Optical control of gene expression in mammalian cells

Trying to start a reboot of the posts here on Brain Windows. Lots of great stuff has come out since the last regular posting period, and unfortunately I don’t have the time to cover it all. One of the most exciting papers of the last few months was Rapid blue-light–mediated induction of protein interactions in living cells published in Nature Methods. This paper reports the  logical extension of previous technologies for photoactivatable transcription we previously covered here, here, and here.

There are two key technical improvements in the system from the Tucker Lab.  First, the genetic light switch, a cryptochrome 2 (CRY2) interaction with cryptochrome-interacting basic-helix-loop-helix protien (CIB1), is activated by blue light rather than the red light of previous switches based on phycocyanobilins.  Second, and more importantly, the cofactors necessary for the switch action (flavin and pterin chromophores), are endogenously expressed in mammalian tissues.  Thus, these switches should be usable in vivo without potentially tricky loading of the cofactors.

Upon illumination, the authors observed rapid translocation (in 1 second!) of fluorescent proteins tagged with CRY2 to cell membranes with CIB1 anchored to it.  They also were able to couple it to Gal4-UAS and Split-Cre expression systems, which let them drive reporter genes such as GFP by blue-light illumination.  I was a bit underwhelmed by the efficacy of the cre-induction, only around 15% of cells expressed the cre-driven EGFP after 24 hours of illumination, but maybe that is due to my ignorance of the current limits of the split-cre system.  That efficacy will certainly need to be improved for the REALLY cool stuff one can imagine doing with this.

What are the cool things?  Well, say you are doing some GCAMP3 imaging of a few hundred cells in the cortex during an awake behavior.  You see an ensemble of neurons whose activity is correlated to some aspect of the behavior, like a motor command, a perception or a decision. You want to prove the function of these neurons, to investigate their coding by subtracting or adding activity directly into this specific functional group. How do we control ONLY this group?

A pan-neuronal channelrhodopsin, or even one packaged in a cre-dependent virus injected into a cre reporter line will not allow you to change the spike patterns of only this ensemble. This ensemble is not differentiable from its neighbors by genetic type, only by functional relevance.  You have to hit its neighbors or shared genetic subtype with the same hammer.  But if you have one of these CRY2-CIB1 split cre switches that drive ChR2 expressed across the cortex, you could shine a blue laser (or presumably a two-photon laser) onto the members of the ensemble and turn on optical control of only that functional group.

Details of course still need to be worked out. What is the 2p cross-section of the system? How do you make it compatible with optical imaging and optical control?  How do you improve the speed and efficacy of the switch? These are things that will come with time.  The power of this technique is even recognized by apparent competitors in the field; Anselm Levskaya closed his packed SfN talk on phycocyanobilin-based optical switches with a shout out to this work.

Stay tuned…
Kennedy MJ, Hughes RM, Peteya LA, Schwartz JW, Ehlers MD, & Tucker CL (2010). Rapid blue-light-mediated induction of protein interactions in living cells. Nature methods, 7 (12), 973-5 PMID: 21037589

Software Update : Ephus, ScanImage & Neuroptikon

Three excellent pieces of neuroscience software have been recently updated or freshly released.  I have used two of them, Ephus and ScanImage, on a daily basis as primary data collection tools. The third, Neuroptikon, is quite useful for post-hoc illustration of neural circuits.

Ephus is a modular Matlab-based electrophysiology program that can control and record many channels of tools and data simultaneously.  Under control of a sophisticated internal looper or external trigger, you can initiate an ephys recording, trigger camera frames, adjust galvo positions, open/close shutters, trigger optical stimulation, punishments, rewards, etc.  It is a workhorse program for non-imaging related in vitro and in vivo electrophysiology experiments.  Ephus is named for the fabled baseball pitch, and pronounced as “EFF-ess”. As with the pitch, it may trick you at first, but eventually you’re sure to hit a home run. Of course, the name also evokes electrophysiology, which is the fundamental orientation of the project, be it optical or electrical.

Ephus 2.1.0 is a major release, and the only official version at this time.  The software is fully described in a publication in Frontiers in Neuroscience. New features include unlimited recording time, with disk streaming, for applications such as EEGs and long traces during in-vivo behavior. A number of additional scripts for in-the-loop control have been added. New configuration/start-up files have been created, with a template to help get up and running quickly. This release also includes a number of bug fixes.

ScanImage is another Matlab-related software program that is used for optical imaging and stimulation of neurons in vitro and in vivo.  It finds much use a control platform for 2-photon imaging, glutamate uncaging and laser-scanning photostimulation.  An early incarnation is described in this paper by Pologruto, et al.  It provides a lot of power right out of the box (bidirectional scanning @ 0.5ms/line, etc) and is easily extensible via custom user function plugins.

Neuroptikon is a sophisticated network visualization tool.  It can build Van Essen-like diagrams of any circuit you like, but it is so much more.  The direction of communication is animated, and subsets of regions and connections can be brought into focus, which greatly eases the clarity of the network.  The diagrams can be built in three-dimensions, to preserve relative topography, or functional grouping.  There is simple GUI-based control, while more complex tasks can use a scripting interface.  This is great software for anyone who needs to imagine information flow in a complex network.

All three tools are released for free use under the HHMI/Janelia Farm open source license.

Download Here :

Ephus 2.1.0

ScanImage 2.6.1

Neuroptikon 0.9.9

Optogenetic induction of memory recall

Speaking of reactivating specific memories, at the 2009 Society for Neuroscience meeting, Matteo Rizzi of Michael Häusser’s lab is presenting the realization of an idea that has been floating around in some research proposals I’ve read over the last year.  Express channelrhodopsin-2 under control of the immediate early gene c-fos, induce a strong memory formation via fear conditioning, and then drive the recall of that memory by stimulating the neurons that are expressing ChR2. Immediate early genes are activated shorty after high levels activity in neurons, though the precise patterns are different depending on which promoter (c-fos, Zif268, etc) you use, making precisely HOW they reflect recent neuronal activity patterns unclear.  Nevertheless, the activation of the c-fos based pattern seems close enough to trigger an identical behavioral response as the conditioned stimulus.

Not yet, but getting closer...

Electrically-induced fear conditioning is probably the most blunt instrument possible, encoding a very powerful, general ‘fear’ memory, and many things can make a mouse freeze. Thus, this is definitely the low-hanging fruit on the ‘reverse-engineering’ memories tree. Understanding how the information in a memory is distributed across participating neurons is going to take a more sophisticated approach and a lot more work. This result is still incredibly cool, and I’m somewhat surprised it worked by driving ChR2 with c-fos in a hundred cells in the dentate gyrus. That has pretty powerful implications for avenues by which memories can be recalled.  Surely the entire memory is not encoded by only the 100 neurons that were activated! How many other neurons participate, and how does the optical stimulation activate the entire ensemble? Is it even necessary to activate the entire ensemble to drive behavior? The poster will be MOBBED.  I look forward to reading the details.

Program#/Poster#:	388.8/GG103
Title:	Memory recall driven by optical stimulation of functionally identified sub-populations of neurons
Location:	South Hall A
Presentation Time:	Monday, Oct 19, 2009, 10:00 AM -11:00 AM
Authors:	*M. RIZZI, K. POWELL, J. HEFENDEHL, A. FERNANDES, M. HAUSSER; Wolfson Inst. for Biomed. Res., UCL, London, United Kingdom
Abstract:	The mammalian brain is capable of storing information in sparse populations of neurons encompassing several brain areas. Immediate recall of this information is possible upon presentation of a cue or context. Most aspects of this process remain unresolved: are the cells involved in information storage also responsible for its recall? What portion of this distributed circuit needs to be reactivated, in order to achieve successful recall? To answer these questions we selectively expressed a genetically encoded optogenetic probe (Boyden et al., 2005) in neurons engaged during the learning of a specific association. A plasmid encoding channelrhodopsin-2 and EGFP under an immediate early gene promoter (c-fos-ChR2-IRES-EGFP) was electroporated in vivo into granule cells (GCs) of the dorsal dentate gyrus of anaesthetized C57BL/6 mice. Mice were allowed to recover, and then underwent classical delay fear conditioning (consisting of 10-20 pairings of a 5 second auditory tone and a 2 second footshock). An optic fiber was implanted intra-cranially to allow optical stimulation of transfected neurons. Light stimulation (λ = 530 nm; 5 Hz) successfully induced recall of the fear memory, measured as freezing behaviour (n = 27 animals). Post-hoc analysis of the transfected tissue revealed that a remarkably small subpopulation of GCs (<~100 cells) was sufficient to cause this effect. We then tested whether any, comparatively sized, subset of GCs could be equally effective. We transfected neurons with a plasmid encoding ChR2 expression under a general promoter (pCAG-ChR2) to obtain ChR2 expression in a random population of cells. Interestingly, optical stimulation of this population was insufficient to induce memory recall (population data: n=30). Our results therefore suggest that recall of a learned association, sparsely stored in neuronal circuits distributed over several brain areas, can be achieved by the simple reactivation of a very small subset of neurons involved in learning this association. Furthermore, our strategy may also be useful for dissecting the complexities associated with memory storage and recall. Support: Gatsby Charitable Foundation; Wellcome Trust

Light-switchable protein interactions

A fully genetically-encoded approach to light-activated transcription is getting closer now that a new, generalizable method of light-switchable protein interactions has been published.  In Nature’s advance online publication, Spatiotemporal control of cell signalling using a light-switchable protein interaction, Anselm Levskaya of the Voigt lab at UCSF and co-authors demonstrate inducible, reversible control of protein binding, localization and signalling in mammalian cells.  

apo-PhyB covalently binds to the chromophore phycocyanobilin (PCB) to form a light-sensitive holoprotein. PhyB undergoes conformational changes between the Pr and Pfr states catalysed by red and infrared light, reversibly associating with the PIF domain only in the Pfr state. This heterodimerization interaction can be used to translocate a YFP-tagged PIF domain to PhyB tagged by mCherry and localized to the plasma membrane by the C-terminal CAAX motif of Kras.

When asked about the possibility that this could be used in-vivo, Levskaya said

The only real caveat for in-vivo work is delivery of the non-native PCB tetrapyrrole. From the literature and my experience with cell culture I suspect it shouldn’t be hard to just administer it directly to animals to get saturating levels for holoprotein formation. It might even be possible just to feed animals Spirulina (where it comes from). There’s nutrition literature that suggests their livers are capable of freeing PCB and getting it into the blood stream.

 

Observing light-induced Cdc42 activation with a TIRF recruitment biosensor

Expression of genetic tools that control neural activity (Channelrhodopsins, Halorhodopsins, DREADDs) in functionally defined populations, such as neurons that are active during a particular task or thought, is the next big leap that needs to be made in systems neuroscience. This may be achieved by combining an imaging technique to identify active neurons, such as G-CaMP3, with photo-switchable transcription. The technique presented in the above paper is one promising avenue which may lead to cell-specific photo-switchable transcription.  Once robust versions of these tools are in place, scientists will begin to work out the complex and thrilling processes of reverse-engineering and manipulation of specific thoughts and memories, at least in mice and rats.

Photoactivated Transcription Revisted

Looks like there has been some new results in the field of photoactivated transcription.  Unlike the fully genetically-encoded systems reviewed in a Journal Club, this uses a hybrid genetic and small molecule approach. In Doxycycline-dependent photoactivated gene expression in eukaryotic systems, Cambridge et al. add the photolabile protecting groups to doxycyclin derivatives, which then function as photoactivatable switches in the commonly used Tet-on system. Dr. Dan O’Connor described the technique as “the path of least resistance to photoactivated transcription.” 

 

Local (left) and global (right) GFP expression following optical uncaging of cyanodoxycyclin

 

 

      The authors were able to get robust gene expression with standard UV irradiation, but also were able to uncage sufficient cyanodoxycycline with two-photon illumination to cause highly localized gene expression in cultures.  In live tadpoles, they stuck to UV for the greater efficiency.

     The standard caveats of the tet system apply. The off-state still has a bit of residual gene expression, which is fine for some applications (like fluorescent tagging), and a dealbreaker for others (cre induction). Drug delivery takes time and comes with diffusion, penetration and clearance issues.  UV penetration through deep tissue is going to be a big technical hurdle to overcome to apply this to full-grown mammals. Blasting living tissue with high power UV usually isn’t a good idea. Despite these caveats, the system clearly works and I’d bet the authors are already applying the system to some next-step applications and biological questions. The potential of selectively turning on genes in functionally identified neurons via light is enormous.  It is one of the most likely eventual avenues into possible optical activation or suppression of specific thought patterns (at least if you are willing to squirt virus into your brain and eat a bunch of nasty antibiotics).

Previews : sCRACM, Red PA-FPs, ATP sensor, Deep tissue PALM

Here is a quick list of papers Brain Windows will be covering in greater depth the next two weeks.

The subcellular organization of neocortical excitatory connections : A new technique, subcellular ChR2-assisted circuit mapping (sCRACM), is used to map neuronal circuitry.  

A genetically encoded fluorescent reporter of ATP:ADP ratio : A new single-FP indicator that reports the relative concentration of ATP to ADP in a cells. 

A bright and photostable photoconvertible fluorescent protein : Evolution of monomeric Eos into a fluorescent protein with better properties for super-resolution imaging.

Photoactivatable mCherry for high-resolution two-color fluorescence microscopy : Evolution of mCherry into a photoactivatable fluorescent protein with better properties for super-resolution imaging.

Multilayer three-dimensional super resolution imaging of thick biological samples : Advanced laser pulse shaping techniques to achieve super-resolution imaging in thick samples.

Journal Club #4 : Photoactivatable transcription

Many organisms regulate gene transcription via sunlight.  In plants, phototaxis, flowering and germination all are light dependent processes. Circadian rhythms in many species is entrained by light. Light-activated transcription is achieved through a variety of mechanisms.  Some of these mechanisms may be usable as a powerful tool to control gene expression in selected cells with high spatial and temporal resolution. When paired with other optical tools, such as genetically-encoded calcium indicators or channelrhodopsins, this technique would give unprecedented specificity in recording and manipulating brain activity. In this journal club, I review two major systems for photoactivateable transcription and their prospects for application in mammalian systems.