De novo missense variants in HDAC3 leading to epigenetic machinery dysfunction are associated with a variable neurodevelopmental disorder.

Histone deacetylase 3 (HDAC3) is a crucial epigenetic modulator essential for various developmental and physiological functions. Although its dysfunction is increasingly recognized in abnormal phenotypes, to our knowledge, there have been no established reports of human diseases directly linked to HDAC3 dysfunction. Using trio exome sequencing and extensive phenotypic analysis, we correlated heterozygous de novo variants in HDAC3 with a neurodevelopmental disorder having variable clinical presentations, frequently associated with intellectual disability, developmental delay, epilepsy, and musculoskeletal abnormalities. In a cohort of six individuals, we identified missense variants in HDAC3 (c.277G>A [p.Asp93Asn], c.328G>A [p.Ala110Thr], c.601C>T [p.Pro201Ser], c. 797T>C [p.Leu266Ser], c.799G>A [p.Gly267Ser], and c.1075C>T [p.Arg359Cys]), all located in evolutionarily conserved sites and confirmed as de novo. Experimental studies identified defective deacetylation activity in the p.Asp93Asn, p.Pro201Ser, p.Leu266Ser, and p.Gly267Ser variants, positioned near the enzymatic pocket. In addition, proteomic analysis employing co-immunoprecipitation revealed that the disrupted interactions with molecules involved in the CoREST and NCoR complexes, particularly in the p.Ala110Thr variant, consist of a central pathogenic mechanism. Moreover, immunofluorescence analysis showed diminished nuclear to cytoplasmic fluorescence ratio in the p.Ala110Thr, p.Gly267Ser, and p.Arg359Cys variants, indicating impaired nuclear localization. Taken together, our study highlights that de novo missense variants in HDAC3 are associated with a broad spectrum of neurodevelopmental disorders, which emphasizes the complex role of HDAC3 in histone deacetylase activity, multi-protein complex interactions, and nuclear localization for proper physiological functions. These insights open new avenues for understanding the molecular mechanisms of HDAC3-related disorders and may inform future therapeutic strategies.

Prevalence and founder effect of DRC1 exon 1-4 deletion in Korean patients with primary ciliary dyskinesia.

Primary ciliary dyskinesia (PCD) is a genetically heterogeneous disorder affecting ciliary structure and function. PCD exhibiting dynein regulatory complex subunit 1 (DRC1) exon 1-4 deletion has been reported in several Japanese PCD patients; however, no large scale studies have been performed. Here, we aimed to determine the prevalence and founder effect of this variant in the Korean population. Using an in-house copy number variation tool, we screened for DRC1 exon 1-4 deletion in 20 patients with PCD and exome data of 1435 patients in the Seoul National University Hospital repository. In cases of suspected DRC1 deletion, confirmatory gap-PCR was performed. In a PCD cohort, three of 20 (15%) patients were positive for DRC1 exon 1-4 deletion (NM_145038.5(DRC1): c.1-3952_540 + 1331del27748-bp) while pathogenic variants were found in CCDC39 (N = 1), DNAAF6 (N = 1), DNAH9 (N = 1). In the 1,435-sample exome data, seven patients (0.49%) were confirmed to have DRC1 exon 1-4 deletion. A chimeric sequence including the junction was searched from the 1000 Genomes Project data repository. One Japanese patient (0.96%) was found to have the same DRC1 exon 1-4 deletion, which was absent in other populations. This study demonstrated that the DRC1 exon 1-4 deletion is a founder mutation based on haplotype analysis. In summary, the prevalence of PCD based on DRC1 exon 1-4 deletion is particularly high in Korean and Japanese populations, which is attributed to the founder effect. Genetic testing for DRC1 exon 1-4 deletion should be considered as an initial screening tool for Korean and Japanese patients with PCD.

Neurotoxicity of phenylalanine on human iPSC-derived cerebral organoids.

Phenylketonuria (PKU) is a common genetic metabolic disorder that causes phenylalanine accumulation in the blood. The most serious symptoms are related to the brain, as intellectual disability, seizure, and microcephaly are commonly found in poorly treated PKU patients and the babies of maternal PKU. However, the mechanism of hyperphenylalaninemia on human neurodevelopment is still unclear. Here we utilized human induced pluripotent stem cell (iPSC)-derived cerebral organoids to investigate the neurotoxicity of hyperphenylalaninemia. Cerebral organoids at days 40 or 100 were treated with different concentrations of phenylalanine for 5 days. After phenylalanine treatments, the cerebral organoids displayed alterations in organoid size, induction of apoptosis, and depletion of neural progenitor cells. However, phenylalanine did not have an impact on neurons and glia, including astrocytes, immature oligodendrocytes, and mature oligodendrocytes. Remarkably, a reduction in the thickness of the cortical rosettes and a decrease in myelination at the intermediate zone were inspected with the elevated phenylalanine concentrations. RNA-seq of phenylalanine-treated organoids revealed that gene sets related to apoptosis, p53 signaling pathway, and TNF signaling pathway via NF-kB were enriched in upregulated genes, while those related to cell cycle and amino acid metabolism were enriched in downregulated genes. In addition, there were several microcephaly disease genes, such as ASPM, LMNB1, and CENPE, ranked at the top of the downregulated genes. These findings indicate that phenylalanine exposure may contribute to microcephaly, abnormal cortical expansion, and myelination lesions in the developing human brain.

Real-time detection of vehicle-originated condensable particulate matter through thermodenuder integrated aerosol measurement method at tailpipes.

Condensable particulate matter (CPM) corresponds to primary particulate matter ≤2.5 µm (PM2.5) obtained through the condensation of gaseous air pollutants caused by temperature drops in the atmosphere. The internal combustion of vehicle engines can produce CPM because of the condensable compounds in the exhaust gas. Conventional CPM measurement methods have been developed for coal-fired power plants with stable emissions through sampling and off-site analyses. They are therefore unsuitable for detecting the rapidly changing vehicle-originated CPM. In addition, the current system for evaluating PM2.5 from vehicles, based on the particle measurement program (PMP) protocol, provides only the emission factors of total PM2.5 (and not CPM separately) at a fixed temperature (∼25 °C) and dilution ratio (∼ × 35). This study reports, for the first time, the development of a real-time detection method for vehicle-originated CPM through a thermodenuder (TD) integrated with real-time aerosol instruments. This method was designed to reduce the loss of CPM due to condensation and diffusion while sampling the exhaust gas. It permits the investigation of the effects of dilution gas temperature (5-45 °C) and dilution ratio (up to × 30) on the formation of CPM. During the feasibility test of this method using a diesel vehicle (Euro-4), the real-time total particle number concentrations (PNs) matched well with those obtained by a PMP protocol-based evaluation system. Moreover, this method detected PNs concentrations ten times higher than the detection limit (4 × 106 particles/cm3) of the PMP-based system. The emission factors of the total PM2.5 with a bulk density (1 g/cm3) measured by this method also showed consistency with the results of the PMP protocol. The mass emission factor of CPM determined by deploying the TD was ∼14.57 mg/km (∼63% contribution to the total PM2.5).

The transcriptomic landscape of caudal cell mass in different developmental stages of the chick embryo.

INTRODUCTION: The caudal cell mass (CCM) is an aggregate of undifferentiated pluripotent cells and the main player in secondary neurulation. Previous studies have elucidated the dynamic fate of the multipotent cell lineages, with a recent interest in the neuromesodermal progenitors. However, a transcriptomic analysis of the CCM during secondary neurulation has not been performed yet. METHODS: We analyzed RNA sequencing data of CCM samples at three different developmental stages of chicken embryos; HH16 (largest CCM phase), HH20 (secondary neural tube formation phase), and HH28 (degeneration phase). RESULTS: The transcriptomic profiles were clearly distinguishable according to developmental stage, and HH20 was shown to have not only intermediate, but also unique properties in secondary neurulation. A total of 10,666 differentially expressed genes, including FGF18 and GDF11, were identified and enriched in several gene ontologies related to embryogenesis or organogenesis. We also found that genes encoding transcription factors, such as TWIST2, IRX4, HOXB4, HOXD13, LIN28A, CDX4, and Brachyury, were among the top-ranked differentially expressed genes. CONCLUSION: Through transcriptomic profiling, we provided a picture of the developmental process of the CCM. We identified several key molecules or pathways involved in secondary neurulation and the pathogenesis of related diseases.

Photobiocidal-triboelectric nanolayer coating of photosensitizer/silica-alumina for reusable and visible-light-driven antibacterial/antiviral air filters.

Outbreaks of airborne pathogens pose a major threat to public health. Here we present a single-step nanocoating process to endow commercial face mask filters with photobiocidal activity, triboelectric filtration capability, and washability. These functions were successfully achieved with a composite nanolayer of silica-alumina (Si-Al) sol-gel, crystal violet (CV) photosensitizer, and hydrophobic electronegative molecules of 1H, 1H, 2H, 2H-perfluorooctyltriethoxysilane (PFOTES). The transparent Si-Al matrix strongly immobilized the photosensitizer molecules while dispersing them spatially, thus suppressing self-quenching. During nanolayer formation, PFOTES was anisotropically rearranged on the Si-Al matrix, promoting moisture resistance and triboelectric charging of the Si-Al/PFOTES-CV (SAPC)-coated filter. The SAPC nanolayer stabilized the photoexcited state of the photosensitizer and promoted redox reaction. Compared to pure-photosensitizer-coated filters, the SAPC filter showed substantially higher photobiocidal efficiency (∼99.99 % for bacteria and a virus) and photodurability (∼83 % reduction in bactericidal efficiency for the pure-photosensitizer filter but ∼0.34 % for the SAPC filter after 72 h of light irradiation). Moreover, after five washes with detergent, the SAPC filter maintained its photobiocidal and filtration performance, proving its reusability potential. Therefore, this SAPC nanolayer coating provides a practical strategy for manufacturing an antimicrobial and reusable mask filter for use during the ongoing COVID-19 pandemic.

Persistent Symptoms After Acute COVID-19 Infection in Omicron Era.

BACKGROUND: We aim to compare the clinical characteristics and subjectively reported symptoms of the acute coronavirus disease (COVID) phase and those of the post-acute COVID phase to examine varying factors that affect the number of persistent symptoms and their categories. METHODS: We categorized 1,122 patients who visited the post coronavirus disease 2019 (COVID-19) clinic into two groups: "acute group" (< 4 weeks following diagnosis of COVID-19) and "post-acute group" (> 4 weeks following diagnosis of COVID-19). We statistically compared clinical characteristics between the two groups and determined which factors are associated with the number of persistent symptoms and their categories. RESULTS: The persistent symptoms of post COVID-19 conditions were classified into three categories as follows: Category A (the prevalence of symptoms is higher in the acute-visit group than in the post-acute-visit group), Category B (the prevalence of symptoms is not different between the two groups) and Category C (the prevalence of symptoms is higher in the post-acute-visit group than in the acute-visit group). Category A mainly included respiratory symptoms. Category B had generalized weakness, weight loss, cardiologic symptoms, hypogeusia, hyposmia, anxiety, and various gastrointestinal symptoms. Category C included fatigue, decreased attention, depression, blurred vision, hair loss, and sexual dysfunction. Anxiety, depression, fatigue and age were also associated with the number of symptoms and their categories, and anxiety is the most correlated factor (P < 0.001) among them. CONCLUSION: The persistent symptoms of post COVID-19 condition involve multi-organ and continue for four weeks or greater. Therefore, long-term observation and multidisciplinary interventions are essential for patients with post COVID-19 conditions.

Evaluation of survival rates of airborne microorganisms on the filter layers of commercial face masks.

After the WHO designated COVID-19 a global pandemic, face masks have become a precious commodity worldwide. However, uncertainty remains around several details regarding face masks, including the potential for transmission of bioaerosols depending on the type of mask and secondary spread by face masks. Thus, understanding the interplay between face mask structure and harmful bioaerosols is essential for protecting public health. Here, we evaluated the microbial survival rate at each layer of commercial of filtering facepiece respirators (FFRs) and surgical masks (SMs) using bacterial bioaerosols. The penetration efficiency of bacterial particles for FFRs was lower than that for SMs; however, the microbial survival rate for all tested masks was >13%, regardless of filtration performance. Most bacterial particles survived in the filter layer (44%-77%) (e.g., the core filtering layer); the outer layer also exhibited significant survival rates (18%-29%). Most notably, survival rates were determined for the inner layers (<1% for FFRs, 3%-16% for SMs), which are in contact with the respiratory tract. Our comparisons of the permeability and survival rate of bioaerosols in each layer will contribute to bioaerosol-face mask research, while also providing information to facilitate the establishment of a mask-reuse protocol.

Graf regulates hematopoiesis through GEEC endocytosis of EGFR.

GTPase regulator associated with focal adhesion kinase 1 (GRAF1) is an essential component of the GPI-enriched endocytic compartment (GEEC) endocytosis pathway. Mutations in the human GRAF1 gene are associated with acute myeloid leukemia, but its normal role in myeloid cell development remains unclear. We show that Graf, the Drosophila ortholog of GRAF1, is expressed and specifically localizes to GEEC endocytic membranes in macrophage-like plasmatocytes. We also find that loss of Graf impairs GEEC endocytosis, enhances EGFR signaling and induces a plasmatocyte overproliferation phenotype that requires the EGFR signaling cascade. Mechanistically, Graf-dependent GEEC endocytosis serves as a major route for EGFR internalization at high, but not low, doses of the predominant Drosophila EGFR ligand Spitz (Spi), and is indispensable for efficient EGFR degradation and signal attenuation. Finally, Graf interacts directly with EGFR in a receptor ubiquitylation-dependent manner, suggesting a mechanism by which Graf promotes GEEC endocytosis of EGFR at high Spi. Based on our findings, we propose a model in which Graf functions to downregulate EGFR signaling by facilitating Spi-induced receptor internalization through GEEC endocytosis, thereby restraining plasmatocyte proliferation.

ICT-Based Health Care Services for Individuals with Spinal Cord Injuries: A Feasibility Study.

In the Republic of Korea, 90.5% of those living with spinal cord injury (SCI) are faced with medical complications that require chronic care. Some of the more common ones include urinary tract infections, pressure sores, and pain symptomatology. These and other morbidities have been recognized to deteriorate the individual's health, eventually restricting their community participation. Telerehabilitation, using information and communication technology, has propelled a modern-day movement in providing comprehensive medical services to patients who have difficulty in mobilizing themselves to medical care facilities. This study aims to verify the effectiveness of health care and management in the SCI population by providing ICT-based health care services. We visited eight individuals living with chronic SCI in the community, and provided ICT-based health management services. After using respiratory and urinary care devices with the provision of home visit occupational therapy, data acquisition was achieved and subsequently entered into a smart device. The entered information was readily accessible to the necessary clinicians and researchers. The clients were notified if there were any concerning results from the acquired data. Subsequently, they were advised to follow up with their providers for any immediate medical care requirements. Digital hand-bike ergometers and specialized seating system cushions are currently in development. The ICT-based health care management service for individuals with SCI resulted in a favorable expected level of outcome. Based on the results of this study, we have proposed and are now in preparation for a randomized clinical trial.

Comprehensive Analysis of the Transcriptional and Mutational Landscape of Follicular and Papillary Thyroid Cancers.

Follicular thyroid carcinoma (FTC) and benign follicular adenoma (FA) are indistinguishable by preoperative diagnosis due to their similar histological features. Here we report the first RNA sequencing study of these tumors, with data for 30 minimally invasive FTCs (miFTCs) and 25 FAs. We also compared 77 classical papillary thyroid carcinomas (cPTCs) and 48 follicular variant of PTCs (FVPTCs) to observe the differences in their molecular properties. Mutations in H/K/NRAS, DICER1, EIF1AX, IDH1, PTEN, SOS1, and SPOP were identified in miFTC or FA. We identified a low frequency of fusion genes in miFTC (only one, PAX8-PPARG), but a high frequency of that in PTC (17.60%). The frequencies of BRAFV600E and H/K/NRAS mutations were substantially different in miFTC and cPTC, and those of FVPTC were intermediate between miFTC and cPTC. Gene expression analysis demonstrated three molecular subtypes regardless of their histological features, including Non-BRAF-Non-RAS (NBNR), as well as BRAF-like and RAS-like. The novel molecular subtype, NBNR, was associated with DICER1, EIF1AX, IDH1, PTEN, SOS1, SPOP, and PAX8-PPARG. The transcriptome of miFTC or encapsulated FVPTC was indistinguishable from that of FA, providing a molecular explanation for the similarly indolent behavior of these tumors. We identified upregulation of genes that are related to mitochondrial biogenesis including ESRRA and PPARGC1A in oncocytic follicular thyroid neoplasm. Arm-level copy number variations were correlated to histological and molecular characteristics. These results expanded the current molecular understanding of thyroid cancer and may lead to new diagnostic and therapeutic approaches to the disease.

A copy number variation in PKD1L2 is associated with colorectal cancer predisposition in korean population.

Recently reported genome-wide association studies have identified more than 20 common low-penetrance colorectal cancer (CRC) susceptibility loci. Recent studies have reported that copy number variations (CNVs) are considered important human genomic variants related to cancer, while the contribution of CNVs remains unclear. We performed array comparative genomic hybridization (aCGH) in 36 CRC patients and 47 controls. Using breakpoint PCR, we confirmed the breakpoint of the PKD1L2 deletion region. High frequency of PKD1L2 CNV was observed in CRC cases. We validated the association between PKD1L2 variation and CRC risk in 1,874 cases and 2,088 controls (OR = 1.44, 95% CI = 1.04-1.98, p = 0.028). Additionally, PKD1L2 CNV is associated with increased CRC risk in patients younger than 50 years (OR = 2.14, 95% CI 1.39-3.30, p = 5.8 × 10-4 ). In subgroup analysis according to body mass index (BMI), we found that the CN loss of PKD1L2 with BMI above or equal to 25 exhibited a significant increase in CRC risk (OR = 2.29, 95% CI 1.29-4.05, p = 0.005). PKD1L2 CNV with BMI above or equal to 25 and age below 50 is associated with a remarkably increased risk of colorectal cancer (OR = 5.24, 95% CI 2.36-11.64, p= 4.8 × 10-5 ). Moreover, we found that PKD1L2 variation in obese patients (BMI ≥ 25) was associated with poor survival rate (p = 0.026). Our results suggest that the common PKD1L2 CNV is associated with CRC, and PKD1L2 CNV with high BMI and/or age below 50 exhibited a significant increased risk of CRC. In obese patients, PKD1L2 variation was associated with poor survival.

Deep resequencing of 131 Crohn's disease associated genes in pooled DNA confirmed three reported variants and identified eight novel variants.

OBJECTIVE: Genome wide association studies (GWAS) and meta-analyses for Crohn's disease (CD) have not fully explained the heritability of CD, suggesting that additional loci are yet to be found and that the known loci may contain high effect rare risk variants that have thus far gone undetected by GWAS. While the cost of deep sequencing remains too high to analyse many samples, targeted sequencing of pooled DNA samples allows the efficient and cost effective capture of all variations in a target region. DESIGN: We performed pooled sequencing in 500 Korean CD cases and 1000 controls to evaluate the coding exon and 5' and 3' untranslated regions of 131 CD associated genes. The identified genetic variants were validated using genotyping in an independent set of 500 CD cases and 1000 controls. RESULTS: Pooled sequencing identified 30 common/low single nucleotide variants (SNVs) in 12 genes and 3 rare SNVs in 3 genes. Our results confirmed a significant association of CD with the following previously reported risk loci: rs3810936 in TNFSF15 (OR=1.83, p<2.2×10(-16)), rs76418789 in IL23R (OR=0.47, p=1.14×10(-8)) and rs2241880 in ATG16L1 (OR=1.30, p=5.28×10(-6)). In addition, novel loci were identified in TNFSF8 (rs3181374, OR=1.53, p=1.03×10(-14)), BTNL2 (rs28362680, OR=1.47, p=9.67×10(-11)), HLA-DQA2 (rs3208181, OR=1.36, p=4.66×10(-6)), STAT3 (rs1053004, OR=1.29, p=2.07×10(-5)), NFKBIA (rs2273650, OR=0.80, p=3.93×10(-4)), NKX2-3 (rs888208, OR=0.82, p=6.37×10(-4)) and DNAH12 (rs4462937, OR=1.13, p=3.17×10(-2)). A novel rare SNV, rs200735402 in CARD9, was shown to have a protective effect (OR=0.09, p=5.28×10(-5)). CONCLUSIONS: Our deep resequencing of 131 CD associated genes confirmed 3 reported risk loci and identified 8 novel risk loci for CD in Koreans, providing new insights into the genetic architecture of CD.

A transforming KIF5B and RET gene fusion in lung adenocarcinoma revealed from whole-genome and transcriptome sequencing.

The identification of the molecular events that drive cancer transformation is essential to the development of targeted agents that improve the clinical outcome of lung cancer. Many studies have reported genomic driver mutations in non-small-cell lung cancers (NSCLCs) over the past decade; however, the molecular pathogenesis of >40% of NSCLCs is still unknown. To identify new molecular targets in NSCLCs, we performed the combined analysis of massively parallel whole-genome and transcriptome sequencing for cancer and paired normal tissue of a 33-yr-old lung adenocarcinoma patient, who is a never-smoker and has no familial cancer history. The cancer showed no known driver mutation in EGFR or KRAS and no EML4-ALK fusion. Here we report a novel fusion gene between KIF5B and the RET proto-oncogene caused by a pericentric inversion of 10p11.22-q11.21. This fusion gene overexpresses chimeric RET receptor tyrosine kinase, which could spontaneously induce cellular transformation. We identified the KIF5B-RET fusion in two more cases out of 20 primary lung adenocarcinomas in the replication study. Our data demonstrate that a subset of NSCLCs could be caused by a fusion of KIF5B and RET, and suggest the chimeric oncogene as a promising molecular target for the personalized diagnosis and treatment of lung cancer.

Noninvasive prenatal diagnosis of duchenne muscular dystrophy: comprehensive genetic diagnosis in carrier, proband, and fetus.

BACKGROUND: Noninvasive prenatal diagnosis of monogenic disorders using maternal plasma and targeted massively parallel sequencing is being investigated actively. We previously demonstrated that comprehensive genetic diagnosis of a Duchenne muscular dystrophy (DMD) patient is feasible using a single targeted sequencing platform. Here we demonstrate the applicability of this approach to carrier detection and noninvasive prenatal diagnosis. METHODS: Custom solution-based target enrichment was designed to cover the entire dystrophin (DMD) gene region. Targeted massively parallel sequencing was performed using genomic DNA from 4 mother and proband pairs to test whether carrier status could be detected reliably. Maternal plasma DNA at varying gestational weeks was collected from the same families and sequenced using the same targeted platform to predict the inheritance of the DMD mutation by their fetus. Overrepresentation of an inherited allele was determined by comparing the allele fraction of 2 phased haplotypes after examining and correcting for the recombination event. RESULTS: The carrier status of deletion/duplication and point mutations was detected reliably through using a single targeted massively parallel sequencing platform. Whether the fetus had inherited the DMD mutation was predicted correctly in all 4 families as early as 6 weeks and 5 days of gestation. In one of these, detection of the recombination event and reconstruction of the phased haplotype produced a correct diagnosis. CONCLUSIONS: Noninvasive prenatal diagnosis of DMD is feasible using a single targeted massively parallel sequencing platform with tiling design.

Interaction of CD99 with its paralog CD99L2 positively regulates CD99L2 trafficking to cell surfaces.

Mouse CD99 and its paralog CD99-like 2 (CD99L2) are surface proteins implicated in cellular adhesion and migration. Although their distributions overlap in a wide variety of cells, their physical/functional relationship is currently unknown. In this study, we show the interaction between the two molecules and its consequence for membrane trafficking of mouse (m)CD99L2. The interaction was analyzed by bimolecular fluorescence complementation, immunoprecipitation, and fluorescence resonance energy transfer assays. When coexpressed, mCD99 formed heterodimers with mCD99L2, as well as homodimers, and the heterodimers were localized more efficiently at the plasma membrane than were the homodimers. Their interaction was cytoplasmic domain-dependent and enhanced mCD99L2 trafficking to the plasma membrane regardless of whether it was transiently overexpressed or endogenously expressed. Surface levels of endogenous mCD99L2 were markedly low on thymocytes, splenic leukocytes, and CTL lines derived from CD99-deficient mice. Importantly, the surface levels of mCD99L2 on mCD99-deficient cells recovered significantly when wild-type mCD99 was exogenously introduced, but they remained low when a cytoplasmic domain mutant of mCD99 was introduced. Our results demonstrate a novel role for mCD99 in membrane trafficking of mCD99L2, providing useful insights into controlling transendothelial migration of leukocytes.

A highly annotated whole-genome sequence of a Korean individual.

Recent advances in sequencing technologies have initiated an era of personal genome sequences. To date, human genome sequences have been reported for individuals with ancestry in three distinct geographical regions: a Yoruba African, two individuals of northwest European origin, and a person from China. Here we provide a highly annotated, whole-genome sequence for a Korean individual, known as AK1. The genome of AK1 was determined by an exacting, combined approach that included whole-genome shotgun sequencing (27.8x coverage), targeted bacterial artificial chromosome sequencing, and high-resolution comparative genomic hybridization using custom microarrays featuring more than 24 million probes. Alignment to the NCBI reference, a composite of several ethnic clades, disclosed nearly 3.45 million single nucleotide polymorphisms (SNPs), including 10,162 non-synonymous SNPs, and 170,202 deletion or insertion polymorphisms (indels). SNP and indel densities were strongly correlated genome-wide. Applying very conservative criteria yielded highly reliable copy number variants for clinical considerations. Potential medical phenotypes were annotated for non-synonymous SNPs, coding domain indels, and structural variants. The integration of several human whole-genome sequences derived from several ethnic groups will assist in understanding genetic ancestry, migration patterns and population bottlenecks.

A targeted glycan-related gene screen reveals heparan sulfate proteoglycan sulfation regulates WNT and BMP trans-synaptic signaling.

A Drosophila transgenic RNAi screen targeting the glycan genome, including all N/O/GAG-glycan biosynthesis/modification enzymes and glycan-binding lectins, was conducted to discover novel glycan functions in synaptogenesis. As proof-of-product, we characterized functionally paired heparan sulfate (HS) 6-O-sulfotransferase (hs6st) and sulfatase (sulf1), which bidirectionally control HS proteoglycan (HSPG) sulfation. RNAi knockdown of hs6st and sulf1 causes opposite effects on functional synapse development, with decreased (hs6st) and increased (sulf1) neurotransmission strength confirmed in null mutants. HSPG co-receptors for WNT and BMP intercellular signaling, Dally-like Protein and Syndecan, are differentially misregulated in the synaptomatrix of these mutants. Consistently, hs6st and sulf1 nulls differentially elevate both WNT (Wingless; Wg) and BMP (Glass Bottom Boat; Gbb) ligand abundance in the synaptomatrix. Anterograde Wg signaling via Wg receptor dFrizzled2 C-terminus nuclear import and retrograde Gbb signaling via synaptic MAD phosphorylation and nuclear import are differentially activated in hs6st and sulf1 mutants. Consequently, transcriptional control of presynaptic glutamate release machinery and postsynaptic glutamate receptors is bidirectionally altered in hs6st and sulf1 mutants, explaining the bidirectional change in synaptic functional strength. Genetic correction of the altered WNT/BMP signaling restores normal synaptic development in both mutant conditions, proving that altered trans-synaptic signaling causes functional differentiation defects.

Whole-exome sequencing identifies mutations of KIF22 in spondyloepimetaphyseal dysplasia with joint laxity, leptodactylic type.

Spondyloepimetaphyseal dysplasia with joint laxity (SEMDJL), leptodactylic (lepto-SEMDJL) or Hall type, is an autosomal-dominant skeletal dysplasia manifesting with short stature, joint laxity with dislocation(s), limb malalignment, and spinal deformity. Its causative gene mutation has not yet been discovered. We captured and sequenced the exomes of eight affected individuals in six unrelated kindreds (three individuals in a family and five simplex individuals). Five novel sequence variants in KIF22, which encodes a member of the kinesin-like protein family, were identified in seven individuals. Sanger sequencing of KIF22 confirmed that c.443C>T (p.Pro148Ser) cosegregated with the phenotype in the affected individuals in the family; c.442C>T (p.Pro148Leu) or c.446G>A (p.Arg149Gln) was present in four of five simplex individuals, but was absent in unaffected individuals in their family and 505 normal cohorts. KIF22 mRNA was detected in human bone, cartilage, joint capsule, ligament, skin, and primary cultured chondrocytes. In silico analysis of KIF22 protein structure indicates that Pro148 and Arg149 are important in maintaining hydrogen bonds in the ATP binding and motor domains of KIF22. We conclude that these mutations in KIF22 cause lepto-SEMDJL.

The effect of word imagery on priming effect under a preconscious condition: an fMRI study.

Semantic priming is affected by the degree of association and how readily a word is imagined. In the association effect, activity in the perisylvian structures including the bilateral inferior frontal gyrus, the left middle temporal gyrus, and the supramarginal gyrus was correlated. However, little is known about the brain regions related to the effect of imagery word under the preconscious condition. Forty word pairs for high (HA)-, low (LA)-, and nonassociation (NA), nonword (NW) conditions were presented. Each 40 association word pairs (HA and LA) included 20 high (HI) and 20 low (LI) imagery prime stimuli, using a visually presented lexical decision task. A trial consisted of 30 ms prime, 30 ms mask, 500 ms probe, and 2-8 s stimulus onset asynchrony. Brain activation was measured using functional magnetic resonance imaging during word discrimination. Behavioral data indicated that the shortest response time (RT) was given for HA words, followed by LA and NA, and NW showed the longest RT (P < 0.01). RT was faster in HI than LI within HA, but not LA conditions (P < 0.01). Functional neuroimaging showed that differential brain regions for high imagery (HI) and low imagery (LI) words within low prime-target word association were observed in the left precuneus, left posterior cingulate gyrus, and right cuneal cortex. The present findings demonstrate that the effect of the degree of imagery on semantic priming occurs during the early stage of language processing, indicating an "automatic imagery priming effect." Our paradigm may be useful to explore semantic deficit related to imagery in various psychiatric disorders.