cytopathological features of a rare variant of PTC (oncocytic subtype) in the background of Hashimoto's thyroiditis. We also briefly discuss the differential diagnosis and diagnostic pitfalls of Hürthle cell lesions, with a review of the literature.

Cellular adequacy for thyroid aspirates prepared by ThinPrep: how many cells are needed?

Although it is well established that ThinPrep introduces artifacts to thyroid aspirates, no criteria have been established for adequacy of such specimens. This study evaluates the adequate number of cells needed to establish the correct diagnosis based on ThinPrep alone. A total of 218 thyroid aspirates prepared by TP with surgical pathology follow-up were reviewed. The cellularity was calculated as follows: Count the total number of clusters, randomly select 10 clusters and count each, calculate the average number per cluster and multiply by the total number of clusters. A minimum number of 6 clusters with 10 cells each was arbitrary established to assume adequacy for a definitive diagnosis. Cytologic diagnoses were classified as: Nondiagnostic (ND), cystic contents, thyroiditis, nodular hyperplasia (NH), follicular/Hurthle (F/H) cell lesion, F/H cell neoplasm, and carcinoma: qualify. Histologic diagnoses were classified as: Cyst (colloid or otherwise), thyroiditis, NH, F/H adenoma, F/H carcinoma, carcinoma: qualify. Appropriate treatment triage was considered to be clinical for the former 4 cytologic categories and surgical for the latter 3 with ND warranting repeat aspiration. The results were subjected to logistic regressions analysis and contingency tables correlating the number of cells with the cytologic and histologic diagnosis as well as with treatment triage. Cellularity of sample was ranked in 10 deciles according to the number of cells and in 4 quartiles according to the number of clusters. The agreement percentage, for both diagnostic and treatment, was computed for each decile and quartile. 146 (67%) cases had cells and received a diagnosis while 72 (33%) were acellular. Of the 146 cases, 21 contained histiocytes or colloid only. 91/146 (62.3%) were correctly diagnosed and 123/146 (84.3%) would have been correctly triaged for treatment based upon the cytologic diagnosis. Samples with 180 cells or fewer had an agreement rate below 50%. Agreement rate increases to 80% when cellularity is 180-320. Above 320 agreement rate remains high but not uniformly. Total number of clusters did not play an independent role and only the number of cells per cluster had a significant correlation with diagnostic agreement. A 25-cell increase in average cells per cluster increases the odds of agreement between diagnoses by 65%.

A metastatic renal carcinoid tumor presenting as breast mass: a diagnostic dilemma

We present clinicopathological and cytological findings of a well-defined breast mass in a patient with history of primary renal carcinoid tumor. Fine-needle aspiration (FNA) cytology showed monotonous tumor cells with plasmacytoid appearance arranged singly and in small clusters. Occasional tumor cells were arranged in acinar architecture resembling glandular differentiation. Tumor cells showed fine speckled chromatin. The unusual location for metastasis of this rare type of carcinoid tumor and overlapping cytological features with primary mammary carcinoma led to an erroneous preliminary cytological diagnosis of primary breast carcinoma with plasmacytoid features. Tumor cells in the corresponding cell block showed strong diffuse positivity for synapthophysin and pan-cytokeratin with weak focal positivity for chromogranin markers. These patterns of immunostaining were similar to the original renal carcinoid tumor. To the best of our knowledge, a few cases of carcinoid tumor metastatic to the breast have been reported in the literature and more than half of these cases were initially misdiagnosed as primary breast carcinoma causing unnecessary surgical treatment. This is a first reported case of metastatic renal carcinoid tumor into breast diagnosed with FNA biopsy. This report highlights the cytological features of well-differentiated neuroendocrine tumor (carcinoid tumor) and its potential diagnostic pitfalls.