Next-generation transcriptome sequencing of the premenopausal breast epithelium using specimens from a normal human breast tissue bank

Introduction

Our efforts to prevent and treat breast cancer are significantly impeded by a lack of knowledge of the biology and developmental genetics of the normal mammary gland. In order to provide the specimens that will facilitate such an understanding, The Susan G. Komen for the Cure Tissue Bank at the IU Simon Cancer Center (KTB) was established. The KTB is, to our knowledge, the only biorepository in the world prospectively established to collect normal, healthy breast tissue from volunteer donors. As a first initiative toward a molecular understanding of the biology and developmental genetics of the normal mammary gland, the effect of the menstrual cycle and hormonal contraceptives on DNA expression in the normal breast epithelium was examined.

Methods

Using normal breast tissue from 20 premenopausal donors to KTB, the changes in the mRNA of the normal breast epithelium as a function of phase of the menstrual cycle and hormonal contraception were assayed using next-generation whole transcriptome sequencing (RNA-Seq).

Results

In total, 255 genes representing 1.4% of all genes were deemed to have statistically significant differential expression between the two phases of the menstrual cycle. The overwhelming majority (221; 87%) of the genes have higher expression during the luteal phase. These data provide important insights into the processes occurring during each phase of the menstrual cycle. There was only a single gene significantly differentially expressed when comparing the epithelium of women using hormonal contraception to those in the luteal phase.

Conclusions

We have taken advantage of a unique research resource, the KTB, to complete the first-ever next-generation transcriptome sequencing of the epithelial compartment of 20 normal human breast specimens. This work has produced a comprehensive catalog of the differences in the expression of protein-coding genes as a function of the phase of the menstrual cycle. These data constitute the beginning of a reference data set of the normal mammary gland, which can be consulted for comparison with data developed from malignant specimens, or to mine the effects of the hormonal flux that occurs during the menstrual cycle.

Characterizing the heterogeneity of triple-negative breast cancers using microdissected normal ductal epithelium and RNA-sequencing

Triple-negative breast cancers (TNBCs) are a heterogeneous set of tumors defined by an absence of actionable therapeutic targets (ER, PR, and HER-2). Microdissected normal ductal epithelium from healthy volunteers represents a novel comparator to reveal insights into TNBC heterogeneity and to inform drug development. Using RNA-sequencing data from our institution and The Cancer Genome Atlas (TCGA) we compared the transcriptomes of 94 TNBCs, 20 microdissected normal breast tissues from healthy volunteers from the Susan G. Komen for the Cure Tissue Bank, and 10 histologically normal tissues adjacent to tumor. Pathway analysis comparing TNBCs to optimized normal controls of microdissected normal epithelium versus classic controls composed of adjacent normal tissue revealed distinct molecular signatures. Differential gene expression of TNBC compared with normal comparators demonstrated important findings for TNBC-specific clinical trials testing targeted agents; lack of over-expression for negative studies and over-expression in studies with drug activity. Next, by comparing each individual TNBC to the set of microdissected normals, we demonstrate that TNBC heterogeneity is attributable to transcriptional chaos, is associated with non-silent DNA mutational load, and explains transcriptional heterogeneity in addition to known molecular subtypes. Finally, chaos analysis identified 146 core genes dysregulated in >90 % of TNBCs revealing an over-expressed central network. In conclusion, use of microdissected normal ductal epithelium from healthy volunteers enables an optimized approach for studying TNBC and uncovers biological heterogeneity mediated by transcriptional chaos.

Abstract 4858: Next-generation whole transcriptome sequencing of thymic malignancies

Background: Thymomas & Thymic Carcinomas are rare malignancies with approximately 500 cases in the US per year. Apart from standard chemotherapy, treatment options are limited for those patients who become refractory to therapy or present with distant metastasis. Further, histological subtyping of these tumors has proven challenging, resulting in substantial discordance between pathologists and hindering the development of targeted therapy. A major impediment to therapeutic advancement is an inadequate understanding of the transcriptional biology of these cancers. Using next-generation sequencing, we embarked on a study to survey the transcriptomes of thymic malignancies to comprehensively identify novel biology by analyzing all full length transcripts expressed in these tissues.

Methods: Frozen thymomas, thymic carcinoma, and normal tissues were obtained from the Indiana University Simon Cancer Center. The WHO (2004 classification) subtypes represented in our sample set include: (4) type A, (2) A/B, (1) B2, (5) B3, (1) C, and (3) normal tissues. Tissues were reviewed and classified by one pathologist (S.B.) who was blinded to subsequent analyses. cDNA libraries were prepared and sequenced on an Applied Biosystems (AB) SOLiD3+ sequencer using a 50bp fragment run. For gene expression, mapping of reads to the genome was performed using the AB BioScope 1.0 Pipeline and outputs imported into Partek Genomics Suite for analysis. In Partek, mapped reads were cross-referenced against known genes from the UCSC database followed by statistical comparison of RPKM values for each gene between subtypes. Dimensionality reduction analyses (PCA & hierarchical clustering) were also performed in Partek.

Results: RNA sequencing of the 16 tissues produced 736 million reads equaling 37GB of data of which 24.4GB (66%) mapped to the human genome. These initial sequencing outputs represent only a portion, as additional paired-end sequencing of these samples is ongoing. In our preliminary data analysis, unsupervised hierarchical clustering of RPKM values from 20,600 RefSeq genes revealed 100% concordance between gene expression clusters and WHO subtype. A subsequent unsupervised clustering of 705 pre-miRNAs also showed substantial concordance between clusters and subtype. When analyzing differential gene expression between the three subtypes most represented in our data set (A, A/B, B3), we report 318 genes to be differentially expressed between A vs. A/B, 799 genes for A/B vs. B3, and 1524 genes for A vs. B3.

Discussion: We report preliminary data from RNA-sequencing of thymic malignancies. Initial analyses reveal that this technology could be used to accurately subtype these tumors. Further paired-end sequencing of these samples and additional tumors is ongoing. Subsequent analyses of these data include identifying gene fusions, mutations, alternative splicing, noncoding RNAs, novel transcribed regions, and potential viral genomes.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4858. doi:10.1158/1538-7445.AM2011-4858

Abstract PD01-08: Decoding the Transcriptional Landscape of Triple-Negative Breast Cancer Using Next-Generation Whole Transcriptome Sequencing

Background: Triple-negative breast cancer (TNBC) has been plagued by the absence of targeted therapies. Discovery of therapeutic targets in TNBC has in part, been hampered by an inadequate understanding of the transcriptional biology of the normal breast as an optimal comparator. Using next-generation sequencing, we embarked on a study to compare the transcriptomes of TNBC and normal breast to comprehensively identify novel targets by analyzing all full length transcripts expressed in these tissues.

Methods: Normal breast tissues from healthy pre-menopausal volunteers with no history of disease were procured from the Susan G. Komen for the Cure® Tissue Bank at the IU Simon Cancer Center. To eliminate bias from stromal tissue, normal tissues were laser capture microdissected for ductal epithelium. cDNA libraries from 10 TNBC tumors and 10 normal breast tissues were sequenced on an Applied Biosystems (AB) SOLiD3 sequencer using 50bp fragment runs. For gene expression, mapping of reads to the genome was performed using the AB BioScope 1.2 Pipeline and outputs imported into Partek Genomics Suite for analysis. In Partek, mapped reads were cross-referenced against known genes from the UCSC database followed by statistical comparison of RPKM values for each gene between TNBC and normal. Dimensionality reduction analyses (PCA & Hierarchical clustering) and identification of Novel Transcribed Regions were also performed in Partek, whereas construction of gene networks was performed using Ingenuity Pathway Analysis. To identify gene fusions, partially mapped reads were interrogated utilizing a novel algorithm that searched for reads spanning exons from two different genes. Fusions that were supported by at least 3 reads (of which 2 had to be unique) were considered candidates and were subsequently validated. Results/Discussion: Sequencing produced 1.1 billion reads equaling 57.3GB of data of which 36.0GB (63%) mapped to the human genome. In comparing RPKM values between TNBC and Normal, we report 7140 RefSeq Genes, 22 pre-miRNAs, 109 lincRNA exons, and 15 ultraconserved regions that were differentially expressed between these tissues (FDR<0.01). Biological interpretation of these results reveals upregulation of genes and miRNAs involved in DNA repair, angiogenesis, and inhibitors of Estrogen Receptor-alpha. Some previous drug targets (e.g. EGFR and c-kit) were not found to be upregulated here which may explain lack of clinical success to date. Conversely, PARP was significantly upregulated and early trial results suggest a strong signal for efficacy with inhibition of PARP. We also surveyed the genome for Novel Transcribed Regions (NTRs), defined as areas of significant transcription where no annotated gene is present. When comparing between TNBC and Normal, we report 6408 NTRs to be differentially expressed (FDR<0.01). Lastly, when analyzing the dataset for gene fusions, we identified several gene fusions in the TNBC samples, though no individual fusion was present in more than one sample.

Conclusion: We report an extensive comparison of the transcriptomes of TNBC and normal ductal epithelium. We identified numerous genes previously unknown to be dysregulated in TNBC that can be utilized for therapeutic discovery.

Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr PD01-08.

Abstract 2216: Next-generation whole transcriptome sequencing of triple-negative breast tumors and normal tissues

Background: Triple-negative breast cancer (TNBC) disproportionally affects pre-menopausal women and women of African-American descent, and has been plagued by the absence of targeted therapies leading to poor survival. The paucity of therapeutic targets in TNBC impels us to utilize new technologies that can determine novel targets on a global scale. Using next-generation sequencing, we embarked on a study to analyze the whole transcriptomes of TNBC tumors compared to normal breast tissues in order to comprehensively identify novel targets by analyzing all full length transcripts expressed in these tissues.

Methods: Normal breast tissues from healthy pre-menopausal volunteers with no history of disease were procured from the Susan G. Komen for the Cure® Tissue Bank at the IU Simon Cancer Center. To eliminate bias from stromal tissue, epithelial cells were laser capture microdissected and RNA extracted from captured cells. cDNA libraries from 10 TNBC tumors and 10 normal breast tissues were subsequently sequenced on an ABI SOLiD3 sequencer using a 50bp fragment run. For gene expression, mapping of reads to the human genome was performed using the ABI Whole Transcriptome Pipeline and outputs were imported into Partek Genomics Suite for analysis. To analyze for gene fusions, reads were mapped to the genome using the SOLiD Analysis Pipeline Tool, followed by an alignment to Refseq to map reads crossing exon-exon junctions. A composite transcriptome was formed from areas of the genome with significant expression (17% of the genome sequence) and served as a concise search space for identifying fusions. Reads not mapping to the genome or to RefSeq (a rich source of fusion reads) were then mapped to the composite transcriptome using BLAT to facilitate a highly accurate split-read alignment. Using a custom developed pipeline, reads that spanned transcribed regions from two different chromosomes, or to loci farther than 200kb apart on the same chromosome, were considered as candidate fusions.

Results/Discussion: Sequencing of the 10 TNBC tumors and 10 normal samples produced 1.1 billion reads equaling 58.15GB of data. Mapping of the reads to the genome revealed 1.6 million transcribed regions (exons) of significant expression. A preliminary analysis of gene expression shows 55.2% of the transcribed loci to have significant differential expression between tumor and normal. Network-node, non-coding RNA, and statistical analyses are currently ongoing. In a further interim analysis, we bioinformatically identified several interchromosomal fusions that were present in a majority of the tumors but were absent in the normal samples. RT-PCR validation of these candidate fusions in a larger validation cohort of TNBC tumors and normal breast tissues is ongoing. A multitude of additional analyses including but not limited to: novel transcripts, alternative splicing, and presence of viral genes are also planned.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2216.

Next-Generation Whole Transcriptome Sequencing of Triple-Negative Breast Tumors and Normal Tissues

Background: Triple-negative breast cancer predominately affects pre-menopausal women and women of African-American descent and has been plagued by the absence of targeted therapies leading to poor survival. Using a new cutting edge technology, next-generation sequencing, we embarked on a study to analyze the whole transcriptomes of triple-negative tumors and normal tissues from pre-menopausal women in order to comprehensively identify new targets by analyzing all full length transcripts expressed in these tissues. This approach is independent of pre-determined gene selection as is common with microarrays, and allows for the analysis of RNA species that have not been previously profiled in breast cancer.Methods: cDNA libraries were created from RNA isolated from 8 triple-negative tumors and 2 normal breast tissues. Triple negative tumors were procured from Origene Technologies and normal breast tissues were procured from the Susan G. Komen for the Cure tissue bank at Indiana University. Normal samples were from healthy pre-menopausal volunteers with no history of disease. In order to eliminate bias from stromal tissue, normal samples were laser capture microdissected for ductal cells and RNA extracted from the excised tissue. cDNA libraries were prepared and subsequently sequenced on an Applied Biosystems (ABI) SOLiD3 sequencer using a 50bp fragment run. Mapping of whole reads to the human genome was performed using the SOLiD Analysis Pipeline Tool software (ABI) followed by a split-read alignment in order to map reads crossing exon-exon junctions. Gene expression profiles for each sample were then created and statistically compared to identify the most differentially expressed genes. In order to analyze for fusion genes, a split-read alignment of non-mapping reads to a composite transcriptome formed from previously mapped reads (clusters) was performed.Results: Sequencing of the 10 samples produced 513 million filtered reads equaling 25.66GB of data. Mapping of the reads to the genome revealed 1.14 million transcribed regions (exons). A preliminary analysis of gene expression shows 55.2% of the transcribed loci to have significant differential expression between tumor and normal. In a further analysis for gene fusions, several candidate fusions were bioinformatically detected. These are currently being reviewed and validated.Discussion: Herein we present a preliminary analysis of the transcriptomes of triple-negative breast cancers in comparison to normal tissues. A multitude of analyses are ongoing, including but not limited to: gene fusions, differentially expressed novel genes, novel transcripts, alternative splicing, intrinsic subtyping, and presence of viral genes. In addition 2 more triple-negative tumors and 8 normal samples will also be sequenced. In the current analysis, differentially expressed non-coding RNAs was highly pervasive among the samples indicating a major role of this RNA species in tumorigenesis. In addition, triple-negative breast cancers may contain fusion genes that could be “drivers” of this malignancy. Further validation of these differentially expressed RNAs and fusion genes in a larger set of samples with subsequent functional studies is planned.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 6134.

The value of avian genomics to the conservation of wildlife

Background

Genomic studies in non-domestic avian models, such as the California condor and white-throated sparrow, can lead to more comprehensive conservation plans and provide clues for understanding mechanisms affecting genetic variation, adaptation and evolution.

Developing genomic tools and resources including genomic libraries and a genetic map of the California condor is a prerequisite for identification of candidate loci for a heritable embryonic lethal condition. The white-throated sparrow exhibits a stable genetic polymorphism (i.e. chromosomal rearrangements) associated with variation in morphology, physiology, and behavior (e.g., aggression, social behavior, sexual behavior, parental care).

In this paper we outline the utility of these species as well as report on recent advances in the study of their genomes.

Results

Genotyping of the condor resource population at 17 microsatellite loci provided a better assessment of the current population's genetic variation. Specific New World vulture repeats were found in the condor genome. Using condor BAC library and clones, chicken-condor comparative maps were generated. A condor fibroblast cell line transcriptome was characterized using the 454 sequencing technology.

Our karyotypic analyses of the sparrow in combination with other studies indicate that the rearrangements in both chromosomes 2^m and 3^a are complex and likely involve multiple inversions, interchromosomal linkage, and pleiotropy. At least a portion of the rearrangement in chromosome 2^m existed in the common ancestor of the four North American species of Zonotrichia, but not in the one South American species, and that the 2^m form, originally thought to be the derived condition, might actually be the ancestral one.

Conclusion

Mining and characterization of candidate loci in the California condor using molecular genetic and genomic techniques as well as linkage and comparative genomic mapping will eventually enable the identification of carriers of the chondrodystrophy allele, resulting in improved genetic management of this disease.

In the white-throated sparrow, genomic studies, combined with ecological data, will help elucidate the basis of genic selection in a natural population. Morphs of the sparrow provide us with a unique opportunity to study intraspecific genomic differences, which have resulted from two separate yet linked evolutionary trajectories. Such results can transform our understanding of evolutionary and conservation biology.

Evolutionary toggling of the MAPT 17q21.31 inversion region

Using comparative sequencing approaches, we investigated the evolutionary history of the European-enriched 17q21.31 MAPT inversion polymorphism. We present a detailed, BAC-based sequence assembly of the inverted human H2 haplotype and compare it to the sequence structure and genetic variation of the corresponding 1.5-Mb region for the noninverted H1 human haplotype and that of chimpanzee and orangutan. We found that inversion of the MAPT region is similarly polymorphic in other great ape species, and we present evidence that the inversions occurred independently in chimpanzees and humans. In humans, the inversion breakpoints correspond to core duplications with the LRRC37 gene family. Our analysis favors the H2 configuration and sequence haplotype as the likely great ape and human ancestral state, with inversion recurrences during primate evolution. We show that the H2 architecture has evolved more extensive sequence homology, perhaps explaining its tendency to undergo microdeletion associated with mental retardation in European populations.

Genome analysis of the platypus reveals unique signatures of evolution

We present a draft genome sequence of the platypus, Ornithorhynchus anatinus. This monotreme exhibits a fascinating combination of reptilian and mammalian characters. For example, platypuses have a coat of fur adapted to an aquatic lifestyle; platypus females lactate, yet lay eggs; and males are equipped with venom similar to that of reptiles. Analysis of the first monotreme genome aligned these features with genetic innovations. We find that reptile and platypus venom proteins have been co-opted independently from the same gene families; milk protein genes are conserved despite platypuses laying eggs; and immune gene family expansions are directly related to platypus biology. Expansions of protein, non-protein-coding RNA and microRNA families, as well as repeat elements, are identified. Sequencing of this genome now provides a valuable resource for deep mammalian comparative analyses, as well as for monotreme biology and conservation.

Gallus GBrowse: a unified genomic database for the chicken

Gallus GBrowse (http://birdbase.net/cgi-bin/gbrowse/gallus/) provides online access to genomic and other information about the chicken, Gallus gallus. The information provided by this resource includes predicted genes and Gene Ontology (GO) terms, links to Gallus In Situ Hybridization Analysis (GEISHA), Unigene and Reactome, the genomic positions of chicken genetic markers, SNPs and microarray probes, and mappings from turkey, condor and zebra finch DNA and EST sequences to the chicken genome. We also provide a BLAT server (http://birdbase.net/cgi-bin/webBlat) for matching user-provided sequences to the chicken genome. These tools make the Gallus GBrowse server a valuable resource for researchers seeking genomic information regarding the chicken and other avian species.

Evolutionary and biomedical insights from the rhesus macaque genome

The rhesus macaque (Macaca mulatta) is an abundant primate species that diverged from the ancestors of Homo sapiens about 25 million years ago. Because they are genetically and physiologically similar to humans, rhesus monkeys are the most widely used nonhuman primate in basic and applied biomedical research. We determined the genome sequence of an Indian-origin Macaca mulatta female and compared the data with chimpanzees and humans to reveal the structure of ancestral primate genomes and to identify evidence for positive selection and lineage-specific expansions and contractions of gene families. A comparison of sequences from individual animals was used to investigate their underlying genetic diversity. The complete description of the macaque genome blueprint enhances the utility of this animal model for biomedical research and improves our understanding of the basic biology of the species.

An ORFeome-based analysis of human transcription factor genes and the construction of a microarray to interrogate their expression

Transcription factors (TFs) are essential regulators of gene expression, and mutated TF genes have been shown to cause numerous human genetic diseases. Yet to date, no single, comprehensive database of human TFs exists. In this work, we describe the collection of an essentially complete set of TF genes from one depiction of the human ORFeome, and the design of a microarray to interrogate their expression. Taking 1468 known TFs from TRANSFAC, InterPro, and FlyBase, we used this seed set to search the ScriptSure human transcriptome database for additional genes. ScriptSure's genome-anchored transcript clusters allowed us to work with a nonredundant high-quality representation of the human transcriptome. We used a high-stringency similarity search by using BLASTN, and a protein motif search of the human ORFeome by using hidden Markov models of DNA-binding domains known to occur exclusively or primarily in TFs. Four hundred ninety-four additional TF genes were identified in the overlap between the two searches, bringing our estimate of the total number of human TFs to 1962. Zinc finger genes are by far the most abundant family (762 members), followed by homeobox (199 members) and basic helix-loop-helix genes (117 members). We designed a microarray of 50-mer oligonucleotide probes targeted to a unique region of the coding sequence of each gene. We have successfully used this microarray to interrogate TF gene expression in species as diverse as chickens and mice, as well as in humans.

UTR reconstruction and analysis using genomically aligned EST sequences

Untranslated regions (UTR) play important roles in the posttranscriptional regulation of mRNA processing. There is a wealth of UTR-related information to be mined from the rapidly accumulating EST collections. A computational tool, UTR-extender, has been developed to infer UTR sequences from genomically aligned ESTs. It can completely and accurately reconstruct 72% of the 3' UTRs and 15% of the 5' UTRs when tested using 908 functionally cloned transcripts. In addition, it predicts extensions for 11% of the 5' UTRs and 28% of the 3' UTRs. These extension regions are validated by examining splicing frequencies and conservation levels. We also developed a method called polyadenylation site scan (PASS) to precisely map polyadenylation sites in human genomic sequences. A PASS analysis of 908 genic regions estimates that 40-50% of human genes undergo alternative polyadenylation. Using EST redundancy to assess expression levels, we also find that genes with short 3' UTRs tend to be highly expressed.