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Supplementary Methods, Figure Legend, Table 1 from Mapping Geographic Zones of Cancer Risk with Epigenetic Biomarkers in Normal Breast Tissue

Supplementary Figure 1 from Mapping Geographic Zones of Cancer Risk with Epigenetic Biomarkers in Normal Breast Tissue

Purpose: Genetic alterations were previously identified in normal epithelia adjacent to invasive cancers. The aim of this study was to determine DNA methylation in histologically normal tissues from multiple geographic zones adjacent to primary breast tumors.Experimental Design: First, methylation status of a 4-kb region of RASSF1A promoter was interrogated using oligonucleotide-based microarray in 144 samples (primary tumors, 47; adjacent normals, 69; reduction mammoplasty tissues, 28). Second, allelic imbalance (AI)/loss of heterozygosity (LOH) surrounding RASSF1A promoter were analyzed in 30 samples (tumors, 8; adjacent normals, 22). Third, global methylation screening of 49 samples (tumors, 12; adjacent normals, 25; reduction mammoplasty, 12) was done by differential methylation hybridization. Real-time quantitative methylation-specific PCR was used to validate the microarray findings.Results: DNA methylation in the core RASSF1A promoter was low in reduction mammoplasty tissues (P = 0.0001) when compared with primary tumors. The adjacent normals had an intermediate level of methylation. The regions surrounding the core were highly methylated in all sample types. Microsatellite markers showed AI/LOH in tumors and some of the adjacent normals. Concurrent AI/LOH and DNA methylation in RASSF1A promoter occurred in two of six tumors. Global methylation screening uncovered genes more methylated in adjacent normals than in reduction mammoplasty tissues. The methylation status of four genes was confirmed by quantitative methylation-specific PCR.Conclusions: Our findings suggest a field of methylation changes extending as far as 4 cm from primary tumors. These frequent alterations may explain why normal tissues are at risk for local recurrence and are useful in disease prognostication.

RNA splicing is an important biological process associated with cancer initiation and progression, yet in pancreatic cancer the role and regulation of splicing is not well understood. From a forward genetic screen in a mouse model of pancreatic cancer, we identified an enrichment of RNA binding proteins (RBPs) associated with the spliceosome. Here, we link deregulation of RBFOX2, an RBP of the FOX family, to pancreatic cancer progression and liver metastasis. We show that RBFOX2 regulation in pancreatic cancer occurs at both the RNA and protein level, and that nuclear localization of RBFOX2 is significantly reduced in poorly differentiated PDAC. Deregulation of RBFOX2 in PDAC is associated with an enrichment of exon exclusion events in transcripts encoding proteins involved in cytoskeletal remodeling and invadopodia programs that potentiate metastatic potential in vivo. Using splice-switching antisense oligonucleotides (AONs) and inducible cDNA isoforms, we demonstrate that RBFOX2 mediated exon exclusion in ABI1 controls the abundance and localization of ABI1 protein isoforms in pancreatic cancer cells, and that ABI1 splice-switching enhances cellular phenotypes associated with cancer cell stemness. Together, our data identify a novel role for RBFOX2 deregulation in promoting PDAC progression through alternative splicing regulation.

BACKGROUND The current report provides results from a large retrospective analysis of intraoperative imprint cytology performed on axillary sentinel lymph nodes (IICN) removed over the course of 2137 breast surgeries (4905 lymph nodes). It is hoped that these results may serve as benchmarks for those interested in using this technique. METHODS The current study included 2078 patients with T1–2 invasive breast carcinoma who underwent sentinel lymph node biopsy (SLNB) and IICN. Lymph nodes were bivalved, imprinted, stained with Diff-Quik (Baxter Diagnostics, McGaw Park, IL), and reviewed by a cytopathologist. A positive intraoperative diagnosis led to immediate complete axillary lymph node dissection (CALND). On final pathology, lymph nodes found to be negative on hematoxylin and eosin staining were submitted for cytokeratin staining. RESULTS Of the 2137 cases for which SLNB was performed, 673 were found to have positive lymph node status on final pathology. Of these 673 cases, 359 were identified by IICN, resulting in a sensitivity rate of 53.3%. The specificity and overall accuracy rates for this technique were 99.5% and 85.0%, respectively. In IDC cases, IICN had a sensitivity rate of 55.5%, compared with 38.7% in ILC cases. Based on these results, the reoperative CALND rate was calculated to be approximately 14.7%, with 54.5% of these reoperative procedures being performed for cases in which lymph nodes positive only for micrometastases were found. Macrometastasis-positive lymph nodes that went undetected by IICN were present in only 154 of the 2137 cases examined (7.2%). CONCLUSIONS IICN accurately predicts final lymph node status in 85.0% of patients. Although the accuracy of this technique varies with tumor size and type, IICN remains a time-efficient and cost-effective adjunct to SLNB. Cancer (Cancer Cytopathol) 2005. © 2004 American Cancer Society.

Since the first description by Frantz in 1959 of a papillary cystic tumor of the pancreas, solid pseudopapillary tumors have been increasing in incidence. However, management of these lesions remains controversial. Patients under the age of 20 years more often undergo local excision than do their older counterparts, resulting in increased recurrence rates. The cause of this discrepancy is not clear but may be related to an inability to make a definitive preoperative diagnosis. The authors report a case of a solid pseudopapillary tumor of the pancreas in a 13-year-old girl in which the diagnosis was established preoperatively by endoscopic ultrasound scan with fine-needle aspiration (EUS-FNA). EUS-FNA represents a diagnostic technique commonly used in adults that may be useful in identifying the rare pediatric patient with pancreatic malignancy.

The current report provides results from a large retrospective analysis of intraoperative imprint cytology performed on axillary sentinel lymph nodes (IIC(N)) removed over the course of 2137 breast surgeries (4905 lymph nodes). It is hoped that these results may serve as benchmarks for those interested in using this technique.The current study included 2078 patients with T1-2 invasive breast carcinoma who underwent sentinel lymph node biopsy (SLNB) and IIC(N). Lymph nodes were bivalved, imprinted, stained with Diff-Quik (Baxter Diagnostics, McGaw Park, IL), and reviewed by a cytopathologist. A positive intraoperative diagnosis led to immediate complete axillary lymph node dissection (CALND). On final pathology, lymph nodes found to be negative on hematoxylin and eosin staining were submitted for cytokeratin staining.Of the 2137 cases for which SLNB was performed, 673 were found to have positive lymph node status on final pathology. Of these 673 cases, 359 were identified by IIC(N), resulting in a sensitivity rate of 53.3%. The specificity and overall accuracy rates for this technique were 99.5% and 85.0%, respectively. In IDC cases, IIC(N) had a sensitivity rate of 55.5%, compared with 38.7% in ILC cases. Based on these results, the reoperative CALND rate was calculated to be approximately 14.7%, with 54.5% of these reoperative procedures being performed for cases in which lymph nodes positive only for micrometastases were found. Macrometastasis-positive lymph nodes that went undetected by IIC(N) were present in only 154 of the 2137 cases examined (7.2%).IIC(N) accurately predicts final lymph node status in 85.0% of patients. Although the accuracy of this technique varies with tumor size and type, IIC(N) remains a time-efficient and cost-effective adjunct to SLNB.

Clinical histories, endoscopic ultrasound (EUS)-guided fine-needle aspiration (FNA) material, and immunohistochemical stains performed on cell block samples of 6 solid-pseudopapillary tumors of the pancreas (SPTPs) were reviewed in the cases of 5 females (13-58 years) and 1 man (57 years); all had abdominal pain. Preliminary cytologic diagnoses at endoscopy included 1 SPTP 2 low-grade neoplasms, and 3 pancreatic endocrine tumors. Variable numbers of branching fragments with central capillaries and myxoid stroma were seen in the smears of 5 of 6 cases but were more apparent in the cell block material of all cases. The cells had bland nuclear features and rare grooves. Extensive necrosis was noted in 1 case and rare mitotic figures in 1. SPTPs showed strong cellular immunoreactivity for vimentin and focal weak keratin reactivity. Neuron-specific enolase, alpha1-antitrypsin, and alpha1-antichymotrypsin stains performed in 2 cases were strongly positive. Subsequent surgical resection confirmed all diagnoses. EUS-guided FNA diagnosis of SPTP is accurate. The characteristic branching papillae with myxoid stroma are best seen in cell block slides. Clinical setting, cytomorphologic features, and immunostains of the cell block help distinguish SPTP from pancreatic endocrine tumors, acinar cell carcinoma, and papillary mucinous carcinoma.