Stories about: genome editing

GALLERY: Forecasting the future of pediatric hematology/oncology

Title image for pediatric hematology/oncology predictionsRecently, the annual ASPHO (American Society for Pediatric Hematology/Oncology) meeting brought together more than 1,100 pediatric hematologists and oncologists, including a team from the Dana-Farber/Boston Children’s Cancers and Blood Disorders Center. Some of the delegates from Dana-Farber/Boston Children’s included:

Based on their discussions with their peers, these are their key takeaways from the meeting:

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Quality assurance for genome editing

Chromosome breaks translocations gene editing CRISPR TALENs ZFNs zinc fingers Frederick Alt
When chromosomes break, the ends can join together in a number of ways, some of which can cause trouble. A new QA method could help researchers avoid making problematic breaks when using gene editing technologies like CRISPR.

Labs the world over are jumping onto the gene editing bandwagon (and into the inevitable patent arguments). And it’s hard to blame them. As these technologies have evolved over the last two decades starting with the zinc finger nucleases (ZFNs), followed by transcription activator-like effector nucleases (TALENs) and CRISPR—they’ve become ever more powerful and easier to use.

But one question keeps coming up: How precise are these systems? After all, a method that selectively mutates, deletes or swaps specific gene sequences (and now can even turn genes on) is only as good as its accuracy.

Algorithms can predict the likely “off-target” edits based on the target’s DNA sequence, but they’re based on limited data. “The algorithms are getting better,” says Richard Frock, PhD, a fellow in the laboratory of Frederick Alt, PhD, at Boston Children’s Hospital. “But you still worry about the one rare off-target effect that’s not predicted but falls in a coding region and totally debilitates a gene.”

Frock, Alt (who leads Boston Children’s Program in Cellular and Molecular Medicine, or PCMM), fellow Jiazhi Hu, PhD, and their collaborators recently turned a method first developed in Alt’s lab for studying broken chromosomes into a quality assurance tool for genome editing. As a bonus, the method—called high-throughput genome translocation sequencing (HTGTS)—also reveals the “collateral damage” gene editing methods might create in a cell’s genome, information that could help researchers make better choices when designing gene editing experiments.

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CRISPR gene editing is creating a buzz in Boston

CRISPR gene editing Boston

You have an immune system. Your cat has an immune system. And bacteria have an immune system, too—one that we’ve tapped to make one of the most powerful tools ever for editing genes.

The tool is called CRISPR (for “clustered regularly interspaced short palindromic repeats”), and it makes use of enzymes that “remember” viral genes and cut them out of bacterial genomes. Applied to bioengineering, CRISPR is launching a revolution. And the Boston Globe reported over the weekend that while researchers at the University of California at Berkeley first developed CRISPR, the technique is booming in labs around Boston.

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A first for CRISPR: Cutting genes in blood stem cells

CRISPR T-cells stem cells HIV gene editing
The CRISPR system (red) at work.

CRISPR—a gene editing technology that lets researchers make precise mutations, deletions and even replacements in genomic DNA—is all the rage among genomic researchers right now. First discovered as a kind of genomic immune memory in bacteria, labs around the world are trying to leverage the technology for diseases ranging from malaria to sickle cell disease to Duchenne muscular dystrophy.

In a paper published yesterday in Cell Stem Cell, a team led by Derrick Rossi, PhD, of Boston Children’s Hospital, and Chad Cowan, PhD, of Massachusetts General Hospital, report a first for CRISPR: efficiently and precisely editing clinically relevant genes out of cells collected directly from people. Specifically, they applied CRISPR to human hematopoietic stem and progenitor cells (HSPCs) and T-cells.

“CRISPR has been used a lot for almost two years, and report after report note high efficacy in various cell lines. Nobody had yet reported on the efficacy or utility of CRISPR in primary blood stem cells,” says Rossi, whose lab is in the hospital’s Program in Cellular and Molecular Medicine. “But most researchers would agree that blood will be the first tissue targeted for gene editing-based therapies. You can take blood or stem cells out of a patient, edit them and transplant them back.”

The study also gave the team an opportunity to see just how accurate CRISPR’s cuts are. Their conclusion: It may be closer to being clinic-ready than we thought.

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Genome editing: A CRISPR way to correct disease

CRISPR Cas9 genome editing Technology sometimes unfolds at a slow, measured pace and sometimes at lightning speed. Right now, we are witnessing what is arguably one of the fastest moving fields in biomedical science: a form of genome editing aptly known as CRISPR.

CRISPR allows researchers to make very precise—some would say crisp—changes to the genomes of human cells and those of other organisms. You might think of it as a kind of guided missile. Its precision is opening the doors to a wide variety of research and, hopefully, medical applications. Indeed, the possibilities seem to be bound only by scientists’ imaginations.

“For a long time, we have been accumulating new knowledge about which gene mutation causes which disease. But until very recently, we haven’t had the ability to go in and correct those mutations,” explains Feng Zhang, PhD, a core member of the Broad Institute of Harvard and MIT, and one of the method’s pioneers. “CRISPR is one of the tools that is starting to allow us to directly go in and do surgery on the genome and replace the mutations.”

CRISPR stands for Clustered Regularly Interspaced Short Palindromic Repeats. While this name is a bit verbose, it points to the technology’s origins: a set of genetic sequences first discovered in bacteria.

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