Featured image above: The peanut (Arachis hypogaea L.) is an important global food source and a staple crop grown in more than 100 countries, with approximately 42 million tonnes produced every year. Credit: ICRISAT
In a world first, under the leadership of University of Western Australia Winthrop Professor Rajeev Varshney, a global team sequenced and identified 50,324 genes in an ancestor of the cultivated peanut, Arachis duranensis.
They decoded the peanut DNA to gain an insight into the legume’s evolution and identify opportunities for using its genetic variability.
Importantly, the researchers have isolated 21 allergen genes, that, when altered, may be able to prevent an allergic response in humans.
The last decade has seen an alarming rise in peanut allergies with almost three in every 100 Australian children suffering, and only 20 per cent growing out of the allergy.
“These 21 characterised genes will be useful in breeding to select the superior varieties in the laboratory such as ones that are non-allergenic,” Varshney says.
They also identified additional genes that would help increase crop productivity and improve peanut nutritional value by altering oil biosynthesis and protein content.
Peanuts or groundnuts (Arachis hypogaea L.) are an important global food source and are a staple crop grown in more than 100 countries, with approximately 42 million tonnes produced every year.
Originating in South America, humans have cultivated peanuts for more than 7,600 years.
With a very high seed oil content of 45–56 per cent, peanut oil contains nearly half of the 13 essential vitamins and 35 per cent of the essential minerals.
Peanuts are also associated with several human health benefits, and have been found to improve cardiovascular health, reduce the risk of certain cancers, and control blood sugar levels.
“This genome sequence has helped to identify genes related to resistance to different diseases, tolerance to abiotic stresses and yield-related traits,” Varshney says.
“By using this ’molecular breeding’ approach, we can also accelerate the breeding process, and generate superior varieties in 3–5 years compared to traditional breeding that takes 6–10 years.”
Varshney says genomics-assisted breeding is a non-GMO or ‘non-transgenic’ approach.
“This is basically a simple breeding process that uses the molecular markers/genes to select the lines in the breeding, and farmers have been growing such varieties for many crops all around the world,” Varshney says.
Since successful genome sequencing was first announced in 2000 by geneticists Craig Venter and Francis Collins, the cost of mapping DNA’s roughly three billion base pairs has fallen exponentially. Venter’s effort to sequence his genome cost a reported US$100 million and took nine months. In March, Veritas Genetics announced pre-orders for whole genome sequencing, plus interpretation and counselling, for US$999.
Another genetics-based start-up, Human Longevity Inc (HLI), believes abundant, relatively affordable sequencing and collecting other biological data will revolutionise healthcare delivery. Founded by Venter, stem cell specialist Robert Hariri and entrepreneur Peter Diamandis, it claims to have sequenced more human genomes than the rest of the world combined, with 20,000 last year, a goal of reaching 100,000 this year and over a million by 2020.
HLI offers to “fully digitise” a patient’s body – including genotypic and phenotypic data collection, and MRI, brain vascular system scans – under its US$25,000 Health Nucleus service. Large-scale machine learning is applied to genomes and phenotypic data, following the efforts at what Venter has called “digitising biology”.
The claim is that artificial intelligence (AI) can predict maladies before they emerge, with “many” successes in saving lives seen in the first year alone. The company’s business includes an FDA-approved stem cell therapy line and individualised medicines. The slogan “make 100 the new 60” is sometimes mentioned in interviews with founders. Their optimism is not isolated. Venture capitalist Peter Thiel admits he takes human growth hormone to maintain muscle mass, confident the heightened risk of cancer will be dealt with completely by a cancer cure, and plans to live to 120.
“We understand what the surgeon needs and we embed that in an algorithm so it’s full automated.”
Bill Maris, CEO of GV (formerly Google Ventures), provocatively said last year that he thinks it’s possible to live to 500. An anit-ageing crusader, biological gerontologist Dr Aubrey de Grey, co-founder and chief science officer of Strategies for Engineered Negligible Senescence (SENS, whose backers include Thiel), has claimed that people alive today might live to 1000.
Longevity expectations are constantly being updated. Consider that, in 1928, American demographer Louis Dublin put the upper limit of the average human lifespan at 64.8. How long a life might possibly last is a complex topic and there’s “some debate”, says Professor of Actuarial Studies at UNSW Michael Sherris.
He says there have been studies examining how long a life could be extended if certain types of mortality, such as cancer, were eliminated, points out Sherris.
“However, humans will still die of something else,” he adds. “The reality is that the oldest person lived to 122.”
Will we see a 1000-year-old human? It isn’t known. What is clear, though, is that efforts to extend health and improve lives have gotten increasingly sophisticated.
The definition of bioengineering has also grown and changed over the years. Now concerning fields including biomaterials, bioinformatics and computational biology, it has expanded with the ability to apply engineering principles at the cellular and molecular level.
Editing out problems to reverse ageing
What if, further than reading and comprehending the code life is written in, it could also be rewritten as desired? A technique enabling this with better productivity and accuracy than any before it, has gotten many excited about this possibility.
“In terms of speed, it’s probably 10 times as quick as the old technology and is five to 10 times as cheap,” says Professor Robert Brink, Chief Scientist at the Garvan Institute of Medical Research’s MEGA Genome Engineering Facility.
The facility uses the CRISPR/Cas9 process to make genetically-engineered mice for academic and research institute clients. Like many labs, Brink’s facility has embraced CRISPR/Cas9, which has made editing plant and animal DNA so accessible even amateurs are dabbling.
First described in a June 2012 paper in Science, CRISPR/Cas9 is an adaptation of bacteria’s defences against viruses. Using a guide RNA matching a target’s DNA, the Cas9 in the title is an endonuclease that makes a precise cut at the site matching the RNA guide. Used against a virus, the cut degrades and kills it. The triumphant bacteria cell then keeps a piece of viral DNA for later use and identification (described sometimes as like an immunisation card). This is assimilated at a locus in a chromosome known as CRISPR (short for clustered regularly spaced short palindromic repeats).
In DNA more complicated than a virus’s, the cut DNA is able to repair itself, and incorporates specific bits of the new material into its sequence before joining the cut back up. Though ‘off-target’ gene edits are an issue being addressed, the technique has grabbed lots of attention. Some claim it could earn a Nobel prize this year. There is hope it can be used to eventually address gene disorders, such as Beta thalassemias and Huntington’s disease.
“Probably the obvious ones are gene therapy, for humans, and agricultural applications in plants and animals,” says Dr George Church of Harvard Medical School.
Among numerous appointments, Church is Professor of Genetics at Harvard Medical School and founding core faculty member at the Wyss Institute for Biologically Inspired Engineering. Last year, a team led by Dr Church used CRISPR to remove one of the major barriers to pig-human organ transplants – retroviral DNA – in pig embryos.
You can have what are called, ‘universal donors’. That’s being used, for example, in making cells that fight cancer.
“We’re now at the point where it used to be that you would have to have a perfect match between donor and recipient of human cells, but that was because you couldn’t engineer either one of them genetically,” he says. “You can engineer the donor so that it doesn’t cause an immune reaction. Now, you can have what are called, ‘universal donors’. That’s being used, for example, in making T cells that fight cancer – what some of us call CAR-T cells. You can use CRISPR to engineer them so that they’re not only effective against your cancer, but they don’t cause immune complications.”
Uncertainty exists in a number of areas regarding CRISPR (including patent disputes, as well as ethical concerns). However, there is no doubt it has promise.
“I think it will eventually have a great impact on medicine,” believes Brink. “It’s come so far, so quickly already that it’s almost hard to predict… Being able to do things and also being able to ensure everyone it’s safe is another thing, but that will happen.”
And as far as acceptance by the general public? Everything that works to overcome nature seems, well, unnatural, at least at first. Then it’s easier to accept once the benefits of are apparent. Church – who believes we could reverse ageing in five or six years – is hopeful about the future. He also feels the world needs people leery about progress, and who might even throw up a “playing God” argument or two.
“I mean it’s good to have people who don’t drive cars and don’t wear clothes and things like that, [and] it’s good to have people who are anti-technology because they give us an alternative way of thinking about things,” he says.
“[Genetic modification] is now broadly accepted in the sense that in many countries people eat genetically-modified foods and almost all countries, they use genetically-modified bacteria to make drugs like Insulin. I think there are very few people who would refuse to take Insulin just because it’s made in bacteria.”
A complete mindshift
Extended, healthier lives are all well and good. However, humans are constrained by the upper limits of what our cells are capable of, believes Dr Randal Koene.
For that and other reasons, the Dutch neuroscientist and founder of Carbon Copies is advancing the goal of Substrate Independent Minds (SIM). The most conservative form (relatively speaking) of SIM is Whole Brain Emulation, a reverse-engineering of our grey matter.
“In system identification, you pick something as your black box, a piece of the puzzle small enough to describe by using the information you can glean about signals going in and signals going out,” he explains, adding that the approach is that of mainstream neuroscience. “The system identification approach is used in neuroscience explicitly both in brain-machine interfaces, and in the work on prostheses.”
No brain much more complicated than a roundworm’s has been emulated yet. Its 302 neurons are a fraction of the human brain’s roughly 100 billion.
Koene believes that a drosophila fly, with a connectome of 100,000 or so neurons, could be emulated within the next decade. He is reluctant to predict when this might be achieved for people.
Precision medicine is opening the doorway to cancer data and offering hope to cancer patients. The power of genomics and the masses of data it creates is transforming cancer research and allowing personalised treatments with more proven effects.
Like hundreds of other cancer researchers, Mark Ragan and his team at The University of Queensland’s Institute for Molecular Bioscience (IMB) need to design experiments based on data from human and cancer genetics. Using data chips and next generation sequencing they must assemble their genetic data, interpret it to understand what genes their data refer to by comparison with other samples, and then classify patients’ cancer into subtypes. If they can’t match to an existing subtype, they identify a new one. Ragan says this intensive work requires access to as much genetic data as possible.
“It would literally be impossible without the data reuse that TCGA and other genome research programs offer”
Doorway to cancer data
Luckily, there are portals with this type of data. One of the first to start collecting cancer genome data was the The Cancer Genome Atlas (TCGA). The initials TCGA also make up the four-letter code of nucleotide bases thymine, cytosine, guanine and adenine that DNA uses to ‘write’ genetic information.
TCGA was started by the US National Institutes of Health (specifically the National Cancer Institute and the National Human Genome Research Institute) in 2006. Ragan says its initial goal was to generate data from researchers across research institutions on two cancer types. Early success expanded the initial goal to collect and profile more than 10,000 samples from over 20 tumour types. While the sample collection phase ended in 2013, data reuse ensures the data generated from those samples are still being analysed. Over 2700 papers have been published by TCGA data so far, including Australian researchers.
The data portal for the TCGA is “amazing” says Ragan. “It’s a really powerful portal that lets you ask questions and interrogate gigantic amounts of cancer genome data, including sequences, survival rates and subtype classifications.”
“Just about everything in it is open access, and the raw data, which isn’t open access, is made available by applying through research institutions’ ethics committees.”
A newer initiative inspired by the success of TCGA, the International Cancer Genome Consortium (ICGC), is an international project in which Ragan’s colleagues play a part. ICGC is built on the TCGA project, which provides about 60% of the patient data in ICGC’s Data Coordination Center. ICGC aims to cover 50 tumour types and currently funds 78 international cancer genome projects like the Australian project at IMB.
“Our research into breast cancer subtypes and survival would literally be impossible without the data reuse that TCGA and other genome research programs offer. We can tell if we’ve discovered a new cancer subtype or not, or even whether the existing data need reinterpreting,” says Ragan.
Knowing a patient’s cancer subtype allows more tailored, evidence-based treatment, potentially increasing survival rates and quality of life by allowing clinicians to more confidently focus on prescribing the drugs most likely to succeed for a particular patient.
One of the exciting things Ragan and other researchers are finding from the data is that some quite different cancer types have a similar genetic basis. This means drugs to treat one type of cancer, such as breast cancer, could be used for another, such as ovarian cancer.
“Instead of waiting 10 years for a new drug to be developed, patients may be able to be treated straight away with a drug that’s already available for another cancer,” says Ragan.
That’s good news for patients, and it also makes drug development, which can cost hundreds of millions of dollars per drug, more cost-effective. This potentially creates a larger market for a given drug, and makes some drugs financially viable that otherwise wouldn’t get to market.
Using miniaturised wine fermentations in 96-well microplates, the Tecan EVO 150 robotic system is screening bacteria for MLF efficiency and response to wine stress factors such as alcohol and low pH.
The bacteria are sourced from the AWRI’s wine microorganism culture collection in South Australia and elsewhere.
The robot can prepare and inoculate multiple combinations of bacteria strains and stress factors in red or white test wine, and then analyse malic acid in thousands of samples over the course of the fermentation.
In one batch, for example, 40 bacteria strains can be screened for MLF efficiency and response to alcohol and pH stress in red wine, with over 6000 individual L-malic acid analyses performed.
The AWRI says that this high-throughput approach provides a quantum leap in screening capabilities compared to conventional MLF testing methods and can be applied to a range of other research applications.
Additionally, the phenotypic data obtained from this research is being further analysed with genomic information, which will identify potential genetic markers for the stress tolerances of malolactic strains.
Scientists have identified two microbes that build bigger and more resilient feed crops, potentially boosting farmers’ bottom lines by millions of dollars.
The biotechnology research conducted at Flinders University in South Australia identified two strains of microbes that dramatically increase the ability of lucerne to fix atmospheric nitrogen, boosting the feed crop’s early growth and resilience, and ultimately its yield.
Research by medical biotechnology PhD student Hoang Xuyen Le drew on the hundreds of strains of endophytic actinobacteria, which grow naturally within legume roots. His research isolated and identified two strains of microbes that in laboratory and glasshouse trials were shown to promote growth in the shoots of the legume plants.
Nitrogen is absorbed by the plants through the formation of external nodules by symbiotic rhizobium bacteria that grow in the nodules. Franco says that following the inoculation of the lucerne seeds with spores of the actinobacteria, the nodules grew significantly larger, fixing greater amounts of nitrogen.
“Up to 50 or even 70 per cent more nitrogen was fixed,” says Franco.
The effect was to substantially improve the establishment of the lucerne, increase its resilience in drought conditions and also boost its yield.
“We found that our two main strains gave us a crop yield increase of 40 to 50 per cent in the glasshouse, and we would look for at least a 20 per cent improvement in the field,” says Franco.
He says as much as 25 per cent of the higher levels of nitrogen persisted in the soil, improving the growing conditions for subsequent crops.
The Flinders biotechnologists will now expand their trials on lucerne in the field, and will also look for similar effects in other legume crops, including peas, chick peas and faba and soya beans.
Further research is required to understand the underlying mechanism of the bugs: while it is likely that their natural propensity to produce bioactive compounds is partly responsible for increasing the general robustness of the inoculated lucerne by reducing disease, they may also be encouraging the growth of rhizobium bacteria in the soil.
Franco says that actinobacteria offer an environmentally friendly way of controlling disease, especially fungal root diseases such as Rhizoctonia, reducing the need for fossil-derived pesticides and fertiliser.
The potential to capture atmospheric nitrogen offers a major environmental benefit.
The legume seed crop, based in the South East of South Australia, is the basis of a national feed industry worth close to $100 million a year.
“This is very good news all round,” says Franco.
This article was first published by The Lead on 22 July 2015. Read the original article here.
The personalised medicine platform, which is being developed and applied with the support of the Cancer Therapeutics CRC, will tailor each child’s cancer treatment to the particular genetics of their individual tumour.
Then, using a combination of in vitro cell growth and testing on mice, treatment will be determined by the response in the laboratory of their own cancer cells to drugs.
The project, led by Professor Michelle Haber, Executive Director of Australia’s Children’s Cancer Institute, in collaboration with the National Institutes of Health in the USA, has been kickstarted with approximately $7.5 million in funding from the CRC budget.
“Although the survival rate of children’s cancer is now about 80%, this still means that on average about three kids in Australia are dying [from the disease] every week,” said Haber, who won the 2014 NSW Premier’s Award for Outstanding Cancer Research.
She said it was clear that individualised treatment is needed. “Two children can have the same diagnosis, but the standard treatment regimen will work for one child and fail with the other,” she explained.
The first step in the new approach is to take cells from a child’s tumour and run them through a set of molecular profiling tests, which reveal the genetic make-up of the cancer.
Haber’s team will soon settle on a panel of about 80 treatable genetic abnormalities for their targeted molecular profiling tests.
“We’ve trawled through the entire literature, pulling out what is known about genes that may be suitable for molecular targeted drug treatment,” she said. “This hasn’t been done for paediatric cancer before.”
The next step is to grow the child’s tumour cells. This is done either in laboratory flasks or in mice with deficient immune systems, known as ‘avatar mice’.
By rapidly scanning the cells, the researchers can test many drugs, either alone or in combinations, to see whether they knock back the cancer. And they don’t just try cancer drugs. Haber said that drugs as disparate as beta-blockers used in heart disease, as well as malaria drugs, can have anti-cancer effects.
Once a drug is shown to work in vitro, the next step is to use it in the avatar mice.
“We have been very excited by the excellent responses of the first patients to have their therapy modified by their treating clinicians, on the basis of information being generated from this new personalised medicine platform,” said Haber.
Clinical trials of the platform, to be spearheaded by Sydney Children’s Hospital, are scheduled for 2017. However, Haber hopes it will be sooner than that.
“The CRC funding is invaluable,” she said. “It is paying for vital staff and their research supplies. Of course, this is just the beginning for the platform and we will only be able to handle a few patients at first.
“Our plan is that, eventually, the treatment platform will be offered to every child in the country who has a high-risk malignancy.”