The Maf-family transcription factor Nrl is a key regulator of photoreceptor differentiation in mammals. Ablation of the Nrl gene in mice leads to functional cones at the expense of rods. We show that a 2.5-kb Nrl promoter segment directs the expression of enhanced GFP specifically to rod photoreceptors and the pineal gland of transgenic mice. GFP is detected shortly after terminal cell division, corresponding to the timing of rod genesis revealed by birthdating studies. In Nrl ؊/؊ retinas, the GFP؉ photoreceptors express S-opsin, consistent with the transformation of rod precursors into cones. We report the gene profiles of freshly isolated flow-sorted GFP؉ photoreceptors from wild-type and Nrl ؊/؊ retinas at five distinct developmental stages. Our results provide a framework for establishing gene regulatory networks that lead to mature functional photoreceptors from postmitotic precursors. Differentially expressed rod and cone genes are excellent candidates for retinopathies.gene profiling ͉ gene regulation ͉ neuronal differentiation ͉ retina ͉ transcription factor E volution of higher-order sensory and behavioral functions in mammals is accompanied by increasingly complex regulation of gene expression (1). As much as 10% of the human genome is presumably dedicated to the control of transcription. Exquisitely timed expression of cell-type-specific genes, together with spatial and quantitative precision, depends on the interaction between transcriptional control machinery and extracellular signals (2, 3). Neuronal heterogeneity and functional diversity result from combinatorial and cooperative actions of regulatory proteins that form complicated yet precise transcriptional networks to generate unique gene expression profiles. A key transcription factor, combined with its cognate regulatory cis-sequence codes, specifies a particular node in the gene regulatory networks that guide differentiation and development (4).The retina offers an ideal paradigm for investigating regulatory networks underlying neuronal differentiation. The genesis of six types of neurons and Müller glia in the vertebrate retina proceeds in a predictable sequence during development (5). Subsets of multipotent retinal neuroepithelial progenitors exit the cell cycle at specific time points and acquire a particular cell fate under the influence of intrinsic genetic program and extrinsic factors (5-7). Pioneering studies using thymidine labeling and retroviral vectors established the order and birthdates of neurons in developing retina (5,(8)(9)(10)). The current model of retinal differentiation proposes that a heterogeneous pool of progenitors passes through states of competence, where it can generate a distinct subset of neurons (5). One can predict that, at the molecular level, this competence is acquired by combinatorial action of specific transcriptional regulatory proteins. Genetic ablation studies of transcription factors involved in early murine eye specification are consistent with combinatorial regulation (11-13).Rod and cone photorecep...

Genetic variants at chromosomes 1q31-32 and 10q26 are strongly associated with susceptibility to age-related macular degeneration (AMD), a common blinding disease of the elderly. We demonstrate, by evaluating 45 tag SNPs spanning HTRA1, PLEKHA1, and predicted gene LOC387715/ARMS2, that rs10490924 SNP alone, or a variant in strong linkage disequilibrium, can explain the bulk of association between the 10q26 chromosomal region and AMD. A previously suggested causal SNP, rs11200638, and other examined SNPs in the region are only indirectly associated with the disease. Contrary to previous reports, we show that rs11200638 SNP has no significant impact on HTRA1 promoter activity in three different cell lines, and HTRA1 mRNA expression exhibits no significant change between control and AMD retinas. However, SNP rs10490924 shows the strongest association with AMD (P ‫؍‬ 5.3 ؋ 10 ؊30 ), revealing an estimated relative risk of 2.66 for GT heterozygotes and 7.05 for TT homozygotes. The rs10490924 SNP results in nonsynonymous A69S alteration in the predicted protein LOC387715/ARMS2, which has a highly conserved ortholog in chimpanzee, but not in other vertebrate sequences. We demonstrate that LOC387715/ARMS2 mRNA is detected in the human retina and various cell lines and encodes a 12-kDa protein, which localizes to the mitochondrial outer membrane when expressed in mammalian cells. We propose that rs10490924 represents a major susceptibility variant for AMD at 10q26. A likely biological mechanism is that the A69S change in the LOC387715/ARMS2 protein affects its presumptive function in mitochondria.aging ͉ genetic association ͉ mitochondria ͉ neurodegeneration ͉ retinal disease

In developed countries, age-related macular degeneration is a common cause of blindness in the elderly. A common polymorphism, encoding the sequence variation Y402H in complement factor H (CFH), has been strongly associated with disease susceptibility. Here, we examined 84 polymorphisms in and around CFH in 726 affected individuals (including 544 unrelated individuals) and 268 unrelated controls. In this sample, 20 of these polymorphisms showed stronger association with disease susceptibility than the Y402H variant. Further, no single polymorphism could account for the contribution of the CFH locus to disease susceptibility. Instead, multiple polymorphisms defined a set of four common haplotypes (of which two were associated with disease susceptibility and two seemed to be protective) and multiple rare haplotypes (associated with increased susceptibility in aggregate). Our results suggest that there are multiple disease susceptibility alleles in the region and that noncoding CFH variants play a role in disease susceptibility.Age-related macular degeneration (AMD; OMIM 603075) is a complex degenerative disorder that primarily affects the elderly. Disease susceptibility is influenced by multiple genetic 1-5 and environmental factors 6-9 . Recently, targeted and genome-wide searches have identified alleles on chromosomes 1q and 10q that are strongly associated with disease susceptibility 10-14 . In each case, the association seems to be robust and has been replicated in multiple samples. We previously showed that the Y402H-encoding variant of CFH is strongly associated with AMD susceptibility in a sample of affected individuals and controls Reprints and permissions information is available online at http://npg.nature.com/reprintsandpermissions/ Note: Supplementary information is available on the Nature Genetics website. After quality assessment of genotype data (see Methods), we tested each SNP for association in 544 unrelated affected individuals and 268 unrelated controls (Fig. 1). As expected, we observed strong association between disease status and the Y402H-encoding variant previously associated with AMD in multiple studies (likelihood ratio test χ 2 = 110.05, P <10 −25 ). Unexpectedly, 20 other variants showed even stronger association. The strongly associated SNPs fell into two linkage disequilibrium (LD) groups (colored in purple and green in Fig. 1), such that, within each group, pairwise r 2 > 0.80, and between groups, pairwise r 2 < 0.50. The Y402H-encoding variant was included in one of the LD groups (the purple group in Fig. 1). The three SNPs showing strongest association are a synonymous SNP in exon 10, rs2274700 (LRT χ 2 = 135.42, P < 10 −30 ) and two intronic SNPs, rs1410996 (LRT χ 2 = 132.70, P < 10 −29 ) and rs7535263 (LRT χ 2 = 130.43, P < 10 −29 ). We observed similar results using a family-based association test 16,17 that incorporated all 726 affected individuals genotyped. Table 1 summarizes results of family-based and case-control single-SNP association tests for rs1061170 (the Y40...

Objective This paper describes the University of Michigan's nine-year experience in developing and using a full-text search engine designed to facilitate information retrieval (IR) from narrative documents stored in electronic health records (EHRs). The system, called the Electronic Medical Record Search Engine (EMERSE), functions similar to Google but is equipped with special functionalities for handling challenges unique to retrieving information from medical text. Materials and Methods Key features that distinguish EMERSE from general-purpose search engines are discussed, with an emphasis on functions crucial to (1) improving medical IR performance and (2) assuring search quality and results consistency regardless of users' medical background, stage of training, or level of technical expertise. Results Since its initial deployment, EMERSE has been enthusiastically embraced by clinicians, administrators, and clinical and translational researchers. To date, the system has been used in supporting more than 750 research projects yielding 80 peer-reviewed publications. In several evaluation studies, EMERSE demonstrated very high levels of sensitivity and specificity in addition to greatly improved chart review efficiency. Discussion Increased availability of electronic data in healthcare does not automatically warrant increased availability of information. The success of EMERSE at our institution illustrates that free-text EHR search engines can be a valuable tool to help practitioners and researchers retrieve information from EHRs more effectively and efficiently, enabling critical tasks such as patient case synthesis and research data abstraction. Conclusion EMERSE, available free of charge for academic use, represents a state-of-the-art medical IR tool with proven effectiveness and user acceptance.

We have characterized comprehensive transcript and proteomic profiles of cell lines corresponding to normal breast (MCF10A), noninvasive breast cancer (MCF7) and invasive breast cancer (MDA-MB-231). The transcript profiles were first analysed by a modified protocol for representational difference analysis (RDA) of cDNAs between MCF7 and MDA-MB-231 cells. The majority of genes identified by RDA showed nearly complete concordance with microarray results, and also led to the identification of some differentially expressed genes such as lysyl oxidase, copper transporter ATP7A, EphB6, RUNX2 and a variant of RUNX2. The altered transcripts identified by microarray analysis were involved in cell-cell or cell-matrix interaction, Rho signaling, calcium homeostasis and copper-binding/sensitive activities. A set of nine genes that included GPCR11, cadherin 11, annexin A1, vimentin, lactate dehydrogenase B (upregulated in MDA-MB-231) and GREB1, S100A8, amyloid b precursor protein, claudin 3 and cadherin 1 (downregulated in MDA-MB-231) were sufficient to distinguish MDA-MB-231 from MCF7 cells. The downregulation of a set of transcripts for proteins involved in cell-cell interaction indicated these transcripts as potential markers for invasiveness that can be detected by methylation-specific PCR. The proteomic profiles indicated altered abundance of fewer proteins as compared to transcript profiles. Antisense knockdown of selected transcripts led to inhibition of cell proliferation that was accompanied by altered proteomic profiles. The proteomic profiles of antisense transfectants suggest the involvement of peptidyl-prolyl isomerase, Raf kinase inhibitor and 80 kDa protein kinase C substrate in mediating the inhibition of cell proliferation.