Several areas are currently worked on within two lab spaces that I am involved in directing: The Control of Gene Expression Lab, which I started in 2001, and the Pediatric Retinal Research Lab (PRRL), which the ERI activated in 2012 in association with the support of the Vision Retinal Research Foundation (VRRF).
Photoreceptor-Maturation Gene-Activation Database: Genome-wide Map of RNA-Polymerase-II Binding
One of the most useful research resources for researchers interested in genes activated in mammalian photoreceptors in vivo, is our mapping of RNA-Polymerase-II (Pol-II) in most genes of the mouse genome. I have programmed a server-link so the research community can compare the presence of Pol-II on photoreceptor genes at age P2 (immature photoreceptors) and age P25 (mature functional photoreceptors) without the need for using any proprietary software. These tracks will load for you in the Genome Browser at UCSC. (Once you get there, find the “Configure” button below the graphical window and set the label area width to 26 characters and text size to 14.) Remember to ZOOM OUT 1.5x, so you see the promoter region of your gene of interest. Substantial amounts of Pol-II may be found throughout the gene as well. Distal (far upstream) and proximal (near the transcription start site) regions of a promoter may have Pol-II peaks because those regions are brought together physically in the promoter activation complex.
Use this link to go there now, and find your gene of interest:
This will load the data for you in a new browser window and begins with the Rhodopsin gene shown. Orange bars show regions of the DNA that had RNA-Polymerase-II bound to them above background controls. There are also “Peak” tracks that indicate the points where the levels of bound polymerase were maximum. An increase in peak value between age P2 and P25, >1.8 fold ratio, indicates a significant expression increase in vivo as rod-photoreceptors matured. So look for your gene. If you would like high resolution maps of the binding peaks in any gene to use for your own research or publications, please contact me (firstname.lastname@example.org). I provide this information, no charge, to other retina researchers. If you have questions, email me.
The current team is listed on our Team Page.
Our Current Research Projects (2018):
- VEGF Mechanisms in the Retinal Vasculature: Funded by the NEI/NIH, to elucidate the molecular basis of the effects of different isoforms of VEGF (Vascular Endothelial Growth Factor) on the blood retinal barrier and specific effects on human vascular endothelial cells. Different isoforms of VEGF vary in their concentrations in conditions such as Diabetic Retinopathy, AMD, and ROP. We have found substantial differences in how isoforms activate retinal vascular endothelial cells.
- Biotechnology: bacterial protein production of recombinant human proteins for research on eye disease treatment. Future drug development with Retinal Solutions.
- Effects of Valproic acid on the degeneration of photoreceptors in mice that have mouse versions of retinitis pigmentosa.
- Development of High-throughput, low-cost targeted DNA-sequencing panels for rare inherited retinal diseases. We have just completed our Stage-1 of development, a proof of concept for the technical process. In other words, to demonstrate that it actually works, and it does! We completing a successful test of what is called “amplicon panel” targeted sequencing using the Illumina DNA-sequencing platform. This method uses hundreds of PCR reactions to amplify all of the exons, intron/exon boundaries, and promoter regions of candidate genes whose DNA-sequences may be altered and cause many different inherited retinal pathologies. At our Stage-1 testing, we designed a panel for seven (7) genes including genes that are often involved in the following diseases: FEVR (Familial Exudative VitreoRetinopathy), Norrie Disease, and Retinoschisis.
Stage-2 of the project will now move to expand from 7 to 10 genes, and then build from that increasing, and to set up an amazing Illumina Sequencing system, the size of a desktop laser printer, in our Pediatric Retinal Research Laboratory.
The practical goal is to establish sequencing of a patient’s DNA for about $250-$300 per person and to share with others how to bring this access to small and medium sized medical practices. That is where most retinal patients are.
The scientific goal is to dramatically increase our knowledge of specific gene changes and how they correlate to different disease characteristics, such as clinical appearance and rate of changes in the retina’s structure and function.
The human goal is to help more families to finally identify the molecular genetic cause of their inherited condition and to give their physicians and genetic counsellors more information to manage and eventually treat their progressive blindness. Speed is important to survey many genes, and this new technology makes this possible. We are one of the first groups to tackle the development of this kind of sequencing panel for retinal disease genes.
If you are a student at Oakland University, you can complete your 490 independent research experiences in ERI laboratories. We also mentor Honors College thesis students, and more recently have added Medical School Capstone Research students, and Engineering Biology Capstone students. Austen Knapp, is our first completing OUWB Medical Student (M4) in the ERI, and has matched to start her Ophthalmology Residency at Cleveland Clinic. Currently, four capstone students work in my group.
If you are interested in learning how to do science in our laboratories, please use the form link for student applicants found in the main menu if you are on a large screen, or click here:
Current Lab Member and Lab Alumni News:
On March 9th, 2018, undergraduate students Jennifer Felisky and Megan Moore both presented talks at the Michigan Academy of Arts, Sciences and Letters hosted at Central Michigan University.
Camryn DeLooff (SUPER program 2013) is currently in the full time MBA program at the internationally renowned business school, the Rotman School of Management, University of Toronto. Quentin Tompkins (SUPER program 2015) has been accepted into several medical schools for fall 2018. Congratulations Quentin. Brandon Metcalf (SUPER program 2014) is now in his M1 year in the OUWB school of medicine. He has also joined our lab again for his medical school capstone research project.
My Philosophy on doing Science well (Ken Mitton).
As for many biomedical, basic-science research labs, my research flows and changes over time as we make new discoveries that lead us to new questions we form even as we uncover the answers to previous questions. That is the nature of basic science, and it is the way science investigation has always brought the most benefits to people and medicine in particular. While many organizations and countries have attempted to focus research support (funding) into specific diseases, it turns out that the overwhelming majority of high-impact medical discoveries have come from “serendipity”. That is, great useful ideas and tools were discovered to treat diseases simply by exploring how things work.
For example, drugs for controlling high cholesterol were not discovered by deciding to start making drugs for treating high cholesterol. In the course of biochemists investigating how our cells make cholesterol in the first place, chemicals were used to block enzymes to help figure out how cholesterol was made. Some of these chemicals then were obviously the idea to become new drugs that could block cholesterol made in the body. Latanoprost, one of the later generation of drugs developed in the 80’s for reducing high intraocular pressure (IOP), was based on the discovery that prostaglandins made by some cells in the eye could increase the aqueous outflow in the eye, and reduce pressure. The basic science was elucidated in animal models. Again, a basic science discovery in the laboratory of physiologist Laszlo Bito at Columbia University, was adopted by a Pharma company as the way to make drugs that mimic natural prostaglandins to produced this new class of drugs. As a result, thousands of people around the world have another class of drugs to reduce their intraocular pressure and reduce their risk of vision loss from Glaucoma.
So, you never really know where benefits will arise for biomedicine. That is why many research funding agencies, such as the NIH (USA) and the MRC (UK), understand the importance of funding physiologists and biochemists to explore how things work. In our case, how things work in the eye, and the retina of the eye.