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2 Target Discovery and Validation Major advances in biomedical research have occurred in the last decade of the 20th century, and these advances will be reflected in improvements in human health care as the 21st century proceeds. Technological advances in the area of genomics have permitted the complete or nearly complete sequencing of the genomes of several species, including humans as well as model organisms, such as the fruit fly, nematode worm, pufferfish, rat, and mouse. Advances in computational abilities and bioinformatics, along with the development of large-scale, high-throughput technologies such as DNA microarrays, have helped to define tissue- and cell-specific patterns of gene transcription, referred to as "transcriptomes." New tools for sequencing proteins have also provided information on the complete protein complements of cellular components, referred to as "proteomics." In parallel with these contributions, studies in "functional genomics" that use a variety of technologies in vitro and in viva have helped to iden- tify and characterize essential and novel functions of genes. In the process of performing these various analyses, thousands of genes have been found to be expressed in the cells and tissues that function in reproduction. At least several hundred of these genes appear to be unique to reproductive cells and tissues, and more than 200 human genes or their counterparts in model organisms have been shown to play roles in reproduction in viva (Matzuk and Lamb, 2002~. Because genes that are highly or exclusively expressed in the reproductive tract continue to be discovered, it is likely that additional functional genomics studies will validate these gene prod- ucts as putative contraceptive targets in men and women. 27

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28 NEW FRONTIERS IN CONTRACEPTIVE RESEARCH Mutations in a particular gene or genes that lead to an infertility phenotype in model organisms would suggest that specific modulation of the same gene product in humans could also, theoretically, result in a contraceptive effect. The more specific the expression and, more impor- tantly, the more specific the function of these genes in the reproductive tract, the less likely it is that a new reproductive tract-specific contra- ceptive would have unwanted side effects. Furthermore, genes whose protein products function as receptors, enzymes, and ion channels or transporter proteins, classes of molecules that have been targeted most commonly by pharmaceuticals (Figure 2.1), would likely be of greatest interest for developing new contraceptive drugs. This chapter provides a brief overview of several of the new method- ologies used in basic biomedical research that could be brought to bear on the identification and validation of novel targets for contraception. Other methods or technologies might also make valuable contributions to the discovery and validation of new targets, but it was not possible to provide a comprehensive review of all possible scientific approaches to contracep- tive research here. The chapter focuses primarily on early stage discovery approaches to research in reproductive biology, which should be viewed Receptors, 45% Enzymes, 28% DNA, 2% Hormones and factors, 1 1% Unknown, 7% channels, 5% receptors, 2% FIGURE 2.1 Molecular targets of drug therapy, with classification according to biochemical criteria. Based on modern standard work in pharmacology, the molecular targets of all known drugs that have been characterized as safe and effective have been collected and listed according to their biochemical nature. SOURCE: Drews, 2000.

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TARGET DISCOVERY AND VALIDATION 29 as a long-term investment in the field, as it will likely take many years, perhaps even decades, to translate the new knowledge into clinically useful and acceptable contraceptives. The chapter also includes a few examples of promising targets that have already been identified and that could potentially be used to develop new contraceptives in a somewhat shorter time frame. Again, a comprehensive list of possible targets was not possible, but a general overview of potential contraceptive targets is provided in the following section. OVERVIEW OF REPRODUCTIVE BIOLOGY Reproduction is a complex process involving many different special- ized cells, tissues, and organs in both the male and the female (Institute of Medicine, 1996; reviewed in Matzuk and Lamb, 2002~. Figure 2.2 provides an overview of the male and female reproductive processes that could potentially be targeted by contraceptives. Recent advances in basic bio- logical research have provided a better understanding of these processes than ever before, and examples of the many genes that may play an im- portant role in reproduction at various stages are shown in Figures 2.3 and 2.4. A small number of germ cells are set aside from somatic cells early in embryogenesis, where they usually remain in an undifferentiated quies- cent state while somatic cells are dividing and forming tissues and organs. In order to form gametes, they must then begin to proliferate and enter meiosis, a process that is unique to germ cells and is required to halve the number of chromosomes in a gamete's nucleus so that it can combine with another haploid gamete at fertilization. Male spermatogenesis is initiated postnatally and is a continuous process characterized by three specific functional phases: proliferation, meiosis, and spermiogenesis. Proliferating cells known as spermatogonia undergo differentiation and enter meiosis as spermatocytes. Once male germ cells complete meiosis to achieve a haploid chromosomal comple- ment, they are called spermatids. Spermatids undergo a process of cellular differentiation known as spermiogenesis, progressing from round to elon- gated spermatids, and culminating in the development of spermatozoa. After spermatogenesis, spermatozoa are released from the Sertoli cells into the seminiferous tubule lumen. In the female, gametes develop in structures called follicles within the ovary. Oogenesis begins as follicles form during prenatal life in humans, and arrests at an early stage of meiosis. Recruitment of individual follicles leads to further growth and development of oocytes, with a resumption of meiosis, and culminates in ovulation, or release of the oocyte into the oviduct. At that point, the oocyte arrests again in a late stage of meiosis

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TARGET DISCOVERY AND VALIDATION Genes Cells Genes Adamts2 Apaf1 Bax Bmp8b Csf1 Dazl Gdnf Camk4 CsnkPa Crem Mtap7 Prm 1 Prm2 Ppptcc ~39562 Growth factors/ receptors Gonadotropins/ receptors Cell-cell adhesion ~ Sertoli cells Peritubular cells Interstitial cells Leydig cells _ Macrophanes _ Steroids and receptors Signal transduction Junctional complexes Proapoptotic/ survival Cell cycle Chromosome pairing/ synapsis _ Homologous recombination _ remodeling ~ .............. Cytoplasmic extrusion Spermiation _ Maturation in genital tract Capacitation Fertilization it, Growth factors Receptors Cytokines Melosis Genomic integrity DNA replication/ repair _ Spermatids ~ .................................................................. .. -............ Differentiation Chromatin packaging Nuclear condensation ~ Spermatozoa ........ - Ivlalurallon Motility Fertilization 31 Fas Gja1 Kit Pi3K Vasa Hyperactivated motility Sperm-zona- egg penetration Nuclear decon de nsati on Slc12a2 Styx Theg Tlp Tnp1 Tnp2 Ube2b 3~5~] P,m1 P~m2 [~752 FIGURE 2.3 Genes involved in the regulation of male reproduction in the mouse. Spermatogenesis requires a complex interaction of the various cellular compart- ments of the testis (seminiferous epithelium containing spermatogenic cells, Sertoli cells, and peritubular myoid cells; the interstitial cell compartment containing the steroidogenic Leydig cells, macrophages, and other interstitial cells; and the vasculature). Targeted mutation of the genes shown affects specific testicular cell types and reproductive function, resulting in male infertility or subfertility in the mouse. SOURCE: Matzuk and Lamb, 2002.

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32 COO integrity GDF9, BMP1 5 PTGER2, PTX3, AMBP A. , Fertilization and pre-implantation development ZP1, ZP2, ZP3, MATER, DNMT10, PEASE, HSF1 Implantation COX2, HOXA10 HOXA11, LIF, IL11 R. NEW FRONTIERS IN CONTRACEPTIVE RESEARCH Pre~y Ovulatlon f(311~e LHR, COX2, PR, ... .. CEBPB NRIP1 , ~ INHA, INHBA, CX37 ERa ERp ~ , FSH, FSHR, IGF1, CCND2, L TAF4B Luteal differentiation/regression PTGFR, P27,CDK4 HMX3, PR, ERa PRL, PRLR F' GDF9, KITL r KITL, KIT, ASH FIGURE 2.4 Female fertility proteins. Knockout mouse models have defined key proteins that function at various stages of follicle formation, folliculogenesis, ovulation, and post-ovulatory events. Several proteins are needed for primordial follicle formation, oocyte and granulose cell (GC) growth and differentiation, ovulation, and the integrity of the cumulus oocyte complex (COC). SOURCE: Matzuk and Lamb, 2002. until fertilized by a sperm. In contrast to males, the formation of follicles in females results in a finite endowment of oocytes. Over the course of a woman's lifetime, there is a precipitous decline in the number of oocytes. The roughly 7 million germ cells in a 20-week-old fetus are reduced to 2 million oocytes at birth, and eventually to 300,000 oocytes at puberty. Only about 400 of those will ever undergo ovulation. Despite this sexual difference in meiosis, many regulators of the process are common to the germ cells of both males and females. Both are controlled from the brain through the production of gonadotropin- releasing hormone (GnRH) by the hypothalamus. GnRH in turn stimu- lates the anterior pituitary to secrete luteinizing hormone (LH) and follicle- stimulating hormone (FSH), both of which are required for normal gamete development as well as steroid hormone production (such as testosterone, estrogen, and progesterone). Chemical communication between develop-

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TARGET DISCOVERY AND VALIDATION 33 ing gametes and their supportive somatic cells via growth factors and cytokines is also essential for egg and sperm production. When sperm leave the testis, they must undergo more morphologic and biochemical changes before they are capable of fertilization. These final developments take place in the epididymis, which also serves as a sperm storage reservoir. During maturation, much of the sperm surface appears to be remodeled. Products secreted by the epithelium of the epididymis mediate these changes. Although the precise components of this epididymal fluid have not been fully identified, it is known that its complex composition changes dramatically along the length of the epididymal tubule. The sperm maturation process continues when sperm enter the female reproductive tract. It is here that they undergo a process known as capaci- tation, during which they acquire the ability to fertilize an egg. For fertili- zation to take place, sperm must be motile and make their way to the oviduct, a step that may involve chemical signals from the egg or com- ponents of the female reproductive tract (Inaba, 2003~. Once a sperm comes in contact with the egg, several events must take place at the proper time in order for fertilization to take place. These include sperm penetra- tion of the egg's cumulus cell layer, binding to the zone pellucida (the egg's protective coat), the sperm acrosome reaction (release of enzymes), penetration through the zone pellucida, and fusion of the sperm and egg plasma membranes. The fertilized egg then progresses through the oviduct for another 72 hours and then enters the uterus. The egg undergoes several mitotic cycles during the first few days after fertilization, eventually forming a blasto- cyst. The blastocyst attaches to the uterine wall and then undergoes multiple steps to complete implantation. Human chorionic gonadotropin (hCG), a hormone released by the early embryo, is involved in events crucial to maintaining early pregnancy, including maintenance of the corpus luteum, which forms on the ovary after ovulation, progesterone production, and, perhaps implantation. STRATEGIES FOR TARGET IDENTIFICATION Recent advances in technology have provided new opportunities to use high-throughput methods to address biological questions on a larger scale than was previously possible. This new approach to biomedical research represents a shift from the traditional, reductionist approach of iAny approach using robotics, automated machines, and computers to process many samples at once.

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34 NEW FRONTIERS IN CONTRACEPTIVE RESEARCH studying one or a very small number of molecules at a time to a larger- scale discovery or systems approach to studying hundreds or even thou- sands of molecules at once (Institute of Medicine, 2003~. For example, with the recent sequencing of entire genomes of many different species, there is now great interest in studying the products of all the genes encoded by the sequences. However, defining the genes2 within a genome is not trivial. Most of an organism's DNA does not actu- ally encode functional genes for proteins or other cellular components. Several approaches are used to identify functional genes (Box 2.1), but each has limitations and is likely to identify a different set of potential genes (Figure 2.5~. These limitations are well known in model organisms such as yeast and are likely to be amplified in the more complex human genome (reviewed by Snyder and Gerstein, 2003~. Thus, a variety of 2The definition of a "gene" has varied over time. A current definition is "a complete chro- mosomal segment responsible for making a functional product" (Snyder and Gerstein, 2003~.

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TARGET DISCOVERY AND VALIDATION / 711 Microarray 1 ,212 188 2,033 / / 106 1 163 Transposon \ / SAGE 35 FIGURE 2.5 Functional genomics is best used in a combined fashion. Illustrated is the number of open reading frames in the yeast genome that were found to be transcribed based on data from microarray hybridization, SAGE, and transposon tagging experiments. Areas of overlap indicate that some transcripts were identi- fied by more than one method. SOURCE: Snyder and Gerstein, 2003. approaches will be needed to identify and validate potential targets for contraceptive development. Some of these methods are described below. Forward Gene Discovery One method used to identify genes that are expressed in a particular cell or tissue type is the expressed sequence tag (EST) approach. This method entails sequencing many small nucleotide fragments, or tags, that have been derived from all the messenger RNAs (mRNAs) expressed in the given cell type. EST sequencing projects have provided publicly avail- able information on more than 100,000 sequences for vertebrate reproduc- tive tract tissues and cell types (e.g., ovary, testis, pituitary gland, oviduct, uterus, cervix, vagina, epididymis, prostate, gametes, and early embryos). These sequences are deposited in the public database at the National Cen- ter for Biotechnology Information3 and are also assembled into clusters at 3See htip://www.ncbi.nIm.nih.gov/.

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36 NEW FRONTIERS IN CONTRACEPTIVE RESEARCH UniGene.4 Complementary DNA (cDNA) subtraction hybridization meth- ods5 and serial analysis of gene expression (SAGE) (Neilson et al., 2000), another method for global gene expression profiling, have also been use- ful to identify genes uniquely expressed in reproductive tissues (Neilson et al., 2000; Wang et al., 2001~. In silica approaches, in which sequences already available in EST and SAGE databases are compared by using spe- cial computer programs to identify those that may be unique to a given tissue or cell type, can also be very powerful analytical methods. For ex- ample, several genes that are expressed exclusively in germ cells (Rajkovic et al., 2001) or epididymal tissues have been identified by this approach (Penttinen et al., 2003~. Because the ESTs are "tags," they are only a partial representation of the full-length mRNA. For transcripts that are long, short-lived, or in low abundance, the full-length mRNA and encoded proteins may be particu- larly difficult to identify. As a result, for a number of novel reproductive tract-specific transcripts, the full-length mRNA sequences and the protein products that they encode may still be unknown. This is problematic because many different mRNAs may be produced from a single gene via alternative splicing, transcription, or processing of the mRNA, and such alterations are known to result in gene transcripts that are unique to the testis (Kleene, 2001~. Hence, full-length transcripts must be determined by complete sequencing of full-length cDNAs. Thus, in certain situations, more exhaustive analysis may be necessary for complete determination of the reproductive tract transcriptome and proteome. The most extensive EST libraries of genes expressed in the male repro- ductive tract have been created by McCarrey and colleagues (McCarrey et al., 1999) and Ko and colleagues (Abe et al., 1998~. These analyses were undertaken with mouse tissues because of the powerful genetics tools that are available for the mouse and the readily available source of material. Thus far, McCarrey and colleagues have sequenced 16,833 cDNA se- quences. Additional sequencing is being done. In addition, the National Institutes of Health (NIH) Specialized Cooperative Centers Program in Reproduction Research has also sequenced alternative gene libraries and 4UniGene is an experimental system for automatically partitioning GenBank sequences into a nonredundant set of gene-oriented clusters. See http://www.ncbi.nlm.nih.gov/ entree / query. f cgi? db =unigene. 5A technique used to identify genes expressed differentially between two tissue samples. A large excess of mRNA from one sample is hybridized to cDNA from the other, and the double-stranded hybrids are removed by physical means. The remaining cDNAs are those that are not represented as RNA in the first sample and, thus, that are presumably expressed uniquely in the second sample. To improve specificity, the process is often repeated several times.

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TARGET DISCOVERY AND VALIDATION 37 tissue sources.6 Although serial analysis of gene expression has been con- ducted with human oocytes (Neilson et al., 2000), full-length sequences for most of the novel sequences and libraries of full-length sequences of human oocytes and early embryos are unavailable at present. Thus, projects to complete the determination of the novel reproductive tract- specific gene sequences of humans and model organisms, such as the mouse, are necessary and will need to include genomic and proteomic analysis of substitute nonhuman primate oocyte and early embryo cDNA libraries, similar to the exhaustive mouse sequence library analysis per- formed by Ko and colleagues (Ko et al., 2000~. Reverse Gene Discovery One of the ways to identify and study gene function is to look for evidence of expression that is, transcription of the gene into RNA. A recently developed technology, DNA microarrays,7 provides a powerful, high-throughput method for studying transcription in specific cell types or tissues (Fodor et al., 1993; Schena et al., 1996~. Microarrays have already been used to generate the data used in thousands of peer-reviewed publi- cations and contributed to many public databases that are now used as research tools by the scientific community as a whole. This technology is widely thought to hold enormous potential for diverse applications, ranging from discovering new drug targets to identifying markers that could predict individual responses to drugs (reviewed by Chicurel and Dalma-Weiszhausz, 2002~. Microarrays that cover all known mouse genes as well as thousands of uncharacterized gene sequences are now being used to examine gene expression in numerous reproductive tissues, including the testis, ovary, and uterus of mice and humans (Borthwick et al., 2003; Burns et al., 2003; Carson et al., 2002; Giudice et al., 2002; Kao et al., 2002; Leo et al., 2001; McLean et al., 2002; reviewed by Schlecht and Primig, 2003; Schultz et al., 2003~. Schultz and colleagues (2003) used microarray analyses of testicu- lar cells to identify 351 mouse genes that appear to be sperm cell specific and that are expressed postmeiotically. The authors estimated that nearly 4 percent of the entire genome may be exclusively expressed in the male germ line. These genes thus represent a large number of germ cell-specific targets for contraceptive development. The databases containing the 6See http://www.nichd.nih.gov/about/cpr/rs/sccprr.htm (accessed August 2003~. 7A DNA microarray consists of a glass microscope slide or silicon chip onto whose surface thousands of specific DNA sequences are spotted. Incubation with a labeled sample of nucleic acid such as mRNA can reveal which of the genes represented on the array are expressed in the sample and their relative levels.

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TARGET DISCOVERY AND VALIDATION 67 gives rise to multiple proteins as a result of alternative transcription and translation start sites. The best-characterized progesterone receptor isoforms are the A and B forms. The A form is generally a repressor of transcription, whereas the B form is the longer protein and is a transcrip- tional activator. Female mice lacking progesterone receptors are infertile because of a defect in the process of ovulation as well as a uterine abnor- mality because of the inability to develop a receptive state and an associ- ated inflammatory infiltration (Lydon et al., 1995~. In the periovulatory period, progesterone receptors are induced in ovarian granulosa cells. Drugs that block periovulatory progesterone synthesis as well as proges- terone receptor antagonists prevent ovulation (Shag et al., 2003~. Collec- tively, these findings demonstrate that events that are initiated by proges- terone and that act on the progesterone receptor are essential for the release of the oocyte from the mature follicle. Selective targeting experi- ments demonstrated that the progesterone receptor isoform required for ovulation is the A form (Mulac-lericevic et al., 2000~. The genes that are regulated by progesterone and that are essential for ovulation have yet to be elucidated, but analysis of differential gene expression through the study of transcript profiles of wild-type and progesterone receptor- deficient ovarian RNA suggests that degradative enzymes including cathepsin L and ADAMTS1 (a member of a family of proteins with a disintegrin and metalloprotease with thrombospondin type 1 repeat) are candidates for proteins that participate in the degradation of the follicle wall and thus release of the egg from the ovary (Richards et al., 2002; Robker et al., 2000~. Understanding the gene and protein networks associ- ated with progesterone action in the periovulatory period could yield new targets, including enzymes, for prevention of ovulation without disrup- tion of ovarian endocrine activity. A number of cytokines have also been identified as potential targets for development of anti-implantation strategies. For example, leukemia inhibitory factor (LIF) is essential for implantation in mice (Bhatt et al., 1991), and there is reason to believe that it plays a similar role in primates (Charnock-Iones et al., 1994; Chen et al., 1995; Cullinan et al., 1996; Vogiagis et al., 1996; Yue et al., 2000~. Interleukin-ll (IL-ll) is intimately involved in early decidualization in mice (Robb et al., 1998) and appears to play a similar role in humans (Dimitriadis et al., 2000, 2002~. Work is under way to develop peptide inhibitors that block activation of the uter- ine LIF and IL-ll signaling pathways (Fairlie et al., 2002~. RECOMMENDATIONS Major advances in identifying and verifying contraceptive targets in males and females have been made since publication of the 1996 Institute

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68 NEW FRONTIERS IN CONTRACEPTIVE RESEARCH of Medicine report. These targets are, in some cases, uniquely and exclu- sively involved in reproduction. The committee recognizes the existence of several promising targets (i.e., proteins that have been shown to play key roles in gamete maturation, function, or interactions) and strongly recommends that these targets be pursued using high-throughput drug discovery approaches (see Chapter 3~. In addition, many more promising targets can be expected from continued work in target discovery using a variety of experimental approaches. Once these potential targets have been identified, they will need to be validated in model organisms through in depth phenotypic analysis using genomic and proteomic approaches. Recommendation 1: Identify and characterize all genes and proteins uniquely or preferentially expressed in the testis, ovary, and repro- ductive tissues; and define the genetic and protein networks in cells relevant to reproduction, including construction of a protein inter- action map for the sperm and the egg. Emphasis should be placed on selective screening methods to iden- tify classes of molecules that have been traditionally targeted by pharma- ceutical compounds, including membrane proteins, enzymes, receptors, and ion channels or transporter proteins. An achievable short-term goal (less than 5 years) is the identification of all genes uniquely or preferen- tially expressed in all relevant reproductive cell and tissue types. This could be accomplished in part through the provision of continued and additional funding for a modest number of laboratories attempting to gen- erate the reproductive transcriptome. However, to complete this task more rapidly, the committee recommends that a broad group of reproductive biologists, bioinformaticists, biochemists, and physiologists convene a meeting with the sole purpose of verifying and annotating all gene expression data obtained through genomic methods. The information generated should then be stored in readily accessible World Wide Web- based databases (e.g., the Mammalian Reproductive Genetics database,33 the Mouse Genome Informatics database,34 or GermOnline35~. Equally im- portant, upkeep of the database will require vigilant review, annotation, and standardization if it is to be a useful and valuable tool for the research community (MacNeil, 2003~. In parallel with genomic approaches, the committee recognizes the need, and unique opportunity, to apply proteomic methods to contracep- tive research. One goal that is being pursued is the creation of sperm and 33See http://mrg.genetics.washington.edu/ (accessed September 2003~. 34See http: / /www.informatics.jax.org/ (accessed September 2003~. 35See http://www.germonline.unibas.ch/ (accessed January 2004~.

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TARGET DISCOVERY AND VALIDATION 69 egg proteome databases. However, this is a large undertaking that will require additional allocation of human resources and financial capital. Recognizing that genes and proteins do not act autonomously, the com- mittee recommends that substantial new resources be devoted to identi- fying and constructing genetic and protein networks as well. This is a more long-term goal (greater than 5 years), but one that should be initi- ated immediately. Genomic and proteomic approaches can also identify metabolic path- ways and enzymes that are involved in the biosynthesis and catabolism of glycoproteins, glycolipids, and other lipids. Functional genomic approaches can reveal the importance of these pathways to reproductive processes. However, these techniques cannot establish the structures of unique carbohydrates on proteins and lipids or the content and organization of lipid domains within membranes. Consequently, different experimental methods are needed to characterize unique features of the glycomes and lipidomes of reproductive tract tissues and gametes. Recommendation 2: Generate a lipidome and glycome of the repro- ductive tract tissues and mature gametes. The glycomes and lipidomes of reproductive tract tissues and gametes have unique features not shared by other somatic tissues, and cell surface lipids and proteins represent logical targets for drugs, particularly small molecules that can interact with carbohydrate structures or insert in hy- drophobic domains. Thus, the committee recommends that the investiga- tion of the novel characteristics of the reproductive glycome and lipidome be pursued with the goal of identifying targets and small molecules that act to selectively disrupt membrane structure and function. The Consor- tium for Functional Glycomics, funded by the National Institute of Gen- eral Medical Sciences, could provide useful research tools for an initiative in reproductive glycomics. Recommendation 3: Validate existing and emerging contraceptive targets by using forward and reverse genetic approaches with model organisms. Some of the identified targets described here will be validated or rejected during the normal progress of typical NIH-sponsored research programs. However, in some circumstances, study sections may not fund studies for the genetic validation of targets with unknown biochemical or molecular functions. To address this bottleneck, the committee recom- mends that a small consortium of investigators (public or private) be funded for the sole purpose of completing the genetic validation of all potential targets. To accomplish this goal most efficiently, newly estab- lished genetic models should be rapidly distributed to the community of

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