Can you really diagnose Alzheimer’s disease with peanut butter and a ruler?

A couple of weeks ago, I came across a news article highlighting a recent study that showed that with just 14 grams (1 tablespoon) of peanut butter and a ruler, an Alzheimer’s disease diagnosis could be confirmed. I found this really interesting because of the simplicity of both the concept and tools used in demonstrating this concept. It never occurred to me that one could run a scientific study with food obtained from a grocery store :-).  Details of the study were published in the journal of the neurological sciences http://www.jns-journ

This article made me wonder if there was something unique about peanut butter that made it better suited for this study or if one could use some other household condiment like oregano to get a similar result. This will be a fun science experiment to try at home. The only risk is we may all end up thinking we have Alzheimer’s disease.




Fascinating CLARITY seminar

Two days ago I went to a BrainMap talk given by Kwanghun Chung about CLARITY, the novel technique you probably all heard about and that transforms intact brain tissue into a hydrogel form that is optically transparent and can be imaged under a microscope. Very interesting talk and amazing 3D visualizations! Here is the link to the paper and videos:

See here for upcoming BrainMap talks at the Martinos Center:

Check it out!



Using confocal microscopy for fluorescence imaging

Confocal microscopy is an essential optical tool in biological research which can be used to study cellular structures as well as sub-cellular components. The main advantages of confocal are the elimination of out-of-focus glare that leads increased resolution and the ability to collect serial optical sections (z-sections) from thick specimens. Hence this method generates better (and certainly prettier!) images than regular widefield microscopy (transmitted light or epifluorescence).

My research work in the Hooker lab, is focused on activity based small molecule fluorescent probes for histone deacetylase (HDAC) imaging. Confocal microscopy has become one of the very useful techniques that I use for HDAC-probe imaging in HeLa-cervical cancer cells. It allows a more precise view of cellular components and thus obtained images permit the development of an advanced understanding of the probe/enzyme of interest.

I have been using the Zeiss LSM510 laser scanning confocal microscope at the Ragon Institute and it’s an enormous help in taking my research project further. If any of you are interested in using a confocal microscope or the microscopy facility, I encouraged you go ahead and do so.

Here’s the link to the Ragon center microscopy core.

I hope this would be a useful bit of info! After all, by using all the technology and tools available to us, we are unraveling the mysteries of biology and taking science one step further.

- Himashinie



Editorial, "Mind how you go" in Nature

I came across an editorial in Nature (thanks RAH) that points to a shift in the focus of treatments for mental illnesss.  The article mentions a shift toward genetics and I would augment that with epigenetics (see blog by Al below).  I am glad that companies like Novartis are re-energized to solve or at least help patients suffering from mental illnesses.  Imaging biomarkers of mental illness are going to be critical since the populations that suffer are so heterogeneous.  A lot has been learned by imaging neurotransmitters, but there are no robust biomarkers for any psychiatric illness.  With time, we'd like to change that. 


What doesn’t kill you makes you smarter: apoptosis and cognitive enhancement by HDAC inhibitors.

Histone deacetylase (HDAC) inhibition has been a recurring topic at the leading edge of preclinical drug design.  Beyond approved utility for cancer treatment – inducing death in cancer cells - HDAC inhibitor drugs may be useful in therapeutic development for addiction, mood-related disorders and cognitive deficits.  

HDACs are a family of enzymes that function in part to control the acetylation modification of histone proteins which organize DNA packaging within the nucleus of a cell.  Dysfunction in HDAC enzyme expression or activity is thought to be an important facet of a number of brain diseases.  Blocking the function of HDACs with small molecule inhibitors may help treat these diseases – potentially by correcting aberrant gene expression.   

For new drugs that might alter brain circuitry, a lot depends on the target tissue exposure (how much drug gets in the brain?) and residence time (how long does it stick around?)

Until recently, these basic questions were largely addressed in literature on HDAC inhibitors.

The two major classes of HDAC inhibitors, hydroxamates and benzamides, feature differences in the number of HDAC family members they inhibit, but differ moreso in their BINDING KINETICS.  Hydroxamates bind their targets very quickly (on the time scale of minutes) and benzamides are s-l-o-w…only maximally binding HDAC targets after a few hours time. 

Binding HDACs over time: Lauffer et al. JBC, 2013

How do these differences impact histone acetylation, gene expression and biology?  Using a cancer cell model, Lauffer and collegues - J.Biol.Chem.  ‘Histone deacetylase inhibitor kinetic rate constants correlate with histone acetylation but not transcription and cell viability’ July, 2013 -  recently outlined the time-dependent effects of hydroxamate and benzamide exposure on histone acetylation.  Logically, the fast-binding hydroxamates induced histone acetylation quickly, whereas benzamides took time.  This histone acetylation was also long lasting for benzamides, in line with slow dissociation kinetics & long residence times of compounds in this class.

Interestingly, for both hydroxamates and benzamides, gene expression profiling experiments and monitoring of cell death indicated that a refined set of genes were altered by both drug classes and that drug exposure time was linked to a large number of the changes. The authors suggest that genes sensitive to the onset kinetics of either hydroxamates or benzamides leading to downstream changes in gene expression and, over extended exposure, inducing cell death.

We understand from Lauffer’s work that differential outcomes (intermediate gene expression changes vs. cell death) can result from HDAC inhibitor residence times.   To understand the biology induced by HDAC inhibition, it is insufficient to focus on histone acetylation and we should instead focus on biological changes in the brain, including behavior as the net output of these changes.

Impacting the HDACs in brain: Hanson et al. PlosOne 2013.

Cognitive deficits associated with neurodegenerative disease and normal aging have been reported to be alleviated in animal models by HDAC inhibitor treatment, including by the well-known hydroxamate, SAHA.   In a report nearly parallel to Lauffer’s work, Hanson et al (Plos One, July 2013, Vol.8 (7)) demonstrated that the hydroxamate HDAC inhibitor, SAHA, indeed suppress HDAC activity and neural activity, consistent with its role as a potential cognitive enhancer.  However, in experiments in mice, almost NO SAHA could be detected in brain, even when very high doses were given.  This was explained in part by the identification that SAHA is actively pumped OUT of the brain by specialized proteins.  However, Hanson’s work underscores the importance of identifying HDAC inhibitors with good brain exposure in order to best understand the biology of behavioral and neurochemical changes.

Advice to consider:

  1. Don’t use histone acetylation as a metric for biological / behavioral change.
  2. Do design experiments to understand dynamic impact of HDAC inhibition in your system.
  3. Don’t use behavioral change as an indicator of drug presence in brain.
  4. Do investigate brain exposure and residence times early in evaluating novel inhibitors.

-Al Schroeder