Abstract 1333: High-quality multi-omic analysis of FFPE samples

Next-generation sequencing analysis of formalin-fixed, paraffin-embedded (FFPE) samples has the potential to lead to major advances in cancer treatment and prevention. These samples present a great opportunity for research because they are associated with clinical records, and millions of samples exist that can be used for retrospective analyses. We previously reported high quality whole-genome sequencing (WGS) results from FFPE tissue with an average of 98% of the genome covered at 20X or greater depth for samples as old as 15 years. In this study, we show high-quality results from performing multi-omic analysis including RNA sequencing (RNA-seq), WGS, methylation array, and microRNA sequencing (miRNA-seq) from the same archival sample. This demonstrates that multiomic analysis of existing cancer samples is technically feasible and opens up multi-omic analysis of these archival FFPE tissues.

Using archival samples derived from breast, non small-cell lung, colorectal, and melanoma tumors, we extracted high-quality, high molecular weight DNA using the WuXi NextCODE SeqPlus method, and RNA was extracted using a rRNA depletion method. Using these extracts, we performed WGS, methylation chip array, RNA-seq, and miRNA-seq analyses. The resulting WGS data had high uniform coverage, and high-quality data was produced from the methylation chips. Results from the FFPE samples were compared to those found in the TCGA data. Analysis of mutation calls in these WGS samples revealed high concordance with those produced from the fresh-frozen whole-exome sequenced TCGA samples. Methylation patterns from our data clustered with samples of the same cancer type in the TCGA dataset. We also saw a similar clustering with the RNA-seq and miRNA-seq results when compared to the TCGA data. In addition, we found that RNA expression was correlated with promoter methylation, and gene expression changes affected by mutation and methylation were identified. In summary, we found an overall clustering of the FFPE samples with samples of the same cancer type and no systemic differences between fresh and FFPE samples were observed. These data demonstrate the feasibility of performing comprehensive, multi-omic profiling of archival FFPE tissues.

Citation Format: Jim Lund, Shannon Bailey, Muhammad Ekram, David Shahbazian, Lorenzo Memeo, Paul Hofman, Richard Williams, Jeff Gulcher. High-quality multi-omic analysis of FFPE samples [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1333.

The clinical utility of genetic risk variants in type 2 diabetes

BACKGROUND

Type 2 diabetes is one of the first success stories in the application of genome-wide linkage and association studies to find genetic variants contributing to its risk.

OBJECTIVE

Are the genetic markers found so far useful in predicting which individuals are more likely to develop type 2 diabetes? Can they find which patients with prediabetes are more likely to convert to type 2 diabetes and therefore may benefit the most from lifestyle or pharmacologic prevention strategies?

METHODS

The literature pertaining to the discovery and replications of genes contributing to type 2 diabetes was focused on.

RESULTS/CONCLUSION

Substantial risk for type 2 diabetes is represented by the top 8 genes, including TCF7L2, and in certain circumstances may be useful for prevention strategies targeted to those with highest risk.

Screen for CACNA1A and ATP1A2 mutations in sporadic hemiplegic migraine patients

The aim of this study was to investigate the involvement of the CACNA1A and ATP1A2 gene in a population-based sample of sporadic hemiplegic migraine (SHM). Patients with SHM (n = 105) were identified in a nationwide search in the Danish population. We sequenced all exons and promoter regions of the CACNA1A and ATP1A2 genes in 100 patients with SHM to search for possible SHM mutations. Novel DNA variants were discovered in eight SHM patients, four in exons of the CACNA1A gene and four in exons of the ATP1A2 gene. Six of the variants were considered non-pathogenic. The causal role of the two remaining DNA variants is unknown until functional studies have been made or independent genetic evidence is discovered. Only very few DNA variants were identified in 100 SHM patients, and regardless of whether the identified variants are causal the CACNA1A and ATP1A2 genes are not major genes in SHM.

The genetic spectrum of a population-based sample of familial hemiplegic migraine

Familial hemiplegic migraine (FHM) is a rare subtype of migraine with aura and transient hemiplegia. FHM mutations are known in three genes, the CACNA1A (FHM1) gene, the ATP1A2 (FHM2) and the SCN1A (FHM3) gene and seem to have an autosomal-dominant mode of inheritance. The aim of this study was to search for FHM mutations in FHM families identified through a screen of the Danish population of 5.2 million people. FHM patients were diagnosed according to the International Classification of Headache Disorders and all FHM patients had a physical and neurological examination by a physician. A total of 147 FHM patients from 44 different families were identified; 43 FHM families participated in this study. Linkage analysis of these families shows clear linkage to the FHM locus (FHM1) on chromosome 19, supportive linkage to the FHM2 locus whereas no linkage was found to the FHM3 locus. Furthermore, we sequenced all exons and promoter regions of the CACNA1A and ATP1A2 genes and screened for the Q1489K mutation in the SCN1A gene. CACNA1A gene mutations were identified in three of the FHM families, two known FHM mutations, R583Q and T666M and one novel C1369Y mutation. Three FHM families were identified with novel mutations in the ATP1A2 gene; a family with a V138A mutation, a family with a R202Q mutation and a family with a R763C mutation. None of the Danish FHM families have the Q1489K mutation in the SCN1A gene. Our study shows that only 14% (6/42) of FHM families in the general Danish population have exonic FHM mutations in the CACNA1A or ATP1A2 gene. The families we identified with FHM mutations in the CACNA1A and ATP1A2 genes were extended, multiple affected families whereas the remaining FHM families were smaller. The existence of many small families in the Danish FHM cohort may reflect less bias in FHM family ascertainment and/or more locus heterogeneity than described previously.

Distinct clinical differences between HLA-Cw*0602 positive and negative psoriasis patients--an analysis of 1019 HLA-C- and HLA-B-typed patients

A major susceptibility gene for psoriasis is located in the major histocompatibility complex class I region on chromosome 6 very close to the HLA-Cw6 gene. We collected a cohort of 1,019 patients with chronic plaque psoriasis. The patients were typed for HLA-C and HLA-B. A total of 654 (64.2%) were HLA-Cw*0602 positive but 365 (35.8%) carried other HLA-C alleles. We confirmed that HLA-Cw*0602 positive patients have younger age of onset (17.5 vs 24.3 years, P<10(-10)), higher incidence of guttate and the eruptive type of psoriasis (P<0.0001), more frequent exacerbations with throat infections (P=0.01), higher incidence of the Koebner's phenomenon (P=0.01), and more extensive disease (P=0.03). A striking new finding was a diverging pattern of disease severity in HLA-Cw*0602 positive and negative patients depending on the age of onset of the disease (P=0.0006). HLA-Cw*0602 positive women also had more frequent remissions during pregnancy (P<0.0001). All types of nail changes were, however, more common in the Cw*0602 negative patients (P=0.003) and they more often had multiple types of nail lesions (P<0.0001). The three ancestral haplotypes of Cw*0602 all conferred an increase in odds ratio but showed no difference in any of the clinical features studied. Our findings indicate that the genetic factor on chromosome 6 has a strong influence on the phenotype of the disease, and underline that differences in clinical features of psoriasis may be to a large extent genetically determined.

Association between the gene encoding 5-lipoxygenase-activating protein and stroke replicated in a Scottish population

Cardiovascular diseases, including myocardial infarction (MI) and stroke, most often occur on the background of atherosclerosis, a condition attributed to the interactions between multiple genetic and environmental risk factors. We recently reported a linkage and association study of MI and stroke that yielded a genetic variant, HapA, in the gene encoding 5-lipoxygenase-activating protein (ALOX5AP), that associates with both diseases in Iceland. We also described another ALOX5AP variant, HapB, that associates with MI in England. To further assess the contribution of the ALOX5AP variants to cardiovascular diseases in a population outside Iceland, we genotyped seven single-nucleotide polymorphisms that define both HapA and HapB from 450 patients with ischemic stroke and 710 controls from Aberdeenshire, Scotland. The Icelandic at-risk haplotype, HapA, had significantly greater frequency in Scottish patients than in controls. The carrier frequency in patients and controls was 33.4% and 26.4%, respectively, which resulted in a relative risk of 1.36, under the assumption of a multiplicative model (P=.007). We did not detect association between HapB and ischemic stroke in the Scottish cohort. However, we observed that HapB was overrepresented in male patients. This replication of haplotype association with stroke in a population outside Iceland further supports a role for ALOX5AP in cardiovascular diseases.

A genome wide linkage disequilibrium screen in Parkinson’s disease

Whole genome screening is increasingly used to identify genetic risk factors for complex diseases. In this study, a genome wide linkage disequilibrium (LD) screen was performed in a cohort of Parkinson's disease (PD) patients from the UK (n = 195) using pooled DNA to facilitate efficient genotyping of 5546 microsatellite markers. Allele frequencies were compared with those found in 2 previously typed disease free control populations, and the most interesting markers were selected for multiple repeat testing among the 3 pools. Markers were then individually genotyped in our original PD cohort and one of the original control groups, and independently in a second cohort of UK PD patients (n = 179), and additional controls. Using this 2-stage approach, we have been unable to find evidence for consistent association of any markers with sporadic PD. Subgroup analysis of the most promising marker shows some evidence that microsatellite marker D1S2886 is associated with familial forms of the disease.

Genome-wide TDT analysis in a localized population with a high prevalence of multiple sclerosis indicates the importance of a region on chromosome 14q

Epidemiological studies show that susceptibility to multiple sclerosis (MS) has a strong genetic component, but apart from the HLA gene complex, additional genetic factors have proven difficult to map in the general population. Thus, localized populations, where MS patients are assumed to be more closely related, may offer a better opportunity to identify shared chromosomal regions. We have performed a genome-wide scan with 834 microsatellite markers in a data set consisting of 54 MS patients and 114 healthy family members. A group of families from a small village were possible to track back to common ancestors living in the 17th century. We used single marker- and haplotype-based transmission disequilibrium test (TDT) analysis and nonparametric linkage analysis to analyze genotyping data. Regions on chromosomes 2q23-31, 6p24-21, 6q25-27, 14q24-32, 16p13-12 and 17q12-24 were found to be in transmission disequilibrium with MS. Strong transmission disequilibrium was detected in 14q24-32, where several dimarker haplotypes were in transmission disequilibrium in affected individuals. Several regions showed modest evidence for linkage, but linkage and TDT were both clearly positive only for 17q12-24. All patients and controls were also typed for HLA class II genes; however, no evidence for a gene-gene interaction was observed.

A whole genome association study in Finnish multiple sclerosis patients with 3669 markers

Multiple sclerosis (MS) is a demyelinating disease of the central nervous system with complex genetic background. In the present study, based in the Finnish population, we typed a large number of microsatellite markers in separately pooled DNA samples from 195 MS patients and 205 controls. A total of 108 markers showed evidence of association. Five genomic regions containing two or more of these markers within a 1-Mb interval were identified, 1q43, 2p16, 4p15, 4q34 and 6p21 (the MHC region). Substantial overlap with previously published linkage genome screens is also seen.

Genome-wide linkage screen of a consanguineous multiple sclerosis kinship

Multiple sclerosis (MS), like Alzheimer's disease (AD) and Parkinson's disease (PD), is a common neurological disorder thought to be caused by the interaction of several genes with unknown environmental factors. In both AD and PD the identification of disease forms inherited in a classic Mendelian fashion has helped investigators elucidate pathogenetic mechanisms. In this study a whole-genome screen, with an average of 608 successful genotypes per person, was performed on nine members of a consanguineous family: the index case, three of her siblings and her daughter, all of whom have been diagnosed with definite MS; as well as the parents of the index case (first cousins), one of her five healthy siblings and her husband (who is also her first cousin). Nonparametric linkage analysis was performed on genotyping data. Based on the presence of consanguinity, the a priori hypothesis was that the disease is transmitted in an autosomal recessive fashion in the pedigree. Linkage analysis revealed a suggestive logarithm of odds (LOD) score of 2.29 on the long arm of chromosome 9. Four of five affected family members were identically homozygous for a haplotype under this peak, spanning approximately 43 cM, while the fifth affected subject and all unaffected family members were heterozygous for the haplotype.

Psoriasis patients who are homozygous for the HLA-Cw*0602 allele have a 2.5-fold increased risk of developing psoriasis compared with Cw6 heterozygotes

BACKGROUND

Psoriasis is strongly associated with certain human leucocyte-associated antigens, especially HLA-Cw*0602. Patients who are HLA-Cw*0602 positive have been reported to have more active disease and a younger age at disease onset than HLA-Cw6-negative patients.

OBJECTIVES

To ascertain whether there are differences in the clinical features and relative risk between HLA-Cw*0602 homozygous and heterozygous psoriasis patients.

METHODS

One thousand and six patients with chronic plaque psoriasis were evaluated clinically and HLA-C typed. In addition, 512 unrelated controls were typed for HLA-C.

RESULTS

Of the patients 646 (64.2%) were HLA-Cw*0602 positive, and 68 (6.8%) were homozygous for this allele. Heterozygosity was associated with a relative risk of developing psoriasis of 8.9 compared with 23.1 for the Cw6 homozygous patients. The homozygous patients also had an earlier disease onset (mean 15.0 vs. 17.8 years, P = 0.04). However, the Cw6 homozygotes did not differ from the heterozygotes with respect to disease severity, guttate onset, distribution of plaques, nail changes or any other clinical parameter recorded.

CONCLUSIONS

Homozygosity for the gene in the major histocompatibility complex region has a major additive impact on the risk of developing psoriasis and predisposes to an earlier disease onset, but does not have any marked influence on the phenotype or the severity of the disease.

The inheritance of hand osteoarthritis in Iceland

OBJECTIVE

To assess the contribution of genetics to hand osteoarthritis (HOA) and its subsets in the Icelandic population.

METHODS

A list of 2,919 HOA patients, constituting 1% of the Icelandic population, was compiled through nationwide sources. This patient list was cross-referenced with a comprehensive Icelandic genealogy database, enabling the use of algorithms to assess familiality of HOA. Two methods were used: the average pairwise kinship coefficient (KC) of the patients, and the relative risk (RR) of HOA in relatives of patients. In each case, the results were compared with 1,000 control sets of similar composition with regard to number, age, and sex, generated from the genealogy database.

RESULTS

The KC for patients was significantly higher than for the control sets and was proportional to the degree of both interphalangeal (IP) and thumb base (first carpometacarpal [CMC] joint) involvement. The RR of HOA in sisters of women in the study was 2.0 (P < 0.001), while the RR in spouses was not significantly different from that in controls. The RR increased with the severity of the disease. Thus, sisters of women with severe IP HOA had an RR of 5.0 and sisters of those with severe first CMC involvement had an RR of 6.9. The increased risk also extended beyond the nuclear family, with significantly increased risk in cousins.

CONCLUSION

Patients seeking medical services for HOA are more related to each other than matched controls, supporting the role of a genetic component in the disease. The genetic influence in both IP and first CMC HOA appears to be similar and increases with increasing severity of the disease.

Genetic factors contribute to the risk of developing endometriosis

BACKGROUND

Endometriosis is known to cluster within nuclear families. The extent of familial clustering can be evaluated in Iceland with its large population-based genealogical database.

METHODS AND RESULTS

Applying several measures of familiality we demonstrated that 750 women with endometriosis were significantly more interrelated than matched control groups. The risk ratio for sisters was 5.20 (P < 0.001) and for cousins 1.56 (P = 0.003). The average kinship coefficient for the patients was significantly higher than that calculated for 1000 sets of 750 matched controls (P < 0.001) and this remained significant when contribution from first-degree relatives was excluded (P < 0.05). The minimum number of ancestors required to account for the group of patients was compared with the minimum number of ancestors required to account for the control groups at different time points in the past. The minimum number of founders for the group of patients was significantly smaller than for the control groups. Affected cousin pairs were as likely to be paternally connected as maternally connected.

CONCLUSIONS

This is the first population-based study using an extensive genealogy database to examine the genetic contribution to endometriosis. A genetic factor is present, with a raised risk in close and more distant relatives, and a definite kinship factor with maternal and paternal inheritance contributing.

Allelic frequencies and patterns of single-nucleotide polymorphisms in candidate genes for asthma and atopy in Iceland

Numerous asthma and atopy loci have been reported in studies demonstrating associations of the asthma-related phenotypes atopy, elevated IgE levels, and bronchial hyperresponsiveness with alleles of microsatellite markers and single-nucleotide polymorphisms (SNPs) within specific cytokine/chemokine and IgE-regulating genes. Although the studies reporting these observations are compelling, most of them lack statistical power. We assessed the nature, pattern, and frequency of SNPs in 24 candidate genes in Iceland and looked for associations with asthma and atopy. We identified 42 SNPs with an average minor allele frequency of 20.3% (asthma) and 20.7% (control). Twenty SNPs (48%) were within coding sequences and 90% of those led to a predicted change in protein sequence. No differences were detected in the allelic frequencies of SNPs in any of these candidate genes between control subjects and the patients with atopic asthma. Moreover, linkage analysis that included 269 patients with atopic asthma uncovered no evidence of linkage to markers associated with these genes. We conclude that this study has failed to produce evidence in support of the notion that variations within these 24 candidate atopy and asthma genes significantly influence the expression of the atopic asthmatic phenotype or contribute to the susceptibility of atopic asthma.

Association between IL-1beta/TNF-alpha-induced glucocorticoid-sensitive changes in multiple gene expression and altered responsiveness in airway smooth muscle

The pleiotropic cytokines interleukin (IL)-1beta and tumor necrosis factor (TNF)-alpha have been implicated in the pathophysiology of asthma. To elucidate the role of these cytokines in the pro-asthmatic state, the effects of IL-1beta and TNF-alpha on airway smooth muscle (ASM) responsiveness and ASM expression of multiple genes, assessed by high-density oligonucleotide array analysis, were examined in the absence and presence of the glucocorticoid dexamethasone (DEX). Administration of IL-1beta/TNF-alpha increased ASM contractility to acetylcholine and impaired ASM relaxation to isoproterenol. These pro-asthmatic- like changes in ASM responsiveness were associated with IL-1beta/ TNF-alpha-induced mRNA expression of a host of proinflammatory genes that regulate transcription, cytokines and chemokines, cellular adhesion molecules, and various signal transduction molecules that regulate ASM responsiveness. In the presence of DEX, the changes induced in ASM responsiveness were abrogated, and most of the IL-1beta/TNF-alpha-mediated changes in proinflammatory gene expression were repressed, although mRNA expression of a small number of genes was enhanced by DEX. Collectively, the observations support the concept that, together with its role as a regulator of airway tone, in response to IL-1beta/TNF-alpha, the ASM expresses a host of glucocorticoid-sensitive genes that contribute to the altered structure and function of the airways in the pro-asthmatic state. We speculate that glucocorticoid-sensitive, cytokine-induced pathways involved in ASM cell signaling represent important targets for new therapeutic interventions.

Endometriosis is not associated with or linked to the GALT gene

OBJECTIVE

To investigate a possible association between the carrier frequency of the N314D mutation in the galactose-1-phosphate uridyl transferase (GALT) gene and endometriosis and linkage to the short arm of chromosome 9, where the GALT gene resides.

DESIGN

Association and linkage study.

SETTING

Population material collected for case and family studies in endometriosis.

PATIENT(S)

Women diagnosed with endometriosis by laparotomy or laparoscopy.

INTERVENTION(S)

Association with the GALT gene investigated by genotyping 85 affected women and 213 unrelated control women and a scan for linkage to chromosome 9 in 205 women from 64 families with endometriosis.

MAIN OUTCOME MEASURE(S)

Multipoint parametric lod scores and frequency of alleles.

RESULT(S)

There was no significant difference in allele frequency for the N314D polymorphism in patients compared with control subjects. No evidence for linkage was found to chromosome 9p, where the GALT gene resides.

CONCLUSION(S)

The experiments reported herein provide no evidence supporting involvement of the GALT locus in the development of endometriosis.

The genealogic approach to human genetics of disease

The goal of modern human genetics is to correlate genes with disease or, more specifically, relate genetic variation to phenotypic variation. Although this correlation is usually straightforward in the Mendelian disorders, it has proved to be much more difficult to find in the common diseases because they appear to be more complex, likely involving an interplay among multiple genes and between genes and the environment. Although the strategy of linkage mapping of families was very successful when it was applied to the rare monogenic diseases, few common diseases have been mapped to statistical significance. Many investigators are now abandoning linkage analysis altogether and are moving to a candidate gene case-control strategy. In this article, we describe a genealogic approach to mapping human disease genes and provide three examples of how we have used it to map common diseases to statistical significance. We focus on a simple population with little historic migration and use a computerized genealogy database to increase the number of patients who can be compared with other affected relatives through high-density microsatellite genotyping. The genealogy helps determine which phenotypic classification is inherited and therefore possible to map. It may represent a more efficient strategy than candidate gene case-control studies for determination of what alleles or haplotypes are shared by patients in a population. We suggest that the genetics community not give up on linkage analysis, nor should it assume that the common diseases are too complex to map.

The inheritance of hip osteoarthritis in Iceland

OBJECTIVE

To assess, in a population-wide study in Iceland, the genetic contribution to hip osteoarthritis (OA) leading to total hip replacement (THR).

METHODS

Information from 2 population-based databases in Iceland was combined: a national registry of all THRs performed between 1972 and 1996, and a genealogy database of all available Icelandic genealogy records for the last 11 centuries. A genetic contribution to THR for OA was assessed by 1) identifying familial clusters of OA patients with THR, 2) applying the minimum founder test (MFT) to estimate the minimum number of ancestors ("founders") that would account for the genealogy of all 2,713 patients with THR for OA, compared with the average number of founders for control lists, 3) calculating an average pairwise kinship coefficient (KC) for the patient list and control lists, and 4) estimating the relative risk (RR) for THR among relatives of OA patients who have undergone the procedure. One thousand matched control lists, each the same size as the patient list, were created using the genealogy database.

RESULTS

A large number of familial clusters of patients with THR for OA were identified. The MFT showed that OA patients descended from fewer founders than did subjects in the control groups (P < 0.001). The average pairwise KC among patients with OA was greater than in the control population (P < 0.001). The RR for THR among siblings of OA patients was 3.05 (95% confidence interval 2.52-3.10).

CONCLUSION

This population-based study shows that Icelandic patients with hip replacement for OA are significantly more related to each other than are matched controls drawn from the Icelandic population. These findings support a significant genetic contribution to a common form of OA and encourage the search for genes conferring an increased susceptibility to OA.

Using quality measures to facilitate allele calling in high-throughput genotyping

Currently, the main limitation in high-throughput microsatellite genotyping is the required manual editing of allele calls. Even though programs for automated allele calling have been available for several years, they have limited capability because accurate data could only be assured by manual inspection of the electropherograms for confirmation. Here we describe the development of a parametric approach to allele call quality control that eliminates much of the time required for manual editing of the data. This approach was implemented in an editing tool, Decode-GT, that works downstream of the allele calling program, TrueAllele (TA). Decode-GT reads the output data from TA, displays the underlying electropherograms for the genotypes, and sorts the allele calls into three categories: good, bad, and ambiguous. It discards the bad calls, accepts the good calls, and suggests that the user inspect the ambiguous calls, thereby reducing dependence on manual editing. For the categorization we use the following parameters: (1) the quality value for each allele call from TrueAllele; (2) the peak height of the alleles; and (3) the size of the peak shift needed to move peaks into the nearest bin. Here we report how we optimized the parameters such that the size of the ambiguous category was minimized, and both the number of miscalled genotypes in the good category and the useable genotypes in the bad category were negligible. This approach reduces the manual editing time and results in <1% miscalls.

Population genomics: laying the groundwork for genetic disease modeling and targeting

The family has proven the most appropriate unit with which to study Mendelian diseases. There are, however, certain limitations on the use of the family as a fundamental unit in the study of common diseases, most of which are complex genetic diseases. The groups that are most likely to yield the genetics of complex diseases are isolated populations with strong founder effects. Therefore, access to such populations is proving to be a precious resource in the work on the genetics of common diseases. The Icelandic population is an excellent population for the study of the genetics of common diseases; it is genetically homogeneous, with founder effects for many traits, and the genealogy of the entire nation is well documented back to the founding days. Furthermore, the nature of the Icelandic national health care system facilitates the assignment of phenotypes in the search for disease genes. Decode Genetics has begun to study of the genetics of 20 of the most common diseases in the Western parts of the world. The company has placed the groundwork for the construction of an encrypted database with information on the health care of the entire nation, genealogy of the entire nation, genotyping information with high density of markers on a large part of the nation (including typing for known disease genes), and resource use in the Icelandic health care system. The plan is to build the database with approval of participating individuals as well as Icelandic government and health care officials. The database will be used to model health care as viewed in the context of genetic predisposition to the development of disease. The database will also be used in the search for drug targets in complex diseases and in the solution of pharmacogenomic problems. Basing the company in Iceland directly benefits the population in terms of employment and return on investment as well as providing the health care system with an information resource which may be used in preventive medicine and in the optimization of health care in Iceland.

Molecular evolution of tau protein: implications for Alzheimer's disease

The brains of patients with Alzheimer's disease contain deposits of hyperphosphorylated tau proteins that have polymerized into insoluble fibrils. These deposits, in neurofibrillary tangles and dystrophic neurites, correlate with loss of cells and synapses, and consequently with dementia. Neurofibrillary pathology occurs in humans, as well as certain ungulates, including goats, sheep, and cows, but not in nonhuman primates. We hypothesize that the differences among species in the propensity to develop neurofibrillary pathology may be attributable to variations in the amino acid sequence of tau proteins. To investigate this hypothesis, we sequenced tau-encoding mRNA transcripts from the brains of rhesus monkey and domesticated goat and compared them with the known sequences of tau mRNAs from humans. The major difference we observed was that some tau mRNAs from rhesus monkey neocortex contain exon 8, whereas this exon has not been found in cortical tau from human or goat. Cows express very low levels of exon 8, and they tend to develop sparse neurofibrillary pathology with aging. We also found a transcribed tau-related pseudogene in rhesus monkey, which may be present in humans. We propose that differences in the expression of tau and tau-related protein sequences may underlie the predilection of human but not monkey brains to develop neurofibrillary degeneration.

Monoclonal antibodies and lectins as probes for investigation of the cell biology of human trabecular meshwork: a preliminary report

Two classes of ligand-binding molecules, (1) monoclonal antibodies (MABs) and (2) lectins, were used as probes to investigate the cell biology of human trabecular cells. We raised MABs by using human trabecular meshwork as the immunogen. One MAB (KAa25D7) consistently recognized two polypeptides with molecular weights of approximately 42 and 49 kilodaltons. The former comigrated with actin and the latter was shown by fractionation and extraction studies to be a macromolecular complex. Four lectins (wheat germ agglutinin, concanavalin A, Phaseolus vulgaris leukoagglutinin I, and Ulex europaeus agglutinin I) were used to identify the glycosylated polypeptides in human trabecular meshwork on Western blots. Compared to normal age-matched controls, there was a significant decrease in binding of the lectins to most polypeptides of the trabecular meshwork samples that were obtained from 4 eyes of 2 patients with primary open-angle glaucoma. Our preliminary studies show that lectins applied to Western blots and MABs are useful methods to probe the cell biology of human trabecular meshwork in health and disease.