Category Archives: Genetics

Fundamental and non fundamental objections of genome editing in humans

3.02.2019 Matthias Wjst

Braun, Schickl and Dabrock try to “map the underlying ethical arguments” (p6ff in “Moral Hazard” 2018) against human genome editing.

The various objections against germline genome editing can basically be divided into (1) fundamental (i.e. against the context of research and application) and (2) non fundamental (i.e. only against the context of application) arguments. The most prevalent fundamental arguments are (a) arguments of human dignity (b) arguments of naturalness and (c) slippery slope… The most common argument within the ethical (as well legal) debate on the use of genome editing techniques, like CRISPR technologies, is the safety argument as a non fundamental objection.

While I think the differentiation of fundamental vs non-fundamental is important for discriminating relevant from irrelevant arguments, the definitions are not fully clear. What is “context of research” – subject, object or objective? And what is “context of application” – the procedural conditions?

“Fundamental” may not be the best label as “fundamental” in German usually claims to be the only right doctrine. Anyway, a fundamental argument will be an argument that cannot be easily overcome by a counter-argument as it is it is deeply grounded, heavy-weighted and basis for other conclusions. A non-fundamental is just a non fundamental argument that can be rebutted immediately or in the foreseeable future.

The classification of fundamental by Braun, Schickl and Dabrock is even problematic as well. “Naturalness” is not a fundamental argument as it is nearly impossible to define a “natural” human genome. IMHO “slippery slope” is also not a logical argument at all – having more fear mongering elements than a strict consequentialist logic.

I would therefore like to split any fundamental objections by the disciplines where they originate: (a) philosophical/theological anthropology (b) biology and (c) sociology.

FUNDAMENTAL OBJECTION
-- anthropology
  .. human dignity
  .. missing embryonal consent
  .. genetic heteronomy
-- biology
  .. off target risks / safety
  .. unknown genetic background effects
  .. unknown next generation effects
  .. dissolution of species boundaries
-- sociology
  .. missing societal consensus
  .. tendency towards eugenics
  .. tendency towards racism
NON FUNDAMENTAL OBJECTION
  .. medical necessity
  .. ethics vote
  .. no pre-tests
  .. no trial exit strategy
  .. conflicts of interest
  .. consent without alternatives
  .. and all other Krimsky rules

Safety could of course could be a fundamental argument as set out by Nüsslein Vollhard: we can not 100% predict from one cell the fate from another cell.

Maybe this very first classification of arguments could be a further step into a more rational ethical discussion.

Braun, Schickl and Dabrock write on the same page in their book that “the potentiality argument … which is considered to be the strongest argument for absolute embryo protection, is increasingly criticized by ethicists” citing Schöne-Seifert et al 2013 and themselves as Schickl et al 2014. Their argument: we can reprogram now adult cells, the potentiality is therefore not a unique property of the human embryo, the embryo therefore has not any unique value, the embryo does not need protection.
I ask – instead of REVOKING potentiality of the human embryo why not EXPANDING potentiality to reprogrammed stem cells?
I have also doubts that a “reprogrammed” stem cell will ever have the unique potentiality of an embryo in situ for 3 reasons:
1. a stem cell is not a de novo creation but just a replication.
2. a stem cell will never replicate the complicated epigenetic pattern of an embryonic cell (which is a unique part of the embryonic identity, putting the Schickl argument in a row of genetic exceptionalism arguments).
3. lastly there is never ever maternal support of a stem cell, ignoring the complex biological support chain of human embryos.

(TBC)

Genetics

Abwehr des Bio-Terrorismus

1.02.2019 Matthias Wjst

Nature hat einen interessanten Beitrag, wie in Zukunft der Bioterrorismus abgewehrt werden soll: Alle Sequenzen, die an die Oligo Fabrik gehen, sollen routinemassig vorher gescreent werden, für was sie codieren. Das wird eine extrem komplexe Aufgabe für die Bioinformatik sein. Wenig Aussicht auf Erfolg hat der Vorschlag allerdings, wenn Biokampfstoffe staatlich gefördert werden.

Genetics

What makes an allele dominant on the molecular level?

25.01.2019 Matthias Wjst

This was a question, I have been asked yesterday.

Although dominance is the property an allele, dominance is not”regulated” on the genomic level but a function of the resulting protein. According to the largely citied Wilkie paper there are numerous mechanisms

reduced gene dosage expression or protein activity
increased gene dosage
ectopic or temporally altered mRNA expression
increased or constitutive protein activity
dominant negative effects
altered structural proteins
toxic protein alterations
new protein functions

In lay terms also explained at biology.stackexchange

… the dominant allele encodes a protein that can perform its function. For example, the dominant allele for the CFTR gene encodes a channel that can let chloride into and out of the cells. The recessive allele, on the other hand encodes a protein that cannot do its job correctly (this also called a loss-of-function mutation). So if you inherit a functional copy from one parent and a non-functional copy from the other parent, you will still have one copy of the protein that can do its job. Only if you get a nonfunctional copy from both parents will you have a recessive condition called cystic fibrosis.

Genetics

IVF eine Zeitbombe?

19.01.2019 Matthias Wjst

Nachdem es also doch so viele IVFs in Deutschland gibt (12.000 IVF bei 785.000 Geburten im Jahr ), wäre es doch mal interessant, was es an Spätwirkungen für die IVF Kinder gibt, sobald sie das niedrige Geburtsgewicht und angeborene Defekte überlebt haben.

S. 22 Jahrbuch Deutsches IVF Register 2018

Aus zwei Gründen ist die Frage allerdings nicht ganz leicht zu beantworten. Erstens gibt es bisher keine IVF Kinder, die bisher älter als 40 Jahre sind und damit gibt es auch keine Erfahrung mit den typischen Krankheiten ab 60 Jahre.
Und zweitens gibt es diverse Krankheiten der Eltern, die überhaupt erst zur IVF geführt haben, aber nicht der IVF selbst angelastet werden können. Zudem sind IVF Mütter deutlich älter als im Durchschnitt was selbst schon ein Krankheitsrisiko für die Kinder bedeutet.

Zumindestens von der Theorie her, ist die IVF nicht ganz ungefährlich für den Embryo, man braucht Hormone und ein künstliches Medium, was vor allem die Methylierungsstatus der Embryos beeinflusst (dazu gibt es mehrere Studien, die wichtigste von 2015). Eigenartigerweise gibt es aber nur wenig klinische Literatur zu dem Thema und Null Information am Deutschen IVF Register. Die fehlenden Studienbasis fiel auch vor kurzem auch dem Independent auf.

Das letzte medizinische Review ist schon etwas angejahrt. Beschriebene Risiken sind vor allem Depression im frühen Erwachsenenalter, Alkoholismus, erhöhter Bluthochdruck, erhöhter Nüchternzucker, erhöhter BMI, vorzeitige Knochenalterung sowie Schilddrüsenerkrankungen.

Eigentlich müsste es regelmässige Kontrolluntersuchungen nach IVF anbieten, am besten im Rahmen klinischer Studien.

Genetics

Could the correction of a deleterious mutation be a disadvantage?

18.01.2019 Matthias Wjst

When working on a forthcoming talk about the ethics of correcting gene defects, I asked myself: Are there any empirical examples where the correction of a so called “deleterious” mutation may be a disadvantage? Or in other words: Are there any beneficial side-effects of otherwise deleterious mutations?

(Don’t answer this with the joke that the Y chromosome is a X with a large deletion :-)

Yes, there are some examples of heterozygote advantage

HBB-p.E6V leads to sickle cell anemia and malaria resistance
CFTR Delta F508 leads to CF and protects against tuberculosis
…

Maybe I am not asking if there are beneficial/deleterious mutations in a single gene – the question here is more about distant / cis-regulating elements. And there seems to be a thesis that

deleterious mutations have long been thought to be unimportant, however this view overlooks the pivotal role of epistasis. The unique experiments presented here give new insights into the historical and highly contingent nature of evolution. While evolution frequently finds a well adapted solution in the long-term, evolving populations will frequently climb suboptimal peaks initially. Deleterious mutations become useful because they aide evolution in reconciling short-term and long-term adaptation.

the thesis made it also into a PNAS paper

It might seem obvious that deleterious mutations must impede evolution. However, a later mutation may interact with a deleterious predecessor, facilitating otherwise inaccessible adaptations. … We studied digital organisms—computer programs that replicate and evolve—to compare adaptation in populations where deleterious mutations were disallowed with unrestricted controls. Control populations achieved higher fitness values because some deleterious mutations acted as stepping stones across otherwise impassable fitness valleys. Deleterious mutations can thus sometimes play a constructive role in adaptive evolution.

Looks like humans shouldn’t interfere with their own evolution as long as the rules are not known… The PNAS paper above has been cited many times, it will take some time to scan these for more empirical examples.

Genetics

Weight Loss Advice

13.01.2019 Matthias Wjst

23andme is again in the headlines

Consumer DNA-testing giant 23andMe Inc. plans to add new wellness offerings it hopes will help its customers shed a few pounds, but some genetics experts say the jury is still out on the science behind the products.
On Tuesday, the Mountain View, California-based company announced a partnership with Lark Health, an artificial-intelligence coaching service that delivers personalized advice for weight loss and diabetes prevention via an app. Lark will allow customers to incorporate weight-related genetic data from 23andMe into its service.

We don’t need artifical intelligence for that, just a simple BMI table
Underweight Below 18.5 Normal 18.5–24.9 Overweight 25.0–29.9 Obesity 30.0 and Above
According to NIH recommendations people who are considered obese (BMI >30) or those who are overweight (BMI of 25-29.9) and have two or more risk factors, it is recommended to lose weight. Even a small weight loss of 5 to 10 percent of your current weight will help lower your disease risk. Point. No need to send your money to 23andme, just give it to a charity now. 23andme has already enough money for selling private data of some other boobies.

Genetics

Genes and environment

10.01.2019 Matthias Wjst

An interesting interview 1999 at Edge reloaded: Children don’t do things half way: children don’t compromise with Judith Rich Harris

How the parents rear the child has no long-term effects on the child’s personality, intelligence, or mental health. […] The trouble is, the evidence is ambiguous. It’s clear that children resemble their biological parents; what isn’t clear is why. Is it the environment the parents provided, or is it the genes they provided? Just knowing there’s a correlation isn’t enough—we have to tease apart the effects of the genes from the effects of the home environment. One way to do it is by looking at adopted kids. And what we find is that the correlation disappears. The adopted child reared in a let’s-read-a book-together home ends up no smarter, on the average, than the one reared in a don’t-bother-me-I’m-watching-TV home. […] In fact, for personality (which is what I’m mainly interested in), only about half the variation from one person to another can be attributed to the genes. More precisely, about half the reliable variance in measured personality characteristics—the variance that remains after measurement error is subtracted—can be attributed to differences in genes. […] They still haven’t acknowledged the fact that whatever genetic predispositions the children have, there’s a good chance the parents have them too. […] In study after study, was that the environment shared by two kids reared in the same home could account for no more than 5 percent of the variance in personality characteristics. […] Well, the way children behave outside their parents’ home is certainly more lasting, because that’s where they’re going to spend their adult lives. […] the impetus comes from the child doing the conforming, not from the group. Tailoring your behavior to that of the other members of your group is something that people of all ages do automatically, usually without even realizing that they’re doing it.

Genetics

Paternal mitochondrial inheritance

28.12.2018 Matthias Wjst

So far I thought this is not happening in humans, but a PNAS paper published this month shows it may be even a genetic trait as the authors found biparental mtDNA inheritance in 17 members in three multi-generation families.
There are around 50-75 mitochondria in a single sperm which appears to be a quite low number (∼0.1%) relative to the number maternal mitochondria.
This unexpected paternal origin of mtDNA raises questions how exactly paternal mtDNA can escape its normal fate of being eliminated from the embryo. Are paternal mitos just being diluted and there is much more (micro-)heteroplasmy than currently known?
I don’t know why the authors didn’t do formal linkage analysis. And I also don’t know if their conclusion is correct “that occasional paternal transmission events seem to have left no detectable mark on the human genetic record” not citing an 1996 PNAS paper

In the majority of mammals—including humans—the midpiece mitochondria can be identified in the embryo even though their ultimate fate is unknown. The “missing mitochondria” story seems to have survived—and proliferated—unchallenged in a time of contention between hypotheses of human origins, because it supports the “African Eve” model of recent radiation of Homo sapiens out of Africa.

In the age of single cell sequencing it may no more be adequate to believe in maternal inheritance alone.

Genetics

CRISPR CAS Babies: Doubt on the Sanger sequences

27.12.2018 Matthias Wjst

Using the new inDelphi (Nature 2018) prediction we can examine the gRNA guided cut used for the CRISPR Baby experiment. The results are somewhat unexpected

Maybe it is difficult to extrapolate from mouse to human embryonic stem cells but one observed event is not even listed here.

The results marked with a star have been observed

The -15 genotype has a probability of less than 0.05%. For +1 genotype the probability is 0.09% and for the -4 deletion it is 3.74%.

Looking therefore again at the Hong Kong slides of He Jiankui, I am getting doubts if the chromatogram of embryo 2 is correct interpreted even if we admit that the labels of embryo 1 and 2 have been switched..

Color enhanced + sharpened version Hong Kong slide. Unfortunately the chromatograms do not expand to the left also.

Embryo 2 does not show a clean sequence at all and certainly not a -4/+1 genotype as indicated everywhere “ATTTTCCATACAG-ATTCAATTCTGGACTAAAATAAATACCT” isn’t even a human sequence at all.

Genetics

Gene Editing

27.12.2018 Matthias Wjst

Die Entwicklung des Gene Editing ist schwer nachvollziehbar ohne detaillierte Kenntnisse der Enzymchemie. Das neueste LJ 12/18 hat ziemlich versteckt auf S.44 eine exzellente Beschreibung von BE1 (mutiertes dCas9 mit APOBEC1-Cytidin-Deaminase, Einzellstrang R Loop), BE2 (Uracil-Glycosylase-Inhibitor), BE3 (dCas9 mit Nick), HF-BE3 (high fidelity), BE4-GAM, BE4max, bis zum ABE 7th generation…

Das Basen-Editing tüftelten David Ruchien Liu und seine Mitarbeiter vom Broad-Institut in Cambridge, USA, aus. Sie kombinierten CRISPR-Cas-Komponenten mit Bestandteilen der mRNA-Editiersysteme, die sowohl Pro- wie auch Eukaryoten benutzen. Liu fasste die Methode in einer Presseerklärung so zusammen: „Wir haben programmierbare molekulare Maschinen entwickelt, die an einer von uns aus- gewählten Stelle im Genom eine Base austauschen, ohne dabei einen Doppelstrangbruch in die DNA einzufügen.“

Was noch fehlt? Die bisherigen BE können bisher nur Pyrimidine C -> T und T -> C, oder Purine A -> G und G -> A Transitionen. Das Problem sind Transversionen von Purinbase nach Pyrimidinbase oder umgekehrt also T -> A oder C->G, denn dafür gibt es keine Enzyme.

Genetics

Verrückte Experimente

16.12.2018 Matthias Wjst

Bisher dachte ich immer, Optogenetik sei die genetische Aufklärung von optischen Anomalien, wie Linsendeformationen oder Netzhauterkrankungen. Aber offensichtlich liege ich damit falsch, wenn ich mir die neue NM Arbeit anschaue, in der ein Hybrid Crispr-Cas9 durch Licht angeschaltet werden kann.

We engineered optogenetic anti-CRISPR variants comprising hybrids of AcrIIA4, a potent Streptococcus pyogenes Cas9 inhibitor, and the LOV2 photosensor from Avena sativa. Coexpression of these proteins with CRISPR–Cas9 effectors enabled light-mediated genome and epigenome editing, and revealed rapid Cas9 genome targeting in human cells.

Die Optogenetik ist ein richtig grosses Feld mittlerweile. Es ist eine interessante Option allemal, die Enzymaktivität intrazellulär an- und abzuschalten zu können.

Die FAZ weiss dazu aber auch ein Experiment, Mäuse auf Knopfdruck im Kreis laufen zu lassen, in dem man den motorischen Cortex über Licht aktiviert. Danke an Juliette Irmer für den Link!

Was für Experimente und was für eine Hybris … Das WSJ zu einem ähnlich gelagerten Tierversuch

The stumbles show the risks of racing ahead with such experiments, even as many governments work to clear regulatory pathways to bring meat, eggs and dairy from gene-edited animals to store shelves. Bioethicists and many geneticists have raised doubts about applying the gene-editing technology to animals and especially humans, given the continued uncertainties in both the science and the lab and field results.

Genetics

Off target sites of the CRISPR CAS babies

14.12.2018 Matthias Wjst

Sure, we don’t know the genome of the Chinese couple (which would be mandatory for any prediction) . And we know only one confirmed off target site that has 5! mismatches

At least I would expect more than 1 off target site.. So we are could check several online services that include the human genome..

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 above, nor any reported de novo mutations (COL4A, CCDC170, NUCB2, GCDH, FTL).

Cas-OFFinder