A new mouse mutant of the Cdh23 gene with early-onset hearing loss facilitates evaluation of otoprotection drugs

Original Article

The Pharmacogenomics Journal advance online publication 20 July 2010; doi: 10.1038/tpj.2010.60

F Han1,4, H Yu1,4, C Tian1, H E Chen1, C Benedict-Alderfer1, Y Zheng1, Q Wang1,5, X Han1 and Q Y Zheng1,2,3

1. Department of Otolaryngology-HNS, Case Western Reserve University, Cleveland, OH, USA
2. Department of Genetics, Case Western Reserve University, Cleveland, OH, USA
3. Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA

Correspondence: Dr QY Zheng, Department of Otolaryngology-HNS, Case Western Reserve University, 11100 Euclid Avenue, LKS 5045, Cleveland, OH 44106, USA. E-mail: qing.zheng@case.edu

4These authors contributed equally to this work.

5Current address: Department of Otolaryngology and HNS, Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, 28 Fuxing Road, Beijing 100853 China.

Received 4 November 2009; Revised 4 June 2010; Accepted 14 June 2010; Published online 20 July 2010.
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Abstract

We report a novel mutation (erlong, erl) of the cadherin 23 (Cdh23) gene in a mouse model for DFNB12 characterized by progressive hearing loss beginning from postnatal day 27 (P27). Genetic and sequencing analysis revealed a 208 T >C transition causing an amino-acid substitution (70S–P). Caspase expression was upregulated in mutant inner ears. Hearing was preserved (up to 35-dB improvement) in pan-caspase inhibitor Z-VAD-FMK-treated mutants compared with untreated mutants (P<0.05). Outer hair cell (OHC) loss in the cochleae of Z-VAD-FMK-treated mutants was significantly reduced compared with those of untreated mice. Thus, the erl mutation can lead to hearing loss through apoptosis. This is the first genetic mouse model of hearing loss shown to respond to otoprotective drug therapy. The short interval from initial hearing loss to deafness (P27–P90) makes this model ideal for screening and validating otoprotective drugs.

Sirt1 improves healthy ageing and protects from metabolic syndrome-associated cancer

FROM NATURE COMMUNICATIONS | for ARTICLE click here.

Daniel Herranz,

Maribel Muñoz-Martin,

Marta Cañamero,

Francisca Mulero,

Barbara Martinez-Pastor,

Oscar Fernandez-Capetillo

& Manuel Serrano

Abstract

Genetic overexpression of protein deacetylase Sir2 increases longevity in a variety of lower organisms, and this has prompted interest in the effects of its closest mammalian homologue, Sirt1, on ageing and cancer. We have generated transgenic mice moderately overexpressing Sirt1 under its own regulatory elements (Sirt1-tg). Old Sirt1-tg mice present lower levels of DNA damage, decreased expression of the ageing-associated gene p16Ink4a, a better general health and fewer spontaneous carcinomas and sarcomas. These effects, however, were not sufficiently potent to affect longevity. To further extend these observations, we developed a metabolic syndrome-associated liver cancer model in which wild-type mice develop multiple carcinomas. Sirt1-tg mice show a reduced susceptibility to liver cancer and exhibit improved hepatic protection from both DNA damage and metabolic damage. Together, these results provide direct proof of the anti-ageing activity of Sirt1 in mammals and of its tumour suppression activity in ageing- and metabolic syndrome-associated cancer.

Original Article

The Pharmacogenomics Journal advance online publication 13 April 2010; doi: 10.1038/tpj.2010.28

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Intronic polymorphism in CYP3A4 affects hepatic expression and response to statin drugs

D Wang¹, Y Guo², S A Wrighton², G E Cooke³ and W Sadee¹

1. ¹Department of Pharmacology, Program in Pharmacogenomics, School of Biomedical Science, Ohio State University, Columbus, OH, USA
2. ²Department of Drug Disposition, Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, USA
3. ³Division of Cardiovascular Medicine, Department of Internal Medicine, College of Medicine, Ohio State University, Columbus, OH, USA

Correspondence: Dr D Wang, Department of Pharmacology, Program in Pharmacogenomics, School of Biomedical Science, College of Medicine, Ohio State University, Columbus, OH 43210, USA. E-mail:wang.808@osu.edu

Received 12 October 2009; Revised 10 March 2010; Accepted 16 March 2010; Published online 13 April 2010.

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Abstract

Cytochrome P450 3A4 (CYP3A4) metabolizes ~50% of all clinically used drugs. Although CYP3A4 expression varies widely between individuals, the contribution of genetic factors remains uncertain. In this study, we measured allelic CYP3A4 heteronuclear RNA (hnRNA) and mRNA expression in 76 human liver samples heterozygous for at least one of eight marker SNPs and found marked allelic expression imbalance (1.6–6.3-fold) in 10/76 liver samples (13%). This was fully accounted for by an intron 6 SNP (rs35599367, C>T), which also affected mRNA expression in cell culture on minigene transfections. CYP3A4 mRNA level and enzyme activity in livers with CC genotype were 1.7- and 2.5-fold, respectively, greater than in CT and TT carriers. In 235 patients taking stable doses of atorvastatin, simvastatin, or lovastatin for lipid control, carriers of the T allele required significantly lower statin doses (0.2–0.6-fold, P=0.019) than non-T carriers for optimal lipid control. These results indicate that intron 6 SNP rs35599367 markedly affects expression of CYP3A4 and could serve as a biomarker for predicting response to CYP3A4-metabolized drugs.

Keywords:

polymorphism; gene expression; CYP3A4; statin; allelic expression imbalance; cytochrome P450

Gene network analysis of oxidative stress-mediated drug sensitivity in resistant ovarian carcinoma cells

Original Article - click here for text.

The Pharmacogenomics Journal advance online publication 17 November 2009; doi: 10.1038/tpj.2009.49

A K Maiti¹

¹A&I, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA

Correspondence: Dr AK Maiti, A&I, Oklahoma Medical Research Foundation, 825 NE13th, Oklahoma City, OK 73104, USA. E-mails: amit-maiti@omrf.org, Akmit123@yahoo.com

Received 23 March 2009; Revised 21 August 2009; Accepted 24 September 2009; Published online 17 November 2009.

Drug resistance in cancer cells involves complex molecular mechanisms and ovarian carcinoma cells become resistant to chlorambucil (Cbl) after continuous treatment. This drug- and ionizing radiation-resistant cells have lower level of endogenous ROS (reactive oxygen species) compared with sensitive cells. Elevation of the cellular ROS level by exogenous ROS generation increases the sensitivity of Cbl to resistant cells. In contrast, antioxidants prevent the sensitization of resistant cells to Cbl by H₂O₂, COS (chronic oxidative stress) or NOO^-. The molecular mechanism of drug sensitivity with COS has been investigated by microarray gene expressions followed by gene network analysis and it reveals that a cdc42/rac1 guanine exchange factor, ARHGEF6, with p53 and DNA-Pkc (PRKDC) is central to induce apoptosis in Cbl^cos (Cbl with COS) cells. mRNA and protein levels of major gene network pathway differ significantly in Cbl^cos cells than in Cbl-treated cells. Moreover, DNA-PKc physically interacts with ARHGEF6 and p53 mostly in the nucleus of Cbl-treated cells, whereas in Cbl^cos-treated cells, its interactions are mostly in the cytoplasm. These results suggest that low doses of Cbl and very low doses of COS together kill Cbl-resistant ovarian carcinoma cells and ARHGEF6 signaling may have an instrumental role in induction of apoptosis in Cbl^cos cells.

Human Genome Sequencing Using Unchained Base Reads on Self-Assembling DNA Nanoarrays

SCIENCE - Published Online November 5, 2009 Science DOI: 10.1126/science.1181498

Reports - Click here for article.

Submitted on September 3, 2009
Accepted on October 23, 2009

Radoje Drmanac ^1*, Andrew B. Sparks ¹, Matthew J. Callow ¹, Aaron L. Halpern ¹, Norman L. Burns ¹, Bahram G. Kermani ¹, Paolo Carnevali ¹, Igor Nazarenko ¹, Geoffrey B. Nilsen ¹, George Yeung ¹, Fredrik Dahl ², Andres Fernandez ¹, Bryan Staker ¹, Krishna P. Pant ¹, Jonathan Baccash ¹, Adam P. Borcherding ¹, Anushka Brownley ¹, Ryan Cedeno ¹, Linsu Chen ¹, Dan Chernikoff ¹, Alex Cheung ¹, Razvan Chirita ¹, Benjamin Curson ¹, Jessica C. Ebert ¹, Coleen R. Hacker ¹, Robert Hartlage ¹, Brian Hauser ¹, Steve Huang ¹, Yuan Jiang ¹, Vitali Karpinchyk ¹, Mark Koenig ¹, Calvin Kong ¹, Tom Landers ¹, Catherine Le ¹, Jia Liu ¹, Celeste E. McBride ¹, Matt Morenzoni ¹, Robert E. Morey ³, Karl Mutch ¹, Helena Perazich ¹, Kimberly Perry ¹, Brock A. Peters ¹, Joe Peterson ¹, Charit L. Pethiyagoda ¹, Kaliprasad Pothuraju ¹, Claudia Richter ¹, Abraham M. Rosenbaum ⁴, Shaunak Roy ¹, Jay Shafto ¹, Uladzislau Sharanhovich ¹, Karen W. Shannon ⁵, Conrad G. Sheppy ¹, Michel Sun ¹, Joseph V. Thakuria ⁴, Anne Tran ¹, Dylan Vu ¹, Alexander Wait Zaranek ⁴, Xiaodi Wu ⁶, Snezana Drmanac ¹, Arnold R. Oliphant ¹, William C. Banyai ¹, Bruce Martin ¹, Dennis G. Ballinger ^1*, George M. Church ⁴, Clifford A. Reid ¹

¹ Complete Genomics, Inc., 2071 Stierlin Court, Mountain View, CA 94043, USA.
² Complete Genomics, Inc., 2071 Stierlin Court, Mountain View, CA 94043, USA.; Present address: Ion Torrent Systems, San Francisco, CA, USA.
³ Complete Genomics, Inc., 2071 Stierlin Court, Mountain View, CA 94043, USA.; Present address: San Diego State University, San Diego, CA, USA.
⁴ Department of Genetics, Harvard Medical School, Cambridge, MA, USA.
⁵ Complete Genomics, Inc., 2071 Stierlin Court, Mountain View, CA 94043, USA.; Present address: Life Technologies, Carlsbad, CA, USA.
⁶ School of Medicine, Washington University, St. Louis, St. Louis, MO, USA.

^* To whom correspondence should be addressed.
Radoje Drmanac , E-mail: rdrmanac@completegenomics.com
Dennis G. Ballinger , E-mail: dballinger@completegenomics.com

Genome sequencing of large numbers of individuals promises to advance the understanding, treatment, and prevention of human diseases, among other applications. We describe a genome sequencing platform that achieves efficient imaging and low reagent consumption with combinatorial probe anchor ligation (cPAL) chemistry to independently assay each base from patterned nanoarrays of self-assembling DNA nanoballs (DNBs). We sequenced three human genomes with this platform, generating an average of 45- to 87-fold coverage per genome and identifying 3.2 to 4.5 million sequence variants per genome. Validation of one genome data set demonstrates a sequence accuracy of about 1 false variant per 100 kilobases. The high-accuracy, affordable cost of $4,400 for sequencing consumables and scalability of this platform enable complete human genome sequencing for the detection of rare variants in large-scale genetic studies.

ADRA1A gene is associated with BMI in chronic schizophrenia patients exposed to antipsychotics

Original Article - click here to go to article.

The Pharmacogenomics Journal advance online publication 17 November 2009; doi: 10.1038/tpj.2009.55

Y-R Liu^1,2,11, E-W Loh^1,11, T-H Lan^1,3,4, S-F Chen⁵, Y-H Yu⁶, Y-H Chang^1,7, C-J Huang⁸, T-M Hu⁹, K-M Lin¹, Y-T Yao² and H-J Chiu¹⁰

1. Division of Mental Health and Addiction Medicine, Institute of Population Health Sciences, National Health Research Institutes, Miaoli County, Taiwan
2. Graduate Institute of Pathology, College of Medicine, National Taiwan University, Taipei, Taiwan
3. Faculty of Medicine, National Yang Ming University, Taipei, Taiwan
4. Department of Psychiatry, Taichung Veterans General Hospital, Taichung, Taiwan
5. Institute of Food Science and Technology, National Taiwan University, Taipei, Taiwan
6. Department of Life Sciences and Institute of Genome Sciences, National Yang Ming University, Taipei, Taiwan
7. Institute of Public Health and Department of Public Health, National Yang Ming University, Taipei, Taiwan
8. Department of Industrial Engineering and Engineering Management, College of Engineering, National Tsing-Hua University, HsinChu, Taiwan
9. Department of Psychiatry, Yu-Li Veterans Hospital, Hualian County, Taiwan
10. Jianan Mental Hospital, Tainan County, Taiwan

Correspondence: Dr H-J Chiu, Department of Health, Jianan Mental Hospital, #80, Lane 870, Jhung-Shan Road, Rende Township, Tainan 717, Taiwan. E-mail: chiu8@mail2000.com.tw

¹¹These authors contributed equally to this study.

Received 28 April 2009; Revised 28 July 2009; Accepted 23 September 2009; Published online 17 November 2009.

Abstract

Noradrenaline and adrenaline are neurotransmitters of the sympathetic nervous system that interact with various adrenergic receptor (ADR) subtypes, and this regulates the basal metabolic rate, thermogenesis and efficiency of energy utilization. We examined a possible role of the gene coding for ADRA1A receptor in weight gain in schizophrenia subjects exposed to antipsychotics. A total of 401 schizophrenia in-patients treated with antipsychotics for >2 years were recruited and a final 394 DNA samples were genotyped. Their body mass indexes (BMIs) were recorded for 12 months and parameterized to be correlated in regression. Among the 58 single-nucleotide polymorphisms (SNPs) genotyped, 44 valid SNPs, which had minor allele frequency 0.03, were analyzed in statistics. Linear regression model with age, gender, diabetes, use of typical antipsychotics and use of atypical antipsychotics as covariates, with or without gender interaction, showed evidence of associations between the ADRA1A gene and BMI. Most of the SNPs associated with BMI are located in the promoter and intron regions, and being female appeared to enhance the gene effect. Our study suggests that the ADRA1A gene is involved in weight gain among schizophrenia patients treated with antipsychotics. Further molecular dissection of the ADRA1A gene warrants better understanding on weight gain mechanisms in schizophrenia.

The modulating effect of the androgen receptor on craving in alcohol withdrawal of men is partially mediated by leptin

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Original Article

The Pharmacogenomics Journal advance online publication 3 November 2009; doi: 10.1038/tpj.2009.56

B Lenz 1,
H Frieling 1,2,
C Jacob 1,
A Heberlein 1,2,
J Kornhuber 1,
S Bleich 1,2 and
T Hillemacher 1,2

1. Department of Psychiatry and Psychotherapy, Friedrich-Alexander-University of Erlangen-Nuremberg, Erlangen, Germany
2. Department of Psychiatry, Socialpsychiatry and Psychotherapy, Hannover Medical School, Hannover, Germany

Correspondence: Dr B Lenz, Department of Psychiatry and Psychotherapy, Friedrich-Alexander-University of Erlangen-Nuremberg, Schwabachanlage 6-10, D-91054 Erlangen, Germany. E-mail: bernd.lenz@uk-erlangen.de

Received 3 August 2009; Revised 2 October 2009; Accepted 6 October 2009; Published online 3 November 2009.
Abstract

We reported recently that a functional relevant CAG trinucleotide repeat of the androgen receptor influences craving of men in alcohol withdrawal. It is known to modulate serum concentrations of leptin, which affects hypothalamic appetite regulation. Its plasma levels are elevated during chronic alcohol consumption, normalize within periods of abstinence and are associated with craving. The aim of this study was to further elucidate the role of leptin in mediating the effects of the mentioned polymorphism on craving in men undergoing alcohol withdrawal. We included 110 male in-patients who were admitted for detoxification treatment. Each one had an established diagnosis of alcohol dependence according to the DSM-IV. Our results show on the one hand negative associations between the number of CAG repeats and (i) leptin serum levels (P<0.01)>P<0.05),>P<0.001).>r=-0.144) accounting for 60% and indirect, leptin-mediated effects (r=-0.096) accounting for 40% of the total effect. Dysregulation of sexual hormones influences human metabolism and seems to affect leptin homeostasis. This report suggests that the investigated polymorphism mediates its effect on craving of men in alcohol withdrawal mostly through the regulation of leptin. Nevertheless future studies are needed to further explore the functionality of the androgen receptor gene in terms of craving.