Anaplastic thyroid cancer: outcome and the mutation/expression profiles of potential targets

Anaplastic thyroid cancer (ATC) is a rare but aggressive malignancy of the thyroid. No effective treatment modalities are currently available. Targeted therapy against protein kinases showed promising results in preclinical studies. Our goal was to assess the mutational status of potential therapeutic targets, as well as the biomarker for immunotherapy in the clinical context. Using allele specific PCR, Sanger sequencing, fragment analysis and immunohistochemistry, we assessed BRAF, KRAS, EGFR mutations and protein overexpression of C-KIT and PDL1 in anaplastic thyroid cancer specimens. Results were compared to clinical information and patient outcome to assess the utility of these biomarkers. There were 13 patients in our study with a median overall survival of 19 weeks. Of the 13 ATC patients, 3 (23 %) had BRAF V600E mutation. C-KIT overexpression was found in 1 (8 %) patient who responded well to a tyrosine kinase inhibitor. PDL1 expression was seen in 3 (23 %) patients, none of them were surgical candidates due to unresectability and poor performance status. KRAS codon 12/13 and EGFR exon 18, 19, 20 and 21 were all wild type in our patients. Protein kinase inhibitors and immunotherapy may be useful adjuvant therapies for ATC.

Early detection of high-grade squamous intraepithelial lesions in the cervix with quantitative spectroscopic imaging

Quantitative spectroscopy has recently been extended from a contact-probe to wide-area spectroscopic imaging to enable mapping of optical properties across a wide area of tissue. We train quantitative spectroscopic imaging (QSI) to identify cervical high-grade squamous intraepithelial lesions (HSILs) in 34 subjects undergoing the loop electrosurgical excision procedure (LEEP subjects). QSI's performance is then prospectively evaluated on the clinically suspicious biopsy sites from 47 subjects undergoing colposcopic-directed biopsy. The results show the per-subject normalized reduced scattering coefficient at 700 nm (An) and the total hemoglobin concentration are significantly different (p<0.05) between HSIL and non-HSIL sites in LEEP subjects. An alone retrospectively distinguishes HSIL from non-HSIL with 89% sensitivity and 83% specificity. It alone applied prospectively on the biopsy sites distinguishes HSIL from non-HSIL with 81% sensitivity and 78% specificity. The findings of this study agree with those of an earlier contact-probe study, validating the robustness of QSI, and specifically An, for identifying HSIL. The performance of An suggests an easy to use and an inexpensive to manufacture monochromatic instrument is capable of early cervical cancer detection, which could be used as a screening and diagnostic tool for detecting cervical cancer in low resource countries.

Expression of microRNA and their gene targets are dysregulated in preinvasive breast cancer

INTRODUCTION

microRNA (miRNA) are short, noncoding RNA that negatively regulate gene expression and may play a causal role in invasive breast cancer. Since many genetic aberrations of invasive disease are detectable in early stages, we hypothesized that miRNA expression dysregulation and the predicted changes in gene expression might also be found in early breast neoplasias.

METHODS

Expression profiling of 365 miRNA by real-time quantitative polymerase chain reaction assay was combined with laser capture microdissection to obtain an epithelium-specific miRNA expression signature of normal breast epithelium from reduction mammoplasty (RM) (n = 9) and of paired samples of histologically normal epithelium (HN) and ductal carcinoma in situ (DCIS) (n = 16). To determine how miRNA may control the expression of codysregulated mRNA, we also performed gene expression microarray analysis in the same paired HN and DCIS samples and integrated this with miRNA target prediction. We further validated several target pairs by modulating the expression levels of miRNA in MCF7 cells and measured the expression of target mRNA and proteins.

RESULTS

Thirty-five miRNA were aberrantly expressed between RM, HN and DCIS. Twenty-nine miRNA and 420 mRNA were aberrantly expressed between HN and DCIS. Combining these two data sets with miRNA target prediction, we identified two established target pairs (miR-195:CCND1 and miR-21:NFIB) and tested several novel miRNA:mRNA target pairs. Overexpression of the putative tumor suppressor miR-125b, which is underexpressed in DCIS, repressed the expression of MEMO1, which is required for ErbB2-driven cell motility (also a target of miR-125b), and NRIP1/RIP140, which modulates the transcriptional activity of the estrogen receptor. Knockdown of the putative oncogenic miRNA miR-182 and miR-183, both highly overexpressed in DCIS, increased the expression of chromobox homolog 7 (CBX7) (which regulates E-cadherin expression), DOK4, NMT2 and EGR1. Augmentation of CBX7 by knockdown of miR-182 expression, in turn, positively regulated the expression of E-cadherin, a key protein involved in maintaining normal epithelial cell morphology, which is commonly lost during neoplastic progression.

CONCLUSIONS

These data provide the first miRNA expression profile of normal breast epithelium and of preinvasive breast carcinoma. Further, we demonstrate that altered miRNA expression can modulate gene expression changes that characterize these early cancers. We conclude that miRNA dysregulation likely plays a substantial role in early breast cancer development.

In thyroid fine-needle aspiration, use of bedside-prepared slides significantly increased diagnostic adequacy and specimen cellularity relative to solution-based samples

BACKGROUND

In the United States, the prevalence among adults of palpable thyroid nodules is 4%-7%, of which 5%-10% may represent thyroid carcinoma. Despite the success of fine-needle aspiration in reducing the need for thyroidectomy, aspirates are inadequate to render a diagnosis in 20% of cases. Minimizing nondiagnostic samples is an important goal in improving this technique. Our objective was to determine whether bedside-prepared slides improve diagnostic adequacy over standard solution-based samples. We further sought to determine the role of needle size.

METHODS

One hundred sixty-two patients were prospectively enrolled. For each, both bedside slides and standard cytology solutions were prepared; the order of preparation alternated from subject to subject. Needle size (21- or 25-gauge) also alternated from subject to subject. Slides were evaluated by pathologists blinded to needle size. The study took place in the endocrinology clinic at Boston Medical Center, the tertiary referral hospital of the Boston University School of Medicine. Key outcomes were diagnostic adequacy and specimen cellularity.

RESULTS

Compared to standard solution-based samples, bedside slides provided more cellular specimens (p < 0.01) and fewer nondiagnostic samples (p = 0.016). When standard solution-based samples were used as the sole method of preparation, 21-gauge needles provided improved diagnostic adequacy.

CONCLUSIONS

Bedside-prepared slides offer improved diagnostic adequacy and specimen cellularity over solution-based samples. The difference may be especially important when using smaller (25-gauge) needles to perform fine-needle aspiration. When solution-based samples are used, larger (21-gauge) needles provide more diagnostic specimens.

Abnormal anal cytology in HIV-infected women

OBJECTIVE

The purpose of this study was to assess the prevalence of and risk factors for abnormal anal cytology and human papillomavirus (HPV) infections in women who are human immunodeficiency virus (HIV) positive.

STUDY DESIGN

We conducted an observational single center study of 100 HIV-infected women with cervical and anal specimens that were obtained for cytologic and high-risk HPV testing with Hybrid Capture 2.

RESULTS

Seventeen women had abnormal anal cytology; 16 women had anal HPV; 21 women had abnormal cervical cytology, and 24 women had cervical HPV. Abnormal anal cytology was associated with cervical HPV infection, abnormal cervical cytology, and anal HPV infection in univariate analysis. In multivariate analysis, abnormal anal cytology was associated with a CD4 count <200 cells/mm(3), a history of sexually transmitted disease, and concurrent cervical cytologic abnormality.

CONCLUSION

HIV-infected women are at high risk for abnormal cytology and HPV infections of both the anus and cervix. Risk factors for abnormal anal cytology include abnormal cervical cytology, cervical and anal HPV infections, and low CD4 count.

Abstract 2153: Copy number variants in histologically normal breast epithelium from reduction mammoplasty controls and breast cancer cases

Whole genome arrays have been used to study DNA aberrations in a wide variety of samples. The genetics of breast cancer has been intensely studied using multiple techniques including whole genome SNP genotyping. Research using genotyping data to study copy number variants (CNVs) has been limited by suboptimal algorithms for segmentation. Recently, a new algorithm has been developed that is easy to use and highly adaptive to individual data sets. Since genomic changes are now appreciated prior to the appearance of malignancy - even in histologically normal epithelium - it was our aim to apply this algorithm and test whether CNVs differ between histologically normal ducts from reduction mammoplasty controls (RM) and histologically normal ducts from breast cancer cases (HN).

Using data imported from Illumina's Human 610-quad beadchip, CNV segmentation and copy number status was calculated using the OmicSoft algorithm. This algorithm utilizes three types of information, the Log2Ratio, B-Allele Frequency and the genotype calls. Segmentation criteria were optimized and then validated on 4 well-characterized breast cancer cell lines (MCF7, MDA-MB-231, T47D, BT474) and these data were compared to publically available Affymetrix SNP6 chip data. The validated segmentation method was then applied to data obtained with the Illumina beadchip from 19 snap-frozen human breast epithelial samples. Ducts from 8 RM (mean age 47y) and 11 HN (mean age 54y) samples from untreated ER+ cancers were identified by a pathologist and captured via laser microdissection. Samples were anonymous and obtained through an IRB approved protocol.

Data from the cell lines were analyzed using OmicSoft's Array Studio. There was good concordance with the publically available data, although the Illumina-generated data had fewer segments. This may be because there are more SNP/CNV markers on the Affy SNP6.0 chip and thus higher resolution. Using the optimized segmentation criteria, small CNVs were detected in all RM and HN samples. In the 8 RM cases, there was an average of 39 segments and 5-12 CNVs per case. The 11 HN cases had an average of 37 segments and 4-12 CNVs per case. The CNVs were small sized (35-400KB) and were more often losses than gains, with approximately 75% and 85% of the CNVs representing losses in RMs and HNs respectively. The gains were low level amplifications with copy number of 3N. The most common loss was on chromosome 3q (97KB), found in 2/8 (25%) RMs and 6/11 (55%) HNs (p=0.18) and had no association with self-identified ethnicity.

OmicSoft's algorithm for segmentation was easy to use and is ideal for CNV analysis because it can be modified to provide optimal segmentation for specific data sets. Small CNVs are detected commonly in histologically normal breast epithelium, but substantial differences in CNVs are not present between RM and HN samples. These changes must occur later in tumor development.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2153.

Early dysregulation of cell adhesion and extracellular matrix pathways in breast cancer progression

Proliferative breast lesions, such as simple ductal hyperplasia (SH) and atypical ductal hyperplasia (ADH), are candidate precursors to ductal carcinoma in situ (DCIS) and invasive cancer. To better understand the relationship of breast lesions to more advanced disease, we used microdissection and DNA microarrays to profile the gene expression of patient-matched histologically normal (HN), ADH, and DCIS from 12 patients with estrogen receptor positive sporadic breast cancer. SH were profiled from a subset of cases. We found 837 differentially expressed genes between DCIS-HN and 447 between ADH-HN, with >90% of the ADH-HN genes also present among the DCIS-HN genes. Only 61 genes were identified between ADH-DCIS. Expression differences were reproduced in an independent cohort of patient-matched lesions by quantitative real-time PCR. Many breast cancer-related genes and pathways were dysregulated in ADH and maintained in DCIS. Particularly, cell adhesion and extracellular matrix interactions were overrepresented. Focal adhesion was the top pathway in each gene set. We conclude that ADH and DCIS share highly similar gene expression and are distinct from HN. In contrast, SH appear more similar to HN. These data provide genetic evidence that ADH (but not SH) are often precursors to cancer and suggest cancer-related genetic changes, particularly adhesion and extracellular matrix pathways, are dysregulated before invasion and even before malignancy is apparent. These findings could lead to novel risk stratification, prevention, and treatment approaches.

Allele Imbalance, or Loss of Heterozygosity, in Normal Breast Epithelium of Sporadic Breast Cancer Cases and BRCA1 Gene Mutation Carriers Is Increased Compared With Reduction Mammoplasty Tissues

Purpose

Normal-appearing breast epithelium can contain genetic abnormalities, including allele imbalance (AI), also referred to as loss of heterozygosity. Whether abnormalities are associated with cancer or cancer risk is unknown.

Patients and Methods

We performed a miniallelotype, using 20 microsatellites, on each of 460 histologically normal, microdissected breast terminal ducto-lobular units (TDLUs) from three groups of women: sporadic breast cancer patients (SP; n = 18), BRCA1 gene mutation carriers (BRCA1; n = 16), and controls undergoing reduction mammoplasty (RM; n = 18). We analyzed the results using Fisher's exact tests, logistic regression, and generalized estimating equations.

Results

AI was increased three-fold in SP and BRCA1 groups compared with RM. Both the number of TDLUs with AI increased (eight [5%] of 162 in the RM group compared with 24 [15%] of 162 in the SP and 22 [16%] of 136 in the BRCA1 groups; P = .0150), and the proportion of patients with AI increased (five [28%] of 18 in the RM group compared with 15 [83%] of 18 in the SP and 13 [81%] of 16 in the BRCA1 groups; P = .0007). The adjusted odds ratios (OR) for AI in TDLU increased in SP (OR = 15.5) and BRCA1 (OR = 13.7) patients compared with RM (P = .0025). This result was particularly evident on chromosome 17q (P = .0393), where more AI was seen in BRCA1 (OR = 12.4) than in SP (OR = 4.9) patients or RM controls.

Conclusion

Increased prevalence of AI in normal-appearing epithelium is associated with breast cancer and increased breast cancer risk. The increased prevalence may reflect dysregulation, even in normal-appearing epithelium, of genomic processes contributing to cancer development. The clinical significance of genetic alterations in the subset of controls remains to be determined.

Quantitative DNA Fingerprinting May Distinguish New Primary Breast Cancer From Disease Recurrence

Purpose

Approximately 10% of women with breast cancer develop a second breast tumor, either a new primary or a recurrence. Differentiating between these entities using standard clinical and pathologic criteria remains challenging. Ambiguous cases arise, and misclassifications may occur. We investigated whether quantitative DNA fingerprinting, based on allele imbalance (AI) or loss of heterozygosity (LOH), could evaluate clonality and distinguish second primary breast cancer from recurrence.

Methods

We developed a scoring system based on the AI/LOH fingerprints of 20 independent breast tumors and generated a decision rule to classify any breast tumor pair as related or unrelated. We validated this approach on eight related tumors (cancers and synchronous positive lymph nodes). Finally, we analyzed paired tumors from 13 women (bilateral cancers, primary tumors and contralateral positive axillary lymph nodes, or two ipsilateral tumors). Each pair's genetic classification was compared with their clinical diagnosis and outcome.

Results

Each independent cancer had a unique fingerprint. Every tumor pair's relationship was quantifiable. Six of eight related tumor pairs were genetically classified correctly, two were indeterminate, and none were misclassified. Among the 13 women with two cancers, four of five clinically indeterminate pairs could be classified genetically. In three of 13 women, the pair's classification contradicted the clinical diagnosis. These women had bilateral cancers genetically classified as related and disease progression. This challenges the paradigm that bilateral cancers represent independent tumors. Overall, women with tumors genetically classified as related had poorer outcomes.

Conclusion

Quantitative AI/LOH fingerprinting is a potentially valuable tool to improve diagnosis and optimize treatment for the growing number of second breast malignancies.

Loss of heterozygosity in serial plasma DNA samples during follow-up of women with breast cancer

We evaluated the potential utility of occult circulating tumor DNA as a molecular marker of disease in subjects previously diagnosed with breast cancer. Using 24 microsatellite markers located at sites of frequent loss of heterozygosity (LOH) or allele imbalance in breast cancer, we analyzed DNA from 16 primary tumors (Stage IIA or more advanced) and 30 longitudinally collected plasma specimens. Clinical data at the time of plasma collection were obtained. All 16 tumors were characterized by an individual pattern of LOH. LOH was detected in 12 of 30 (40%) plasma samples, taken from 8 of 14 (57%) subjects. However, the number of LOH in plasma was small (n = 15), and the mean proportion of LOH was much lower than in the tumors (0.05 vs. 0.52). Although infrequent, 12 of 15 (80%) plasma LOH were concordant with abnormalities in the paired tumors, and the mean percent LOH was higher than in normal plasmas, suggesting that they were authentic tumor-derived abnormalities. We found, despite this, no association, between plasma LOH and tumor stage or clinical status at time of blood collection (i.e., LOH was as common in subjects with no evident disease as in those with evident disease). In addition, detection of LOH was not consistent between serial samples from 5 of 11 subjects (45%), despite stable clinical conditions. No association with clinical outcome was evident, although the sample size was small. Microsatellite instability in plasma was infrequent, nonconcordant with paired tumor and inconsistent in serial samples. This pilot study suggests that identifying tumor-specific LOH in the plasma of breast cancer subjects may not be useful for detecting occult metastases or for monitoring disease. Other detection techniques may be more promising, but circulating tumor DNA may not be a sufficiently accurate reflection of breast cancer clinical status or tumor activity.

Loss of heterozygosity or allele imbalance in histologically normal breast epithelium is distinct from loss of heterozygosity or allele imbalance in co-existing carcinomas

To better understand early steps in human breast carcinogenesis, we examined allele imbalance or loss of heterozygosity (LOH), in co-existing normal-appearing breast epithelium and cancers. We microdissected a total of 173 histologically normal ducts or terminal ductolobular units (TDLUs) and malignant epithelial samples from 18 breast cancer cases, and examined their DNA for LOH at 21 microsatellite markers on 10 chromosome arms. Fourteen of 109 (13%) normal ducts/TDLUs, from 8 of 18 (44%) cases, contained LOH. The location of these 14 ducts/TDLUs appeared unrelated to distance from the cancer. LOH in normal-appearing epithelium involved only single markers, whereas LOH in cancers commonly encompassed all informative markers on a chromosome arm. In only 1 of 14 (7%) ducts/TDLUs with LOH, was the same LOH seen in the co-existing cancer. Global differences in LOH per arm in normal-appearing tissue were not demonstrated, but less LOH was seen at 11q and 17p than at 1q (P = 0.002), 16q (P = 0.01), and possibly 17q (P = 0.06). These results indicate that in a large fraction of women with breast cancer, histologically normal breast epithelium harbors occult aberrant clones. Individual clones rarely are precursors of co-existing cancers. However, they might constitute a reservoir from which proliferative lesions or second cancers develop once additional genetic abnormalities occur, they could contribute to intratumoral genetic heterogeneity, and they are consistent with a role for genetic instability early in tumorigenesis.