Abstract P3-07-01: Towards a therapeutically relevant subtyping scheme for triple-negative breast cancer (TNBC), profiling results from A Randomized, TNBC Enrolling trial to confirm Molecular profiling Improves Survival (ARTEMIS)

Triple-negative breast cancer is a highly diverse group of cancers, with poor prognosis, and currently, there are no targeted drugs available in the clinic. In TNBC around 50% percent of the patients respond to chemotherapy, while, the other 50% percent relapse with poor prognosis. There is a need to understand better the targetable mechanisms driving TNBC via integrative analysis of gene-expression, copy-number, and mutational data.

Samples from 220 triple-negative breast cancer (TNBC) pts treated with NACT were prioritized for transcriptomic and genomic profiling. Non-negative matrix factorization was used on array-based profiling to identify six robust (ARTEMIS) subtypes. Comparing ARTEMIS subtypes with Vanderbilt subtypes, revealed significant overlap with 4/6 clusters while identifying two new clusters. Logistic regression on ssGSEA scores vs. subtypes revealed several pathways, selectively enriched specific subtypes. CL1/IM (Immune subtype), was enriched in INFg and INFa, while CL2 (MYC/mTOR), showed enrichment of several proliferation-related pathways. In addition, LAR and M (Mesenchymal) pts formed overlapping clusters, using either method.

Two new subtypes did not associate significantly with any of the previous subtypes. The majority of the tumors from the Vanderbilt BL2 and MSL were reclassified into a CL5 (ANGIO) cluster, which was enriched in angiogenesis geneset, including targetable genes like VEGF and FGFR. Also, an MYO (CL3) subtype was identified, with myogenesis-related genes. Of note, TIL (tumor infiltrating lymphocytes) and LAR quantification using IHC were associated with respective ARTEMIS subtypes. Finally, the IM subtype was significantly associated with higher rates of RCB 0-I and the M (CL4) subtype was associated with higher rates of RCB II-III, irrespective of the neoadjuvant treatment regimen.

ARTEMIS subtypes are a novel classification system for TNBC that is focused on therapeutic translation. Further, we show a possibility to classify previously un-classified (UNS) tumors, which will be validated using additional cohorts (TCGA/METABRIC).

Citation Format: Seth S, Huo L, Rauch G, Lau R, Gilcrease M, Adrada B, Piwnica-Worms H, Symmans WF, Draetta G, Futreal AP, Moulder S, Chang JT. Towards a therapeutically relevant subtyping scheme for triple-negative breast cancer (TNBC), profiling results from A Randomized, TNBC Enrolling trial to confirm Molecular profiling Improves Survival (ARTEMIS) [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P3-07-01.

Abstract OT2-01-14: Triple-negative first-line study: Neoadjuvant trial of nab-paclitaxel and atezolizumab, a PD-L1 inhibitor, in patients with triple negative breast cancer (TNBC) (NCT02530489)

BACKGROUND: TNBC has an especially poor prognosis in patients (pts) whose tumor does not respond to anthracycline and taxane-based chemotherapy. Approximately 50% will have chemo-insensitive disease (CID) resulting in extensive residual disease at the time of surgery. 40-80% of these pts will recur < 3 years. Recently developed molecular profiling techniques to identify TNBC subsets detect distinct molecular hallmarks. We designed a clinical trial to identify and characterize CID (ARTEMIS: A Randomized, TNBC Enrolling trial to confirm Molecular profiling Improves Survival). Treatment naïve pts with localized TNBC undergo a pretreatment biopsy followed by anthracycline-based chemotherapy (AC). During AC the molecular profile is determined; these results along with the response assessment (clinical exam/diagnostic imaging) will identify CID and guide the second phase of neoadjuvant chemotherapy. Tumor-infiltrating lymphocytes (TIL) have been identified as having prognostic and predictive significance in TNBC pts leading to higher pCR rates post NACT. However, the tumor microenvironment also contains regulatory T cells and myeloid-derived suppressor cells that are immunosuppressive. Programmed death ligand 1 (PD-L1) is expressed in 20% TNBC. Targeting this may lead to a more durable response as compared to chemotherapy alone.

PRIMARY OBJECTIVE: Evaluate the rate of pathologic complete response (pCR)/RCB-0 + residual cancer burden (RCB)-I responses in TNBC pts, determined to have CID after anthracycline-based chemotherapy, then treat with atezolizumab + nab-paclitaxel preoperatively.

TRIAL DESIGN AND STATISITCAL METHODS: Pts deemed to have CID on the ARTEMIS trial can enter this non-randomized phase II study. Pts without response to their initial chemotherapy cycles have a low likelihood (5%) of achieving pCR with additional cycles of chemotherapy. It would be clinically meaningful for pCR to improve to 20%. Counting pCR (RCB-0) or RCB-I as response given similar survival outcomes, a two-stage Gehan-type design will be employed with 14 pts in the first stage. If at least one pt responds, 23 more will be added. This design has a 49% chance of terminating after the first stage if the true response rate is 0.05, 23% chance if the true rate is 0.10, 10% if the true rate is 0.15 and 4% if the true rate is 0.20. If accrual continues to the second stage, the 95% confidence interval for a 0.20 response rate will extend from 0.10 to 0.35.

BRIEF ELIGIBILITY CRITERIA: Inclusion: localized TNBC enrolled onto ARTEMIS and determined to have CID at the time of response assessment after anthracycline chemotherapy, adequate organ, bone marrow and cardiac parameters. Exclusion: prior immunotherapy, IBC, history of autoimmune disease, HIV, Hep-B, Hep-C, active tuberculosis, pregnant.

CORRELATIVE SCIENCE: Evaluate the presence and phenotype of TIL and other immune cell populations in tumor tissue pre/post treatment; determine changes in expression of co-stimulatory and co-inhibitory molecules on tumor cells and immune cells in the microenvironment; evaluate the immune repertoire and cytokine responses in serially collected peripheral blood mononuclear cells and serum respectively.

Citation Format: Litton JK, Moulder S, Helgason T, Clayborn AR, Rauch GM, Gilcrease M, Adrada BE, Huo L, Hess KR, Symmans WF, Thompson A, Tripathy D, Mittendorf EA. Triple-negative first-line study: Neoadjuvant trial of nab-paclitaxel and atezolizumab, a PD-L1 inhibitor, in patients with triple negative breast cancer (TNBC) (NCT02530489) [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr OT2-01-14.

Abstract OT2-01-20: Phase IIB study of neoadjuvant panitumumab combined with carboplatin and paclitaxel (PaCT) for anthracycline-resistant triple-negative breast cancer (TNBC)

BACKGROUND: Approximately 50% of patients with TNBC treatedwithstandardtaxane/anthracycline-based neoadjuvant chemotherapy (NACT)have chemo-insensitive disease (CID), i.e., residual disease burden (RCB)-II/III at the time of surgery, and 40-80% of patients develop recurrence within 3 years. Recent developments in molecular profiling have identified subsets of TNBC with distinct, targetable molecular features. We developed a clinical trial to identify and characterize CID (ARTEMIS: A Randomized, TNBC-Enrolling trial to confirm Molecular profiling Improves Survival). In ARTEMIS, patients with localized TNBC will undergo a pretreatment biopsy, then begin anthracycline-based NACT. During NACT, we use molecular profiling and response assessment to identify CID and allocate patients to alternative therapies to overcome CID. Epidermal growth factor receptor (EGFR) is overexpressed in 25-30% of TNBC. In preclinical studies, suppression of EGFR signaling has shown efficacy in controlling cancers through suppression of the stem cell population, enhanced apoptosis via MAPK/PI3K signaling, and modulation of epithelial-mesenchymal transition (EMT). Moreover, in a phase II trial of triple negative inflammatory breast cancer, neoadjuvant PaCT yielded significantly higher pathologic complete response (pCR) rates than historic control. Taken together, we hypothesize that using PaCT to suppress EGFR in TNBC will enhance the pCR rate.

OBJECTIVES: Primary objective: determine pCR and RCB-0/I rates in TNBC patients with CID given PaCT. Secondary objective: determine the benefit of using baseline genomic signatures to develop an alternative second phase of NACT.

TRIAL DESIGN AND STATISTICAL METHODS: Patients with >10% volume reduction for non-CID or <80% for CID will enroll in a biomarker-guided, experimental, nonrandomized phase II study and be given PaCT (panitumumab 2.5 mg/kg, carboplatin AUC 5, paclitaxel 80 mg/m2). Because pCR rates in pts with CID with additional cycles of taxane-based therapy are low (∼5%), a 20% response rate (RCB-0 or RCB-I) will be considered clinically meaningful. A two-stage Gehan-type design will be employed. If at least 1 of 14 patients responds, 23 more patients will be added, for a total of 37 patients. This design has a 49% chance of terminating after the first stage if the true response rate is 0.05, 23% if the rate is 0.10, 10% if the rate is 0.15, and 4% if the rate is 0.20. If accrual continues to the second stage and 37 patients are enrolled, the 95% confidence interval for a 0.20 response rate will be 0.10 to 0.35.

BRIEF ELIGIBILITY CRITERIA: Inclusion: localized TNBC; enrolled in ARTEMIS trial; adequate organ, bone marrow, and cardiac parameters; Exclusion: pregnant or lactating, known or suspected metastasis.

CORRELATIVE SCIENCE: Circulating tumor cells (CTCs) and cell free (cf) DNA in baseline and subsequent blood samples, EGFR expression (immunohistochemistry), stem cell/EMT/apoptosis marker changes in tissue and CTCs, PD-L1 glycosylation for EGFR sensitivity.

Citation Format: Lim B, Helgason T, Hess KR, Piwnica-Worms H, Yang W, Adrada BE, Rauch GM, Gilcrease M, Symmans FW, Huo L, Mittendorf EA, Thompson A, Stacy M-TL, Debu T, Ueno NT. Phase IIB study of neoadjuvant panitumumab combined with carboplatin and paclitaxel (PaCT) for anthracycline-resistant triple-negative breast cancer (TNBC) [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr OT2-01-20.

Abstract P3-14-02: Targeting the PI3K/AKT/mTOR pathway for the treatment of mesenchymal triple-negative breast cancer (TNBC): Evidence of efficacy and proof of concept from a phase I trial with dose expansion of mTOR inhibition in combination with liposomal doxorubicin and bevacizumab

Background: Approximately 30% of TNBCs are characterized by microarray as claudin-low, mesenchymal or mesenchymal stem cell-like and, unlike basal TNBCs, these tumors frequently harbor aberrations in the PI3K/AKT/mTOR axis, raising the possibility of targeting this axis to enhance chemotherapy response. Assays to clinically identify mesenchymal TNBCs are under development, but published results confirm that up to 30% are metaplastic breast cancers (MpBCs), a chemo-refractory group of tumors that contain a mixture of epithelial and mesenchymal components, making them identifiable by microscopy. As such, MpBCs serve as surrogates of response for potential regimens to treat mesenchymal TNBC.

Methods: Patients (pts) with advanced TNBC (N=64) were treated with liposomal doxorubicin (D), bevacizumab (A) and the mTOR inhibitors temsirolimus (T) or everolimus (E). D and A were administered IV on day 1 with T (IV on days 1, 8 and 15) or E (continuous daily oral administration) using 21 day cycles. Response was assessed every 6 weeks using RECIST. When available, archived tissue was evaluated for aberrations in the PI3K pathway using standard assays.

Results: Fifty-two MpBC pts were treated with DAT (N=39) or DAE (N=13). Median age was 58 (range 37-79); median # of prior regimens for metastatic disease was 1 (range 0-5). The objective response rate (ORR) was 21% [complete response (CR)=4 (8%); partial response (PR)=7 (13%)] and 10 (19%) pts had stable disease (SD)≥6 months for a clinical benefit rate (CBR) of 40%. Tissue was available for testing in 43 pts and 32 (74%) had a PI3K pathway activating aberration (Table 1).

Response According to PI3K Pathway AberrationPI3K Pathway AberrationN (%)CRPRSD≥6monthsCBRORRAny PI3K Pathway Aberration*32 (74)46444%31%PIK3CA Mutation19 (59)23447%26%p.H1047R12 (38)21350%25%p.E545K6 (19)02150%33%p.G1007R1 (3)010100%100%p.E545A1 (3)0000%0%p.H1047Y1 (3)0000%0%p.K111E1 (3)0000%0%p.E542K1 (3)0000%0%PIK3CA Amplification1 (3)010100%100%PTEN Mutation5 (16)0000%0%PTEN Loss5 (16)02040%40%AKT1 p.E17K Mutation2 (6)0000%0%AKT2 Amplification1 (3)100100%100%PIK3R1 Mutation2 (6)01050%50%NF2 Mutation1 (3)100100%100%No PI3K Pathway Aberration11 (26)00545%0%*Some tumors had >1 aberration detected

PI3K pathway activation was associated with a significant improvement in ORR (31 vs 0%; P=0.043) but not CBR (44 vs 45%; P=1.000) or progression-free survival (median 5.1 vs 2.9 months; P=0.352). A pt with 5 year+ durable CR (on maintenance everolimus) had a mutation in NF2. To emphasize the importance of pt selection, it is notable that 12 pts with non-metaplastic TNBC were also treated with DAT, and only 1 pt had a response (CR/PR=1; SD≥6 months=0), for a CBR that was significantly worse than pts with MpBC (8 vs 40%; P=0.045).

Conclusions: Using MpBC as a surrogate of response, DAT/DAE has significantly better activity in mesenchymal compared to non-selected TNBC. Response is enhanced in pts with PI3K pathway activation. DAT/DAE should be tested in non-metaplastic, mesenchymal TNBC once a diagnostic assay is available.

Citation Format: Basho RK, Gilcrease M, Murthy RK, Helgason T, Booser DJ, Karp DD, Meric-Bernstam F, Wheler JJ, Valero V, Albarracin C, Litton J, Chavez-MacGregor M, Ibrahim NK, Murray JL, Koenig KB, Hong D, Subbiah V, Kurzrock R, Janku F, Moulder S. Targeting the PI3K/AKT/mTOR pathway for the treatment of mesenchymal triple-negative breast cancer (TNBC): Evidence of efficacy and proof of concept from a phase I trial with dose expansion of mTOR inhibition in combination with liposomal doxorubicin and bevacizumab. [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 P3-14-02.

Inhibition of the phosphoinositide 3-kinase pathway for the treatment of patients with metastatic metaplastic breast cancer

BACKGROUND

Mesenchymal/metaplastic breast cancers (MpBCs) are often triple-negative (TNBC), and chemo-refractory, and can harbor phosphoinositide 3-kinase (PI3kinase) alterations; thus, therapy with mTor inhibitors may demonstrate activity.

PATIENTS AND METHODS

Patients with mesenchymal/MpBC treated with temsirolimus-based regimens were evaluated. Mutational analyses [polymerase chain reaction (PCR)-based DNA sequencing method, mass spectrometric detection (Sequenom MassARRAY), or next-generation sequencing] as well as loss of phosphatase and tensin homolog (PTEN) (immunohistochemistry) were performed (archived tissue when available).

RESULTS

Twenty-three patients (one of whom was on two separate trials) were treated using temsirolimus-containing regimens: temsirolimus alone (n = 1 patient) or combined with the following: liposomal doxorubicin and bevacizumab (DAT, n = 18); liposomal doxorubicin (DT, n = 1); paclitaxel and bevacizumab (TAT, n = 2); paclitaxel (TT, n = 1); carboplatin and bevacizumab (CAT, n = 1). Response rate [complete response (CR) + partial response (PR)] was 25% across all regimens; 32% in the anthracycline-based regimens [DAT and DT (CR = 2, PR = 4; N = 19)]. An additional two patients achieved stable disease (SD) ≥6 months [total SD ≥6 months/CR/PR = 8 (33%)]. Molecular aberrations in the PI3K pathway were common: PIK3CA mutation = 6/15 (40%), PTEN mutation = 3/11 (27%), and PTEN loss = 2/11 (18%). A point mutation in the NF2 gene (K159fs*16; NF2 alterations can activate mTor) was found in one patient who attained CR (3+ years). Of the eight patients who achieved SD ≥6 months/CR/PR, all 4 patients with available tissue had a molecular aberration that activate the PIK3CA/Akt/mTOR axis: PIK3CA mutation = 2; PTEN loss = 1; NF2 aberration = 1.

CONCLUSIONS

DAT has activity in MpBCs including complete CRs. Molecular aberrations that can activate the PI3 K/Akt/mTOR axis are common in MpBC.

Abstract P5-20-09: Tumor mutational analysis and therapy outcomes for patients (pts) with metastatic/unresectable locally advanced myoepithelial/metaplastic breast cancer treated with PI3K targeted therapy

Background: Metaplastic breast cancers are considered a chemorefractory subset of triple negative breast cancers. Molecular profiling has demonstrated that metaplastic tumors are enriched for epithelial-to-mesenchymal transition (EMT), frequently express myoepithelial differentiation, make up a component of the ‘claudin-low’ subtype, and harbor relatively high rates of mutations/activation of the PI3kinase pathway (Hennessy, Cancer Research, 2009; Prat, Breast Cancer Res, 2010).

Methods: Data from pts with myoepithelial/metaplastic breast cancer treated within the Center for Targeted Therapy using regimens with known inhibitors of the PI3K pathway were evaluated to determine response to therapy. Mutational analyses were performed in archived tumor samples when available.

Results: 23 pts have been treated using 6 different therapy regimens and one pt was treated on two separate clinical trials for a total of 24 analyzable outcomes. Patients were treated with liposomal doxorubicin, bevacizumab and the mTOR inhibitor, temsirolimus (DAT, n=17); liposomal doxorubicin and temsirolimus (DT, n=1); paclitaxel, bevacizumab and temsirolimus (TAT, n=3); paclitaxel and temsirolimus (TT, n=1), paclitaxel in combination with an experimental PI3K inhibitor (TEx, n=1), or temsirolimus alone (tem, n=1). Response was measured every two cycles using RECIST criteria. Most pts had received prior chemotherapy, median of 2 prior regimens (range 0–7). Three patients were not evaluated for response, one who died of pneumonia during cycle 2 (DAT) and two who have not yet completed 2 cycles of therapy (DAT, TEx). Response rate (CR+PR) was 35% (CR = 2, PR=4, SD≥6 months=2, SD<6 months=2, PD/death=7) with the anthracycline based regimens, DAT and DT; whereas, stable disease was the best response seen thus far with the paclitaxel based regimens or temsirolimus alone: TAT (SD<6months=2, PD=1), TT (SD<6months=1), tem (SD<6months=1). 8 of 9 tumors tested (89%) were found to have mutations that would lead to activation of the PI3K pathway: PIK3CA=5 (62%), PTEN=2 (25%) and NF2=1(13%). The two patients with CR from DAT had mutations in NF2 and PIK3CA, respectively. Both patients remain in CR (2+ years and 1+ year respectively) after discontinuing protocol therapy, and both continue maintenance everolimus.

Conclusion: Activating mutations in the PI3K pathway are common in metaplastic breast cancers, a tumor subtype that shares molecular features with claudin-low and mesenchymal/mesenchymal-stem cell like triple negative breast cancers. DAT has demonstrated activity in myoepithelial/metaplastic breast cancer including two durable CRs to therapy. This regimen should be explored in larger, randomized trials to test superiority to chemotherapy alone.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P5-20-09.

Abstract P5-03-05: Histone deacetylase (HDAC)-inhibitor mediated reprogramming drives cancer cells to the pentose phosphate metabolic pathway

Recent studies have shown that energy metabolism in human pluripotent cells contrasts sharply with energy metabolism in differentiated cell types. Specifically, it has been shown that nuclear reprogramming from somatic cells to induced pluripotent stem cells is associated with a switch from oxidative to glycolytic metabolism. Whether a metabolic switch also occurs in reprogrammed/dedifferentiated breast cancer cells is unknown. Moreover, the function of the metabolic state in stemness is poorly understood and no data are available on whether breast cancer stem cells (CSCs) are metabolically different from committed cancer cells. Herein we demonstrated that HDAC inhibitors reprogram committed single aldefluor negative breast cancer cells into aldefluor positive cells (10.3 ± 2.8 vs 21.3 ±3.7% untreated vs treated P <0.05, representing an average of 5 single cell derived clones) and promoted tumor initiation from non-initiating committed cells (p = 0.004). Further, induced stem-like cells were resistant to taxol and salinomycin, a drug previously described to target CSCs. These reprogrammed cancer cells have enhanced activity of the pentose phosphate pathway (PPP) with upregulation of G6PD expression and activity and higher levels of NADPH and ROS. Hypothesizing that CSCs may favor the PPP in order to survive and self renew, we used G6PD inhibitors, 6-AN and Imatinib, to target mammosphere formation and aldefluor activity in HDAC inhibition induced stem-like cells. Not only was there a significant decrease in mammospheres from reprogrammed cells, the aldefluor activity was totally blocked at a concentration that does not affect proliferation. This work demonstrates that HDAC inhibition mediated cancer cell dedifferentiation promotes metabolic reprogramming and highlights an FDA approved drug that targets metabolism in stem cell plasticity. Further functional endpoint studies are underway to validate these findings.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P5-03-05.

Abstract P2-06-09: Mucin4 Is Associated with the Loss of Estrogen-Receptor-α in Breast Cancer

Data suggests that breast carcinomas that overexpress the HER2 oncoprotein are more resistant to endocrine treatments such as tamoxifen (Tam) or estrogen deprivation (ED) via aromatase inhibitors. To investigate possible mechanisms of endocrine resistance in vivo, we performed a gene microarray analysis on estrogen receptor-(ER)+, HER2-overexpressing xenograft tumors that are de novo resistant to tamoxifen treatment and acquire resistance to ED therapy. A large number of genes were upregulated, including several members of the mucin family of genes. This corroborated our finding from histological staining of the resistant tumors that indicated striking increases of mucin vacuoles when compared to sensitive tumors. These vacuoles were located mostly intracellularly and stained positive for mucins with mucicarmine. We were particularly interested in one particular mucin, mucin4 (MUC4) because previous studies have suggested its role in stabilizing and enhancing HER2 signaling. Quantitative realtime PCR confirmed the microarray results and showed that there was an approximately 156-fold increase in MUC4 transcript between the ED-sensitive and ED-resistant tumors, with a 65-fold increase between the early Tam and late Tam-resistant tumors. Immunohistochemistry confirmed that this upregulation in these two treatment groups was present also at the protein level. Furthermore, western blot analysis of these tumors demonstrated that resistant tumors have downregulation of ER protein and its downstream effectors with corresponding increase in total HER2 protein levels. These tumors have seemingly shifted away from the ER pathway to signaling via the growth factor signaling pathway. Preliminary experiments where MUC4 protein was stably overexpressed in ER+, HER2-overexpressing cells model these results in vitro with a downregulation of ER protein and downstream effectors, showing that ER expression and activity are affected. Furthermore, immunohistochemical analysis of 73 primary human invasive breast carcinomas suggests that MUC4 is associated with estrogen-receptor negative tumors (P=0.05). This clinical data validates the preclinical studies for investigating a possible mechanism for the loss of ER, and suggest MUC4 as an inviting biomarker for endocrine treatment and a potential therapeutic target for endocrine resistant breast cancer.

Crosstabulation of MUC4 and ER

DNA methylation profiles of lung tumors

Aberrant methylation of CpG islands in promoter regions of tumor cells is one of the major mechanisms for silencing of tumor suppressor genes. We determined the frequency of aberrant promoter methylation of the p16, adenomatous polyposis coli (APC), H-cadherin (CDH13), glutathione S-transferase P1 (GSTP1), O6-methylguanine-DNA-methyltransferase (MGMT), retinoic acid receptor beta-2 (RAR beta), E-cadherin (CDH1), and RAS association domain family 1A (RASSF1A) genes in 198 tumors consisting of small cell lung cancers [SCLCs (n = 43)], non-small cell lung cancers [NSCLCs (n = 115)], and bronchial carcinoids (n = 40). The profile of methylated genes in the two neuroendocrine tumors (SCLC and carcinoids) were very different from that of NSCLC. However, whereas the overall pattern of aberrant methylation of carcinoids was similar to that of SCLC, carcinoids had lower frequencies of methylation for some of the genes tested. There were also significant differences in the methylation profiles between the two major types of NSCLC, adenocarcinoma and squamous cell carcinoma. We performed cluster analysis and found that SCLCs clustered with other SCLCs and carcinoids but not with NSCLCs, whereas the NSCLCs tended to cluster together. Within NSCLCs, adenocarcinomas and squamous cell carcinomas clustered with their respective histological types. Finally, we compared the methylation profiles of SCLC and NSCLC tumors and their respective cell lines (n = 44). In general, methylation frequencies were higher in tumor cell lines, but these differences were seldom significant. Thus, tumor cell lines appear to be suitable models to study aberrant DNA methylation. We conclude that SCLC, carcinoids, squamous cell carcinomas, and adenocarcinomas of the lung have unique profiles of aberrant methylation. Our findings should help us understand differences in the pathogenetic mechanisms of lung cancers.

Aberrant methylation and simian virus 40 tag sequences in malignant mesothelioma

Aberrant promoter methylation and resultant silencing of several genes plays an important role in the pathogenesis of many tumor types. We compared the methylation profile of 66 malignant mesotheliomas (MMs) and 40 lung adenocarcinomas using methylation-specific PCR for seven genes frequently methylated in lung cancer. We also compared the methylation frequencies of these genes as well as the methylation index, a reflection of all of the gene frequencies, with the presence of SV40 large T-antigen (Tag) sequences, histological subtype, and patient survival. Our major findings are: (a) with the exception of the RASSF1A promoter of the RASSF1 gene, frequencies of aberrant methylation were significantly lower in MMs than in adenocarcinomas; (b) the frequency of RASSF1A aberrant methylation and the value of the methylation index were significantly higher in SV40 sequence positive MM than in negative MM; and (c) the methylation index was higher in epithelial MM than in sarcomatous/mixed MM. Our results demonstrate a relationship between SV40 and aberrant methylation in MMs.

Aberrant methylation of the adenomatous polyposis coli (APC) gene promoter 1A in breast and lung carcinomas

The adenomatous polyposis coli (APC) gene is a tumor suppressor gene associated with both familial and sporadic cancer. Despite high rates of allelic loss in lung and breast cancers, point mutations of the APC gene are infrequent in these cancer types. Aberrant methylation of the APC promoter 1A occurs in some colorectal and gastric malignancies, and we investigated whether the same mechanism occurs in lung and breast cancers. The methylation status of the APC gene promoter 1A was analyzed in 77 breast, 50 small cell (SCLC), and 106 non-small cell (NSCLC) lung cancer tumors and cell lines and in 68 nonmalignant tissues by methylation-specific PCR. Expression of the APC promoter 1A transcript was examined in a subset of cell lines by reverse transcription-PCR, and loss of heterozygosity at the gene locus was analyzed by the use of 12 microsatellite and polymorphic markers. Statistical tests were two-sided. Promoter 1A was methylated in 34 of 77 breast cancer tumors and cell lines (44%), in 56 of 106 NSCLC tumors and cell lines (53%), in 13 of 50 SCLC cell lines (26%), and in 3 of 68 nonmalignant samples (4%). Most cell lines tested contained the unmethylated or methylated form exclusively. In 27 cell lines tested, there was complete concordance between promoter methylation and silencing of its transcript. Demethylation with 5-aza-2'-deoxycytidine treatment restored transcript 1A expression in all eight methylated cell lines tested. Loss of heterozygosity at the APC locus was observed in 85% of SCLCs, 83% of NSCLCs, and 63% of breast cancer cell lines. The frequency of methylation in breast cancers increased with tumor stage and size. In summary, aberrant methylation of the 1A promoter of the APC gene and loss of its specific transcript is frequently present in breast and NSCLC cancers and cell lines and, to a lesser extent, in SCLC cell lines. Our findings may be of biological and clinical importance.

Loss of expression and aberrant methylation of the CDH13 (H-cadherin) gene in breast and lung carcinomas

Expression of some members of the cadherin family is reduced in several human tumors, and CDH13 (H-cadherin), located on chromosome 16q24.2-3, may function as a tumor suppressor gene. In human tumors, loss of expression of many tumor suppressor genes occurs by aberrant promoter region methylation. We examined the methylation status of the CDH13 promoter in breast and lung cancers and correlated it with mRNA expression using methylation-specific PCR and reverse transcription-PCR. Methylation was frequent in primary breast tumors (18 of 55, 33%) and cell lines (7 of 20, 35%). In lung cancers, methylation was present more frequently in non-small cell lung cancer tumors (18 of 42, 43%) and cell lines (15 of 30, 50%) than in small cell lung cancer cell lines (6 of 30, 20%; P = 0.03). Only the methylated or unmethylated forms of the gene were present in most (73 of 80, 91%) tumor cell lines. CDH13 expression was present in 24 of 30 (80%) of nonmethylated tumor lines. All 18 methylated lines tested lacked expression irrespective of whether the unmethylated form was present, confirming biallelic inactivation in methylated lines. Gene expression was restored in all five methylated cell lines tested after treatment with the demethylating agent 5'-aza-2-deoxycytidine. Our results demonstrate frequent aberrant methylation of CDH13 in breast and lung cancers accompanied by loss of gene expression, although expression may occasionally be lost by other mechanisms.

Glomus tumor of the uterine cervix

Two examples of glomus tumors of the cervix that were incidental findings in patients with uterine leiomyomas are described. The first occurred in a 52-year-old woman with two small uterine leiomyomas and an endometrial polyp. The second occurred in a 39-year-old woman with a large uterine leiomyoma. The glomus tumors were located deep in the cervical stroma and were 0.8 and 0.4 cm in maximal dimension, respectively. The tumors were composed of nests or trabeculae of small cells with round or ovoid hyperchromatic nuclei and eosinophilic or clear cytoplasm. The cells closely surrounded slitlike capillaries and were immunoreactive for smooth muscle actin and muscle specific actin. To our knowledge, no similar tumors have been reported in the cervix.