Expansions of DNA repeats are very hard to analyze. A method developed by researchers at the Max Planck Institute for Molecular Genetics in Berlin allows for a detailed look at these previously inaccessible regions of the genome. It combines nanopore sequencing, stem cell, and CRISPR-Cas technologies. The method could improve the diagnosis of various congenital diseases and cancers in the future.
Large parts of the genome consist of monotonous regions where short sections of the genome repeat hundreds or thousands of times. But expansions of these "DNA repeats" in the wrong places can have dramatic consequences, like in patients with Fragile X syndrome, one of the most commonly identifiable hereditary causes of cognitive disability in humans. However, these repetitive regions are still regarded as an unknown territory that cannot be examined appropriately, even with modern methods.
A research team led by Franz-Josef Mller at the Max Planck Institute for Molecular Genetics in Berlin and the University Hospital of Schleswig-Holstein in Kiel recently shed light on this inaccessible region of the genome. Mller's team was the first to successfully determine the length of genomic tandem repeats in patient-derived stem cell cultures. The researchers additionally obtained data on the epigenetic state of the repeats by scanning individual DNA molecules. The method, which is based on nanopore sequencing and CRISPR-Cas technologies, opens the door for research into repetitive genomic regions, and the rapid and accurate diagnosis of a range of diseases.A gene defect on the X chromosomeIn Fragile X syndrome, a repeat sequence has expanded in a gene called FMR1 on the X chromosome. "The cell recognizes the repetitive region and switches it off by attaching methyl groups to the DNA," says Mller. These small chemical changes have an epigenetic effect because they leave the underlying genetic information intact. "Unfortunately, the epigenetic marks spread over to the entire gene, which is then completely shut down," explains Mller. The gene is known to be essential for normal brain development. He states: "Without the FMR1 gene, we see severe delays in development leading to varying degrees of intellectual disability or autism."
Female individuals are, in most cases, less affected by the disease, since the repeat region is usually located on only one of the two X chromosomes. Since the unchanged second copy of the gene is not epigenetically altered, it is able to compensate for the genetic defect. In contrast, males have only one X chromosome and one copy of the affected gene and display the full range of clinical symptoms. The syndrome is one of about 30 diseases that are caused by expanding short tandem repeats.
First precise mapping of short tandem repeats
In this study, Mller and his team investigated the genome of stem cells that were derived from patient tissue. They were able to determine the length of the repeat regions and their epigenetic signature, a feat that had not been possible with conventional sequencing methods. The researchers also discovered that the length of the repetitive region could vary to a large degree, even among the cells of a single patient.
The researchers also tested their process with cells derived from patients that contained an expanded repeat in one of the two copies of the C9orf72 gene. This mutation leads to one of the most common monogenic causes of frontotemporal dementia and amyotrophic lateral sclerosis. "We were the first to map the entire epigenetics of extended and unchanged repeat regions in a single experiment," says Mller. Furthermore, the region of interest on the DNA molecule remained physically wholly unaltered. "We developed a unique method for the analysis of single molecules and for the darkest regions of our genome - that's what makes this so exciting for me."
Tiny pores scan single molecules
"Conventional methods are limited when it comes to highly repetitive DNA sequences. Not to mention the inability to simultaneously detect the epigenetic properties of repeats," says Bjrn Brndl, one of the first authors of the publication. That's why the scientists used Nanopore sequencing technology, which is capable of analyzing these regions. The DNA is fragmented, and each strand is threaded through one of a hundred tiny holes ("nanopores") on a silicon chip. At the same time, electrically charged particles flow through the pores and generate a current. When a DNA molecule moves through one of these pores, the current varies depending on the chemical properties of the DNA. These fluctuations of the electrical signal are enough for the computer to reconstruct the genetic sequence and the epigenetic chemical labels. This process takes place at each pore and, thus, each strand of DNA.
Genome editing tools and bioinformatics illuminate "dark matter"Conventional sequencing methods analyze the entire genome of a patient. Now, the scientists designed a process to look at specific regions selectively. Brndl used the CRISPR-Cas system to cut DNA segments from the genome that contained the repeat region. These segments went through a few intermediate processing steps and were then funneled into the pores on the sequencing chip.
"If we had not pre-sorted the molecules in this way, their signal would have been drowned in the noise of the rest of the genome," says bioinformatician Pay Giesselmann. He had to develop an algorithm specifically for the interpretation of the electrical signals generated by the repeats: "Most algorithms fail because they do not expect the regular patterns of repetitive sequences." While Giesselmann's program "STRique" does not determine the genetic sequence itself, it counts the number of sequence repetitions with high precision. The program is freely available on the internet.
Numerous potential applications in research and the clinic"With the CRISPR-Cas system and our algorithms, we can scrutinize any section of the genome - especially those regions that are particularly difficult to examine using conventional methods," says Mller, who is heading the project. "We created the tools that enable every researcher to explore the dark matter of the genome," says Mller. He sees great potential for basic research. "There is evidence that the repeats grow during the development of the nervous system, and we would like to take a closer look at this."
The physician also envisions numerous applications in clinical diagnostics. After all, repetitive regions are involved in the development of cancer, and the new method is relatively inexpensive and fast. Mller is determined to take the procedure to the next level: "We are very close to clinical application."
Reference: Giesselmann et al. 2019.Analysis of short tandem repeat expansions and their methylation state with nanopore sequencing. Nature Biotechnology.DOI: https://doi.org/10.1038/s41587-019-0293-x.
This article has been republished from the following materials. Note: material may have been edited for length and content. For further information, please contact the cited source.
- US government considers ethics of aborted tissue research - Pregnancy Help News - August 7th, 2020
- Plant Stem Cell Market 2020 Share Growing Rapidly With Latest Trends, Development, Revenue, Demand And Forecast To 2029 - Owned - August 7th, 2020
- Stem Cell Cartilage Regeneration Market Size, Global Analytical Overview, Key Players, Regional Demand, Trends and Forecast To 2026 - Bulletin Line - August 7th, 2020
- Covid-19 Impact on Global Stem Cell Assay Market Set Explosive Growth By 2019 2027 | Merck & Co., Thermo Fisher Scientific, GE Healthcare,... - August 7th, 2020
- Why cultivated meat is about to have its Tesla Roadster moment - Massive Science - August 7th, 2020
- Platelet Rich Plasma and Stem Cell Alopecia Treatment Market to Reach a Value of Approximately US$ 450.5 Mn by the End of 2026 - Science Examiner - August 6th, 2020
- Covid-19 Impact on 2021-2026 Stem Cell Manufacturing Market Segmentation, Analysis by Recent Trends, Development & Growth by Regions - Owned - August 6th, 2020
- Cell Transplantatio Therapy Market Global Research and Analysis 2020 - Owned - August 6th, 2020
- National STEM Scholars Announced for 2020 - PR Web - August 6th, 2020
- US government considers ethics of aborted tissue research - Catholic News Agency - August 6th, 2020
- Cell Viability Assays Market by Production Analysis, Current Trends 2024 Analysis of Regions with Top vendors, Market Dynamics, Types, Applications,... - August 6th, 2020
- Stem Cell Assay Market Study for 2020 to 2027 providing information on Key Players, Growth Drivers and Industry challenges - Bulletin Line - August 6th, 2020
- Allogeneic Stem Cells Market 2020-2024: Business Overview, Industry Size and Share, Opportunities, Impact of Drivers, Key Venders, Types, Applications... - August 5th, 2020
- Cancer Stem Cell Therapeutics Market Emerging Trends, Business Opportunities, Segmentation, Production Values, Supply-Demand, Brand Shares and... - August 5th, 2020
- IMAC Holdings Receives FDA Authorization to Initiate Clinical Study of Its Umbilical Cord-Derived Allogenic Mesenchymal Stem Cells for the Treatment... - August 5th, 2020
- Hematopoietic Stem Cell Transplantation (HSCT) Market 2020: Regen Biopharma Inc, China Cord Blood Corp, CBR Systems Inc, Escape Therapeutics Inc,... - August 5th, 2020
- BioTech Life Sciences Initiates New Study of Anti-Aging Formulas in Helping COVID-19 'Long-Haulers' and Those Suffering With Chronic Fatigue Syndrome... - August 5th, 2020
- COVID-19 Industry Impact On Autologous Stem Cell and Non-Stem Cell Based Therapies Market Revenue Develop Rapidly By 2019 2027 | Fibrocell Science,... - August 5th, 2020
- Nerve Repair and Regeneration Market worth $9.7 billion by 2025 - Exclusive Report by MarketsandMarkets - PRNewswire - August 5th, 2020
- Teams Working to Image Protein Clumps in Parkinson's Share $8.5M Prize - Parkinson's News Today - August 5th, 2020
- Placental Stem Cell Collection and Storage Market 2020 Segmented by Major Market Players, Types, Applications and Countries Forecast to 2026 - Market... - August 4th, 2020
- Nerve Repair and Regeneration Market worth $9.7 billion by 2025 - Exclusive Report by MarketsandMarkets - PR Newswire UK - August 4th, 2020
- Cell Isolation Technology Market 2020 Segmented by Major Market Players, Types, Applications and Countries Forecast to 2026 - Market Research Posts - August 4th, 2020
- Justin Thomas wins WGC-FedEx St. Jude Invitational and moves to No. 1 world ranking - Commercial Appeal - August 4th, 2020
- Latest Research on Autologous Cell Therapy Market 2020 by Application, Industry Share, End User with top players BioTime, Inc., BrainStorm Cell... - August 4th, 2020
- Stem Cell Assay Market to Witness Huge Growth By Top Players Merck & Co., Thermo Fisher Scientific, GE Healthcare, Agilent Technologies, Bio-Rad... - August 4th, 2020
- Stem Cell Cartilage Regeneration Market Outlook, Strategies, Challenges, Advancements, Geography Trends and Growth, Applications and Forecast 2026 -... - August 4th, 2020
- Cell Expansion Market Detailed Analysis of Current Industry Figures with Forecasts Growth By 2027 - CueReport - August 4th, 2020
- Cell Banking Outsourcing Market Size 2020 Industry Share, Strategies, Growth Analysis, Regional Demand, Revenue, Key Players and 2026 Forecast... - August 3rd, 2020
- 'Year of Preparations for the Next Fifty Years' will contribute to country's development process - Emirates News Agency - August 3rd, 2020
- Stem Cell Therapy Market Latest Trends, Development, Revenue, Demand And Forecast To 2022 - Market Research Correspondent - August 3rd, 2020
- Cell Proliferation Kit Market 2020-2026 analysis examined in new market research report with Focusing Key players like - BD Biosciences, GE... - August 3rd, 2020
- Research Antibodies Market 2020 to Witness Lucrative Growth in Coming Years with Top Key Players Abcam plc. Agilent Technologies, Merck KGaA - Market... - August 3rd, 2020
- Stem Cell Banking Outsourcing Market Research Report to 2026 COVID-19 Impact on Industry Size, Growth Share, Future Trends, Price, Top Key Players... - August 3rd, 2020
- Impact of Covid-19 on Stem Cell Banking Market 2020 | Enormous Growth with Recent Trends & Demand - Market Research Posts - August 3rd, 2020
- Animal Stem Cell Therapy Market to Reach US$ Million at xx% CAGR During the Forecast Period 2017 2025 - Bulletin Line - August 3rd, 2020
- Stem Cell Alopecia Treatment Market Share Worldwide Industry Growth, Size, Statistics, Opportunities and Forecasts up to 2027 - Owned - August 3rd, 2020
- How Airway Cells Work Together in Regeneration and Aging - Technology Networks - August 2nd, 2020
- Stem Cell Characterization Kits Market Research Report and Outlook by 2018 to 2026 - Owned - August 2nd, 2020
- Cell Expansion Market Set to Surpass US$XX Million by the end of 2017 2025 - Owned - August 2nd, 2020
- Global Multiple Myeloma Therapeutics Market 2020 | With Top Growing Companies & Coronavirus (COVID-19) Impact Analysis | Amgene, Inc., Celgene... - August 2nd, 2020
- Biotechnology Reagents Market Analysis and Forecast by Rapid Growth Rate 2020 Value Share Analysis by Regions, Industry Size, Key Insights till 2024 -... - August 2nd, 2020
- Personalized Cell Therapies Market to Witness Astonishing Growth by 2025 - Owned - August 2nd, 2020
- Why Superman 5 With Christopher Reeve Never Happened - Screen Rant - August 1st, 2020
- Research On Global Stem Cell Cartilage Regeneration Market (impact of COVID-19), Analysis, Overview, Growth Forecast, Top key players Anika... - August 1st, 2020
- Readers ask about antibody tests, chimeras and public health and privacy - Finance Brokerage - August 1st, 2020
- Gene variants and susceptibility to schizophrenia - The Hindu - August 1st, 2020
- How COVID-19 Pandemic Will Impact Australia & New Zealand Research Antibodies Market Business Opportunity, And Growth 2020-2026 Bulletin Line -... - August 1st, 2020
- FDA Approves Monjuvi(R) (tafasitamab-cxix) in Combination with Lenalidomide for the Treatment of Adu - PharmiWeb.com - August 1st, 2020
- Animal Stem Cell Therapy Market Growth, Trends and Value Chain 2019-2025 - Owned - August 1st, 2020
- Global Allogeneic Stem Cell Therapy Market 2020 Research by Business Analysis, Growth Strategy and Industry Development to 2025 - Galus Australis - August 1st, 2020
- Global Stem Cell Assay Market 2020 Trends Analysis and Coronavirus (COVID-19) Effect Analysis | Key Players Market With COVID-19 Impact Analysis, In... - August 1st, 2020
- Cell Therapy Manufacturing Market is estimated to reach close to USD 11 Billion by 2030, predicts Roots Analysis - Market Research Posts - August 1st, 2020
- Global Cytokine Market 2020 Top Countries Data Industry Size, Share, Business Growth, Revenue, Trends, Market Demand Penetration and Forecast to By... - August 1st, 2020
- What's On The Ballot? A Summary Of The 12 State Propositions For November 2020 Election - KHTS Radio - July 31st, 2020
- Covid-19 Impact on Global Adipose Derived Stem Cell Therapy Market Strategies, Comparison, Shares, Demand, Supply, Challenges and Forecast to 2026 -... - July 31st, 2020
- Personalized Cell Therapies Market Trends, Outlook, and Opportunity Analysis up to 2021 focuses on major key players PCT Cell Therapy Services, LLC... - July 31st, 2020
- Stem Cell And Platelet Rich Plasma Prp Alopecia Therapies Market Size, Share, Types, Products, Trends, Growth, Applications and Forecast 2020 to 2027... - July 31st, 2020
- Limited Reporting of Adverse Events Tied to Regenerative Treatments Leaves Consumers Vulnerable - The Pew Charitable Trusts - July 31st, 2020
- How airway cells work together in regeneration and aging - Newswise - July 31st, 2020
- Global Animal Stem Cell Therapy Market 2020 Trends Analysis and Coronavirus (COVID-19) Effect Analysis | Key Players Market With COVID-19 Impact... - July 31st, 2020
- New Trends of Stem Cell Banking Market with Worldwide Industry Analysis to 2025 - Owned - July 31st, 2020
- Scientists to speed creation of pig vaccines - FarmingUK - July 30th, 2020
- Cell Culture Market Research Report by Product, by End User, by Application - Global Forecast to 2025 - Cumulative Impact of COVID-19 - GlobeNewswire - July 30th, 2020
- Research report covers the Stem Cell and Platelet Rich Plasma (PRP) Alopecia Therapies Market Forecasts and Growth, 2019-2025 - Market Research... - July 30th, 2020
- Trending Now: COVID-19 impact on 3D Cell Cultures Market Variables, Information, Emerging Trends, Analysis and Forecast 2020-2026 | Sigma, Lonza, 3D... - July 30th, 2020
- Global Covid-19 impact on Stem Cell Storage Market Insights and Upcoming Trends to Forecast till 2025| CCBC, CBR, ViaCord, Esperite, Vcanbio - Owned - July 30th, 2020
- Trending Now: Stem Cell Source Market Growth by Top Companies, Trends by Types and Application, Forecast to 2026| BD Bioscience, Beckman Coulter, Ge... - July 30th, 2020
- Covid-19 Impact on Global Stem Cell Drugs Market by Technology, Solutions, Application, Price, Demand Analysis and Growth Opportunities to 2026 -... - July 30th, 2020
- Michael J. Fox Foundation Announces Winners of the "Ken Griffin Alpha-synuclein Imaging Competition" to Develop Game-Changing Tool for... - July 30th, 2020
- Cancer Stem Cell Therapeutics Market 2020 Global Trend, Segmentation and Opportunities Forecast To 2027 | Merck KGA, LONZA Group AG, Novartis, etc. -... - July 30th, 2020
- Cell Separation by Membrane Filtration Technology Market: In-depth Analysis of the Global Industry with Future Estimations till 2029 - Owned - July 30th, 2020
- Hematopoietic Stem Cell Transplantation Market Outlook | Recent Trends and Growth Forecast 2020 2027 - Owned - July 30th, 2020
- Mesoblast sees lasting need for COVID treatment beyond a vaccine - Sydney Morning Herald - July 30th, 2020
- UAE leads Covid-19 research in the Middle East - The National - July 30th, 2020
- Demand for Cryopreservation Equipment Market to Experience a Significant Dip in 2020, Influenced by COVID-19 Pandemic 2020-2029 | Thermo Fisher... - July 30th, 2020
- Plant Stem Cell Market Size, Share, Trends Analysis and Growth Forecast by Type and Application from 2020-2026 - Bulletin Line - July 30th, 2020
- Literature Review of Surgical Treatment in Idiopathic Full-Thickness M | OPTH - Dove Medical Press - July 29th, 2020
- Peripheral Nerve Repair Devices Market Research Report by Device, by Application, by End User - Global Forecast to 2025 - Cumulative Impact of... - July 29th, 2020
- Stem Cell Therapy Market Analysis and Forecast 2019 | By Top Players Magellan, Medipost Co., Ltd, Osiris Therapeutics, Inc., Kolon TissueGene, Inc.,... - July 29th, 2020