A team of researchers affiliated with Ludwig Cancer Research and the Karolinska Institutet in Sweden report in the current issue of Nature Methods a dramatically improved technique for analyzing the genes expressed within a single cell—a capability of relevance to everything from basic research to future cancer diagnostics.
"There are cells in tumors and in healthy tissues that are not present in sufficient numbers to permit analysis using anything but single-cell methods," explains senior author, Rickard Sandberg, PhD. "This method allows us to identify rare and important subpopulations of cells in all sorts of tissues. We can also use it to tease apart, more rigorously than ever before, how the expression of unique suites of genes transform cells from one state to another as, say, an embryo develops into an organism, or a tumor becomes metastatic."
Traditional approaches, which depend on the collective analysis of gene expression in millions of cells at once, tend to obscure biologically significant differences in the genes expressed by specialized cells within a particular kind of tissue. Single-cell analysis of gene expression overcomes this limitation. The leading method for such analysis—Smart-seq—was developed in 2012 by the biotechnology firm Illumina, together with Sandberg's laboratory.
To develop the new technique, named Smart-seq2, Sandberg's team conducted more than 450 experiments to improve upon their initial method. The new procedure consistently captures three to four times as many RNA molecules, which often translates into 2,000 more genes per cell than current methods allow. It also captures far more full-length gene sequences, a steep challenge in such studies, which often capture only partial sequences of expressed genes. This will permit researchers to conduct a more granular analysis of how subtle differences between the same genes in different people—known as single nucleotide polymorphisms (or SNPs)—contribute to differences in biology and disease.
The new method is likely to be of great value to cancer research. Identifying rare sub-populations of cells in tumors and understanding their role in the survival and progression of cancers can provide invaluable information for the development of diagnostics and targeted therapies. A study recently published by Ludwig researchers described, for example, how certain subpopulations of cells in melanomas can be pushed into a drug-susceptible state and then destroyed by chemotherapy. More such strategies might be devised as researchers get a better handle on the cellular species found in different types of tumors, and the patterns of gene expression that define them.
Because Smart-seq2 relies on off-the-shelf reagents, it costs roughly a twentieth as much as the commercialized kit, which should allow researchers to conduct sophisticated analyses of single cells on a much larger scale. It can also be improved further by the scientific community, since its constituent components and rationale are both open to the public.
Armed with the more effective and affordable Smart-seq2, Sandberg's lab is now moving ahead on projects that require a large-scale, single-cell gene expression analysis. "Now all researchers can do their own single-cell gene expression analysis by buying the components of the process described in this paper and assembling their own kits," says Sandberg.
Explore further: Sensitive technique for taking RNA inventory of individual cells offers powerful tool
More information: Smart-seq2 for sensitive full-length transcriptome profiling in single cells, DOI: 10.1038/nmeth.2639
Medical Xpress on facebook
Related Stories
New genomic sequencing method enables 'smarter' anaysis of individual cells
Jul 22, 2012
Only by viewing a Seurat painting at close range can you appreciate the hidden complexities of pointillism – small, distinct dots of pure color applied in patterns to form an image from a distance. Similarly, biologists ...
Sensitive technique for taking RNA inventory of individual cells offers powerful tool
Jul 04, 2013
Every cell is a hectic messaging center, with thousands of genes churning out messenger RNA (mRNA) transcripts for translation into functional proteins. Accordingly, sequencing the mRNA content of an individual ...
Homing in on developmental epigenetics
Aug 23, 2013
Germ cells have unique molecular features that enable them to perform the important task of transmitting genetic information to the next generation. During development from their embryonic primordial state, ...
Researchers challenge long-held assumption of gene expression in embryonic stem cells
Jul 03, 2013
Whitehead Institute researchers have determined that the transcription factor Nanog, which plays a critical role in the self-renewal of embryonic stem cells, is expressed in a manner similar to other pluripotency markers. ...
Short-term gene-expression 'memory' is inherited in proteins associated with DNA, new research finds
Aug 06, 2013
(Phys.org) —By studying a gene in yeast, a team of scientists has found that modifications to histones—proteins associated with DNA—can control whether or not a gene is allowed to function and may be ...
Recommended for you
Getting rid of unwanted visitors
Sep 20, 2013
Gut-dwelling bacteria are attracting increasing attention, particularly those associated with human diseases. Helicobacter pylori is found in the stomach of humans, where it may cause chronic gastritis and ...
Lifestyle influences metabolism via DNA methylation
Sep 20, 2013
An unhealthy lifestyle leaves traces in the DNA. These may have specific effects on metabolism, causing organ damage or disease. Scientists of Helmholtz Zentrum München have now identified 28 DNA alterations associated with ...
Researchers tease apart workings of a common gene
Sep 19, 2013
Researchers at Weill Cornell Medical College have discovered why a tiny alteration in a brain gene, found in 20 percent of the population, contributes to the risk for anxiety, depression and memory loss.
Want to better understand the accuracy of your human genome sequencing?
Sep 19, 2013
As new high-throughput "Next Generation" DNA sequencing methods are moving into clinical applications, understanding accuracy of variants is critical. Numerous recent studies have demonstrated that different ...
New approach to early diagnosis of chronic renal diseases in children
Sep 18, 2013
New mutations of the different pathologies found in renal diseases have been discovered by researchers from the University of Oviedo, Spain.
Whole DNA sequencing reveals mutations, new gene for blinding disease
Sep 16, 2013
Retinitis pigmentosa (RP) is a genetic disease that causes progressive loss of vision and is caused by mutations in more than 50 genes. Conventional methods for identification of both RP mutations and novel RP genes involve ...
User comments
© Medical Xpress 2011-2013, Phys.org network
A team of researchers affiliated with Ludwig Cancer Research and the Karolinska Institutet in Sweden report in the current issue of Nature Methods a dramatically improved technique for analyzing the genes expressed within a single cell—a capability of relevance to everything from basic research to future cancer diagnostics.
"There are cells in tumors and in healthy tissues that are not present in sufficient numbers to permit analysis using anything but single-cell methods," explains senior author, Rickard Sandberg, PhD. "This method allows us to identify rare and important subpopulations of cells in all sorts of tissues. We can also use it to tease apart, more rigorously than ever before, how the expression of unique suites of genes transform cells from one state to another as, say, an embryo develops into an organism, or a tumor becomes metastatic."
Traditional approaches, which depend on the collective analysis of gene expression in millions of cells at once, tend to obscure biologically significant differences in the genes expressed by specialized cells within a particular kind of tissue. Single-cell analysis of gene expression overcomes this limitation. The leading method for such analysis—Smart-seq—was developed in 2012 by the biotechnology firm Illumina, together with Sandberg's laboratory.
To develop the new technique, named Smart-seq2, Sandberg's team conducted more than 450 experiments to improve upon their initial method. The new procedure consistently captures three to four times as many RNA molecules, which often translates into 2,000 more genes per cell than current methods allow. It also captures far more full-length gene sequences, a steep challenge in such studies, which often capture only partial sequences of expressed genes. This will permit researchers to conduct a more granular analysis of how subtle differences between the same genes in different people—known as single nucleotide polymorphisms (or SNPs)—contribute to differences in biology and disease.
The new method is likely to be of great value to cancer research. Identifying rare sub-populations of cells in tumors and understanding their role in the survival and progression of cancers can provide invaluable information for the development of diagnostics and targeted therapies. A study recently published by Ludwig researchers described, for example, how certain subpopulations of cells in melanomas can be pushed into a drug-susceptible state and then destroyed by chemotherapy. More such strategies might be devised as researchers get a better handle on the cellular species found in different types of tumors, and the patterns of gene expression that define them.
Because Smart-seq2 relies on off-the-shelf reagents, it costs roughly a twentieth as much as the commercialized kit, which should allow researchers to conduct sophisticated analyses of single cells on a much larger scale. It can also be improved further by the scientific community, since its constituent components and rationale are both open to the public.
Armed with the more effective and affordable Smart-seq2, Sandberg's lab is now moving ahead on projects that require a large-scale, single-cell gene expression analysis. "Now all researchers can do their own single-cell gene expression analysis by buying the components of the process described in this paper and assembling their own kits," says Sandberg.
Explore further: Sensitive technique for taking RNA inventory of individual cells offers powerful tool
More information: Smart-seq2 for sensitive full-length transcriptome profiling in single cells, DOI: 10.1038/nmeth.2639
Medical Xpress on facebook
Related Stories
New genomic sequencing method enables 'smarter' anaysis of individual cells
Jul 22, 2012
Only by viewing a Seurat painting at close range can you appreciate the hidden complexities of pointillism – small, distinct dots of pure color applied in patterns to form an image from a distance. Similarly, biologists ...
Sensitive technique for taking RNA inventory of individual cells offers powerful tool
Jul 04, 2013
Every cell is a hectic messaging center, with thousands of genes churning out messenger RNA (mRNA) transcripts for translation into functional proteins. Accordingly, sequencing the mRNA content of an individual ...
Homing in on developmental epigenetics
Aug 23, 2013
Germ cells have unique molecular features that enable them to perform the important task of transmitting genetic information to the next generation. During development from their embryonic primordial state, ...
Researchers challenge long-held assumption of gene expression in embryonic stem cells
Jul 03, 2013
Whitehead Institute researchers have determined that the transcription factor Nanog, which plays a critical role in the self-renewal of embryonic stem cells, is expressed in a manner similar to other pluripotency markers. ...
Short-term gene-expression 'memory' is inherited in proteins associated with DNA, new research finds
Aug 06, 2013
(Phys.org) —By studying a gene in yeast, a team of scientists has found that modifications to histones—proteins associated with DNA—can control whether or not a gene is allowed to function and may be ...
Recommended for you
Getting rid of unwanted visitors
Sep 20, 2013
Gut-dwelling bacteria are attracting increasing attention, particularly those associated with human diseases. Helicobacter pylori is found in the stomach of humans, where it may cause chronic gastritis and ...
Lifestyle influences metabolism via DNA methylation
Sep 20, 2013
An unhealthy lifestyle leaves traces in the DNA. These may have specific effects on metabolism, causing organ damage or disease. Scientists of Helmholtz Zentrum München have now identified 28 DNA alterations associated with ...
Researchers tease apart workings of a common gene
Sep 19, 2013
Researchers at Weill Cornell Medical College have discovered why a tiny alteration in a brain gene, found in 20 percent of the population, contributes to the risk for anxiety, depression and memory loss.
Want to better understand the accuracy of your human genome sequencing?
Sep 19, 2013
As new high-throughput "Next Generation" DNA sequencing methods are moving into clinical applications, understanding accuracy of variants is critical. Numerous recent studies have demonstrated that different ...
New approach to early diagnosis of chronic renal diseases in children
Sep 18, 2013
New mutations of the different pathologies found in renal diseases have been discovered by researchers from the University of Oviedo, Spain.
Whole DNA sequencing reveals mutations, new gene for blinding disease
Sep 16, 2013
Retinitis pigmentosa (RP) is a genetic disease that causes progressive loss of vision and is caused by mutations in more than 50 genes. Conventional methods for identification of both RP mutations and novel RP genes involve ...
User comments
© Medical Xpress 2011-2013, Phys.org network
0 comments:
Post a Comment