Level of Comfort with Making Changes to the DNA of an Organism

Level of Comfort with Making Changes to the DNA of an Organism

Curator: Aviva Lev-Ari, PhD, RN

The Voice of  Aviva Lev-Ari, PhD, RN   Level of Comfort with Making Changes to the DNA of an Organism, Volume 2 (Volume Two: Latest in Genomics Methodologies for Therapeutics: Gene Editing, NGS and BioInformatics, Simulations and the Genome Ontology), Part 2: CRISPR for Gene Editing and DNA Repair

My prospects are that Jennifer A. Doudna and Emmanuelle Charpentier will be awarded the Nobel Prize for their joint contribution to the study of  the many different flavors of the enzyme Cas9 that occur naturally. The Basic Research that has led to development of the Gene Editing technology and to Clinical Applications will better the human condition negatively affected by genetic and genomic alterations.

Citation of Prof. Jennifer A. Doudna, UC, Berkeley


The Structural Biology of CRISPR-Cas Systems

Curr Opin Struct Biol. 2015 Feb 24;30C:100-111

Authors: Jiang F, Doudna JA

“Work that started off as a very basic science project with our collaborator Emmanuelle and seeing how it turned into this incredible technology.”

Doudna: It’s really important for people to appreciate that this technology grew out of a project to figure out how a basic process in biology worked. Many discoveries are made via basic science and working to understand a process. You can do careful work and obtain data that allow you to deduce something fundamental about nature. That was very much the origin of this system here. That’s something great to emphasize. There’s a tendency now in our country and Europe to emphasize “translational research.” Maybe there is not as much of an appreciation of basic science as there should be. That kind of research was critical with Cas9. A lot of non-scientists don’t understand the process. Scientists are just curious about the world and we’ve chosen particular kinds of questions. We are doing it for the purpose of understanding our world and life.


Doudna: We need to learn how efficiently it works. What’s the best way to deliver it safely and efficiently? Not only efficiency, but also what are the off-target levels? How do we minimize that? What would be a safe level if any of off-targets? I’d like to see basic research like what happens to the DNA in germ cells or pre-germ cells when a double-stranded break occurs? What is the repair process like in those specific cells? Those answers would be interesting from a basic science perspective as well as informing future potential clinical applications.





AWARDS for the Discovery

Images of the Award Ceremonies


Jennifer Doudna, cosmology teams named 2015 Breakthrough Prize winners

Jennifer Doudna, The winner of the 2014 Lurie Prize in the Biomedical Sciences

CRISPR-Cas9 Discovery and Development of Programmable Genome Engineering – Gabbay Award Lectures in Biotechnology and Medicine – Hosted by Rosenstiel Basic Medical Sciences Research Center, 10/27/14 3:30PM Brandeis University, Gerstenzang 121

Doudna was a Searle Scholar and received a 1996 Beckman Young Investigators Award, the 1999 NAS Award for Initiatives in Research and the 2000 Alan T. Waterman Award. She was elected to the National Academy of Sciences in 2002 and to the Institute of Medicine in 2010. In 2014, Doudna was awarded the Lurie Prize in Biomedical Sciences from the Foundation for the National Institutes of Health as well as the Dr. Paul Janssen Award for Biomedical Researchand Breakthrough Prize in Life Sciences, both shared with Emanuelle Charpentier.




Discovery Presented in Science, Nov 2014


Jennifer A. Doudna* and Emmanuelle Charpentier*
Science Nov 2014; 346(6213) 1258096:1077 – 1087.

Discovery Context: Delineating a Role for CRISPR-Cas9 in Pharmaceutical Targeting

Author & Curator: Larry H. Bernstein, MD, FCAP, Chief Scientific Officer, Leaders in Pharmaceutical Intelligence, Boston, MA



Comprehensive Coverage of the Discovery by the Team at Leaders in Pharmaceutical Business Intelligence


Content Consultant: Larry H Bernstein, MD, FCAP

Genomics Orientations for Individualized Medicine

Volume One

Larry H Bernstein, MD, FCAP, Senior Editor

Leaders in Pharmaceutical Business Intelligence, Boston



Stephen J. Williams, PhD, Editor

Leaders in Pharmaceutical Business Intelligence, Philadelphia



Aviva Lev-Ari, PhD, RN, Editor

Editor-in-Chief BioMed E-Book Series

Leaders in Pharmaceutical Business Intelligence, Boston


Chapter 21

21.1 Introducing CRISPR/Cas9 Gene Editing Technology – Works by Jennifer A. Doudna

21.1.1 Ribozymes and RNA Machines – Work of Jennifer A. Doudna

Reporter: Aviva Lev-Ari, PhD, RN

21.1.2 Evaluate your Cas9 gene editing vectors: CRISPR/Cas Mediated Genome Engineering – Is your CRISPR gRNA optimized for your cell lines?

Reporter: Aviva Lev-Ari, PhD, RN

21.1.3 2:15 – 2:45, 6/13/2014, Jennifer Doudna “The biology of CRISPRs: from genome defense to genetic engineering”

Reporter: Aviva Lev-Ari, PhD, RN

21.1.4  Prediction of the Winner RNA Technology, the FRONTIER of SCIENCE on RNA Biology, Cancer and Therapeutics  & The Start Up Landscape in BostonGene Editing – New Technology The Missing link for Gene Therapy?

Curator: Aviva Lev-Ari, PhD, RN


21.2 CRISPR in Other Labs

21.2.1 CRISPR @MIT – Genome Surgery

Curator: Aviva Lev-Ari, PhD, RN

21.2.2 The CRISPR-Cas9 System: A Powerful Tool for Genome Engineering and Regulation

Yongmin Yan and Department of Gastroenterology, Hepatology & Nutrition, University of Texas M.D. Anderson Cancer, Houston, USADaoyan Wei*

21.2.3 New Frontiers in Gene Editing: Transitioning From the Lab to the Clinic, February 19-20, 2015 | The InterContinental San Francisco | San Francisco, CA

Reporter: Aviva Lev-Ari Ph.D. RN

21.2.4 Gene Therapy and the Genetic Study of Disease: @Berkeley and @UCSF – New DNA-editing technology spawns bold UC initiative as Crispr Goes Global

Reporter: Aviva Lev-Ari Ph.D. RN

21.2.5 CRISPR & MAGE @ George Church’s Lab @ Harvard

Genome Engineering: CRISPR & MAGE 
Multiplex Automated Genome Engineering (MAGE), is an intentionally broad term. In practice, it has come to be associated with a very efficient oligonucleotide allele-replacment (lambda red beta), so far restricted mainly to E.coli. CRISPR, in contrast, works in nearly every organism tested.

Relevant companies: EnEvolvEgenesisEditas.

Editas (NextBigFuture, 28-Nov-2013, Brian Wang)
A Call to Fight Malaria One Mosquito at a Time by Altering DNA (NY Times, 17-Jul-2014, Carl Zimmer)

* Vectors: Addgene
* Computational: Center for Causal Consequences of Variation (CCV)

Relevant Lab Publications:
2013 Probing the limits of genetic recoding in essential genes. Science.
2013 Genomically Recoded Organisms Impart New Biological Functions. Science.
2013 CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nature Biotech.
2009 Programming cells by multiplex genome engineering and accelerated evolution. Nature.






Potential Outcomes of Human Germ-line Engineering

  • Baltimore, et al. propose path forward for human germline engineering in Science

In a new perspectives piece in Science, Nobel Laureate David Baltimore and co-authors including Jennifer Doudna and George Church, chart a potential path forward for human genomic engineering involving germline modification. See also accompanying Bioethics piece by Gretchen Vogel as well, “Embryo engineering alarm”.

human germline editing policy

In the piece, entitled “A prudent path forward for genomic engineering and germline gene modification” calls for further discussion and assessment of key potential benefits and risks to moving forward with this technology. The illustration included here is from the piece.

The piece is reflective to a large extent of conclusions from a recent meeting held in Napa on this issue.

The summary statement is as follows:  “A framework for open discourse on the use of CRISPR-Cas9 technology to manipulate the human genome is urgently needed.”

They make 4 more specific recommendations.

  1. Strongly discourage clinical application of this technology at this time.
  2. Create forums for education and discussion
  3. Encourage open research to evaluate the utility of CRISPR-Cas9 technology for both human and nonhuman model systems.
  4. Hold an international meeting to consider these issues and possibly make policy recommendation.




Don’t edit the human germ line

12 March 2015

Heritable human genetic modifications pose serious risks, and the therapeutic benefits are tenuous, warn Edward Lanphier, Fyodor Urnov and colleagues.



It is thought that studies involving the use of genome-editing tools to modify the DNA of human embryos will be published shortly1.

There are grave concerns regarding the ethical and safety implications of this research. There is also fear of the negative impact it could have on important work involving the use of genome-editing techniques in somatic (non-reproductive) cells.

We are all involved in this latter area of work. One of us (F.U.) helped to develop the first genome-editing technology, zinc-finger nucleases2 (ZFNs), and is now senior scientist at the company developing them, Sangamo BioSciences of Richmond, California. The Alliance for Regenerative Medicine (ARM; in which E.L., M.W. and S.E.H. are involved), is an international organization that represents more than 200 life-sciences companies, research institutions, non-profit organizations, patient-advocacy groups and investors focused on developing and commercializing therapeutics, including those involving genome editing.



  • Practical Plan for Managing Human Germline Genetic Modification

CRISPR-Cas9 gene editing technology is a game changer on many levels both inside and soon outside the lab. There is a growing sense of urgency amongst biomedical scientists to take a proactive approach to current and future use of CRISPR technology in human germ cells and embryos.

These concerns have been heightened by rumors of multiple papers currently in various stages of peer review that will reportedly describe CRISPR-mediated gene editing of human embryos. A number of scientists and scientific organizations have recently come out with policy statements on human germline genetic modification: Lanphier, et al.NatureBaltimore, et al. Science, and ISSCR.

I’ve outlined a proposed plan (see figure below) that I call ABCD for simplicity to try to practically manage the situation with human germline genetic modification. This plan shares a few key features with some of those already proposed by others, but in some ways it is different or more specific. This ABCD idea is just a possible plan coming from one person (me) with the intention of positively adding to the overall dialogue.ABCD Plan Human Germline Modification

My view is that in vitro research on genetically modified human germ cells and early embryos–with appropriate training and oversight–is ethical and can in fact be of great value. Such work will provide new, valuable information about gene editing itself and early human development, fertility, and more. Therefore, such research should not be prohibited, but should only be conducted under certain conditions.



  • Engineering the Perfect Baby

Scientists are developing ways to edit the DNA of tomorrow’s children. Should they stop before it’s too late?

Antonio Regalado on March 5, 2015



Paul Knoepfler Interview with Jennifer Doudna, April 2015


Paul Knoepfler

Associate Professor at UC Davis

A Conversation with Jennifer Doudna on Cas9 and Human Germline Gene Editing

Jennifer DoudnaI’m doing a series of interviews with leaders in the field on human germline modification. The first interview in this series was with George Church.

Today is the second in this series and is a conversation I had with Dr. Jennifer Doudna, a pioneer in CRISPR-Cas9 technology.

Doudna is a Professor in MCB and Chemistry as well as Li Ka Shing Chancellor’s Chair in Biomedical and Health Sciences at UC Berkeley. She is also an HHMI Investigator.

You can read more about the Doudna lab’s research here. She is not only an internationally respected researcher, but also continues to lead efforts to catalyze discussion on the potential future applications of CRISPR-Cas9 technology including dialogue on possible future work in the human germline.

An initial meeting was held earlier this year in Napa that led to a recent commentary piece in Science. Other views have been published as well including Lanphier, et al. inNature and I have put out there my own perspectives with a roadmap I call the ABCD plan.

I followed up on the Napa meeting in today’s interview with Doudna and also touched on other important issues related to CRISPR-Cas9 technology.

What specifically sparked the Napa meeting? Did you help to start the ball rolling?

Doudna: The Napa meeting was organized by myself and my colleagues at the Innovative Genomics Initiative. We had ethical concerns regarding potential applications of genome editing because CRISPR-Cas9 is widely adapted and so simple. We felt it was important to convene a meeting of stakeholders.

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