Why is a Dolphin Not a Cat?

How repurposing non-coding elements in the genome gave rise to the great 'mammalian radiation'

Friday, 30 January 2015

Exploring gene regulation in 20 mammals

provides insights into the mammalian radiation

that occurred over 100 million years ago. Credit:

Spencer Phillips, EMBL-EBI.

New research shows how evolution has given rise to a rich diversity of species by repurposing functional elements shared by all mammals. Published in Cell by scientists at the European Bioinformatics Institute (EMBL-EBI) and the University of Cambridge Cancer Research UK-Cambridge Institute (CRUK CI), the study demonstrates how methods for understanding human biology can be used to understand a broad range of species.

Mammals all share a common ancestor, and they share a lot of the same genes. So what exactly makes a dolphin not a cat, and how did we all start to diverge from one another millions of years ago? Part of the answer lies in how - and when - genes are regulated. This latest research explores the evolution of gene regulation in 20 mammalian species, and provides deep insights into the 'mammalian radiation', a time of rapid morphological evolution that occurred shortly after the asteroid impact that caused the extinction of the dinosaurs.

Leveraging findings from a study comparing the genome sequences of 29 mammals, and with the help of conservation organisations such as the UK Cetacean Strandings Investigation Programme and the Copenhagen Zoo, the team were able to study and compare gene regulation in liver cells from 20 key species including the naked mole rat, human, Tasmanian devil, dolphin and Sei whale.

"What we've shown is that evolution repurposes things that exist in all species, to make each species unique," explains Paul Flicek, head of Vertebrate Genomics at EMBL-EBI.

"By looking at gene promoters and enhancers in many different mammals, we demonstrated that species-specific enhancers come from ancient DNA - that evolution captures DNA that's been around for a long time, and uses it for gene regulation in specific tissues."

Evolution has two ways to turn changes in the genome into differences between species: it can change a protein sequence, or it can change the way promoters or enhancers control that protein's expression. Today's study also shows that in some cases evolution uses both strategies at once. When amino acid sequences evolve very quickly, important regulation changes occur at the same time: the protein-coding sequence and the corresponding regulatory sequence change synergistically.

Gathering the samples - the experimental efforts were led by Diego Villar of CRUK CI - took well over two years, and the experiments themselves produced a staggering volume of data. Analysing the results brought the team to a new frontier in bioinformatics.

"People spend a lot of time and money trying to understand human biology, so most of the tools we have are designed to study human genomes," explains Camille Berthelot of EMBL-EBI, who led the computational work.

"The reference data we have for the less studied species, like the Sei whale or Tasmanian devil, are nothing like the pored-over datasets we have for the human genome. A lot of what we did involved benchmarking, and making sure the methods and algorithms were fit for this kind of comparison."

"What inspired this work was a desire to get on top of the mountain, look out and see what is going on in the landscape of molecular evolution across the breadth of mammalian space," says Duncan Odom of CRUK CI and Wellcome Trust Sanger Institute.

"What's exciting about this study is that we now know we can start to answer questions about the functional genetics of many under-explored species - questions we usually can ask only of humans and mice. We can use tools developed to study humans to understand the biology of all kinds of animals, whether they're blackbirds or elephants, and explore their relationship with one another. This research has given us new insights into mammalian evolution, and proven how powerful these methods can be."

Source: EMBL

Contact: Mary Todd Bergman

Reference:

Enhancer Evolution across 20 Mammalian Species

Diego Villar, Camille Berthelot, Sarah Aldridge, Tim F. Rayner, Margus Lukk, Miguel Pignatelli, Thomas J. Park, Robert Deaville, Jonathan T. Erichsen, Anna J. Jasinska, James M.A. Turner, Mads F. Bertelsen, Elizabeth P. Murchison, Paul Flicek, Duncan T. Odom

Cell, Volume 160, Issue 3, p554–566, 29 January 2015, DOI: http://dx.doi.org/10.1016/j.cell.2015.01.006

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Mitochondrial Donation: How Many Women Could Benefit?

Two and a Half Thousand Women Could Benefit from Mitochondrial Donation in the UK

Thursday, 29 January 2015

Almost 2,500 women of child-bearing age in the UK are at risk of transmitting mitochondrial disease to their children, according to the most recent estimates published today in the New England Journal of Medicine.

The research offers the most recent evidence yet of how many families could potentially be helped by new IVF techniques to prevent mitochondrial disease, which would be permitted by new regulations on which a vote in parliament is imminent.

Mitochondrial diseases are caused by inherited mutations in the DNA contained in mitochondria - tiny structures present in every cell that generate energy. Mitochondrial diseases can be devastating and particularly affect tissues that have high energy demands - brain, muscle (including heart), liver and kidney.

New IVF-based techniques have been developed which have the potential to prevent the transmission of serious mitochondrial disease. Known as 'mitochondrial donation' the techniques involve removing faulty mitochondria inherited from the mother and replacing them with the healthy mitochondria of another woman. The nuclear DNA, containing 99.9% of genetic material from the mother and father, remains unchanged.

Researchers at the Wellcome Trust Centre for Mitochondrial Research at Newcastle University, which will be the first to offer mitochondrial donation if parliament agrees to new regulations of the Human Fertilisation and Embryology Act (1990), have now calculated how many women have disease-causing mutations in their mitochondrial DNA in order to estimate how many could potentially benefit. The new regulations only allow for mitochondrial donation to prevent mitochondrial disease and set no precedent for genetic manipulation of nuclear DNA.

They calculate that 2,473 women in the UK, and 12,423 women in the US, aged between 15 and 44 years, are at risk of passing on potentially lethal mitochondrial DNA disease to their children. This equates to an average of 152 births per year in the UK, and 778 births per year in the US.

The estimates were made by identifying the number of women in North East England who are at risk of passing on mitochondrial disease to their children and extrapolating the figure to the rest of the UK, based on the relative number of women of child-bearing age in the North East compared to the UK as a whole. A similar method was used for the US figures. The study did not account for variance due to ethnicity or potentially different fertility rates in different parts of the UK.

Researchers also assessed the fertility of women with mitochondrial DNA mutations. To do this they compared fertility data from their patients' to data about the general population, obtained from the UK Office for National Statistics. They found that mitochondrial mutation has no statistically significant effect on fertility rate.

Dr Gráinne Gorman from the Wellcome Trust Centre for Mitochondrial Research at Newcastle University, and joint first author of the paper, said:

"Our estimate of how many women could benefit from mitochondrial donation is based on our data from North East England, where we have very detailed insight into how many women are affected. We are confident that there are a similar number of women across the UK at risk of passing on mitochondrial disease to their children."

Professor Doug Turnbull, Director of the Wellcome Trust Centre for Mitochondrial Research at Newcastle University, and an author of the paper, said:

"Our findings have considerable implications for all countries that are considering allowing mitochondrial donation techniques. In the UK we are waiting for parliament to decide whether to support these regulations. This would allow women who carry these mutations greater reproductive choice. "

Source: Wellcome Trust 

Contact: Clare Ryan 

Reference:

Mitochondrial Donation: How many women could benefit? 

Gráinne S. Gorman, John P. Grady, Yi Ng, Andrew M. Schaefer, Richard J. McNally, Patrick F. Chinnery, Patrick Yu Wai Man, Mary Herbert, Robert W. Taylor, Robert McFarland, and Doug M. Turnbull

New England Journal of Medicine, January 28, 2015 DOI: 10.1056/NEJMc1500960

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New Cells May Help Treat Diabetes

U. Iowa group creates insulin-producing cells that normalize blood-sugar levels in diabetic mice

Thursday, 29 January 2015

University of Iowa researchers reprogrammed

human skin cells to create induced pluripotent

stem cells, which were then differentiated in a

stepwise fashion to create insulin-producing cells.

When these cells were transplanted into diabetic

mice, the cells secreted insulin and reduced the

blood sugar levels of the mice to normal or near-

normal levels. The image shows the insulin-

producing cells (right) and precursor cells (left).

Credit: University of Iowa.

Starting from human skin cells, researchers at the University of Iowa have created human insulin-producing cells that respond to glucose and correct blood-sugar levels in diabetic mice. The findings may represent a first step toward developing patient-specific cell replacement therapy for type 1 diabetes.

In the new study, published Jan. 28 in the journal PLOS ONE, the UI team led by Nicholas Zavazava, MD, PhD, UI professor of internal medicine, reprogrammed human skin cells to create induced pluripotent stem (iPS) cells, which were then coaxed into forming insulin-producing cells. When these cells were transplanted into diabetic mice, the cells secreted insulin and reduced the blood sugar levels of the mice to normal or near-normal levels.

Although the cells were not as effective as pancreatic cells in controlling blood sugar levels, Zavazava says that the results are an "encouraging first step" toward the goal of generating effective insulin-producing cells that can be used to potentially cure type 1 diabetes.

"This raises the possibility that we could treat patients with diabetes with their own cells," says Zavazava, who also is a member of the Fraternal Order of Eagles Diabetes Research Center at the UI.

"That would be a major advance, which will accelerate treatment of diabetes."

In type 1 diabetes, a person's immune system attacks and destroys the pancreatic beta cells that produce insulin. Although it is possible to treat type 1 diabetes with pancreas transplants from deceased donors, the demand for transplants far exceeds the availability of donated organs.

Zavazava's team is among several groups aiming to create an alternative source of insulin-producing pancreatic cells that can be transplanted into patients with type 1 diabetes. However, the UI study is the first to use human iPS cells to create the insulin-producing cells. Creating these cells from a patient's own cells would not only eliminate the need to wait for a donor pancreas, but would also mean patients could receive transplants without needing to take immunosuppressive drugs. Using iPS cells rather than embryonic stem cells as a starting point also avoids the ethical concerns some people have with using embryonic stem cells.

In the mouse study, the insulin-producing cells were placed under the kidney capsule - a thin membrane layer that surrounds the kidney - where they developed into an organ-like structure with its own blood supply. This new "organ" secreted insulin and gradually corrected the blood sugar levels in the diabetic mice over a period of several months. In addition, after the mice became normoglycemic, the glucose levels stayed steady.

By developing the cells in a stepwise fashion, the UI team was able to collect and use only those cells that would develop into pancreatic cells. This meant they were able to remove very immature (undifferentiated) cells that could form tumours. None of the mice developed tumours from the transplanted cells.

Source: University of Iowa

Contact: Jennifer Brown

Reference:

Human iPS Cell-Derived Insulin Producing Cells Form Vascularized Organoids under the Kidney Capsules of Diabetic Mice

Raikwar SP, Kim E-M, Sivitz WI, Allamargot C, Thedens DR and Nicholas Zavazava

PLoS ONE 10(1): e0116582 (2015), doi:10.1371/journal.pone.0116582

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Mammalian Heart Regenerative Capacity Depends on Severity of Injury

Full recovery and normal function restored in mouse models following mild injury

Friday, 23 January 2015

This is a neonatal mouse heart showing basal

level of proliferating cardiomyocytes. (Red-

cardiomyocytes; Green- proliferating

cardiomyocytes; RV-right ventricle; LV-left

ventricle.) Credit: The Saban Research Institute

of Children's Hospital Los Angeles. 

A new study by researchers at Children's Hospital Los Angeles has shown that neonatal mouse hearts have varying regenerative capacities depending upon the severity of injury. Using cryo-injury - damaging the heart through exposure to extreme cold in order to mimic cellular injury caused by myocardial infarction - investigators found that neonatal mouse hearts can fully recover normal function following a mild injury, though fail to regenerate after a severe injury.

Published online by the journal Developmental Biology, the study suggests that cardiac regeneration strategies should be based on the type and severity of heart injury.

"Using models such as zebrafish and neonatal mice that regenerate their hearts naturally, we can begin to identify important molecules that enhance heart repair," said Ellen Lien, PhD, of The Saban Research Institute of Children's Hospital Los Angeles. Lien, who was senior author on the paper, is also an assistant professor at the Keck School of Medicine of the University of Southern California.

New born mice have shown the capacity for heart regeneration, but it is rapidly lost by seven days after birth. Approaches to extend this regenerative capacity in a mammalian model, from the neonatal period to the juvenile or adult period, could help identify new treatment options for humans.

Acute myocardial infarction, commonly known as a heart attack, can be classified according to the extent of damage to the heart muscle. Severe, or trans-mural injury, is associated with a blood supply blockage to the full thickness of the heart. Non-trans-mural injury indicates a blockage that penetrates only partially through the heart muscle. The investigators were able to develop models for both types of injury.

In addition to differences in regenerative capacity, the investigators also found an indicator of tissue fibrosis or "scarring", profibrotic marker PAI-1, was markedly elevated only after trans-mural injury. In both models post-injury, the cells that form heart muscle, cardiomyocytes, did not increase significantly. However, responses to cardiac injury repair in the outer layer of the heart (epicardium) and blood vessels (revascularization) - were present.

"If we can figure out how to activate this youthful type of myocardial regeneration program in humans, it will be a major clinical breakthrough," said David Warburton, OBE, DSc, MD, director of Developmental Biology and Regenerative Medicine at The Saban Research Institute of CHLA. Warburton is also a professor at the Keck School of Medicine of USC and was co-author on the paper.

Source: Children's Hospital Los Angeles

Contact: Jennifer Jing

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Do Viruses Make Us Smarter?

Do Viruses Make Us Smarter?

Monday, 12 January 2015

A new study from Lund University in Sweden indicates that inherited viruses that are millions of years old play an important role in building up the complex networks that characterise the human brain.

Researchers have long been aware that endogenous retroviruses constitute around five per cent of our DNA. For many years, they were considered junk DNA of no real use, a side-effect of our evolutionary journey.

In the current study, Johan Jakobsson and his colleagues show that retroviruses seem to play a central role in the basic functions of the brain, more specifically in the regulation of which genes are to be expressed, and when. The findings indicate that, over the course of evolution, the viruses took an increasingly firm hold on the steering wheel in our cellular machinery. The reason the viruses are activated specifically in the brain is probably due to the fact that tumours cannot form in nerve cells, unlike in other tissues.

"We have been able to observe that these viruses are activated specifically in the brain cells and have an important regulatory role. We believe that the role of retroviruses can contribute to explaining why brain cells in particular are so dynamic and multifaceted in their function. It may also be the case that the viruses' more or less complex functions in various species can help us to understand why we are so different", says Johan Jakobsson, head of the research team for molecular neurogenetics at Lund University.

The article, based on studies of neural stem cells, shows that these cells use a particular molecular mechanism to control the activation processes of the retroviruses. The findings provide us with a complex insight into the innermost workings of the most basal functions of the nerve cells. At the same time, the results open up potential for new research paths concerning brain diseases linked to genetic factors.

"I believe that this can lead to new, exciting studies on the diseases of the brain. Currently, when we look for genetic factors linked to various diseases, we usually look for the genes we are familiar with, which make up a mere two per cent of the genome. Now we are opening up the possibility of looking at a much larger part of the genetic material which was previously considered unimportant. The image of the brain becomes more complex, but the area in which to search for errors linked to diseases with a genetic component, such as neurodegenerative diseases, psychiatric illness and brain tumours, also increases".

Source: Lund University

Contact: Johan Jakobsson

Reference:

TRIM28 represses transcription of endogenous retroviruses in neural progenitor cells

Liana Fasching, Adamandia Kapopoulou, Rohit Sachdeva, Rebecca Petri, Marie E. Jönsson, Christian Männe, Priscilla Turelli, Patric Jern, Florence Cammas, Didier Trono, Johan Jakobsson

Cell Reports, 2015 Jan 6;10(1):20-8, doi: 10.1016/j.celrep.2014.12.004

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Researchers Grow Functional Tissue-engineered Intestine from Human Cells

Regenerative medicine technique brings surgeons one step closer to helping patients

Thursday, 08 January 2015

This is the principal investigator Tracy C.

Grikscheit of The Saban Research Institute of

Children's Hospital Los Angeles. Credit:

Children's Hospital Los Angeles. 

A new study by researchers at Children's Hospital Los Angeles has shown that tissue-engineered small intestine grown from human cells replicates key aspects of a functioning human intestine. The tissue-engineered small intestine they developed contains important elements of the mucosal lining and support structures, including the ability to absorb sugars, and even tiny or ultra-structural components like cellular connections.

Published online January 8 by the American Journal of Physiology: GI & Liver, the work brings surgeons one step closer to helping human patients using this regenerative medicine technique.

Tissue-engineered small intestine (TESI) grows from stem cells contained in the intestine and offers a promising treatment for short bowel syndrome (SBS), a major cause of intestinal failure, particularly in premature babies and newborns with congenital intestinal anomalies. TESI may one day offer a therapeutic alternative to the current standard treatment, which is intestinal transplantation, and could potentially solve its largest challenges - donor shortage and the need for lifelong immunosuppression.

Tracy C. Grikscheit, MD, a principal investigator in The Saban Research Institute of CHLA and its Developmental Biology and Regenerative Medicine program, is also a pediatric surgeon at Children's Hospital Los Angeles and an assistant professor of surgery at the Keck School of Medicine of the University of Southern California.

Grikscheit aims to help her most vulnerable young patients, including babies who are born prematurely and develop a devastating disease called necrotizing enterocolitis (NEC), where life-threatening intestinal damage requires removal of large portions of the small intestine. Without enough intestinal length, the babies are dependent on intravenous feeding, which is costly and may cause liver damage. NEC and other contributors to intestinal failure occur in 24.5 out of 100,000 live births, and the incidence of SBS is increasing. Nearly a third of patients die within five years.

CHLA scientists had previously shown that TESI could be generated from human small intestine donor tissue implanted into immunocompromised mice. However, in those initial studies - published in July 2011 in the biomedical journal Tissue Engineering, Part A - only basic components of the intestine were identified. For clinical relevance, it remained necessary to more fully investigate intact components of function such as the ability to form a healthy barrier while still absorbing nutrition or specific mechanisms of electrolyte exchange.

The new study determined that mouse TESI is highly similar to the TESI derived from human cells, and that both contain important building blocks such as the stem and progenitor cells that will continue to regenerate the intestine as a living tissue replacement. And these cells are found within the engineered tissue in specific locations and in close proximity to other specialized cells that are known to be necessary in healthy human intestine for a fully functioning organ.

"We have shown that we can grow tissue-engineered small intestine that is more complex than other stem cell or progenitor cell models that are currently used to study intestinal regeneration and disease, and proven it to be fully functional as it develops from human cells," said Grikscheit.

"Demonstrating the functional capacity of this tissue-engineered intestine is a necessary milestone on our path toward one day helping patients with intestinal failure."

Source: Children's Hospital Los Angeles

Contact: Debra Kain

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Newer Genome Editing Tool Shows Promise in Engineering Human Stem Cells

Johns Hopkins study could advance use of stem cells for treatment and disease research

Tuesday, 06 January 2015

A powerful “genome editing” technology known as CRISPR has been used by researchers since 2012 to trim, disrupt, replace or add to sequences of an organism’s DNA. Now, scientists at Johns Hopkins Medicine have shown that the system also precisely and efficiently alters human stem cells.

In a recent online report on the work in Molecular Therapy, the Johns Hopkins team says the findings could streamline and speed efforts to modify and tailor human-induced pluripotent stem cells (iPSCs) for use as treatments or in the development of model systems to study diseases and test drugs.

“Stem cell technology is quickly advancing, and we think that the days when we can use iPSCs for human therapy aren’t that far away,” says Zhaohui Ye, Ph.D., an instructor of medicine at the Johns Hopkins University School of Medicine.

“This is one of the first studies to detail the use of CRISPR in human iPSCs, showcasing its potential in these cells.”

CRISPR originated from a microbial immune system that contains DNA segments known as clustered regularly interspaced short palindromic repeats. The engineered editing system makes use of an enzyme that nicks together DNA with a piece of small RNA that guides the tool to where researchers want to introduce cuts or other changes in the genome.

Previous research has shown that CRISPR can generate genomic changes or mutations through these interventions far more efficiently than other gene editing techniques, such as TALEN, short for transcription activator-like effector nuclease.

Despite CRISPR’s advantages, a recent study suggested that it might also produce a large number of “off-target” effects in human cancer cell lines, specifically modification of genes that researchers didn’t mean to change.

To see if this unwanted effect occurred in other human cell types, Ye, Linzhao Cheng, Ph.D., a professor of medicine and oncology in the Johns Hopkins University School of Medicine; and their colleagues pitted CRISPR against TALEN in human iPSCs, adult cells reprogrammed to act like embryonic stem cells. Human iPSCs have already shown enormous promise for treating and studying disease.

The researchers compared the ability of both genome editing systems to either cut out pieces of known genes in iPSCs or cut out a piece of these genes and replace it with another. As model genes, the researchers used JAK2, a gene that when mutated causes a bone marrow disorder known as polycythemia vera; SERPINA1, a gene that when mutated causes alpha1-antitrypsin deficiency, an inherited disorder that may cause lung and liver disease; and AAVS1, a gene that’s been recently discovered to be a “safe harbour” in the human genome for inserting foreign genes.

Their comparison found that when simply cutting out portions of genes, the CRISPR system was significantly more efficient than TALEN in all three gene systems, inducing up to 100 times more cuts. However, when using these genome editing tools for replacing portions of the genes, such as the disease-causing mutations in JAK2 and SERPINA1 genes, CRISPR and TALEN showed about the same efficiency in patient-derived iPSCs, the researchers report.

Contrary to results of the human cancer cell line study, both CRISPR and TALEN had the same targeting specificity in human iPSCs, hitting only the genes they were designed to affect, the team says. The researchers also found that the CRISPR system has an advantage over TALEN: It can be designed to target only the mutation-containing gene without affecting the healthy gene in patients, where only one copy of a gene is affected.

The findings, together with a related study that was published earlier in a leading journal of stem cell research (Cell Stem Cell), offer reassurance that CRISPR will be a useful tool for editing the genes of human iPSCs with little risk of off-target effects, say Ye and Cheng.

“CRISPR-mediated genome editing opens the door to many genetic applications in biologically relevant cells that can lead to better understanding of and potential cures for human diseases,” says Cheng.

Source: Johns Hopkins Medicine

Contact: Marin Hedin

Reference:

Efficient and Allele-Specific Genome Editing of Disease Loci in Human iPSCs

Cory Smith, Leire Abalde-Atristain, Chaoxia He, Brett R Brodsky, Evan M Braunstein, Pooja Chaudhari, Yoon-Young Jang, Linzhao Cheng and Zhaohui Ye

Molecular Therapy, December 16, 2014; doi:10.1038/mt.2014.226

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