Genetic Engineering Mosquitos Resistant to Malaria

Posted on March 21, 2007 by Steven F. Palter, MD

The BBC is reoprting that a new geneticaly medified mosquito has been created that is relatively reistant to malaria.

The study publsihed in PNAS reports

The approach exploits the fact that the health of infected mosquitoes is itself compromised by the parasite they spread. Insects that cannot be invaded by the parasite are therefore likely to be fitter and out-compete their disease-carrying counterparts.

BBC says;

The organism is passed to humans through the bite of the Anopheles mosquito. Each year it makes 300 million people ill and causes a million deaths worldwide. Some 90% of cases are in sub-Saharan Africa, where a child dies of malaria every 30 seconds.

Before you spill all of your quinine out, the malaria variation tested was a rdent one and the researchers predict tit will be 10-20 years before GM mosq’s will be released into the wild.

Many people do not realize that the gene for sickle cell anemia functions in a similar fashion. While deadly in its full disease form, the carrier state (or sickle cell trait) confers a relative immunity to malria and is likely the reason this genetic variation is so common in the Africal population.

While on the subject of GM mosquitos there have been frankencreatures and frankenpets before that have a fluorescent gene stuck into their genome.

The most famous is Glofish. For more info – Here’s how the fluorescent glofish are made. Nothing like genetic engineering to create cute pets. Hey why not knock out growth hormone so you kitten never grows up!

Flawed Research: The Hidden Weakness of Peer Review & More Falsified Stem Cells

Posted on February 15, 2007 by Steven F. Palter, MD

The point of this post is not about stem cell research it is about flaws in the peer review process. However, I need to start with a little timely news and some background first.

In yet another blow to stem cell research, New Scientist reports today that one of the best-known stem cell papers in the past five years, describing adult cells that seemed to hold the same promise as embryonic stem cells is based on likely flawed (or false) data.

Everyone will recall the Korean Stem cell-cloning mess recently. There, Hwang Woo Suk admitted that none of the 11 tailor-made cell colonies he claimed to have created actually exist (and that women were coerced to donate their eggs). More details of this fiasco are reported here and the retraction of the paper from the journal Science here.

The latest stem cell mess-scenario seems to be yet another garden variety data falsification. The new paper prints data that is later found to be exactly used in another paper from the same group but on different cells – (coincidence- methinks not)!

What’s more interesting to docinthemachine here is the inherent flaws in the peer review system. Its just like that old bad legal joke: a jury of your peers means a group of people too stupid or lazy to get out of jury duty (a sad commentary on civic duty and the legal system but hey that’s another post for the politico-blogs). Unfortunately, the medical peer review process shares some similarities. I have served as a journal reviewer for many journals and have reviewed original research since I was a resident through fellowship and on as an assistant professor. I have several disquieting observations. Since I have an extensive network of colleagues, mentors, and mentees (is that a word?) from many different departments and universities (many who just have sought my advice) the following cannot be taken as representative of any particular person I have worked with. Sorry – not naming names here.

Where Peer Review Fails:

1) the trickle down review. A journal reviewer is chosen to review submitted manuscripts based on his past academic accomplishments, expertise in the area of research, and reputation. However, it is commonplace for academic faculty members, division directors, and departmental chairs to pass the reviews on to junior faculty and fellows-in-training. On the positive side, when done collaboratively this can be an excellent leaning opportunity for the junior person. They do extensive research on the topic and prepare an exhaustive report for the senior faculty member who sits down with them and prepares the final review teaching all along the way. Yes, but we’re not in Kansas anymore Toto! On the bad side, the lazy senior faculty member passes it on the junior (lacking in the expertise or knowledge) who does his best but does an inadequate job. The lazy mentor simply says thanks, signs his name, and passes the crap off as his own. Yep, seen it happen.

2) The lazy reviewer. A journal submission goes to more than one reviewer. Often the reviewers see the comments from the other reviewer. On many occasions I have completed my review with a dozen points for the author to fix, clarify, or amend. Sometimes these include very serious research flaws. Heck, I take the job seriously. All the more reason I get shocked to see the other reviewer chime back with 2-3 lines of comments, at least one of which is spelling or grammar. They just did not give it much effort. This reminds of the couples that come in where the wife speaks little English and the husband translates. I ask a question, he translates. She goes on for 5 minutes passionately answering to him- sounds pretty concerned to me. He turns to me and replies “she says no”. Something is getting lost in the translation and it’s not accidental. I remember a seminal paper I wrote along co-authors who are world famous pioneers and leaders in reproductive medicine. This thing was infamous in my circles since it went through more than 35 major revision drafts over 7 years before my mentor judged it complete. (for those interested it was a reappraisal of the basic theory of the role of estrogen in human follicular and egg development refuting classical theories – Are Estrogens of Import to Primate/Human Ovarian Folliculogenesis? from Endocrine Reviews and can be found here). Well I remember my shock when the reviewers comments came back with pages of suggestions! This guy did MASSIVE research double checking and commenting on minutia in the paper but did 1000% his job as a reviewer (we went on the address all of his concerns).

3) Bad reviewer choice A. Some journals have a shortage of good reviewers. As a result they have a second tier group who just don’t meet the muster in terms of qualifications. Happens more with very clinically oriented journals. A related issue is in some of the newer surgical journals. Many of the leading surgeons on the”cutting edge” (sorry) are amazing pioneers but not necessarily researchers. Many of the lead academics are amazing researcher but not pioneers in these fields. Therefore the reviewer tends to be only 1/2 of what’s needed.

4) Bad reviewer choice B. The reviewer gets a paper to review that he is really not a expert on. In the best case he taps out and declines the review. In the worst case he accepts to do the review but misses a lot. I have seen this one getting calls “hey Steve- you’re an expert on so and so – I got this paper to review but don’t know anything about this – can you give it a look?”

5) The editor over-ruling the reviewer. Reviewer finds errors and recommends rejection. Editor accepts the paper and it goes on the be revealed to be a bad study. Seen it happen.

I even remember a teaching conference we ran briefly when I was at Yale “bad research papers”. We would pull papers that really had flaws and have the fellows comment on what was wrong to teach methodologies etc.

All in all the medical literature is a living breathing organism. That’s why internet research by inadequately trained or educated readers can be so faulty. You can find SOME paper to support both sides of an argument or hypothesis. A real expert knows them all and weighs the bunch on their merits and methodology to try to come to the best conclusion. A single paper taken out of its context of the entire literature is just a piece of the puzzle. If you don’t know research methods and the other studies you are getting set up to draw incorrect conclusions. This is one of the problems in the courtroom where in expert testimony papers are weighed equally. It’s the reason why I never draw conclusions on areas where I am not an expert.

In a sense this is at the basis of the trend towards evidence based medicine. Instead of just an expert or committee’s opinion research is judged and ranked according to its quality and conclusions drawn and then the results apllied to the individual patient. It’s a mantra for the modern specialist! You can read a nice piece on EBM from BMJ here including this definition:

Evidence based medicine is the conscientious, explicit, andjudicious use of current best evidence in making decisions aboutthe care of individual patients. The practice of evidence basedmedicine means integrating individual clinical expertise withthe best available external clinical evidence from systematicresearch. By individual clinical expertise we mean the proficiencyand judgment that individual clinicians acquire through clinicalexperience and clinical practice. Increased expertise is reflectedin many ways, but especially in more effective and efficientdiagnosis and in the more thoughtful identification and compassionateuse of individual patients’ predicaments, rights, and preferencesin making clinical decisions about their care. By best availableexternal clinical evidence we mean clinically relevant research,often from the basic sciences of medicine, but especially frompatient centered clinical research into the accuracy and precisionof diagnostic tests (including the clinical examination), thepower of prognostic markers, and the efficacy and safety oftherapeutic, rehabilitative, and preventive regimens. Externalclinical evidence both invalidates previously accepted diagnostictests and treatments and replaces them with new ones that aremore powerful, more accurate, more efficacious, and safer

For those wishing to go deep into this area check out extensive resources at UW EMB here and the categories of research levels of evidence here.

You can read my thoughts about the future of electronic medical research and publishing here.

MORE: great discussion on the flaws of the peer review process on the thread at slashdot. Obviously over fraud and falsified data is at the top of the crap heap.

New Device Filters Blood- Kills Tumor Cells and Captures Stem Cells

Posted on January 5, 2007 by Steven F. Palter, MD

Stemcapture is a new company commercializing a neat device licenses from the University of Rochester. As reported in what’s next in health

Associate Professor Michael King of the University of Rochester Biomedical Engineering Department has invented a device that filters the blood for cancer and stem cells. When he captures cancer cells, he kills them. When he captures stem cells, he harvests them for later use in tissue engineering, bone marrow transplants, and other applications that treat human disease and improve health. With Nichola Charles, Jared Kanofsky, and Jane L. Liesveld of the University of Rochester, King wrote about his discoveries in “Using Protein-Functionalized Microchannels for Stem Cell Separation,” Paper No. ICNMM2006-96228, Proceedings of the ASME, June 2006. King’s team includes scientists at StemCapture, Inc., a Rochester company that bought the University patent for King’s technique in November 2005 to build the cancer-killing and stem cell-harvesting devices. The technique can be used in vivo, meaning a device is inserted in the body, or in vitro, in which case the device resides outside of the body – either way, the device kills cancer cells and captures stem cells, which grow into blood cells, bone, cartilage, and fat.

Basically this is a high tech molecular based blood filter. It has great potential for cancer therapeutics.

Read much more about the technology and the research behind it (along with a video of the mechanism) here at the U or R

How the stem cell capture works- Selectins:

When King was working at the University of Pennsylvania from 1999 to 2001, one of his labmates discovered that bone marrow stem cells stick to adhesive proteins called selectins more strongly than other cells — including blood cells — stick to selectins. When King came to the University of Rochester in early 2002, he started studying the adhesion of blood cells to the vascular wall, the inner lining of the blood vessels. During inflammation, the vascular wall presents surface selectins that adhere specifically to white blood cells. These selectins cause the white blood cells to roll slowly along the vascular wall, seeking signals that tell them to crawl out of the bloodstream. This is how white blood cells migrate to bacterial infections and tissue injuries. King set out to find a way to duplicate this natural process.

How the tumor capture works

Another exciting application of King’s invention is filtering the blood for cancer cells and triggering their death, an innovative, new method to prevent the spread of cancer. When someone has a primary cancer tumor, a small number of cancer cells circulates through the bloodstream. In a process called metastasis, these cells are transmitted from the primary tumor to other locations in the body, where they form secondary, cancerous growths.

As a cancer cell flows along the implanted surface, King’s device captures it and delivers an apoptosis signal, a biochemical way of telling the cancer cell to kill itself. Within two days, that cancer cell is dead. Normal cells are left totally unharmed because the device selectively targets cancer cells.

The apoptosis signal is delivered by a molecule called TRAIL that coats the cancer-killing device. Cancer cells have five types of proteins that recognize and bind to TRAIL, but only two trigger cell death. The other three are called decoy receptors. Healthy cells contain a lot of decoy receptors, giving them a natural protection against TRAIL, whereas cancer cells mainly express the two receptors that signal cell death.

Sniffing Out Disease-”Smellcheck”

Posted on January 5, 2007 by Steven F. Palter, MD

Defensetech reports on DARPA’s new “smell-out the terrorist program“. Ok stop laughing and read on:

Cutting edge military R&D from DARPA has developed a way to smell out bad guys- literally. Move over fingerprints and biometrics- this is what I call “smellcheck”.

Darpa’s “Unique Signature Detection Project (formerly known as the Odortype Detection program)” aims to sniff out genetic markers in “human emanations (urine, sweat, etc.)” that “can be used to identify and distinguish specific high-level-of-interest individuals within groups of enemy troops.”

Sniffing out Organ Donors: There is real science behind this. National Geographic reported on some of the basic science mouse research behind this. Michael Leon, a neurobiologist at the University of California, Irvine studied mice and found that specific molecules excreted in urine were related to MHC molecules. The MHC (major histocompatibility complex) antigens are molecules on the surface of cells that the body uses to recognize self vs non-self. The MHC genes are the genes that code for these molecules. Whena person is “matched” for an organ or bone marrow transplant these are the factors that are being matched.

Read more very technical article about the details of tissue typing for transplants with HLA and MHC typing here

Read about the standard methods of matching and volunteer to be a bone marrow donor at the national marrow donation program here

Therefore– this new military technology being used to sniff out terrorists in a group could be used to rapidly and noninvasively screen large groups of people for potential transplant matches.

This medical concept has already been tested. An article in Nature Genetics from UC Illinois reported that:

The smell signature also applies to health. Beauchamp’s team at Monell discovered that mice, for example, can distinguish older and younger genetically identical mice. They also use odor to identify animals infected with the Mammary Tumor Virus before any signs of disease are present. In Cambridge, England, dogs are being tested for their ability to sniff out traces of human prostate cancer in urine samples. Beauchamp anticipates that many diseases may have chemical signatures that may provide early diagnoses.

DT reports- Darpa’s smell detector is part of a larger, $15 million-per-year effort to develop “novel sensors” for U.S. troop operating in “urban settings.” The goal of the Urban Vision program is “to enable the warfighter to ‘see’ movers within a building using a variety of fused multi-spectral techniques.” The “Enemy Dismount Intrusion Detection program,” on the other hand, “will develop a chemical sensor that is capable of providing an advanced warning of the presence of enemy troops or combatants by detecting the chemical emissions… that are common to all humans.”

Update: docinthemachine nominated for best medical technology blog of 2006 – please vote for us here

The Power of Genetics and IVF Embryos- and the Controversy

Posted on November 20, 2006 by Steven F. Palter, MD

I am just about to finish an IVF cycle I am doing with a lovely couple. They are in one of the best prognosis groups. He has children from a previous marriage as does she. She had a tubal ligation and “only” has blocked tubes (this is the best prognosis group for IVF). She is 37 years old and while not as young as the highest chance group her chances should be outstanding.

So why in heck am I writing this pleasant little musing on them? Where is the technology in the story? Well they decided they wanted PGS (preimplantation genetic screening). This cutting edge technology can be used to screen embryos for genetic diseases and also to test for major genetic abnormalities leading to miscarriage. Approximately 20-30% of early human pregnancies will miscarry due to genetic abnormalities. These are commonly trisomies or monosomies where there is loss of addition of a chromosome (supposed to be only 1 from mom and 1 from dad of each).

In PGS we biopsied each little embryo removing a single cell called a blastomere from an 8 cell day 3 of development embryo. It’s tested overnight and Voila! I got the report today— 10/12 of her embryos were genetically abnormal and incompatible with life! This is the power of this new genetic technology. So luckily 2 of them can lead to a live born baby and I’ll be putting those 2 in tomorrow on day 5 of development.

What’s the controvery DITM?

1) I also get information about the sex of the embryo and people are increasingly requesting this for sex-selection. Should we being doing gender selection? A leading researcher once said last time I checked “gender was not a disease”

2) It has recently been discovered that a “mosaicism” occurs in human embryos. This could lead to high rates of inaccurate results from single embryo biopsies. This is an amazing new discovery–human embryos were thought to undergo orderly cell divisions all equal. NOT TRUE! We know now that every so often (how often we do not know) there is an uneven division of just one cell so its offspring cells are abnormal but all the others are normal- and it may be that those 2 abnormal one will die but the normal cells happily grow! This means that unless we do multiple cell biopsies (and remember there are only 6-10 little cells in an embryo at this stage) we will think it’s abnormal when it is not…

The answers in the future:

1) multiple cell biopsies

2) very large cell number biopsies at the blastocyst stage of development with instant genetic results (day 5 of development cell numbers skyrocket)

3) other markers of normalcy

Metabolomics-Machine Tests IVF Embryo’s Waste to Achieve Pregnancy

Posted on November 17, 2006 by Steven F. Palter, MD

8-cell human embryo from Gold Coast IVF

Next in my series of updates from my visit to the Annual Meeting of the ASRM (American Society for Reproductive Medicine) is a potentially amazing technology to help identify a healthy embryo in a dish. IVF (in vitro fertilization) has become our most powerful toiol to help infertile couples achieve a pregnancy. More than 100,000 procedures are performed each year in the USA alone. We have come so very far since the birth of Louise Brown 30 years ago (she’s a mon herself now). The technology has progressed to the point where getting eggs and sperm and having them joing to make an embryo is no longer the hurdle it one was. However, picking a healthy embryo from the group growing in the dish remains an inexact science. Today this process is based upon morphology. We have a very crude grading system based esentially on the speed of division of the cells and on how regular the cells appear. This yields a rough system with a grade from 1-5. This would be like your doctor looking at you from across the street and estimating if you were healthy. You’ll get correct information only some of the time. Well the powerful new technique of PGS (preimplantation genetic screening) where we biopsy a growing embryo and test its genetics has shown recently that fully 1/2 of apparently good looking embryos are genetically abnormal and incompatible of leading to a living baby.

Metabolomics is the study of the small-molecule metabolite byproducts left behind from cellular processes. In simple terms it’s like examining poop. The concept is that by measuring the collection of all the byproducts of the cells metabolism you can get a snapshot of the physiology of a cell or embryo and that translates to health.

Molecular Biometrics is looking to turn this new science of metabolomics into a noninvasive test to pick the healthy viable embryo from the dish and increase the chances of pregnancy. I know the Medical Director and the President from my days when I was Clinic Chief of Infertility at Yale University and my former fellow is one of their researchers. I spoke with them at length about ther work.

As they say in their press release:

The study was designed to assess embryo viability using a novel technology developed by Molecular Biometrics based on themetabolomic profiling of Oxidative Stress (OS) biomarkers. The goal of the technology is to
identify metabolomic differences in viable verses non-viable embryos so only the highest quality embryos can be selected for transfer in IVF. This non-invasive test analyzes OS biomarkers in normally discarded culture media. The biomarkers are quantified using Molecular Biometrics’ proprietary spectroscopic analysis and advanced bioinformatics. The study group concluded that detectable differences exist in the metabolomic profiles found in culture media obtained from embryos that cause pregnancy compared to those that do not. The reported metabolomic parameters were established using two different forms of spectroscopic analysis, Raman and Near Infrared (NIR) spectroscopy, with media samples obtained from three different IVF programs. The metabolomic method achieved high sensitivity and specificiity >85%.

The bigest advantage in addition to increased pregnancy rates would be that if we can identify a healthy embryo destined to implant, then we can put fewer back into the uterus and lower the risk of multiple pregnancies from IVF treatments. Another study found the system could also identify normal vs abnormal sperm. If it is proven to work this would be a breakthrough technology.

First A Spider-Goat Next a Spider-Man

Posted on October 10, 2006 by Steven F. Palter, MD

My last post was on Nexia Biotechnologies tranfection of a goat with a gene to produce spider silk. I wanted to elaborate on the technology behind the process. A complete description is available from the company.

As a fertility specialist I know this technology well since it involves in vitro fertilization (IVF) and is the basis of what will become human gene therapy. As they write:

The first method uses microinjection of the genetic construct into a fertilized egg. This traditional method of pronuclear microinjection involves literally injecting the genetic construct into the pronucles of a one-celled fertilized egg with an extra-fine needle. The genetic construct will merge itself with the fertilized egg’s native DNA and once this is achieved, the egg is transferred to a recipient goat and the pregnancy follows its normal course. The second method uses nuclear transfer technology. In this method, the nucleus of a cell containing the genetic construct of interest is fused to a recipient fertilized egg whose native DNA has been previously removed and the resulting egg is transferred to a recipient goat.

Ok folks- both these methods already exist in humans! The first method is the basis of how gene therapy is planned to be done in humans. . This single cell is then analyzed quickly for signs of genetic diseases and I can pick the healthy embryos (without the disease) to implant into the mother’s womb. This is called PGD or preimplantation genetic diagnosis. The current human research is trying to refine the process (and safety) of inserting genes like was done with the goat. Step one: fix sickle cell anemia or Tay Sach’s Disease. Potentially eliminate it from the gene pool as well. There are dangers however- genes for genetic diseases in some cases have potential beneficial effects that would be eliminated (like sickle cell carriers having resistance to malaria). More ominous is potential “down-stream effects” where changing one gene may have ripple-like effects on other seemingly unrelated genes. Most researchers I know in this field are looking at somatic cell gene therapies (only affects the non reproductive tissues) so “problems” are not passed on to offspring as would be with germ-cell (egg and sperm affected) techniques.

The second technique was a promising technique to deal with age related infertility. There is a high level of egg dysfunction from the eggs of older women. Researchers in infertility took eggs from an older woman and removed the gene-containing nuclei and used it to replace the nuclei of the egg from a young donor. In theory, if the old egg was genetically normal but had poor supporting stuff then placing it in a young egg host would lead to increased fertility. This technique has essentially been banned by the FDA. I was present at a meeting of the ASRM in SAn Antonio where researchers I know with collaborators in China reported on results doing this on humans. The pregnancies did not survive. The legal and ethical ramifications are huge and reviewed here.

Spider Silk Uses Reported- Mutant GoatSpider They Missed

Posted on October 10, 2006 by Steven F. Palter, MD

This sucker spins webs.

Med gadget reports on a review of uses of spider silk. All kinds of neat potential spider-tech uses are mentioned in the article they quote.

“Dr. Randolph V. Lewis from the Department of Molecular Biology, University of Wyoming, wrote a great review article about spider silk and its multiple possible uses for biomed industry. From the press release that features an interview he gave to the American Chemical Society”

This article does not mention my favorite scary mutant spider product “biosteel”. I origially heard about this from a talk I attended at a medical meeting by a rep from DARPA (who have a hand in all things amazing and terrifying). Biosteel is a product made with transgenic technology by Nexia Biotechnologies. In short, the gene for spider-dragline-silk (the long toughest but non-sticky thread they use to drop to the ground in emergencies) has been transfected into goats. Yes goats. Then these mutant genetic chimera animals excrete the spider silk protein by the bucketful in their milk. Yes its true.

The company reportedly has been having difficulties spinning the stuff into usable forms and progress as been behind schedule. You can imagine where this (and the DARPA connection) is going – flexible wearable armor made of the strongest fabric even known. Spiderman did not need Kevlar.

In medicine, there are many potential uses I can imagine- all kinds of joint and tendon replacements, ligaments, heart valves, cut-proof surgeon gloves, etc. See my follow-up post on the technology behind this and how it can be used to make a spider-man.