Identification of a New Enhancer That Promotes Sox9 Expression by a Comparative Analysis of Mouse and Sry-Deficient Amami Spiny Rat

INTRODUCTION

Testis differentiation is initiated by the SRY gene on the Y chromosome in mammalian species. However, the Amami spiny rat, Tokudaia osimensis, lacks both the Y chromosome and the Sry gene and acquired a unique Sox9 regulatory mechanism via a male-specific duplication upstream of Sox9, without Sry. In general mammalian species, the SRY protein binds to a testis-specific enhancer to promote SOX9 gene expression. Several enhancers located upstream of Sox9/SOX9 have been reported in mice and humans. In particular, the binding of SRY to the highly conserved enhancer Enh13 is thought to be a common mechanism underlying testis differentiation and sex determination in mammals.

METHODS

Sequences of T. osimensis homologues of three Sox9 enhancers that were previously reported in mice, Enh8, Enh14, and Enh13, were determined. We performed in vitro assays to confirm enhancer activity involved in Sox9 regulation in T. osimensis.

RESULTS

T. osimensis Enh13 showed enhancer activity when co-transfected with NR5A1 and SOX9. Mouse Enh13 was activated by NR5A1 and SRY; however, T. osimensis Enh13 did not respond to SRY, even though the binding sites of SRY and NR5A1 were conserved. To identify the key sequence that is present in mouse but absent from T. osimensis, we performed reporter gene assays using vectors in which partial sequences of T. osimensis Enh13 were replaced with mouse sequences. For T. osimensis Enh13 in which the second half (approximately 430 bp) was replaced with the corresponding mouse sequence, activity in response to NR5A1 and SRY was recovered. Further, reporter assays revealed that multiple regions in the second half of the mouse Enh13 sequence are required for the response to NR5A1 and SRY. The latter 49 bp was particularly important and contained four binding sites for three transcription factors, POU2F1, HOXA3, and GATA1.

CONCLUSION

We showed that there are unknown sequences responsible for the interaction between NR5A1 and SRY and mEnh13 based on comparative analyses of Sry-dependent and Sry-independent species. Our comparative analyses revealed new molecular mechanisms underlying mammalian sex determination.

Exome-wide benchmark of difficult-to-sequence regions using short-read next-generation DNA sequencing

Next-generation DNA sequencing (NGS) in short-read mode has recently been used for genetic testing in various clinical settings. NGS data accuracy is crucial in clinical settings, and several reports regarding quality control of NGS data, primarily focusing on establishing NGS sequence read accuracy, have been published thus far. Variant calling is another critical source of NGS errors that remains unexplored at the single-nucleotide level despite its established significance. In this study, we used a machine-learning-based method to establish an exome-wide benchmark of difficult-to-sequence regions at the nucleotide-residue resolution using 10 genome sequence features based on real-world NGS data accumulated in The Genome Aggregation Database (gnomAD) of the human reference genome sequence (GRCh38/hg38). The newly acquired metric, designated the 'UNMET score,' along with additional lines of structural information from the human genome, allowed us to assess the sequencing challenges within the exonic region of interest using conventional short-read NGS. Thus, the UNMET score could provide a basis for addressing potential sequential errors in protein-coding exons of the human reference genome sequence GRCh38/hg38 in clinical sequencing.

Y Chromosome Genomic Variations and Biological Significance in Human Diseases and Health

The Y chromosome is a haploid genome unique to males with no genes essential for life. It is easily transmitted to the next generation without being repaired by recombination, even if a major genomic structural alteration occurs. On the other hand, the Y chromosome genome is basically a region transmitted only from father to son, reflecting a male-specific inheritance between generations. The Y chromosome exhibits genomic structural differences among different ethnic groups and individuals. The Y chromosome was previously thought to affect only male-specific phenotypes, but recent studies have revealed associations between the Y chromosomes and phenotypes common to both males and females, such as certain types of cancer and neuropsychiatric disorders. This evidence was discovered with the finding of the mosaic loss of the Y chromosome in somatic cells. This phenomenon is also affected by environmental factors, such as smoking and aging. In the past, functional analysis of the Y chromosome has been elucidated by assessing the function of Y chromosome-specific genes and the association between Y chromosome haplogroups and human phenotypes. These studies are currently being conducted intensively. Additionally, the recent advance of large-scale genome cohort studies has increased the amount of Y chromosome genomic information available for analysis, making it possible to conduct more precise studies of the relationship between genome structures and phenotypes. In this review, we will introduce recent analyses using large-scale genome cohort data and previously reported association studies between Y chromosome haplogroups and human phenotypes, such as male infertility, cancer, cardiovascular system traits, and neuropsychiatric disorders. The function and biological role of the Y chromosome in human phenotypes will also be discussed.

The Neo-X Does Not Form a Barr Body but Shows a Slightly Condensed Structure in the Okinawa Spiny Rat (Tokudaia muenninki)

X chromosome inactivation (XCI) is an essential mechanism for gene dosage compensation between male and female cells in mammals. The Okinawa spiny rat (Tokudaia muenninki) is a native rodent in Japan with XX/XY sex chromosomes, like most mammals; however, the X chromosome has acquired a neo-X region (Xp) by fusion with an autosome. We previously reported that dosage compensation has not yet evolved in the neo-X region; however, X-inactive-specific transcript (Xist) RNA (long non-coding RNA required for the initiation of XCI) is partially localized in the region. Here, we show that the neo-X region represents an early chromosomal state in the acquisition of XCI by analyses of heterochromatin and Barr body formation. We found no evidence for heterochromatin formation in the neo-X region by R-banding by acridine orange (RBA) assays and immunostaining of H3K27me3. Double-immunostaining of H3K27me3 and HP1, a component of the Barr body, revealed that the entire ancestral X chromosome region (Xq) showed a bipartite folded structure. By contrast, HP1 was not localized to the neo-X region. However, BAC-FISH revealed that the signals of genes on the neo-X region of the inactive X chromosome were concentrated in a narrow region. These findings indicated that although the neo-X region of the inactive X chromosome does not form a complete Barr body structure (e.g., it lacks HP1), it forms a slightly condensed structure. These findings combined with the previously reported partial binding of Xist RNA suggest that the neo-X region exhibits incomplete inactivation. This may represent an early chromosomal state in the acquisition of the XCI mechanism.

Optical Genome Mapping for a Patient with a Congenital Disorder and Chromosomal Translocation

We performed optical genome mapping (OGM), a newly developed cytogenetic technique, for a patient with a disorder of sex development (DSD) and a 46,XX,t(9;11)(p22;p13) karyotype. The results of OGM were validated using other methods. OGM detected a 9;11 reciprocal translocation and successfully mapped its breakpoints to small regions of 0.9-12.3 kb. OGM identified 46 additional small structural variants, only three of which were detected by array-based comparative genomic hybridization. OGM suggested the presence of complex rearrangements on chromosome 10; however, these variants appeared to be artifacts. The 9;11 translocation was unlikely to be associated with DSD, while the pathogenicity of the other structural variants remained unknown. These results indicate that OGM is a powerful tool for detecting and characterizing chromosomal structural variations, although the current methods of OGM data analyses need to be improved.

Genetic variants of G-protein coupled receptors associated with pubertal disorders

Background

The human hypothalamic-pituitary-gonadal (HPG) axis is the regulatory center for pubertal development. This axis involves six G-protein coupled receptors (GPCRs) encoded by KISS1R, TACR3, PROKR2, GNRHR, LHCGR, and FSHR.

Methods

Previous studies have identified several rare variants of the six GPCR genes in patients with pubertal disorders. In vitro assays and animal studies have provided information on the function of wild-type and variant GPCRs.

Main Findings

Of the six GPCRs, those encoded by KISS1R and TACR3 are likely to reside at the top of the HPG axis. Several loss-of-function variants in the six genes were shown to cause late/absent puberty. In particular, variants in KISS1R, TACR3, PROKR2, and GNRHR lead to hypogonadotropic hypogonadism in autosomal dominant, recessive, and oligogenic manners. Furthermore, a few gain-of-function variants of KISS1R, PROKR2, and LHCGR have been implicated in precocious puberty. The human HPG axis may contain additional GPCRs.

Conclusion

The six GPCRs in the HPG axis govern pubertal development through fine-tuning of hormone secretion. Rare sequence variants in these genes jointly account for a certain percentage of genetic causes of pubertal disorders. Still, much remains to be clarified about the molecular network involving the six GPCRs.

P-175 Relationship Between oocytes with sERC and Ploidy

Study question

We investigated the effects of the presence or absence of sERC on subsequent embryonic development and the ploidy of embryos.

Summary answer

The acquisition rates for euploidy embryos were similar to those for the embryos derived from oocytes without smooth endoplasmic reticulum cluster (sERC).

What is known already

The effects of the presence of sERC have been reported on embryonic development processes and pregnancy rate after embryo transfer (ET). In this study, we investigated the effects of the presence of sERC not only on embryonic development and pregnancy rate, but also on the ploidy of embryos from the oocytes with sERC.

Study design, size, duration

The subjects comprised women from whom oocytes were collected from January 2019 to November 2021. The group with the oocytes with sERC was designated as sERC(+), and the other group without sERC as sERC(-).

Participants/materials, setting, methods

Retrospective analysis was performed using a time-lapse system (EmbryoScope+). They were divided into two groups according to the presence of sERC. The groups were compared for fertilization rate, degeneration rate, abnormal fertilization rate (1PN, 3PN, 2.1PN), blastocyst rate, and good-quality-blastocyst rate after ICSI. The prognosis of the transferred embryos was followed up on. In addition, the embryos that were subjected to NGS analysis were investigated for effects of the presence of sERC on their ploidies.

Main results and the role of chance

The sERC(+) group exhibited a significantly lower fertilization rate (74.8%) compared to that of the sERC(-) group (82.4%, P < 0.01). The sERC(+) group exhibited a significantly higher abnormal fertilization rate (14.8%) compared to that of the sERC(-) group (6.6%, P < 0.01). The sERC(+) group showed a significantly higher blastocyst formation rate (57.4%) compared to the sERC(-) group (45.2%, P < 0.01). With respect to after ET prognosis, eight women gave birth with no confirmed congenital anomality. At the very least, the presence of sERC has been shown to have no effect on childbirth. The investigation on ploidy showed that the oocytes in the sERC(+) group included 24.2% euploidy (8/33), 9.1% mosaic (3/33), and 66.7% aneuploidy (22/33) embryos, while the oocytes in the sERC(-) group included 30.4% euploidy (137/451), 12.4% mosaic (56/451), and 57.2% aneuploidy (258/451) embryos. Thus, there was no difference due to the presence of sERC. Three out of the eight euploidy blastocysts in the sERC (+) group had been transferred, one of which reached childbirth.

Limitations, reasons for caution

PGT-A is still under clinical research in Japan.

Wider implications of the findings

Many reports suggested that oocytes with sERC can be used as embryos appropriate for transfer when they develop into blastocysts. The investigation into the ploidy of sERC(+)-derived blastocysts in this study confirmed that the presence of sERC did not affect the ploidy of embryos and that these embryos were transferable.

Trial registration number

not applicable

P-163 Effects of Early Modes of Cell Division on Blastocyst Ploidy

Study question

Abnormal cleavage (AC) has been confirmed at early development. We performed an NGS analysis on AC-derived blastocysts to investigate ploidy of the resulting embryos.

Summary answer

Group in which AC occurred during second division showed significantly higher rates for embryos appropriate for transfer than group where AC occurred during first division.

What is known already

Early division is important in embryogenesis and serves as an indicator of subsequent embryonic development. The occurrence of AC during early development can be identified with the advent of the time-lapse incubator, which in turn has led to difficulties in determining whether such AC-derived blastocysts can be used embryo transfer. In this study, we performed NGS analysis on AC-derived blastocysts to investigate the ploidy of the resulting embryos.

Study design, size, duration

The subjects comprised women from whom oocytes were collected for NGS analysis from January 2019 to November 2021. Retrospective analysis was performed using a time-lapse system (EmbryoScope+). Embryos were categorized into two groups: those with abnormal divisions observed during the first and second divisions and those in which normal divisions were observed in the same cycle.

Participants/materials, setting, methods

The group with AC observed was designated the AC group and the other with normal divisions as the Normal Cleavage (NC) group. Within the AC group, the subgroup with AC observed during first division was designated as the First (AC-F) group and the subgroup with AC observed during second division as the Second (AC-S) group for comparing the acquisition rates for euploidy embryos and embryos appropriate for transfer.

Main results and the role of chance

The AC group (17.3%) showed a significantly lower rate of good blastocyst formation than did the NC group (53.4%) (P < 0.01). The cutoff point for mosaicism was defined as > 20% of abnormal cells. Percentage <20 were classified as normal (euploid); >80, abnormal (aneuploidy); and 20-80, mosaic. Using a cutoff of 50% to differentiate ‘‘low’’ mosaics from ‘‘high’’ mosaics. There was no difference between the two groups in the acquisition rates for euploidy embryos (30.8-35.1%) and the embryos appropriate for transfer, including low-mosaic ones (44.3-46.1%). There also was no difference in the acquisition rates for euploidy embryos (24.0-37.0%) between the AC-F and AC-S groups. However, the AC-S group (59.3%) showed significantly higher acquisition rates than the AC-F group (32.0%) for the embryos appropriate for transfer, including low-mosaic ones (P < 0.05).

Limitations, reasons for caution

PGT-A is still under clinical research in Japan.

Wider implications of the findings

The group in which AC occurred during second division showed significantly higher acquisition rates for the embryos appropriate for transfer than the group in which AC occurred during first division. This indicates that the most important factor for identifying euploidy embryos is going through the two-cell phase during first division.

Trial registration number

not applicable

POS0755 SAFETY, TOLERABILITY, PHARMACOKINETICS, AND PHARMACODYNAMICS OF A SINGLE ORALLY ADMINISTERED DOSE OF ENPATORAN IN A PHASE I STUDY OF HEALTHY JAPANESE AND CAUCASIAN PARTICIPANTS

Background

Enpatoran, a novel, highly selective and potent dual toll-like receptor (TLR) 7 and TLR8 inhibitor, is in development for the treatment of autoimmune disorders including systemic and cutaneous lupus erythematosus. A first-in-human study in healthy participants has shown that enpatoran is well-tolerated and has a linear pharmacokinetic (PK) profile.

Objectives

To compare the PK parameters, safety, and tolerability of single ascending oral doses of enpatoran in a Phase I study in Japanese and Caucasian participants, and to explore a potential PK/pharmacodynamic (PD) relationship.

Methods

A single-centre, open-label, sequential dose group study enrolled healthy Japanese and Caucasian participants into three dose cohorts. Each Caucasian participant was matched by body weight (± 20%), height (± 15%) and sex to a Japanese participant. Participants received a single orally administered enpatoran dose of 100 mg, 200 mg, or 300 mg as a film-coated tablet under fasting conditions. PK parameters, (maximum plasma concentration [Cmax]; area under the plasma concentration–time curve (AUC) from time 0 to infinity [AUC0-inf]; AUC from time 0 to the last sampling time [AUC0-tlast]) determined using noncompartmental analysis, were estimated post-dose from Day 1–3. Safety was assessed from Day -1 to 8. PK (exposure) between the two ethnic groups was compared using an analysis of covariance (ANCOVA) model including ethnic group, natural log-transformed dose, and ethnic group by natural log dose interaction. Ex vivo secretion of cytokines (PD) under stimulated (using the TLR7/8 agonist, R848) and unstimulated conditions, was assessed pre- and post-dose. A panel of cytokines was analysed by multiplex immunoassay; IL-6 was considered the primary PD biomarker.

Results

The study included 36 male participants (18 Japanese and 18 Caucasian) with a mean (± SD) age of 35.1 (± 10.8) years and mean (± SD) body mass index of 23.1 (± 2.1) kg/m2. Each dose group included six Japanese and six Caucasian participants. The geometric mean enpatoran plasma exposure parameters (Cmax, AUC0-inf, and AUC0-tlast) were consistent between the two ethnic groups for each dose level (Table 1) and indicated dose proportionality. ANCOVA modeling demonstrated comparable exposure between the two groups (geometric least square mean ratio [Japanese/Caucasian;90% CI] of Cmax: 0.9409 [0.7855–1.1270]; AUC0-inf: 0.8959 [0.7497–1.0704] and AUC0-tlast: 0.8963 [0.7511–1.0695]). Treatment-emergent adverse events (TEAEs) were observed in six Japanese (n = 0, 100 mg; n = 3, 200 mg; n = 3, 300 mg) and four Caucasian (n = 1, 100 mg; n = 0, 200 mg; n = 3, 300 mg) participants. There we no serious TEAEs; most were mild and not dose dependent. Treatment-related TEAEs were mild diarrhoea, mild flatulence, and moderate headache. There were no deaths, withdrawals, or early terminations due to TEAEs. Administering enpatoran effectively reduced ex vivo stimulated cytokine release, with maximal inhibition observed at 2 hours post-dose (IL-6: mean ≥99%). High inhibition levels were sustained through 24 hours in a dose-dependent manner (IL-6: mean ~76–97%). The pattern of cytokine release inhibition was consistent across doses and ethnic groups.

Table 1.

PK parameters in Japanese and Caucasian participants at the three enpatoran dose levels

Parameter100 mg200 mg300 mgJapaneseCaucasianJapaneseCaucasianJapaneseCaucasianN = 6N = 6N = 6N = 6N = 6N = 6Cmax139175260245486490(ng/mL)AUC0-inf7749481910185028403330(h*ng/mL)AUC0-tlast7589311880183028103270(h*ng/mL)

All values are Geometric mean.

Cmax, maximum plasma concentration AUC0-inf, area under the plasma concentration–time curve (AUC) from time 0 to infinity; AUC0-tlast, AUC from time 0 to the last sampling time.

Conclusion

There were no relevant ethnic differences in PK, PD, and safety between healthy Japanese and Caucasian participants across a range of single oral enpatoran doses, thus supporting the inclusion of Asian participants in future global Phase II studies.

Acknowledgements

We would like to thank those who took part in the study. This study was sponsored by the healthcare business of Merck KGaA, Darmstadt, Germany (CrossRef Funder ID: 10.13039/100009945), who funded medical writing support by Bioscript Stirling Ltd.

Disclosure of Interests

Sathej Gopalakrishnan Shareholder of: Merck Healthcare KGaA, Employee of: Merck Healthcare KGaA, Axel Krebs-Brown Employee of: Merck Healthcare KGaA, Marco Nogueira Filho Employee of: Merck Healthcare KGaA, Yoshihiro Kuroki Employee of: Merck Biopharma Co., Ltd., Angelika Bachmann Employee of: Merck Healthcare KGaA, Andreas Becker Shareholder of: Merck Healthcare KGaA, Employee of: Merck Healthcare KGaA, Frank Schippers Employee of: Merck Healthcare KGaA, Markus Fluck Shareholder of: Merck Healthcare KGaA, Employee of: Merck Healthcare KGaA, Özkan Yalkinoglu Employee of: Merck Healthcare KGaA, Lena Klopp-Schulze Employee of: Merck Healthcare KGaA

Correction: Extra-mitochondrial citrate synthase initiates calcium oscillation and suppresses age-dependent sperm dysfunction

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Construction of JRG (Japanese reference genome) with single-molecule real-time sequencing

In recent genome analyses, population-specific reference panels have indicated important. However, reference panels based on short-read sequencing data do not sufficiently cover long insertions. Therefore, the nature of long insertions has not been well documented. Here, we assembled a Japanese genome using single-molecule real-time sequencing data and characterized insertions found in the assembled genome. We identified 3691 insertions ranging from 100 bps to ~10,000 bps in the assembled genome relative to the international reference sequence (GRCh38). To validate and characterize these insertions, we mapped short-reads from 1070 Japanese individuals and 728 individuals from eight other populations to insertions integrated into GRCh38. With this result, we constructed JRGv1 (Japanese Reference Genome version 1) by integrating the 903 verified insertions, totaling 1,086,173 bases, shared by at least two Japanese individuals into GRCh38. We also constructed decoyJRGv1 by concatenating 3559 verified insertions, totaling 2,536,870 bases, shared by at least two Japanese individuals or by six other assemblies. This assembly improved the alignment ratio by 0.4% on average. These results demonstrate the importance of refining the reference assembly and creating a population-specific reference genome. JRGv1 and decoyJRGv1 are available at the JRG website.

Researchers in Japan have assembled a Japanese reference genome, which includes sequences missing from the international reference genome, as well as others specific to East Asian populations. A team led by Masao Nagasaki and Masayuki Yamamoto sequenced a Japanese individual using a method, which produces longer sequences than previous technologies. Using this approach, they identified thousands of sequences spanning 2.5 million bases, which were absent in the international reference genome. Many of these were sequences able to move within the genome. They showed that the majority of these sequences are also present in early humans and chimpanzees, demonstrating that their absence from the current reference is due to deletions or limitations of earlier sequencing methodologies. In addition to providing a population-specific reference, these findings demonstrate the importance of continually improving the international reference genome.

Genome analyses for the Tohoku Medical Megabank Project towards establishment of personalized healthcare

Personalized healthcare (PHC) based on an individual's genetic make-up is one of the most advanced, yet feasible, forms of medical care. The Tohoku Medical Megabank (TMM) Project aims to combine population genomics, medical genetics and prospective cohort studies to develop a critical infrastructure for the establishment of PHC. To date, a TMM CommCohort (adult general population) and a TMM BirThree Cohort (birth+three-generation families) have conducted recruitments and baseline surveys. Genome analyses as part of the TMM Project will aid in the development of a high-fidelity whole-genome Japanese reference panel, in designing custom single-nucleotide polymorphism (SNP) arrays specific to Japanese, and in estimation of the biological significance of genetic variations through linked investigations of the cohorts. Whole-genome sequencing from >3,500 unrelated Japanese and establishment of a Japanese reference genome sequence from long-read data have been done. We next aim to obtain genotype data for all TMM cohort participants (>150,000) using our custom SNP arrays. These data will help identify disease-associated genomic signatures in the Japanese population, while genomic data from TMM BirThree Cohort participants will be used to improve the reference genome panel. Follow-up of the cohort participants will allow us to test the genetic markers and, consequently, contribute to the realization of PHC.

Identification of somatic mutations in postmortem human brains by whole genome sequencing and their implications for psychiatric disorders

AIM

Somatic mutations in the human brain are hypothesized to contribute to the functional diversity of brain cells as well as the pathophysiology of neuropsychiatric diseases. However, there are still few reports on somatic mutations in non-neoplastic human brain tissues. This study attempted to unveil the landscape of somatic mutations in the human brain.

METHODS

We explored the landscape of somatic mutations in human brain tissues derived from three individuals with no neuropsychiatric diseases by whole-genome deep sequencing at a depth of around 100. The candidate mutations underwent multi-layered filtering, and were validated by ultra-deep target amplicon sequencing at a depth of around 200 000.

RESULTS

Thirty-one somatic mutations were identified in the human brain, demonstrating the utility of whole-genome sequencing of bulk brain tissue. The mutations were enriched in neuron-expressed genes, and two-thirds of the identified somatic single nucleotide variants in the brain tissues were cytosine-to-thymine transitions, half of which were in CpG dinucleotides.

CONCLUSION

Our developed filtering and validation approaches will be useful to identify somatic mutations in the human brain. The vulnerability of neuron-expressed genes to mutational events suggests their potential relevance to neuropsychiatric diseases.

Biallelic mutations in SZT2 cause a discernible clinical entity with epilepsy, developmental delay, macrocephaly and a dysmorphic corpus callosum

Mutations in SZT2 were first reported in 2013 as a cause of early-onset epileptic encephalopathy. Because only five reports have been published to date, the clinical features associated with SZT2 remain unclear. We herein report an additional patient with biallelic mutations in SZT2. The proband, a four-year-old girl, showed developmental delay and seizures from two years of age. Her seizures were not intractable and readily controlled by valproate. She showed mildly dysmorphic facies with macrocephaly, high forehead, and hypertelorism, and also had pectus carinatum. An EEG showed epileptic discharges which rarely occurred. A brain MRI revealed a short and thick corpus callosum. Whole-exome sequencing detected compound heterozygous biallelic mutations (c.8596dup (p.Tyr2866Leufs^∗42) and c.2930-17_2930-3delinsCTCGTG) in SZT2, both of which were novel and predicted to be truncating. This case suggested a broad phenotypic spectrum arises from SZT2 mutations, forming a continuum from epileptic encephalopathy and severe developmental delay to mild intellectual disability without epilepsy. The characteristic thick and short corpus callosum observed in 7/8 cases with epilepsy, including the proband, but not in three non-syndromic cases, appears to be specific, and thus useful for indicating the possibility of SZT2 mutations. This feature has the potential to make loss of SZT2 a clinically discernible disorder despite a wide clinical spectrum.

Surfactant protein D inhibits activation of non-small cell lung cancer-associated mutant EGFR and affects clinical outcomes of patients

Tyrosine kinase inhibitor (TKI)-sensitive and TKI-resistant mutations of epidermal growth factor receptor (EGFR) are associated with lung adenocarcinoma. EGFR mutants were previously shown to exhibit ligand-independent activation. We have previously demonstrated that pulmonary surfactant protein D (SP-D, SFTPD) suppressed wild-type EGFR signaling by blocking ligand binding to EGFR. We herein demonstrate that SFTPD downregulates ligand-independent signaling in cells harboring EGFR mutations such as TKI-sensitive exon 19 deletion (Ex19del) and L858R mutation as well as TKI-resistant T790M mutation, subsequently suppressing cellular growth and motility. Lectin blotting and ligand blotting in lung cancer cell lines suggested that EGFR mutants express oligomannose-type N-glycans and interact with SFTPD directly. Cross-linking assay indicated that SFTPD inhibits ligand-independent dimerization of EGFR mutants. We also demonstrated that SFTPD reduced dimerization-independent phosphorylation of Ex19del and T790M EGFR mutants using point mutations that disrupted the asymmetric dimer interface. It was confirmed that SFTPD augmented the viability-suppressing effects of EGFR-TKIs. Furthermore, retrospective analysis of 121 patients with lung adenocarcinoma to examine associations between serum SFTPD levels and clinical outcome indicated that in TKI-treated patients with lung cancer harboring EGFR mutations, including Ex19del or L858R, high serum SFTPD levels correlated with a lower number of distant metastases and prolonged overall survival and progression-free survival. These findings suggest that SFTPD downregulates both TKI-sensitive and -resistant EGFR mutant signaling, and SFTPD level is correlated with clinical outcome. These findings illustrate the use of serum SFTPD level as a potential marker to estimate the efficacy of EGFR-TKIs.

Genome evolution in the allotetraploid frog Xenopus laevis

To explore the origins and consequences of tetraploidy in the African clawed frog, we sequenced the Xenopus laevis genome and compared it to the related diploid X. tropicalis genome. We demonstrate the allotetraploid origin of X. laevis by partitioning its genome into two homeologous subgenomes, marked by distinct families of “fossil” transposable elements. Based on the activity of these elements and the age of hundreds of unitary pseudogenes, we estimate that the two diploid progenitor species diverged ~34 million years ago (Mya) and combined to form an allotetraploid ~17–18 Mya. 56% of all genes are retained in two homeologous copies. Protein function, gene expression, and the amount of flanking conserved sequence all correlate with retention rates. The subgenomes have evolved asymmetrically, with one chromosome set more often preserving the ancestral state and the other experiencing more gene loss, deletion, rearrangement, and reduced gene expression.

Initiation of recombination suppression and PAR formation during the early stages of neo-sex chromosome differentiation in the Okinawa spiny rat, Tokudaia muenninki

Background

Sex chromosomes of extant eutherian species are too ancient to reveal the process that initiated sex-chromosome differentiation. By contrast, the neo-sex chromosomes generated by sex-autosome fusions of recent origin in Tokudaia muenninki are expected to be evolutionarily ‘young’, and therefore provide a good model in which to elucidate the early phases of eutherian sex chromosome evolution. Here we describe the genomic evolution of T. muenninki in neo-sex chromosome differentiation.

Results

FISH mapping of a T. muenninki male, using 50 BAC clones as probes, revealed no chromosomal rearrangements between the neo-sex chromosomes. Substitution-direction analysis disclosed that sequence evolution toward GC-richness, which positively correlates with recombination activity, occurred in the peritelomeric regions, but not middle regions of the neo-sex chromosomes. In contrast, the sequence evolution toward AT-richness was observed in those pericentromeric regions. Furthermore, we showed genetic differentiation between the pericentromeric regions as well as an accelerated rate of evolution in the neo-Y region through the detection of male-specific substitutions by gene sequencing in multiple males and females, and each neo-sex–derived BAC sequencing.

Conclusions

Our results suggest that recombination has been suppressed in the pericentromeric region of neo-sex chromosomes without chromosome rearrangement, whereas high levels of recombination activity is limited in the peritelomeric region of almost undifferentiated neo-sex chromosomes. We conclude that PAR might have been formed on the peritelomeric region of sex chromosomes as an independent event from spread of recombination suppression during the early stages of sex chromosome differentiation.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-015-0514-y) contains supplementary material, which is available to authorized users.

Rare variant discovery by deep whole-genome sequencing of 1,070 Japanese individuals

The Tohoku Medical Megabank Organization reports the whole-genome sequences of 1,070 healthy Japanese individuals and construction of a Japanese population reference panel (1KJPN). Here we identify through this high-coverage sequencing (32.4 × on average), 21.2 million, including 12 million novel, single-nucleotide variants (SNVs) at an estimated false discovery rate of <1.0%. This detailed analysis detected signatures for purifying selection on regulatory elements as well as coding regions. We also catalogue structural variants, including 3.4 million insertions and deletions, and 25,923 genic copy-number variants. The 1KJPN was effective for imputing genotypes of the Japanese population genome wide. These data demonstrate the value of high-coverage sequencing for constructing population-specific variant panels, which covers 99.0% SNVs of minor allele frequency ≥0.1%, and its value for identifying causal rare variants of complex human disease phenotypes in genetic association studies.

The Tohoku Medical Megabank Organization establishes a biobank with detailed patient health care and genome information. Here the authors analyse whole-genome sequences of 1,070 Japanese individuals, allowing them to catalogue 21 million single-nucleotide variants including 12 million novel ones.

Comparative genome and transcriptome analyses of the social amoeba Acytostelium subglobosum that accomplishes multicellular development without germ-soma differentiation

BACKGROUND

Social amoebae are lower eukaryotes that inhabit the soil. They are characterized by the construction of a starvation-induced multicellular fruiting body with a spore ball and supportive stalk. In most species, the stalk is filled with motile stalk cells, as represented by the model organism Dictyostelium discoideum, whose developmental mechanisms have been well characterized. However, in the genus Acytostelium, the stalk is acellular and all aggregated cells become spores. Phylogenetic analyses have shown that it is not an ancestral genus but has lost the ability to undergo cell differentiation.

RESULTS

We performed genome and transcriptome analyses of Acytostelium subglobosum and compared our findings to other available dictyostelid genome data. Although A. subglobosum adopts a qualitatively different developmental program from other dictyostelids, its gene repertoire was largely conserved. Yet, families of polyketide synthase and extracellular matrix proteins have not expanded and a serine protease and ABC transporter B family gene, tagA, and a few other developmental genes are missing in the A. subglobosum lineage. Temporal gene expression patterns are astonishingly dissimilar from those of D. discoideum, and only a limited fraction of the ortholog pairs shared the same expression patterns, so that some signaling cascades for development seem to be disabled in A. subglobosum.

CONCLUSIONS

The absence of the ability to undergo cell differentiation in Acytostelium is accompanied by a small change in coding potential and extensive alterations in gene expression patterns.

Mutations in the testis-specific enhancer of SOX9 in the SRY independent sex-determining mechanism in the genus Tokudaia

SRY (sex-determining region Y) is widely conserved in eutherian mammals as a sex-determining gene located on the Y chromosome. SRY proteins bind to the testis-specific enhancer of SOX9 (TES) with SF1 to upregulate SOX9 expression in undifferentiated gonads of XY embryos of humans and mice. The core region within TES, named TESCO, is an important enhancer for mammalian sex determination. We show that TESCO of the genus Tokudaia lost enhancer activity caused by mutations in its SRY and SF1 binding sites. Two species of Tokudaia do not have the Y chromosome or SRY, and one species has multiple SRYs located on the neo-Y chromosome consisting of the Y fused with an autosome. The sequence of Tokudaia TESCO exhibited more than 83% identity with mouse TESCO, however, nucleotide substitution(s) were found in two out of three SRY binding sites and in five out of six SF1 binding sites. TESCO of all species showed low enhancer activity in cells co-transfected with SRY and SF1, and SOX9 and SF1 in reporter gene assays. Mutated TESCO, in which nucleotide substitutions found in SRY and SF1 binding sites were replaced with mouse sequence, recovered the activity. Furthermore, SRYs of the SRY-positive species could not activate the mutated TESCO or mouse TESCO, suggesting that SRYs lost function as a sex-determining gene any more. Our results indicate that the SRY dependent sex-determining mechanism was lost in a common ancestor of the genus Tokudaia caused by nucleotide substitutions in SRY and SF1 binding sites after emergence of a new sex-determining gene. We present the first evidence for an intermediate stage of the switchover from SRY to a new sex-determining gene in the evolution of mammalian sex-determining mechanism.

Monozygotic Twins with Discordant Sex

A nine-year-old girl with short stature was referred to the department of pediatrics at Kyushu University. The clinical diagnosis was Turner syndrome; karyotypic analysis performed on peripheral blood, using GTG techniques, demonstrated a 45,X/47,XYY (17:83) mosaicism. Her twin brother, a phenotypically normal male, had the same karyotype; 45,X/47,XYY (3:97) on peripheral blood. Their skin fibroblast karyotypes showed the same mosaicism, ie. 45,X/47,XYY (41:59 and 31:69 respectively). On eleven biochemical genetic markers the twin pair were concordant, thus the likelihood of monozygosity was 0.99527034. In addition, the analysis of variable number of tandem repeat (VNTR) markers revealed the likelihood of monozygosity to be 0.99944386. The most plausible explanation of the X/XYY mosaicism was nondisjunction of the Y in the first cleavage division of the 46,XY zygote. A disproportionate rate of cell populations with 45,X and 47.XYY in the twinning process of the X/XYY embryo, especially in the germ lines, would result in discordant sex in twin pairs.

Co-option of Sox3 as the male-determining factor on the Y chromosome in the fish Oryzias dancena

Sex chromosomes harbour a primary sex-determining signal that triggers sexual development of the organism. However, diverse sex chromosome systems have been evolved in vertebrates. Here we use positional cloning to identify the sex-determining locus of a medaka-related fish, Oryzias dancena, and find that the locus on the Y chromosome contains a cis-regulatory element that upregulates neighbouring Sox3 expression in developing gonad. Sex-reversed phenotypes in Sox3(Y) transgenic fish, and Sox3(Y) loss-of-function mutants all point to its critical role in sex determination. Furthermore, we demonstrate that Sox3 initiates testicular differentiation by upregulating expression of downstream Gsdf, which is highly conserved in fish sex differentiation pathways. Our results not only provide strong evidence for the independent recruitment of Sox3 to male determination in distantly related vertebrates, but also provide direct evidence that a novel sex determination pathway has evolved through co-option of a transcriptional regulator potentially interacted with a conserved downstream component.

In vivo function and evolution of the eutherian-specific pluripotency marker UTF1

Embryogenesis in placental mammals is sustained by exquisite interplay between the embryo proper and placenta. UTF1 is a developmentally regulated gene expressed in both cell lineages. Here, we analyzed the consequence of loss of the UTF1 gene during mouse development. We found that homozygous UTF1 mutant newborn mice were significantly smaller than wild-type or heterozygous mutant mice, suggesting that placental insufficiency caused by the loss of UTF1 expression in extra-embryonic ectodermal cells at least in part contributed to this phenotype. We also found that the effects of loss of UTF1 expression in embryonic stem cells on their pluripotency were very subtle. Genome structure and sequence comparisons revealed that the UTF1 gene exists only in placental mammals. Our analyses of a family of genes with homology to UTF1 revealed a possible mechanism by which placental mammals have evolved the UTF1 genes.

Phasic synaptic incorporation of GluR2-lacking AMPA receptors at gonadotropin-releasing hormone neurons is involved in the generation of the luteinizing hormone surge in female rats

Reproductive success depends on a robust and appropriately timed preovulatory luteinizing hormone (LH) surge, which is induced by the activation of gonadotropin-releasing hormone (GnRH) neurons in response to positive feedback from increasing estrogen levels. Here we document an increase in postsynaptic GluR2-lacking Ca2+ -permeable AMPA-type glutamate receptors (CP-AMPARs) at synapses on GnRH neurons on the day of proestrus in rats, coincident with the increase in estrogen levels. Functional blockade of CP-AMPARs depressed the synaptic responses only on the day of proestrus and concomitantly attenuated the LH surge. Thus, the phasic synaptic incorporation of postsynaptic CP-AMPARs on GnRH neurons is involved in the generation of the LH surge.

Evolutionary history of novel genes on the tammar wallaby Y chromosome: Implications for sex chromosome evolution

We report here the isolation and sequencing of 10 Y-specific tammar wallaby (Macropus eugenii) BAC clones, revealing five hitherto undescribed tammar wallaby Y genes (in addition to the five genes already described) and several pseudogenes. Some genes on the wallaby Y display testis-specific expression, but most have low widespread expression. All have partners on the tammar X, along with homologs on the human X. Nonsynonymous and synonymous substitution ratios for nine of the tammar XY gene pairs indicate that they are each under purifying selection. All 10 were also identified as being on the Y in Tasmanian devil (Sarcophilus harrisii; a distantly related Australian marsupial); however, seven have been lost from the human Y. Maximum likelihood phylogenetic analyses of the wallaby YX genes, with respective homologs from other vertebrate representatives, revealed that three marsupial Y genes (HCFC1X/Y, MECP2X/Y, and HUWE1X/Y) were members of the ancestral therian pseudoautosomal region (PAR) at the time of the marsupial/eutherian split; three XY pairs (SOX3/SRY, RBMX/Y, and ATRX/Y) were isolated from each other before the marsupial/eutherian split, and the remaining three (RPL10X/Y, PHF6X/Y, and UBA1/UBE1Y) have a more complex evolutionary history. Thus, the small marsupial Y chromosome is surprisingly rich in ancient genes that are retained in at least Australian marsupials and evolved from testis-brain expressed genes on the X.

Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development

BACKGROUND

We present the genome sequence of the tammar wallaby, Macropus eugenii, which is a member of the kangaroo family and the first representative of the iconic hopping mammals that symbolize Australia to be sequenced. The tammar has many unusual biological characteristics, including the longest period of embryonic diapause of any mammal, extremely synchronized seasonal breeding and prolonged and sophisticated lactation within a well-defined pouch. Like other marsupials, it gives birth to highly altricial young, and has a small number of very large chromosomes, making it a valuable model for genomics, reproduction and development.

RESULTS

The genome has been sequenced to 2 × coverage using Sanger sequencing, enhanced with additional next generation sequencing and the integration of extensive physical and linkage maps to build the genome assembly. We also sequenced the tammar transcriptome across many tissues and developmental time points. Our analyses of these data shed light on mammalian reproduction, development and genome evolution: there is innovation in reproductive and lactational genes, rapid evolution of germ cell genes, and incomplete, locus-specific X inactivation. We also observe novel retrotransposons and a highly rearranged major histocompatibility complex, with many class I genes located outside the complex. Novel microRNAs in the tammar HOX clusters uncover new potential mammalian HOX regulatory elements.

CONCLUSIONS

Analyses of these resources enhance our understanding of marsupial gene evolution, identify marsupial-specific conserved non-coding elements and critical genes across a range of biological systems, including reproduction, development and immunity, and provide new insight into marsupial and mammalian biology and genome evolution.

JTT-130, a novel intestine-specific inhibitor of microsomal triglyceride transfer protein, ameliorates impaired glucose and lipid metabolism in Zucker diabetic fatty rats

AIM

Microsomal triglyceride transfer protein (MTP) takes part in the mobilization of triglyceride-rich lipoproteins from enterocytes and hepatocytes. We investigated the effects of JTT-130, a novel intestine-specific MTP inhibitor, on impaired glucose and lipid metabolism in Zucker diabetic fatty (ZDF) rats.

METHODS

Male ZDF rats were fed a regular powdered diet with or without JTT-130 as a food admixture (0.01-0.02%) for 6 weeks. Food intake, body weight, blood biochemical parameters, fecal lipid contents, hepatic lipid contents, tissue mRNA levels and glucose utilization in adipose tissues were assessed. An intraperitoneal glucose tolerance test (IPGTT) and histological analysis of the pancreas were performed.

RESULTS

JTT-130 treatment decreased food intake, glycated hemoglobin, plasma levels of glucose, triglycerides and total cholesterol, hepatic levels of triglycerides and cholesterol and hepatic mRNA levels of glucose-6-phosphatase, phosphoenolpyruvate carboxykinase and fructose-1,6-bisphosphatase. JTT-130 treatment increased fecal levels of free fatty acids and cholesterol, plasma levels of glucagon-like peptide-1 and peptide YY, mRNA levels of glucose transporter 4 (GLUT4) and lipoprotein lipase in adipose tissues and GLUT4 in muscle and glucose utilization in adipose tissues. Plasma insulin decreased after 2 weeks and increased after 4 weeks of JTT-130 treatment. Plasma glucose in the JTT-130-treated rats was lower with higher plasma insulin than in the control rats during the IPGTT. The islets of the JTT-130-treated rats were larger and contained more insulin than those of the control rats.

CONCLUSIONS

JTT-130 ameliorates impaired glucose and lipid metabolism in the ZDF rats thereby suggesting that JTT-130 could be useful for prevention and treatment of type 2 diabetes.

Identification of tammar wallaby SIRH12, derived from a marsupial-specific retrotransposition event

In humans and mice, there are 11 genes derived from sushi-ichi related retrotransposons, some of which are known to play essential roles in placental development. Interestingly, this family of retrotransposons was thought to exist only in eutherian mammals, indicating their significant contributions to the eutherian evolution, but at least one, PEG10, is conserved between marsupials and eutherians. Here we report a novel sushi-ichi retrotransposon-derived gene, SIRH12, in the tammar wallaby, an Australian marsupial species of the kangaroo family. SIRH12 encodes a protein highly homologous to the sushi-ichi retrotransposon Gag protein in the tammar wallaby, while SIRH12 in the South American short-tailed grey opossum is a pseudogene degenerated by accumulation of multiple nonsense mutations. This suggests that SIRH12 retrotransposition occurred only in the marsupial lineage but acquired and retained some as yet unidentified novel function, at least in the lineage of the tammar wallaby.

JTT-130, a novel intestine-specific inhibitor of microsomal triglyceride transfer protein, suppresses high fat diet-induced obesity and glucose intolerance in Sprague-Dawley rats

AIM

Microsomal triglyceride transfer protein (MTP) takes part in the mobilization and secretion of triglyceride-rich lipoproteins from enterocytes and hepatocytes. We investigated the effects of JTT-130, a novel intestine-specific MTP inhibitor, on high fat diet-induced obesity and glucose intolerance.

METHODS

Male Sprague-Dawley rats were fed a 3.1% fat diet or a 35% fat diet with or without JTT-130 as a food admixture (0.029%). Food intake, body weight, abdominal fat, hepatic triglyceride, faecal free fatty acids and plasma levels of glucagon-like peptide-1 (GLP-1) and peptide YY (PYY) were assessed. Plasma levels of glucose and insulin were measured during intraperitoneal glucose tolerance tests. In addition, indirect calorimetry was performed on rats fed with a 35% fat diet.

RESULTS

JTT-130 treatment decreased body weights, abdominal fat and hepatic triglyceride with suppression of food intake and elevation of faecal free fatty acids and plasma GLP-1 and PYY levels in rats fed with the 35% fat diet, whereas no significant effects on these parameters except for increased faecal free fatty acids were observed in rats fed with the 3.1% fat diet. JTT-130 treatment decreased plasma levels of glucose and insulin during intraperitoneal glucose tolerance tests on rats fed with the 35% fat diet, but not on rats fed with the 3.1% fat diet. JTT-130-treated rats showed increased O(2) consumption and CO(2) production on a 35% fat diet.

CONCLUSIONS

JTT-130 suppresses high fat diet-induced obesity and glucose intolerance with suppression of food intake and fat absorption and could be useful for prevention and treatment of obesity and obesity-related insulin resistance.

In vivo morphometric analysis of inflammatory condylar changes in rat temporomandibular joint

OBJECTIVE

Injection of complete Freund's adjuvant (CFA) into the temporomandibular joint (TMJ) causes acute swelling around the joint and subsequent morphological alterations in the condyle. We aimed to evaluate changes in the three-dimensional architecture of the condyle induced with CFA.

MATERIALS AND METHODS

The CFA was injected into the unilateral TMJ of rats and morphological changes in the condyle were assessed repeatedly for 14 days by in vivo micro-CT.

RESULTS

Osseous abnormalities of condyle were first observed at 3-5 days after CFA injection on the tomographic images, and the condylar deformation became more obvious thereafter. Among 12 condyles examined at 14 days postinjection, osteophytosis was observed in all of the specimens and bone erosion coexisted in five condyles. None of the saline-treated condyles showed architectural changes. Significant changes were detected in the mesiolateral and rostrocaudal widths of the CFA-treated condyles at 10-14 days postinjection (P < 0.01). The extent of both condylar bone formation and resorption was greater in the CFA-injected TMJs than in saline-injected TMJs (P < 0.05).

CONCLUSION

These results indicate that CFA causes dynamic morphological changes in the condyle and that our experimental approach will provide new insights into the subacute inflammatory processes in the TMJ.

Integrated quantitative analysis of the phosphoproteome and transcriptome in tamoxifen-resistant breast cancer

Quantitative phosphoproteome and transcriptome analysis of ligand-stimulated MCF-7 human breast cancer cells was performed to understand the mechanisms of tamoxifen resistance at a system level. Phosphoproteome data revealed that WT cells were more enriched with phospho-proteins than tamoxifen-resistant cells after stimulation with ligands. Surprisingly, decreased phosphorylation after ligand perturbation was more common than increased phosphorylation. In particular, 17β-estradiol induced down-regulation in WT cells at a very high rate. 17β-Estradiol and the ErbB ligand heregulin induced almost equal numbers of up-regulated phospho-proteins in WT cells. Pathway and motif activity analyses using transcriptome data additionally suggested that deregulated activation of GSK3β (glycogen-synthase kinase 3β) and MAPK1/3 signaling might be associated with altered activation of cAMP-responsive element-binding protein and AP-1 transcription factors in tamoxifen-resistant cells, and this hypothesis was validated by reporter assays. An examination of clinical samples revealed that inhibitory phosphorylation of GSK3β at serine 9 was significantly lower in tamoxifen-treated breast cancer patients that eventually had relapses, implying that activation of GSK3β may be associated with the tamoxifen-resistant phenotype. Thus, the combined phosphoproteome and transcriptome data set analyses revealed distinct signal transcription programs in tumor cells and provided a novel molecular target to understand tamoxifen resistance.

Effect of alendronate on bone metabolic indices and bone mineral density in patients treated with high-dose glucocorticoid: a prospective study

SUMMARY

This prospective study, in the very early phase after initiation of glucocorticoid (GC) treatment, showed that alendronate was effective in suppressing accelerated bone resorption and subsequent decrease in bone mineral density (BMD) at the lumbar spine of patients with high-dose GC treatment.

INTRODUCTION

How bisphosphonates affect bone metabolism and BMD of patients with high-dose GC in the early phase, especially within 1 month is unclear.

METHODS

We examined the prospective effects of daily 5 mg alendronate on bone metabolism and BMD in 20 patients with high-dose GC (at least 40 mg prednisolone/day) and compared them to 34 high-dose GC-treated patients without alendronate.

RESULTS

Serum levels of calcium decreased at day 28 in the alendronate group. Urinary calcium excretion significantly increased after day 7 in both groups. The increase in serum parathyroid hormone (PTH) level at day 7 in the control group was not observed in the alendronate group, but PTH levels increased at day 28 and month 3 in the alendronate group. As for the bone turnover markers, the serum osteocalcin level decreased in both alendronate and control groups, but serum bone-type alkaline phosphatase levels did not show significant changes. Although the urinary type I collagen cross-linked N-telopeptide (NTX) level showed significant increases on days 7 and 28 in the control group; such early increases in urinary NTX were not observed in the alendronate group. Thereafter, the urinary NTX levels fell slowly in the alendronate group significantly. BMD at the lumbar spine significantly decreased from month 1 in the control group, whereas in the alendronate group, BMD at the lumbar spine maintained almost the same level at all time points observed.

CONCLUSION

Alendronate was effective in suppressing bone resorption and subsequent BMD decrease at the lumbar spine in patients with high-dose GC treatment.

Increasing antiviral activity of surfactant protein d trimers by introducing residues from bovine serum collectins: dissociation of mannan-binding and antiviral activity

Collectins contribute to host defence through interactions with glycoconjugates on pathogen surfaces. We have prepared recombinant trimeric neck and carbohydrate recognition domains (NCRD) of collectins, and we now show that the NCRD of bovine conglutinin and CL-46 (like that of CL-43) have greater intrinsic antiviral activity for influenza A virus (IAV) than the human SP-D NCRD (hSP-D-NCRD). The three serum collectins differ from SP-D by having insertions adjacent to amino acid 325 and substitution of hydrophobic residues for arginine 343. We previously showed that a three amino acid (RAK) insertion, as found in CL-43, increases antiviral activity and mannan-binding activity of the hSP-D-NCRD, while the substitution of valine at 343, as in conglutinin, more strongly increased these activities. Mannan-binding activity of collectins has been considered to predict for ability to bind to high mannose glycans on viruses or other pathogens. We now show, however, that combined mutants containing the RAK insertion and R343V or R343I substitutions have greatly increased mannan-binding ability, but lower IAV binding or inhibiting activity than mutants containing R343V or R343I substitutions only. These findings indicate differences in the recognition of glycan structures of mannan and IAV by the NCRD and emphasize the importance of the flanking sequences in determining the differing interactions of human SP-D and bovine serum collectins with mannose-rich glycoconjugates on IAV and other pathogens. Of interest, we show conservation of some monoclonal antibody-binding epitopes between bovine collectin NCRD and hSP-D, suggesting shared structural motifs.

Diagnostic accuracy of microcomputed tomography for osseous abnormalities in the rat temporomandibular joint condyle

OBJECTIVES

Our aim was to investigate the diagnostic accuracy of in vivo micro-CT for osseous abnormalities of the rat temporomandibular joint (TMJ) condyle, using macroscopic observations as the "gold standard".

METHODS

A 30 TMJ arthritis model was prepared by injecting inflammatory complete Freund's adjuvant (CFA) into one side of the TMJ cavities of rats. The TMJ condyles were then imaged using micro-CT. The samples were macroscopically evaluated for osseous abnormalities, including erosions, osteophytes, flattening and concavity. The micro-CT images were independently assessed for abnormalities using the same criteria. Images in three planes were produced using the micro-XYZ technique with the micro-CT equipment.

RESULTS

According to the macroscopic observations, 26 of the 60 rat condyles showed osseous abnormalities. The micro-XYZ images detected abnormalities in 25 of the condyles. The condyle diagnostic accuracy of micro-CT was 0.98, the sensitivity was 0.96 and the specificity was 1.0.

CONCLUSIONS

Good diagnostic results were obtained using micro-CT. It is therefore an effective technique for the evaluation of osseous abnormalities in the rat TMJ condyle.

The identification and functional implications of human-specific "fixed" amino acid substitutions in the glutamate receptor family

BACKGROUND

The glutamate receptors (GluRs) play a vital role in the mediation of excitatory synaptic transmission in the central nervous system. To clarify the evolutionary dynamics and mechanisms of the GluR genes in the lineage leading to humans, we determined the complete sequences of the coding regions and splice sites of 26 chimpanzee GluR genes.

RESULTS

We found that all of the reading frames and splice sites of these genes reported in humans were completely conserved in chimpanzees, suggesting that there were no gross structural changes in humans after their divergence from the human-chimpanzee common ancestor. We observed low KA/KS ratios in both humans and chimpanzees, and we found no evidence of accelerated evolution. We identified 30 human-specific "fixed" amino acid substitutions in the GluR genes by analyzing 80 human samples of seven different populations worldwide. Grantham's distance analysis showed that GRIN2C and GRIN3A are the most and the second most diverged GluR genes between humans and chimpanzees. However, most of the substitutions are non-radical and are not clustered in any particular region. Protein motif analysis assigned 11 out of these 30 substitutions to functional regions. Two out of these 11 substitutions, D71G in GRIN3A and R727H in GRIN3B, caused differences in the functional assignments of these genes between humans and other apes.

CONCLUSION

We conclude that the GluR genes did not undergo drastic changes such as accelerated evolution in the human lineage after the divergence of chimpanzees. However, there remains a possibility that two human-specific "fixed" amino acid substitutions, D71G in GRIN3A and R727H in GRIN3B, are related to human-specific brain function.

BAC library construction and BAC end sequencing of five Drosophila species: the comparative map with the D. melanogaster genome

We constructed and characterized arrayed bacterial artificial chromosome (BAC) libraries of five Drosophila species (D. melanogaster, D. simulans, D. sechellia, D. auraria, and D. ananassae), which are genetically well characterized in the studies of meiosis, evolution, population genetics, and developmental biology. The BAC libraries comprise 8,000 to 12,500 clones for each species, estimated to cover the most of the genomes. We sequenced both ends of most of these BAC clones with a success rate of 91%. Of these, 53,701 clones consisting of non-repetitive BAC end sequences (BESs) were mapped with reference of the public D. melanogaster genome sequences. The BES mapping estimated that the BAC libraries of D. auraria and D. ananassae covered 47% and 57% of the D. melanogaster genome, respectively, and those of D. melanogaster, D. sechellia, and D. simulans covered 94-97%. The low coverage by BESs of D. auraria and D. ananassae may be due to the high sequence divergence with D. melanogaster. From the comparative BES mapping, 111 possible breakpoints of chromosomal rearrangements were identified in these four species. The breakpoints of the major chromosome rearrangement between D. simulans and D. melanogaster on the third chromosome were determined within 20 kb in 84E and 30 kb in 93E/F. Corresponding breakpoints were also identified in D. sechellia. The BAC clones described here will be an important addition to the Drosophila genomic resources.

Measurement of B(Ds{+}-->mu+nu(mu))

We present a measurement of the branching fraction B(D{s}{+}-->mu{+}nu{mu}) using a 548 fb{-1} data sample collected by the Belle experiment at the KEKB e{+}e{-} collider. The D{s} momentum is determined by reconstruction of the system recoiling against DKgammaX in events of the type e{+}e{-}-->D{s}{*}DKX, D{s}{*}-->D{s}gamma, where X represents additional pions or photons from fragmentation. This full-reconstruction method provides high resolution in the neutrino momentum and thus good background separation, equivalent to that achieved by experiments at the tau-charm factories. We obtain the branching fraction B(D{s}{+}-->mu{+}nu{mu})=[6.44+/-0.76(stat)+/-0.57(syst)]x10{-3}, implying a D{s} decay constant of f{D{s}}=[275+/-16(stat)+/-12(syst)] MeV.