Gary Churchill
Senior Editor

Gary A. Churchill received his SB degree in Mathematics from Massachusetts Institute of Technology in 1983 and PhD in Biostatistics in 1988 from the University of Washington, Seattle. He is currently Professor and the Karl Gunnar Johannsen Chair in Computational Biology at the Jackson Laboratory. Churchill’s research addresses statistical applications in genetics and molecular biology. He has played a central role in the establishment of genetics resources including the Collaborative Cross and Diversity Outbred mouse populations. He is co-director of the JAX Center for Aging Research. He was chosen as a 2019 Fellow of the American Association for the Advancement of Science for his contributions to the field of systems genetics to study aging and metabolic disease.

Why Publish in G3: Genes|Genomes|Genetics?

Beatriz Vicoso
Associate Editor, Empirical Population and Evolutionary Genetics

Beatriz Vicoso is an evolutionary biologist with a broad interest in how and why genomes change over time. Her research has focused on the evolution of sex chromosomes, such as the X and Y of fruit flies and mammals or the Z and W of birds and butterflies. During her PhD in Brian Charlesworth’s lab at the University of Edinburgh, she compared how genes evolve on the X and other chromosomes of the model organism Drosophila. During her postdoc in Doris Bachtrog’s lab at University of California, Berkeley and since 2015 in her own group at the Institute of Science and Technology Austria, she has examined the genome sequence and gene expression of various model and non-model organisms, and Vicoso has used them to investigate the origin and diversity of sex chromosomes on a broad phylogenetic scale.

Why publish in GENETICS?

GSA’s new audio interview series is designed to help you discover and share interesting perspectives from the genetics community—even when you only have five minutes to spare.

The excitement of science is meant to be shared.

What if you could hear scientists share—in their own words—the value of their work using yeast, flies, worms, and other genetic research organisms?

What if, at the same time, you would gain insights into some very cool biology and inspiration to talk even more about your own work to broader audiences? 

What if you could do all this by just grabbing a snippet—a few minutes here and there between running a gel or going to a seminar? 

And, what if you could share these short snippets with friends and family outside science (you know, the ones who don’t get that “fruit fly obsession”), so they glimpse why this kind of work is so important? After all, people outside science may want to know how science discoveries are made and how discoveries might benefit them, even if the endpoints of the research are not totally obvious from the get-go.

GSA is thrilled to introduce SNPets. 

Join me and our genetics colleagues—Nobel Prize winners, GSA leaders, and other scientists making breakthrough discoveries—as they discuss the sometimes-twisty roads to their discoveries, how their research organisms made it all possible, and what the scientific community means to them. 

Got a minute? Check out a SNPet for a quick pop of inspiration. 

GSA President Hugo Bellen announces a new seminar series on tools and resources for exploring gene function across organisms. 

Some of us are worried about the future of the research enterprise, especially funding support for science in our favorite model organism. Why worry? One of the main drivers of this concern is that some believe our work is not directly relevant to human biology. This is often based on the idea it is difficult to quickly translate basic discoveries into directly applicable medical paradigms. Yet, the model organisms that many of us study have been the driving force for most biomedical discoveries. More than 90% of the Nobel prizes in Medicine or Physiology in the past 40 years have been awarded for research carried out in model organisms such as mice, rats, Xenopus, worms, and flies. These include the discovery of monoclonal antibodies (mouse), RNAi technology (worms), CRISPR technology (bacteria), cell cycle and cancer (yeast), signaling pathways, and development (flies), and so many others. Such discoveries in fundamental biology have propelled advances in medicine, and I believe they will remain at the forefront.  

Genetics offers numerous important features for such advances, because genetic manipulations are the most elegant type of manipulations for answering biological questions. Is there a less intrusive experiment than changing a single nucleotide among millions or billions of bases and asking: what are the in vivo consequences? The answer is a flat no in my opinion! 

Despite the obvious relevance of our work to human biology, some are averse to a human-centric vision of research for good reasons, as nicely illustrated by the examples above. Diseases should not per se dictate our research because we don’t yet know where the next breakthrough will come from. Serendipity and curiosity are major players in discovery. 

Yet, I see no reason not to search for a middle ground. This is especially the case in the area of genetics, as the evolutionary conservation of genes and their function has been critical to understanding most biological processes across organisms. Forward genetic screens and evolution-based studies in model organisms have led, and will continue to lead, to discovery of many basic aspects of biology as they are unbiased and probe a very diverse set of biological functions.  

Doing biological research is not always a forced choice between creating fundamental knowledge or developing targeted medical applications. Both outcomes can result from the same efforts. Indeed, human genetics has advanced basic biology, from Archibald Garrod helping renew the understanding of Mendel’s laws by studying a rare disease, to prion biology revealed by Creutzfeldt-Jakob disease. The last ten years have seen remarkable changes as another set of scientists—human geneticists—have joined the cohort of screeners. They, like many of us, observe phenotypes (of patients) and attempt to identify the causative genes.  This approach has gained tremendous strength with the ability to sequence all exomes (WES) and genomes (WGS). WES or WGS of an affected individual and a few direct family members allows the identification of variants in one or a few genes that may be causative, especially for very rare diseases. 

Surprisingly, more than 50% of the orthologues of these genes have been poorly characterized in vivo in any organism, leaving a wide knowledge gap. Because an estimated 6,000–13,000 rare disease associated genes remain to be discovered, we have a full plate of genes and variants to tackle. Note that more than 80% of new human disease genes that have been discovered in the past few years are conserved in worm, flies and, more obviously, in vertebrates.

How can a scientist study the function of these genes, especially when the phenotypes associated with the loss of these genes in model organisms may be more subtle than many of the genes that have been characterized already? One productive approach is to generate clean loss-of-function tools using state-of-the-art genetic technologies and then to perform systematic phenotyping at many different levels, including transcriptomics, metabolomics, histological screens, as well as behavioral screens of the many collections of mutants available in yeast, worms, flies, fish, and more recently, mouse. 

Another approach is to team up with other model organism researchers who are performing similar screens and share data to identify genes and pathways to help define their function. 

A third approach is to identify researchers who are attempting to define the function of certain genes based on their scientific interest but are not even aware that others are interested in orthologues in other species.  The latter challenge can now be solved if open communication and collaborative ventures are explored at the onset. For example, a human geneticist may identify an evolutionarily conserved gene that has been poorly characterized in model organisms and may be interested in collaborating with a model organism researcher. Alternatively, a model organism researcher may have identified a conserved gene and wonder if a human geneticist has identified patients that carry variants in the orthologous human gene. Recent databases and online platforms now allow scientists to explore these unpublished data, connect, and explore or initiate collaborations.  These include GeneMatcher, ModelMatcher, and numerous international ventures designed to match researchers and clinicians with common interests. 

GSA is exploring ways to introduce the model organism community to these approaches.  In addition, there are now many databases that attempt to centralize knowledge from many model organisms to help geneticists explore gene function across evolution, such as the Monarch Initiative and the Alliance of Genome Research, as well as databases to integrate clinical and scientific databases such as MARRVEL. GSA will organize a series of seminars this year to introduce these opportunities and provide tips and tutorials to help explore the available websites and databases. We believe that these seminars will be useful to investigators at all career stages and across different model organisms, as well as for human biologists. We hope this will add a new dimension to research, reveal unanticipated phenotypes, speed up discovery, allow new funding opportunities, and lead to the discovery of new fundamental aspects of biology. 

Sign up for the Seminars Now!

AP-2 transcription factors, which control sleep in flies and worms, are confirmed to do the same in mammals.

Humans are not alone in their deep need for sleep. Almost all animals, even tiny nematode worms and fruit flies, suffer when deprived of their Z’s, but little is known about how sleep is controlled. New work published in GENETICS advances our understanding of this mysterious physiological state by pinpointing a key gene family that affects sleep architecture.

Two research groups independently conducted parallel studies on neural crest-derived AP-2 transcription factors in mice. Their work demonstrates that the associated genes play a conserved role in mammalian sleep, though there is some evolutionary divergence and added complexity in mammals compared to invertebrates.

From Worms to Mice

Henrik Bringmann leads the Max Planck Research Group on Sleeping and Waking. In 2013, his laboratory screened C. elegans worms for mutations affecting sleep. AP-2 deletion mutants showed no detectable sleep, suggesting these transcription factors are important regulators of the process. In 2016, Bringmann led another study showing that AP-2 transcription factors are also needed for sleep in Drosophila. 

“Sleep appears to have evolved at least 600 million years ago and has been conserved since then, which suggests that many fundamental principles of sleep regulation are conserved,” said Bringmann. “This said, sleep is more complex in humans than in worms or flies, so we need mammalian models to understand additional levels of complexity.”

The researchers’ next step was to establish whether a similar sleep-regulating role is played by related genes in mammals, the TFAP2 genes. In their most recent study, the team generated mice that were heterozygous knockouts for either Tfap2a or Tfap2b and compared each mutant to wild-type littermates. In addition to analyzing sleep duration and brain waves, they examined symptoms of sleep deprivation such as memory loss and stress resistance.

Since the AP-2 transcription factors promote sleep in invertebrates, researchers initially expected that the equivalent genes would also promote sleep in mice. They were therefore surprised to find that while losing Tfap2bfunction reduced both sleep quality and quantity, Tfap2a mutants slept for the typical amount of time and the quality of their sleep was actually higher than wild-type. This result suggests that the function of AP-2 transcription factors has diverged over the course of evolution, perhaps to allow sleep quality to be fine-tuned in either direction.

Working Backwards from Human Disorders

Meanwhile, another research group also published an article in the same issue of GENETICS examining the effects of two specific TFAP2B mutations in mice. Yu Hayashi of Kyoto University  and University of Tsukuba said his lab was inspired to pursue this avenue of research by a paper in PNAS. That study described multiple human families with mutations in TFAP2B that are associated with a rare disorder known as Char syndrome. Two of these families exhibited symptoms of disordered sleep, including sleepwalking and extremely shortened sleep.

“We were astonished to read about a family that slept just two to three hours per night and had no signs of fatigue. We thought that maybe analyzing this gene can help us understand what sleep is for in the first place,” said Hayashi. “We even thought that maybe this mutation might somehow substitute for the function of sleep. Could there be a way to help humans need less sleep?”

To answer these questions, Hayashi’s team set out to replicate those families’ specific TFAP2B point mutations in mouse models. They measured both how long the mice stayed awake and the duration of different sleep phases compared to wild-type mice and heterozygous knockouts. The results showed that TFAP2B helps determine the amount of nonrapid eye movement sleep (NREMS). However, the effects of the point mutations in mice did not match the symptoms observed in humans—the mice did not sleepwalk or show dramatically shortened sleep.

In the mice that carried the same mutation as the human family with short sleep, female mice showed fragmented sleep, while male mice did not. This result was unforeseen because there was no reported gender difference in the human family. “It was surprising for me to see the gender difference,” said lead author Ayaka Nakai, a graduate student in the Hayashi lab. It is possible that future research may uncover sex differences in sleep regulation.

In terms of generating a model of fatigue-free short sleep, the results did not match their initial hopes—sleep was reduced overall in heterozygous mutant mice, but it was generally fragmented rather than shortened. However, the results clearly established TFAP2B’s important role in sleep architecture and laid the groundwork for learning more about how sleep works.

Next Steps

Ultimately, said Bringmann, “it was satisfying to hear that both approaches converged on the same conclusions regarding TFAP2B’s role in sleep.” Together, these two papers establish that AP-2 transcription factors contribute to sleep control in mammals—just as they do in flies and worms.

The gene’s evolutionary conservation is a key lesson from the study, said Nakai.

For Nakai and Yu, the next research step is creating knockdown mice that have Tfap2b downregulated only in the nervous system. This will allow them to observe the neural effect of a homozygous loss-of-function mutation, which is developmentally lethal if the knockout is genome-wide. Studying a homozygous knockdown may offer clearer insights into how the gene affects neuron specification and activity.

Next, Bringmann is interested in examining other mammalian AP-2 paralogs, but he says invertebrates will continue to be important for identifying other genes that contribute to sleep regulation. “Going back and forth between different models will be the future of sleep research for the next years, and this will be facilitated by looking at homologous genes and conserved principles.”

CITATION:

Functional Divergence of Mammalian TFAP2a and TFAP2b Transcription Factors for Bidirectional Sleep Control

Yang Hu, Alejandra Korovaichuk,  Mariana Astiz, Henning Schroeder, Rezaul Islam, Jon Barrenetxea, Andre Fischer, Henrik Oster and Henrik Bringmann

GENETICS 2020 216: 735-752. 

https://doi.org/10.1534/genetics.120.303533

Sleep Architecture in Mice Is Shaped by the Transcription Factor AP-2β

Ayaka Nakai, Tomoyuki Fujiyama, Nanae Nagata, Mitsuaki Kashiwagi, Aya Ikkyu, Marina Takagi, Chika Tatsuzawa, Kaeko Tanaka, Miyo Kakizaki, Mika Kanuka, Taizo Kawano, Seiya Mizuno, Fumihiro Sugiyama, Satoru Takahashi, Hiromasa Funato, Takeshi Sakurai, Masashi Yanagisawa and Yu Hayashi

GENETICS 2020 216:753-764

https://doi.org/10.1534/genetics.120.303435

Courtesy of Lernestorod via Pixabay

Written by members of the GSA Early Career Scientist Communication and Outreach Subcommittee: Carla Bautista Rodriguez, Université Laval; Zach Grochau-Wright, University of Arizona; Angel F. Cisneros Caballero, Université Laval

Disrupting the complex and delicate balance of a genome can have devastating consequences. In humans, for example, extra copies of individual chromosomes can result in diseases, and whole-genome duplications often occur in cancer. However, extra genome copies can also provide advantages. From our morning coffee to pharmaceutical production to the origins of vertebrates, genome duplication has had many implications for our lives. Research in model organisms is helping illuminate how and why.

Our early origins

Genomes contain the information needed for the development and metabolism of living organisms. As humans, our genome is composed of 46 chromosomes. These come in 23 pairs because we inherit one half of each pair from our parents. However, organisms sometimes receive unusual numbers of chromosomes. These events can range from receiving extra copies of individual chromosomes to extra copies of the whole genome!

The number of chromosome copies an organism has is referred to as ploidy. For example, haploids have one full set of chromosomes, diploids (like humans) have two, and polyploids have more than two. One of the ways ploidy can change is through errors in cell division. Cells have to replicate their genome before they divide, so  they can assign a full copy to each of their daughter cells. However the cells fail to divide sometimes, which results in a whole-genome duplication. Changes in ploidy can also result from the interbreeding of different species. This happens particularly often in plants.

When these extra copies are passed onto future generations, they can become a source for novel genetic material. One example is hinted at by curious patterns in the human genome. Some human chromosomes have long stretches of similar genes organized in the same order. Genome-scale analyses across a range of vertebrate species showed that many of these long stretches come in four copies. What is the origin of these groups of four? One possibility could be many successive duplications of individual genes. However, this is unlikely because it would require a very large number of individual events. The most likely explanation is that the ancestor of all vertebrates underwent two rounds of whole-genome duplication. These early events could have set the stage for the evolution of vertebrates and the subsequent origin of many different species, including humans.

When more is more: genome duplication and adaptation

Sometimes, polyploidy can be an advantage. Selmecki and colleagues performed an experiment where they generated haploid, diploid, and tetraploid strains of the model organism Saccharomyces cerevisiae, also known as baker’s yeast. They grew each strain in an environment where the complex sugar raffinose was the primary source of carbon. Raffinose is more difficult to metabolize than simpler sugars like glucose, so this new environment placed selective pressure on the yeast strains to adapt to the new source of energy. Selmecki and colleagues found that tetraploid yeast strains adapted faster than haploid and diploid strains to this challenging environment. The scientists then used mathematical modeling and whole genome sequencing to examine what allowed tetraploids to adapt so rapidly. They reasoned that, for duplicated genes, as long as one of the copies retains its function, the other copies can accumulate mutations that might otherwise be harmful to fitness. These additional mutations ultimately mean more genetic variation for natural selection to act on the population. Thus, the increase in variation probably helped tetraploids find the beneficial mutations for raffinose metabolism quickly.

Genome duplications have played a major role in generating the diversity of plant species we see today. They have been associated with 15% and 31% of speciation events in flowering plants and ferns, respectively. One reason for this is that polyploid plants are unable to reproduce with parent species due to different chromosome numbers. Similar to the yeast experiment above, polyploid plants have been found to evolve into different ecological niches faster than their diploid relatives. Again, this has been linked to increased genetic diversity following polyploidization.

Polyploids make food, drink, and drugs

Polyploid species have been widely used by humans for thousands of years. Today, humans still benefit from polyploidy in fields such as agriculture, industry, and biotechnology.

You can thank a polyploid for your morning coffee, for example, since coffee plants are tetraploid. This is not an isolated case; domesticated crops tend to be polyploids more often than their wild relatives. Some of these crops are widely used, including wheat crops, which are tetraploid or hexaploid, and potato crops, which have ploidy ranging from diploid, triploid, tetraploid, to pentaploid. Fruits also show high ploidy levels, like octoploid strawberries. The reason there are so many polyploid crops is because they usually have larger cells and organs than their diploid progenitors, allowing more biomass to be obtained from a single plant.

Polyploid microorganisms are also used in industrial applications. Since polyploidy tends to increase the ability of microbes to resist environmental stresses, it has been widely used in the brewing industry where cells must endure high osmotic stress and high alcohol concentrations. For instance, beer and baking yeasts and some wine hybrid strains are usually triploid and tetraploid. This is explained by the fact that the increase in ploidy is not only accompanied by an increase in size, but also, greater respiratory activity.

Recently, polyploidy has been used to make biotechnological products. For instance, ploidy has been manipulated for the enhanced production of phyto-pharmaceuticals. Since polyploidization increases the size of cells and organs and plant organs are the source of secondary metabolites, increasing ploidy can improve the bioproduction of these metabolites. For instance, tetraploids of Cannabis sativa showed an 80% increase in marijuana-like activity, and triploids or tetraploids of Papaver somniferum showed an increase of 100% in morphine concentration.

Nature constantly offers unexpected innovations. All these examples reveal that unusual numbers of chromosomes are not always harmful, and have had important evolutionary implications. In fact, genome duplications have helped shape our world, leaving a lasting impact on our economic activities and on our own human genome.

About the authors:

Carla Bautista Rodriguez

Zach Grochau-Wright

Angel F. Cisneros Caballero

Acknowledgments:

We would like to thank Jacob Steenwyk, Axelle Marchant, Diana Ascencio, and Souhir Marsit for useful comments.

A better way to make endogenous reporters in C. elegans

CRISPR systems for gene editing have revolutionized biological research, but the method still has limitations. While it is usually straightforward to delete parts of the genome using CRISPR, large insertions can be a challenge. This has been the case even for the nematode Caenorhabditis elegans, one of the most established model organisms. But now, work published in GENETICS by Vicencio, Martínez-Fernández, Serrat, and Cerón has produced a more effective way to use CRISPR to insert longer stretches of DNA into the nematodes’ genomes.

A method for adding long DNA fragments is essential because many genes of interest, including important fluorescent reporter genes, are too long to be effectively inserted using existing methods. In fact, the team embarked on the work after attempts to insert a gene into the nematodes using another CRISPR-based technique repeatedly failed—a problem also reported in at least one other publication. In contrast, they found that their method, called Nested CRISPR, could efficiently add segments of DNA up to 792 base pairs long. They also achieved insertions of 927 base pairs, although the efficiency was lower.

In their method, the gene is inserted in two CRISPR-based steps. First, a short fragment with nucleotides from each end of the gene is inserted into the target site. Next, this fragment is replaced by the full-length insertion via homology-directed repair.

Their results mean that when insertions of a few hundred base pairs are needed, Nested CRISPR is a viable alternative to current methods involving extrachromosomal or randomly inserted DNA. The Nested CRISPR technique may even be broadly applicable to other organisms, particularly through the authors’ one-shot approach to achieve the two editing steps in a single injection.

It’s not completely clear why this group and others have had difficulty reproducing the level of efficiency reported for an existing CRISPR-based method for inserting DNA segments of this length into C. elegans. Slight differences in reagents among labs may be partially to blame for the lack of reproducibility of some laboratory methods, including those used for genome editing, but the authors of this study believe that won’t be an issue in the case of Nested CRISPR because all the reagents are commercially available and affordable. The availability of these premade reagents may also make it easier for researchers with less experience in gene editing (or molecular cloning in general) to perform the technique, allowing them to pursue projects that they otherwise may have avoided. The group has called for the C. elegans community to come together to evaluate the utility of methods such as theirs for inserting long stretches of DNA—which may become even more important as the field continues to hurtle forward.

CITATION:

Efficient Generation of Endogenous Fluorescent Reporters by Nested CRISPR in Caenorhabditis elegans
Jeremy Vicencio, Carmen Martínez-Fernández, Xènia Serrat, Julián Cerón
GENETICS 2019 211(4): 1143-1154; https://doi.org/10.1534/genetics.119.301965
https://www.genetics.org/content/211/4/1143

An automated drug screening approach gives insight into rare NGLY1 deficiency.

Sometimes, diagnosing and treating an illness is straightforward. Other times, the diagnosis is challenging while the treatment is simple—or vice versa. In the case of a rare disease like NGLY1 Deficiency, both diagnosis and treatment can feel unreachable. The complex challenges of rare diseases prompt outside-the-box approaches—such as the partnership between a rare disease funding body and a fundamental research group. In an article published in G3, Portillo Rodriguez et al. report findings from just such a partnership, outlining a drug screening methodology used to shed light on this rare disease.

N-glycanase 1 (NGLY1) is an enzyme responsible for cleaving sugars from proteins as part of the endoplasmic reticulum-associated degradation (ERAD) pathway, which oversees the breakdown of misfolded proteins. In humans, lack of NGLY1 leads to a condition that baffled clinicians and evaded identification until just a few years ago. NGLY1 Deficiency causes global developmental delay, seizures, floppy body, and an inability to produce tears; fewer than 50 patients with the condition have ever been identified, making research on treatments extremely difficult.

Funding for rare disease research can be hard to come by through standard mechanisms—with so few people affected, scarce research funds are rarely diverted their way. When their daughter Grace was diagnosed with NGLY1 Deficiency, Matt and Kristen Wilsey started the Grace Science Foundation, dedicated to finding a cure for the disease and others like it. In 2017, Grace Science partnered with Perlara, a biotech public benefit corporation (bioPBC) that uses model organisms to discover treatments for rare disease. Their goal is to use high-throughput methodologies in model organisms to identify drugs that could impact the rare disease in question.

The report by Portillo Rodriguez et al. is the first publication to come out of this NGLY1 partnership. The researchers developed an assay that let them efficiently screen a collection of 2,650 compounds for any that might modulate NGLY1-related phenotypes. They first generated a new Drosophila model of NGLY1 Deficiency by introducing a nonsense mutation into Pngl, the fly homolog of NGLY1; this model has a readily identifiable larval size phenotype, which let them perform their screen in 96-well plates with three larvae per well. Each well contained a different drug from the Microsource Spectrum compound library; an automated workflow imaged the plates and quantified the size of the larvae to determine which, if any, of the chemicals modified the mutant phenotype.

The screen produced a single validated hit: 20-hydroxyecdysone (20E), which is an important signaling hormone that drives metamorphosis and molting in arthropods. While 20E is not a good drug candidate for human patients, the implication of the neuroendocrine axis in the pathophysiology of the Drosophila phenotype gives us more information into the mechanism of NGLY1/Pngl than we previously had.

Anything we can learn about the molecular players that contribute to rare disease brings us closer to finding interventions for patients—as does the availability of a validated screening platform. Because model organisms like Drosophila are so amenable to high-throughput screening of whole organism phenotypes, the hope is that approaches like these will bring people with rare diseases one step closer to treatments.

Citation

Defects in the Neuroendocrine Axis Contribute to Global Development Delay in a Drosophila Model of NGLY1 Deficiency
Tamy Portillo Rodriguez, Joshua D. Mast, Tom Hartl, Tom Lee, Peter Sand, Ethan O. Perlstein
G3: Genes, Genomes, Genetics July 1, 2018 vol. 8 no. 7 2193-2204;
https://doi.org/10.1534/g3.118.300578
http://www.g3journal.org/content/8/7/2193

A suppressor screen in C. elegans uncovers previously unknown flexibility in the genetics underlying extracellular membranes.

In nearly all animal tissues, thin barriers called basement membranes anchor outward-facing layers of cells—the linings of lungs, the top layers of skin, the insides of blood vessels—to the connective tissues that support them. Mutations disrupting any major basement membrane component are often incompatible with human life, and partial loss of function can lead to diseases such as muscular dystrophy.

In the nematode C. elegans, as in humans, mutations in basement membrane components can be lethal. New work published in GENETICS by Gotenstein et al. shows that this lethality can be rescued by mutations in certain membrane structural components. Worms, like other animals, rely on enzymes called peroxidasins to crosslink basement membrane constituents and thus increase their structural integrity. This crosslinking is critical during development; disabling the peroxidasin PXN-2, for example, prevents worms from surviving beyond the embryonic or larval stage.

Unexpectedly, Gotenstein et al. discovered that gain-of-function mutations in a few proteins that make up the basement membrane itself, including perlecan and type IV collagen, can prevent the dysfunctions caused by pxn-2 mutations. Mutations that affect part of the extracellular domain of LET-805, a transmembrane protein thought to help the basement membrane adhere to the epidermis, also suppressed the mutant phenotype. Mutations that suppressed the phenotype of pxn-2 mutants also restored normal development in worms with mutations in spon-1, which is also important for basement membrane assembly.

SPON-1’s precise role in basement membrane formation isn’t fully understood, but its molecular mechanism is thought to be different from that of PXN-2, implying that the newly discovered suppressor mutations affect the basement membrane broadly, rather than being narrowly involved in individual pathways. The unanticipated flexibility in the formation of the basement membrane offers a new perspective on this vital, highly conserved structure, unlocking a new realm of possible mechanisms to explore.

CITATION:

Genetic Suppression of Basement Membrane Defects in Caenorhabditis elegans by Gain of Function in Extracellular Matrix and Cell-Matrix Attachment Genes
Jennifer R. Gotenstein, Cassidy C. Koo, Tiffany W. Ho, Andrew D. Chisholm
Genetics 2018 208: 1499-1512; https://doi.org/10.1534/genetics.118.300731
http://www.genetics.org/content/208/4/1499

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New evidence for genome instability in fly tumors suggests key similarities—and differences—from human disease processes.

Human cancers display a variety of abnormal genomic features, including increased numbers of single nucleotide variants (SNVs) and copy number variants (CNVs). However, a 2014 study on a fruit fly tumor detected no elevation of SNVs or CNVs compared to non-tumor tissues, raising questions about how well the fly tumors, which are sometimes used in cancer research, represent cancer in humans. Rossi et al. investigated whether this was generally the case in malignant neoplasms in flies by sequencing the genomes of 17 such tumors caused by mutations in four different genes.

To address this question, the researchers used a process called allografting: they dissected tumors from fly larvae, then implanted them into the abdomens of adult flies. Each time the tumors filled up the abdomens of their hosts, the tumors were removed, and some of the tumor cells were allografted again into new fly hosts. This approach allowed them to monitor which types of mutations accumulate over many rounds of cell division. Without these successive iterations of allografting, they would have been limited to studying mutations that occur over the comparatively short lifespan of the hosts.

In all of the allografted tumors, the researchers found increases in SNVs and CNVs similar in number to those seen in human cancers, and in the case of CNVs, with a similar size distribution. Also as in humans, the increases in the number of mutations varied from one tumor type to the next. However, they also found that the CNVs weren’t distributed in any discernable pattern, no two allografts had SNVs affecting the same genes, and the CNVs and SNVs often weren’t retained from one allograft to later allografts. This implies that these mutations may merely be byproducts of genome instability in the tumors and thus don’t contribute to malignancy, whereas in humans, it’s thought that the accumulation of such mutations as tumors age is a driver of malignancy.

One important consideration, though, is that studies looking for genetic variants correlated with cancer in humans often have much larger sample sizes, which might reveal associations this fly study could not identify. Still, because flies are important model organisms for cancer research, furthering our understanding of the similarities and differences between human and fly tumors, as Rossi et al. have done, is essential.

CITATION:

Drosophila Larval Brain Neoplasms Present Tumour-Type Dependent Genome Instability
Fabrizio Rossi, Camille Stephan-Otto Attolini, Jose Luis Mosquera, Cayetano Gonzalez
G3: Genes|Genomes|Genetics 2018 8: 1205-1214; https://doi.org/10.1534/g3.117.300489
http://www.g3journal.org/content/8/4/1205