Thomas V O Hansen

Large recurrent microdeletions associated with schizophrenia.

Reduced fecundity, associated with severe mental disorders, places negative selection pressure on risk alleles and may explain, in part, why common variants have not been found that confer risk of disorders such as autism, schizophrenia and mental retardation. Thus, rare variants may account for a larger fraction of the overall genetic risk than previously assumed. In contrast to rare single nucleotide mutations, rare copy number variations (CNVs) can be detected using genome-wide single nucleotide polymorphism arrays. This has led to the identification of CNVs associated with mental retardation and autism. In a genome-wide search for CNVs associating with schizophrenia, we used a population-based sample to identify de novo CNVs by analysing 9,878 transmissions from parents to offspring. The 66 de novo CNVs identified were tested for association in a sample of 1,433 schizophrenia cases and 33,250 controls. Three deletions at 1q21.1, 15q11.2 and 15q13.3 showing nominal association with schizophrenia in the first sample (phase I) were followed up in a second sample of 3,285 cases and 7,951 controls (phase II). All three deletions significantly associate with schizophrenia and related psychoses in the combined sample. The identification of these rare, recurrent risk variants, having occurred independently in multiple founders and being subject to negative selection, is important in itself. CNV analysis may also point the way to the identification of additional and more prevalent risk variants in genes and pathways involved in schizophrenia.

Ancient human genome sequence of an extinct Palaeo-Eskimo

We report here the genome sequence of an ancient human. Obtained from ∼4,000-year-old permafrost-preserved hair, the genome represents a male individual from the first known culture to settle in Greenland. Sequenced to an average depth of 20×, we recover 79% of the diploid genome, an amount close to the practical limit of current sequencing technologies. We identify 353,151 high-confidence single-nucleotide polymorphisms (SNPs), of which 6.8% have not been reported previously. We estimate raw read contamination to be no higher than 0.8%. We use functional SNP assessment to assign possible phenotypic characteristics of the individual that belonged to a culture whose location has yielded only trace human remains. We compare the high-confidence SNPs to those of contemporary populations to find the populations most closely related to the individual. This provides evidence for a migration from Siberia into the New World some 5,500 years ago, independent of that giving rise to the modern Native Americans and Inuit.

Disruption of the neurexin 1 gene is associated with schizophrenia

Deletions within the neurexin 1 gene (NRXN1; 2p16.3) are associated with autism and have also been reported in two families with schizophrenia. We examined NRXN1, and the closely related NRXN2 and NRXN3 genes, for copy number variants (CNVs) in 2977 schizophrenia patients and 33 746 controls from seven European populations (Iceland, Finland, Norway, Germany, The Netherlands, Italy and UK) using microarray data. We found 66 deletions and 5 duplications in NRXN1, including a de novo deletion: 12 deletions and 2 duplications occurred in schizophrenia cases (0.47%) compared to 49 and 3 (0.15%) in controls. There was no common breakpoint and the CNVs varied from 18 to 420 kb. No CNVs were found in NRXN2 or NRXN3. We performed a Cochran-Mantel-Haenszel exact test to estimate association between all CNVs and schizophrenia (P = 0.13; OR = 1.73; 95% CI 0.81-3.50). Because the penetrance of NRXN1 CNVs may vary according to the level of functional impact on the gene, we next restricted the association analysis to CNVs that disrupt exons (0.24% of cases and 0.015% of controls). These were significantly associated with a high odds ratio (P = 0.0027; OR 8.97, 95% CI 1.8-51.9). We conclude that NRXN1 deletions affecting exons confer risk of schizophrenia.

Birt-Hogg-Dubé syndrome: diagnosis and management

Birt-Hogg-Dubé syndrome (BHD) is an autosomal dominant condition characterised clinically by skin fibrofolliculomas, pulmonary cysts, spontaneous pneumothorax, and renal cancer. The condition is caused by germline mutations in the FLCN gene, which encodes folliculin; the function of this protein is largely unknown, although FLCN has been linked to the mTOR pathway. The availability of DNA-based diagnosis has allowed insight into the great variation in expression of FLCN, both within and between families. Patients can present with skin signs and also with pneumothorax or renal cancer. Preventive measures are aimed mainly at early diagnosis and treatment of renal cancer. This Review gives an overview of current diagnosis and management of BHD.

RNA‐binding IMPs promote cell adhesion and invadopodia formation

Oncofetal RNA‐binding IMPs have been implicated in mRNA localization, nuclear export, turnover and translational control. To depict the cellular actions of IMPs, we performed a loss‐of‐function analysis, which showed that IMPs are necessary for proper cell adhesion, cytoplasmic spreading and invadopodia formation. Loss of IMPs was associated with a coordinate downregulation of mRNAs encoding extracellular matrix and adhesion proteins. The transcripts were present in IMP RNP granules, implying that IMPs were directly involved in the post‐transcriptional control of the transcripts. In particular, we show that a 5.0 kb CD44 mRNA contained multiple IMP‐binding sites in its 3′UTR, and following IMP depletion this species became unstable. Direct knockdown of the CD44 transcript mimicked the effect of IMPs on invadopodia, and we infer that CD44 mRNA stabilization may be involved in IMP‐mediated invadopodia formation. Taken together, our results indicate that RNA‐binding proteins exert profound effects on cellular adhesion and invasion during development and cancer formation.

Copy number variations of chromosome 16p13.1 region associated with schizophrenia

Deletions and reciprocal duplications of the chromosome 16p13.1 region have recently been reported in several cases of autism and mental retardation (MR). As genomic copy number variants found in these two disorders may also associate with schizophrenia, we examined 4345 schizophrenia patients and 35 079 controls from 8 European populations for duplications and deletions at the 16p13.1 locus, using microarray data. We found a threefold excess of duplications and deletions in schizophrenia cases compared with controls, with duplications present in 0.30% of cases versus 0.09% of controls (P=0.007) and deletions in 0.12 % of cases and 0.04% of controls (P>0.05). The region can be divided into three intervals defined by flanking low copy repeats. Duplications spanning intervals I and II showed the most significant (P=0.00010) association with schizophrenia. The age of onset in duplication and deletion carriers among cases ranged from 12 to 35 years, and the majority were males with a family history of psychiatric disorders. In a single Icelandic family, a duplication spanning intervals I and II was present in two cases of schizophrenia, and individual cases of alcoholism, attention deficit hyperactivity disorder and dyslexia. Candidate genes in the region include NTAN1 and NDE1. We conclude that duplications and perhaps also deletions of chromosome 16p13.1, previously reported to be associated with autism and MR, also confer risk of schizophrenia.

Dwarfism and Impaired Gut Development in Insulin-Like Growth Factor II mRNA-Binding Protein 1-Deficient Mice

ABSTRACT Insulin-like growth factor II mRNA-binding protein 1 (IMP1) belongs to a family of RNA-binding proteins implicated in mRNA localization, turnover, and translational control. Mouse IMP1 is expressed during early development, and an increase in expression occurs around embryonic day 12.5 (E12.5). To characterize the physiological role of IMP1, we generated IMP1-deficient mice carrying a gene trap insertion in the Imp1 gene. Imp1−/− mice were on average 40% smaller than wild-type and heterozygous sex-matched littermates. Growth retardation was apparent from E17.5 and remained permanent into adult life. Moreover, Imp1−/− mice exhibited high perinatal mortality, and only 50% were alive 3 days after birth. In contrast to most other organs, intestinal epithelial cells continue to express IMP1 postnatally, and Imp1−/− mice exhibited impaired development of the intestine, with small and misshapen villi and twisted colon crypts. Analysis of target mRNAs and global expression profiling at E12.5 indicated that Igf2 translation was downregulated, whereas the postnatal intestine showed reduced expression of transcripts encoding extracellular matrix components, such as galectin- 1, lumican, tenascin-C, procollagen transcripts, and the Hsp47 procollagen chaperone. Taken together, the results demonstrate that IMP1 is essential for normal growth and development. Moreover, IMP1 may facilitate intestinal morphogenesis via regulation of extracellular matrix formation.

Collection of blood, saliva, and buccal cell samples in a pilot study on the danish nurse cohort : Comparison of the response rate and quality of genomic DNA

In this study, we compared the response rates of blood, saliva, and buccal cell samples in a pilot study on the Danish nurse cohort and examined the quantity and quality of the purified genomic DNA. Our data show that only 31% of the requested participants delivered a blood sample, whereas 72%, 80%, and 76% delivered a saliva sample, buccal cell sample via mouth swabs, or buccal cell sample on FTA card, respectively. Analysis of purified genomic DNA by NanoDrop and agarose gel electrophoresis revealed that blood and saliva samples resulted in DNA with the best quality, whereas the DNA quality from buccal cells was low. Genotype and PCR analysis showed that DNA from 100% of the blood samples and 72% to 84% of the saliva samples could be genotyped or amplified, whereas none of the DNA from FTA cards and only 23% of the DNA from mouth swabs could be amplified and none of the DNA from swabs and 94% of the DNA from FTA cards could be genotyped. Our study shows that the response rate of self-collection saliva samples and buccal cell samples were much higher than the response rate of blood samples in our group of Danish nurses. However, only the quality of genomic DNA from saliva samples was comparable with blood samples as accessed by purity, genotyping, and PCR amplification. We conclude that the use of saliva samples is a good alternative to blood samples to obtain genomic DNA of high quality and it will increase the response rate considerably in epidemiologic studies. (Cancer Epidemiol Biomarkers Prev 2007;16(10):2072–6)

The genetic prehistory of the New World Arctic

Introduction Humans first peopled the North American Arctic (northern Alaska, Canada, and Greenland) around 6000 years ago, leaving behind a complex archaeological record that consisted of different cultural units and distinct ways of life, including the Early Paleo-Eskimos (Pre-Dorset/Saqqaq), the Late Paleo-Eskimos (Early Dorset, Middle Dorset, and Late Dorset), and the Thule cultures. Genetic origins of Paleo-Eskimos and Neo-Eskimos. All Paleo-Eskimos represent a single migration pulse from Siberia into the Americas, independent of the Neo-Eskimo Thule people (ancestors of modern-day Inuit) and the related extinct Sadlermiut population. The Siberian Birnirk people were likely cultural and genetic ancestors of modern-day Inuit. We also show ancient admixture between the Paleo- and Neo-Eskimo lineages, occurring at least 4000 years ago. Rationale We addressed the genetic origins and relationships of the various New World Arctic cultures to each other and to modern-day populations in the region. We obtained 26 genome-wide sequences and 169 mitochondrial DNA sequences from ancient human bone, teeth, and hair samples from Arctic Siberia, Alaska, Canada, and Greenland, and high-coverage genomes of two present-day Greenlandic Inuit, two Siberian Nivkhs, one Aleutian Islander, and two Athabascan Native Americans. Twenty-seven ancient samples were radiocarbon dated for accurate cultural assignment, of which 25 were corrected for marine reservoir effect to account for the dominant marine component in these individuals’ diets. Results Nuclear and mitochondrial DNA data unequivocally show that the Paleo-Eskimos are closer to each other than to any other present-day population. The Thule culture represents a distinct people that are genetic and cultural ancestors of modern-day Inuit. We additionally find the Siberian Birnirk culture (6th to 7th century CE) as likely cultural and genetic ancestors of the Thule. The extinct Sadlermiut people from the Hudson Bay region (15th to 19th century CE), considered to be Dorset remnants, are genetically closely related to Thule/Inuit, rather than the Paleo-Eskimos. Moreover, there is no evidence of matrilineal gene flow between Dorset or Thule groups with neighboring Norse (Vikings) populations settling in the Arctic around 1000 years ago. However, we do detect gene flow between the Paleo-Eskimo and Neo-Eskimo lineages, dating back to at least 4000 years. Conclusion Our study has a number of important implications: Paleo-Eskimos likely represent a single migration pulse into the Americas from Siberia, separate from the ones giving rise to the Inuit and other Native Americans, including Athabascan speakers. Paleo-Eskimos, despite showing cultural differences across time and space, constituted a single population displaying genetic continuity for more than 4000 years. On the contrary, the Thule people, ancestors of contemporary Inuit, represent a population replacement of the Paleo-Eskimos that occurred less than 700 years ago. The long-term genetic continuity of the Paleo-Eskimo gene pool and lack of evidence of Native American admixture suggest that the Saqqaq and Dorset people were largely living in genetic isolation after entering the New World. Thus, the Paleo-Eskimo technological innovations and changes through time, as evident from the archaeological record, seem to have occurred solely by movement of ideas within a single resident population. This suggests that cultural similarities and differences are not solid proxies for population movements and migrations into new and dramatically different environments, as is often assumed. Arctic genetics comes in from the cold Despite a well-characterized archaeological record, the genetics of the people who inhabit the Arctic have been unexplored. Raghavan et al. sequenced ancient and modern genomes of individuals from the North American Arctic (see the Perspective by Park). Analyses of these genomes indicate that the Arctic was colonized 6000 years ago by a migration separate from the one that gave rise to other Native American populations. Furthermore, the original paleo-inhabitants of the Arctic appear to have been completely replaced approximately 700 years ago. Science, this issue 10.1126/science.1255832; see also p. 1004 Early Arctic humans differed from both present-day Inuit and Native Americans. [Also see Perspective by Park] The New World Arctic, the last region of the Americas to be populated by humans, has a relatively well-researched archaeology, but an understanding of its genetic history is lacking. We present genome-wide sequence data from ancient and present-day humans from Greenland, Arctic Canada, Alaska, Aleutian Islands, and Siberia. We show that Paleo-Eskimos (~3000 BCE to 1300 CE) represent a migration pulse into the Americas independent of both Native American and Inuit expansions. Furthermore, the genetic continuity characterizing the Paleo-Eskimo period was interrupted by the arrival of a new population, representing the ancestors of present-day Inuit, with evidence of past gene flow between these lineages. Despite periodic abandonment of major Arctic regions, a single Paleo-Eskimo metapopulation likely survived in near-isolation for more than 4000 years, only to vanish around 700 years ago.

The Biology of Cholecystokinin and Gastrin Peptides

Cholecystokinin (CCK) and gastrin together constitute a family of homologous peptide hormones, which are both physiological ligands for the gastrin/CCK-B receptor, whereas the CCK-A receptor binds only sulfated CCK-peptides. CCK peptides are mainly produced in small intestinal endocrine I-cells and in cerebral neurons. CCK peptides regulate pancreatic enzyme secretion and growth, gallbladder contraction, intestinal motility, satiety and inhibit gastric acid secretion. Moreover, they are potent neurotransmitters in the brain and the periphery. CCK peptides are derived from proCCK and have the bioactive heptasequence -Tyr(SO4)-Met-Gly-Trp-Met-Asp-Phe-NH2 as their C-terminus. The dominant forms in plasma are CCK-58, CCK-33, CCK-22 and CCK-8, whereas CCK-8 is the major transmitterform. Due to scarcity of specific assays, knowledge about CCK in disease is still limited. Gastrin peptides are mainly synthetized in antroduodenal G-cells, from where they are released to blood to regulate gastric acid secretion and mucosal growth. Small amounts are synthetized further down the intestinal tract, in the foetal pancreas, in a few cerebral and peripheral neurons, in the pituitary gland and in spermatozoes. Gastrin peptides are derived from progastrin and all have the C-terminal bioactive hexasequence -Tyr (SO4)-Gly-Trp-Met-Asp-Phe-NH2. The major gastrin forms in tissue and plasma are gastrin-34 and gastrin-17, but also gastrin-71, -14 and -6 have been identified. Gastrin peptides are secreted in excessive amounts from gastrinomas and are expressed at lower levels in bronchogenic, colorectal, gastric, ovarian and pancreatic cancers. A carcinogenetic significance of gastrin peptides remains, however, to be proven.