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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.

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.

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.

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.

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

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.

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

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.