Engineering Babies One Crispr at a Time

 

By Sophie Balmer, PhD

Over the past few weeks, the scientific community has been overwhelmed with major advances in human embryonic research. Whether researchers report for the second time the use of Crispr to edit the human germline or extend the conditions of in vitro culture of human embryos (also here), these issues have been all over the news. However, as all topics can not be raised in only one post, therefore, I will focus on genome editing studies.

 

About a year ago, one research group in China reported the first genome editing of human embryos using Crispr technology. Although these embryos were not viable due to one additional copy of each chromosome, this study quickly became highly controversial and raised strong concerns. The public and scientific communities questioned whether editing the human germline for therapeutic benefits was legitimate, leading to numerous ethical discussions. A few of weeks ago, a second study reported genome editing of embryos reinforcing the debate around this issue. Additionally, several research proposal involving genomic modification of healthy human embryos’ DNA have been validated recently in other countries. In this post, I want to address several questions. What are the possible advances or consequences of such work? What is the current legislation on human genome editing worldwide? Are these studies as alarming as what is written in some newspaper articles?

 

The emergence of the Crispr technology a few years ago has revolutionized the way scientists work since this method greatly improves the efficiency of DNA alteration of model organisms. However, this powerful tool has also raised many concerns, notably on the possibility to easily tweak the human genome and generate modified embryos.

In the eyes of the general public, this kind of experiment resonates with science fiction books or movies. Because of the high potential of this technique, it is crucial to inform everyone correctly to avoid clichés. Recently, one of my favorite comedian and television host John Oliver depicted in a very bright and amusing way how small scientific advances are sometimes presented in the media. Although the examples he uses are dramatic, every scientific breakthrough gets its share of overselling to the public. In the case of gene-editing of human embryos, pretending we are about to use eugenics principles to engineer babies and their descendants with beneficial genes is pure fiction. However, to prevent any potential malpractice from happening, clear ethical discussions and regulations need to be established and then explained to the public to prevent misunderstanding of these issues.

Within the scientific community, last year’s results triggered the need for new discussions and regulations on human cloning. Modifying the genome of human embryos involves modifying the germline as well, leading eventually to the transmission of the genetic alteration to future generations. However, the consequences of such transmission are unknown. Potentially, this could resolve a number of congenital genetic diseases for the individual him/herself and be used for gene therapy but would result in generations of genetically modified humans.

 

Because of cultural and ethical differences between countries, the legislation (if there is any) around working with human embryos or cells derived from human embryos (hESC for human embryonic stem cells) is variable. International ethical committees have only been able to establish guidelines as instituting international laws on human cloning is impossible. Ultimately, each country is responsible for enforcing these rules. Most countries and international ethics committees agree on a ban on reproductive and therapeutic human cloning. Moreover, following last year published experiments, a summit held in December 2015 gathered experts from all around the world. The consortium concluded that gene-editing of embryos used to establish pregnancy should not be performed (for now) and to follow up on all-related issues, new sets of guidelines are coming out imminently.

 

Still, it seems difficult to get an idea of the consensus depending on the countries in which scientists perform experiments. There is range of possibilities when working with human samples: some countries completely prohibit any manipulation of human embryos or hESC while others authorize genetic modification of the embryo for research purposes only under specific conditions. In between several nations authorize research exclusively on already derived lines of hESC and others authorize derivation of hESC but no manipulation of the embryos themselves.

Besides these general rules and as of today, three countries have approved proposals for gene-editing of human embryos: China, the UK and Sweden. Research proposals in both European countries have authorized Crispr targeting of specific genes in healthy human embryos to assess the function of these genes during early human development. However, these embryos can not be used for in vitro fertilization (IVF) and have to be destroyed at the end of the study. The purpose of these studies would be to confirm what has been described in hESC and in mammalian model systems and contribute to our knowledge of human development.

 

On the other hand, both published studies from China focused on Crispr targeting towards clinical therapies of an incurable blood disease or HIV. The overall purpose of such projects is to test the use of the Crispr technology for gene therapy. Although rendering embryos immune to several diseases using Crispr is an attractive possibility, it seems more urgent to probe the validity of the technique in humans and assess whether the mechanisms of human embryonic development are similar to what has been hypothesized. Gene therapies have already been successfully attempted in humans using other techniques to modify the genome. Yet, the modifications were targeted towards specific cells in already-born individuals. Again, modifying the genome of embryos implies that the mutation will be inherited in future generations and is in a large part the reason of this debate. Moreover, Crispr targeting still leads to unspecific modification of the genome, although very promising results show that newly engineered cas9 could lead to very specific targeting. The consequences of such off-target modification are unknown and could be disastrous for the following generations.

 

Overall, no research proposal dares to consider genetically modified embryos to establish pregnancy but as research moves faster, increasing demand for ethical discussion and regulations are brought forward. As more studies come out, it will be interesting to follow the evolution of this debate. Additionally, informing clearly the population of the possibilities and outcomes of ongoing projects should be a priority so that they can give an informed consent towards such research. In any case, a clear boundary needs to be established between selecting the fittest embryo by pre-implantation genetic diagnosis, which is routinely performed for IVF and playing the sorcerer’s apprentice with human embryo’s

How Low Can You Go? Designing a Minimal Genome

By Elizabeth Ohneck, PhD

How many genes are necessary for life? We humans have 19,000 – 20,000 genes, while the water flea Daphnia pulex has over 30,000 and the microbe Mycoplasma genitalium has only 525. But how many of these genes are absolutely required for life? Is there a minimum number of genes needed for a cell to survive independently? What are the functions of these essential genes? Researchers from the J. Craig Venter Institute and Synthetic Genomics, Inc., set out to explore these questions by designing the smallest cellular genome that can maintain an independently replicating cell. Their findings were published in the March 25th version of Science.

The researchers started with a modified version of the Mycoplasma mycoides genome, which contains over 900 genes. Mycoplasmas are simplest cells capable of autonomous growth, and their small genome size provides a good starting point for building minimal cells. To identify genes unnecessary for cell growth, the team used Tn5 transposon mutagenesis, in which a piece of mobile DNA is introduced to the cells and randomly “jumps” into the bacterial chromosome, thereby disrupting gene function. If many cells were found to have the transposon inserted into the same gene at any position in the gene sequence, and these cells were able to grow normally, the gene was considered non-essential, since its function was not required for growth; such genes were candidates for deletion in a minimal genome. In some genes, the transposon was only found to insert at the ends of the genes, and cells with these insertions grew slowly; such genes were considered quasi-essential, since they were needed for robust growth but were not necessary for cell survival. Genes which were never found to contain the transposon in any cells were considered essential, since cells that had transposon insertions in these genes did not survive; these essential genes were required in the minimal genome.

The researchers then constructed genomes with various combinations of non-essential and quasi-essential gene deletions using in vitro DNA synthesis and yeast cells. The synthetic chromosomes were transplanted into Mycoplasma capricolum, replacing its normal chromosome with the minimized genome. If the M. capricolum survived and grew in culture, the genome was considered viable. Some viable genomes, however, caused the cells to grow too slowly to be practical for further experiments. The team therefore had to find a compromise between small genome size and workable growth rate.

The final bacterial strain containing the optimized minimal genome, JCVI-syn3.0, had 473 genes, a genome smaller than any autonomously replicating cell found in nature. Its doubling time was 3 hours, which, while slower than the 1 hour doubling time of the M. mycoides parent strain, was not prohibitive of further experiments.

What genes were indispensable for an independently replicating cell? The 473 genes in the minimal genome could be categorized into 5 functional groups: cytosolic metabolism (17%), cell membrane structure and function (18%), preservation of genomic information (7%), expression of genomic information (41%), and unassigned or unknown function (17%). Because the cells were grown in rich medium, with almost all necessary nutrients provided, many metabolic genes were dispensable, aside from those necessary to effectively use the provided nutrients (cytosolic metabolism) or transport nutrients into the cell (cell membrane function). In contrast, a large proportion of genes involved in reading, expressing, replicating, and repairing DNA were maintained (after all, the presence of genes is of little use if there is no way to accurately read and maintain them). As the cell membrane is critical for a defined, intact cell, it’s unsurprising that the minimal genome also required many genes for cell membrane structure.

Of the 79 genes that could not be assigned to a functional category, 19 were essential and 36 were quasi-essential (necessary for rapid growth). Thirteen of the essential genes had completely unknown functions. Some were similar to genes of unknown function in other bacteria or even eukaryotes, suggesting these genes may encode proteins of novel but universal function. Those essential genes that were not similar to genes in any other organisms might encode novel, unique proteins or unusual sequences of genes with known function. Studying and identifying these genes could provide important insight into the core molecular functions of life.

One of the major advancements resulting from this study was the optimization of a semi-automated method for rapidly generating large, error-free DNA constructs. The technique used to generate the genome of JCVI-syn3.0 allows any small genome to be designed and built in yeast and then tested for viability under standard laboratory conditions in a process that takes about 3 weeks. This technique could be used in research to study the function of single genes or gene sets in a well-defined background. Additionally, genomes could be built to include pathways for the production of drugs or chemicals, or to enable cells to carry out industrially or environmentally important processes. The small, well-defined genome of a minimal cell that can be easily grown in laboratory culture would allow accurate modeling of the consequences of adding genes to the genome and lead to greater efficiency in the development of bacteria useful for research and industry.

Epigenetic Inheritance, Trauma and the Holocaust

 

By Alison Bernstein, PhD

Since my research interests focus on environmental impacts on health and how epigenetic processes mediate those effects, my mother sent me this article, “Study of Holocaust survivors finds trauma passed on to children’s genes“, from The Guardian. This article reports the recent paper, “Holocaust exposure induced intergenerational effects on FKBP5 methylation“, in Biological Psychiatry. I get overly excited by teachable moments so I decided to take the opportunity to teach some more epigenetics (see my pages on Facebook or Google+ for my Intro to Epigenetics series).

Epigenetics literally means “over the genome”. It encompasses all meiotically and mitotically heritable changes in gene expression that are not coded in the DNA sequence itself. If we break that down, there are some key points to note:

  • “Not coded in the DNA”: There is no change in the DNA sequence. Thus, for these to be heritable, there must be mechanisms of inheritance besides DNA replication.
  • “Changes in gene expression”: The underlying assumption of all epigenetic studies should be that these changes alter gene expression (or change how inducible or repressible gene expression is, but that’s harder to measure).
  • “Meiotically and mitotically heritable”: This means heritable through cell division, but not necessarily heritable from parent to offspring.

Epigenetics generally refers to 4 mechanisms: DNA methylation (and other modifications to cytosine), histone modifications, non-coding RNAs, and long-range chromatin interactions (3D structure of chromosomes). In this paper, the authors focused on DNA methylation and identified changes in DNA methylation that occur in people who were in a Nazi concentration camp, witnessed or experienced torture, or hid from the Nazis during World War II. Similar changes were seen in their children. This transmission of a trait from parents to children is called intergenerational inheritance.

The effects of severe stress and other exposures has been shown to be inherited intergenerationally, multigenerationally (to grandchildren) and sometimes even transgenerationally (to great-grandchildren), both in animals and in people. The Dutch famine of 1944 and the polybrominated biphenyl exposure in Michigan in 1978 have provided evidence that exposures that occur prior to conception and in utero can have lasting effects on subsequent generations. However, it is difficult to separate out the different mechanisms that contribute to the inheritance of traits to subsequent generations. Thus, it is an important research question to ask how the effects of trauma, stress and other exposures are passed from generation to generation. This is the question the scientists wanted to address in this paper: is there an epigenetic component to the intergenerational inheritance of the effects of trauma?

Epigenetic Inheritance

This paper provides direct evidence in humans that the epigenetic effects of pre-conception stress can be seen in both parents and offspring. The authors looked at one specific gene only – FKBP5 – because it is known to be involved in the response to high glucocorticoid levels (a biological signal for stress) and is a possible novel target for antidepressant medication. They looked for changes in DNA methylation in glucocorticoid response elements within this gene. Response elements are sequences of DNA that bind to specific transcription factors and regulate transcription of genes. In this case, glucocorticoid response elements are bound by glucocorticoid hormones and their receptors to regulate expression of the gene containing the response element. They found changes in DNA methylation in these specific elements of the specific FKBP5 gene in Jewish Holocaust survivors and their children, but not in other Jewish people of similar age. This observed change in DNA methylation of the FKBP5 gene was in the opposite direction in parents and offspring, yet we do not yet have an explanation as to why this change would be different in parents and offspring. Thus, it is actually impossible to say from the results of this paper if these epigenetic changes are due to direct effects of stress and high glucocorticoid levels (or other shared environmental factors) or to inheritance of epigenetic marks.

Let’s say a woman or girl lived through the Holocaust. She and her eggs were exposed to high glucocorticoid levels, and other effects, due to stress. If a woman was pregnant during this time, she, her eggs and her in utero daughters’ eggs were exposed. So that’s 2, and possibly, 3 generations directly exposed to the stress. Until you get to the 4th generation, there is still a possibility of direct exposure. It might be epigenetic, but it is also possible that it’s still a result of direct exposure. Changes must be observed in the generation the great-grandchildren to definitively say that they are epigenetically inherited and not a result of direct exposure. In general, the great-grandchildren are the first generation that was definitely not directly exposed to the stressor. However, in this case, they looked at preconception stress, so looking at the 3rd generation (grandchildren) would be sufficient to differentiate between epigenetic inheritance and direct exposure.

This paper only looks at parents and their children. So the eggs that produced ALL those children were directly exposed (since females are born with all their eggs) to the trauma. It’s possible that high glucocorticoid levels directly affect the methylation of FKBP5 in the eggs as well in cells of the parent. The discussion of the paper itself goes into this, but the article overlooked this point and it’s a really important point to understand if you are interested in epigenetic inheritance.

From the discussion section of the paper:

“The main finding in this study is that Holocaust survivors and their offspring have methylation changes on the same site in a functional intronic region of the FKBP5 gene, a GR binding sequence in intron 7, but in the opposite direction. To our knowledge, these results provide the first demonstration of transmission of preconception stress effects resulting in epigenetic changes in both exposed parents and their offspring in adult humans. Bin 3/site 6 methylation was not associated with the FKBP5 risk-allele, and could not be attributed to the offspring’s own trauma exposure, their own psychopathology, or other examined characteristics that might independently affect methylation of this gene. Yet, it could be attributed to Holocaust exposure in the F0.

It is not possible to infer mechanisms of transmission from these data. It was not possible to disentangle the influence of parental gender, including in utero effects, since both Holocaust parents were survivors. Epigenetic effects in maternal or paternal gametes are a potential explanation for epigenetic effects in offspring, but blood samples will not permit ascertainment of gamete dependent transmission. What can be detected in blood samples is parental and offspring experience-dependent epigenetic modifications. Future prospective, longitudinal studies of high risk trauma survivors prior to conception, during pregnancy and postpartum may uncover sources of epigenetic influences.”

The paper reports evidence that the epigenetic effects of stress and trauma can be seen in both parents and offspring. However, there are a lot of variables that may cause similar epigenetic changes in parents and offspring. Further studies are needed to really know what the mechanism of these shared epigenetic marks are, before we can confidently assert that the epigenetic changes observed in parents and offspring are due to epigenetic inheritance. As with all good science, this paper answers a question while, at the same time, raising additional questions for future research.

This article was originally published on The Sound of Science blog in August 2015.

Leaving Your Mark on the World

By Danielle Gerhard

 

The idea that transgenerational inheritance of salient life experiences exists has only recently entered the world of experimental research. French scientist Jean-Baptiste Lamarck proposed the idea that acquired traits throughout an organism’s life could be passed along to offspring. This theory of inheritance was originally disregarded in favor of Mendelian genetics, or the inheritance of phenotypic traits isn’t a blending of the traits but instead a specific combination of alleles to form a unique gene encoding the phenotypic trait. However, inheritance is much more complicated than either theory allows for. While Lamarckian inheritance has largely been negated by modern genetics, recent findings in the field of genetics have caused some to revisit l’influence des circonstances, or, the influence of circumstances.

 

Over the past decade, efforts have shifted towards understanding the mechanisms underlying the non-Mendelian inheritance of experience-dependent information. While still conserving most of the rules of Mendelian inheritance, new discoveries like epigenetics and prions challenge the central dogma of molecular biology. Epigenetics is the study of heritable changes in gene activity as a result of environmental factors. These changes do not affect DNA sequences directly but instead impact processes that regulate gene activity such as DNA methylation and histone acetylation.

 

Epigenetics has transformed how psychologists approach understanding the development of psychological disorders. The first study to report epigenetic effects on behavior came from the lab of Michael Meany and Moshe Szyf at McGill University in the early 2000s. In a 2004 Nature Neuroscience paper they report differential DNA methylation in pups raised by high licking and grooming mothers compared to pups raised by low licking and grooming mother. Following these initial findings, neuroscientists have begun using epigenetic techniques to better understand how parental life experiences, such as stress and depression, can shape the epigenome of their offspring.

 

Recent research coming out from the lab of Tracy Bale of the University of Pennsylvania has investigated the heritability of behavioral phenotypes. A 2013 Journal of Neuroscience paper found that stressed males went on to produce offspring with blunted hypothalamic pituitary (HPA) axis responsivity. In simpler terms, when the offspring were presented with a brief, stressful event they had a reduction in the production of the stress hormone corticosterone (cortisol in humans), symptomatic of a predisposition to psychopathology. In contrast, an adaptive response to acute stressors is a transient increase in corticosterone that signals a negative feedback loops to subsequently silence the stress response.

 

The other key finding from this prior study is the identification of nine small non-coding RNA sperm microRNAs (miRs) increased in stressed sires. These findings begin to delve into how paternal experience can influence germ cell transmission but does not explain how selective increases in these sperm miRs might effect oocyte development in order to cause the observed phenotypic and hormonal deficits seen in adult offspring.

 

A recent study from the lab published in PNAS builds off of these initial findings to further investigate the mechanisms underlying transgenerational effects of paternal stress. Using the previously identified nine sperm miRs, the researchers performed a multi-miR injection into single-cell mouse zygotes that were introduced into healthy surrogate females. To confirm that all nine of the sperm miRs were required to recapitulate the stress phenotype, another set of single-cell mouse zygotes were microinjected with a single sperm miR. Furthermore, a final set of zygotes received none of the sperm miRs. Following a normal rearing schedule, the adult offspring were briefly exposed to an acute stressor and blood was collected to analyze changes in stress hormones. As hypothesized, male and female adult offspring from the multi-miR group had a blunted stress response relative to both controls.

 

To further investigate potential effects on neural development, the researchers dissected out the paraventricular nucleus (PVN) of the hypothalamus, a region of the brain that has been previously identified by the group to be involved in regulation of the stress response. Using RNA sequencing and gene set enrichment analysis (GSEA) techniques they found a decrease in genes involved in collagen formation and extracellular matrix organization which the authors go on to hypothesize could be modifying cerebral circulation and blood brain barrier integrity.

 

The final experiment in the study examined the postfertilization effects of multi-miR injected zygotes. Specifically, the investigators were interested in the direct, combined effect of the nine identified sperm miRs on stored maternal mRNA. Using a similar design as the initial experiment, the zygote mRNA was collected and amplified 24 hours after miR injection in order to examine differential gene expression. The researchers found that microinjection of the nine sperm miRs reduced stored maternal mRNA of candidate genes.

 

This study is significant as it has never been shown that paternally derived miRs play a regulatory role in zygote miR degradation. In simpler terms, these findings contradict the conventional belief that zygote development is solely maternally driven. Paternal models of transgenerational inheritance of salient life experiences are useful as they avoid confounding maternal influences in development. Studies investigating the effects of paternal drug use, malnutrition, and psychopathology are ongoing.

 

Not only do early life experiences influence the epigenome passed down to offspring but recent work out of the University of Copenhagen suggests that our diet may also have long-lasting, transgenerational effects. A study that will be published in Cell Metabolism next year examined the effects of obesity on the epigenome. They report differential small non-coding RNA expression and DNA methylation of genes involved in central nervous system development in the spermatozoa of obese men compared to lean controls. Before you start feeling guilty about the 15 jelly donuts you ate this morning, there is hope that epigenetics can also work in our favor. The authors present data on obese men who have undergone bariatric surgery-induced weight loss and they show a remodeling of DNA methylation in spermatozoa.

 

Although still a nascent field, epigenetics has promise for better understanding intergenerational transmission of risk to developing a psychopathology or disease. The ultimate goal of treatment is to identify patterns of epigenetic alternations across susceptible or diagnosed individuals and develop agents that aim to modify epigenetic processes responsible for regulating genes of interest. I would argue that it will one day be necessary for epigenetics and pharmacogenetics, another burgeoning field, to come into cahoots with one another to not only identify the epigenetic markers of a disease but to identify the markers on an person by person basis. However, because the fields of epigenetics and pharmacogenetics are still in the early stages, the tools and techniques currently available limit them. As a result, researchers are able to extract correlations in many of their studies but unable to determine potential causality. Therefore, longitudinal, transgenerational studies like those from the labs of Tracy Bale and others are necessary to provide insight into the lability of our epigenome in response to lifelong experiences.

Development On the Fly: An Interview with Dr. Thomas Gregor

By John McLaughlin

 

Thomas Gregor is a biophysicist and Professor at Princeton University. His Laboratory for the Physics of Life uses both Drosophila melanogaster and Dictyostelium discoideum as model systems to understand developmental processes from a physical perspective.

 

Could you briefly describe your educational path from undergraduate to faculty member at Princeton?

TG: As an undergraduate, I studied physics in Geneva, and then moved into theoretical physics and math. I came to Princeton, initially for a theoretical physics PhD; I switched during my time here to theoretical biophysics and then realized that it makes sense to combine this with experiments. I ended up doing a PhD between three complementary disciplines. My main advisor was Bill Bialek, a theoretical physicist. My other two were David Tank, an experimental neuroscientist, and Eric Wieschaus, a fly geneticist. So I had both experiment and theory, from a biological and a physical side. I then went to Tokyo for a brief post-doc, during which I continued in that interface. But I changed model organisms: I switched from a multicellular, embryonic system to looking at populations of single cells [the social amoeba Dictyostelium discoideum]. As a physicist you’re not married to model organisms. When I came back to start my lab at Princeton in 2009, I kept both the fly and the amoeba systems.

 

What is the overall goal of your lab’s research program?

TG: Basically, to find physical principles behind biological phenomena. How can we come up with a larger, principled understanding that goes beyond the molecular details of any one particular system? I mostly look at genetic networks and try to understand their global properties.

 

Do you think the approaches of biologists and physicists are very different, and if so are they complementary?

TG: I’m driven by the physical aspects of things, but I’m also realistic enough to see what can now be done in biological systems, in terms of data collection and what we can test. To find the overlap between them is kind of an art, and I think that’s where I’m trying to come in.

 

Do you have any scientific role models who have shaped how you approach science?

TG: The three that I mentioned: Bialek influenced me in the types of questions that speak to me; Tank had a very thorough experimental approach that taught me how to make real, physics-style measurements; and Wieschaus brought a lot of enthusiasm and knowledge of the system.

 

Your lab has been studying developmental reproducibility and precision, in the patterning of the fly Drosophila melanogaster. In a 2014 paper1, you showed that levels of the anterior determinant bicoid mRNA vary by only ~9% between different embryos. This is a very similar value to the ~10% variation in Bicoid protein levels between embryos, which you demonstrated several years earlier2. So it seems that this reproducibility occurs even at the mRNA level.

TG: Before going into this, the general thought in the field is that things were very noisy initially, and as the developmental path goes along it becomes more refined and things become more precise. This paper basically asked whether the precision is inherited from the mother, or the embryo needs to acquire it. Because the fluctuations in mRNA, from the mother, completely mimic the fluctuations in protein that the zygote expresses, that told us that the mother lays the groundwork, and passes on a very reproducible pattern. So there’s no necessity for a mechanism that reduces fluctuations from the mRNA to the protein level.

 

Continuing on the theme of precision: in a separate paper from the same year3, your lab showed that the wing structure among different adult flies is identical to within less than a single cell width. Did you have any prior expectations going into this study, and did the results surprise you?

TG: Before looking at the wing, I had kind of made up my mind. I had first seen single cell precision in patterning of gene expression boundaries in the embryo. But I also knew that it’s always better to make a measurement first, and it seems that things are much more precise and reproducible in biology than we think, given the idea of “sloppiness” that we have.

 

Do you think that a high level of reproducibility is a general feature of development, or varies widely among different types of species?

TG: It’s a philosophical question in a way, because I haven’t looked. I think what we found in the embryo is not special to the fly; specific mechanisms for getting there might be unique to the fly. For instance, we have also shown in a recent paper from 2013 that transcription is just as noisy in flies as it is in bacteria, hugely noisy. So, physical mechanisms like temporal and spatial averaging seem enough to reduce the high ubiquitous noise that transcription has to the very fine, reproducible patterns that you see in the fly. The specific mechanisms that reduce noise will be very different from species to species, but I think overall the fact that development is precise and reproducible is something we may one day be able to call a principle.

 

If you could make any changes to scientific institutions, such as the current funding system, journal peer review, etc. what would they be?

TG: One thing that might be nice is if we didn’t have to fund graduate students for the first five years of their career; it would be nice to have more streamlined training grants, not only for U.S. but also international graduate students. And so, graduate students wouldn’t have to worry. They should be free to choose a school based on their scientific interests.

For peer review in journals, the problem is the sheer volume of output is becoming so high. One way to keep a peer review system, is either to pay the reviewers money, or to put everything on the bioRxiv [bio archive is a pre-print server for the life sciences] and let some other means determine how to evaluate a paper. I don’t read papers from looking at the top journals’ table of contents every week, I read them because I see people talk about it on Twitter, or my colleagues tell me I should look at that paper, or because I hear about the work in a talk and decide to see what else the guy is doing.

A lot of people are advocating the new metrics – citations, citation rates, H-index – which are so dependent on the particular field and not necessarily a good measure of impact. In 100 years, are we going to look more at those papers than the ones that currently get very few citations? We don’t know. I don’t think the solution is out there yet.

 

Do you have any advice for young scientists – current PhD students or post-doctoral fellows – for being successful in science?

TG: My advice would be to focus on one very impactful finding. If it’s very thorough and good science, it will be seen. Also, nothing comes from nothing. You need to put in the hours if you want to get a job in academia. And I think that’s one of the ways to measure a good scientist, because knowledge in experimental science comes from new, good data.


What are some future goals of your lab’s research?

TG: We’ve been looking at the genetic network in the fly embryo, trying to understand properties of that network. Medium term, we want to incorporate a slightly different angle, which is looking at the link between transcriptional regulation and the 3D architecture of the genome. In the living embryo, we want to look at how individual pieces of DNA interact, and how that influences transcription and eventually patterning. In the longer term, I don’t know yet; I just got tenure, so I need to sit back. Everything is open. That is what’s nice about being a physicist; you’re not married to your biological past so much.

 

In your opinion, what are the most exciting developments happening in biology right now, whether in your own field or elsewhere?

TG: It’s definitely the fact that so many different disciplines have stormed into biology, making it a very multidisciplinary science. I think it makes the life sciences a very vibrant, communal enterprise. Hopefully the next decades will show the fruits of those interactions.

 

This question is asked very often: How do you balance your lab and family life?

TG: When you start thinking about having a family in science, things become much more complicated. Since I’ve had children, my workload went down a lot. My wife is also a scientist, and for her it’s much harder because she’s not yet tenured. As much as people look at the CV and see how many high-profile papers you have, they should also look at it and see your family and life situation. And for women in science, despite all the efforts that have been made, I don’t think we’re there yet.

 

References

[ordered_list style=”decimal”]

  1. Petkova, MD et al. Maternal origins of developmental reproducibility. Current Biology. 2014. 24(11).
  2. Gregor, T et al. Probing the limits to positional information. Cell. 2007. 130(1).
  3. Abouchar, L et al. Fly wing vein patterns have spatial reproducibility of a single cell. J R Soc Interface. 2014. 11(97).

[/ordered_list]

 

 

CRISPR/Cas9: More Than a Genome Editor

By Rebecca Delker, PhD

 

The bacterial defense system, CRISPR/Cas9, made huge waves in the biomedical community when the seemingly simple protein-RNA complex of Type II CRISPR systems was engineered to target DNA in vitro and in complex eukaryotic genomes. The introduction of double-strand breaks using CRISPR/Cas9 in a targeted fashion opened the portal to highly affordable and efficient site-specific genomic editing in cells derived from yeast to man.

 

To get a sense of the impact CRISPR technology has had on biological research, one simply needs to run a search of the number of publications containing CRISPR in the title or abstract over the past handful of years; the results practically scream in your face. From 2012, the year of the proof-of-principle experiment demonstrating the utility of engineered Cas9, to 2015, CRISPR publications rose steadily from a mere 138 (in 2012) to >1000 (at the time of this post). Publications more than doubled between the years of 2012 and 2013, as well as between 2013 and 2014. Prior to the use of CRISPR as a technology, when researchers studied the system for the (very cool) role it plays in bacterial defense, publications-per-year consistently fell below 100. In other words, it’s a big deal.

 

In fact, during my 10 years at the bench I have never witnessed a discovery as transformative as CRISPR/Cas9. Overnight, reverse genetics on organisms whose genomes were not amenable to classical editing techniques became possible. And with the increasing affordability of high-throughput sequencing, manipulation of the genomes of non-model organisms is now feasible. Of course there are imperfections with the technology that require greater understanding to circumvent (specificity, e.g.), but the development of CRISPR as a tool for genomic engineering jolted biological research, fostering advances more accurately measured in leaps rather than steps. These leaps – and those expected to occur in the future – landed the discoverers of CRISPR/Cas9 at the top of the list of predicted recipients of the Nobel Prize in Chemistry; though they didn’t win this year (the award went to researchers of the not-totally-unrelated field of DNA repair), I anticipate that a win lies ahead. The rapid success of CRISPR genome editing has also sparked patent battles and incited public debate over the ethics of applying the technology to human genomes. With all of the media attention, it’s hard not to know about CRISPR.

 

The transformative nature of CRISPR/Cas9 does not, however, end with genome editing; in fact, an even larger realm of innovation appears when you kill the enzymatic activity of Cas9. No longer able to cut DNA, dead Cas9 (dCas9) becomes an incredibly good DNA-binding protein guided to its target by a programmable RNA molecule (guide RNA, gRNA). If we think of active Cas9 as a way to better understand genes (through deletions and mutations), then dCas9 is the route to get to know the genome a bit better – a particularly enticing mission for those, including myself, invested in the field of Genomics. From high-throughput targeted gene activation and repression screens to epigenome editing, dCas9 is helping scientists probe the genome in ways that weren’t possible before. Here, I put forth some of the best (in my humble opinion) applications, actual and potential, of CRISPR technology that go beyond genome editing.

 

Cas9 and Functional (Epi)Genomics

 

For many years the genome was considered as the totality of all genes in a cell; the additional junk DNA found was merely filler between the necessary gene units, stitching together chromosomes. We’ve come a long way since this naiveté, especially in recent years. We understand that the so-called junk DNA contains necessary regulatory information to get the timing and position of gene expression correct; and now, more than ever, we have a greater appreciation for the genome as a complex macromolecule in its own right, participating in gene regulation rather than acting as a passive reservoir of genetic material. The genome, it has been shown, is much more than just its sequence.

 

The epigenome, consisting of a slew of modifications to the DNA and the histones around which the DNA is wrapped, as well as the 3D organization of the genome in the nucleus, collaborates with DNA binding proteins to accurately interpret sequence information to form a healthy, functional cell. While mutations and/or deletions can be made – more easily, now, with Cas9 – to genomic sequences to test functionality, it is much harder to conduct comparable experiments on the epigenome, especially in a targeted manner. Because of the inability to easily perturb features of the epigenome and observe the consequences, our understanding of it is limited to correlative associations. Distinct histone modifications are associated with active versus inactive genes, for example; but, how these modifications affect or are affected by gene expression changes remains unknown.

 

Taking advantage of the tight binding properties of dCas9, researchers have begun to use the CRISPR protein as a platform to recruit a variety of functionalities to a genomic region of interest. Thus far, this logic has most commonly been employed to activate and/or repress gene expression through recruitment of dCas9 fused to known transcriptional activator or repressor proteins. Using this technique, scientists have conducted high-throughput screens to study the role of individual – or groups of – genes in specific cellular phenotypes by manipulating the endogenous gene locus. And, through a clever extension of the gRNA to include a hairpin bound by known RNA-binding proteins, the targeted functionality has been successfully transferred from dCas9 to the gRNA, allowing for simultaneous activation and repression of independent genes in the same cell with a single dCas9 master regulator – the beginnings of a simple, yet powerful, synthetic gene circuit.

 

Though powerful in its ability to decipher gene networks, dCas9-based activation and repression screens are still gene-centric; can this recruitment technique help us better understand the epigenome? The first attempts at addressing this question used dCas9 to target histone acetyltransferase, p300, to catalyze the acetylation of lysine 27 on histone 3 (H3K27) at specific loci. The presence of H3K27 at gene regulatory regions has been known to be strongly associated with active gene expression at the corresponding gene(s), but the direction of the histone modification-gene expression relationship remained in question. Here, Hilton et al. demonstrate that acetylation of regulatory regions distal to gene promoters strongly activates gene expression, demonstrating causality of the modification.

 

More recently, recruitment of a dCas9-KRAB repressor fusion to known regulatory regions catalyzed trimethylation of lysine 9 on histone 3 (H3K9) at the enhancer and associated promoters, effectively silencing enhancer activity. Though there have only been a few examples published, it will likely not be long until researchers employ this technique for the targeted analysis of additional epigenome modifiers. Already, targeted methylation, demethylation and genomic looping have been accomplished using the DNA-binders, Zinc Finger Nucleases and TALEs. With the increased simplicity in design of gRNAs, dCas9 is predicted to surpass these other proteins in its utility to link epigenome modifications with gene expression data.

 

Visualization of Genomic Loci

 

When you treat dCas9 as a bridge between DNA and an accessory protein, just as in the recruitment of activators, repressors and epigenome modifiers, there are few limits to what can be targeted to the genome. Drawing inspiration from the art of observation that serves as the foundation of scientific pursuit, researchers have begun to test whether dCas9 can be used to visualize genomic loci and observe their position, movements, and interactions simply by recruiting a fluorescent molecule to the locus of interest.

 

This idea, of course, is not entirely new. In situ hybridization techniques (ISH, and its fluorescent counterpart, FISH) have been successfully used to label locus position in fixed cells but cannot offer any information about the movement of chromosomes in living cells. Initial studies to conquer this much harder feat made use of long tracts of repetitive DNA sequence bound by its protein binding partner fused to fluorescing GFP; though surely an advance, this technique is limited because of the requirement to engineer the repetitive DNA motifs prior to imaging.

 

To circumvent this need, researchers have recently made use of TALEs and dCas9 (and here) carrying fluorescent tags to image unperturbed genomic loci in a variety of live cell cultures. The catch is that both TALEs and dCas9 perform much better when targeting repetitive regions, such that multiple copies of the fluorescent molecule are recruited, enhancing the intensity of the signal. Tiling of fluorescent dCas9 across a non-repetitive region using 30-70 neighboring gRNAs (a task made much more feasible with CRISPR versus TALEs) can similarly pinpoint targeted loci, albeit with much higher background. As is, the technique lacks the resolution desired for live imaging, but current advances in super-resolution microscopy and single-molecule tracking, as well as improvements in the brightness of fluorescent molecules available, will likely spur improvements in dCas9 imaging in the coming years.

 

Finally, dCas9 is not only useful in live cells. CASFISH, an updated Cas9-mediated FISH protocol, has been successfully used to label genomic loci in fixed cells and tissue. This updated version holds many benefits over traditional FISH including a streamlined protocol; but, most notably, CASFISH does not require the denaturation of genomic DNA, a necessary step for the hybridization of FISH probes, eliminating positional artifacts due to harsh treatment of the cells. Unfortunately, as of now, CASFISH also suffers from a need for repetitive sequences or tiling of gRNAs to increase signal intensity at the locus of interest.

 

Targeting RNA with Cas9

 

From cutting to tagging to modifying, it is clear that Cas9 has superstar potential when teamed up with double-stranded DNA (dsDNA); however, recent data suggests that this potential may not be limited to DNA. Mitchell O’Connell and colleagues at Berkeley found that Cas9 could bind and cleave single-stranded RNA (ssRNA) when annealed to a short DNA oligonucleotide containing the necessary NGG sequence. In addition, the authors made use of dCas9 and biotin-tagged gRNA to capture and immobilize targeted messenger RNA from cell extract. Though it remains to be shown, this proof-of-principle binding of dCas9 suggests that it is plausible to recruit a variety of functionalities to RNA as has been done for dsDNA. Recruitment of RNA processing factors through Cas9 could potentially enhance translation, generate known RNA editing events (deamination, e.g.), regulate alternative splicing events, or even allow visualization of RNA localization with conjugated fluorescent molecules. Again, each of these processes requires no modification to the RNA sequence or fixation, both of which can disrupt normal cell physiology.

 

Improving CRISPR Technology

 

The development of CRISPR technology, particularly the applications discussed here, is still in its infancy. It will likely take years of research for Cas9 and dCas9 to reach their full potential, but advances are underway. These developments pertain not only to the applications discussed here, but also genome engineering.

 

Specificity of Cas9

 

Cas9’s biggest flaw is its inability to stay focused. Off-target (OT) binding (and here) of Cas9 and DNA cutting have been reported and both present problems. With particular relevance to dCas9-based applications, promiscuous binding of Cas9 to regions of the genome that contain substantial mismatches to the gRNA sequence raises concerns of non-specific activity of the targeted functionality. Efforts to reduce OT binding are needed to alleviate these concerns, but progress has been made with the finding that truncated gRNA sequences are less tolerant of mismatches, reducing off-target Cas9 activity, if not also binding.

 

Temporal Precision of Cas9

 

One of the most exciting developments in dCas9 genome targeting is the potential to manipulate the genome and epigenome in select cell populations within a whole animal to gain spatial resolution in our understanding of genome regulation; however, as we have learned over the years, gene expression patterns don’t only change with space, but also time. A single cell, for example, will alter its transcriptome at different points during development or in response to external stimulus. The development of split versions of Cas9 (and dCas9), which require two-halves of the protein to be expressed simultaneously for function, will not only improve spatial specificity of Cas9 activity but holds the potential to restrict its activity temporally. Drug-inducible and photoactivatable (!) versions of split Cas9 restrict function to time windows of drug treatment or light activation, respectively. In addition, a ligand-sensitive intein has been shown to temporally control Cas9 activity by releasing functional Cas9 through protein splicing only in the presence of ligand.

 

Expanding the CRISPR Protein Repertoire

 

Finally, CRISPR technology will likely benefit from taking all of the weight off of the shoulders of Cas9. Progress toward designing Cas9 molecules with altered PAM specificity, as well as the isolation of Cas9 from different species of bacteria, has helped expand the collection of genomic sites that can be targeted. It has also enabled multiplexing of orthogonal CRISPR proteins in a single cell to effect multiple functions simultaneously. More recently, the Zhang lab isolated an alternative type II CRISPR protein, Cpf1, purified from Francisella novicida. Cas9’s new BFF is also able to cut genomic DNA (as shown in human cells), but in a slightly different fashion than Cas9, generating sticky overhangs rather than blunt ends. Cpf1 also naturally harbors an alternate PAM specificity; rather than targeting sequences upstream of NGG, it prefers T-rich signatures (TTN), further expanding the genomes and genomic sites that can be targeted.

 

CRISPR/Cas9 has already proven to be one of the most versatile tools in the biologist’s toolbox to manipulate the genomes of a variety of species, but its utility continues to grow beyond these applications. Targeting Cas9 to the mitochondria rather than the nucleus can specifically edit the mitochondrial genome, with implications for disease treatment. Cas9 has been used for in vitro cloning experiments when traditional restriction enzymes just won’t do. And, by directly borrowing the concept of Cas9 immunity from bacteria, researchers have enabled enhanced resistance to viruses in plants engineered with Cas9 and gRNAs. While we ponder what innovative technique will come next, it’s important to think about how this cutting-edge technology that promises to bolster both basic and clinical research came to be: this particular avenue of research was paved entirely by machinery provided by the not-so-lowly bacteria. That’s pretty amazing, if you ask me.

Taking Genome Editing out of the Lab: Cause for Concern?

By Rebecca Delker, PhD

Genome editing – the controlled introduction of modifications to the genome sequence – has existed for a number of years as a valuable tool to manipulate and study gene function in the lab; however, because of inefficiencies intrinsic to the methods used, the technique has, until now, been limited in scope. The advent of CRISPR/Cas9 genome editing technology, a versatile, efficient and affordable technique, not only revolutionized basic cell biology research but has opened the real possibility of the use of genome editing as a therapy in the clinical setting and as a defense against pests destructive to the environment and human health.

 

CRISPR – Clustered Regularly Interspaced Short Palindromic Repeats – when teamed up with the nuclease, Cas9, to form CRISPR/Cas9 serves as a primitive immune system for bacteria and archaea, able to tailor a specific response to an invading virus. During viral invasion, fragments of the invader’s foreign genome are incorporated between the CRISPR repeats, forever encoding a memory of the attack in the bacterial genome. Upon future attack by the same virus, these memories can be called upon by transcribing the fragments to RNA, which, through Watson-Crick base-pairing, guide Cas9 to the viral genome, targeting it for destruction by induced double strand breaks (DSBs).

 

While an amazing and inspiring piece of biology in its own right, the fame of CRISPR/Cas9 did not skyrocket until the discovery that this RNA/nuclease team could be programmed to target specific sequences and induce DSBs in the complex genomes of all species tested. Of course the coolness factor of CRISPR technology does not end with the induction of DSBs but rather the use of these breaks to modify the genome. Taking advantage of a cell’s natural DNA repair machinery, CRISPR-induced breaks can be repaired by re-gluing the broken ends in a manner that results in the insertion or deletion of nucleotides – indels, for short – that disrupt gene function. More interesting for genome editing, though, DSBs can also serve as a portal for the insertion of man-made DNA fragments in a site-specific fashion, allowing the insertion of foreign genes or replacement of faulty genes.

 

CRISPR/Cas9 is not the first technology developed to precisely edit genomes. The DNA-binding (and cutting) engineered proteins, TALENS and Zinc Finger Nuclease (ZFNs), came into focus first but, compared to the RNA-guided Cas9 nuclease, are just a bit clunky – more complex in design with lower efficiency and less affordable. Even prior to these techniques, the introduction of recombinant DNA technology in the 1970s allowed the introduction of foreign DNA into the genomes of cells and organisms. Mice could be made to glow green using a jellyfish gene before the use of nucleases – just less efficiently. Now, the efficiency of Cas9 and the general ease of use of the technology paired with the decreased costs of genome sequencing enable scientists to edit the genome of just about any species, calling to mind the plots of numerous sci-fi films.

 

While it is unlikely that we will find ourselves in a GATTACA-like situation anytime soon, the potential for the application of CRISPR genome editing to human genomes has sparked conversation in the scientific literature and popular press. Though genome modification of somatic cells (regulators of body function) is generally accepted as an enhanced version of gene therapy, editing of germline cells (carriers of hereditary information) has garnered more attention because of the inheritance of the engineered modifications by generations to come. Many people, including some scientists, view this as a line that should never be crossed and argue that there is a slippery slope between editing disease-causing mutations and creating designer babies. Attempts by a group at Sun Yat-sen University in China to test the use of CRISPR in human embryos was referred to by many as irresponsible and their paper was rejected from top journals including Nature and Science. It should be noted, however, that this uproar occurred despite the fact that the Chinese scientists were working with non-viable embryos in excess from in vitro fertilization and with approval by the appropriate regulatory organizations.

 

Modifying human beings is unnatural; and, as such, seems to poke and prod at our sense of morality, eliciting the knee-jerk response of no. But, designer babies aside, how unethical is it to target genes to prevent disease – the ultimate preventative medicine, if you will? It is helpful to address this question in a broader context. All medical interventions – antibiotics, vaccinations, surgeries – are unnatural, but (generally) their ethics are not questioned because of their life-saving capabilities. If we look specifically at reproductive technology, there is precedent for controversial innovation. In the 1970s when the first baby was born by in vitro fertilization (IVF), people were skeptical of scientists making test-tube babies­ in labs. Now, it is a widely accepted technique and more than 5 million babies have been born with IVF.

 

Moving the fertilization process out of the body allowed for the unique possibility to prevent the transmission of genetic diseases from parent to child. Pre-Implantation Genetic Diagnosis (PGD), the screening of eggs or embryos for genetic mutations, allows for the selection of embryos that are free of disease for implantation. More recently, the UK (although not the US) legalized mitochondrial replacement therapy – a technique that replaces faulty mitochondria of the parental egg with that of a healthy donor either prior to or post fertilization. Referred to in the press as the creation of three-parent babies because genetic material is derived from three sources, this technique aims to prevent the transmission of debilitating mitochondrial diseases from mother to child. To draw clearer parallels to germline editing, mitochondria – energy producing organelles that are the likely descendants of an endosymbiotic relationship between bacteria and eukaryotic cells – contain their own genome. Thus, although mitochondrial replacement is often treated as separate from germline editing because nuclear DNA is left untouched, the genomic content of the offspring is altered. There are, of course, naysayers who don’t think the technique should be used in humans, but largely this is not because of issues of morality; rather, their opposition is rooted in questions of safety.

 

Germline editing could be the next big development in assisted reproductive technology (ART), but, like mitochondrial replacement and all other experimental therapies, safety is of utmost concern. Most notably, the high efficiency of CRISPR/Cas9 relative to earlier technologies comes at a cost. It has been demonstrated in a number of model systems, including the human embryos targeted by the Chinese group, that in addition to the desired insertion, CRISPR results in off-target mutations that could be potentially dangerous. Further, because our understanding of many genetic diseases is limited, there remains a risk of unintended consequences due to unknown gene-environmental interactions or the interplay of the targeted gene and other patient-specific genomic variants. The voluntary moratorium on clinical applications of germline editing in human embryos suggested by David Baltimore and colleagues is fueled by these unknowns. They stress the importance of initiating conversations between scientists, bioethicists, and government agencies to develop policies to regulate the use of genome editing in the clinical setting. Contrary to suggestions by others (and here), these discussions should not impede the progress of CRISPR research outside of the clinical setting. As a model to follow, a group of UK research organizations have publically stated their support for the continuation of genome editing research in human embryos as approved by the Human Fertilisation and Embryology Authority (HFEA), the regulatory organization that oversees the ethics of such research. Already, a London-based researcher has requested permission to use CRISPR in human embryos not as a therapeutic but to provide insight into early human development.

 

Much of the ethics of taking genome editing out of the lab is, thus, intertwined with safety. It is unethical to experiment with human lives without taking every precaution to prevent harm and suffering. Genome editing technology is nowhere near the point at which it is safe to attempt germline modifications, although clinical trials are in progress testing the efficacy of ZFN-based editing of adult cells to reduce viral titers in patients with HIV. This is not to say that we will never be able to apply CRISPR editing to germline cells in a responsible and ethical manner, but it is imperative that it be subject to regulations to assure the safety of humans involved, as well as to prevent the misuse of the technology.

 

This thought process must also be extended to the application of CRISPR to non-human species, especially because it does not typically elicit the same knee-jerk response as editing human progeny. CRISPR has been used to improve the efficiency of so-called gene drives, which guarantee inheritance of inserted genes, in yeast and fruit flies; and they have been proposed for use in the eradication of malaria by targeting the carrier of disease, the Anopheles mosquito. It is becoming increasingly important to consider the morality of our actions with regard to other species, as well as the planet, when developing technologies that benefit humanity. When thinking about the use of CRISPR-based gene drives to manipulate an entire species it is of utmost importance to take into consideration unintended consequences to the ecosystem. Though the popular press has not focused much on these concerns, a handful of scientific publications have begun to address these questions, releasing suggested safety measures.

 

There is no doubt that CRISPR is a powerful technology and will become more powerful as our understanding of the system improves. As such, it is critical to discuss the social implications of using genome editing as a human therapeutic and an environmental agent. Such discussions have begun with the convention in Napa attended by leading biomedical researchers and will likely continue with similar meetings in the future. This dialogue is necessary to ensure equal access to beneficial genome-editing therapies, to develop safeguards to prevent the misuse of technology, and to make certain that the safety of humans and our planet is held in the highest regard. However, too much of the real estate in today’s press regarding CRISPR technology has been fear-oriented (for example) and we run the risk of fuelling the anti-science mentality that already plagues the nation. Thus, it is equally important to focus on the good CRISPR has done and will continue to do for biological and biomedical research.

 

We are rapidly entering a time when the genomes of individuals around the world will be sequenced completely, along with many other organisms on the planet; however, this is just the tip of the iceberg of our understanding of the complex translation of this genome into life. For over a decade we have known the complete sequence of the lab mouse, but our understanding of the cellular processes within this mouse is still growing every day. Thus, there is an important distinction to be made between knowing a DNA sequence and understanding it well enough to be able to make meaningful (and safe) modifications. CRISPR genome editing technology, as it is applied in basic biology, is helping us make this leap from knowing to understanding in order to inform the creation of remedies for diseases that impact people, animals and our planet; and it is doing so with unprecedented precision and speed.

 

We must strike a balance that enables the celebration and use of the technology to advance knowledge, while assuring that the proper regulations are in place to prevent premature use in humans and hasty release into the environment. Or, as CRISPR researcher George Church remarked: “We need to think big, but also think carefully.”

 

Double Strand Breaks For The Win

 

By Rebecca Delker, PhD

The blueprint of an organism is its genome, the most fundamental code necessary for life. The carefully ordered – and structured – composition of As, Ts, Cs and Gs provides the manual that each cell uses to carry out its diverse function. As such, unintended alterations to this code often produce devastating consequences, manifesting themselves in disease phenotypes. From mutations to insertions and deletions, changes in the sequence of nucleotides alter the cell’s interpretation of the genome, like changing the order of words in a sentence. However, arguably one of the most threatening alterations is the double-strand break (DSB), a fracture in the backbone of the helical structure, splitting a linear piece of DNA in two, as if cut by molecular scissors. While the cell has a complex set of machinery designed to repair the damage, this process can be erroneous generating deletions, or even worse, translocations – permanently reordering the pages of the manual and ultimately transforming the cell. Given the central role translocations can play in oncogenic transformation, DSBs have understandably received a bad rap; but, as can be expected, not all is black and white and it’s worth asking whether there is an upside to DSBs.

 

One such commendable pursuit of the DSB serves to expand the capabilities of our genome. While it is true that the genome is the most basic code necessary for life, many of the processes within a cell actually require changes to the code. These can occur at all levels of the Central Dogma – modifications of proteins, RNA, and even DNA. B- and T-lymphocytes, cells that provide a good amount of heft to our immune system, are notable for their DNA editing skills. Tasked with protecting an organism from billions of potential pathogens, B- and T-cells must generate receptors specific for each unique attack. Rather than encoding each of these receptors in the genome – an impossibility due to size restrictions – B- and T-lymphocytes use DSBs to cut and paste small gene fragments to build a myriad of different receptor genes, each with a unique sequence and specificity (reviewed here). For immune cells, and for the survival of the organism, these DSBs are essential. Although tightly controlled, DNA rearrangements in immune cells are mechanistically similar to the sinister DSB-induced translocations that promote cancer formation; however, rather than causing disease, they help prevent it.

 

New research published this summer points to exciting, and even more unusual uses of DSBs in the regulation of gene expression. In a quest to understand the molecular effects of DSBs that are causally linked to a variety of neurological disorders, Ram Madabhushi, Li-Huei Tsai and colleagues instead discovered a necessary role for DSBs in the response of neurons to external stimulus. To adapt to the environment and generate long-term memories, changes in the “morphology and connectivity of neural circuits” occur in response to neuron-activation. This synaptic plasticity relies on a rapid increase in gene expression of a select set of early-response genes responsible for initiating the cascade of cellular changes needed for synaptogenic processes. In their paper published in Cell this summer, the authors reveal that the formation of DSBs in the promoter of early-response genes induces gene expression in response to neuron stimulation.

 

By treating neuronal cells with etoposide, an inhibitor of type-II topoisomerase enzymes (TopoII) that causes DSB formation, the researchers expected to find that DSBs interfere with transcription. In fact, most genes found to be differentially expressed in cells treated with the drug showed a decrease in expression; however, a small subset of genes, including the early-response genes, actually increased. Through a series of in vivo and ex vivo experiments, the researchers showed that even in the absence of drug treatment, DSB formation in the promoters of early-response genes is critical for gene expression – beautifully weaving a connection between neuronal activation, DSB formation and the rapid initiation of transcription in this subset of genes.

 

The serendipitous discovery of the positive effect of etoposide on gene expression lead the researchers to focus in on the role of topoisomerases, the guardians of DNA torsion, in DSB formation. As a helical structure composed of intertwined strands, nuclear processes like replication and transcription cause the over- or under-twisting of the DNA helix, leading the DNA molecule to twist around itself to relieve the torsional stress and form a supercoiled structure. Topoisomerases return DNA to its relaxed state by generating breaks in the DNA backbone – single-strand breaks by type I enzymes and DSBs by type II – untwisting the DNA and religating the ends. While etoposide can artificially force sustained DSBs, physiological TopoII-induced breaks are typically too transient to allow recognition by DNA repair proteins. The finding that TopoIIb-induced DSBs at the promoters of neuronal early-response genes are persistent and recognized by DNA repair machinery suggests a non-traditional role for TopoII enzymes, and DSBs, in transcription initiation and regulation.

 

In fact, the contribution of TopoII and DSBs in the regulation of neuronal genes may not be so niche. Another study published recently found a similar relationship between transcriptional activation and Topo-mediated DSB formation. Using the primordial cells of the germline in C. elegans as a model system, Melina Butuči, W. Matthew Michael and colleagues found that the abrupt increase in transcription as embryonic cells switch from a dependence on maternally provided RNA and protein to activation of its own genome induced widespread DSB formation. Amazingly, TOP-2, the C. elegans ortholog of TopoII is required for break formation; but, in contrast to neuronal activation, these DSBs occur in response to transcription rather than as a causative agent.

 

These recent studies build upon a growing recognition of a potentially intimate relationship between DSBs, torsion and transcription. DNA repair proteins, as well as topoisomerase enzymes have been shown to physically interact with transcription factors and gene regulatory elements; topoisomerase I and II facilitate the transcription of long genes; and, as in neuronal cells, studies of hormone-induced gene expression in cell culture reveal an activation mechanism by which TopoIIb induces DSBs selectively in the promoters of hormone-sensitive genes. Thus, DSBs may constitute a much broader mechanism for the regulation of gene-specific transcription than previously thought.

 

Given the grave danger associated with creating breaks in the genome, it is curious that the use of DSBs evolved to be an integral component of the regulation of transcription – an inescapable and ubiquitously employed process; however, as we expand our understanding of transcription to include the contribution of the higher-order structure of DNA, the utility of this particular evolutionary oddity comes into focus. Genomic DNA is not naked, but rather wrapped around histone proteins and packaged in the 3D space of the nucleus such that genomic interactions influence gene expression. Changes in the torsion and supercoiling of DNA have been associated with histone exchange, as well as changes in the affinity of DNA-binding proteins for DNA. In addition, the necessity of topoisomerase for the transcription of long genes occurs early as RNA polymerase transitions from initiation to elongation, suggesting that the role of TopoI and II is not to relieve transcription-induced torsion, but rather to resolve an inhibitory, likely 3D, genomic structure that is specific to genes of longer length. A similar mechanism may be involved at the neuronal early-response genes. In these cells, genomic sites of TopoIIb-binding and DSB-formation significantly overlap binding sites of CTCF – a crucial protein involved in genomic looping and higher-order chromatin structure – and, again, DNA breaks may function to collapse a structure constraining gene activation. Whatever the exact mechanisms at play here, these results inspire further inquiry into the relationship between DSBs, genome topology and transcription.

 

A cell’s unique interpretation of the genome via distinct gene expression programs is what generates cell diversity in multicellular organisms. Immune cells, like B- and T-lymphocytes, are different from neurons, which are different from skin cells, despite working from the same genomic manual. In B- and T-cells, DSBs are essential to piece together DNA fragments in a choose-your-own-adventure fashion to produce a reorganization of the manual necessary for cell function. And, as is emphasized in this growing body of research, DSBs function along with a variety of other molecular mechanisms to highlight, underline, dog-ear, and otherwise mark-up the genome in a cell-specific manner to facilitate the activation and repression of the correct genes at the correct time. Here, DSBs may not reorder the manual, but, nevertheless, play an equally important role in promoting proper cell function.

 

Lethal Weapon: How Many Lethal Mutations Do We Carry?

 

By John McLaughlin

Many human genetic disorders, such as cystic fibrosis and sickle cell anemia, are caused by recessive mutations with a predictable pattern of inheritance. Tracking hereditary disorders such as these is an important part of genetic counseling, for example when planning a family. In fact, there exists an online database dedicated to medical genetics, Mendelian Inheritance in Man, which contains information on most human genetic disorders and their associated phenotypes.

 

The authors of a new paper in Genetics set out to estimate the number of recessive lethal mutations carried in the average human’s genome. The researchers’ rationale for specifically focusing on recessive mutations is their higher potential impact on human health; because deleterious mutations that are recessive are less likely to be purged by selection, they can be maintained in heterozygotes with little impact on fitness, and therefore occur in greater frequency. For the purposes of their analysis, recessive lethal disorders (i.e. caused by a recessive lethal mutation) were defined by two main criteria: first, when homozygous for its causative mutation, the disease leads to the death or effective sterility of its carrier before reproductive age, and second, mutant heterozygotes do not display any disease symptoms.

 

For this study, the researchers had access to an excellent sample population, a religious community known as the Hutterian Brethren. This South Dakotan community of ~1600 individuals is one of three closely related groups that migrated from Europe to North America in the 19th century. Importantly, the community has maintained a detailed genealogical record tracing back to the original 64 founders, which also contains information on individuals affected by genetic disorders since 1950. An additional bonus is that the Hutterites practice a communal lifestyle in which there is no private property; this helps to reduce the impact of confounding socioeconomic factors on the analysis.

 

Four recessive lethal genetic disorders have been identified in the Hutterite pedigree since their more detailed records began: cystic fibrosis, nonsyndromic mental retardation, restrictive dermopathy, and myopathy. To estimate the number of recessive lethal mutations carried by the original founders, the team used both the Hutterite pedigree and a type of computational simulation known as “gene dropping”. In a typical gene dropping simulation, alleles are assigned to a founder population, the Mendelian segregation and inheritance of these alleles across generations is simulated, and the output is compared with the known pedigree. One simplifying assumption made during the analysis is that no de novo lethal mutations had arisen in the population since its founding; therefore, any disorders arising in the pedigree are attributed to mutations carried by the original founder population.

 

After combining the results from many thousands of such simulations with the Hutterite pedigree, the authors make a final estimate of roughly one or two recessive lethal mutations carried per human genome (the exact figure is ~0.58). What are the implications of this estimate for human health? Although mating between more closely related individuals has been long known to increase the probability of recessive mutations homozygosing in offspring, a more precise risk factor was generated from this study’s mutation estimate. In the discussion section it is noted that mating between first cousins, although fairly rare today in the United States, is expected to increase the chance of a recessive lethal disorder in offspring by ~1.8%.

 

Perhaps the most interesting finding from this paper was the consistency of the predicted lethal mutation load across the genomes of different animal species. The authors compared their estimates for human recessive lethal mutation number to those from previous studies examining this same question in fruit fly and zebrafish genomes, and observed a similar value of one or two mutations per genome. Of course, the many simplifying assumptions made during their analyses should be kept in mind; the estimates are considered tentative and will most likely be followed up with similar future work in other human populations. It will certainly be interesting to see how large-scale studies such as this one will impact human medical genetics in the future.

 

Cancer DNA: The New Frontier for Preventing and Curing Cancer

By Jesica Levingston Mac Leod, PhD

 

DNA Biomarkers are the hot topic in oncology right now, and the more precise, easy and effective they may be to detect cancer, the better.  This cutting edge technique has its origins in the discovery that fetuses shed fragments of DNA into the bloodstreams of the mothers, so do normal and cancer cells. The strategy to search for the most accurate “bar code” for each type of cancer is been approach from a bunch of oncologists around the world.

Researchers from the National Cancer institute, MD, published this month in the Lancet, a correlative biomarker study for lymphoma. In the study publish by Roschewski and col., they detected circulating tumor DNA encoding the clonal immunoglobulin gene sequence (VDJ) in the serum of patients with diffuse large-B-cell lymphoma. The VDJ immunoglobulin genes contain unique sequences that are markers of clonality. Malignant cell VDJ gene sequences could be detected in the serum of patients with diffuse large B-cell lymphoma and used to predict clinical disease recurrence after treatment. For this, they used next-generation DNA sequencing to analyze cell-free circulating tumor DNA in patients assigned to one of three different treatment protocols during a period of 20 years. They concluded that “Surveillance circulating tumor DNA identifies patients at risk of recurrence before clinical evidence of disease in most patients and results in a reduced disease burden at relapse. Interim circulating tumor DNA is a promising biomarker to identify patients at high risk of treatment failure.”

Earlier this year, Hyman and col., reported the analysis of a biomarker (the mutant BRAF(V600E)) in 2 systemic histiocytic disorders characterized by accumulation and infiltration of histiocytes in multiple tissues of the body, leading to organ compromise. These researchers from Memorial Sloan Kettering Cancer Center, New York, showed that in plasma and urinary samples cell free DNA provides a reliable method to detect the mutation that is a biomarker for these disorders, and it can monitor response to therapy in these disorders.

In Australia, the group of doctors  Tie, Cosgrove and col., identified and validated 3 protein-based biomarkers in independent cohorts of colorectal cancer (n = 145 and n = 197), which could be translated to a reliable, non-invasive blood-based screening test. The biomarker “winners” were selected by Elisa kits, and they are the following proteins: Insulin like growth factor binding protein 2 (IGFBP2), Dickkopf-3 (DKK3), and Pyruvate kinase M2(PKM2). (3) Anyways, this article is bout DNA markers: So, in a follow up study Tie and col. detected circulating tumor DNA in a high proportion of treatment naïve metastatic colorectal cancer patients. Moreover, they described that early changes in circulating tumor DNA during first-line chemotherapy predict the later radiologic response.  On other notes, they also reported that the intake of aspirin is not associated with improvements in survival in colon cancer patients, yeah, bad news for the daily aspirin takers.

Studying the blood samples of healthy elders (“wellderlies”, adults age 80 plus), the team lead by doctor Eric Topol, at the SCRIP center, is trying to find the immune response that attacked and effectively destroyed cancer cells. There is a high probability that these healthy elders had had abnormal cell/cells in their bodies at some point of their lives, which they attacked and destroyed, generating immune memory and powerful anti-cancer antibodies. In fact, a member of the team, Doctor Brunie Felding, had discovered that one of the proteins recognized by “wellderly” antibodies was Apolipoprotein E, suggesting that antibodies against this protein may help develop a targeted therapy against highly-expressing ApolipoproteinE cancers.

These new discoveries, plus the recently  FDA approval of three new immuno-oncology therapy drugs, called PD-1 inhibitors,  are bright examples of the importance of cancer research funding and support from the public to the government officers.

One of the most influential bioinformaticians/molecular biologists, Dr. George Church, genetics professor at Harvard, thinks that “the DNA is the ultimate computer code and we are all computer programmers”. Therefore, the study of the DNA fragments can help to solve multiple problems… it is working for cancer therapy, and it could be useful to treat even the most common disease: aging.