Immune Checkpoint Inhibitors: Has Cancer Met its Match?

The cover of S. Mukerjee's book, The Emporer of All Maladies: The Biology of Cancer. Used courtesy of Wikimedia and WLU.
The cover of S. Mukerjee’s book, The Emporer of All Maladies: The Biology of Cancer. Used courtesy of Wikimedia and WLU.

Dr. Drew M. Pardoll, Johns Hopkins University School of Medicine in Baltimore, in his 2012 review, “The blockade of immune checkpoints in cancer immunotherapy” published in Nature Reviews Cancer (1) writes:

“The myriad of genetic and epigenetic alterations that are characteristic of all cancers provide a diverse set of antigens that the immune system can use to distinguish tumour cells from their normal counterparts.”

Tumors have antigens, so we should be able to address/attack these antigens with our immune system, right?

Various immune mediators as therapeutic agents against cancer have entered and mostly flopped in clinical trials over the past 30 or more years. As a graduate student in the 1980s I remember IL-2 and interferon raising many hopes. More recently, drugs against chronic myeloid leukemia and CLL have shown early promise. However, so far cancer cells have mostly won against these therapies. Yet recent news points to some exciting new therapeutic agents, that over the past 15 years or so, and in and out of clinical trials, are getting a leg up in the cancer battle. These drugs are immune checkpoint inhibitors.

Continue reading “Immune Checkpoint Inhibitors: Has Cancer Met its Match?”

Culturing the Unculturable Bacteria

Culturing bacteria is't always this easy.
Culturing bacteria is’t always this easy.

It is estimated that all the bacterial species so far described represent only a tiny fraction of the total. The rest remain unknown to science because they are “unculturable” in standard (or known) laboratory media. Given that many antibiotics were first isolated from environmental bacteria, it seems likely that these as yet unknown organisms could also be a rich source of potential new drug candidates. The desperate need for new strategies to combat multi-drug resistant infections gives impetus to studies investigating how we can culture some of these “unculturable” bacteria and uncover their potential as a source of much-needed new treatments. 

Continue reading “Culturing the Unculturable Bacteria”

Announcing the 10th Annual Wisconsin Stem Cell Symposium: Engineering Limb Regeneration

Image courtesy of James Monaghan, Ph.D., Northeastern University, Boston, MA
Image courtesy of James Monaghan, Ph.D., Northeastern University, Boston, MA

On April 22, 2015, the BTC Institute and Promega Corporation will host the 10th Annual Wisconsin Stem Cell Symposium — Engineering Limb Regeneration: Recapitulating Normal Development and Regeneration? Our colleagues at the University of Wisconsin-Madison have put together an outstanding list of presenters who will address advances – and challenges – associated with this field of research.
Continue reading “Announcing the 10th Annual Wisconsin Stem Cell Symposium: Engineering Limb Regeneration”

Chikungunya Virus and the Promise of a Virus-Like Particle Vaccine

My family and I just returned from a week-long camping trip along the North Shore of Lake Superior in Minnesota. It is beautiful country, filled with lakes, rivers, ponds—and mosquitoes, lots and lots of mosquitoes. We went prepared for the worse. We had a screen tent, head nets and tubes and tubes of insect repellent because in this area of the world, mosquitoes are a flying, buzzing, picnic-ruining, itch-inducing pest. In the US, though, a pest is really all they are. In other areas of the world they are a flying, buzzing, disease-carrying, deadly menace.

Image courtesy of James Gathany and the CDC
Image courtesy of James Gathany and the CDC

Mosquitos act as vectors for many diseases including malaria, Dengue fever, Yellow fever, encephalitis, West Nile Virus and chikungunya virus. Many of these diseases are deadly; in fact, mosquitoes are responsible for more human deaths than any other animal (~725,000 deaths annually). Although most of these diseases have a long and infamous history, two of them, West Nile virus (first identified in 1932) and chikungunya virus (first identified in 1950), are relative new comers on the world health stage. Continue reading “Chikungunya Virus and the Promise of a Virus-Like Particle Vaccine”

Hope for Treatment of Carbapenem-Resistant Bacteria

Structure of the antibiotic meropenem
Structure of the antibiotic meropenem
Last month brought some hopeful news on the subject of antibiotic resistance. A paper published in Nature on June 26 described the isolation of a fungal compound that restored the antibiotic sensitivity of carbapenem-resistant enterobacteria. An editorial accompanying the paper took encouragement from the article–considering it a sign that the well of potential sources of new antimicrobial agents, and agents that inhibit resistance mechanisms, is not yet dry:

But the reservoir of natural products with the potential to act as antibacterial drugs has not yet been exhausted. In contrast to general thinking by drug companies, screening for such products may well still have a bright future” Nature News and Views: “Antibiotic resistance: To the rescue of old drugs” Meziane-Cherif & Courvalin, Nature 510, 477–478.

The emergence of bacteria that are resistant to antibiotics has been an object lesson in the relentlessness of natural selection; the moment a new antibiotic is developed and introduced, the countdown to the emergence of resistance begins. The race to keep the one step ahead of emerging resistance mechanisms has been going on since antibiotics were first introduced.

The history of the development of penicillin and related antibiotics is both an illustration of the ingenuity of scientists and of the never-ending nature of this battle with emerging resistance. The Nature paper is the latest installment in that story. Continue reading “Hope for Treatment of Carbapenem-Resistant Bacteria”

From Soot, Turpentine and Walnut Oil to Bio-Inks with Living Cells: Printing Reinvents Itself in 3D and Comes Alive

Gutenberg-Style Printing Press.
Gutenberg-Style Printing Press (Replica). Wikimedia Commons.

Printing has been an integral part of society since the first movable type printing press was invented by Johannes Gutenberg in the 15th century. And yet, many recent headlines have heralded its impending death.  As everything from books to newspapers transitioned to digital media, the traditional printing techniques seemed destined for the history books and museums. However, even before the popularity of printing started to fade, some of the concepts were being reimagined in amazing, new—and three dimensional— ways. Continue reading “From Soot, Turpentine and Walnut Oil to Bio-Inks with Living Cells: Printing Reinvents Itself in 3D and Comes Alive”

Ghost of the Himalayas (Snow Leopard) Caught on Camera In a Successful Hunt

Snow LeopardPaul Steyn has posted an amazing series of photographs taken by Adam Riley in Hemis National Park in the Himalayas on the National Geographic News web site. These photographs are the  first photo documentation of a successful snow leopard hunt, and underscore the amazing biology of this area. If you are interested in learning more, we have another blog post about early work to isolate induced pluripotent stem cells from adult animals–an attempt to compliment the habitat preservation and other efforts to save this incredible hunter before it truly becomes a ghost.

From Where, the Dog’s Ancient Ancestor

We’ve learned this year, 2013, that Europe may be the original home to domestic dogs, a title previously claimed by East Asia and the Middle East. A recent study published in Science magazine may put to rest the debate.

In their report, Thalmann and Wayne (1) used an evidential gold standard, DNA from mitochondria of fossilized ancient dog and wolf remains, to reach the conclusion that dogs originated from a now extinct line of European gray wolves.

In 2002, researchers from Sweden and China collaborated to compared first the mitochondrial DNA and later the complete mitochondrial genomes and Y chromosomes from a hundreds of wolves, coyotes and modern dogs from around the world (2). Their results showed the greatest genetic diversity from canids from East Asia. Such genetic diversity can be a marker of a species’ origin.

In 2010 Wayne, et al. (3) analyzed 48,000 markers from across the genome of gray wolves and dogs, again from around the world. The dogs were found to have more genetic material in common with Middle Eastern wolves than with those from East Asia. Wayne and colleagues found this a yes to dogs’ origins lying in the Middle East.

A criticism of the analysis done with modern dog DNA is that this DNA has been mixed with that from wolves. In addition, dog-dog breeding over the 15,000 to 30,000 years since this domestication, could confound results. Prior to the current study, critics called for analysis of ancient DNA remains only.

Wayne had collected DNA from ancient remains and due to recent collaboration with geneticist Thalmann, now had the lab-power to analyze those remains.

In this work, Wayne and Thalmann looked at mitochondrial DNA from ancient remains, those of 18 wolves and dogs. The fossils  ranging in age from 1,000 to 36,000 years. Eight of the samples were classified as dog-like and 10 samples were wolf-like in nature. They compared the ancient mitochondrial DNA samples to those of modern animals, including 77 dogs from an assortment of breeds, as well as 49 wolves and 4 coyotes. They then built a sort of a canid family tree, demonstrating relatedness in the animals whose DNA was analyzed.

Thalmann and Wayne’s finding showed that 1) the DNA of modern dogs more closely resembled that of ancient gray wolves than modern wolves, and 2) the geographic location of the wolves who’s DNA was most closely resembled, was Europe.

It is important to note that Thalmann and Wayne did not compare ancient remains from animals from the Middle East, nor did they have access to ancient remains from East Asia. In addition, there is criticism of the use of mitochondrial DNA, which represents only the maternal dog lineage. Thus there is more work to be done to finalize the ancestral home of the modern dog.

This work does, however, push back the origins of domesticated dogs to between 18,000 and 32,000 years ago, significant because the domestication timeline was previously believed to coincide with the rise of farming by our human ancestors. Domestic canines are now believed to have been part of humans lives far before farming was a way of life, back in the hunter-gatherer days.

There are those who believe that domestication of wolves, selectively bred to become modern dogs occurred simultaneously at more than one geographic region. Wolves were once found in many locations around the world and their usefulness to and domestication by humans would seem odd if only embraced by people from a single part of the world.

    References

  1. Thalmann, O. et al. Science (2013) 342, 871–874
  2. Savolainen P, Zhang YP, et al. (2002)
  3. Wayne, R.K. et al. (2010) Nature 464(7290), 898-902. 

Remembering Frederick Sanger and Sanger Sequencing

It is with sadness that we recognize the passing of Dr. Frederick Sanger. Sanger is known to molecular biologists and biochemists worldwide for his DNA sequencing technique, which won for him the 1980 Nobel prize in Chemistry.

Also noteworthy, Sanger’s laboratory accomplished the first complete genome sequence, that of a viral DNA genome more than 5,000 base pairs in length.

The 1980 prize was Sanger’s second Nobel award, his first awarded in 1958 for determining the chemical structure of proteins. In this work, Sanger elucidated not only the amino acids that comprised insulin but also the order in which the amino acids occurred.

About Sanger Sequencing
Sanger DNA sequencing is also known as the chain-termination method of sequencing. The Sanger technique uses dideoxynucleotides or ddNTPs in addition to typical deoxynucleotides (dNTPs) in the reaction. ddNTPs result in termination of the DNA strand because ddNTPs lack the 3’-OH group required for phosphodiester bond formation between nucleotides. Without this bond, the chain of nucleotides being formed is terminated.

Sanger sequencing requires a single-stranded DNA, a DNA primer (either radiolabeled or with a fluorescent tag), DNA polymerase, dNTPs and ddNTPs. Four reactions are set up, one for each nucleotide, G, A, T and C. In each reaction all four dNTPs are included, but only one ddNTP (ddATP, ddCTP, ddGTP or ddTTP) is added. The sequencing reactions are performed and the products denatured and separated by size using polyacrylamide gel electrophoresis.

Diagram of Sanger dideoxy sequencing. (Courtesy  of Wikipedia and Estevez, J.)
Diagram of Sanger dideoxy sequencing. (Courtesy of Wikipedia and Estevez, J.)

This reaction mix results in various lengths of fragments representing, for instance, the location of each A nucleotide in the sequence, because while there is more dATP than ddATP in the reaction, there is enough ddATP that each ATP ultimately instead is replaced with a ddATP, resulting in chain termination. Separation by gel electrophoresis reveals the size of these ddATP-containing fragments, and thus the locations of all A nucleotide in the sequence. Similar information is provided for GTP, CTP and TTP.

The Maxam and Gilbert DNA sequencing method had the advantage at the time of being used with double-stranded DNA. However, this method required DNA strand separation or fractionation of the restriction enzyme fragments, resulting in a somewhat more time-consuming technique, compared to the 1977 method published by Sanger et al.

Dr. Sanger was born in Gloucestershire, U.K. in 1918, the son of a physician. Though he initially planned to follow his father into medicine, biochemistry became his life-long passion and area of research endeavor. Sanger retired at age 65, to spend more time at hobbies of gardening and boating.

References

Sanger, F. , Nicklen, S. and Coulson, A.R. (1977) DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. USA 74, 5463-7.

Maxam, A.M. and Gilbert, W. (1977) A New Method for Sequencing DNA. Proc. Natl. Acad. Sci. USA

There is something special about seeing the original Sanger publication from 1977, available here as a scan.

TB Vaccine News

Mycobacterium tuberculosis (Ziehl Neelsen stain). Photo credit: Centers for Disease Control and Prevention.
Mycobacterium tuberculosis (Ziehl Neelsen stain). Photo credit: Centers for Disease Control and Prevention.
A paper published last week in Science Translational Medicine describes promising results from a phase 1 clinical trial of a new anti-tuberculosis vaccine. The vaccine, composed of a human Adenoviral vector expressing a Mycobacterium tuberculosis antigen, generated an immune response in people with and without previous exposure to the current anti-tuberculosis (BCG) vaccine.

Mycobacterium tuberculosis, discovered by Robert Koch in 1882, is the organism that causes tuberculosis—commonly known as TB. After introduction of the BCG (Bacille Calmette-Guérin ) vaccine in 1919 and antibiotic treatment in the 1950s, the hope was that TB would be finally consigned to history—that Mycobacteruim tuberculosis would be a name only associated with the pre-antibiotic era and would not be a part of the 21st century world. However, over the last 30 years the emergence of multi-drug resistance and the worldwide HIV epidemic have led to the re-emergence of TB to the point where the following statements are true: Continue reading “TB Vaccine News”