Systems genetics analysis of pharmacogenomics variation during antidepressant treatment.

Selective serotonin reuptake inhibitors (SSRIs) are the most widely used antidepressants, but the efficacy of the treatment varies significantly among individuals. It is believed that complex genetic mechanisms play a part in this variation. We have used a network based approach to unravel the involved genetic components. Moreover, we investigated the potential difference in the genetic interaction networks underlying SSRI treatment response over time. We found four hub genes (ASCC3, PPARGC1B, SCHIP1 and TMTC2) with different connectivity in the initial SSRI treatment period (baseline to week 4) compared with the subsequent period (4-8 weeks after initiation), suggesting that different genetic networks are important at different times during SSRI treatment. The strongest interactions in the initial SSRI treatment period involved genes encoding transcriptional factors, and in the subsequent period genes involved in calcium homeostasis. In conclusion, we suggest a difference in genetic interaction networks between initial and subsequent SSRI response.

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.

Expanding the range of ZNF804A variants conferring risk of psychosis.

A trio of genome-wide association studies recently reported sequence variants at three loci to be significantly associated with schizophrenia. No sequence polymorphism had been unequivocally (P<5 × 10(-8)) associated with schizophrenia earlier. However, one variant, rs1344706[T], had come very close. This polymorphism, located in an intron of ZNF804A, was reported to associate with schizophrenia with a P-value of 1.6 × 10(-7), and with psychosis (schizophrenia plus bipolar disorder) with a P-value of 1.0 × 10(-8). In this study, using 5164 schizophrenia cases and 20,709 controls, we replicated the association with schizophrenia (odds ratio OR = 1.08, P = 0.0029) and, by adding bipolar disorder patients, we also confirmed the association with psychosis (added N = 609, OR = 1.09, P = 0.00065). Furthermore, as it has been proposed that variants such as rs1344706[T]-common and with low relative risk-may also serve to identify regions harboring less common, higher-risk susceptibility alleles, we searched ZNF804A for large copy number variants (CNVs) in 4235 psychosis patients, 1173 patients with other psychiatric disorders and 39,481 controls. We identified two CNVs including at least part of ZNF804A in psychosis patients and no ZNF804A CNVs in controls (P = 0.013 for association with psychosis). In addition, we found a ZNF804A CNV in an anxiety patient (P = 0.0016 for association with the larger set of psychiatric disorders).

Utility and adoption of CYP2D6 and CYP2C19 genotyping and its translation into psychiatric clinical practice.

OBJECTIVE: To describe clinical utility and adoption of routinely offered CYP2D6 and CYP2C19 genotyping (CYP test) in daily clinical practice of a psychiatric centre. METHOD: We described psychiatrists translations of CYP test results in patients with genotypes indicating poor or ultrarapid metabolizer status and treated with at least one CYP-dependent drug based on a retrospective review of medical records. Complementary, we used ethnographic participant observation and qualitative interviews to identify the barriers and incentives for the use of CYP test results. RESULTS: The cohort study included 101 of 1932 cases genotyped between 2003 and 2009. In 53 of 101 cases, test results were addressed in medical records. The most frequent response was to monitor drug concentrations (23 cases), observe for adverse events (18 cases) and adjust dosage (13 cases). In 33 of 101 cases, results were mentioned in the discharge letter. The ethnographic study indicated a poor adoption of the CYP test in clinical praxis. Test results were lost in workflows and knowledge transfer between laboratory and clinician and were absent from clinical routines, treatment conferences and educational fora. CONCLUSION: The CYP test has not gained foothold in clinical practice, and its potential clinical benefits are not utilized.

Use of a balloon catheter in management of the pelvic space following laparoscopic abdominoperineal excision.

AIM: Management of the pelvic space following laparoscopic abdominoperineal excision remains controversial. We describe a simple technique for obliteration of the pelvic space after laparoscopic abdominoperineal excision. METHOD: Pneumoperitoneum was re-established after completion of the operative procedure and a Foley catheter Ch. 24 was inserted through the right lower port under direct vision. The balloon of the catheter, placed in the presacral space, was filled with 50 ml of sterile saline and connected to passive drainage. The catheter was removed 10 days postoperatively. RESULTS: This technique was used in 15 patients with the median age of 74 years (range 63-86). Eleven patients were treated with preoperative chemoradiotherapy. The median length of hospital stay was 9 days (range 5-11). Two patients (13.3%) treated with chemoradiotherapy developed a superficial perineal wound infection and four patients (26.6%) had a deep pelvic abscess, which required surgical drainage. The median time of perineal wound healing was 3 months (range 2-8). The median follow-up time was 36 months (range 18-60). None of the patients developed perineal hernia or intestinal obstruction in the follow-up period. One patient underwent small bowel resection due to stenosis caused by radiation enteritis. There was no local recurrence, but two patients developed distant metastases after 12 months. CONCLUSION: Our results suggest that filling the pelvic cavity with a balloon catheter for 10 days results in the creation of a thin, fibrotic peritoneal layer which keeps the small intestine out of the pelvis and prevents loops of intestine adhering in the pelvic cavity.

Bioassay-guided isolation of apigenin with GABA-benzodiazepine activity from Tanacetum parthenium.

Extracts of Tanacetum parthenium are used in the prophylactic treatment of migraine and have also been used in Danish folk medicine for the treatment of epilepsy. An ethanol extract of T. parthenium showed high affinity for the GABA(A)-benzodiazepine site. An ethanol extract of T. parthenium was fractionated by VLC on silica and preparative C18 HPLC. Each step was monitored with the GABA(A)-benzodiazepine bioassay. The fractionation led to the isolation of apigenin, which may be responsible for CNS-effects of T. parthenium extracts.

Effective population size dynamics reveal impacts of historic climatic events and recent anthropogenic pressure in African elephants.

Two hundred years of elephant hunting for ivory, peaking in 1970-1980s, caused local extirpations and massive population declines across Africa. The resulting genetic impacts on surviving populations have not been studied, despite the importance of understanding the evolutionary repercussions of such human-mediated events on this keystone species. Using Bayesian coalescent-based genetic methods to evaluate time-specific changes in effective population size, we analysed genetic variation in 20 highly polymorphic microsatellite loci from 400 elephants inhabiting the greater Samburu-Laikipia region of northern Kenya. This area experienced a decline of between 80% and 90% in the last few decades when ivory harvesting was rampant. The most significant change in effective population size, however, occurred approximately 2500 years ago during a mid-Holocene period of climatic drying in tropical Africa. Contrary to expectations, detailed analyses of four contemporary age-based cohorts showed that the peak poaching epidemic in the 1970s caused detectable temporary genetic impacts, with genetic diversity rebounding as juveniles surviving the poaching era became reproductively mature. This study demonstrates the importance of climatic history in shaping the distribution and genetic history of a keystone species and highlights the utility of coalescent-based demographic approaches in unravelling ancestral demographic events despite a lack of ancient samples. Unique insights into the genetic signature of mid-Holocene climatic change in Africa and effects of recent poaching pressure on elephants are discussed.

Selectivity among dipeptidyl peptidases of the S9b family.

Dipeptidyl peptidase IV is a serine protease with an indirect role in antihyperglycaemia via degradation of the incretin hormones glucagon-like peptide 1 and glucose-dependent insulinotropic polypeptide. Inhibition of the DPP-IV is thus a potential therapeutic strategy for type 2 diabetes. In this study, we have investigated upon selectivity of dipeptidyl peptidase IV compared to two other members of the S9b family, dipeptidyl peptidase 8 and 9, based on kinetic analyses of the pancreatic peptide hormones neuropeptide Y and peptide YY. We report a striking 250-fold preference for cleavage of neuropeptide Y compared to peptide YY observed for DPP-8/-9, but not for DPP-IV. This difference appears to be linked to differences in the S1' pocket within the active site, particularly via flexibility of the oxyanion stabilizing residue Y547. These aspects are discussed in relation to available protein structures of DPP-IV and data on DPP-IV selective inhibitors.

Identification and evaluation of Peruvian plants used to treat malaria and leishmaniasis.

Households in eleven geographically and ethnically distinct areas in Loreto, Peru, were interviewed about their knowledge and use of plants, for the treatment of malaria and leishmaniasis. The survey resulted in 988 use records representing 118 plant-taxa for malaria and 289 use-records representing 85 plant-taxa for leishmaniasis. In both cases the 10 most frequently reported taxa accounted for about half of all the use-records. Plant material was collected and extracts were screened for in vitro inhibition of Plasmodium and Leishmania parasites. In the case of Plasmodium, extracts of 11 of the 13 most frequently reported plants showed significant growth inhibitory activity, while only a few plant extracts inhibited the growth of Leishmania parasites.

Population Pharmacokinetics of Methylphenidate in Healthy Adults Emphasizing Novel and Known Effects of Several Carboxylesterase 1 (CES1) Variants.

The aim of this study was to identify demographic and genetic factors that significantly affect methylphenidate (MPH) pharmacokinetics (PK), and may help explain interindividual variability and further increase the safety of MPH. d-MPH plasma concentrations, demographic covariates, and carboxylesterase 1 (CES1) genotypes were gathered from 122 healthy adults and analyzed using nonlinear mixed effects modeling. The structural model that best described the data was a two-compartment disposition model with absorption transit compartments. Novel effects of rs115629050 and CES1 diplotypes, as well as previously reported effects of rs71647871 and body weight, were included in the final model. Assessment of the independent and combined effect of CES1 covariates identified several specific risk factors that may result in severely increased d-MPH plasma exposure.

Possible involvement of endogenous retroviruses in the development of autoimmune disorders, especially multiple sclerosis.

Endogenous retroviruses are normal elements in vertebrate genomes. Many aspects concerning these genomic elements are still uncertain. In mice some endogenous retroviral sequences seem to be involved in the regulation of immune responses and there is even evidence that a retroviral element is responsible for the development of an autoimmune disease in a mouse strain. Whether endogenous retroviruses also contribute to the development of autoimmune diseases in humans is not known, but it is an interesting possibility. Below we briefly review endogenous retroviruses as potential etiological factors in autoimmunity and we discuss a possible association between MS and endogenous retroviruses on the basis of results from our laboratory.

Expression of endogenous retroviruses in blood mononuclear cells and brain tissue from multiple sclerosis patients.

OBJECTIVES: To compare the expression of endogenous retroviruses in MS patients and controls. MATERIAL AND METHODS: Peripheral blood mononuclear cells were obtained from 22 MS patients, a corresponding number of matched healthy donors and five patients with other central nervous system disease. Also brain specimens from MS patients and controls were obtained. Transcripts of various endogenous retroviruses in these samples were detected by RNA-PCR. RESULTS: Several endogenous retroviral sequences were transcribed in peripheral blood mononuclear cells and brain tissue from MS patients as well as controls. A composite transcript of an endogenous retrovirus and a zinc finger sequence was more frequently found in healthy donors than in MS patients. CONCLUSION: Some endogenous retroviruses are normally transcribed in white blood cells and brain tissue. The significance of those findings, which concerned the composite transcripts of the zinc finger sequence and its associated endogenous retrovirus is uncertain.

Localization of KCNQ5 in the normal and epileptic human temporal neocortex and hippocampal formation.

The KCNQ family of voltage-dependent non-inactivating K+ channels is composed of five members, four of which (KCNQ2-5) are expressed in the CNS and are responsible for the M-current. Mutations in either KCNQ2 or KCNQ3 lead to a hereditary form of dominant generalized epilepsy. Using specific antisera to the KCNQ2, KCNQ3 and KCNQ5 subunits, we found that KCNQ3 co-immunoprecipitated with KCNQ2 and KCNQ5 subunits, but no association was detected between KCNQ2 and KCNQ5. Intense KCNQ5 immunoreactivity was found to be widely distributed throughout the temporal neocortex and the hippocampal formation. In these structures, both pyramidal and non-pyramidal neurons and a population of glial cells in the white matter expressed the KCNQ5 subunit. In the sclerotic areas of the CA fields of epileptic patients, a marked loss of KCNQ5 immunoreactive pyramidal neurons was found in relation with the loss of neurons in these regions. However, in the regions adjacent to the sclerotic areas, the distribution and intensity of KCNQ5 immunostaining was apparently normal. The widespread distribution of KCNQ5 subunits, its persistence in pharmacoresistant epilepsy, along with the significant role of the M-current in the control of neuronal excitability, makes this protein a possible target for the development of anticonvulsant drugs.

Genetic susceptibility to multiple sclerosis: detection of polymorphic nucleotides and an intron in the 3' untranslated region of the major histocompatibility complex class II transactivator gene.

The master player in the transcriptional regulation of major histocompatibility (MHC) class II genes is a factor known as the MHC class II transactivator (CIITA). In this study we searched for polymorphisms in the 5' and 3' ends of the human CIITA gene to assess whether or not there is an association between alleles of this gene and multiple sclerosis (MS). Polymorphism screening based upon detection of single strand conformational changes (SSCP analysis) followed by sequencing revealed six single nucleotide variations, namely one in the promoter utilized by B cells and five in the 3' untranslated region (UTR) of the gene. Determination of alleles at these polymorphic sites was facilitated by treatment of amplified DNA fragments with a panel of appropriate restriction enzymes. The distributions of CIITA alleles did not differ between MS patients and control subjects (p > 0.05). After subgrouping of the patients into relapsing-remitting MS and primary progressive MS we found that the distribution of promoter alleles in the latter of these two patient groups differed from that of healthy control subjects (p = 0.04). There was no evidence of linkage disequilibrium between the polymorphic site in the B cell specific promoter and those in the 3' UTR. Based upon the polymorphic sites in the 3' UTR we identified two common CIITA haplotypes which were present at similar frequencies in patients and control subjects. Assuming that susceptibility to MS depends upon type of MHC class II molecule as well as the amounts of expressed class II molecules we tested for interaction between DR15 status and CIITA alleles. No such interaction was detected. Unexpectedly, we identified an intron in the 3' UTR of the human as well as the mouse CIITA gene. Due to the proximity of these introns to the termination codon in both the human and mouse CIITA gene, the mechanism for regulation of transcript stability known as nonsense-mediated decay is probably not involved in the posttranscriptional control of the expression of these genes. So far, the function and significance of the intron in the human and mouse CIITA genes are unknown.

A novel haplotype of the endogenous retrovirus, HRES-1, in patients with multiple sclerosis and healthy individuals.

In this study we searched for genetic variation in a segment of the human endogenous retrovirus, HRES-1, which encodes a potential autoantigen of 28 kDa. The purpose was to further investigate a possible association between this endogenous retrovirus and multiple sclerosis (MS). Fragments amplified from the HRES-1 region in question were subjected to single strand conformational analysis (SSCP analysis) and sequencing if the SSCP migration pattern suggested presence of polymorphisms. Using this approach a synonymous G --> C substitution, creating an NciI site, was found. Our sequence data also revealed an additional nucleotide in the region encoding the 28-kDa protein, i.e. a nucleotide not present in the first published sequence. This finding has implications for future studies of the 28-kDa HRES-1 protein since the additional nucleotide changes the reading frame of this protein. The detection of the Nci polymorphism allowed us to define a novel haplotype of HRES-1 distinct from the three previously known HRES-1 haplotypes. On comparison of the distribution of these four haplotypes in MS patients and healthy individuals we found a statistically significant difference (P = 0.03) but the contribution from the novel haplotype to this was modest.

Large number of polymorphic nucleotides and a termination codon in the env gene of the endogenous human retrovirus ERV3.

The terminal portion of the pol gene and the entire env gene of the human endogenous retrovirus ERV3 was screened for polymorphic nucleotides. For this purpose fragments amplified from the desired regions of ERV3 were subjected to single strand conformational analysis (SSCP analysis). Using this approach, we detected 13 polymorphic nucleotides, namely four in the pol gene and nine in the env gene. Three of the nucleotide substitutions were synonymous (not affecting the amino acid code). One of the non-synonymous nucleotide substitutions changed an arginine codon to a termination codon. The alleles at the different polymorphic sites could be arranged into five ERV3 haplotypes, two of which were new. To evaluate the possible significance of the termination codon, which precludes expression of a putative immunoregulatory factor, we examined samples of DNA from patients with multiple sclerosis, a demyelinating disease of presumed autoimmune etiology. We did not find an association between the ERV3 allele with the termination codon and this disease. Perhaps the presence of a stop codon combined with the high number of non-synonymous nucleotide substitutions in the reading frame of the env gene reflects absence of selective constraints during evolution. Obviously, our findings contradict the assumption that the reading frame of the ERV3 env gene has been conserved throughout evolution.

Sequencing and detection of polymorphisms in the 5' end of the human endogenous retroviral element, HRES-1.

Fragments of the 5' long terminal repeat (LTR) of the human endogenous retroviral element, HRES-1, were amplified. Single strand conformation analysis of these fragments in combination with sequencing revealed two polymorphic nucleotides, namely a HindIII and an Eco571 polymorphic site. Moreover, a number of differences from the previously published HRES-1 LTR sequence were detected. The linkage pattern of the two polymorphisms suggested the existence of three allelic forms of HRES-1. The frequencies of the genotypes and alleles of HRES-1 were determined in 158 individuals. The detection of HRES-1 markers may be useful to study associations between this endogenous retrovirus and various diseases.

Association between the endogenous retrovirus HRES-1 and multiple sclerosis in the United Kingdom--evidence of genetically different disease subsets?

In the present study we determined the frequencies of four haplotypes of the human T-cell lymphotropic virus-related endogenous sequence, HRES-1, in 110 multiple sclerosis (MS) patients and 100 healthy control subjects from the United Kingdom. We found evidence of an association between this endogenous retrovirus and MS (p < 0.01), in particular reflecting an increased frequency of HRES-1 haplotype 1 in the group of patients. There was no significant difference in the distribution of HRES-1 haplotypes between relapsing-remitting MS and the primary progressive form of the disease. The odds ratio for HRES-1 haplotype 1 and MS did not differ significantly between individuals positive for HLA-DR2 and DR2-negative individuals. Comparison of the observations from the present study with previous results implicated HRES-1 as a marker of genetic heterogeneity in MS.

Three allelic forms of the human endogenous retrovirus, ERV3, and their frequencies in multiple sclerosis patients and healthy individuals.

A possible association between the endogenous retrovirus, ERV3, and multiple sclerosis (MS) was examined. Samples of DNA from 74 MS patients and 159 healthy blood donors were subjected to enzymatic amplification followed by single strand conformational analysis to detect polymorphisms in the long terminal repeats of ERV3. Using this approach we detected six single base pair variations and a drop-out of a nucleotide. The linkage pattern of these base pair variations enabled us to define three allelic forms of ERV3. Polymorphisms exclusively present in the group of patients were not found and the distribution of the three allelic forms did not differ significantly between the group of controls and the MS group. Neither was there a significant difference in the distribution of the three alleles between MS patients with the progressive form and patients with relapsing/remitting MS. Our results are not in support of an association between ERV3 and MS.

Serum concentration of the aminopropeptide of type I procollagen in patients on haemo- and peritoneal dialysis.

Using an ELISA technique, the aminopropeptide of type I procollagen (PINP) was measured in serum from patients with chronic renal failure treated with haemodialysis (HD) (n = 19) or continuous ambulatory peritoneal dialysis (CAPD) (n = 14), and compared to the commonly used bone markers. The serum concentrations for PINP, compared to healthy controls were significantly increased in both the HD-group (p < 0.00001) and the CAPD-group (p < 0.00001). In the HD-group a close correlation was found between PINP and parathyroid hormone (PTH) (R(s) = 0.745; p = 0.00026) and between PINP and total alkaline phosphatase (R(s) = 0.623; p = 0.004), but in the CAPD-group the corresponding p-values were 0.17 and 0.06 only. No significant difference was found between the HD and CAPD patients with respect to serum levels of PINP, PTH, total alkaline phosphatase, or ionized calcium. In the HD-patients, a significantly higher level of serum phosphate was found compared to in the CAPD-patients. The present study demonstrates a close correlation between PTH, total alkaline phosphatase and PINP, which indicates that PINP might be used as a marker for evaluating increased bone turnover in patients with chronic renal failure treated with haemodialysis, and perhaps also in patients treated with peritoneal dialysis, and that the ideal biochemical parameters to analyse changes in bone metabolism in these patients may be a combination of the initiating hormone (PTH) and PINP as a marker of the effect of PTH on bone metabolism.