Author: Kari Kenefick

Immune Checkpoint Inhibitors: Has Cancer Met its Match?

Posted on by Kari Kenefick
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?”

Differentiating but not Mature Adipocytes Provide a Defense Against S. aureus Infection

Posted on by Kari Kenefick

http://upload.wikimedia.org/wikipedia/commons/6/65/Blausen_0012_AdiposeTissue.png
Cross-section of skin and adipose tissue enlargement. Used courtesy of Wikimedia Commons, Blausen.

A basic tenet of immunology is that antibodies produced by B cells are very important and specific immunoprotective agents, released in response to infection.

However, antibodies do not supply immediate protection. The invading organism needs to get into the host, meet up with T cells and then B cells, in order for antibody production to occur. If the host has seen this particular pathogen previously, the antibody response occurs somewhat more quickly, but we’re still talking about days. If the invading organism is a bacterium, it can multiply and double in numbers in just hours. Thus an infection could potentially gain a foothold in a body prior to an antibody response.

Fortunately we have a more rapid, first line of defense to invading pathogens, a cellular response. In the case of a puncture or skin wound, epithelial cells, mast cells and leukocytes are activated quickly in response to pathogens. Neutrophils and monocytes also aid the cellular response.

Now a recently published report demonstrates that fat cells also play a part in the cellular response to invading bacteria. R. Gallo et al. published a study on Jan. 2 in Science, providing more in depth information on the role of adipocytes in the host response to the bacterium Staphylococcus aureus (S. aureus). Continue reading “Differentiating but not Mature Adipocytes Provide a Defense Against S. aureus Infection”

Insights into the Function of P7C3 Compounds in Neuroprotection

Posted on by Kari Kenefick

The multiple Lombardi trophies won by Pittsburgh Steelers. Image used under Wikimedia Creative Commons, and attributed to daveynin.
The multiple Lombardi trophies won by Pittsburgh Steelers. Image used under Wikimedia Creative Commons, and attributed to daveynin.

It is fall and the season for American football. For this football fan, watching the game is a bit less enjoyable than it used to be, as more and more information is available about the serious and permanent brain injuries suffered by football players.

In the introduction to a recent paper in the journal Cell, “P7C3 Neuroprotective Chemicals Function by Activating the Rate-Limiting Enzyme in NAD Salvage”, not a word about American football is mentioned.

However, the paper begins, “No substantive therapeutics are available for the treatment of almost any form of disease entailing nerve death” (1). The authors list a range of neurodegenerative disorders such as Huntington’s, Alzheimers and Parkinson’s diseases, as well as ALS  or Lou Gherig’s disease. They also note that there are currently no effective treatments for trauma to the brain or peripheral nervous system.

The authors note that a chemical treatment that could interfere with nerve cell death would have a “transformative impact in modern medicine”. Continue reading “Insights into the Function of P7C3 Compounds in Neuroprotection”

Novel Cell Surface Markers Identified that Differentiate White, Beige and Brown Adipocytes

Posted on by Kari Kenefick

2012 CDC-based data on U.S. obesity percentages by state.
2012 CDC-based data on U.S. obesity percentages by state.

Estimates of obesity in the U.S. range from 30% (Centers for Disease Control data) to 70% (persons selling online and television audience-focused weight-loss programs). We are a nation of fat or fat-obsessed persons, and rightfully so. CDC data shows that the cost of obesity, in 2008 dollars, was estimated at $147 billion. That amount of money would buy a lot of french fries or cheesecake or __ (name your poison).

We all help pay those high-dollar amounts in terms of rising healthcare costs, thus there is considerable interest in finding ways to not only avoid, but also to combat obesity.

In recent years researchers working to understand body fat biology have produced exciting information on differences in types of fat. For instance, we now understand that in addition to white adipose tissue, animals and humans also have brown and beige adipose tissue. White adipose tissue or WAT is commonly found in humans and mice subcutaneously and in visceral fat. Brown adipose tissue or BAT, and beige adipose, is less common, and in humans and mice, is found in deeper cervical, supraclavical and paraspinal areas.

Continue reading “Novel Cell Surface Markers Identified that Differentiate White, Beige and Brown Adipocytes”

Dark Chocolate Benefits Improved by Fiber

Posted on by Kari Kenefick

Add pomegranate to your chocolate, says researcher Finley, to aid it's digestion, health benefits.
Add pomegranate to your chocolate, says researcher Finley, to aid it’s digestion and health benefits.

For chocolate lovers (and chocolate makers) it has been a great decade or so. Scientific research continues to prove what our brains have been saying for years; chocolate really IS good for us.

Research over the past decade or so has studied dark chocolate and its polyphenolic compounds, such as catechin and epicatechin, for their effects on inflammation, and cardiac and endothelial cell function. Today, from the American Chemical Society meeting in Dallas, TX, we learn new details about how dark chocolate brings its health benefits.

Before beneficial compounds in dark chocolate can reach the heart and other tissues in the body, digestive processes must occur to release the beneficial compounds from the chocolate.

Researcher John Finley and cohorts from Louisiana State University created a model digestive system by which to study what happens when cocoa combines with typical gut bacteria.

Their research showed that bacterial species in the colon ferment the fiber found in cocoa, which in turn aids in digestion of the larger polyphenols in cocoa, into smaller, more easily absorbed molecules. These smaller molecules, the catechins and epicatechins then enter the bloodstream and exert their anti-inflammatory effects.

Finley emphasized the role of dietary fiber, such as the fiber in the cocoa powders tested in this research, in the digestion process. He noted that prebiotics, carbohydrates in foods like raw garlic or cooked whole wheat flour, while not digested by humans, aid digestion and absorption of healthful food components, in this case polyphenols in dark chocolate.  Continue reading “Dark Chocolate Benefits Improved by Fiber”

From Where, the Dog’s Ancient Ancestor

Posted on by Kari Kenefick

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

Posted on by Kari Kenefick

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.

Priming an Effective T cell Response to Cancer

Posted on by Kari Kenefick

Cancer vaccines have been in progress for some time now. But a vaccine that is highly effective against cancer is not currently available.

However, an interesting report from Stanford University School of Medicine researchers, Dr. Irving Weissman, et al. shows some promise in a development of an altered means of stimulating the immune system, that could result in a stronger immune response and ultimately a better cancer vaccine. The paper by Weissman et al. was published electronically ahead of print in PNAS USA, May 20, 2013: “Anti-CD47 antibody-mediated phagocytosis of cancer by macrophages primes an effective antitumor T-cell response.”

Schematic of a macrophage engulfing, digesting and presenting parts of a pathogen or foreign cell to the cell surface.
Schematic of a macrophage engulfing, digesting and presenting parts of a pathogen or foreign cell to the cell surface.

Continue reading “Priming an Effective T cell Response to Cancer”

Walking the Dog, Prefrontal Cortex Engaged

Posted on by Kari Kenefick

A favorite walk: the dog park.

A friend and I were recently at a local dog park, walking his Sheltie and Australian shepherd, and my two standard poodles. Our dogs are not daily visitors to the dog park, and while his dogs are well-behaved and subtle in their approach to other dogs, my poodles’ enthusiasm is not always in their best interest.

In addition, one of my dogs seems to take issue with certain of the protection dog breeds,  like German Shepherds, as well as some of the sled dog breeds. Generally, if a dog has pointed ears, I am on the alert for bad behavior.

For that matter, the protection dogs don’t seem to much care for fluffy, bouncy poodles. Annoying, you know? A dog’s trying to keep order and make the world safe, and here comes that poodle, bouncing along without a care in the world. There’s a lot of danger out there and the poodles are simply not paying attention. They jog along meeting people and dogs like they are running for mayor; darn poodles.

Occasionally it has seemed that the attitude problem is not exclusive to my dog.

People often say, “Oh, standard poodles are such smart dogs”. But you’d think a smart dog would not choose a big, guard dog breed with which to make trouble. Continue reading “Walking the Dog, Prefrontal Cortex Engaged”

A Food for Happiness? Go Fish

Posted on by Kari Kenefick

Salmon, smoked
Salmon is a good source of omega-3 fatty acids.

We’ve heard that omega-3 fatty acids, such as those from various fish sources, have important anti-inflammatory, as well as cardiac health benefits.

In fact, WebMD has an Omega-3 Fatty Acid Fact Sheet with so much positive health information that you may add “Buy wild-caught salmon” to your list of things to do on the way home tonight.

In other words, eating fish is a no-brainer, right? Continue reading “A Food for Happiness? Go Fish”