Abstract PD05-09: Whole-genome progression of breast cancer from early neoplasia to invasive carcinoma

Cancer evolution involves cycles of genomic damage, epigenetic deregulation, and increased cellular proliferation that eventually culminate in the carcinoma phenotype. Early breast neoplasias include usual ductal hyperplasia, columnar cell lesions, and flat epithelial atypia and some are thought to represent precursor stages. To elucidate their role in cancer evolution we performed comparative whole genome sequencing of early neoplasias, matched normal tissue, and carcinomas from six patients. The identified somatic mutations served as lineage markers to build trees that relate the tissue samples. On the basis of the lineage trees we inferred the order, timing, and rates of mutational events. We find that in a subset of cases, the last common ancestor of an early neoplasm and a carcinoma was hypermutated and had several aneuploidies, and that evolution further accelerated in the carcinoma lineage. In contrast to highly advanced tumors that are the focus of much of current cancer genome sequencing, the early neoplasia genomes, and the carcinomas as well, harbor a striking paucity of potentially functional somatic point mutations. The earliest significant events we could detect, those changes that occurred in common ancestors of neoplastic and tumor cells, are aneuploidies. Several aneuploidies are recurrent, suggesting that they are among the earliest genomic events that predispose breast tissue to eventual development of invasive carcinoma.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr PD05-09.

Partitioning of tissue expression accompanies multiple duplications of the Na+/K+ ATPase alpha subunit gene

Vertebrate genomes contain multiple copies of related genes that arose through gene duplication. In the past it has been proposed that these duplicated genes were retained because of acquisition of novel beneficial functions. A more recent model, the duplication-degeneration-complementation hypothesis (DDC), posits that the functions of a single gene may become separately allocated among the duplicated genes, rendering both duplicates essential. Thus far, empirical evidence for this model has been limited to the engrailed and sox family of developmental regulators, and it has been unclear whether it may also apply to ubiquitously expressed genes with essential functions for cell survival. Here we describe the cloning of three zebrafish alpha subunits of the Na(+),K(+)-ATPase and a comprehensive evolutionary analysis of this gene family. The predicted amino acid sequences are extremely well conserved among vertebrates. The evolutionary relationships and the map positions of these genes and of other alpha-like sequences indicate that both tandem and ploidy duplications contributed to the expansion of this gene family in the teleost lineage. The duplications are accompanied by acquisition of clear functional specialization, consistent with the DDC model of genome evolution.

A double-deletion mutation in the Pitx3 gene causes arrested lens development in aphakia mice

The recessive aphakia (ak) mouse mutant is characterized by bilateral microphthalmia due to a failure of lens morphogenesis. We fine-mapped the ak locus to the interval between D19Umi1 and D19Mit9, developed new polymorphic markers, and mapped candidate genes by construction of a BAC contig. The Pitx3 gene, known to be expressed in lens primordia, shows zero recombination with the ak mutation on our intersubspecific intercross panel representing 1170 meioses. A recent report described a deletion in the intergenic region between Gbf1 and Pitx3 as the possible ak mutation. Our results differ in that we find not only the distant intergenic deletion, but also a much larger deletion directly in the Pitx3 gene, eliminating exon 1 and extending into intron 1 and the promoter region. Pitx3 transcript levels are severely reduced in ak/ak mice from E11.5 to newborn (5 +/- 1% of the wildtype levels at E13.5), while an involvement of the flanking Gbf1 and Cig30 genes in the aberrant lens development is highly unlikely based on expression analysis. We conclude that the ak mutation consists of two deletions, the larger of which removes part of Pitx3, indicating a crucial role of this gene in early lens development.

A novel member of the F-box/WD40 gene family, encoding dactylin, is disrupted in the mouse dactylaplasia mutant

Early outgrowth of the vertebrate embryonic limb requires signalling by the apical ectodermal ridge (AER) to the progress zone (PZ), which in response proliferates and lays down the pattern of the presumptive limb in a proximal to distal progression. Signals from the PZ maintain the AER until the anlagen for the distal phalanges have been formed. The semidominant mouse mutant dactylaplasia (Dac) disrupts the maintenance of the AER, leading to truncation of distal structures of the developing footplate, or autopod. Adult Dac homozygotes thus lack hands and feet except for malformed single digits, whereas heterozygotes lack phalanges of the three middle digits. Dac resembles the human autosomal dominant split hand/foot malformation (SHFM) diseases. One of these, SHFM3, maps to chromosome 10q24 (Refs 6,7), which is syntenic to the Dac region on chromosome 19, and may disrupt the orthologue of Dac. We report here the positional cloning of Dac and show that it belongs to the F-box/WD40 gene family, which encodes adapters that target specific proteins for destruction by presenting them to the ubiquitination machinery. In conjuction with recent biochemical studies, this report demonstrates the importance of this gene family in vertebrate embryonic development.

Serrate2 is disrupted in the mouse limb-development mutant syndactylism

The mouse syndactylism (sm) mutation impairs some of the earliest aspects of limb development and leads to subsequent abnormalities in digit formation. In sm homozygotes, the apical ectodermal ridge (AER) is hyperplastic by embryonic day 10.5, leading to abnormal dorsoventral thickening of the limb bud, subsequent merging of the skeletal condensations that give rise to cartilage and bone in the digits, and eventual fusion of digits. The AER hyperplasia and its effect on early digital patterning distinguish sm from many other syndactylies that result from later failure of cell death in the interdigital areas. Here we use positional cloning to show that the gene mutated in sm mice encodes the putative Notch ligand Serrate. The results provide direct evidence that a Notch signalling pathway is involved in the earliest stages of limb-bud patterning and support the idea that an ancient genetic mechanism underlies both AER formation in vertebrates and wing-margin formation in flies. In addition to cloning the sm gene, we have mapped three modifiers of sm, for which we suggest possible candidate genes.

Gen(om)e duplications in the evolution of early vertebrates

Phylogenetic analyses and sequence surveys of developmental regulator gene families indicate that two large-scale gene duplications, most likely genome duplications, occurred in ancestors of vertebrates. Relaxed constraints allowed duplicated and thus redundant genes to diverge in a two stage mechanism. Neutral changes dominated at first but then positively selected regulatory changes evolved the novel and increasingly complex vertebrate developmental program.

A molecular evolutionary framework for eukaryotic model organisms

BACKGROUND

Implicit in the characterization of a model organism is the hope that insights into its biology can be extended to other species. For this hope to be fulfilled, the phylogenetic position of the model organism within a larger evolutionary framework must be known. We focus here on major model organisms of developmental genetics and cell biology. We first consider the positions of the nematode Caenorhabditis elegans and the arthropod Drosophila melanogaster within a phylogeny of the major advanced metazoan groups. Then we consider the evolutionary relationships between fungi (represented by Saccharomyces cerevisiae and Schizosaccharomyces pombe), plants, and animals.

RESULTS

We show, by a direct comparison with small subunit ribosomal RNA (18 S rRNA), that RNA polymerase II is an appropriate molecule for addressing the phylogenetic branchings in the early evolution of eukaryotes. The results from the analyses of newly determined and previously published sequences of the two largest subunits of RNA polymerase II suggest the following. Firstly, that plants and animals share a last common ancestor that excludes fungi, the lineage of which originated earlier. Secondly, that the lineage leading to the nematode Caenorhabditis elegans diverged earlier from the Metazoa than the lineages of arthropods, deuterostomes, annelids and molluscs. Finally, that deuterostomes arose from within protostomes.

CONCLUSIONS

RNA polymerase II is well-suited for the elucidation of the evolutionary relationships among eukaryotes. We emphasize the implications of our results for other biological disciplines in addition to molecular evolution, as a phylogenetic framework allows predictions and inferences to be made about the existence of fundamental biological mechanisms elucidated in model organisms.

Early evolution of photosynthesis: clues from nitrogenase and chlorophyll iron proteins

Chlorophyll (Chl) is often viewed as having preceded bacteriochlorophyll (BChl) as the primary photoreceptor pigment in early photosynthetic systems because synthesis of Chl requires one fewer enzymatic reduction than does synthesis of BChl. We have conducted statistical DNA sequence analyses of the two reductases involved in Chl and BChl synthesis, protochlorophyllide reductase and chlorin reductase. Both are three-subunit enzymes in which each subunit from one reductase shares significant amino acid identity with a subunit of the other, indicating that the two enzymes are derived from a common three-subunit ancestral reductase. The "chlorophyll iron protein" subunits, encoded by the bchL and bchX genes in the purple bacterium Rhodobacter capsulatus, also share amino acid sequence identity with the nitrogenase iron protein, encoded by nifH. When nitrogenase iron proteins are used as outgroups, the chlorophyll iron protein tree is rooted on the chlorine reductase lineage. This rooting suggests that the last common ancestor of all extant photosynthetic eubacteria contained BChl, not Chl, in its reaction center, and implies that Chl-containing reaction centers were a late invention unique to the cyanobacteria/chloroplast lineage.

Estimating the fraction of invariable codons with a capture-recapture method

A codon-based approach to estimating the number of variable sites in a protein is presented. When first and second positions of codons are assumed to be replacement positions, a capture-recapture model can be used to estimate the number of variable codons from every pair of homologous and aligned sequences. The capture-recapture estimate is compared to a maximum likelihood estimate of the number of variable codons and to previous approaches that estimate the number of variable sites (not codons) in a sequence. Computer simulations are presented that show under which circumstances the capture-recapture estimate can be used to correct biases in distance matrices. Analysis of published sequences of two genes, calmodulin and serum albumin, shows that distance corrections that employ a capture-recapture estimate of the number of variable sites may be considerably different from corrections that assume that the number of variable sites is equal to the total number of positions in the sequence.

Diversification of the Wnt gene family on the ancestral lineage of vertebrates

Diversification of the Wnt genes, a family of powerful developmental regulator molecules, is inferred by molecular evolutionary analyses. Fifty-five recently determined partial sequences from a variety of vertebrates and invertebrates, together with 17 published sequences, mostly from the mouse and Drosophila melanogaster, are analyzed. Wnt-1 through -7 originated before the last common ancestor of arthropods and deuterostomes lived. Another round of gene duplication, involving Wnt-3, -5, -7, and -10, occurred after the echinoderm lineage arose, on the ancestral lineage of jawed vertebrates. Increased constraints were imposed on the Wnt genes when jawed vertebrates originated, as indicated by an overall 4-fold lower rate of amino acid replacements in jawed vertebrates compared with invertebrates and jawless vertebrates. The Wnt genes are thus inferred to have undergone a disproportionately high amount of structural and functional evolution in the relatively short time (approximately 100 million years) between the origin of the echinoderm lineage and the first diversification of jawed vertebrates. A model is presented for the relationship of functional diversification of developmental regulators and their rates of amino acid replacement.

Molecular phylogeny

The avalanche of molecular sequence data from a wide variety of organisms and genes makes the construction and testing of evolutionary trees a widespread and demanding activity. We present the most recent advances in the interpretation of molecular data, as well as recent phylogenetic results affecting both molecular evolutionary biology and other areas of biological research.

Bacterial DNA in Clarkia fossils

For the growing number of investigators who study ancient DNA, the most stimulating paper published during 1990 reported the determination of a chloroplast DNA sequence from a plant compression fossil found in a Miocene deposit at Clarkia, Idaho (Golenberg et al. 1990). During August 1990, S.P. took part in an excavation at the Clarkia site organized by Dr C. J. Smiley of the Tertiary Research Center, University of Idaho. Analysis of extracts prepared from the plant remains shows that the high molecular mass (HMM) DNA that can be detected in some extracts from Clarkia fossils is mostly, if not exclusively, of bacterial origin. Further work aimed at the retrieval of plant sequences from these remains should therefore not be confined to extracts where HMM DNA is seen.

Compositional statistics: an improvement of evolutionary parsimony and its application to deep branches in the tree of life

We present compositional statistics, a new method of phylogenetic inference, which is an extension of evolutionary parsimony. Compositional statistics takes account of the base composition of the compared sequences by using nucleotide positions that evolutionary parsimony ignores. It shares with evolutionary parsimony the features of rate invariance and the fundamental distinction between transitions and transversions. Of the presently available methods of phylogenetic inference, compositional statistics is based on the fewest and mildest assumptions about the mode of DNA sequence evolution. It is therefore applicable to phylogenetic studies of the most distantly related organisms or molecules. This was illustrated by analyzing conservative positions in the DNA sequences of the large subunit of RNA polymerase from three archaebacterial groups, a eubacterium, a chloroplast, and the three eukaryotic polymerases. Internally consistent results, which are in accord with our knowledge of organelle origin and archaebacterial physiology, were achieved.