Re: Common Descent: From Monkey To Man

From: Preston Garrison (garrisonp@uthscsa.edu)
Date: Fri Mar 28 2003 - 22:33:52 EST

  • Next message: John Burgeson: "Re: appearance of age and the goodness of God"

    Josh Bembenek wrote:

    >ASA Folks:
    >
    >I have heard several times from various responses that the fact that
    >humans and apes are related through common descent is most supported
    >by the fact that both genomes have incorporated the same retrovirus
    >at the same locus on some chromosome. I have thought about this a
    >lot, and I came across the following discussion of the gene therapy
    >trials that have recently been halted due to issues discussed in the
    >article below. Question: How do we know that the related virus
    >insertions into the chromosome between man and apes are indeed
    >derived through common descent and not similar viruses attacking
    >both organisms and inserting themselves at similar loci? In the
    >case below, we have random insertion in two patients to the same
    >loci giving the same cancer phenotype. In your answer, please refer
    >to the original findings so I can learn more about the virus
    >insertions that support common descent of monkey to man.
    >
    >Josh

    Josh,

    What seems to be going on here, at least as interpreted by the
    researchers, is not site specific insertion, but selection for cells
    in which the virus inserted near a particular gene. I'm not a gene
    therapy expert, but I think it works like this. They isolate some
    pre-lymphocyte cells of a particular type from the patient and
    transform them in mass with the engineered retrovirus vector. They
    may then select for cells that have the vector incorporated, based on
    some selectable marker in the vector. I'm not sure that they would do
    that or not. They would do it if the transformation is inefficient.
    But they didn't apparently clone from a single transformant cell,
    since they assume in their analysis that the cells they injected back
    into the patient had the vector inserted at various sites. After the
    cells are in the patient, some of them behave well and go to the
    marrow and start producing the desired corrected lymphocytes.
    However, it turns out that some element(s) of this virus can interact
    "in cis" (if the virus inserts next to or within) with this LMO1 gene
    to give a cell that is unregulated for growth and/or programmed cell
    death. That rare cell grows out to give the leukemia. The reason it
    happened in two patients is that they are transforming and injecting
    enough cells to make it fairly likely that in each patient at least
    one cell will have the insertion somewhere near the LMO1 gene. Of
    course, it would be interesting to know if the two insertions
    occurred at exactly the same site or only in the same vicinity, which
    is much more likely. There are such things as hotspots for virus
    insertion, probably based on chromatin structure or sites related to
    normal recombination. It's possible something like that contributed
    here, but I believe that in general retroviruses are not very site
    specific.

    As to your larger question on endogenous retroviruses at the same
    site in different species, a mechanism corresponding to that above
    would require that there be a selective advantage of the insertion at
    the same exact location for both species. There may be a few sites
    where there was a selective advantage, but that would be dubious for
    the vast majority. Even in that case, you wouldn't expect the
    insertion to occur at exactly the same site. Insertion at exactly the
    same site in humans and other primates is I think known to be the
    case for some retrovirus insertions where the region has been
    sequenced in more than one species. Other transposable elements,
    particularly L1 elements and Alu elements are present in mammalian
    genomes in much larger numbers than retroviruses (L1 > 10^5; Alu >
    10^6) and thus provide thousands more examples of the same thing.
    These elements are so frequent in the genome that almost any segment
    over a few kb that is sequenced in both human and chimp or gorilla
    will have examples of this. Some particular insertions can be shown
    to be present only after a certain point in primate evolution. That
    is, they may be present only in chimps, gorilla and human and not in
    more primitive primates or other mammals. For one paper among many
    that show this see:

    Genomics 18, 29-36, 1993.
    Fixation times of retroposons in the ribosomal DNA spacer of humans
    and other primates.
    Abstract
       We have investigated the presence/absence of two types of retroposed
       sequences found in human ribosomal DNA in equivalent positions in
       chimpanzee, gorilla, orangutan, gibbon, and rhesus monkey rDNA. These
       sequences are one pseudogene derived from the single-copy cdc27hs gene and
       seven complete Alu elements. The 2-kb pseudogene is present in the apes
       but not in Old World monkeys, indicating fixation in an ape ancestor. Five
       of the Alu elements are shared by the whole set of primates studied,
       indicating insertion and fixation prior to the split of the ape and Old
       World monkey lineages. One is absent only from the rhesus monkey rDNA, and
       another is absent from both gibbon and rhesus rDNA, indicating fixation at
       different times in primate evolutionary history. Since branching times for
       the primate phylogenetic tree are known from a combination of the fossil
       record and multiple molecular data sets, it is possible to compare Alu
       fixation times determined from the phylogenetic information with those
       calculated from Alu element mutation rates.

    For a paper looking at retrovirus insertions in more detail, see:

    UI - 99398695
    AU - Johnson WE
    AU - Coffin JM
    TI - Constructing primate phylogenies from ancient retrovirus sequences.
    TA - Proc Natl Acad Sci U S A
    PG - 10254-60
    SB - M
    SB - X
    CY - UNITED STATES
    IP - 18
    VI - 96
    JC - PV3
    AA - Author
    EM - 199912
    AB - The genomes of modern humans are riddled with thousands of endogenous
           retroviruses (HERVs), the proviral remnants of ancient viral
    infections of
           the primate lineage. Most HERVs are nonfunctional, selectively neutral
           loci. This fact, coupled with their sheer abundance in primate genomes,
           makes HERVs ideal for exploitation as phylogenetic markers. Endogenous
           retroviruses (ERVs) provide phylogenetic information in two ways: (i) by
           comparison of integration site polymorphism and (ii) by orthologous
           comparison of evolving, proviral, nucleotide sequence. In this study,
           trees are constructed with the noncoding long terminal repeats (LTRs) of
           several ERV loci. Because the two LTRs of an ERV are identical
    at the time
           of integration but evolve independently, each ERV locus can provide two
           estimates of species phylogeny based on molecular evolution of the same
           ancestral sequence. Moreover, tree topology is highly sensitive to
           conversion events, allowing for easy detection of sequences involved in
           recombination as well as correction for such events. Although
    other animal
           species are rich in ERV sequences, the specific use of HERVs in
    this study
           allows comparison of trees to a well established phylogenetic standard,
           that of the Old World primates. HERVs, and by extension the ERVs of other
           species, constitute a unique and plentiful resource for studying the
           evolutionary history of the Retroviridae and their animal hosts.
    AD - Department of Molecular Microbiology, Tufts University School
    of Medicine,
           Boston, MA 02111, USA.
    PMID- 0010468595
    SI - GENBANK
    URLF- http://www.pnas.org/cgi/content/full/96/18/10254
    URLS- http://www.pnas.org/cgi/content/abstract/96/18/10254
    EDAT- 1999/09/01 09:00
    MHDA- 1999/09/01 09:00
    SO - Proc Natl Acad Sci U S A 1999 Aug 31;96(18):10254-60

    >
    >Second cancer case halts gene-therapy trials
    >
    >ERIKA CHECK
    >
    >[WASHINGTON]
    >A. & H.-F. MICHLER/SPL
    >
    >Blood cancer: leukaemia has been detected in two patients who have
    >received gene therapy.
    >The world of gene therapy was shaken last year when a child treated
    >in a French trial developed leukaemia. Researchers had pinned their
    >hopes on this being an unfortunate one-off. Now those hopes have
    >been dashed with the emergence of a second, almost identical case
    >that could jeopardize the future of gene therapy.
    >
    >The latest case centres on a three-year-old boy treated in a
    >gene-therapy trial led by Alain Fischer at the Necker Hospital for
    >Sick Children in Paris. Just under three years ago, the child was
    >cured of severe combined immunodeficiency disease (SCID), a
    >condition that disrupts the development of the immune system. But
    >researchers revealed last week that the boy was diagnosed with
    >leukaemia just days before Christmas.
    >
    >The news last August that a child in Fischer's trial had developed
    >cancer left nations divided over their regulatory response (see
    >Nature 419, 545546; 2002). This time there was greater accord.
    >Britain has stopped the world's only active SCID trial, and the US
    >Food and Drug Administration (FDA) has suspended more than two dozen
    >similar gene-therapy trials in a variety of diseases trials it had
    >allowed to continue after August's incident.
    >
    >The setback is all the more serious because it arises in a trial
    >that was widely viewed as gene therapy's only true success. Fisher
    >has so far cured nine boys including the two who now have
    >leukaemia out of 11 patients. And when the first child was
    >diagnosed with cancer, some argued that it was an isolated event
    >(see Nature 420, 595; 2002).
    >
    >But Christof von Kalle of the Cincinnati Children's Hospital says
    >analysis of the two boys' cells shows that the same molecular events
    >probably caused the cancers. In both boys, the retroviral vector
    >used to deliver the corrective gene has integrated itself into a
    >stretch of DNA in or near a gene called LMO2, which can cause
    >childhood leukaemias. Scientists are now satisfied that the disease
    >behaves enough like leukaemia to describe it as such.
    >
    >Kalle estimates that the vector is likely to insert itself near to
    >LMO2 in between 1-in-50,000 and 1-in-100,000 cells. And because each
    >child in the trial receives a dose of about a million corrected
    >cells, each patient could carry at least one cell with the vector
    >near LMO2. Kalle is analysing samples from all of the children
    >about 15 in all who have been treated in SCID gene-therapy trials
    >to find out whether they are carrying such cells.
    >
    >In the meantime, an FDA advisory committee on gene therapy will meet
    >on 28 February to decide what the adverse event means for other
    >studies. The American Society of Gene Therapy will also convene a
    >committee to examine data from human and animal trials of retroviral
    >vectors. And the National Institutes of Health's Recombinant DNA
    >Advisory Committee (RAC) postponed its planned meeting on 17
    >January, but will convene shortly to discuss these issues.
    >
    >At their last meetings, both the FDA committee and the RAC
    >recommended that gene therapy in SCID could proceed with appropriate
    >monitoring and informed-consent programmes. RAC chair Ted Friedmann
    >of the University of California, San Diego, says that this approach
    >is "still valid", although it could be revised in light of the new
    >case.
    >
    >The case is an enormous setback for the field and for patients
    >with SCID. "The treatment works very well," Fischer says, "but the
    >risk is not acceptable."
    >
    >
    >
    >
    >
    >
    >P.S. This is my response to Stephen's comment earlier:
    >
    >Just wanted to stimulate interesting discussion, but also know that
    >I don't have excessive time to nurture the thread (I have started
    >threads before and not kept up with them.)
    >
    >
    >>From: "Stephen J. Krogh" <panterragroup@mindspring.com>
    >>To: "asa" <asa@calvin.edu>
    >>Subject: RE: leaving
    >>Date: Wed, 26 Mar 2003 18:33:55 -0600
    >>
    >>Jon,
    >>
    >>So sorry you feel like leaving. If you don't find the conversations
    >>stimulating, feel free to start your own thread that you would find
    >>interesting. My archives show that you have posted 16 times since December.
    >>That last being this notice that you are leaving, like we are supposed to
    >>notify the media regarding your departure.
    >>
    >>
    >>Stephen J. Krogh, P.G.
    >>The PanTerra Group
    >>http://panterragroup.home.mindspring.com
    >>
    >>==========================================
    >>
    >>> -----Original Message-----
    >>> From: asa-owner@lists.calvin.edu [mailto:asa-owner@lists.calvin.edu]On
    >>> Behalf Of jdac
    >>> Sent: Wednesday, March 26, 2003 4:08 PM
    >>> Cc: asa
    >>> Subject: leaving
    >>>
    >>>
    >>> Regretfully I am finding the volume of emails on subjects I find
    >>> uninteresring and unhelpful overwhelming. Farewell.
    >>>
    >>> Jon
    >>>
    >>>
    >>
    >
    >
    >_________________________________________________________________
    >MSN 8 with e-mail virus protection service: 2 months FREE*
    >http://join.msn.com/?page=features/virus

    -- 
    


    This archive was generated by hypermail 2.1.4 : Fri Mar 28 2003 - 22:35:09 EST