Bret Taback

Profiling epigenetic inactivation of tumor suppressor genes in tumors and plasma from cutaneous melanoma patients

Aberrant methylation of CpG islands in promoter regions of tumor suppressor genes (TSG) has been demonstrated in epithelial origin tumors. However, the methylation profiling of tumor-related gene promoter regions in cutaneous melanoma tumors has not been reported. Seven known or candidate TSGs that are frequently hypermethylated in carcinomas were assessed by methylation-specific polymerase chain reaction (MSP) in 15 melanoma cell lines and 130 cutaneous melanoma tumors. Four TSGs were frequently hypermethylated in 86 metastatic tumor specimens: retinoic acid receptor-β2 (RAR-β2) (70%), RAS association domain family protein 1A (RASSF1A) (57%), and O6-methylguanine DNA methylatransferase (MGMT) (34%), and death-associated protein kinase (DAPK) (19%). Hypermethylation of MGMT, RASSF1A, and DAPK was significantly lower in primary melanomas (n=20) compared to metastatic melanomas. However, hypermethylation of RAR-β2 was 70% in both primary and metastatic melanomas. Cell lines had hypermethylation profiles similar to those of metastatic melanomas. The analysis of these four markers of metastatic tumors demonstrated that 97% had ⩾1 gene(s) and 59% had ⩾2 genes hypermethylated. The methylation of genes was verified by bisulfite sequencing. The mRNA transcripts could be re-expressed in melanoma cell lines having hypermethylated genes following treatment with 5′-aza 2′-deoxycytidine (5Aza-dC). Analysis of melanoma patients’ plasma (preoperative blood; n=31) demonstrated circulating hypermethylated MGMT, RAR-β2, and RASSF1A DNA for at least one of the markers in 29% of the patients. Our findings indicate that the incidence of TSG hypermethylation increases during tumor progression. Methylation of TSG may play a significant role in cutaneous melanoma progression.

Distinct Hypermethylation Profile of Primary Breast Cancer Is Associated with Sentinel Lymph Node Metastasis

Purpose: Gene promoter region hypermethylation is a significant event in primary breast cancer. However, its impact on tumor progression and potential predictive implications remain relatively unknown. Experimental Design: We conducted hypermethylation profiling of 151 primary breast tumors with association to known prognostic factors in breast cancer using methylation-specific PCR for six known tumor suppressor and related genes: RASSF1A, APC, TWIST, CDH1, GSTP1, and RAR-β2. Furthermore, correlation with sentinel lymph node (SLN) tumor status was assessed as it represents the earliest stage of metastasis that is readily detected. Hypermethylation for any one gene was identified in 147 (97%) of 151 primary breast tumors. The most frequently hypermethylated gene was RASSF1A (81%). Results: Hypermethylation of the CDH1 was significantly associated with primary breast tumors demonstrating lymphovascular invasion (P = 0.008), infiltrating ductal histology (P = 0.03), and negative for the estrogen receptor (P = 0.005), whereas RASSF1A and RAR-β2 gene hypermethylation were significantly more common in estrogen receptor–positive (P < 0.001) and human epidermal growth factor receptor 2–positive (P < 0.001) tumors, respectively. In multivariate analysis, hypermethylation of GSTP1 and/or RAR-β2 was significantly associated with patients having macroscopic SLN metastasis compared with those with microscopic or no sentinel node metastasis (odds ratio, 4.59; 95% confidence interval, 2.02-10.4; P < 0.001). In paired SLN metastasis, CDH1 was the most frequently methylated gene (90%) and provides evidence in patients corroborating its role in the clinical development of metastasis. Conclusion: Hypermethylation profiling of primary breast tumors is significantly associated with known pathologic prognostic factors and may have additional clinical and pathologic utility for assessing patient prognosis and predicting early regional metastasis.

Serum Vascular Endothelial Growth Factor and Fibronectin Predict Clinical Response to High-Dose Interleukin-2 Therapy

PURPOSE High-dose interleukin-2 (IL-2) induces durable therapeutic responses in a small subset of patients with metastatic melanoma and renal cell carcinoma, but simple pretreatment predictors of response have not been identified. PATIENTS AND METHODS To identify predictive biomarkers of clinical response, sera from patients treated with high-dose IL-2 were collected for analysis using a customized, multiplex antibody-targeted protein array platform that surveyed expression of soluble factors associated with tumor immunobiology. Soluble factors associated with clinical responses were analyzed using a multivariate permutation test, and survival outcomes were determined using Kaplan-Meier and log-rank tests. RESULTS A training set from 10 patients identified 68 potentially relevant soluble factors that were then tested in an independent validation set of 49 patients. Class comparison revealed a cluster of 11 biomarkers that were associated with therapeutic outcome. Vascular endothelial growth factor (VEGF) and fibronectin were identified as independent predictors of response. In particular, high levels of these proteins were correlated with lack of clinical response and decreased overall survival. CONCLUSION Serum VEGF and fibronectin are easily measured pretreatment biomarkers that could serve to exclude patients unlikely to respond to IL-2 therapy.

Prognostic Significance of Molecular Upstaging of Paraffin-Embedded Sentinel Lymph Nodes in Melanoma Patients

PURPOSE Detection of micrometastases in sentinel lymph nodes (SLNs) is important for accurate staging and prognosis in melanoma patients. However, a significant number of patients with histopathology-negative SLNs subsequently develop recurrent disease. We hypothesized that a quantitative realtime reverse transcriptase polymerase chain reaction (qRT) assay using multiple specific mRNA markers could detect occult metastasis in paraffin-embedded (PE) SLNs to upstage and predict disease outcome. PATIENTS AND METHODS qRT was performed on retrospectively collected PE SLNs from 215 clinically node-negative patients who underwent lymphatic mapping and sentinel lymphadenectomy for melanoma and were followed up for at least 8 years. PE SLNs (n = 308) from these patients were sectioned and assessed by qRT for mRNA of four melanoma-associated genes: MART-1 (antigen recognized by T cells-1), MAGE-A3 (melanoma antigen gene-A3 family), GalNAc-T (beta1-->4-N-acetylgalactosaminyl-transferase), and Pax3 (paired-box homeotic gene transcription factor 3). RESULTS Fifty-three (25%) patients had histopathology-positive SLNs by hemotoxylin and eosin and/or immunohistochemistry. Of the 162 patients with histopathology-negative SLNs, 48 (30%) had nodes that expressed at least one of the four qRT markers, and these 48 patients also had a significantly increased risk of disease recurrence by a Cox proportional hazards model analysis (P <.0001; risk ratio, 7.48; 95% CI, 3.70 to 15.15). The presence of > or = one marker in histopathology-negative SLNs was also a significant independent prognostic factor by multivariate analysis for overall survival (P =.0002; risk ratio, 11.42; 95% CI, 3.17 to 41.1). CONCLUSION Molecular upstaging of PE histopathology-negative SLNs by multiple-marker qRT assay is a significant independent prognostic factor for long-term disease recurrence and overall survival of patients with early-stage melanoma.

Sentinel Lymph Node Biopsy for Local Recurrence of Breast Cancer After Breast-Conserving Therapy

BackgroundLymphatic mapping (LM) with sentinel lymph node (SLN) biopsy has revolutionized the surgical staging of primary breast cancer, but its utility and feasibility have not been established in patients with ipsilateral breast tumor recurrence (IBTR) after breast-conserving surgery (BCS) and radiation.MethodsWe reviewed our breast cancer database to identify all patients who underwent preoperative lymphoscintigraphy for IBTR and whose primary tumor had been managed by BCS, SLN biopsy and/or axillary node dissection, and adjuvant breast irradiation.ResultsPreoperative lymphoscintigraphy identified migration to the regional nodal drainage basins in 11 (73%) of 15 patients, as follows: 5 ipsilateral axillary, 1 supraclavicular, 2 internal mammary, 2 interpectoral, and 3 contralateral axillary. Two patients demonstrated drainage to two nodal basins. In four patients, no drainage was observed. Intraoperative LM with radioisotope plus blue dye identified at least 1 SLN in 11 of 14 patients, and histopathologic evaluation revealed metastasis in 3 patients (2 contralateral axillary and 1 ipsilateral axillary). During preoperative lymphoscintigraphy, the radiocolloid migration time tended to be longer and the drainage pathways more variable than those associated with primary tumors.ConclusionsLM/SLN biopsy can be successfully performed in patients with IBTR after prior BCS, axillary surgical staging, and adjuvant radiation. This approach illustrates variations in the lymphatic drainage of recurrent breast tumors and may permit the identification of regional metastasis not noted with conventional imaging techniques.

Allelic Imbalance of 12q22–23 Associated with APAF-1 Locus Correlates with Poor Disease Outcome in Cutaneous Melanoma

Cutaneous melanoma is a highly aggressive tumor that is relatively resistant to chemotherapy and radiotherapy. This resistance may be in part due to inhibition of apoptosis. Apoptotic protease activating factor-1(APAF-1), a candidate tumor suppressor gene, mediates p53-induced apoptosis, and its loss promotes oncogenic transformation. To determine whether loss of the APAF-1 locus influences tumor progression, we assessed loss of heterozygosity microsatellites on the APAF-1 locus (12q22–23) in 62 primary and 112 metastatic melanomas. We discovered that frequency of allelic imbalance was significantly higher in metastatic tumors (n = 36 of 98; 37%) than in primary melanomas (n = 10 of 54; 19%; P = 0.02). In metastatic melanomas, APAF-1 loss significantly correlated with a worse prognosis (P < 0.05) in the patients, and its loss during melanoma tumor progression suggests that APAF-1 is a tumor suppressor gene. Furthermore, loss of heterozygosity was frequent in the 12q22–23 chromosome region centromeric to the APAF-1 locus suggesting that other tumor-related genes may be present in the 12q22–23 region. In summary, the study demonstrates that allelic imbalance in the 12q22–23 region is a genomic surrogate of poor disease outcome for cutaneous melanoma patients.

Quantification of Circulating DNA in the Plasma and Serum of Cancer Patients

Abstract: A variety of tumor‐genetic alterations have been identified circulating free‐form in the plasma and serum of cancer patients that may have diagnostic and prognostic implications. Currently, no consensus exists as to whether plasma or serum is preferable for circulating nucleic acid analysis, and the impact of collection and processing on yield is unknown. We prospectively assessed DNA content in paired plasma and serum obtained from 10 patients with AJCC stage IV advanced metastatic melanoma. Blood (30 mL) was collected from each patient as follows: 10 mL each was processed immediately for serum and plasma and an additional 10 mL was incubated overnight at 37°C and processed for serum. In addition, blood was collected from 25 normal healthy donor volunteers to determine the concentration of free DNA circulating in paired plasma and serum. DNA was isolated from 800 μl of plasma or serum and quantified. Median‐free DNA concentrations were fourfold greater in serum than in the corresponding plasma sample. Serum isolated from blood allowed to clot overnight yielded four times more DNA than serum processed immediately. Among normal healthy volunteers, only serum contained detectable free DNA. These findings provide conclusive evidence that elevated levels of circulating DNA could be identified consistently in patients with cancer than in normal healthy donors. Furthermore, the method of blood processing may significantly affect the levels of circulating nucleic acids and impact the investigators results. Significant consideration must be given to the methods by which circulating nucleic acids are obtained for clinical analysis.

Circulating Nucleic Acids and Proteomics of Plasma/Serum: Clinical Utility

Abstract: Circulating tumor‐specific nucleic acids have been identified in plasma, serum, and other body fluids from cancer patients with tumors originating in almost any organ site. Polymerase chain reaction provides a highly sensitive and specific technique for the detection of these genetic changes in a limited amount of tissue/fluid. The presence of elevated levels of free DNA/RNA in many medical conditions, malignancy, and infectious processes is being investigated for screening, diagnosis, prognosis, surveillance for occult disease progression, identifying potential therapeutic targets, and monitoring treatment response. Additionally, elevated fetal DNA/RNA in maternal blood is being used to determine gender identity, assess chromosomal abnormalities, and monitor pregnancy‐associated complications. Questions remain on the etiology, characteristics, stability, and potential pathologic consequences of cell‐free DNA/RNA in the circulation. Nevertheless, nucleic acid‐based assays that monitor plasma, serum, and body fluids provide a noninvasive, facile, and practical method for assessing patients. Proteomic profiling may prove complementary to a total functionality approach in providing a comprehensive evaluation of the patients disease.

Peptide nucleic acid clamp PCR: A novel K-ras mutation detection assay for colorectal cancer micrometastases in lymph nodes

Inaccurate staging of colorectal cancer (CRC) has been attributed to the failure to detect lymph node metastases by conventional pathology. We have previously reported the use of lymphatic mapping to accurately identify those lymph nodes most likely to harbor micrometastatic disease and permit focused pathologic examination. Mutation of K‐ras allele at codons 12 or 13 occurs frequently in early stages of CRC development. The purpose of our study was to assess sentinel lymph nodes (SLN) for occult CRC micrometastases using a unique peptide nucleic acid (PNA) clamp PCR assay specific for K‐ras mutations. Seventy‐two paraffin‐embedded primary CRC and paired SLN were evaluated by PNA clamp PCR for K‐ras mutations. Thirty primary tumors (42%) were positive for K‐ras mutations, and in 5 of these cases the SLN were positive for metastases by Hematoxylin and Eosin staining. PNA clamp PCR identified occult metastases in an additional 6 patients, upstaging 24% of K‐ras positive primary CRCs (p = 0.014). No K‐ras mutations were detected among the 20 noncancer lymph nodes assessed. This study demonstrates the utility, specificity and sensitivity of PNA clamp PCR assay in identifying occult micrometastases in the SLN of CRC patients by single‐base mutation analysis.

Molecular Clonality of In-Transit Melanoma Metastasis

In-transit melanoma is characterized by an aggressive pattern of recurrence that is associated with a poorer prognosis. Because in-transit melanoma is considered to result from the intralymphatic trapping of melanoma cells between the primary tumor and regional lymph nodes, it provides an excellent model to assess genetic events associated with early metastasis. The hypothesis of this study was to determine whether in-transit metastases are clonal in origin and therefore, may have specific genetic alterations uniquely associated with this disease and the development of early metastasis. This was assessed using loss of heterozygosity (LOH) analysis for specific DNA microsatellite loci. Seventy-nine paraffin-embedded in-transit melanoma lesions from 25 patients (range, 2 to 9 lesions per patient; average, 3.4 lesions per patient) were assessed for LOH using eight microsatellite DNA markers on six chromosomes. In 19 of 25 patients (76%) LOH was demonstrated for at least one marker. The most frequent microsatellite marker demonstrating LOH was D9S157 (56%). Using LOH microsatellite markers to assess intertumor heterogeneity, six of 79 tumors (7.6%) demonstrated different profiles when compared to other lesions from the same patient. In-transit metastases from those patients demonstrating intertumor heterogeneity were further assessed using laser capture microdissection and DNA analysis, and revealed no significant intratumor heterogeneity. In conclusion, LOH was frequently observed in in-transit melanoma metastasis. Based on LOH analysis, in-transit metastases are clonal in origin. The establishment of clinically successful in-transit melanoma metastasis requires specific genetic events that seem to be unique and homogeneous for each patient.