Society for Neuroscience Conference 2014 Continued


Let me emphasize that the huge number of posters and talks at the SfN conference made it impossible to attend all of them, so my recollections here are some of the high points that I was able to take in. There is a lot of terrific science going on out there and these conferences are windows into it.

One poster described a feeding study in rats. One group of rats received a diet rich in omega-3 fatty acids, which are found in fish oils and soy. Another group was fed a standard laboratory diet that tends to skim on the omega-3 fatty acids. In the brains of the omega-3-fed rats, the expression off the gene that encodes Brain Derived Neurotropic Factor or BDNF increased significantly.

This is significant because BDNF promotes the survival of nerve cells (neurons) by playing a role in the growth, maturation (differentiation), and maintenance of these cells. In the brain, BDNF protein is active at the connections between nerve cells (synapses), where cell-to-cell communication occurs. The synapses can change and adapt over time in response to experience, a characteristic called synaptic plasticity, and BDNF regulates synaptic plasticity, which is important for learning and memory.

When these researchers examined why the BDNF gene was unregulated in rats fed the omega-3-rich diet, they discovered that the starting point of the gene, which is called the promoter was nice and clear. In the standard diet rats, the promoter of the BDNF gene was chemically modified with methyl (-CH3) groups. In the absence of the methyl groups, the transcription factor CTCF was able to bind and increase the rate of transcription. If the promoter was chemically modified with methyl groups, then a protein called MeCP2 bound to the promoter and prevented expression of BDNF.

This group looked further and discovered that the omega-3-rich diet seemed to influence the expression of BDNF by means of the balance of reduced and oxidized versions of electron carriers in cells, in particular, the ratio of NAD+ to NADH. NAD is a major electron carrier in cells and the ratio of NAD+, the oxidized version of this molecule, to the reduced version of this molecule, NADH, is a measure of the energy charge of the cell and how well-fed the individual is. More importantly, NAD is a substrate for another regulator of gene expression called Sirtuins.

Sirtuins are protein deacetylases, but they are unusual deacetylases since many of them they do not simply hydrolyze acetyl-lysine residues. Instead they couple lysine deacetylation to NAD hydrolysis. This hydrolysis produces O-acetyl-ADP-ribose, which is the deacetylated substrate and nicotinamide, which is an inhibitor of sirtuin activity. The dependence of sirtuins on NAD links their enzymatic activity directly to the energy status of the cell via the cellular NAD:NADH ratio.

The fact that a diet high in omega-3 fatty acids affects the NAD/NADH ratio is significant for Alzheimer’s disease because the sirtuin, SIRT1, deacetylates and coactivates the promoter for the gene that encodes the retinoic acid receptor beta gene, which subsequently upregulates the expression of alpha-secretase (ADAM10). Alpha-secretase is able to suppress beta-amyloid production. ADAM10 activation by SIRT1 also induces the Notch signaling pathway, which is known to repair neuronal damage in the brain. All of this begins with a dietary factor that actually protects the brain from Alzheimer’s disease by profound changes in gene expression.

Another poster from an Italian group used the 5XFAD mouse model of Alzheimer’s disease to test a growth factor called “painless Nerve Growth Factor” on mice with protein plaque formation in their brains. The growth factor was given by placing droplets of the growth factor in the noses of the mice while they were anesthetized. The results were stunning. Normally, 5XFAD mice get plaques quickly in their brains and lots of them. However, the growth factor was able to rescue the onset of behavioral deficits and reduces, although not eliminate, plaque formation. Other brain-specific pathologies found in these mice were reduced, such as astrocytosis. The wandering white cells in the brain known as microglia did a better job of gobbling up protein aggregates and clearing them from the brain, and the markers of inflammation were significantly reduced. I asked the investigator if there were plans to try to move this to clinical trials, and she said that she was unable to do so because of a lack of funding. Maybe someone will collaborate with this dear lady to make it so?

In another poster, the overexpression of an enzyme called heparanase in the brain decreased the burden of protein aggregates in the brains of mice with Alzheimer’s disease. I was not able to get into the details of this poster because of time.

In another poster, a very energetic young man told me about his very interesting work with a Parkinson’s disease model in rodents. If mice are administered a drug called MPTP (short for 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine), the dopamine-using neurons in the brain will specifically take up this drug in high concentrations and it will kill them. Therefore, this drug is an excellent model system to study Parkinson’s disease in mice.

Prokineticin-2 is a gene that is expressed in high quantities in the surviving dopamine-using neurons that came from the brains of Parkinson’s disease patients after their deaths. When Prokineticin-2 was overexpressed in cultured dopaminergic neurons, they unregulated a protein called Bcl-2. Bcl-2 is one of the group of proteins can protect cells from dying. Therefore, Prokineticin-2 is a prosurvival protein.

Next, this chap switched from a culture system to a “in a living animal” system or an in vivo system. By using genetically engineered viruses that overexpressed Prokineticin-2 in the brains of mice, he discovered that this viruses did not adversely affect the mice and he did in fact achieve high levels of Prokineticin-2 in the brains of mice with this recombinant viruses. The overexpression did not affect the mice in the least. When he did the same experiment with MPTP-treated mice – oh, just to be clear, he overexpressed Prokineticin-2 first and then administered the MPTP because it takes about 30 days for the viruses to properly upregulate Prokineticin-2 – he saw decreased inflammation in the brain, and increase in Bcl-2 and Pink1 expression in the brain (both of these genes are pro-survival genes), and the behavioral problems of the mice never emerged with the severity of the MPTP mice. When he examined TH – an enzyme that makes the neurotransmitter dopamine, he saw that levels of this enzyme were up too. This means that the dopamine-using neurons were surviving. Is this cool stuff or what?

That’s enough for now. More later.

Physical Cues Push Mature Cells into Induced Pluripotent Stem Cells


Bioengineers from the laboratory of Song Li at UC Berkeley have used physical cues to help push mature cells to de-differentiate into embryonic-like cells known as induced pluripotent stem cells.

Essentially, Li and his coworkers grew skin fibroblasts from human skin and mouse ears on surfaces with parallel grooves 10 micrometers apart and 3 micrometers high, in a special culture medium. This procedure increased the efficiency of reprogramming of these mature cells four-fold when compared to cells grown on a flat surface. Growing cells in scaffolds of nanofilbers aligned in parallel had similar effects.

Li’s study could significantly advance the protocols for making induced pluripotent stem cells (iPSCs). Normally iPSCs are made by genetically engineering adult cells so that they overexpress four different genes: Oct-4, Sox-2, Klf-4, and c-Myc. To put these genes into the cells, genetically modified viruses are used, or plasmids (small circles of DNA). Initially, Shinya Yamanaka, the scientist who invented iPSCs, and his co-workers used retroviruses that contained these four genes. When fibroblasts were infected with these souped-up retroviruses, the viruses inserted their viral DNA into the genomes of the host cells and expressed these genes.

retrovirus_life_cycle

Shinya Yamanaka won the Nobel Prize for this work in Physiology or Medicine in 2012 for this work. Unfortunately, retroviruses and can cause insertional mutations when they integrate into the genome (Zheng W., et al., Gene. 2013 Apr 25;519(1):142-9), and for this reason they are not the preferred way of making iPSCs. There are other viral vectors that do not integrate into the genome of the host cell (e.g., Sendai virus; see Chen IP, et al., Cell Reprogram. 2013 Dec;15(6):503-13). There are also techniques that use plasmids, which encode the four genes but do not integrate into the genome of the host cell. Finally, synthetic messenger RNAs that encode these four genes have also been used to make iPSCs (Tavernier G,, et al., Biomaterials. 2012 Jan;33(2):412-7).

The use of physical cues to make iPSCs may replace the need for gene overexpression, just as the use of particular chemicals can replace the need for particular genes (Zhu, S. et al. Cell Stem Cell 7, 651–655 (2010); Li, Y. et al. Cell Res. 21, 196–204 (2011)). If physical cues can replace the need for the overexpression of particular genes, then this discovery could revolutionize iPSC derivation; especially since the overexpression of particular genes in mature cells tends to cause genome instability in cells (Doris Steinemann, Gudrun Göhring, and Brigitte Schlegelberger. Am J Stem Cells. 2013; 2(1): 39–51).

“Our study demonstrates for the first time that the physical features of biomaterials can replace some of these biochemical factors and regulate the memory of a cell’s identity,” said study principal investigator Song Li, UC Berkeley, Professor of bioengineering. “We show that biophysical signals can be converted into intracellular chemical signals that coax cells to change.”

a, Scanning electron micrograph of PDMS membranes with a 10 μm groove width. All grooves were fabricated with a groove height of 3 μm. b, The top row shows phase contrast images of flat and grooved PDMS membranes with various widths and spacings. The bottom row shows fibroblast morphology on various PDMS membranes. Images are fluorescence micrographs of the nucleus (DAPI, blue) and actin network (phalloidin, green; scale bars, 100 μm). c, Reprogramming protocol. Colonies were subcultured and expanded or immunostained and quantified by day 12–14. d, Fluorescence micrograph showing the morphology of iPSC colonies generated on flat and grooved membranes (scale bar, 1 mm). Groove dimensions were 10 μm in width and spacing, denoted as 10 μm in this and the rest of the figures. Double-headed arrow indicates microgroove orientation of alignment. e, Reprogramming efficiency of fibroblasts transduced with OSKM and cultured on PDMS membranes with flat or grooved microtopography. The number of biological replicates, n, used for this experiment was equal to 6. Groove width and spacing were varied between 40, 20 and 10 μm. Differences of statistical significance were determined by a one-way ANOVA, followed by Tukey’s post-hoc test. * indicates significant difference (p<0.05) compared with the control flat surface. f, Reprogramming efficiency in fibroblasts transduced with OSK (n = 4). *p<0.05 (two-tailed, unpaired t-test) compared with the control flat surface. Error bars represent one standard deviation. g, Immunostaining of a stable iPSC line expanded from colonies generated on 10 μm grooves. These cells express mESC-specific markers Oct4, Sox2, Nanog and SSEA-1 (scale bar, 100 μm). h, The expanded iPSCs in g were transplanted into SCID mice to demonstrate the formation of teratomas in vivo (scale bar, 50 μm).
a, Scanning electron micrograph of PDMS membranes with a 10 μm groove width. All grooves were fabricated with a groove height of 3 μm. b, The top row shows phase contrast images of flat and grooved PDMS membranes with various widths and spacings. The bottom row shows fibroblast morphology on various PDMS membranes. Images are fluorescence micrographs of the nucleus (DAPI, blue) and actin network (phalloidin, green; scale bars, 100 μm). c, Reprogramming protocol. Colonies were subcultured and expanded or immunostained and quantified by day 12–14. d, Fluorescence micrograph showing the morphology of iPSC colonies generated on flat and grooved membranes (scale bar, 1 mm). Groove dimensions were 10 μm in width and spacing, denoted as 10 μm in this and the rest of the figures. Double-headed arrow indicates microgroove orientation of alignment. e, Reprogramming efficiency of fibroblasts transduced with OSKM and cultured on PDMS membranes with flat or grooved microtopography. The number of biological replicates, n, used for this experiment was equal to 6. Groove width and spacing were varied between 40, 20 and 10 μm. Differences of statistical significance were determined by a one-way ANOVA, followed by Tukey’s post-hoc test. * indicates significant difference (p<0.05) compared with the control flat surface. f, Reprogramming efficiency in fibroblasts transduced with OSK (n = 4). *p

To boost the efficiency of mature cell reprogramming, scientists also use a chemical called valproic acid, which dramatically affects global DNA structure and expression.

“The concern with current methods is the low efficiency at which cells actually reprogram and the unpredictable long-term effects of certain imposed genetic or chemical manipulations,” said the lead author of this study Timothy Downing. “For instance, valproic acid is a potent chemical that drastically alters the cell’s epigenetic state and can cause unintended changes inside the cell. Given this, many people have been looking at different ways to improve various aspects of the reprogramming process.”

This new study confirms and extends previous studies that showed that mechanical and physical cues can influence cell fate. Li’s group showed that physical and mechanical cues can not only affect cell fate, but also the epigenetic state and cell reprogramming.

a, Scanning electron micrograph of nanofibres showing fibre morphology in aligned and random orientations (scale bar, 20 μm). Confocal fluorescence micrograph of fibroblasts cultured on nanofibres (DAPI (blue) and phalloidin (green) staining; scale bar, 100 μm). b, Western blotting analysis for fibroblasts cultured on random and aligned nanofibres for three days. c, Fibroblasts were transduced with OSKM and seeded onto nanofibre surfaces, followed by immunostaining for Nanog expression (red) at day 12. Nuclei were stained with DAPI in blue; scale bar, 500 μm. d, Quantification of colony numbers in c (n = 5). *p<0.05 (two-tailed, unpaired t-test) compared with the control surface with random nanofibres. e, Fibroblasts were micropatterned into single-cell islands of 2,000 μm2 area with a CSI value of 1 (round) or 0.1 (elongated). After 24 h, cells were immunostained for AcH3, H3K4me2 or H3K4me3 (in green). Phalloidin staining (red) identifies the cell cytoskeleton for cell shape accuracy. The white arrowhead indicates the location of the nucleus (scale bars, 20 μm). f, Quantification of fluorescence intensity in e (n = 34, 20 and 34 for AcH3, H3K4me2 and H3K4me3, respectively). *p<0.05 (two-tailed, unpaired t-test) compared with the circular micropatterned cells (CSI = 1). Error bars represent one standard deviation.
a, Scanning electron micrograph of nanofibres showing fibre morphology in aligned and random orientations (scale bar, 20 μm). Confocal fluorescence micrograph of fibroblasts cultured on nanofibres (DAPI (blue) and phalloidin (green) staining; scale bar, 100 μm). b, Western blotting analysis for fibroblasts cultured on random and aligned nanofibres for three days. c, Fibroblasts were transduced with OSKM and seeded onto nanofibre surfaces, followed by immunostaining for Nanog expression (red) at day 12. Nuclei were stained with DAPI in blue; scale bar, 500 μm. d, Quantification of colony numbers in c (n = 5). *p

“Cells elongate, or example, as they migrate throughout the body,” said Downing, who is a research associate in Li’s lab. “In the case of topography, where we control the elongation of a cell by controlling the physical microenvironment, we are able to more closely mimic what a cell would experience in its native physiological environment. In this regard, these physical cues are less invasive and artificial to the cell and therefore less likely to cause unintended side effects.”

Li and his colleagues are studying whether growing cells on grooved surfaces eventually replace valproic acid and even replace other chemical compounds in the reprogramming process.

“We are also studying whether biophysical factors could help reprogram cells into specific cell types, such as neurons,” said Jennifer Soto, a UC Berkeley graduate student in bioengineering who was also a co-author on this paper.

Timothy Downing, et al., Nature Materials 12, 1154–1162 (2013).  

Expanding Blood-Making Stem Cells for Use in Patients


John Dick is a senior scientist at the University Health Network’s McEwen Centre for Regenerative Medicine and a professor at the University of Toronto. He is also the senior investigator for a study that includes a collaboration between Canadian and Italian stem cell scientists that examined ways to expand human blood stem cells for human use.

A new master control gene was identified in this study that, when manipulated, could increase stem cell production.

In the words of Dick, “For the first time in human blood stem cells, we have established that a new class of non-coding RNA called miRNA represents a new tactic for manipulating these cells, which opens the door to expanding them for therapeutic uses.”

In 2011, Dick’s research group published a landmark paper in which he and his colleagues succeeded in isolating “CD49f+” cells. Just one of these CD49f+ cells could reconstitute an entire blood-cell making system in bone marrow. It has been known for some time that the population of blood cell-making stem cells in bone marrow is rather heterogeneous, and some cells have tremendous regenerative capacities, but others shown only slight regenerative abilities. DIck’s group isolated bone marrow stem cells that could replenish the whole blood-making system of a laboratory animal (see Notta, et al., Science 333, 218-221).

Dick has also pioneered the field of cancer stem cells when his lab identified leukemia stem cells in 1994 (Lapidot T, et al., Nature. 367, 645-8.) and colon cancer cells in 2007 (O’Brien CA, et al. Nature. 445, 106-10).

The lead author of this study, Eric Lechman, recounted his laboratory work with a master control gene known as microRNA 126 or miR-126. THis small RNA normally silences the expression of many genes, and thus keeps stem cells in a quiescent, dormant state. His strategy in working with miR-126 was to introduce new binding sites into the cell for miR-126 in order to lower the concentration of free miR-126 inside the cell. To do this, he infected stem cells with a genetically engineered virus that was loaded with miR-126 binding sites. The results were remarkable.

According to Lechman, “The virus acted like a sponge and mopped up the specific miRNA in the cells. This enabled the expression of normally expressed genes to become prominent, after which we observed a long-term expansion of the blood stem cells without exhaustion or malignant transformation.”

Given the difficult many labs have has growing sufficient quantities of blood stem cells in the laboratory, this finding could completely revolutionize blood stem cell research and clinical treatments with these stem cells.

According to Dick, “We’ve shown that if you remove the miRNA you can expand the stem cells while keeping their identity intact. That’s the key to long-term stem cell expansion for use in patients.”