Magnetically functionalized hydrogels for high-throughput genomic applications

Single-cell genomics has revolutionized tissue analysis by revealing the genetic program of individual cells. The key aspect of the technology is the use of barcoded beads to unambiguously tag sequences originating from a single cell. The generation of unique barcodes on beads is mainly achieved by split-pooling methods, which are labor-intensive due to repeated washing steps. Towards the automation of the split-pooling method, we developed a simple method to magnetize hydrogel beads. We show that these hydrogel beads provide increased yields and washing efficiencies for purification procedures. They are also fully compatible with single-cell sequencing using the BAG-Seq workflow. Our work opens the automation of the split-pooling technique, which will improve single-cell genomic workflows.

FABP5 Inhibition against PTEN-Mutant Therapy Resistant Prostate Cancer

Resistance to standard of care taxane and androgen deprivation therapy (ADT) causes the vast majority of prostate cancer (PC) deaths worldwide. We have developed RapidCaP, an autochthonous genetically engineered mouse model of PC. It is driven by the loss of PTEN and p53, the most common driver events in PC patients with life-threatening diseases. As in human ADT, surgical castration of RapidCaP animals invariably results in disease relapse and death from the metastatic disease burden. Fatty Acid Binding Proteins (FABPs) are a large family of signaling lipid carriers. They have been suggested as drivers of multiple cancer types. Here we combine analysis of primary cancer cells from RapidCaP (RCaP cells) with large-scale patient datasets to show that among the 10 FABP paralogs, FABP5 is the PC-relevant target. Next, we show that RCaP cells are uniquely insensitive to both ADT and taxane treatment compared to a panel of human PC cell lines. Yet, they share an exquisite sensitivity to the small-molecule FABP5 inhibitor SBFI-103. We show that SBFI-103 is well tolerated and can strongly eliminate RCaP tumor cells in vivo. This provides a pre-clinical platform to fight incurable PC and suggests an important role for FABP5 in PTEN-deficient PC.

P11.64.A Long-term follow up and translational data from the ReoGlio phase Ib trial of GM-CSF and intravenous pelareorep (Reovirus) alongside standard of care in GBM

BACKGROUND

We previously reported safety data from a phase Ib, open-label study of intravenous oncolytic virus pelareorep with GM-CSF alongside standard chemoradiotherapy in newly diagnosed glioblastoma confirming that the combination is well tolerated. We now report on long-term follow up and analysis of translational samples from tumour and blood in a subset of patients.

METHODS

15 patients with newly diagnosed GBM were treated with GM-CSF 50μg subcutaneously on days 1-3 and intravenous pelareorep on days 4-5 in weeks 1 and 4 of chemoradiotherapy, and subsequently in week 1 of each adjuvant temozolomide course: 7 patients received 1x1010TCID50 (dose level 1); 8 received 3x1010TCID50 (dose level 2). The primary objective was to determine the maximum tolerated dose of pelareorep and GM-CSF with standard chemoradiotherapy. Following a protocol amendment we also collected survival data in all patients up to August 2021. Serial blood samples were taken from three patients, at baseline, during chemoradiotherapy and in the first adjuvant cycle. Peripheral blood mononuclear cells were analysed for immune checkpoint expression by flow cytometry, RNAseq gene expression and T-cell receptor clonality, whilst plasma cytokines were quantified by Luminex.

RESULTS

This combination was well tolerated with 87% of patients completing treatment as planned. Survival data analysis showed that median OS was 12.6 months in dose level 1 and 16.1 months in dose level 2, median OS for all patients was 13.1 months. The 24-month survival estimate for all patients was 25.0%, 16.7% for dose level 1 and 33.3% for dose level 2. One patient in dose level 1 remains alive at 43 months post registration without further treatment. Laboratory data showed that pelareorep infusion resulted in inflammatory cytokine and chemokine secretion, immune checkpoint modulation, and upregulation of inflammatory pathways. There was also increased peripheral clonal tumour-specific T-cell proliferation following pelareorep infusion.

CONCLUSION

Although based on small numbers, these long-term follow up data suggest this may be an active combination in a subset of GBM patients. Translational data confirm that pelareorep potentially activates tumour-targeting immune pathways in GBM, with consequential immune checkpoint modulation. These data support a combination clinical trial of pelareorep, radiotherapy and immune checkpoint blockade in GBM.

Parity-induced changes to mammary epithelial cells control NKT cell expansion and mammary oncogenesis

Pregnancy reprograms mammary epithelial cells (MECs) to control their responses to pregnancy hormone re-exposure and carcinoma progression. However, the influence of pregnancy on the mammary microenvironment is less clear. Here, we used single-cell RNA sequencing to profile the composition of epithelial and non-epithelial cells in mammary tissue from nulliparous and parous female mice. Our analysis indicates an expansion of γδ natural killer T-like immune cells (NKTs) following pregnancy and upregulation of immune signaling molecules in post-pregnancy MECs. We show that expansion of NKTs following pregnancy is due to elevated expression of the antigen-presenting molecule CD1d on MECs. Loss of CD1d expression on post-pregnancy MECs, or overall lack of activated NKTs, results in mammary oncogenesis. Collectively, our findings illustrate how pregnancy-induced changes modulate the communication between MECs and the immune microenvironment and establish a causal link between pregnancy, the immune microenvironment, and mammary oncogenesis.

Chromosomal instability accelerates the evolution of resistance to anti-cancer therapies

Aneuploidy is a ubiquitous feature of human tumors, but the acquisition of aneuploidy typically antagonizes cellular fitness. To investigate how aneuploidy could contribute to tumor growth, we triggered periods of chromosomal instability (CIN) in human cells and then exposed them to different culture environments. We discovered that transient CIN reproducibly accelerates the acquisition of resistance to anti-cancer therapies. Single-cell sequencing revealed that these resistant populations develop recurrent aneuploidies, and independently deriving one chromosome-loss event that was frequently observed in paclitaxel-resistant cells was sufficient to decrease paclitaxel sensitivity. Finally, we demonstrated that intrinsic levels of CIN correlate with poor responses to numerous therapies in human tumors. Our results show that, although CIN generally decreases cancer cell fitness, it also provides phenotypic plasticity to cancer cells that can allow them to adapt to diverse stressful environments. Moreover, our findings suggest that aneuploidy may function as an under-explored cause of therapy failure.

192 An Audit of The Delivery of Paediatric Orthopaedic Services at The Bristol Royal Children’s Hospital in Response to The British Orthopaedic Association Standards for Trauma (BOAST) COVID-19 Guidance

Introduction

Guidance from the BOAST helped structure our paediatric orthopaedic service n response to COVID-19. We assessed our compliance with 'BOAST COVID-19 standards', whether it is possible to run a safe and effective paediatric orthopaedic service.

Method

We performed a prospective audit of clinic and theatre data (16th March to 30th April 2020), from the paediatric orthopaedic department at the BRCH against the 'BOAST COVID-19 standards'. We also performed a retrospective audit.

Results

Patients booked into acute fracture clinic (AFC) and fracture clinic follow-up (FFO) reduced by 40% and 48% respectively from 2019 to 2020. A virtual fracture clinic (VFC) was implemented with an increasing trend seen. The number of patient initiated follow-up appointments increased in AFC and FFO from 16% to 75% and 12% to 35% respectively. Radiography was reduced; only 17% and 39% of AFC and FFO patients respectively required radiographs. On-call referrals and trauma cases dropped by 50% with similar case mix year-on-year. All elective operating was cancelled in 2020.

Conclusions

By reducing clinic admissions and theatre throughput, it was possible to run an effective paediatric orthopaedic service in a busy tertiary referral centre. Our aim now is to determine the long-term efficacy, cost, and sustainability of our COVID-19 service.

Intraductal Transplantation Models of Human Pancreatic Ductal Adenocarcinoma Reveal Progressive Transition of Molecular Subtypes

Pancreatic ductal adenocarcinoma (PDAC) is the most lethal common malignancy, with little improvement in patient outcomes over the past decades. Recently, subtypes of pancreatic cancer with different prognoses have been elaborated; however, the inability to model these subtypes has precluded mechanistic investigation of their origins. Here, we present a xenotransplantation model of PDAC in which neoplasms originate from patient-derived organoids injected directly into murine pancreatic ducts. Our model enables distinction of the two main PDAC subtypes: intraepithelial neoplasms from this model progress in an indolent or invasive manner representing the classical or basal-like subtypes of PDAC, respectively. Parameters that influence PDAC subtype specification in this intraductal model include cell plasticity and hyperactivation of the RAS pathway. Finally, through intratumoral dissection and the direct manipulation of RAS gene dosage, we identify a suite of RAS-regulated secreted and membrane-bound proteins that may represent potential candidates for therapeutic intervention in patients with PDAC. SIGNIFICANCE: Accurate modeling of the molecular subtypes of pancreatic cancer is crucial to facilitate the generation of effective therapies. We report the development of an intraductal organoid transplantation model of pancreatic cancer that models the progressive switching of subtypes, and identify stochastic and RAS-driven mechanisms that determine subtype specification.See related commentary by Pickering and Morton, p. 1448.This article is highlighted in the In This Issue feature, p. 1426.

Integrated Computational Pipeline for Single-Cell Genomic Profiling

PURPOSE

Copy-number profiling of multiple individual cells from sparse sequencing may be used to reveal a detailed picture of genomic heterogeneity and clonal organization in a tissue biopsy specimen. We sought to provide a comprehensive computational pipeline for single-cell genomics, to facilitate adoption of this molecular technology for basic and translational research.

MATERIALS AND METHODS

The pipeline comprises software tools programmed in Python and in R and depends on Bowtie, HISAT2, Matplotlib, and Qt. It is installed and used with Anaconda.

RESULTS

Here we describe a complete pipeline for sparse single-cell genomic data, encompassing all steps of single-nucleus DNA copy-number profiling, from raw sequence processing to clonal structure analysis and visualization. For the latter, a specialized graphical user interface termed the single-cell genome viewer (SCGV) is provided. With applications to cancer diagnostics in mind, the SCGV allows for zooming and linkage to the University of California at Santa Cruz Genome Browser from each of the multiple integrated views of single-cell copy-number profiles. The latter can be organized by clonal substructure or by any of the associated metadata such as anatomic location and histologic characterization.

CONCLUSION

The pipeline is available as open-source software for Linux and OS X. Its modular structure, extensive documentation, and ease of deployment using Anaconda facilitate its adoption by researchers and practitioners of single-cell genomics. With open-source availability and Massachusetts Institute of Technology licensing, it provides a basis for additional development by the cancer bioinformatics community.

Novel insights into breast cancer copy number genetic heterogeneity revealed by single-cell genome sequencing

Copy number alterations (CNAs) play an important role in molding the genomes of breast cancers and have been shown to be clinically useful for prognostic and therapeutic purposes. However, our knowledge of intra-tumoral genetic heterogeneity of this important class of somatic alterations is limited. Here, using single-cell sequencing, we comprehensively map out the facets of copy number alteration heterogeneity in a cohort of breast cancer tumors. Ou/var/www/html/elife/12-05-2020/backup/r analyses reveal: genetic heterogeneity of non-tumor cells (i.e. stroma) within the tumor mass; the extent to which copy number heterogeneity impacts breast cancer genomes and the importance of both the genomic location and dosage of sub-clonal events; the pervasive nature of genetic heterogeneity of chromosomal amplifications; and the association of copy number heterogeneity with clinical and biological parameters such as polyploidy and estrogen receptor negative status. Our data highlight the power of single-cell genomics in dissecting, in its many forms, intra-tumoral genetic heterogeneity of CNAs, the magnitude with which CNA heterogeneity affects the genomes of breast cancers, and the potential importance of CNA heterogeneity in phenomena such as therapeutic resistance and disease relapse.

Cells in the body remain healthy by tightly preventing and repairing random changes, or mutations, in their genetic material. In cancer cells, however, these mechanisms can break down. When these cells grow and multiply, they can then go on to accumulate many mutations. As a result, cancer cells in the same tumor can each contain a unique combination of genetic changes.

This genetic heterogeneity has the potential to affect how cancer responds to treatment, and is increasingly becoming appreciated clinically. For example, if a drug only works against cancer cells carrying a specific mutation, any cells lacking this genetic change will keep growing and cause a relapse. However, it is still difficult to quantify and understand genetic heterogeneity in cancer.

Copy number alterations (or CNAs) are a class of mutation where large and small sections of genetic material are gained or lost. This can result in cells that have an abnormal number of copies of the genes in these sections. Here, Baslan et al. set out to explore how CNAs might vary between individual cancer cells within the same tumor.

To do so, thousands of individual cancer cells were isolated from human breast tumors, and a technique called single-cell genome sequencing used to screen the genetic information of each of them. These experiments confirmed that CNAs did differ – sometimes dramatically – between patients and among cells taken from the same tumor. For example, many of the cells carried extra copies of well-known cancer genes important for treatment, but the exact number of copies varied between cells. This heterogeneity existed for individual genes as well as larger stretches of DNA: this was the case, for instance, for an entire section of chromosome 8, a region often affected in breast and other tumors.

The work by Baslan et al. captures the sheer extent of genetic heterogeneity in cancer and in doing so, highlights the power of single-cell genome sequencing. In the future, a finer understanding of the genetic changes present at the level of an individual cancer cell may help clinicians to manage the disease more effectively.

Multiplex accurate sensitive quantitation (MASQ) with application to minimal residual disease in acute myeloid leukemia

Measuring minimal residual disease in cancer has applications for prognosis, monitoring treatment and detection of recurrence. Simple sequence-based methods to detect nucleotide substitution variants have error rates (about 10⁻³) that limit sensitive detection. We developed and characterized the performance of MASQ (multiplex accurate sensitive quantitation), a method with an error rate below 10⁻⁶. MASQ counts variant templates accurately in the presence of millions of host genomes by using tags to identify each template and demanding consensus over multiple reads. Since the MASQ protocol multiplexes 50 target loci, we can both integrate signal from multiple variants and capture subclonal response to treatment. Compared to existing methods for variant detection, MASQ achieves an excellent combination of sensitivity, specificity and yield. We tested MASQ in a pilot study in acute myeloid leukemia (AML) patients who entered complete remission. We detect leukemic variants in the blood and bone marrow samples of all five patients, after induction therapy, at levels ranging from 10⁻² to nearly 10⁻⁶. We observe evidence of sub-clonal structure and find higher target variant frequencies in patients who go on to relapse, demonstrating the potential for MASQ to quantify residual disease in AML.

Single-Chromosomal Gains Can Function as Metastasis Suppressors and Promoters in Colon Cancer

High levels of cancer aneuploidy are frequently associated with poor prognosis. To examine the relationship between aneuploidy and cancer progression, we analyzed a series of congenic cell lines that harbor single extra chromosomes. We found that across 13 different trisomic cell lines, 12 trisomies suppressed invasiveness or were largely neutral, while a single trisomy increased metastatic behavior by triggering a partial epithelial-mesenchymal transition. In contrast, we discovered that chromosomal instability activates cGAS/STING signaling but strongly suppresses invasiveness. By analyzing patient copy-number data, we demonstrate that specific aneuploidies are associated with distinct outcomes, and the acquisition of certain aneuploidies is in fact linked with a favorable prognosis. Thus, aneuploidy is not a uniform driver of malignancy, and different aneuploidies can uniquely influence tumor progression. At the same time, the gain of a single chromosome is capable of inducing a profound cell state transition, thereby linking genomic plasticity, phenotypic plasticity, and metastasis.

Guidelines for safe transfer of the brain-injured patient: trauma and stroke, 2019: Guidelines from the Association of Anaesthetists and the Neuro Anaesthesia and Critical Care Society

The location of care for many brain-injured patients has changed since 2012 following the development of major trauma centres. Advances in management of ischaemic stroke have led to the urgent transfer of many more patients. The basis of care has remained largely unchanged, however, with emphasis on maintaining adequate cerebral perfusion as the key to preventing secondary injury. Organisational aspects and training for transfers are highlighted, and we have included an expanded section on paediatric transfers. We have also provided a table with suggested blood pressure parameters for the common types of brain injury but acknowledge that there is little evidence for many of our recommendations. These guidelines remain a mix of evidence-based and consensus-based statements. We have received assistance from many organisations representing clinicians who care for these patients, and we believe our views represent the best of current thinking and opinion. We encourage departments to review their own practice using our suggestions for audit and quality improvement.

Copolymerization of single-cell nucleic acids into balls of acrylamide gel

We show the use of 5′-Acrydite oligonucleotides to copolymerize single-cell DNA or RNA into balls of acrylamide gel (BAGs). Combining this step with split-and-pool techniques for creating barcodes yields a method with advantages in cost and scalability, depth of coverage, ease of operation, minimal cross-contamination, and efficient use of samples. We perform DNA copy number profiling on mixtures of cell lines, nuclei from frozen prostate tumors, and biopsy washes. As applied to RNA, the method has high capture efficiency of transcripts and sufficient consistency to clearly distinguish the expression patterns of cell lines and individual nuclei from neurons dissected from the mouse brain. By using varietal tags (UMIs) to achieve sequence error correction, we show extremely low levels of cross-contamination by tracking source-specific SNVs. The method is readily modifiable, and we will discuss its adaptability and diverse applications.

Utility of Single-Cell Genomics in Diagnostic Evaluation of Prostate Cancer

A distinction between indolent and aggressive disease is a major challenge in diagnostics of prostate cancer. As genetic heterogeneity and complexity may influence clinical outcome, we have initiated studies on single tumor cell genomics. In this study, we demonstrate that sparse DNA sequencing of single-cell nuclei from prostate core biopsies is a rich source of quantitative parameters for evaluating neoplastic growth and aggressiveness. These include the presence of clonal populations, the phylogenetic structure of those populations, the degree of the complexity of copy-number changes in those populations, and measures of the proportion of cells with clonal copy-number signatures. The parameters all showed good correlation to the measure of prostatic malignancy, the Gleason score, derived from individual prostate biopsy tissue cores. Remarkably, a more accurate histopathologic measure of malignancy, the surgical Gleason score, agrees better with these genomic parameters of diagnostic biopsy than it does with the diagnostic Gleason score and related measures of diagnostic histopathology. This is highly relevant because primary treatment decisions are dependent upon the biopsy and not the surgical specimen. Thus, single-cell analysis has the potential to augment traditional core histopathology, improving both the objectivity and accuracy of risk assessment and inform treatment decisions.Significance: Genomic analysis of multiple individual cells harvested from prostate biopsies provides an indepth view of cell populations comprising a prostate neoplasm, yielding novel genomic measures with the potential to improve the accuracy of diagnosis and prognosis in prostate cancer. Cancer Res; 78(2); 348-58. ©2017 AACR.

Effect of Blood Collection Tube Type and Time to Processing on the Enumeration and High-Content Characterization of Circulating Tumor Cells Using the High-Definition Single-Cell Assay

CONTEXT

- As circulating tumor cell (CTC) assays gain clinical relevance, it is essential to address preanalytic variability and to develop standard operating procedures for sample handling in order to successfully implement genomically informed, precision health care.

OBJECTIVE

- To evaluate the effects of blood collection tube (BCT) type and time-to-assay (TTA) on the enumeration and high-content characterization of CTCs by using the high-definition single-cell assay (HD-SCA).

DESIGN

- Blood samples of patients with early- and advanced-stage breast cancer were collected into cell-free DNA (CfDNA), EDTA, acid-citrate-dextrose solution, and heparin BCTs. Time-to-assay was evaluated at 24 and 72 hours, representing the fastest possible and more routine domestic shipping intervals, respectively.

RESULTS

- We detected the highest CTC levels and the lowest levels of negative events in CfDNA BCT at 24 hours. At 72 hours in this BCT, all CTC subpopulations were decreased with the larger effect observed in high-definition CTCs and cytokeratin-positive cells smaller than white blood cells. Overall cell retention was also optimal in CfDNA BCT at 24 hours. Whole-genome copy number variation profiles were generated from single cells isolated from all BCT types and TTAs. Cells from CfDNA BCT at 24-hour TTA exhibited the least noise.

CONCLUSIONS

- Circulating tumor cells can be identified and characterized under a variety of collection, handling, and processing conditions, but the highest quality can be achieved with optimized conditions. We quantified performance differences of the HD-SCA for specific preanalytic variables that may be used as a guide to develop best practices for implementation into patient care and/or research biorepository processes.

Whole-genome single-cell copy number profiling from formalin-fixed paraffin-embedded samples

A substantial proportion of tumors consist of genotypically distinct subpopulations of cancer cells. This intratumor genetic heterogeneity poses a substantial challenge for the implementation of precision medicine. Single-cell genomics constitutes a powerful approach to resolve complex mixtures of cancer cells by tracing cell lineages and discovering cryptic genetic variations that would otherwise be obscured in tumor bulk analyses. Because of the chemical alterations that result from formalin fixation, single-cell genomic approaches have largely remained limited to fresh or rapidly frozen specimens. Here we describe the development and validation of a robust and accurate methodology to perform whole-genome copy-number profiling of single nuclei obtained from formalin-fixed paraffin-embedded clinical tumor samples. We applied the single-cell sequencing approach described here to study the progression from in situ to invasive breast cancer, which revealed that ductal carcinomas in situ show intratumor genetic heterogeneity at diagnosis and that these lesions may progress to invasive breast cancer through a variety of evolutionary processes.

TGF-β reduces DNA ds-break repair mechanisms to heighten genetic diversity and adaptability of CD44+/CD24- cancer cells

Many lines of evidence have indicated that both genetic and non-genetic determinants can contribute to intra-tumor heterogeneity and influence cancer outcomes. Among the best described sub-population of cancer cells generated by non-genetic mechanisms are cells characterized by a CD44+/CD24- cell surface marker profile. Here, we report that human CD44+/CD24- cancer cells are genetically highly unstable because of intrinsic defects in their DNA-repair capabilities. In fact, in CD44+/CD24- cells, constitutive activation of the TGF-beta axis was both necessary and sufficient to reduce the expression of genes that are crucial in coordinating DNA damage repair mechanisms. Consequently, we observed that cancer cells that reside in a CD44+/CD24- state are characterized by increased accumulation of DNA copy number alterations, greater genetic diversity and improved adaptability to drug treatment. Together, these data suggest that the transition into a CD44+/CD24- cell state can promote intra-tumor genetic heterogeneity, spur tumor evolution and increase tumor fitness.

Effects of storage at -20°C on ischaemia-modified albumin results

Background: Ischaemia-modified albumin (IMA) is being studied as a new marker for reversible ischaemia in patients presenting with possible cardiac chest pain. The conditions under which samples are stored prior to analysis may be critical in influencing the analytical result and hence the cut-off used in any particular study.

Methods: Sixty-eight samples taken during a study assessing the performance of IMA for risk stratification in patients presenting with possible cardiac chest pain were analysed both within 2.5 h of collection and after periods of storage at -20°C.

Results: Samples stored at -20°C yielded IMA values on average 3 units higher than those analysed within 2.5 h (mean 90.5 vs. 87.5; P < 0.00001). A Bland-Altman plot showed that the difference was not concentration dependent.

Conclusions: These results indicate that decision cut-offs will be influenced by conditions of sample storage prior to IMA analysis, and that these should be stated in detail for each study.

SMASH, a fragmentation and sequencing method for genomic copy number analysis

Copy number variants (CNVs) underlie a significant amount of genetic diversity and disease. CNVs can be detected by a number of means, including chromosomal microarray analysis (CMA) and whole-genome sequencing (WGS), but these approaches suffer from either limited resolution (CMA) or are highly expensive for routine screening (both CMA and WGS). As an alternative, we have developed a next-generation sequencing-based method for CNV analysis termed SMASH, for short multiply aggregated sequence homologies. SMASH utilizes random fragmentation of input genomic DNA to create chimeric sequence reads, from which multiple mappable tags can be parsed using maximal almost-unique matches (MAMs). The SMASH tags are then binned and segmented, generating a profile of genomic copy number at the desired resolution. Because fewer reads are necessary relative to WGS to give accurate CNV data, SMASH libraries can be highly multiplexed, allowing large numbers of individuals to be analyzed at low cost. Increased genomic resolution can be achieved by sequencing to higher depth.

Interactive analysis and assessment of single-cell copy-number variations

We present Ginkgo (http://qb.cshl.edu/ginkgo), a user-friendly, open-source web platform for the analysis of single-cell copy-number variations (CNVs). Ginkgo automatically constructs copy-number profiles of cells from mapped reads and constructs phylogenetic trees of related cells. We validated Ginkgo by reproducing the results of five major studies. After comparing three commonly used single-cell amplification techniques, we concluded that degenerate oligonucleotide-primed PCR is the most consistent for CNV analysis.

Abstract POSTER-TECH-1114: Single-cell molecular profiling of fluid biopsies of epithelial ovarian cancer

The immediate goal of this project is to identify rare circulating tumor cells (CTC) in the bloodstream of epithelial ovarian cancer (EOC) patients and to apply high content, single cell assays that will yield information on morphology, protein expression and genomic structure. The ultimate goal is to develop a minimally invasive “fluid biopsy” for ovarian patients that can provide detailed information on the patient’s response to therapy, early warnings of potential resistance or relapse, and genetic predictors for the most appropriate therapy.

The onset of pharmacogenomics has opened the door to a future of precision-guided therapies for cancer. Although as yet not implemented in all cancers, the idea of matching therapy to the molecular genetic characteristics of an individual cancer has been realized for specific classes of breast, lung and prostate cancers. For metastatic ovarian cancer patients the most efficient and convenient way to monitor the continuous state of the patient is through the presence of circulating epithelial cells (CTCs) that are shed from metastatic sites into the bloodstream. The difficulty, of course, is detecting and isolating these cells from the tens of millions of endothelial leukocytes (white blood cells) in a standard blood draw.

We have created the HD-CTC assay for visualizing these rare CTC from blood samples and measuring their morphology, protein expression and genomic structure. Briefly, after initial processing to remove red blood cells, the blood samples are deposited on glass slides, stained and examined with a high-speed optical scanner. Epithelial (cancer) cells are distinguished from white blood cells by the presence of a complex of cytokeratin molecules in the cell. Each epithelial cell is imaged and its position recorded along with morphometric data including overall cell and nuclear size and shape. The positional information is used to retrieve individual cells for DNA extraction and DNA sequencing. The DNA sequence is initially converted into a genomic profile of copy number variation (CNV) and can be further sequenced for single nucleotide mutations.

With support from the Rivkin Foundation we will obtain blood samples from up to 20 Stage 4 epithelial ovarian cancer patients at sequential times during their cycles of treatment and perform full HD-CTC assays including CTC enumeration, protein expression and genomic analysis of individual cells in order to determine the specific genetic alterations present in each cell and the degree of variation present within each case. Coupled with clinical information, including C125 levels and response to therapy, plus genetic information from bulk primary and metastatic tissue, we expect to establish the landscape of the circulating cell compartment in EOC and begin to understand the relationship of CTC to the metastatic behavior and patient prognosis.

Citation Format: Carmen Ruiz Velasco, Asya Stepansky, Angel Dago, Anders Carlson, Anand Kolatkar, Jude Kendall, James Hicks , Peter Kuhn. Single-cell molecular profiling of fluid biopsies of epithelial ovarian cancer [abstract]. In: Proceedings of the 10th Biennial Ovarian Cancer Research Symposium; Sep 8-9, 2014; Seattle, WA. Philadelphia (PA): AACR; Clin Cancer Res 2015;21(16 Suppl):Abstract nr POSTER-TECH-1114.

Abstract 4735: Single-cell sequencing from formalin-fixed paraffin-embedded breast cancers: a powerful tool to address intratumor genetic heterogeneity

Background: At diagnosis, tumors often consist of multiple, genotypically distinct cell populations. Genome sequencing of single cells has opened new avenues of investigation, yet the application of this technology remains limited to fresh/frozen tissue samples. Here, we describe and validate a method to perform single-cell massively parallel sequencing using DNA extracted from individual nuclei from FFPE tumor samples.

Methods: Tissue sections are deparaffinized and the area of interest microdissected, DNA is reverse-crosslinked and the extracellular matrix is digested. Extracted single nuclei are then FACS-sorted, lysed and the whole genome repaired using a broad-spectrum DNA-repair enzyme cocktail. Repaired DNA is whole genome amplified (WGA) using GenomePlex WGA4 (Sigma-Aldrich) with modifications for heavily damaged genomic templates. Illumina sequencing libraries are generated using standard approaches followed by multiplex sequencing on an Illumina HiSeq2000. To obtain copy number (CN) profiles, single-cell sequencing data are mapped to the reference genome with PCR duplicates removed. Uniquely mapped reads are allocated and counted in genomic intervals of variable length (bins) with CN states roughly proportional to the number of allocated sequencing reads. Bin counts are then normalized on the basis of GC-content, segmented and transformed to CN values to identify long contiguous regions of equivalent CN.

Results: As a proof-of-principle we performed single-cell CN profiling on two aneuploid synchronous ductal carcinomas in situ (DCIS)/invasive ductal carcinomas (IDCs), where both FFPE and frozen material was available. Using our novel methodology, 24 single nuclei were multiplexed/lesion. An average of 3 million reads/cell (average coverage of 0.1X/cell) was obtained, providing sufficient data to infer CN profiles of single cells accurately. These data were successfully employed to identify non-neoplastic cells and distinct clonal lineages of neoplastic cells within each lesion. The data obtained from the analysis of FFPE samples were concordant with those obtained from the analysis of matched frozen samples.

Conclusions: We developed a robust procedure to perform single-cell massively parallel sequencing of individual nuclei isolated from FFPE samples, providing the opportunity to unlock pathology archives for studies aiming to catalog and dissect the biological and clinical relevance of intra-tumor genetic heterogeneity.

Citation Format: Luciano G. Martelotto, Rita A. Sakr, Timour Baslan, Linda Rodgers, Hilary Cox, Jude Kendall, Tari A. King, Britta Weigelt, James Hicks, Jorge S. Reis-Filho. Single-cell sequencing from formalin-fixed paraffin-embedded breast cancers: a powerful tool to address intratumor genetic heterogeneity. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4735. doi:10.1158/1538-7445.AM2015-4735

Abstract 2989: Intra-tumor heterogeneity and clonal changes in the progression of DCIS to invasiveness: Combined tumor bulk and single cell analysis

INTRODUCTION: Ductal carcinoma in situ (DCIS) is a clonal intraductal proliferation of epithelial cells which acts as a non-obligate precursor of invasive breast cancer (IBC), yet the genetic events leading to the acquisition of invasive behavior remain unclear. We hypothesize that DCIS is composed of mosaics of genetically diverse tumor cell clones, and that the process of invasion is an evolutionary bottleneck. To test this hypothesis we performed a detailed characterization of the repertoire of genetic alterations and intra-tumor genetic heterogeneity in synchronously diagnosed DCIS and IBC using NextGen sequencing of bulk tumor and single cells.

METHODS: DNA extracted from fresh frozen, microdissected DCIS, IBC and adjacent normal tissue was subjected to whole exome sequencing on an Illumina HiSeq2000. Reads were aligned to the reference human genome hg19. Single nucleotide variants (SNVs) were called by MuTect, and gene copy number alterations were determined using VarScan2. Single nuclei were isolated from 100μm serial sections microdissected to separate DCIS and IBC. Individual nuclei were FACS-sorted into a 96-well plate, lysed and whole genome amplified. Amplified DNA samples were barcoded, pooled and sequenced on a HiSeq2000. Single cell sequencing data were mapped to the reference genome and uniquely mapped reads were allocated into bins, normalized, segmented and CN values generated.

RESULTS: In 6 cases of synchronous DCIS and IBC, a median of 41 and 47 non-synonymous mutations were found in each component, respectively. The somatic mutations identified in both DCIS and adjacent IBC components affected known driver breast cancer genes, including AKT1, PIK3CA, GATA3, MAP2K4 and TP53. Interestingly, we also found mutations restricted to either DCIS or IBC: ATRX (IBC-3); ALK and PKD2 (IBC-5); ESR1 (DCIS-5). The gene copy number profiles of matched DCIS and IBC were similar in all 6 pairs, however we also identified gene copy number alterations restricted either to DCIS or IBC: 1q gain (IBC-5); 3p and 3q losses (DCIS-6); 12p homozygous deletion (DCIS-4). Single cell sequencing of two cases (3 and 4) revealed that the majority of cells from both DCIS and IBC were derived from a common precursor lineage with shared copy number losses and gains. Both sets of DCIS-IBC pairs in these cases displayed elements of a subclonal structure with dominant clones alongside genetically diverse derivatives as well as genetic heterogeneity reflected in variable copy number alterations and non-modal clones.

CONCLUSION: Synchronous DCIS and IBC share founder genetic events, but also harbor somatic genetic alterations restricted to either the DCIS or IBC components, demonstrating that although DCIS is a precursor of IBC, intra-tumor genetic heterogeneity is present at the DCIS stage. Changes in clonal composition likely take place in the progression from DCIS to IBC.

Citation Format: Rita A. Sakr, Luciano G. Martelotto, Timour Baslan, Charlotte KY Ng, Jude Kendall, Linda Rodgers, Hilary Cox, Mike Riggs, Sean D'Itali, Asya Stepansky, Narciso Olvera, Tari A. King, Britta Weigelt, Jorge S. Reis-Filho, James Hicks. Intra-tumor heterogeneity and clonal changes in the progression of DCIS to invasiveness: Combined tumor bulk and single cell analysis. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2989. doi:10.1158/1538-7445.AM2015-2989

Optimizing sparse sequencing of single cells for highly multiplex copy number profiling

Genome-wide analysis at the level of single cells has recently emerged as a powerful tool to dissect genome heterogeneity in cancer, neurobiology, and development. To be truly transformative, single-cell approaches must affordably accommodate large numbers of single cells. This is feasible in the case of copy number variation (CNV), because CNV determination requires only sparse sequence coverage. We have used a combination of bioinformatic and molecular approaches to optimize single-cell DNA amplification and library preparation for highly multiplexed sequencing, yielding a method that can produce genome-wide CNV profiles of up to a hundred individual cells on a single lane of an Illumina HiSeq instrument. We apply the method to human cancer cell lines and biopsied cancer tissue, thereby illustrating its efficiency, reproducibility, and power to reveal underlying genetic heterogeneity and clonal phylogeny. The capacity of the method to facilitate the rapid profiling of hundreds to thousands of single-cell genomes represents a key step in making single-cell profiling an easily accessible tool for studying cell lineage.

The contribution of de novo coding mutations to autism spectrum disorder

Whole exome sequencing has proven to be a powerful tool for understanding the genetic architecture of human disease. Here we apply it to more than 2,500 simplex families, each having a child with an autistic spectrum disorder. By comparing affected to unaffected siblings, we show that 13% of de novo missense mutations and 43% of de novo likely gene-disrupting (LGD) mutations contribute to 12% and 9% of diagnoses, respectively. Including copy number variants, coding de novo mutations contribute to about 30% of all simplex and 45% of female diagnoses. Almost all LGD mutations occur opposite wild-type alleles. LGD targets in affected females significantly overlap the targets in males of lower intelligence quotient (IQ), but neither overlaps significantly with targets in males of higher IQ. We estimate that LGD mutation in about 400 genes can contribute to the joint class of affected females and males of lower IQ, with an overlapping and similar number of genes vulnerable to contributory missense mutation. LGD targets in the joint class overlap with published targets for intellectual disability and schizophrenia, and are enriched for chromatin modifiers, FMRP-associated genes and embryonically expressed genes. Most of the significance for the latter comes from affected females.

Role of SWI/SNF in acute leukemia maintenance and enhancer-mediated Myc regulation

Cancer cells frequently depend on chromatin regulators to maintain their malignant phenotype. Brg1, an ATPase subunit of SWI/SNF, is known to suppress tumor formation in several cell types. Vakoc and colleagues now show that leukemia cells instead rely on Brg1 to support their oncogenic transcriptional program, which includes Myc as a key target. Brg1 is critical to sustain transcription factor occupancy and enable long-range looping interactions with the Myc promoter. These findings thus implicate enhancer-mediated Myc regulation in leukemia pathogenesis.

Cancer cells frequently depend on chromatin regulatory activities to maintain a malignant phenotype. Here, we show that leukemia cells require the mammalian SWI/SNF chromatin remodeling complex for their survival and aberrant self-renewal potential. While Brg1, an ATPase subunit of SWI/SNF, is known to suppress tumor formation in several cell types, we found that leukemia cells instead rely on Brg1 to support their oncogenic transcriptional program, which includes Myc as one of its key targets. To account for this context-specific function, we identify a cluster of lineage-specific enhancers located 1.7 Mb downstream from Myc that are occupied by SWI/SNF as well as the BET protein Brd4. Brg1 is required at these distal elements to maintain transcription factor occupancy and for long-range chromatin looping interactions with the Myc promoter. Notably, these distal Myc enhancers coincide with a region that is focally amplified in ∼3% of acute myeloid leukemias. Together, these findings define a leukemia maintenance function for SWI/SNF that is linked to enhancer-mediated gene regulation, providing general insights into how cancer cells exploit transcriptional coactivators to maintain oncogenic gene expression programs.

The contribution of de novo and rare inherited copy number changes to congenital heart disease in an unselected sample of children with conotruncal defects or hypoplastic left heart disease

Congenital heart disease (CHD) is the most common congenital malformation, with evidence of a strong genetic component. We analyzed data from 223 consecutively ascertained families, each consisting of at least one child affected by a conotruncal defect (CNT) or hypoplastic left heart disease (HLHS) and both parents. The NimbleGen HD2-2.1 comparative genomic hybridization platform was used to identify de novo and rare inherited copy number variants (CNVs). Excluding 10 cases with 22q11.2 DiGeorge deletions, we validated de novo CNVs in 8 % of 148 probands with CNTs, 12.7 % of 71 probands with HLHS and none in 4 probands with both. Only 2 % of control families showed a de novo CNV. We also identified a group of ultra-rare inherited CNVs that occurred de novo in our sample, contained a candidate gene for CHD, recurred in our sample or were present in an affected sibling. We confirmed the contribution to CHD of copy number changes in genes such as GATA4 and NODAL and identified several genes in novel recurrent CNVs that may point to novel CHD candidate loci. We also found CNVs previously associated with highly variable phenotypes and reduced penetrance, such as dup 1q21.1, dup 16p13.11, dup 15q11.2-13, dup 22q11.2, and del 2q23.1. We found that the presence of extra-cardiac anomalies was not related to the frequency of CNVs, and that there was no significant difference in CNV frequency or specificity between the probands with CNT and HLHS. In agreement with other series, we identified likely causal CNVs in 5.6 % of our total sample, half of which were de novo.

The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA

The maize genome, with its large complement of transposons and repeats, is a paradigm for the study of epigenetic mechanisms such as paramutation and imprinting. Here, we present the genome-wide map of cytosine methylation for two maize inbred lines, B73 and Mo17. CG (65%) and CHG (50%) methylation (where H = A, C, or T) is highest in transposons, while CHH (5%) methylation is likely guided by 24-nt, but not 21-nt, small interfering RNAs (siRNAs). Correlations with methylation patterns suggest that CG methylation in exons (8%) may deter insertion of Mutator transposon insertion, while CHG methylation at splice acceptor sites may inhibit RNA splicing. Using the methylation map as a guide, we used low-coverage sequencing to show that parental methylation differences are inherited by recombinant inbred lines. However, frequent methylation switches, guided by siRNA, persist for up to eight generations, suggesting that epigenetic inheritance resembling paramutation is much more common than previously supposed. The methylation map will provide an invaluable resource for epigenetic studies in maize.

Genomic heterogeneity of circulating tumor cells in castration-resistant prostate cancer (CRPC) revealed by single-cell sequencing

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Background: Circulating tumor cells (CTC) provide an opportunity to sample multiple metastatic tumor sites through a single blood draw – a ”fluid biopsy.” NextGen DNA sequencing provides the means to obtain detailed genetic information from captured cells prior to and during treatment. Here we demonstrate the use of DNA sequencing to interrogate genome-wide copy number variations (CNV) at the single-cell level in CTC isolated from pts with CRPC. Methods: Pre- and post-treatment blood samples were obtained from pts treated at MSKCC. EpCAM+ events were collected singly and in groups by cytometric flow sorting and were subjected to DNA amplification and Illumina NextGeneration sequencing. Parallel samples were assayed using the Veridex CellSearch method to ensure the presence of malignant cells. Results: Samples with up to 50 EpCAM+ events analyzed in bulk displayed CNV patterns expected from published CRPC data. Subsequent single cell analyses showed that the method could reliably detect common genomic markers in CRPC, including AR amplification, PTEN and RB1 loss, and the TMPRSS-ERG fusion. Individual genomic CNV profiles obtained from 125 single cells isolated from 15 patients were then analyzed. Using unsupervised clustering, cells from each pt showed a closely related lineage structure, consistent with an evolution from a common ancestor. The degree of genomic heterogeneity within CTC from an individual pt was highly variable, with R2 correlation coefficients ranging from >0.92 (nearly homogeneous) to <0.75 (mixed populations). Two pts harbored separate subpopulations with both amplified AR and non-amplified AR cells and another displayed mixtures of genetic markers that changed over the course of treatment. Conclusions: The observed variation in complexity of CTC populations in CRPC pts underscores the importance of being able to sample and analyze multiple cells from an individual pt on multiple occasions and with real time analytics. Doing so is essential to understand and identify mechanisms of resistance so that they can be targeted effectively. Supported by STARR Cancer Consortium, NCI SPORE in Prostate Cancer; Department of Defense; Prostate Cancer Foundation.

De novo gene disruptions in children on the autistic spectrum

Exome sequencing of 343 families, each with a single child on the autism spectrum and at least one unaffected sibling, reveal de novo small indels and point substitutions, which come mostly from the paternal line in an age-dependent manner. We do not see significantly greater numbers of de novo missense mutations in affected versus unaffected children, but gene-disrupting mutations (nonsense, splice site, and frame shifts) are twice as frequent, 59 to 28. Based on this differential and the number of recurrent and total targets of gene disruption found in our and similar studies, we estimate between 350 and 400 autism susceptibility genes. Many of the disrupted genes in these studies are associated with the fragile X protein, FMRP, reinforcing links between autism and synaptic plasticity. We find FMRP-associated genes are under greater purifying selection than the remainder of genes and suggest they are especially dosage-sensitive targets of cognitive disorders.

Rare de novo and transmitted copy-number variation in autistic spectrum disorders

To explore the genetic contribution to autistic spectrum disorders (ASDs), we have studied genomic copy-number variation in a large cohort of families with a single affected child and at least one unaffected sibling. We confirm a major contribution from de novo deletions and duplications but also find evidence of a role for inherited "ultrarare" duplications. Our results show that, relative to males, females have greater resistance to autism from genetic causes, which raises the question of the fate of female carriers. By analysis of the proportion and number of recurrent loci, we set a lower bound for distinct target loci at several hundred. We find many new candidate regions, adding substantially to the list of potential gene targets, and confirm several loci previously observed. The functions of the genes in the regions of de novo variation point to a great diversity of genetic causes but also suggest functional convergence.

A RSC/nucleosome complex determines chromatin architecture and facilitates activator binding

How is chromatin architecture established and what role does it play in transcription? We show that the yeast regulatory locus UASg bears, in addition to binding sites for the activator Gal4, sites bound by the RSC complex. RSC positions a nucleosome, evidently partially unwound, in a structure that facilitates Gal4 binding to its sites. The complex comprises a barrier that imposes characteristic features of chromatin architecture. In the absence of RSC, ordinary nucleosomes encroach over the UASg and compete with Gal4 for binding. Taken with our previous work, the results show that both prior to and following induction, specific DNA-binding proteins are the predominant determinants of chromatin architecture at the GAL1/10 genes. RSC/nucleosome complexes are also found scattered around the yeast genome. Higher eukaryotic RSC lacks the specific DNA-binding determinants found on yeast RSC, and evidently Gal4 works in those organisms despite whatever obstacle broadly positioned nucleosomes present.

Genome-Wide DNA Methylation Profiles of Breast Tumors Reveal Loci Associated with Relapse Risk

Background:Breast cancer prognosis is used in determining the course of adjuvant therapy for patients. Clinical prognostic indices like the Nottingham Prognostic Index have poor specificity, overestimate the risk of disease recurrence and necessitate more specific and robust prognostic markers. Prognostic gene expression markers are already in clinical use and show improved decision support. Methylation of CpG islands, an important regulator of gene expression, is reported to be disregulated in tumors, thus making methylation markers an important alternative to gene expression markers. We present the results of a genome-wide study that explored loci whose methylation status was significantly associated with recurrence risk.Methods:We used 108 frozen primary breast cancer specimens with ten year follow-up and extensive clinical data including histopathological measurements to identify potential epigenetic markers associated with recurrence risk. Using a previously validated array based method (Kamalakaran et. al., Nucleic Acids Research, 2009) we performed genome-wide measurements of differential CpG island methylation covering over 150,000 loci. We evaluated each locus for its ability to stratify patients into good or poor prognosis groups depending on its methylation status. Statistical significance was established using permutation analysis with appropriate multiple testing corrections. Prognostic markers independent of histopathological factors (ER, PR, HER2, tumor size, grade, node status, age) were identified using multivariate Cox regression analysis.Results:The methylation status of several loci proximal to genes significantly stratified samples independent of other clinical variables. Demethylation of several loci were associated with poor prognosis including ADAMTS4 (Hazard Ratio = 17.5, p-value&lt;&lt;0.001), a metalloproteinase previously implicated in the progression of glioma; DNA Topoisomerase I (HR = 3.81; 95% CI = 1.953-7.462; p&lt;&lt;0.001), implicated in chemotherapy resistance; and JMJD2C (HR = 3.7; 95% CI = 1.828-7.519; p&lt;&lt;0.001), which was found to be frequently amplified in esophageal cancers. The methylation of several loci also had significant association with poor prognosis, such as several members in the forkhead box family (FOXF1, FOXG1B, FOXJ1, FOXL2) and FHL1 (HR = 4.78; 95% CI = 2.38-9.62; p&lt;&lt;0.001). We selected several loci to form an ensemble classifier with statistically significant performance on our dataset. We show that this classifier achieved much higher specificity when compared to the Nottingham Prognostic Index, while maintaining high sensitivity.Discussion:Our retrospective study of genome-wide DNA methylation in breast cancer has identified several novel markers for prognosis. We found methylation deregulation of CpG islands proximal to genes implicated in metastasis and chemotherapy resistance is associated with poor prognosis. Furthermore, the potential for clinical benefit of these markers is their ability to jointly identify significantly larger number of low-risk patients compared to the Nottingham Prognostic Index.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 4046.

Subtype Dependent Alterations of the DNA Methylation Landscape in Breast Cancer

Background: The diversity of breast cancers at the clinical, histopathological and molecular level reflects variation in underlying biology and affects the clinical implications for patients. Gene expression studies have identified five breast cancer subtypes with distinct expression profiles – Luminal A, Luminal B, basal, ErbB2 enriched and Normal-Like. DNA methylation is an important regulator of gene expression that is also known to be deregulated in tumors. We set out to determine the relationship between DNA methylation and breast cancer subtypes in 108 breast cancer samples with previously determined expression subtypes.Methods: We performed high-throughput genome-wide scans of CpG methylation in 108 tumors and 11 normal tissues using our previously validated Methylation Oligonucleotide Microarray Analysis (MOMA) method [Kamalakaran, S et al. Nucleic Acids Research, 2009)]. We identified loci that were most varied across all tumors or had the most significant alterations and performed unsupervised hierarchical clustering on those loci. We then used a genetic algorithm based feature selection method to identify a subset of those loci that could cluster the sample set by expression subtype. We then characterized the loci contributing to subsetting and where possible, the relationship between methylation and gene expression.Results: Unsupervised hierarchical clustering using the 500 most differentially methylated loci across all tumors and 100 most significant altered loci between tumors and Normal tissues clustered the tumors into 3 major clusters – 82% of Cluster I belonged to Luminal Subtypes (22 Luminal A and 4 Luminal B), and 86% of Cluster II samples were of Basal or ErbB2+ subtypes. Cluster III did not show any expression subtype specific enrichment, but contained samples whose expression subtype was inconclusive with weak correlations to multiple expression subtypes. Interestingly, methylation loci that contributed to this clustering were not localized to CpG islands immediately upstream of genes, with 354 loci far from gene transcription start sites. These non-geneic loci did not show any significant regulatory potential based on cross-species conservation measures and no clear function could be assigned to these regions. The remaining 146 loci could be mapped to known genes. Gene expression microarray measurements were available for 79 of these geneic loci and 36 showed significant correlation of methylation to expression levels (p&lt;0.05), implying possible functional effects of the methylation on gene expression. Additionally, distinct subtype specific patterns of methylation could also be detected in known cancer associated genes. CpG islands in the HOXA gene cluster and many other homeobox genes were significantly more methylated in Luminal A tumors.Conclusions: Our results suggest that there are subtype dependant genome-wide alterations in the methylation landscape in breast cancers, especially near homeobox genes. Many more CpG islands with no apparent functional significance get methylated according to subtype in addition to those CpG islands associated with genes with known cancer related functions.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 1144.

Inferring tumor progression from genomic heterogeneity

Cancer progression in humans is difficult to infer because we do not routinely sample patients at multiple stages of their disease. However, heterogeneous breast tumors provide a unique opportunity to study human tumor progression because they still contain evidence of early and intermediate subpopulations in the form of the phylogenetic relationships. We have developed a method we call Sector-Ploidy-Profiling (SPP) to study the clonal composition of breast tumors. SPP involves macro-dissecting tumors, flow-sorting genomic subpopulations by DNA content, and profiling genomes using comparative genomic hybridization (CGH). Breast carcinomas display two classes of genomic structural variation: (1) monogenomic and (2) polygenomic. Monogenomic tumors appear to contain a single major clonal subpopulation with a highly stable chromosome structure. Polygenomic tumors contain multiple clonal tumor subpopulations, which may occupy the same sectors, or separate anatomic locations. In polygenomic tumors, we show that heterogeneity can be ascribed to a few clonal subpopulations, rather than a series of gradual intermediates. By comparing multiple subpopulations from different anatomic locations, we have inferred pathways of cancer progression and the organization of tumor growth.

Microduplications of 16p11.2 are associated with schizophrenia

Recurrent microdeletions and microduplications of a 600 kb genomic region of chromosome 16p11.2 have been implicated in childhood-onset developmental disorders1-3. Here we report the strong association of 16p11.2 microduplications with schizophrenia in two large cohorts. In the primary sample, the microduplication was detected in 12/1906 (0.63%) cases and 1/3971 (0.03%) controls (P=1.2×10^-5, OR=25.8). In the replication sample, the microduplication was detected in 9/2645 (0.34%) cases and 1/2420 (0.04%) controls (P=0.022, OR=8.3). For the series combined, microduplication of 16p11.2 was associated with 14.5-fold increased risk of schizophrenia (95% C.I. [3.3, 62]). A meta-analysis of multiple psychiatric disorders showed a significant association of the microduplication with schizophrenia, bipolar disorder and autism. The reciprocal microdeletion was associated only with autism and developmental disorders. Analysis of patient clinical data showed that head circumference was significantly larger in patients with the microdeletion compared with patients with the microduplication (P = 0.0007). Our results suggest that the microduplication of 16p11.2 confers substantial risk for schizophrenia and other psychiatric disorders, whereas the reciprocal microdeletion is associated with contrasting clinical features.

Updates to the RMAP short-read mapping software

SUMMARY

We report on a major new version of the RMAP software for mapping reads from short-read sequencing technology. General improvements to accuracy and space requirements are included, along with novel functionality. Included in the RMAP software package are tools for mapping paired-end reads, mapping using more sophisticated use of quality scores, collecting ambiguous mapping locations and mapping bisulfite-treated reads.

AVAILABILITY

The applications described in this note are available for download at http://www.cmb.usc.edu/people/andrewds/rmap and are distributed as Open Source software under the GPLv3.0. The software has been tested on Linux and OS X platforms.

CONTACT

andrewds@usc.edu; mzhang@cshl.edu

Methylation detection oligonucleotide microarray analysis: a high-resolution method for detection of CpG island methylation

Methylation of CpG islands associated with genes can affect the expression of the proximal gene, and methylation of non-associated CpG islands correlates to genomic instability. This epigenetic modification has been shown to be important in many pathologies, from development and disease to cancer. We report the development of a novel high-resolution microarray that detects the methylation status of over 25,000 CpG islands in the human genome. Experiments were performed to demonstrate low system noise in the methodology and that the array probes have a high signal to noise ratio. Methylation measurements between different cell lines were validated demonstrating the accuracy of measurement. We then identified alterations in CpG islands, both those associated with gene promoters, as well as non-promoter-associated islands in a set of breast and ovarian tumors. We demonstrate that this methodology accurately identifies methylation profiles in cancer and in principle it can differentiate any CpG methylation alterations and can be adapted to analyze other species.

Copy number alterations in pancreatic cancer identify recurrent PAK4 amplification

Pancreatic cancer is one of the most lethal of all cancers. The median survival is six months and less than 5% of those diagnosed survive five years. Recurrent genetic deletions and amplifications in 72 pancreatic adenocarcinomas, the largest sample set analyzed to date for pancreatic cancer, were defined using comparative genomic hybridization The recurrent genetic alterations identified target a number of previously well-characterized genes, as well as regions that contain possible new oncogenes and tumor suppressor genes. We have focused on chromosome 19q13, a region frequently found amplified in pancreatic cancer and demonstrate how boundaries of common regions of mutation can be mapped and how a gene, in this case PAK4 amplified on chromosome19q13, can be functionally validated. We show that although the PAK4 gene is not activated by mutation in cell lines with gene amplification, an oncogenic form of the KRAS2 gene is present in these cells and oncogenic KRAS2 can activate PAK4. In fact in the three samples we identified with PAK4 gene amplification, the KRAS2 gene was activated and genomically amplified. The kinase activity of the PAK4 protein is significantly higher in cells with genomic amplification as compared to cells without amplification. Our study demonstrates the utility of analyzing copy number data in a large set of neoplasms to identify genes involved in cancer. We have generated a useful dataset which will be particularly useful for the pancreatic cancer community as efforts are undertaken to sequence the pancreatic cancer genome.