Tag Archives: Genome Editing

Off target sites of the CRISPR CAS babies

14.12.2018 admin

Unfortunately we don’t know the genome of the Chinese parents which would be necessary for any prediction of genome mutations in the twins . So far we only know one confirmed off target site from Dr. He’s Hongkong slides that reports 5 mismatches.

At least I would expect for statistical reasons, some 1 bp mismatch, some 2bp, some 3bp…, but not just one 5bp off target site.
So we could check several online services with the know sgRNA sequence that Dr. He used.

CRISPOR

CRISPOR finds one region with 2 mismatches (intergenic) and 13 with 3 mismatches (7 intergenic hits, 5x introns (ST8SIA6, CTD-2532D12.5, CNTN5, C2D3, RABGAP1) and 1x exon of ACACA). This doesn’t match the reported off target sequence.

Cas-OFFinder

Cas-OFFinder identifies 5 regions with 2 mismatches (1x intergenic, 2x sites in LIMCH1, 1x intergenic, 1 in BPIFC).

CCtop (yes, I was waiting for that name :-)

COS finds only one intergenic region with 3 mismatches.

CRISPRSCAN

has the best explanation of what it does but cannot search from sgRNA to off-target as many other online tools.

OFFspotter

is spotting 1 intergenic region with 2 mismatches, 3 with 3 mismatches (2 intergenic, 1 in RP11-238K6.1).

Taken these five different predictions together, I can’t make conclusion but think that we need to resequence the families with much higher coverage (150-200x fold coverage) and even compare the mutations with the phenotype of the children.

Genetics

Phenotype of the CRISPR CAS babies

13.12.2018 admin

CCR5 annotation, including the known delta32 Mutation and the three mutations introduced by He Jiankui. PAM=Protospacer adjacent motif, DSB=putative double strand break.

From the CCR5 sequence we get the following amino acid sequences

>sp|WT.P51681|CCR5_HUMANC-Cchemokinereceptortype5OS=HomosapiensOX=9606GN=CCR5PE=1SV=1
MDYQVSSPIYDINYYTSEPCQKINVKQIAARLLPPLYSLVFIFGFVGNMLVILILINCKR
LKSMTDIYLLNLAISDLFFLLTVPFWAHYAAAQWDFGNTMCQLLTGLYFIGFFSGIFFII
LLTIDRYLAVVHAVFALKARTVTFGVVTSVITWVVAVFASLPGIIFTRSQKEGLHYTCSS
HFPYSQYQFWKNFQTLKIVILGLVLPLLVMVICYSGILKTLLRCRNEKKRHRAVRLIFTI
MIVYFLFWAPYNIVLLLNTFQEFFGLNNCSSSNRLDQAMQVTETLGMTHCCINPIIYAFV
GEKFRNYLLVFFQKHIAKRFCKCCSIFQQEAPERASSVYTRSTGEQEISVGL

>sp|-32.P51681|CCR5_HUMANC-Cchemokinereceptortype5OS=HomosapiensOX=9606GN=CCR5PE=1SV=1
MDYQVSSPIYDINYYTSEPCQKINVKQIAARLLPPLYSLVFIFGFVGNMLVILILINCKR
LKSMTDIYLLNLAISDLFFLLTVPFWAHYAAAQWDFGNTMCQLLTGLYFIGFFSGIFFII
LLTIDRYLAVVHAVFALKARTVTFGVVTSVITWVVAVFASLPGIIFTRSQKEGLHYTCSS
HFPY
IKDSHLGAGPAAACHGHLLLGNPKNSASVSK

>sp|-15.P51681|CCR5_HUMANC-Cchemokinereceptortype5OS=HomosapiensOX=9606GN=CCR5PE=1SV=1
MDYQVSSPIYDINYYTSEPCQKINVKQIAARLLPPLYSLVFIFGFVGNMLVILILINCKR
LKSMTDIYLLNLAISDLFFLLTVPFWAHYAAAQWDFGNTMCQLLTGLYFIGFFSGIFFII
LLTIDRYLAVVHAVFALKARTVTFGVVTSVITWVVAVFASLPGIIFTRSQKEGLHYTCS
SQYQFWKNFQTLKIVILGLVLPLLVMVICYSGILKTLLRCRNEKKRHRAVRLIFTI
MIVYFLFWAPYNIVLLLNTFQEFFGLNNCSSSNRLDQAMQVTETLGMTHCCINPIIYAFV
GEKFRNYLLVFFQKHIAKRFCKCCSIFQQEAPERASSVYTRSTGEQEISVGL

>sp|-4.P51681|CCR5_HUMANC-Cchemokinereceptortype5OS=HomosapiensOX=9606GN=CCR5PE=1SV=1
MDYQVSSPIYDINYYTSEPCQKINVKQIAARLLPPLYSLVFIFGFVGNMLVILILINCKR
LKSMTDIYLLNLAISDLFFLLTVPFWAHYAAAQWDFGNTMCQLLTGLYFIGFFSGIFFII
LLTIDRYLAVVHAVFALKARTVTFGVVTSVITWVVAVFASLPGIIFTRSQKEGLHYTCSS
HFP
YSINSGRISRH

>sp|+1.P51681|CCR5_HUMANC-Cchemokinereceptortype5OS=HomosapiensOX=9606GN=CCR5PE=1SV=1
MDYQVSSPIYDINYYTSEPCQKINVKQIAARLLPPLYSLVFIFGFVGNMLVILILINCKR
LKSMTDIYLLNLAISDLFFLLTVPFWAHYAAAQWDFGNTMCQLLTGLYFIGFFSGIFFII
LLTIDRYLAVVHAVFALKARTVTFGVVTSVITWVVAVFASLPGIIFTRSQKEGLHYTCSS
HFPY
KSVSILEEFPDIKDSHLGAGPAAACHGHLLLGNPKNSASVSK

The -15/WT genotype will have both, a normal and a slightly shortened CCR5 giving no HIV protection at all. The -4/+1 genotype may suffer the fate of non-sense mediated decay. Here are the amino acid predictions for each genotype (I reverted to Topcocns as Protter had some problems in generating correct plots).

Wildtype: There are 7 transmembrane alpha helices I to VII, connected by three extracellular loops (ECL1–3) and three intracellular loops (ICL1–3). ECL2, forms a β-hairpin structure (Tan 2013).

Nana -4 genotype has a much shorter predicted amino acid sequence with missing G protein coupling. Resembles delta 32.

Nana +1 genotype is somewhat longer but missing helices VI and VII. No analogue known.

Lulu -15: resembles wild type, however, will be sensitive to allosteric changes by small-molecule CCR5 inhibitors .

From the original AJHG paper, however, also delta 32 carriers may be HIV infected. As there exists also non-CCR5 dependent virus replication, also Nana is at risk of HIV infection when being virus exposed.

Genetics, Password, Philosophy, Theology

Der chinesische Menschenversuch

26.11.2018 admin

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Philosophy

Ich bin nur dann für technische Neuerungen, wenn sie im Einklang mit sozialen Werten stehen

14.11.2018 admin

Aus einer Umfrage (Technikradar acatech 2018)

Genetics, Philosophy

More human embryos edited

3.08.2017 admin

technologyreview.com writes

Now Mitalipov is believed to have broken new ground both in the number of embryos experimented upon and by demonstrating that it is possible to safely and efficiently correct defective genes that cause inherited diseases.
Although none of the embryos were allowed to develop for more than a few days—and there was never any intention of implanting them into a womb—the experiments are a milestone on what may prove to be an inevitable journey toward the birth of the first genetically modified humans. […] Reached by Skype, Mitalipov declined to comment on the results, which he said are pending publication. But other scientists confirmed the editing of embryos using CRISPR. “So far as I know this will be the first study reported in the U.S.”

For a few moments of fame, scientists take every risk, even “mass destruction and proliferation”.
It reminds me to the first gene therapy trial by French Anderson who was later stripped of tenure, fired from his faculty position and barred from the campus of his university.

Genetics, Software

Safety conditions for genome editing

13.03.2017 admin

I would like to see two points added to current CRISPR/Cas9 guidelines.

First of all, the current gene therapies are not being entered into the clinical trial databases on a regular basis. Maybe as the number of treated patients go down to a single individual or as there is no control group. I would really like the recommendation of a priori entry into clinicaltrials.gov or clinicaltrialsregister.eu (or some newly designed gene therapy databases). Just to get towards a clear risk/ benefit ratio.

Second, there should be some way to recognize gene editing. Some barcode as we used it already long ago, an artificial sequence that indicates the new insert. epigenie.com summarized the current approaches by last summer: Gestalt/Jay Shendure, barcode/Stephen R. Quake, scartrace/Jan Philipp Junker, hgRNA/Prasant Mali, mScribe/Tim Lu. Something like the FLAG-tag. Or more recently

R. Kalhor et al., “Rapidly evolving homing CRISPRbarcodes,” Nature Methods, doi:10.1038/nmeth.4108, 2016.
S.D. Perli et al., “Continuous genetic recording with self-targeting CRISPR-Cas in human cells,” Science, doi: 10.1126/science.aag0511, 2016.

Philosophy

Gene Doping using CRISPR/Cas

25.11.2015 admin

After some first experiments in human embryos, there is a new Chinese paper in the Journal of Molecular Biology showing that also gene doping is possible in mammals. Myostatin deficiency otherwise leads to some really impressive super strength children while it is now possible to knockout this gene artificially. Hopefully the WADA will test for myostatin gene activity in Rio 2016!
Addendum 4 Dec15: An International Summit Statement On Human Gene Editing says

It would be irresponsible to proceed with any clinical use of germline editing unless and until (i) the relevant safety and efficacy issues have been resolved, based on appropriate understanding and balancing of risks, potential benefits, and alternatives, and (ii) there is broad societal consensus about the appropriateness of the proposed application.

Both conditions are unlikely to be ever met.