The Harry M. Zweig Memorial Fund for Equine Research

Horse Genome Project: Functional Genomics through Equine Microarrays

Dr. Douglas F. Antczak

Over the past 10 years grants from the Zweig Fund have provided very important support for the Cornell portion of the Horse Genome Project. This support has made Zweig and Cornell key partners in the global effort to characterize the genome of the horse. Tremendous progress has been made by the Horse Genome Project researchers, resulting in new diagnostic tests for disease-causing genes and a rapidly growing understanding of the genetic basis of health and disease of the horse.

The Horse Genome Project has developed many new ways of mapping genes in the horse, and these gene maps are being used by researchers around the world to study equine inherited diseases. A second major outcome of the Horse Genome Project is the development of laboratory assays for assessing the actions of thousands of genes in single experiments. This global approach to gene expression and gene activity holds immense promise for equine medicine and surgery. Global, genome-wide assays for gene function make use of new laboratory devices called microarrays. Microarrays contain collections of thousands of different genes that are attached to glass microscope slides in defined patterns. They can be used in so-called hybridization experiments to compare the level of gene expression in cells or tissues under different environmental conditions. For example, white blood cells from normal horses and horses infected with a virus can be compared to determine how the horse is responding to this insult. The cellular response to traumatic injury can also be assessed using microarrays. Because the assays test for the activity of thousands of genes, it is possible to identify new targets for drug therapy using this approach.

Objective: The objective of this proposal is to characterize and to begin to use the first large-scale equine microarray. The array is being developed by Horse Genome Project scientists, who have assembled DNA sequences from a collection of over 8,000 horse genes. This represents approximately one third of the estimated 25,000 genes of the horse. Microarrays are available commercially for human and mouse studies, but not for horses. Microarrays have been constructed for cattle, pigs, and dogs, but the horse is lagging behind in these studies. The equine microarray is currently the highest priority of the Horse Genome Project.

The array is being constructed with a new grant from the Morris Animal Foundation. However, the requested budget for this project was cut from $500,000 to $300,000 by the Foundation. Even so, it is one of the largest grants ever made by Morris.

Cornell was chosen as one of the sites to evaluate and validate the new microarray, but only limited funds are available from the Morris grant for this purpose. Therefore we seek support from the Zweig Fund to supplement the funds from the Morris grant. This will enable us to continue our high-level participation in the Horse Genome Project and conduct a first-rate evaluation of this exciting new assay.

Specific Aims:

Aim 1 (year 1) would compare the new horse-specific array with a commercial 44,000 gene human array using control and test horse lymphocytes and placental cells. The validation process would include bioinformatic (statistical) analyses and verification of microarray results with selected testing of individual gene expression using conventional assays.

Aim 2 (year 2) would use the horse array to assay test and control samples from projects of five Cornell equine researchers. The samples would be provided by the individual investigators, but the assays would be performed by a single technician to ensure quality control. The resultant data would be returned to the investigators for use in developing new experimental approaches and projects.

Progress in 2004 and 2005: The past two years were very productive for the Cornell Horse Genome Project Laboratory. The focus of the Zweig-funded research in my laboratory was to apply information and resources from the Horse Genome Project to problems in equine immunology. In these efforts we were very successful. Our group published 6 scientific papers in the past two years with Zweig Fund support, and some of them are very important landmarks in studies of the horse immune system.

With respect to the two main aims of the previous grant, under the first aim we obtained DNA sequences from 9,000 horse genes, and these sequences are being used in the construction of the horse microarray described above. Our research supported the Horse Genome Project application to the Morris Animal Foundation that will fund the construction of the microarray ($300,000 grant shared among six institutions).

Under the second aim, Dr. Bettina Wagner, co-investigator on our previous Zweig grant, developed a new system for making monoclonal antibodies to equine immune system molecules. Dr. Wagner's expertise in this area earned her a place on a new major US Department of Agriculture grant that will develop new immunological reagents for the horse and other domestic animal species (~$500,000 per year for 4 years total funding to be shared among three main laboratories, one of which is Dr. Wagner's).

Finally, a new 5 year NIH grant was awarded to my laboratory in 2005 for our studies of pregnancy immunology ($175,000 per year direct costs). Key preliminary data for this project was obtained with Zweig-supported research in equine genomics.

Two graduate students in my lab, Drs. Paige Adams and Becky Tallmadge, completed PhD theses on equine immunology projects. Several undergraduates and veterinary students worked on Zweig-related projects during this time, and two earned authorship on papers.

Conclusions: Financial support from the Zweig Fund for the Horse Genome Project has been heavily leveraged with new grants for horse genomics from national funding agencies. Furthermore, information about the equine genome has been important in the development of new individual research projects, such as the new NIH grant to my laboratory. Most importantly, the Zweig Fund's continued support of horse genomics research makes Cornell and Zweig important stakeholders in the future of equine medicine and surgery.