Combining Genomic Sequencing and Stem Cell Technology to Understand Disease

New York Stem Cell Foundation and Personalgenomes.org working together to accelerate research

Monday, 09 December 2013

Today, the New York Stem Cell Foundation (NYSCF) Research Institute and PersonalGenomes.org  announced a partnership to identify genetic and environmental contributions to trait and disease development. Cell lines generated by NYSCF will complement genomic data and medical histories contributed by participants in the Harvard Personal Genome Project (PGP), creating a unique and powerful resource to help researchers identify causes of disease.

"Mapping human genetics has laid the groundwork for personalized medicine to tailor treatments to patients on a level not previously achievable. And, now with stem cells, we can take this a step further: we can test and refine drugs on a patient's actual diseased cells," said Susan L. Solomon, CEO of NYSCF.

"Our challenge, going forward, is to leverage the tremendous amount of information from the PGP as the world's only open access source of human genome, microbiome and disease data into a resource for testing causes and cures. We are using PGP stem cells for studying human mutations, gene editing therapies, and novel transplantation methods. That is why we see such value in the integration of these new stem cell technologies through this partnership with NYSCF," said George Church, PhD, Professor of Genetics Harvard Medical School and Founder of the PGP.

To achieve this goal, NYSCF scientists will generate stem cell lines from skin samples of participants in the Harvard PGP. These cell lines can then be studied and compared to data gathered by the PGP including whole genomes, medical histories, body microbiomes and hundreds of other traits from over 3,000 participants. This tool will help achieve the joint goal of "functionalizing" personal genetics for all individuals, meaning using personal genetic information to make informed medical and health decisions.

In 2001, the Human Genome Project (HGP) finished the first draft of the human genome, sequencing most of the 3 billion base pairs that compose human DNA. This took over ten years and cost nearly $3 billion. Today, human genome sequencing is higher quality and can be completed in a day for a little over $1000 enabling researchers an unprecedented look at the building blocks of both normal development and disease.

To additionally speed up the pace of discovery, the PGP developed the open consent framework which enables research studies to make genetic and medical data freely available online to the public and for researchers to analyse and begin to tie underlying genetic patterns or sequences to the development of traits and diseases. Similarly, NYSCF makes cell lines available to researchers in its efforts to find treatments and cures for disease.

Initially, 50 PGP participants will donate skin samples for generation of induced pluripotent stem (iPS) cell lines, which are genetically matched, self-renewing cells that can become any of the body's cell types. Clinicians at dermatology clinics will perform a punch biopsy, a minor procedure to obtain a skin sample, on consenting participants.

These skin samples are then sent to the NYSCF Research Institute, where scientists will derive iPS cells using the NYSCF Global Stem Cell Array™, a novel robotic technology that automates the generation of iPS cell lines. Unlike traditional, by-hand methods to procure stem cells, the Array create standardized, quality controlled cells, enabling scientists to compare stem cells from different participants.

NYSCF scientists will take these iPS cells and derive different adult cell types of interest for research investigations. These cells, which reflect the participants' genetics, provide a powerful tool to study how genetic differences between people can affect disease development and trait expression. Additionally, NYSCF will make these cells available to the broader scientific community through the NYSCF repository.

"Overlaid with medical data, these stem cell models provide a more complete picture of each participant, effectively functionalizing stem cell technology," said Scott Noggle, PhD, Director of the NYSCF Laboratory and NYSCF – Charles Evans Senior Research Fellow for Alzheimer's Disease.

Source: New York Stem Cell Foundation 

Contact: David McKeon

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Human Stem Cells Predict Efficacy of Alzheimer Drugs

Researchers from the University of Bonn use reprogrammed patient neurons for drug testing

Saturday, 07 December 2013

Once established such neural stem cells can be

used to continuously generate neurons for drug

testing and disease modelling. Depicted is an

immunofluorescence staining where proteins

characteristic of neural stem cells are labelled

with fluorescing antibodies (Nestin in green,

Dach1 in red). Credit: Jerome Mertens/Uni.

Bonn.

Why do certain Alzheimer medications work in animal models but not in clinical trials in humans? A research team from the University of Bonn and the biomedical enterprise LIFE & BRAIN GmbH has been able to show that results of established test methods with animal models and cell lines used up until now can hardly be translated to the processes in the human brain. Drug testing should therefore be conducted with human nerve cells, conclude the scientists. The results are published by Cell Press in the journal Stem Cell Reports.

In the brains of Alzheimer patients, deposits forms that consists essentially of beta-amyloid and are harmful to nerve cells. Scientists are therefore searching for pharmaceutical compounds that prevent the formation of these dangerous aggregates. In animal models, certain non-steroidal anti-inflammatory drugs (NSAIDs) were found to a reduced formation of harmful beta-amyloid variants. Yet, in subsequent clinical studies, these NSAIDs failed to elicit any beneficial effects.

"The reasons for these negative results have remained unclear for a long time", says Prof. Dr. Oliver Brüstle, Director of the Institute for Reconstructive Neurobiology of the University of Bonn and CEO of LIFE & BRAIN GmbH.

"Remarkably, these compounds were never tested directly on the actual target cells – the human neuron", adds lead author Dr. Jerome Mertens of Prof. Brüstle's team, who now works at the Laboratory of Genetics in La Jolla (USA).

This is because, so far, living human neurons have been extremely difficult to obtain. However, with the recent advances in stem cell research it has become possible to derive limitless numbers of brain cells from a small skin biopsy or other adult cell types.

Scientists transform skin cells into nerve cells

Now a research team from the Institute for Reconstructive Neurobiology and the Department of Neurology of the Bonn University Medical Center together with colleagues from the LIFE & BRAIN GmbH and the University of Leuven (Belgium) has obtained such nerve cells from humans. The researchers used skin cells from two patients with a familial form of Alzheimer's Disease to produce so-called induced pluripotent stem cells (iPS cells), by reprogramming the body's cells into a quasi-embryonic stage. They then transformed the resulting so-called "jack-of-all-trades cells" into nerve cells.

Using these human neurons, the scientists tested several compounds in the group of non-steroidal anti-inflammatory drugs. As control, the researchers used nerve cells they had obtained from iPS cells of donors who did not have the disease. Both in the nerve cells obtained from the Alzheimer patients and in the control cells, the NSAIDs that had previously tested positive in the animal models and cell lines typically used for drug screening had practically no effect. The values for the harmful beta-amyloid variants that form the feared aggregates in the brain remained unaffected when the cells were treated with clinically relevant dosages of these compounds.

Metabolic processes in animal models differ from humans

"In order to predict the efficacy of Alzheimer drugs, such tests have to be performed directly on the affected human nerve cells", concludes Prof. Brüstle's colleague Dr. Philipp Koch, who led the study.

Why do NSAIDs decrease the risk of aggregate formation in animal experiments and cell lines but not in human neurons? The scientists explain this with differences in metabolic processes between these different cell types.

"The results are simply not transferable", says Dr. Koch.

The scientists now hope that in the future, testing of potential drugs for the treatment of Alzheimer's disease will be increasingly conducted using neurons obtained from iPS cells of patients.

"The development of a single drug takes an average of ten years", says Prof. Brüstle.

"By using patient-specific nerve cells as a test system, investments by pharmaceutical companies and the tedious search for urgently needed Alzheimer medications could be greatly streamlined".

Source: University of Bonn 

Contact: Dr. Oliver Brüstle

Reference:

APP Processing in Human Pluripotent Stem Cell-Derived Neurons is Resistant to NSAID-Based Gamma-Secretase Modulation 

Jerome Mertens, Kathrin Stüber, Patrick Wunderlich, Julia Ladewig, Jaideep C. Kesavan, Rik Vandenberghe, Mathieu Vandenbulcke, Philip van Damme, Jochen Walter, Oliver Brüstle, Philipp Koch

Stem Cell Reports, 05 December 2013, DOI: 10.1016/j.stemcr.2013.10.011

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Oldest Hominine DNA Sequenced

Mitochondrial genome of a 400,000-year-old representative of the genus Homo sequenced

Thursday, 05 December 2013

This is a skeleton of a Homo heidelbergensis 

from Sima de los Huesos, a unique cave site in

Northern Spain. Credit: Javier Trueba, Madrid 
Scientific Films. 

Using novel techniques to extract and study ancient DNA researchers at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, have determined an almost complete mitochondrial genome sequence of a 400,000-year-old representative of the genus Homo from Sima de los Huesos, a unique cave site in Northern Spain, and found that it is related to the mitochondrial genome of Denisovans, extinct relatives of Neanderthals in Asia. DNA this old has until recently been retrieved only from the permafrost.

Sima de los Huesos (SH), the "bone pit", is a cave site in Northern Spain that has yielded the world's largest assembly of Middle Pleistocene hominine fossils, consisting of at least 28 skeletons, which have been excavated and pieced together over the course of more than two decades by a Spanish team of palaeontologists led by Juan-Luis Arsuaga. The fossils are classified as Homo heidelbergensis but also carry traits typical of Neanderthals. Until now it had not been possible to study the DNA of these unique hominines.

Matthias Meyer at work in the clean lab. 
Credit: Max Planck Institute for 
Evolutionary Anthropology. 

Matthias Meyer and his team from the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, have developed new techniques for retrieving and sequencing highly degraded ancient DNA. They then joined forces with Juan-Luis Arsuaga and applied the new techniques to a cave bear from the Sima de los Huesos site. After this success, the researchers sampled two grams of bone powder from a hominine thigh bone from the cave. They extracted its DNA and sequenced the genome of the mitochondria or mtDNA, a small part of the genome that is passed down along the maternal line and occurs in many copies per cell. The researchers then compared this ancient mitochondrial DNA with Neanderthals, Denisovans, present-day humans, and apes.

The Sima de los Huesos hominines lived

approximately 400,000 years ago during the

Middle Pleistocene. Credit: Javier Trueba, 
Madrid Scientific Films.

From the missing mutations in the old DNA sequences the researchers calculated that the Sima hominine lived about 400,000 years ago. They also found that it shared a common ancestor with the Denisovans, an extinct archaic group from Asia related to the Neanderthals, about 700,000 years ago.

"The fact that the mtDNA of the Sima de los Huesos hominine shares a common ancestor with Denisovan rather than Neanderthal mtDNAs is unexpected since its skeletal remains carry Neanderthal-derived features", says Matthias Meyer.

Considering their age and Neanderthal-like features, the Sima hominines were likely related to the population ancestral to both Neanderthals and Denisovans. Another possibility is that gene flow from yet another group of hominines brought the Denisova-like mtDNA into the Sima hominines or their ancestors.

"Our results show that we can now study DNA from human ancestors that are hundreds of thousands of years old. This opens prospects to study the genes of the ancestors of Neanderthals and Denisovans. It is tremendously exciting" says Svante Pääbo, director at the Max Planck Institute for Evolutionary Anthropology.

Prof. Juan Luis Arsuaga, Director of the Centro

Mixto de Evolución and Compòrtamiento

Humanos in Madrid, Spain. Credit: Javier 
Trueba, Madrid Scientific Films. 

"This unexpected result points to a complex pattern of evolution in the origin of Neanderthals and modern humans. I hope that more research will help clarify the genetic relationships of the hominines from Sima de los Huesos to Neanderthals and Denisovans" says Juan-Luis Arsuaga, director of the Center for Research on Human Evolution and Behaviour. The researchers are now pursuing this goal by focusing on retrieving DNA from more individuals from this site and on retrieving also nuclear DNA sequences.

Source: Max-Planck-Gesellschaft 

Contact: Dr. Matthias Meyer

Reference:

A mitochondrial genome sequence of a hominine from Sima de los Huesos

Matthias Meyer, Qiaomei Fu, Ayinuer Aximu-Petri, Isabelle Glocke, Birgit Nickel, Juan-Luis Arsuaga, Ignacio Martínez, Ana Gracia, José María Bermúdez de Castro, Eudald Carbonell and Svante Pääbo

Nature, 4 December 2013, DOI: 10.1038/nature12788

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Human Stem Cells Converted to Functional Lung Cells

Possibility of generating lung tissue for transplant using a patient's own cells

Monday, 02 December 2013

For the first time, scientists have succeeded in transforming human stem cells into functional lung and airway cells. The advance, reported by Columbia University Medical Center (CUMC) researchers, has significant potential for modelling lung disease, screening drugs, studying human lung development, and, ultimately, generating lung tissue for transplantation. The study was published today in the journal Nature Biotechnology.

Human skin cells can now be reprogrammed into

induced pluripotent stem cells, which are similar

to human embryonic stem cells, and then into

functional lung and airway cells. Such cells have

potential for use in disease modelling, drug

screening, the study of lung development, and the

generation of lung tissue for transplantation.

Credit: Hans-Willem Snoeck, M.D., Ph.D.,

Columbia University Medical Center.

"Researchers have had relative success in turning human stem cells into heart cells, pancreatic beta cells, intestinal cells, liver cells, and nerve cells, raising all sorts of possibilities for regenerative medicine," said study leader Hans-Willem Snoeck, MD, PhD, professor of medicine (in microbiology & immunology) and affiliated with the Columbia Center for Translational Immunology and the Columbia Stem Cell Initiative.

"Now, we are finally able to make lung and airway cells. This is important because lung transplants have a particularly poor prognosis. Although any clinical application is still many years away, we can begin thinking about making autologous lung transplants — that is, transplants that use a patient's own skin cells to generate functional lung tissue."

The research builds on Dr. Snoeck's 2011 discovery of a set of chemical factors that can turn human embryonic stem (ES) cells or human induced pluripotent stem (iPS) cells into anterior foregut endoderm — precursors of lung and airway cells. (Human iPS cells closely resemble human ES cells but are generated from skin cells, by coaxing them into taking a developmental step backwards. Human iPS cells can then be stimulated to differentiate into specialized cells — offering researchers an alternative to human ES cells.)

In the current study, Dr. Snoeck and his colleagues found new factors that can complete the transformation of human ES or iPS cells into functional lung epithelial cells (cells that cover the lung surface). The resultant cells were found to express markers of at least six types of lung and airway epithelial cells, particularly markers of type 2 alveolar epithelial cells. Type 2 cells are important because they produce surfactant, a substance critical to maintain the lung alveoli, where gas exchange takes place; they also participate in repair of the lung after injury and damage.

The findings have implications for the study of a number of lung diseases, including idiopathic pulmonary fibrosis (IPF), in which type 2 alveolar epithelial cells are thought to play a central role.

"No one knows what causes the disease, and there's no way to treat it," says Dr. Snoeck.

"Using this technology, researchers will finally be able to create laboratory models of IPF, study the disease at the molecular level, and screen drugs for possible treatments or cures."

"In the longer term, we hope to use this technology to make an autologous lung graft," Dr. Snoeck said.

"This would entail taking a lung from a donor; removing all the lung cells, leaving only the lung scaffold; and seeding the scaffold with new lung cells derived from the patient. In this way, rejection problems could be avoided." Dr. Snoeck is investigating this approach in collaboration with researchers in the Columbia University Department of Biomedical Engineering.

"I am excited about this collaboration with Hans Snoeck, integrating stem cell science with bioengineering in the search for new treatments for lung disease," said Gordana Vunjak-Novakovic, co-author of the paper and Mikati Foundation Professor of Biomedical Engineering at Columbia's Engineering School and professor of medical sciences at Columbia University College of Physicians and Surgeons.

Source: Columbia University Medical Center

Contact: Karin Eskenazi

Reference:

Highly efficient generation of airway and lung epithelial cells from human pluripotent stem cells

Sarah X L Huang, Mohammad Naimul Islam, John O'Neill, Zheng Hu, Yong-Guang Yang, Ya-Wen Chen, Melanie Mumau, Michael D Green, Gordana Vunjak-Novakovic, Jahar Bhattacharya & Hans-Willem Snoeck

Nature Biotechnology, 01 December 2013, doi:10.1038/nbt.2754

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http://cellnews-blog.blogspot.com/

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