The Heroes of CRISPR Lander, Eric S.
Cell,
01/2016, Letnik:
164, Številka:
1-2
Journal Article
Recenzirano
Odprti dostop
Three years ago, scientists reported that CRISPR technology can enable precise and efficient genome editing in living eukaryotic cells. Since then, the method has taken the scientific community by ...storm, with thousands of labs using it for applications from biomedicine to agriculture. Yet, the preceding 20-year journey—the discovery of a strange microbial repeat sequence; its recognition as an adaptive immune system; its biological characterization; and its repurposing for genome engineering—remains little known. This Perspective aims to fill in this backstory—the history of ideas and the stories of pioneers—and draw lessons about the remarkable ecosystem underlying scientific discovery.
Eric Lander provides his perspectives on the personal stories of scientists who discovered the CRISPR system, unraveled its molecular mechanisms, and repurposed it as a powerful tool for biological research and biomedicine.
Recent advances in genome engineering technologies based on the CRISPR-associated RNA-guided endonuclease Cas9 are enabling the systematic interrogation of mammalian genome function. Analogous to the ...search function in modern word processors, Cas9 can be guided to specific locations within complex genomes by a short RNA search string. Using this system, DNA sequences within the endogenous genome and their functional outputs are now easily edited or modulated in virtually any organism of choice. Cas9-mediated genetic perturbation is simple and scalable, empowering researchers to elucidate the functional organization of the genome at the systems level and establish causal linkages between genetic variations and biological phenotypes. In this Review, we describe the development and applications of Cas9 for a variety of research or translational applications while highlighting challenges as well as future directions. Derived from a remarkable microbial defense system, Cas9 is driving innovative applications from basic biology to biotechnology and medicine.
The sequence of the human genome has dramatically accelerated biomedical research. Here I explore its impact, in the decade since its publication, on our understanding of the biological functions ...encoded in the genome, on the biological basis of inherited diseases and cancer, and on the evolution and history of the human species. I also discuss the road ahead in fulfilling the promise of genomics for medicine.
Celotno besedilo
Dostopno za:
DOBA, IJS, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Lessons from the Cancer Genome Garraway, Levi A.; Lander, Eric S.
Cell,
03/2013, Letnik:
153, Številka:
1
Journal Article
Recenzirano
Odprti dostop
Systematic studies of the cancer genome have exploded in recent years. These studies have revealed scores of new cancer genes, including many in processes not previously known to be causal targets in ...cancer. The genes affect cell signaling, chromatin, and epigenomic regulation; RNA splicing; protein homeostasis; metabolism; and lineage maturation. Still, cancer genomics is in its infancy. Much work remains to complete the mutational catalog in primary tumors and across the natural history of cancer, to connect recurrent genomic alterations to altered pathways and acquired cellular vulnerabilities, and to use this information to guide the development and application of therapies.
Large noncoding RNAs are emerging as an important component in cellular regulation. Considerable evidence indicates that these transcripts act directly as functional RNAs rather than through an ...encoded protein product. However, a recent study of ribosome occupancy reported that many large intergenic ncRNAs (lincRNAs) are bound by ribosomes, raising the possibility that they are translated into proteins. Here, we show that classical noncoding RNAs and 5′ UTRs show the same ribosome occupancy as lincRNAs, demonstrating that ribosome occupancy alone is not sufficient to classify transcripts as coding or noncoding. Instead, we define a metric based on the known property of translation whereby translating ribosomes are released upon encountering a bona fide stop codon. We show that this metric accurately discriminates between protein-coding transcripts and all classes of known noncoding transcripts, including lincRNAs. Taken together, these results argue that the large majority of lincRNAs do not function through encoded proteins.
Display omitted
•Ribosome occupancy levels of lincRNAs are similar to classical ncRNAs and 5′ UTRs•Ribosome occupancy does not distinguish between protein-coding and noncoding RNAs•Protein-coding RNAs show ribosome release at stop codons, and known ncRNAs do not•lincRNAs do not show evidence of ribosome release for any open reading frame
A reanalysis of ribosome profiling data from mammalian noncoding RNAs reveals that, although many large ncRNAs engage with ribosomes, the binding pattern is different from messenger RNAs, which is consistent with the ncRNAs operating through mechanisms that do not rely on protein coding potential.
Cancer cells within individual tumors often exist in distinct phenotypic states that differ in functional attributes. While cancer cell populations typically display distinctive equilibria in the ...proportion of cells in various states, the mechanisms by which this occurs are poorly understood. Here, we study the dynamics of phenotypic proportions in human breast cancer cell lines. We show that subpopulations of cells purified for a given phenotypic state return towards equilibrium proportions over time. These observations can be explained by a Markov model in which cells transition stochastically between states. A prediction of this model is that, given certain conditions, any subpopulation of cells will return to equilibrium phenotypic proportions over time. A second prediction is that breast cancer stem-like cells arise de novo from non-stem-like cells. These findings contribute to our understanding of cancer heterogeneity and reveal how stochasticity in single-cell behaviors promotes phenotypic equilibrium in populations of cancer cells.
Display omitted
► Cancer cell populations interconvert between phenotypic states ► Cell-state transitions can be described with a stochastic Markov model ► Markov model predicts convergence to equilibrium phenotypic proportions ► Cancer stem cells can arise de novo from noncancer stem cells
Lung adenocarcinoma, the most common subtype of non-small cell lung cancer, is responsible for more than 500,000 deaths per year worldwide. Here, we report exome and genome sequences of 183 lung ...adenocarcinoma tumor/normal DNA pairs. These analyses revealed a mean exonic somatic mutation rate of 12.0 events/megabase and identified the majority of genes previously reported as significantly mutated in lung adenocarcinoma. In addition, we identified statistically recurrent somatic mutations in the splicing factor gene U2AF1 and truncating mutations affecting RBM10 and ARID1A. Analysis of nucleotide context-specific mutation signatures grouped the sample set into distinct clusters that correlated with smoking history and alterations of reported lung adenocarcinoma genes. Whole-genome sequence analysis revealed frequent structural rearrangements, including in-frame exonic alterations within EGFR and SIK2 kinases. The candidate genes identified in this study are attractive targets for biological characterization and therapeutic targeting of lung adenocarcinoma.
Display omitted
► Exome and genome characterization of somatic alterations in 183 lung adenocarcinomas ► U2AF1, RBM10, and ARID1A are among newly identified recurrently mutated genes ► Structural variants include activating in-frame fusion of EGFR ► Epigenetic and RNA deregulation proposed as a potential lung adenocarcinoma hallmark
Whole-exome and whole-genome sequencing of 183 lung adenocarcinoma tumor/normal DNA pairs reveals new candidate genes as attractive targets for biological characterization and therapeutic targeting of lung cancer.
Brave New Genome Lander, Eric S
The New England journal of medicine,
07/2015, Letnik:
373, Številka:
1
Journal Article
Recenzirano
Odprti dostop
Genome editing holds great therapeutic promise, but its application in humans would require not only overcoming serious technical challenges but also addressing serious risks and fraught ethical ...issues.
Fifty years ago, microbiologists sparked the recombinant-DNA revolution with the discovery that bacteria have innate immune systems based on restriction enzymes. These enzymes bind and cut invading viral genomes at specific short sequences, and scientists rapidly repurposed them to cut and paste DNA in vitro — transforming biologic science and giving rise to the biotechnology industry.
Ten years ago, microbiologists discovered that bacteria also harbor adaptive immune systems, and subsequent progress has been breathtakingly rapid.
1
Between 2005 and 2009, microbial genetic studies conducted by the laboratories of Mojica, Jansen, Koonin, Horvath, van der Oost, Sontheimer, Marraffini, and others revealed that . . .
Clonal evolution is a key feature of cancer progression and relapse. We studied intratumoral heterogeneity in 149 chronic lymphocytic leukemia (CLL) cases by integrating whole-exome sequence and copy ...number to measure the fraction of cancer cells harboring each somatic mutation. We identified driver mutations as predominantly clonal (e.g., MYD88, trisomy 12, and del(13q)) or subclonal (e.g., SF3B1 and TP53), corresponding to earlier and later events in CLL evolution. We sampled leukemia cells from 18 patients at two time points. Ten of twelve CLL cases treated with chemotherapy (but only one of six without treatment) underwent clonal evolution, predominantly involving subclones with driver mutations (e.g., SF3B1 and TP53) that expanded over time. Furthermore, presence of a subclonal driver mutation was an independent risk factor for rapid disease progression. Our study thus uncovers patterns of clonal evolution in CLL, providing insights into its stepwise transformation, and links the presence of subclones with adverse clinical outcomes.
Display omitted
► Whole-exome analysis of clonal heterogeneity in 149 chronic lymphocytic leukemias ► Earlier and later mutations in the temporal evolution of CLL are identified ► Clonal evolution is commonly seen with treatment, typically in a branched pattern ► A subclonal driver in a pretreatment sample is associated with adverse outcome
The intratumoral heterogeneity in 149 chronic lymphocytic leukemia (CLL) cases was evaluated by whole-exome sequencing. The evolutionary patterns of distinct clones enabled a temporal ordering of mutations in CLL, revealed the association of clonal evolution with chemotherapy, and linked the presence of subclonal driver mutations with adverse clinical outcomes.
Eric Lander, Françoise Baylis, Feng Zhang, Emmanuelle Charpentier, Paul Berg and specialists from seven countries call for an international governance framework.
PDF
