With about 1 in 8 women in the United States expected to develop breast cancer in their lifetime, breast cancer remains the most common malignancy in women. Though heavily studied, its complexity creates significant challenges to diagnosis, prognosis, and treatment. One of the major problems is that causal DNA mutations of the disease vary from case to case. Human breast cancer falls into four major molecular subtypes (luminal A and B, HEWithR2-enriched, and basal-like), and these subtypes are associated with significant differences in prognosis and survival.

In the December issue of GENETICS, Li et al. explored the possibility that overarching gene regulatory mechanisms modulate the varying pathways of the four major breast cancer subtypes.

The researchers used publicly available sequencing, gene expression, and clinical data collected from over 3,000 human breast cancer cases across three cohorts.  To this data, they applied the methods of machine learning, a powerful tool for selecting a small number of genes that can discriminate tumor samples into the four subtypes, and mutual information modeling, a method to accurately capture nonlinear interactions between regulators and their regulons .

They identified 16 master regulator genes (MR16) that shape different tumor subtypes. The master regulators are transcription factor genes that play a pivotal role in modulating downstream pathways or gene networks. Gene expression patterns from all three cohorts indicated that the MR16 can be divided into two groups that regulate cancer-related genes in opposite directions. For example, one group up-regulates cell cycle gene expression in only the HER2-enriched and the basal-like subtypes. Conversely, another group of the MR16 down-regulates cell cycle gene expression in those same subtypes. These results reveal a gene regulatory program that affects tumor progression in breast cancer.

Li et al. also sought to associate DNA mutations with gene regulatory pathway changes in tumor subtypes. They found an association of mutations of the gene TP53 with the previously described upregulation of cell cycle pathways in HER2-enriched and basal-like subtypes. This suggests that cell cycle pathway changes may be the characteristic genomic changes in the two subtypes, which opens a potential avenue to design new therapies.

Taken together, these findings help clarify gene regulatory programs in breast cancer, bringing us closer to using precision medicine to treat this complex disease.

CITATION

Li, R., Campos, J. & Iida, J. (2015) A Gene Regulatory program in Human Breast Cancer. Genetics, 201(4), 1341-1348. doi:10.1534/genetics.115.180125

http://www.genetics.org/content/201/4/1341

What if we could eradicate malaria by engineering a mosquito population that doesn’t transmit the disease? What if we could control invasive species that outcompete natural populations? What if we could get rid of insecticide-resistant pests not by developing new chemical treatments, but instead by changing the population itself and driving it toward extinction?

Although scientists have long-imagined the potential of biological interventions to solve challenges like these, the ability of the CRISPR/Cas9 system to precisely edit genetic material, coupled with gene drive systems, offers a hope of success that’s within reach. But this potential gain also carries potential risks.

Much of the increasing attention to gene drive, including recent news coverage, has raised questions about whether these constructs can have their desired effect without simultaneously causing ecological harm.

A new report from Unckless et al. in the October issue of GENETICS builds on recent experimental work being carried out in the field by using mathematical models to estimate how quickly such gene replacement can spread through a population.

Modeling several scenarios using a Wright-Fisher model as their foundation, Unckless et al. demonstrate that adding modified genes through the mutagenic chain reaction (MCR) can have dramatic effects, with these genes fixing in populations after only a few generations, much more quickly that they would as a result of natural selection. Moreover, gene drive allows the potential of a particular allele to spread through a population, even if there is selection operating against it. The efficiency of these methods allow effects of this biological control strategy to appear very quickly, which may prove extraordinarily effective. That very speed and efficiency, which on one hand would be beneficial, also brings some level of risk for unintended consequences that are difficult if not impossible to control.

“We need to consider the population dynamics of gene drive in designing these types of strategies,” emphasizes study author Rob Unckless. “The outcome will vary considerably based on the strength of drive, fitness consequences, and dominance, and other factors. This means that we can’t expect to insert any old mutation into any old site in the genome and expect that within tens of generations, the population will be fixed for that mutation.” But this result may be possible in some instances.

“We need to try these techniques in very limited scales – first cages then enclosures – to assess how it spreads,” said Unckless.

Unckless also suggests that modeling should be done with multiple constructs, including beneficial mutations, deleterious mutations, different conversion efficiencies, and rates of non-homologous end joining, among others. In their paper, Unckless and colleagues explain how the math meets the applied: this modeling of MCR population dynamics can both put bounds on the frequency trajectories expected from the release of an MCR, but it may also identify possible choke points for controlling and preventing the expansion of an escaped or mutated MCR allele in a natural population.

Although Unckless suggests there’s more work to be done to assess the potential and peril of gene drives, early indications suggest the possibility of dramatic effect.

CITATION:
Unckless, R.L., Messer, P.W., Connallon, T., & A.G. Clark. 2015. Modeling the Manipulation of Natural Populations by Mutagenic Chain Reaction. GENETICS, 201:425-431 doi:http://doi.org/10.1534/genetics.115.177592

The effects of neurodegenerative diseases can be devastating for patients and their families. In 2007, the United Nations stated that 1 in 6 people in the world are affected by neurological disorders including diseases like Huntington’s, Alzheimer’s, and amyotrophic lateral sclerosis (ALS). With over 600 characterized neurological disorders yet very few treatments, it is imperative that continued research efforts elucidate the mechanisms underlying these diseases in the hopes of developing targeted and effective treatments. As part of the FlyBook inaugural chapters published in the October issue of GENETICS, McGurk et al. put forth the fly as an in vivo model for human neurodegenerative disease and describe how the fly is a vital tool for providing mechanistic insight.

As most Biology 101 students can tell you, the fly has been a widely-used tool in biological research for over 100 years! Gene manipulation in Drosophila can be fast and relatively simple, and, with short generation times, fly lines are maintained with relative ease. Additionally, fly models offer unique advantages specific to studies of the nervous system, as the organism has a central nervous system that bears striking similarities to that of mammals, though is less complex.  The Drosophila genome is also much smaller than the human genome, allowing easier interpretation of results from gene manipulation studies.

McGurk et al. adds to previous reviews on the subject of fly models of neurodegenerative disease by focusing and describing select studies to emphasize the strengths of such approaches. To do this, McGurk et al. describe studies on polyQ diseases and ALS. PolyQ diseases, a group of diseases that include Huntington’s, are characterized by the expansion of a CAG trinucleotide repeat within the respective gene. Transgenic flies that express the expanded repeat mutation show neurodegenerative effects remarkably reminiscent to those seen in humans. These studies illustrate the power of fly to recapitulate human disease features, providing a system with which to elucidate causal genetic mechanisms.

ALS, also known as Lou Gehrig’s Disease, is the most prevalent of a group of motor neuron diseases that involve the death of neurons. Affecting as many as 30,000 Americans, ALS onsets in individuals as adults, impacting the spinal cord and leading to paralysis and, ultimately, death. For the most part, the cause of this tragic disease has been veiled in mystery for decades, but recent advances in identifying the genetic underpinnings of the disease have been facilitated by enhanced genomic technologies. These findings indicate that many genes related to the disease are involved in RNA biology, suggesting that such activities are involved in the pathology of the disease. Focusing on one such identified gene, TDP-43, McGurk et al. illustrate the power of fly models to investigate this disease. Fly studies for example, were critical for the identification of ATAXIN-2 as a gene that modifies, and consequently adjusts the toxicity of, TDP-43. Researchers proceeded to investigate this modifier and found that mutations in this gene were regularly found in ALS patient populations, characterizing it as a definitive ALS disease gene. This illustrates the impact of combining findings from model organisms with those of genetic analyses to expand our understanding of disease.

Although flies look quite different from humans, flies share a remarkable amount of similarity to mammalian neurodegenerative disease pathologies. The examples described by McGurk et al. illustrate the power of such models and the breadth of understanding that can come from them.  With the necessity for the development of therapeutics for the hundreds of neurological disorders looming, perhaps the solution is in approaches that combine the historic model system of the fruit fly with the sequencing innovations that develop further everyday.

CITATIONS:

McGurk, L., Berson A., & Bonini, N. 2015. Drosophila as an In Vivo Model for Human Neurodegenerative Disease. GENETICS, 201 (2): 377-402. doi:http://doi.org/10.1534/genetics.115.179457

Bilen, J., & Bonini, N. 2005. Drosophila as a Model for Human Neurodegenerative Disease. Annual Review of Genetics, 39:153-171. doi:http://doi.org/10.1146/annurev.genet.39.110304.095804

Over the last decade, advances in next-generation sequencing technology have given rise to many findings increasing our understanding of human disease and natural variation within species. Sequencing of the exome, the small fraction of the genome encompassing all exons of protein coding genes, has gained popularity as an inexpensive alternative to sequencing the entire genome. In a recent issue of G3, Warr et al. review details of the method of exome sequencing, its uses in humans and other species, and its potential benefits.

Researchers first used whole exome sequencing (WES) in a clinical setting only a few years ago. A 15-month-old male child presented with an inflammatory bowel disease, in a particularly rare form that stumped conventional diagnostic tools. A team of researchers used WES but were forced to analyze the sequencing data manually, as analytical software for WES had yet to be developed. Despite this impediment, the team was able to identify a variant that led to the proper diagnosis. This first success sparked the now-extensive clinical use of WES, proving particularly useful for difficult-to-diagnose cases, prenatal diagnosis, and identifying disease in young patients who have not yet exhibited full symptoms.  

While exome sequencing for humans has been used primarily to discover disease-related variants, the same technology has been applied to agricultural species to identify variants leading to unwanted phenotypes and mutations involved in traits relevant to efficient production. Plant genomes are often extremely complex, limiting the possibility of genome re-sequencing. As a result, many economically important crops like wheat and barley have seen very little genetic improvement. Recently, WES has been applied to wheat, soybean, rice, and barley, allowing researchers to identify variants involved in unwanted or desired phenotypes.

Despite the obvious utility of WES, several important considerations and limitations must be kept in mind. WES is dependent on a well-annotated genome. Without one, causative genes can be missed. This is a particularly important consideration for non-human species that may have incomplete reference genomes.

When comparing whether to use whole genome sequencing or whole exome sequencing, Warr et al. stress that researchers must consider the benefits of each. Even though the cost of whole genome sequencing is decreasing, WES remains significantly less pricey,  and allows researchers to sequence more samples and gain statistical power. Also, keep in mind that the development of technology for storing and analyzing the data produced by whole genome sequencing lags behind the sequencing technology itself. On the other hand, the data gleaned using WES is (in size) 100 times less than that of whole genome sequencing.

Compared to WES, whole genome sequencing covers the whole genome with more consistent coverage, does not have reference sequence bias, and provides more accurate detection of variants. Warr et al. state that while whole genome sequencing will inevitably take a leading role in sequencing studies, until storage and analytical tools catch up to handle the data produced, whole exome sequencing offers a positive ratio of cost:benefits well worth considering.

CITATION:

Warr, A., Robert, C., Hume, D., Archibald, A., Deeb, N. & M. Watson (2015). Exome Sequencing: Current and Future Perspectives. G3, 5(8), 1543-1550. http://doi.org/10.1534/g3.115.018564

A vast number of species depend on sexual reproduction for survival. Sex facilitates adaptation and rids populations of deleterious mutations. Despite the benefits of this process, sex can be remarkably costly and disrupt already advantageous genetic combinations. Only 20% of fungal species have been observed to reproduce sexually, and a long-standing mystery for researchers is whether a lack of observation indicates sex is truly absent or only infrequent.

Candida albicans is a commensal fungal species that is an opportunistic human pathogen — sometimes it lives benignly in the human digestive tract, and sometimes it causes deadly infections. Although this species can mate, mating has never been observed in isolates from humans. This observation is perplexing, considering that humans are thought to be the major habitat of the species. For C. albicans, sex is particularly costly, involving the loss of a chromosome, as well as a complex epigenetic switch. In the August issue of GENETICS, Zhang et al. explored whether mating was under selection, which would be expected if it is ultimately adaptive for this species.

In C. albicans, four genes at the MTL locus are required to mate. Zhang et al. determined if these genes maintained their function of controlling mating and if this function was under selection by comparing the number of nonsynonymous mutations to the number of synonymous mutations. They found the number of synonymous mutations greatly outnumbered nonsynonymous mutations, suggesting that genetic changes which interfere with gene function are minimized. This finding, in addition to evidence on the frequency of mutations that abolish mating, suggest that the process is under selection.

To be under selection, mating must generate progeny of increased fitness. Even if sexual reproduction is rare, significant fitness differences between progeny of sexual and asexual reproduction would allow the fitter genotypes to become more frequent over generations. By comparing growth rates in a novel environment of progeny of sexual reproduction with their ancestors, Zhang et al. show that mating produces fitter offspring, confirming the process is adaptive. Experiments in an animal model of commensal colonization indicated though that in the natural environment  the progeny of mating rarely survives in competition with the parents.

The genetic defects that are necessary for mating occur quite frequently in populations of C. albicans, and doom strains to extinction. Mating can potentially fix these defects and save these strains from extinction. The researchers therefore suggest that mating is not costly to the species at all, as it is restricted to these strains that would have been doomed regardless. This benefit to the species as a whole may explain why mating remains under selection for C. albicans.

CITATION:

Zhang, N., Magee, B. B., Magee, P. T., Holland, B. R., Rodrigues, E., Holmes, A. R., Cannon, R.D., & J. Schmid (2015). Selective Advantages of a Parasexual Cycle for the Yeast Candida albicans. Genetics, 200(4), 1117–32. http://doi.org/10.1534/genetics.115.177170

For Lake Whitefish, history has repeated itself. Across the St. John River region that spans Québec and Maine, these freshwater fish have continually evolved in the same way. Within the many individual lakes in this area, Lake Whitefish have diverged into two groups differentiated by size and body shape. These two groups, known as “dwarf” and “normal,” give geneticists a powerful model to study parallel evolution.

In the July issue of G3, Laporte et al. clarify the genetic mechanisms that underlie parallel phenotypic changes in these Lake Whitefish populations. Do parallel phenotypes indicate genetic parallelism, in which body shape in each population evolved via the same genetic mechanism? Or could such changes in morphology occur through multiple genetic routes?

In five different lakes, the authors found dwarf individuals had larger eyes, more slender bodies, and longer tails than their normal counterparts. Normal and dwarf Lake Whitefish use different ecological niches in each lake: normal species feed on benthos while dwarf species feed on zooplankton. The differences between the two morphological types of whitefish match the traits expected to be selected for by their given niches.

With phenotypic differences confirmed, the investigators next explored how many genes are involved in determining body shape. The authors identified 138 quantitative trait loci (QTL) underlying this variation, with each shape trait associated with an average of five QTL. This finding suggests many genes influence body shape, in line with the theory that rapid adaptation of complex traits involves simultaneous selection at many loci.

Then, the authors tested for genetic parallelism using a method that accounted for multiple genes involved in the trait. This method tested for selection on the identified QTL and revealed genetic parallelism in three of the five lakes. The remaining two lake populations each showed no evidence of genetic parallelism with the other lakes. This supports the conclusion that those three lake populations followed the same genetic routes as they diverged, while the other two each underwent unique mechanisms to reach the same phenotypic differentiation. Laporte et al. therefore conclude that both genetic parallelism and multiple genetic routes underlie the parallel evolution of body shape in the Lake Whitefish.

CITATION:

Laporte M, Rogers SM, Dion-Côté A-M, Normandeau E, Gagnaire P, Dalziel AC, Chebib J, Bernatchez L. (2015) RAD-QTL Mapping Reveals Both Genome-Level Parallelism and Different Genetic Architecture Underlying the Evolution of Body Shape in Lake Whitefish (Coregonus clupeaformis) Species Pairs. G3, 5(7): 1481-1491 doi:10.1534/g3.115.019067 http://www.g3journal.org/content/5/7/1481.full

Bdelloid rotifers have been veiled in mystery for decades. Despite extensive studies of this class of tiny freshwater invertebrates, no one has observed any trace of sex: no proven males, hermaphrodites, mating, or meiosis. Unlike other asexual organisms, which tend to be short-lived in evolutionary history, the apparently asexual bdelloid rotifers have managed to persist for millions of years and have diverged into hundreds of species. Such persistence without sexual reproduction challenges the view that sex is essential for the long-term evolutionary success of eukaryotes. Do these populations somehow avoid the accumulation of detrimental mutations thought to occur with asexual reproduction, or have we simply been investigating them under the wrong conditions?

A study by Signorovitch et al. published in the June issue of GENETICS sought to answer this question by using a method of population genetics that allowed the investigators to look for evidence of infrequent or atypical sex in bdelloid genomes.

By comparing genome sequences of individuals descended from a common ancestor, researchers are able to find clues to the population’s mode of reproduction. For any two individuals in an asexual population, the phylogenetic distance between a sequence in one individual and its homolog in the other should be the same for all such sequence pairs. That is because all the sequences in these individuals have been evolving independently of each other for the same number of generations. But if genetic material has been transferred between individuals in the population (as in sexual reproduction), two individuals may be closely related at one sequence, but more distantly related at its homolog. Signorovitch et al. searched for evidence of this phylogenetic pattern—called allele sharing— in the genomes of a species of bdelloid collected from geographically diverse sites.

The results clearly demonstrate that three of six individuals sampled from a mitochondrial clade show allele sharing consistent with sexual reproduction. At each of four genomic regions, a particular individual shared one of its alleles with a second individual and shared its other allele with a third individual. This suggests that genetic material was transferred between individuals via a cross.

Study species, Macrotrachela quadricornifera, and its eggs at right. Provided by Dr. Matthew Meselson

Finding three closely-related individuals in a small sample of geographically well-separated bdelloids suggests that lines that have experienced recent crossing have a fitness advantage over lines that have not, leading to the predominance of the prior. In support of this possibility, Signorovitch et al. cite a study indicating that the loss of sex in the water flea Daphnia pulex (which cycles between asexual and sexual reproduction) is followed by surprisingly rapid extinction. This is thought to be due to the effects of gene conversion, which allows the expression of accumulated recessive deleterious mutations. If bdelloids are also cyclically sexual, Signorovitch et al. propose, then descendents from recent outcrossing that restores heterozygosity would have enhanced fitness and become predominant in the sampled clade.

The evidence for sexual reproduction seems incompatible with previous work that concluded these organisms lack the homologous chromosome pairs needed for standard meiosis, a necessary process for sexual reproduction. The authors hypothesize that bdelloids may undergo a rare type of meiosis that can function without homologous chromosomes. Observed in plants of the Oenothera genus, this involves parental genomes segregating without assortment or crossing over. In other words, segregation is achieved without side-by-side chromosome pairing and without assortment or crossing over, enabling chromosomes of the same parentage to stay together generation after generation.

Signorovitch et al. discovered that a population previously thought to evolve without sex does in fact experience a unique form of sexual exchange. While these organisms remain enigmatic, the authors provide a glimpse into how bdelloid rotifers may have persisted through time.

CITATIONS:

Signorovitch, A., J. Hur, E. Gladyshev & M. Meselson (2015). Allele Sharing and Evidence for Sexuality in a Mitochondrial Clade of Bdelloid Rotifers, Genetics, 200(2), 581-590. doi: http://dx.doi.org/10.1534/genetics.115.176719 http://www.genetics.org/content/200/2/581.full

Tucker, A. E., M. S. Ackerman, B. D. Eads, S. Xu, and M. Lynch (2013) Population-genomic insights into the evolutionary origin and fate of obligately asexual Daphnia pulex. Proc. Natl. Acad. Sci. USA 110: 15740–15745 http://dx.doi.org/10.1073/pnas.1313388110

Umen, J. G (2015) Lost and Found: The Secret Sex Lives of Bdelloid Rotifers, Genetics, 200(2), 409-412, doi: http://dx.doi.org/10.1534/genetics.115.176388  http://www.genetics.org/content/200/2/409.short?rss=1