Genome Editing: Risks and Rewards

Fifty years ago, the recombinant DNA revolution begun with the discovery of restriction enzymes which provides bacteria with innate immune system. These enzymes gave rise to the modern biotechnology industry.

Ten years ago, scientists discovered that bacteria also harbor adaptive immune system now known as CRISPR-Cas9 system which cut invading DNA that matches “guide RNAs” encoded in specific bacterial genome regions containing clustered regularly interspaced short palindromic repeats. Now this system is thought to have the potential for editing the genome in living human cells. It holds great therapeutic promise. For example, we can use it to delete the CCR5 gene in a patient’s immune cells, conferring the resistance to HIV. In normal population 1% of population lacks the functional copies of this gene and are thus naturally resistant to HIIV virus. CCR5 gene encodes a membrane receptor and this receptor is a requirement for the HIV virus entry as the virus binds to it. Thus, no functional receptor, no virus binding and no intrusion and free viruses are cleared away from the circulation by immune cells, mainly by macrophages. This pose no unique ethical issues because it affects only a patient’s own somatic cells.

However, the technology also raises eyebrows when it comes to editing human germ line DNA, in which changes cause permanent, heritable changes and may be to used in highly unethical applications such as for “designer babies” or “genetically modified humans.”

Various potential applications in germ line editing, however, must be considered. The most common argument for germline editing concerns preventing devastating monogenic diseases, such as Huntington’s disease. Though avoiding the roughly 3600 rare monogenic disorders caused by known disease genes is a compelling goal. Genome editing would add substantial value only when all embryos would be affected — for example, when one parent is homozygous for a dominant disorder or both parents are homozygous for a recessive disorder. But such situations are vanishingly rare for most monogenic diseases. For dominant Huntington’s disease, for example, the total number of homozygous patients in the medical literature is measured in dozens. For most recessive disorders, cases are quite infrequent (1 per 10,000 to 1 per million). 

It has been only about a decade since we first read the human genome. We should exercise great caution before we begin to rewrite it.

From: Brave New Genome, Eric S. Lander, Ph.D., The Broad Institute. A lengthier version of this article was published on June 3, 2015, at NEJM.org.

Engineered insulin could offer better diabetes control

Molecule stays in the bloodstream and is turned on when blood sugar levels are too high.

Anne Trafton | MIT News Office
February 9, 2015

For patients with diabetes, insulin is critical to maintaining good health and normal blood-sugar levels. However, it’s not an ideal solution because it can be difficult for patients to determine exactly how much insulin they need to prevent their blood sugar from swinging too high or too low.

Patients with Type I diabetes lack insulin, which is normally produced by the pancreas and regulates metabolism by stimulating muscle and fat tissue to absorb glucose from the bloodstream. Insulin injections, which form the backbone of treatment for diabetes patients, can be deployed in different ways. Some people take a modified form called long-acting insulin, which stays in the bloodstream for up to 24 hours, to ensure there is always some present when needed. Other patients calculate how much they should inject based on how many calories they consume or how much sugar is present in their blood.

The MIT team (Daniel Anderson and Robert Langer) set out to create a new form of insulin that would not only circulate for a long time, but would be activated only when needed — that is, when blood-sugar levels are too high. This would prevent patients’ blood-sugar levels from becoming dangerously low, a condition known as hypoglycemia that can lead to shock and even death.

To create this glucose-responsive insulin, the researchers first added a hydrophobic molecule called an aliphatic domain, which is a long chain of fatty molecules dangling from the insulin molecule. This helps the insulin circulate in the bloodstream longer, although the researchers do not yet know exactly why that is. One theory is that the fatty tail may bind to albumin, a protein found in the bloodstream, sequestering the insulin and preventing it from latching onto sugar molecules.

The researchers also attached a chemical group called PBA, which can reversibly bind to glucose. When blood-glucose levels are high, the sugar binds to insulin and activates it, allowing the insulin to stimulate cells to absorb the excess sugar.

The research team created four variants of the engineered molecule, each of which contained a PBA molecule with a different chemical modification, such as an atom of fluorine and nitrogen. They then tested these variants, along with regular insulin and long-acting insulin, in mice engineered to have an insulin deficiency.

In vitro fertilization: how safe is it?

IN VITRO FERTILIZATION FALLOUT

Mouse offspring conceived by in vitro fertilization are metabolically different from naturally conceived mice.

By Jyoti Madhusoodanan | January 1 | 2015 The Scientist

Embryos formed by in vitro fertilization (IVF) experience very different early conditions from naturally conceived embryos. In previous studies, Paolo Rinaudo of the University of California, San Francisco, and colleagues observed that IVF-conceived female mice were more insulin resistant and metabolized glucose poorly compared to normally conceived females, and that IVF mice of both sexes showed altered gene expression, which led them to wonder what might cause such lasting metabolic and transcriptional changes.

Rinaudo’s team transferred IVF-conceived and normally conceived blastocysts into recipient mice. Two months later, when the animals were young adults, the researchers examined their liver, muscle, fat, and pancreatic tissues for metabolic parameters.

Across tissues, the researchers observed many differences in metabolite levels between the IVF and natural cohorts. The normal sex disparities in fat metabolites shrank among the IVF mice, while in liver tissue the disparity was exaggerated. Fat tissue from IVF females also showed greater signs of oxidative stress. These alterations in metabolism and in underlying gene expression could play a role in the dysfunctional glucose metabolism and insulin resistance observed previously in mice.

The results suggest that the genome of IVF-conceived embryos “is utilized in a very different way, which translates into [their later] ability to handle metabolic changes,” says reproductive biologist Mark Green of the University of Melbourne in Australia. The big question, says Rinaudo, is “to discover if what happens in animals is true in human children.”

S.K. Feuer et al., “Sexually dimorphic effect of in vitro fertilization (IVF) on adult mouse fat and liver metabolomes,” Endocrinology, 155:4554-67, 2014.

Prevention of muscular dystrophy in mice by CRISPR/Cas9–mediated editing of germline DNA

Duchenne muscular dystrophy (DMD) is an inherited X-linked disease caused by mutations in the gene encoding dystrophin, a protein required for muscle fiber integrity. Dystrophin is a large cytoskeletal structural protein essential formuscle cellmembrane integrity. Without it, muscles degenerate, causing weakness and myopathy.

DMD affects approximately 1 in 3500 boys, death of patients usually occurs by age 25, typically from breathing complications and cardiomyopathy. Hence, therapy for DMD necessitates sustained rescue of skeletal, respiratory, and cardiac muscle structure and function. Although the genetic cause of DMD was identified nearly three decades ago, and several gene- and cell-based therapies have been developed to deliver functional Dmd alleles or dystrophin-like protein to diseased muscle tissue, numerous therapeutic challenges have remained and presently and there is no effective treatment.

In a recent study, researchers used clustered regularly interspaced short palindromic repeat/Cas9 (CRISPR/Cas9)–mediated genome editing to correct the dystrophin gene (Dmd) mutation in the germline of mdx mice, amodel for DMD, and then monitored muscle structure and function. Genome editing produced genetically mosaic animals containing 2 to 100% correction of the Dmd gene.The degree of muscle phenotypic rescue in mosaic mice exceeded the efficiency of gene correction, likely reflecting an advantage of the corrected cells and their contribution to regenerating muscle.With the anticipated technological advances that will facilitate genome editing of postnatal somatic cells, this strategymay one day allowcorrection of disease-causing mutations in the muscle tissue of patients with DMD. (Science, Sept 5 2014)

Sorting cells with sound waves

Acoustic device that separates tumor cells from blood cells could help assess cancer’s spread.

Researchers from MIT, Pennsylvania State University, and Carnegie Mellon University have devised a new way to separate cells by exposing them to sound waves as they flow through a tiny channel. Their device, about the size of a dime, could be used to detect the extremely rare tumor cells that circulate in cancer patients’ blood, helping doctors predict whether a tumor is going to spread.

Separating cells with sound offers a gentler alternative to existing cell-sorting technologies, which require tagging the cells with chemicals or exposing them to stronger mechanical forces that may damage them.

To sort cells using sound waves, scientists have previously built microfluidic devices with two acoustic transducers, which produce sound waves on either side of a microchannel. When the two waves meet, they combine to form a standing wave (a wave that remains in constant position). This wave produces a pressure node, or line of low pressure, running parallel to the direction of cell flow. Cells that encounter this node are pushed to the side of the channel; the distance of cell movement depends on their size and other properties such as compressibility.

However, these existing devices are inefficient: Because there is only one pressure node, cells can be pushed aside only short distances.

The new device overcomes that obstacle by tilting the sound waves so they run across the microchannel at an angle — meaning that each cell encounters several pressure nodes as it flows through the channel. Each time it encounters a node, the pressure guides the cell a little further off center, making it easier to capture cells of different sizes by the time they reach the end of the channel.

 

Want to live 100+ years!

By 2050, the number of people over the age of 80 will triple globally. These demographics could come at great cost to individuals and economies.

The problems of old age come as a package. More than 70% of people over 65 have two or more chronic conditions such as arthritis, diabetes, cancer, heart disease and stroke.

Restricting calorie intake in mice or introducing mutations in nutrient-sensing pathways can extend lifespans by as much as 50%. And these ‘Methuselah mice’ are more likely than controls to die without any apparent diseases.

The current tools for extending healthy life — better diets and regular exercise — are effective. But there is room for improvement, especially in personalizing treatments.

Longevity pathways identified in model organisms seem to be conserved in humans and can be manipulated in similar ways. Genetic surveys of centenarians implicate hormonal and metabolic systems. Long-term calorie restriction in humans induces drastic metabolic and molecular changes that resemble those of younger people, notably in inflammatory and nutrient-sensing pathways.

Several molecular pathways that increase longevity in animals are affected by approved and experimental drugs. Cancer and organ-rejection drugs such as rapamycin extend lifespan in mice and worms by muting the mTOR pathway, which regulates processes from protein synthesis to cell proliferation and survival. The sirtuin proteins, involved in a similar range of cellular processes, are activated by high concentrations of naturally occurring compounds (such as the resveratrol found in red wine) and extend lifespan in metabolically abnormal obese mice. A plethora of natural and synthetic molecules affect pathways that are shared by ageing, diabetes and metabolic syndrome. (Luigi Fontana, Brian K. Kennedy, Valter D. Longo, Douglas Seals& Simon Melov, Nature 511, 405–407 (24 July 2014) doi:10.1038/511405a)

 

 

Cell sugar coat and cancer

Cell membranes are covered with sugar-conjugated proteins. New findings suggest that the physical properties of this coating, which is more pronounced in cancer cells, regulate cell survival during tumour spread.

The cell membrane serves as a signalling interface that allows cells to exchange information with their environment. It is constructed from lipids and contains both transmembrane and lipid-tethered proteins, which can be further modified through the covalent addition of sugars to build glycoproteins. Cancer cells frequently have higher levels of glycoproteins, such as mucin-1, than do healthy cells, and individual glycoproteins can transduce environmental signals that directly promote malignancy. However, glycoproteins also collectively organize into a glycocalyx.

Integrins are transmembrane receptors that bind extracellular matrix (ECM) proteins and are key interpreters and integrators of both the biochemical composition and the mechanical properties of the extracellular space. Cells with a thick glycocalyx are more efficient at receiving cell-survival signals through integrins, owing to the kinetic-trap properties of the glycocalyx. This may facilitate metastatic spread by enabling cancer cells to survive in the varied tissue and fluid environments they must traverse to colonize distant organs.

Integrin-based cell-matrix signalling is important for many steps in metastasis, including the migration of cancer cells out of the primary tumour and through the ECM, their entry into the vasculature, survival in the circulation, adhesion to the vessel wall, exit from the vasculature, and migration to and proliferative expansion in a distant organ. By reducing the rate of integrin binding and promoting clustering at existing adhesion sites, bulky glycoproteins act to promote a stable interaction between the cancer cells and the ECM.

We expect that the optimal glycocalyx thickness for supporting different aspects of cancer-cell behaviour, including invasion, vascular spread and metastatic colonization, varies. But how cancer cells adapt their glycocalyx to the diverse surroundings that they experience during metastasis is an interesting open question. Andrew J. Ewald & Mikala Egeblad, Nature511,298–299(17 July 2014)doi:10.1038/nature13506)