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Targeted cancer therapeutics are promised to have a major impact on cancer treatment and survival. Successful application of these novel treatments requires a molecular definition of a patient's disease typically achieved through the use of tissue biopsies. Alternatively, allowing longitudinal monitoring, biomarkers derived from blood, isolated either from circulating tumor cell derived DNA (ctcDNA) or circulating cell-free tumor DNA (ccfDNA) may be evaluated. In order to use blood derived templates for mutational profiling in clinical decisions, it is essential to understand the different template qualities and how they compare to biopsy derived template DNA as both blood-based templates are rare and distinct from the gold-standard. Using a next generation re-sequencing strategy, concordance of the mutational spectrum was evaluated in 32 patient-matched ctcDNA and ccfDNA templates with comparison to tissue biopsy derived DNA template. Different CTC antibody capture systems for DNA isolation from patient blood samples were also compared. Significant overlap was observed between ctcDNA, ccfDNA and tissue derived templates. Interestingly, if the results of ctcDNA and ccfDNA template sequencing were combined, productive samples showed similar detection frequency (56% vs 58%), were temporally flexible, and were complementary both to each other and the gold standard. These observations justify the use of a multiple template approach to the liquid biopsy, where germline, ctcDNA, and ccfDNA templates are employed for clinical diagnostic purposes and open a path to comprehensive blood derived biomarker access.

Background: Effective treatments for advanced breast cancer are limited leaving palliative care as the only option for patients. The development of effective treatments has been challenging in part due to the biologic heterogeneity of the disease. The challenges to improve patient outcomes are represented by the availability of diagnostic technologies allowing real-time access to the genetic drivers of disease in each individual patients and the ability to match such information with novel targeted therapies. Blood based tests have a long history of providing real-time evidence in medicine. Thus blood derived templates could fill this role in genetic diagnosis. To perform, any technology for molecular analysis of tumor cells from blood must overcome limiting amounts of template and high signal to noise. Current efforts are directed to develop blood based tests for circulating biomarkers that can describe the molecular changes in breast cancer. We investigated the ability to productively sequence tumor cells recovered from whole blood. Methods: EpCAM expressing Circulating tumor cells (CTCs) were recovered from 49 patients with metastatic breast cancer on the LiquidBiopsy™ platform (Cynvenio Biosystems, Inc). CTC events were characterized using a nuclear stain (DAPI), Cytokeratin expression and absence of CD45. DNA template recovered from this population was case control sequenced with the Life Technologies AmpliSeq targeted resequencing panel on an Ion Torrent Platform using a CLIA validated sequencing pipeline and a sensitivity of 1%. Somatic single nucleotide variants (SNV) present in CTC but not the germline were identified. Critically, the false positive score for 31 normal donors thus evaluated was zero. Results: Circulating target cells were detected in all 49 patients with metastatic BC (CTC Median 28, range 2 - 4098). Upon resequencing, shared germline polymorphisms were observed in CTC and germline populations. In contrast, SNV were detected in EpCAM enriched populations but not germline in 32% of samples (allele frequency 1.0%-49.6% with 2417-22068 x coverage). Enumeration of cytokeratin expressing cells was predictive of neither the presence nor the allele frequency of detectable SNV. Interestingly mutations in the gene for PIK3ca accounted for 20% of the mutations observed including variants at K111E, E542K, E545K, and H1047L. Mutations were also observed in TP53 (8%), and MET, FGFR2, SMAD4. Twenty samples had tissue biopsy sequence data available and of those, 11 contained mutations that were evaluable in the CTC. All but one mutation were absent in the evaluable tissue biopsy Conclusions: CTC recovered by EpCAM selection directly from blood can be sequenced by NGS. The predictive value of the CK+ phenotype as a surrogate marker for mutation bearing cells is not supported by these data. Even with a relatively narrow 50 gene target platform, cancer relevant SNVs were detected in >30% of the patients, making targeted NGS of CTCs a promising approach for biomarker discovery and validation in MBC. Citation Format: William Strauss, Jessamine Winer-Jones, Laura Austin, Paul W Dempsey, Massimo Cristofanilli. The LiquidBiopsy in metastatic breast cancer (MBC): A novel diagnostic platform for next generation sequencing (NGS) of circulating tumor cells (CTCs) [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P5-10-07.

Defining the identity of embryonic stem (ES) cells in quantitative molecular terms is a prerequisite to understanding their functional characteristics. Little is known about the role of microRNAs (miRNAs) in the regulation of ES cell identity. Statistical analysis of miRNA expression revealed unique expression signatures that could definitively classify mouse ES (mES), embryoid bodies (mEB), and somatic tissues. Analysis of these data sets also provides further confirmation of the nonrestrictive expression of miRNAs during murine development. Using combined genome-wide expression analyses of both miRNAs and mRNAs, we observed both negative and positive correlations in gene expression between miRNAs and their predicted targets. ES-specific miRNAs were positively correlated with their predicted targets, suggesting that mES-specific miRNAs may have a different role or mechanism in regulating their targets in mES maintenance or differentiation. The concept of cellular identity has changed with technology; this study redefines cellular identity by a generic statistical method of known dimension.

During the last decade, a variety of critical biological processes, including early embryo development, cell proliferation, differentiation, apoptosis, and metabolic regularity, have been shown to be genetically regulated by a large gene family encoding a class of tiny RNA molecules termed microRNAs (miRNAs). All miRNAs share a common biosynthetic pathway and reaction mechanisms. The sequence of many miRNAs is found to be conserved, in their mature form, among different organisms. In addition, the evolutionary appearance of multicellular organisms appears to correlate with the appearance of the miRNA pathway for regulating gene expression. The miRNA pathway has the potential to regulate vast networks of gene products in a coordinate manner. Recent evidence has not only implicated the miRNA pathway in regulating a vast array of basic cellular processes but also specialized processes that are required for cellular identity and tissue specificity. A survey of the literature shows that some miRNA pathways are conserved virtually intact throughout phylogeny while miRNA diversity also correlates with speciation. The number of miRNA genes, the expression of miRNAs, and target diversities of miRNAs tend to be positively correlated with morphological complexities observed in animals. Thus, organismal complexity can be estimated by the complexity of the miRNA circuitry. The complexity of the miRNA gene families establishes a link between genotypic complexity and phenotypic complexity in animal evolution. In this paper, we start with the discussion of miRNA conservation. Then we interpret the trends in miRNA conservation to deduce miRNA evolutionary trends in metazoans. Based on these conservation patterns observed in each component of the miRNA regulatory system, we attempt to propose a global insight on the probable consistency between morphological evolution in animals and the molecular evolution of miRNA gene activity in the cell.

This abstract was withdrawn by the authors.

1091 Background: Triple negative breast cancer (TNBC) remains the most aggressive subtype of breast cancer in which up to 1/3 of all patients will relapse early and distantly. There remains no proven method to monitor and detect early recurrence. This study examines the utility of serial liquid biopsies using a multi-template approach (identification and analysis of cell-free DNA (cfDNA) and circulating tumor cells (CTCs)) as a solution. Methods: 210 patients (average 53 yrs.) with confirmed diagnosis of TNBC, within 3 years of completion of therapy (mean 25 mos.), and in full remission were enrolled. Liquid biopsies were performed quarterly to look for cancer specific genomic mutations not seen in germ line controls, but in cfDNA and CTCs using a custom 27-gene breast cancer panel. Prior validation of our gene panel demonstrated a false positive rate of 0.001-0.0007% in normal cfDNA and cell-based controls. Results: Each subject had on average 3.0 serial samples collected to date. 169 patients (80.4%) had evidence of mutations in at least one sample. Seventy-five percent of cfDNA and 36% of CTC samples examined have been found to bear mutations. The total number of samples with orthogonally (either between template or between draws) confirmed signal was 16.9%. Seven patients (3.3%) have developed documented evidence of recurrence, one in the axilla and the others with visceral/distant metastases. Of the patients that have recurred, all had a persistent mutation on consecutive blood draws or evidence of genomic mutations in both cfDNA and CTCs. Conclusions: The majority of TNBC patients in our study post-treatment were found to have genomic mutations on at least one liquid biopsy sample – either cfDNA or CTC. But, very few had a persistent presence of mutations in subsequent samples and 96.7% of our patients have remained NED. Unlike patients who remained NED, patients who recurred displayed persistent evidence of mutations on serial draws or in both cfDNA and CTC samples. To date our recurrence rate is lower than predicted. This study highlights the need for serial monitoring using a multi-template approach to better fully understand patient specific tumor biology and kinetics. The trial is ongoing. Clinical trial information: NCT02639832.

The noncoding RNA Xist has been shown to be essential for X-chromosome inactivation and to coat the inactive X-chromosome (Xi). Thus, an important question in understanding the formation of Xi is whether the binding reaction of Xist is necessary for X-chromosome inactivation. In this article, we demonstrate the failure of X-chromosome silencing if the association of Xist with the X-chromosome is inhibited. The chromatin-binding region was functionally mapped and evaluated by using an approach for studying noncoding RNA function in living cells that we call peptide nucleic acid (PNA) interference mapping. In the reported experiments, a single 19-bp antisense cell-permeating PNA targeted against a particular region of Xist RNA caused the disruption of the Xi. The association of the Xi with macro-histone H2A is also disturbed by PNA interference mapping.

Most conditional expression vectors designed for mammalian cells have been valuable systems for studying genes of interest by regulating their expressions. The available vectors, however, are reliable for the short-length cDNA clones and not optimal for relatively long fragments of genomic DNA or long cDNAs. Here, we report the construction of two bacterial artificial chromosome (BAC) vectors, capable of harboring large inserts and shuttling among Escherichia coli, yeast, and mammalian cells. These two vectors, pEYMT and pEYMI, contain conditional expression systems which are designed to be regulated by tetracycline and mouse interferons, respectively. To test the properties of the vectors, we cloned in both vectors the green fluorescence protein (GFP) through an in vitro ligation reaction and the 17.8-kb-long X-inactive-specific transcript (Xist) cDNA through homologous recombination in yeast. Subsequently, we characterized their regulated expression properties using real-time quantitative RT-PCR (TaqMan) and RNA-fluorescent in situ hybridization (FISH). We demonstrate that these two BAC vectors are good systems for recombination-based cloning and regulated expression of large genes in mammalian cells.

We have extended our earlier work to show that individual 14-20mer peptide nucleic acid probes directed against interspersed alpha-satellite sequences can specifically identify chromosomes. Peptide nucleic acid (PNA) probes were used to detect chromosomal abnormalities and repeat structure in the human genome by fluorescence in situ hybridization (FISH). The hybridization of a single PNA probe species directed against a highly abundant alpha-satellite DNA repeat sequence was sufficient to absolutely identify a chromosome. Selection of highly repetitive or region-specific DNA repeats involved DNA database analysis. Distribution of a specific repeat sequence in human genome was estimated through two means: a computer program "whole genome" approach based on approximately 400 Mb (12%) human genomic sequence. The other method involved directed search for alpha satellite sequences. In total, approximately 240 unique DNA repeat candidates were found. Forty-two PNA probes were designed for screening chromosome-specific probes. Ten chromosome-specific PNA probes for human Chromosomes (Chrs) 1, 2, 7, 9, 11, 17, 18, X, and Y have been identified. Interphase and metaphase results demonstrate that chromosome-specific PNA probes are capable of detecting simple aneuploidies (trisomies) in human. Another set of PNA probes showed distinct banding-like patterns and could be used as sequence-specific stains for chromosome "bar coding". Potential application of PNA probes for investigating repeat structure and function is also discussed.

The satellite repeat structure of the mammalian centromere contains the CENP-B protein binding site. Using the peptide nucleic acid-fluorescence in situ hybridization (PNA-FISH), we show by direct PNA-DNA binding that all detectable CENP-B sites in a mammalian genome might have the same sequence. Two species-specific PNA 17-mers, pMm and pMc, were identified from CENP-B binding sites of Mus musculus and M. caroli, respectively. Fluorescence in situ hybridization confirmed that pMc hybridized to M. caroli centromeres only; however, pMm cross-hybridized to M. musculus and human centromeres. By using a series of CENP-B PNA 17-mers containing 1, 2, 3, 5, and 7 base-pair mismatches to their DNA counterparts, we further demonstrate that PNA-FISH can discriminate between two CENP-B DNA sequences that differ by a single base-pair in mouse and human centromeres, suggesting the degree of conservation of CENP-B sequences throughout the genome. In comparison with DNA oligonucleotides, PNA oligomers demonstrate the higher sequence specificity, improved stability, reproducibility, and lower background. Therefore, PNA oligomers have significant advantages over DNA oligonucleotide probes in analyzing microsatellites in a genome.

To identify novel cis-regulatory elements responsible for the tissue-restricted expression pattern of the Wilms' tumor-1 (WT1) gene, we mapped a total of 11 DNase I-hypersensitive sites in the 5'-flanking region and first intron of the human gene, six of which were specific for WT1 expressing cell lines. A 1.4-kilobase (kb) fragment from the mouse wt1 5'-flanking region contained cross-hybridizing sequence with significant homology to a region of DNase I hypersensitivity in the human WT1 gene which bound to nuclear matrix in human fetal kidney 293 cells. None of the DNase I-hypersensitive sites/matrix attachment regions, either alone or in combination, were sufficient for tissue-specific WT1 expression in transient and stably transfected cell lines. However, stable transfection of an approximately 620-kb yeast artificial chromosome (YAC) that carried the entire mouse wt1 locus into 293 cells resulted in wt1 (trans)gene expression at a level of approximately 30% of the endogenous human gene. Deletion of the 1.4-kb cross-hybridizing mouse fragment, located approximately 15 kb upstream of the transcription start site, caused complete loss of wt1 gene expression in the YAC-transfected 293 cells. In summary, we have identified a far upstream element that contains a region of DNase I hypersensitivity and that binds to nuclear matrix. This element includes phylogenetically conserved sequence and is required, although not sufficient, for mouse wt1 gene expression in human fetal kidney cells in culture.

X inactivation results in inactivation of one X chromosome to compensate for gene dosage differences between mammalian females and males. It requires the X-inactivation center (Xic) and Xist in cis. We report that introducing 450 kb of murine Xic/Xist sequences onto autosomes activates female dosage compensation in male ES cells. Xist is induced upon differentiation and can be expressed from both endogenous and ectopic loci, suggesting that elements for counting and choosing Xs are present in the transgene. Differentiating transgenic ES cells undergo excessive cell death. Postnatally, Xist is expressed only from the transgene. Ectopic Xist RNA structurally associates with the autosome and may inactivate a marker gene in cis. These results argue that the Xic is contained within 450 kb and that these sequences are sufficient for chromosome counting, choosing, and initiation of X inactivation.

Introduction The presence of Circulating Tumor Cells (CTC) has been observed in advanced cancer patients and studies have indicated that these cells contribute to the process of metastasis. Historically CTCs with metastatic potential have been characterized as cells that are EpCAM positive, Cytokeratin positive (CK+), and CD45 negative. We report the results of a prospective study challenging these historical definitions of circulating tumor cells. Description In a prospective study, patients with metastatic breast cancer there were about to start a new systemic therapy were enrolled The samples and representative tissue were collected at baseline. The patients were predominantly female (97%) and all had stage IV disease. From these whole blood samples a LiquidBiopsy® was performed using the “MultiTemplate” format which directly compares CTC, circulating cell free (CCF), and WBC patient-matched DNA in a NGS based resequencing test. Of 22 patients, 18 biopsy samples were successfully evaluated; the balance had insufficient tissue or DNA for analysis. Summary The LiquidBiopsy compared two phenotypic definitions for CTC capture. Tumor cell populations were enriched using epithelial targeted capture and compared to a novel cocktail of antibodies. The cocktail of reagents gave 77% average recovery of engineered samples when a target receptor was present on cell lines representing the spectrum of breast cancer subtypes. This enrichment protocol was applied to serial patient samples. Epithelial based enrichment served as a control and showed an average recovered purity of 10.7% CK+ cells. By comparison, cocktail selection enriched populations with on average 8.8% CK+ cell populations but a larger range of cells than epithelial selection. Importantly, the median number of CK+ cells recovered from cocktail capture was almost twice that of epithelial capture alone. (median of 35.8 vs 22.1 for cocktail and epithelial respectively). The median CD45+ non-target cells background was 80 and 155 cells respectively. This background supports sequencing detection of mutations present at >1%. ccfDNA sample was purified from the same tube of blood. The average concentration of patient matched ccfDNA recovered was 7.3 ng/mL. The combined results of ctcDNA and ccfDNA template sequencing gave productive samples showed similar detection frequency (55% vs 58%), were temporally flexible, and were complementary both to each other and the “gold standard” (FFPE). Conclusions The data from this prospective clinical study reveals subsets of CTC, including an important cohort that is not detected using the standard definition for epithelial CTCs. Furthermore, we present evidence for the successful use of a “Multi-Template” approach to the liquid biopsy, where germline, ctcDNA, and ccfDNA templates are employed for clinical diagnostic purposes and justifies the redefinition of CTC phenotype based upon cell surface biomarkers and mutation content. Citation Format: William M. Strauss, Chris Carter, Erich Klem, Jill Simmons, Keerthi Gogineni, Ruth O’Regan, Laura Austin, Paul W. Dempsey, Massimo Cristofanilli. Multi-template analysis in metastatic breast cancer blood samples. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1388.

Molecular complementation of mutant phenotypes by transgenic technology is a potentially important tool for gene identification. A technology was developed that allows the transfer of a physically intact yeast artificial chromosome (YAC) into the germ line of the mouse. A purified 150-kilobase YAC encompassing the murine gene Col1a1 was efficiently introduced into embryonic stem (ES) cells via lipofection. Chimeric founder mice were derived from two transfected ES cell clones. These chimeras transmitted the full length transgene through the germ line, generating two transgenic mouse strains. Transgene expression was visualized as nascent transcripts in interphase nuclei and quantitated by ribonuclease protection analysis. Both assays indicated that the transgene was expressed at levels comparable to the endogenous collagen gene.

We have developed a pair of vectors for exchanging yeast artificial chromosome (YAC) arms by targeted homologous recombination. These conversion vectors allow the introduction of copy-number control elements into YACs constructed with pYAC4 or related vectors. YACs modified in this way provide an enriched source of DNA for genetic or biochemical studies. A LYS2 gene on the conversion vector provides a genetic selection for the modified YACs after transformation with appropriately prepared vector. A background of Lys+ clones that do not contain modified YACs is also present. However, clones with converted YACs can be distinguished from this background by counter-screening for loss of the original p YAC4 TRP1 arm (Trp- phenotype). The elimination of yeast replication origins (ARS elements) from the conversion vectors increased the frequency of Lys+ Trp- clones, but resulted in weaker amplification. Several YACs have been converted with these vectors, and the fate of the transformed DNA and of the resident YAC DNA has been systematically investigated.

All hybridization methods depend upon the ability of denatured DNA to reanneal when complementary strands are present in an environment near but below their Tm (melting temperature). A detailed procedure is described in which bacteriophage plaques or bacterial colonies bound to a filter membrane are detected by hybridization with a radioactive probe. Hybridization proceeds on prewet filters placed in a sealable plastic bag. After hybridization the filters are removed from the sealed bag, excess probe is washed off, and the filters are autoradiographed to identify the clones that have hybridized with the probe. An Alternate Protocol differs mainly in that formamide is not used in the hybridization solution.

MicroRNAs (miRNAs) are small non-coding RNA molecules that regulate mRNAs through a sequence-specific mechanism. By virtue of their structure and mechanism of action, computational methods have been devised to investigate the encoding of miRNA genes and the targets of miRNA action. A variety of assumptions have predicated the implementation of these various computational solutions. Evolutionary sequence conservation, secondary structure, and folding energetics are some of the assumptions that have been used. The success of these different computational solutions has been evaluated for both elucidation of new miRNAs and deducing targets of miRNA action. While the focus is on search techniques for new miRNAs, we have compared the programs miRseeker, miRScan, PalGrade, ProMiR, and miRAlign as examples of implementation of these techniques. For these programs, a benchmark comparison between theoretical estimation and actual identification is possible. We have also compared the target prediction programs TargetScanS, PicTar, DIANA-microT, miRanda, and RNAhybrid. However, it is difficult to rigorously assess the benchmark performance of these programs due to the difficulty in confirming their theoretical predictions.

Development in mammals is a complex process requiring gene expression to be spatially and temporally well-regulated. Factors modulate gene functioning by controlling transcription, translation, or mRNA degradation. microRNAs (miRNAs) are a group of small RNA molecules (∼22 nucleotides) that attenuate gene activity posttranscriptionally by suppressing translation or destabilizing mRNAs. miRNAs have been recently validated to regulate many animal developmental events including proliferation, differentiation, and apoptosis. Many miRNAs display intriguing expression and functioning patterns throughout these pathways. Here we will review achievements to date about studies of how miRNAs affect a variety of animal developmental transitions, from the formation of early embryos to the generation of highly specialized tissues. Birth Defects Research (Part C) 78:129–139, 2006. © 2006 Wiley-Liss, Inc.

During different periods of mammalian development, global changes in gene expression occur. Developmental changes in global gene expression have been modeled as a restrictive process. To test the restriction model of global changes in gene expression, we have used embryonic stem (ES) cells as a model system for the early mammalian embryo. ES cells are pluripotent cells that can contribute to all cellular lineages of the developing mammalian fetus and are derived from early embryonic cells. Using this model system, we have studied a new class of RNAs called microRNAs that have been identified and shown to play a role in the direct regulation of messenger RNAs. Here we report the expression signature for 248 microRNAs in 13 independent murine ES cells, embryoid bodies, and somatic tissues. The expression profile for 248 mouse microRNAs was determined for embryonic stem cells, embryoid bodies, mouse embryos, mature heart, lung, liver, kidney, and brain. Characteristic microRNA expression signatures were observed for each evaluated sample. When the characteristic microRNA signatures for developmentally ordered samples were compared, immature samples exhibited a less complex microRNA transcript profile than did mature samples. Our data support a progressive model of microRNA gene expression. Based on the progressive increase in complexity of micro- RNA expression, we hypothesize that the mammalian developmental program requires a temporal coupling of expression between microRNAs and messenger RNAs to enable the developmental potential observed in mammalian ontogeny.

The noncoding RNA Xist has been shown to direct the mammalian dosage compensation pathway. Expression of the Xist RNA is regulated through an uncharacterized post-transcriptional mechanism, thought to involve Xist RNA stability. We have previously demonstrated that Xist RNA isoforms contain different 3' ends. In this report we analyze the expression patterns of Xist RNA isoforms and show the Xist RNA long form (L-isoform) is the predominant form in early development. Significant amounts of both the short form (S-isoform) and the L-isoform were found in the female soma. We also define the precise sequence structure of the Xist RNA isoforms 3' ends and show the S-isoform and the L-isoform are structurally dissimilar. Our data show both the S-isoform and L-isoform are cleaved from the same primary transcript. However, the S-isoform is subsequently post-transcriptionally polyadenylated, while the L-isoform is not post-transcriptionally polyadenylated. Sequence organization of the L-isoform shows that there are at least five different nonadenylated L-isoforms in the female soma and only one in embryonic stem (ES) cells. This stem cell-and somatic cell-specific processing may suggest a role for Xist RNA processing in the regulation of Xist RNA expression.

In the setting of inactivated DNA damage-sensitive checkpoints, critically shortened telomeres promote chromosomal instability and the types of widespread cytogenetic alterations that characterize most human carcinomas. Using a direct telomere fluorescence in situ hybridization technique, we analyzed 114 invasive breast carcinomas, 29 carcinoma in situ lesions, 10 benign proliferative lesions, and different normal epithelial components of the male and female breast. We found marked telomere shortening in the majority (52.5%) of invasive carcinomas; smaller subsets of invasive carcinoma demonstrated moderate telomere shortening (17.5%) or normal telomere lengths (21%), while a small subgroup (5%) contained elongated telomeres. Strikingly, the majority (78%) of ductal carcinoma in situ demonstrated markedly or moderately shortened telomeres. Surprisingly, unlike all other normal epithelia studied to date, moderate telomere shortening was observed in benign secretory cells in approximately 50% of histologically-normal terminal duct lobular units (from which most breast cancer is thought to arise), while such shortening was not seen in myoepithelial cells or normal large lactiferous ducts of the female breast or male breast ducts (from which breast cancer infrequently arises). We postulate that such shortening is the result of hormonally driven, physiological proliferation, and may delineate a population of epithelial cells at risk for subsequent malignant transformation.

Both cell free DNA (cfDNA) and circulating tumor cells (CTC) represent important possible templates for mutation analysis of clinical samples with different theoretical advantages for a clinical test. cfDNA is easy to access and isolate, while CTC can provide both DNA as well as RNA for clinical testing. We have tested matched cfDNA and CTC DNA in a Next Generation sequencing test of clinical samples. Both cfDNA and CTC samples provided sufficient quantity for a direct sequencing clinical test. No whole genome amplification was required. The test consisted of coupling these purification technologies to an amplicon re-sequencing panel of 50 cancer-associated genes using a CLIA validated sequencing pipeline for single nucleotide variant (SNV) mutations with a sensitivity of 1%. Typically using this pipeline, blood borne cancer cells are isolated, extracted, sequenced and analyzed in 7 days. In the CLIA setting, the validated DNA sequencing process applied to breast cancer patient samples, has demonstrated useful and actionable clinical data. Results of SNV detection from known clinical positive control samples were quite definitive. We observed perfect concordance in True Positive (TP) SNV detection between the cfDNA and CTC templates. The only discordant results observed were in the detection of False Positives (FP). Using the identical software for SNV detection and variant calls, CTC templates exhibited ∼5x greater sensitivity in our sample set. cfDNA samples showed a much greater noise spectrum of FP. As blood samples are routinely fixed at collection, we evaluated whether fixation might contribute to the cfDNA observed high FP frequency. Our experimental results conclusively show that fixation did not contribute to increased FP observed with cfDNA. Whereas CTC samples showed zero FP over the reportable range, the cfDNA samples exhibited variable FP output ranging from 0 to >10 FP per sample. To extend the capabilities of sequencing rare cells, several RNA sequencing panels have been developed that allow for both SNV, expression, and fusion transcript detection. Although these panels have not been successfully used with cell free templates, they have been successfully applied to rare cell templates and promise to be an important capability for clinical use of CTC in the future. Looking at both lung and breast cancer derived samples we have measured both SNV, CNV (expression based), and fusion transcripts. We describe simultaneous detection of SNV mutations (KRAS: G12S, STK11:Q37*, PIK3CA:E545K, EGFR:L858R, EGFR:T790M, TP53:R273H) as well as fusion transcripts events EML4-ALK.E6aA20.AB374361, and EML4-ALK.E13A20.AB462411. In summary, both cfDNA and CTC derived DNA provided concordant results in SNV mutation detection. cfDNA exhibited a much higher FP rate as compared to CTC DNA. We further demonstrate that rare cells can provide useful template for RNA sequencing. Citation Format: William M. Strauss, Erich Klem, Maria Cuellar, Jill Simmons, Jessamine Winer-Jones, Paul W. Dempsey. Molecular platforms for mutation analysis from whole blood derived clinical samples by nextgen sequencing. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2846. doi:10.1158/1538-7445.AM2014-2846

There are a number of different procedures for the preparation of genomic DNA. They all start with some form of cell lysis, followed by deproteination and recovery of DNA. The main differences between various approaches lie in the extent of deproteination and in molecular weight of the DNA produced. The isolation procedure described here is relatively brief and relies on the powerful proteolytic activity of proteinase K combined with the denaturing ability of the ionic detergent SDS.

This unit provides protocols for characterizing DNA segments cloned in YACs and for purifying YACs from yeast chromosomes. The first basic protocol describes Southern blotting and partial-digest restriction analysis of YACs. These methods are useful for determining the size and complexity of the cloned insert DNA, the presence and location of particular restriction sites or sequences, and even the species of origin of the insert DNA (indicated by hybridization to species-specific repetitive elements such as Alu repeats). The second basic protocol describes gel purification of YACs for use in procedures requiring pure YAC DNA, such as mammalian-cell transformation and subcloning into smaller insert vectors. The third basic protocol details characterizing and analyzing YACs: in vivo fragmentation via homologous recombination with specialized fragmentation vectors containing specific probe sequences or repetitive elements, followed by Southern blotting with YAC- and human-derived probes.

Murine Xist is an essential transcript for X chromosome inactivation (X inactivation). According to recently revised structure, Xist is at least 17.8 kb long. It consists of seven exons and there are two major transcripts in female somatic cells. In this study we further defined the molecular structures of the two isoforms, namely short (S) and long (L) forms by northern blot and RNAse protection assay (RPA). The following lines of evidences suggest that mouse Xist depends on differential polyadenylation, not alternative splicing, to generate the two RNA isoforms: (1) only one band was detectable with the northern probes spanning the 3' end of Xist. (2) RPA showed the 3' termini of both S and L forms, and there are putative polyadenylation signals and hairpin structures close to these ends. (3) Analyses by splice site prediction program did not show any evidence of splice motifs in the sequence of L form. (4) Alignments between Xist 3' end (ESTs) and genomic sequence support the absence of splicing event in the region. The newly revised structure of Xist isoforms may have different stability and roles in the process of X inactivation.

The XIST gene plays an essential role in X Chromosome (Chr) inactivation during the early development of female humans. It is believed that the XIST gene, not encoding a protein, functions as an RNA. The XIST cDNA is unusually long, as its full length is reported to be 16.5 kilobase pairs (kb). Here, comparison of sequences from the genomic interval downstream to the 3' end of the human XIST gene against the human EST database brought to light a number of human EST sequences that are mapped to the region. Furthermore, PCR amplification of human cDNA libraries and RNA fluorescence in situ hybridization (RNA-FISH) demonstrate that the human XIST gene has additional 2.8 kb downstream sequences which have not been documented as a part of the gene. These data show that the full-length XIST cDNA is, in fact, 19.3 kb, not 16.5 kb as previously reported. The newly defined region contains an intron that may be alternatively spliced and seven polyadenylation signal sequences. Sequences in the newly defined region show overall sequence similarity with the 3' terminal region of mouse Xist, and three subregions exhibit quite high sequence conservation. Interestingly, the new intron spans the first two sub-regions that are absent in one of the two isoforms of mouse Xist. Taken together, we revise the structure of human XIST cDNA and compare cDNA structures between human and mouse XIST/Xist. al. 1992). This gene, called XIST/Xist (X inactive specific transcript), shows several interesting features. First, both human and mouse XIST/Xist cDNA are unusually long, reportedly 16.5 kb and 17.8 kb, respectively (Brown et al. 1992; Hong et al. 1999). Second, the transcript does not seem to encode a protein, on the basis of the lack of a significant open reading frame, absence of the Xist RNA from polysomes, and localization of the transcript in the nucleus (Brockdorff et al. 1992; Brown et al. 1992). Third, the XIST/Xist RNA physically associates with, or 'coats,' the inactive X Chr (Brown et al. 1992; Clemson et al. 1996). Fourth, XIST/Xist transcripts can be observed as early as the four-cell stage, and upon the initiation of X-inactivation, the steady-state level of the transcript rises dramatically, apparently by stabilization of the RNA (Panning et al. 1997; Sheardown et al. 1997). Although the function of XIST/Xist is not known, deletion of the gene leads to failure of X-inactivation, and knock-out mice die around the gastrulation stage (Marahrens et al. 1997; Penny et al. 1996). In this report, we revise the structure of the human XIST cDNA and discuss structural features of the newly defined region.

The goal of this grant is to establish a new biological system for studying the progression of prostate cancer. We propose a technology we have previously developed to help define X-chromosome inactivation to increase our understanding of the molecular biology of prostrate cancer. Using a mouse model, our goal is to induce functional Loss of Heterozygosity (LOH) on a particular chromosome at various specified times during development or life span. Specifically, we plan to induce LOH only in mouse prostatic tissues. We are particularly interested in evaluating sites of allelic loss previously identified to be associated with prostate cancer (7q, 8p, 10p, 10q, 13q, 16q, 18q) in humans and understanding the effect of LOH on syntenic mouse chromosomes. We believe this approach has the potential to increase our knowledge of the acquisition and progression of prostate cancer. A systematic experimental approach for creating LOH can help define new prostate specific tumor suppressor genes. As human chromosome 8p is most frequently associated with prostate cancer (80% of primary and metastatic prostate cancers show this chromosomal variant, our mouse model system will initially focus on the development of those mouse chromosomes syntenic with human chromosome 8p. This technology would augment the positional cytogenetic approach to understanding the genetic complexity of prostate cancer.

In this report, we present structural data for the murine Xist gene. The data presented in this paper demonstrate that the murine Xist transcript is at least 17.4 kb, not 14.3 kb as previously reported. The new structure of the murine Xist gene described herein has seven exons, not six. Exon VII encodes an additional 3.1 kb of information at the 3′ end. Exon VII contains seven possible sites for polyadenylation; four of these sites are located in the newly discovered 3′ end. Consequently, it is possible that several distinct transcripts may be produced through differential polyadenylation of a primary transcript. Alternative use of polyadenylation signals could result in size changes for exon VII. Two major species of Xist are detectable by Northern analysis, consistent with differential polyadenylation. In this paper, we propose a model for the role of the Xist 3′ end in the process of X-chromosome counting and choice during embryonic development.

11040 Background: Recently a succession of new hormonal therapies has emerged, highlighting the need for biomarkers to guide the management of HSPC. Biomarker development in HSPC has been hampered by the absence of primary tumor tissue in men who undergo radiation or present with metastatic disease. CTCs can address this challenge by providing real-time cancer tissue for biomarker analysis in HSPC. To test this approach we conducted a pilot of CTC capture and targeted NGS in HSPC. Methods: Under IRB approval, blood samples from patients with HSPC were labeled with EpCAM ferrofluid and placed into the LiquidBiopsy platform (Cynvenio Biosystems, Inc.), an immunoaffinity-based microfluidic device tailored to query genomic events. CTCs were identified by CK, CD45 and DAPI expression. A matched WBC pellet served as a control representing germline sequence. Amplicon libraries were generated using Life Technologies AmpliSeq 2.0 and sequenced on an Ion Torrent platform. Somatic single nucleotide variants (SNV) present in CTCs but not in WBC were identified. Results: CTCs were detected in all 8 patients with HSPC (CTC median 64.5, range 17-217). Germline variants were consistently detected in matched CTC and WBC samples. Significant SNVs (occurring in > 1% of DNA in a sample) were found in 4 of 8 CTC samples (range 1-5 SNVs/sample, frequency 1.2%-11.9% with 620X-14,422X coverage). Notably, 3 patients had biochemical recurrence only (no clinical metastases) yet still yielded CTCs associated with SNVs in KIT, APC, RET, SMAD4 and PTEN. One patient who had untreated metastatic disease had the highest number of CTCs which harbored 4 SNVs. Conclusions: This pilot demonstrates the feasibility of using CTCs as real-time disease relevant substrate for NGS to identify personalized genomic targets in HSPC. A high number of CTCs were detectable in all patients and CTC germline variants correlated with matched WBC controls. Encouragingly, even with a relatively narrow, primary tumor-derived AmpliSeq platform, cancer relevant SNVs were detected in half of the patients including those with only biochemical recurrence, making targeted NGS of CTCs a promising approach for biomarker discovery and validation in HSPC.

580 Background: The treatment of advanced breast cancer demands systemic therapies that can address disease heterogeneity and the development of treatment resistance without a “real-time” molecular window into disease biology. New technologies have focused on increased capture and molecular analysis of circulating tumor cells (CTCs) including cells undergoing epithelial mesenchymal transition (EMT). We conducted a pilot experiment to test the efficiency of capture and cytokeratin (CK) detection and the presence of single point variants (SNV) to determine the best utility of scoring alternatives for CTC. Methods: EpCAM expressing CTC were recovered from breast cancer patients using CellSearch (Veridex) and LiquidBiopsy (Cynvenio Biosystems). EpCAM recovery and CK scoring were indexed in spiked samples and in 12 inflammatory breast cancer (IBC) patient samples using antibodies against CKs 7, 8 or CKs 1-8, 10, 13-16, 18, 19. Additionally, LiquidBiopsy template was analyzed using an Ampliseq 1.0 panel on the IonTorrent PGM. SNV present in the CTC but not white blood cell (WBC) negative controls were identified and where possible, compared to tissue biopsy SNV analyzed using Foundation One (Foundation Medicine). Results: CTCs were detected using CellSearch 10/12 (83%) (range 0-2502 CTC/7.5ml) and LiquidBiopsy 12/12 (100%) (range 6-2800 CTC/7.5mL). More CK positive events were scored using CKs 1-8, 10, 13-16, 18, 19 than CKs 7, 8 in patient samples. Upon sequencing, shared germline polymorphisms were observed in CTC and WBC. Conversely, 1 or 2 SNV were detected in the Epcam selected population but not WBC controls from 6/12 patients (frequency 1.1%-2.1% with 520-5160x coverage) with SNV observed in TP53, MPL, PIK3ca, MET and IDH1. All but one of the PIK3ca mutations were absent in evaluable tissue biopsy. Conclusions: CTC recovery and scoring are two separate events. Altered CK detection emphasized the need to tailor CTC classification to specific disease settings. Sequence analysis showed one correlated SNV among 6 evaluable comparisons to tissue reflecting variable analysis as well as the biologic disparity of metastatic disease. This pilot demonstrates the feasibility of using CTC for molecular analysis.

Introduction: Personalizing cancer care relies on accurate detection of actionable genomic aberrations in tumor cells. Conventionally, this strategy relies on analysis of primary tumor samples, which are often temporally and biologically distinct from recurrent, metastatic or treatment-resistant disease. As an alternative, CTCs offer real-time cancer tissue for analysis that may more accurately represent the current state of a patient's disease. In this pilot, we used CTCs as source material for targeted NGS across a range of malignancies. Methods: Under IRB approval, blood samples from patients with advanced cancer were labeled with EpCAM ferrofluid and placed into the LiquidBiopsy® platform (Cynvenio Biosystems, Inc.), an immunoaffinity-based microfluidic device tailored to query genomic events. CTCs were identified by CK, CD45 and DAPI expression. A matched WBC pellet served as a control representing germline sequence. Amplicon libraries were generated using Life Technologies AmpliSeq 2.0 and sequenced with an Ion Torrent sequencer. When available, matched formalin fixed paraffin embedded (FFPE) primary tumor tissue from the same patient was analyzed in parallel. Somatic single nucleotide variants (SNV) present in CTCs or FFPE samples but not in WBC were identified. Results: CTCs were detected in 18 of 19 patients with advanced prostate (8), breast (6), renal cell (2), bladder (1), lung (1) and rectal (1) cancer (CTC median 54, range 15-421). Germline SNPs were consistently detected across WBC, CTC and FFPE samples. Significant SNVs (occurring in > 1% of DNA in a sample) were found in 6 of 18 patient CTC samples (range 1-6 SNVs/sample, frequency 1.1%-11.9% with 620X-14,422X sequence coverage depth). Numerous SNVs were identified in all 9 matched primary tumor FFPE specimens but did not correlate with the SNVs identified in the CTCs. Conclusion: This pilot demonstrates the feasibility of using CTCs as a real-time disease relevant substrate for NGS to identify personalized genomic targets. A high number of CTCs were detectable across malignancies, and CTC germline variants correlated with matched WBC controls. Cancer relevant SNVs were detected in a third of patients even using the relatively narrow primary tumor derived AmpliSeq platform. The FFPE specimens generated a high number of SNVs but did not correlate with CTC profiles, likely reflecting biological disparity between early localized tumors and advanced metastatic disease, as well as genomic artifacts introduced into primary tumor specimens by FFPE preservation. These data demonstrate the feasibility and potential biological and technical advantages of CTCs over traditional FFPE samples for genomic analysis in the pursuit of personalized cancer medicine. Citation Format: Stephen V. Liu, Paul W. Dempsey, William Strauss, Yucheng Xu, Tong Xu, Jessamine Winer-Jones, Tim J. Triche, David I. Quinn, Janine McMurdie, Andre Defusco, Amir Goldkorn. Targeted next-generation sequencing (NGS) of circulating tumor cells (CTCs) and matched primary tumors. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr LB-227. doi:10.1158/1538-7445.AM2013-LB-227

Sequence analysis and quantitative allele specific PCR (QPCR) methods permit genetic profiling of cancer for targeted therapeutic selection; such personalized treatments have been associated with improved outcomes in cancer. Circulating tumor cells (CTC) offer a minimally-invasive opportunity for serial patient sampling, and potentially a means of tracking the molecular evolution that underlies the behavior and response phenotype of the disease including potential therapeutic response markers. Acquiring these types of patient profiles requires a platform and workflow providing reliable detection and recovery of small numbers of mutation-bearing CTC from a blood sample. Availability of such an enabling platform is a necessary prerequisite to the clinical correlation studies needed to demonstrate the utility of mutation-bearing CTC to patient care. We have successfully purified CTCs and converted them into DNA template of sufficient purity and quality to support multiple non-overlapping advanced molecular characterizations. Beginning with whole human blood spiked with defined numbers of cultured cancer cells as surrogates for CTCs, cells were successfully fluid-phase labeled using an anti-EpCAM antibody ferrofluid. Using a proprietary microfluidic sheath flow technology, EpCAM positive, cytokeratin staining cells were selected from 2 to 4 ml of labeled blood. This method produced sufficient DNA template for multiple analyses per patient sample. QPCR analysis of these templates demonstrated reproducible detection of fewer than 1% target cells in a background of non-target cells, allowing detection of the KRAS G12S mutation from as few as 5 recaptured cancer cells. The same DNA templates were then used for hybrid capture and next-generation sequencing of a panel of more than 200 cancer-related genes. This sequencing platform was able to detect multiple somatic mutations in genomic DNA templates produced from samples containing as few as 10 cancer cells per milliliter of blood. Together these data provide initial proof-of-concept for a system capable of detecting and characterizing mutations across any specified set of genes within purified CTC populations. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4554. doi:1538-7445.AM2012-4554

There are a number of different procedures for the preparation of genomic DNA. They all start with some form of cell lysis, followed by deproteinization and recovery of DNA. The main differences between various approaches lie in the extent of deproteinization and in molecular weight of the DNA produced. The isolation procedure described here is relatively brief and relies on the powerful proteolytic activity of proteinase K combined with the denaturing ability of the ionic detergent SDS.

We describe methods for rapid production and screening of yeast artificial chromosome (YAC) libraries. Utilizing complete restriction digests of mouse genomic DNA for ligations in agarose, a 32,000-clone library was produced and screened in seven weeks. Screening was accomplished by subdividing primary transformation plates into pools of approximately 100 clones which were transferred into a master glycerol stock. These master stocks were used to inoculate liquid cultures to produce culture "pools," and ten pools of 100 clones were then combined to yield superpools of 1,000 clones. Both pool and superpool DNA was screened by polymerase chain reaction (PCR) and positive pools representing 100 clones were then plated on selective medium and screened by in situ hybridization. Screening by the two tiered PCR assay and by in situ hybridization was completed in 4-5 days. Utilizing this methodology we have isolated a 150 kb clone spanning the alpha 1(I) collagen (Col1a1) gene as well as 40 kb clones from the Hox-2 locus. To characterize the representation of the YAC library, the size distribution of genomic Sal I fragments was compared to that of clones picked at random from the library. The results demonstrate significant biasing of the cloned fragment distribution, resulting in a loss of representation for larger fragments.

Characterization of tumors that arise spontaneously in the AKR mouse indicates that they are derived from cells of a distinct T-cell lineage. Cells in this subclass bear surface antigens, designated Tpre, Tthy, Tind, and Tsu, which are encoded by genes in the Tsu linkage group on murine chromosome 12. We have examined the rearrangement and expression of genes encoding the T-cell alpha, beta, and gamma chains in these tumors. Although these cells contain alpha-chain mRNA, they do not produce a normal-sized beta-chain mRNA. Most of them also lack gamma-chain mRNA. Each thymic leukemia was derived from a cell arrested at a different stage of development as defined by their expression of terminal deoxynucleotidyl transferase and Thy-1 mRNA. The data presented here are consistent with a model in which thymocytes expressing Tpre, Tthy, Tind, or Tsu undergo somatic development parallel to the development of other T cells. However, these thymocytes do not appear to differentiate into cells bearing alpha-beta heterodimers of the T-cell antigen receptor.

The human T cell receptor gamma locus, including eleven variable-region, five joining-region, and two constant-region segments, is contained in 160 kilobases. During T cell somatic development these genes undergo rearrangement by deletion of the sequences separating the variable and joining regions. The molecular map of this locus was completely defined by deletion mapping and restriction mapping. Restriction fragments were resolved by standard agarose electrophoresis and field inversion electrophoresis. These studies demonstrate that the deletions in this locus, which occur during the formation of a functional T cell receptor gamma-chain gene, range from 50 to 145 kilobases in length. These studies also provide a structural basis for understanding the development of the gamma-chain peptide repertoire, and extends the potential of the emerging pulsed-field electrophoretic technology.

Cerebral ring hemorrhages were observed in four species of monkeys with various forms of anemia. The lesions resembled those described in humans with a variety of diseases, including pernicious anemia. The pale centers of most lesions were surrounded by rings of erythrocytes. Also observed were petechiae, pale foci without hemorrhage, and glial nodules. Ultrastructural study revealed that the pale cores were foci of degenerating neurites associated with infiltration of fibrin into the finest interstitial spaces. Leakage of firbinogen and erythrocytes apparently occurred from capillary sized vessels. A few of these were thrombosed, some were normal and some had only small fibrin thrombi in apparent apposition to damaged endothelial tight junctions. These findings suggest that a primary effect of anemia and other insults associated with ring hemorrhages is damage to tight junctions. Consequent fibrinous exudation clogs the interstitium and results in neuritic degeneration.

Examination of the histocompatibility region of the nonobese diabetic (NOD) mouse with antibodies against class II glycoproteins (products of immune response genes of the major histocompatibility complex I-A and I-E), hybrid T-cell clones, and mixed-lymphocyte cultures and analysis of restriction fragment length polymorphisms indicate that the NOD mouse has a unique class II major histocompatibility complex with no expression of surface I-E, no messenger RNA for I-E alpha, and an I-A not recognized by any monoclonal antibodies or hybrid T-cell clones studied. In crosses of NOD mice with control C3H mice, the development of diabetes was dependent on homozygosity for the NOD mouse's unique major histocompatibility region.