Detection of elusive DNA copy-number variations in hereditary disease and cancer through the use of noncoding and off-target sequencing reads

Copy-number variants (CNVs) play a substantial role in the molecular pathogenesis of hereditary disease and cancer, as well as in normal human interindividual variation. However, they are still rather difficult to identify in mainstream sequencing projects, especially involving exome sequencing, because they often occur in DNA regions that are not targeted for analysis. To overcome this problem, we developed OFF-PEAK, a user-friendly CNV detection tool that builds on a denoising approach and the use of "off-target" DNA reads, which are usually discarded by sequencing pipelines. We benchmarked OFF-PEAK on data from targeted sequencing of 96 cancer samples, as well as 130 exomes of individuals with inherited retinal disease from three different populations. For both sets of data, OFF-PEAK demonstrated excellent performance (>95% sensitivity and >80% specificity vs. experimental validation) in detecting CNVs from in silico data alone, indicating its immediate applicability to molecular diagnosis and genetic research.

Loss-of-function variants in UBAP1L cause autosomal recessive retinal degeneration

PURPOSE

Inherited retinal diseases (IRDs) are a group of monogenic conditions that can lead to progressive blindness. Their missing heritability is still considerable, due in part to the presence of disease genes that await molecular identification. The purpose of this work was to identify novel genetic associations with IRDs.

METHODS

Patients underwent a comprehensive ophthalmological evaluation using standard-of-care tests, such as detailed retinal imaging (macular optical coherence tomography and short-wavelength fundus autofluorescence) and electrophysiological testing. Exome and genome sequencing, as well as computer-assisted data analysis were used for genotyping and detection of DNA variants. A minigene-driven splicing assay was performed to validate the deleterious effects of 1 of such variants.

RESULTS

We identified 8 unrelated families from Hungary, the United States, Israel, and The Netherlands with members presenting with a form of autosomal recessive and nonsyndromic retinal degeneration, predominantly described as rod-cone dystrophy but also including cases of cone/cone-rod dystrophy. Age of disease onset was very variable, with some patients experiencing first symptoms during their fourth decade of life or later. Myopia greater than 5 diopters was present in 5 of 7 cases with available refractive data, and retinal detachment was reported in 2 cases. All ascertained patients carried biallelic loss-of-function variants in UBAP1L (HGNC: 40028), a gene with unknown function and with homologies to UBAP1, encoding a protein involved in ubiquitin metabolism. One of these pathogenic variants, the intronic NM_001163692.2:c.910-7G>A substitution, was identified in 5 unrelated families. Minigene-driven splicing assays in HEK293T cells confirmed that this DNA change is responsible for the creation of a new acceptor splice site, resulting in aberrant splicing.

CONCLUSION

We identified UBAP1L as a novel IRD gene. Although its function is currently unknown, UBAP1L is almost exclusively expressed in photoreceptors and the retinal pigment epithelium, hence possibly explaining the link between pathogenic variants in this gene and an ocular phenotype.

The p.C759F Variant in USH2A Is a Pathogenic Mutation: Systematic Literature Review and Meta-Analysis of 667 Genotypes

BACKGROUND

Although the p.C759F (c.2276G>T, p.Cys759Phe) variant in the USH2A gene has been identified in association with retinal degeneration by several authors, its pathogenicity has been questioned once by the publication of two unaffected homozygotes from a single family.

OBJECTIVES

The objective of the study was to ascertain the role of p.C759F in hereditary retinal disease.

METHODS

We examined 87 research articles reporting on patients carrying this variant and then used this information as primary data for a series of meta-analytical tests.

RESULTS

Independent statistical analyses showed that p.C759F (i) is highly enriched in patients with respect to healthy individuals, (ii) represents a clear-cut recessive allele causing disease when it is in trans with other mutations, (iii) is pathogenic in homozygotes.

CONCLUSIONS

Our results confirm that p.C759F is a bona fide mutation, leading to retinal blindness according to a recessive pattern of inheritance.

Novel Cu(II) complexes as DNA-destabilizing agents and their DNA nuclease activity

Here, we report a series of four novel Cu complexes, namely 2-(piperidin-1-ylmethyl)quinoline copper(II) nitrate, [LACu(NO3)2] (Cu1), 4-(quinolin-2-ylmethyl)morpholine copper(II) nitrate, [LBCu(NO3)2] (Cu2), 4-(quinolin-2-ylmethyl)morpholine copper(II) chloride, [LBCuCl2] (Cu3), and 2-(piperidin-1-ylmethyl)pyridine copper(II) chloride, [LCCu(μ-Cl)Cl]2 (Cu4). X-ray diffraction studies revealed that the geometry around the Cu(II) center could be best described as distorted octahedral in Cu1 and Cu2, whereas Cu3 and Cu4 showed distorted tetrahedral and square pyramidal geometries, respectively. DNA binding studies showed that Cu complexes Cu1-3 containing quinoline interacted via minor groove binding, whereas the Cu4 complex containing pyridine interacted via intercalation. All Cu complexes containing quinoline and pyridine caused destabilization of DNA at specific homogeneous G-C regions. The Cu1-3 complexes as groove binders destabilized the DNA structure much more than the Cu4 complex as an intercalator. Regarding groove binders, the Cu2 complex containing quinoline and morpholine caused the highest distortion and destabilization of the DNA structure, leading to high DNA cleavage efficiency.

[Deepening the Action on Salt Reduction in China-suggestions on strategy and implementation plan]

Excessive sodium/salt intake is the leading dietary risk factor for the loss of healthy life in the Chinese population. The "Healthy China 2030" Action Plan set the goal of reducing salt intake by 20% by 2030. However, salt intake in China is still at a very high level in the world, with adults reaching 11 g/d, more than twice the recommended limit of 5 g/d. The current policies and action plans of China have targeted catering workers, children, adolescents, and home chefs in salt, oil, and sugar reduction actions. However, there are still obvious deficiencies in the coordinated promotion and implementation. This study, therefore, proposed a set of comprehensive strategies (named CHRPS that is composed of communication and education, salt reduction in home cooking, salt reduction in restaurants, reducing salt content in pre-packaged food, and surveillance and evaluation) and key implementation points for further deepening the salt reduction action in China. These strategies were developed based on the main sources of dietary sodium for Chinese residents, the status of"knowledge, attitude and practice"in salt reduction, evidence of effective intervention measures, existing policies and requirements, and the salt reduction strategies of the World Health Organization and experience from some other countries. As a scientific reference, the CHRPS strategies will help the government and relevant organizations quickly implement salt reduction work and facilitate the earlier realization of China's salt reduction goal.

Effectiveness and Safety of Acupotomy on Lumbar Spinal Stenosis: A Pragmatic, Pilot, Randomized Controlled Trial

Purpose

In Korea, complex treatments such as acupotomy, acupuncture, and physical therapy are performed for lumbar spinal stenosis (LSS). Although there are reports of acupotomy as monotherapy or acupuncture treatment for LSS, pragmatic studies are lacking. Therefore, this study aimed to determine the effectiveness and safety of acupotomy for LSS to provide baseline evidence for a large-scale study.

Materials and Methods

This pragmatic randomized controlled pilot study enrolled 34 participants and randomly assigned them to two groups (n=17/group). The intervention was conducted for 8 weeks. Acupotomy plus and usual care groups received acupuncture (17 acupoints) and interferential current therapy (ICT) twice weekly; however, the acupotomy plus group received an additional acupotomy (7 acupoints) for treatment of the usual care group. The primary outcome was measured using visual analog scales (VAS), and secondary outcomes were assessed using the self-rated walking distance, short-form McGill Pain Questionnaire (SF-MPQ), and the Oswestry Disability Index (ODI). Outcome measurements were conducted at baseline and 4, 8, and 12 weeks after the commencement of the intervention. Adverse events were assessed at each visit. Hematological and biochemical examinations were performed at screening and week 8.

Results

Overall, 33 of the 34 participants completed the study, and one participant in the usual care group dropped out. In both groups, VAS scores at weeks 4, 8, and 12 significantly improved compared to baseline. Also, self-rated walking distance, SF-MPQ, and ODI scores were significantly improved at weeks 4, 8, and 12 than at baseline. However, there were no significant differences in the time-dependent and group-to-time interactions between the two groups. In addition, no severe adverse reactions were reported, and there were no significant differences in hematological and biochemical results.

Conclusion

This study provides baseline data for large-scale studies on the effectiveness and safety of acupotomy in LSS.

Clinical Trial Number

KCT0006234.

The global burden of sudden infant death syndrome from 1990 to 2019: a systematic analysis from the Global Burden of Disease study 2019

BACKGROUND

Sudden infant death syndrome (SIDS) still remains one of the leading causes of infant death worldwide, especially in high-income countries. To date, however, there is no detailed information on the global health burden of SIDS.

AIMS

To characterize the global disease burden of SIDS and its trends from 1990 to 2019 and to compare the burden of SIDS according to the socio-demographic index (SDI).

DESIGN

Systematic analysis based on the Global Burden of Disease (GBD) 2019 data.

METHODS

Epidemiological data of 204 countries from 1990 to 2019 were collected via various methods including civil registration and vital statistics in the original GBD study. Estimates for mortality and disease burden of SIDS were modeled. Crude mortality and mortality rates per 100 000 population were analyzed. Disability-adjusted life years (DALYs) and DALY rates were also assessed.

RESULTS

In 2019, mortality rate of SIDS accounted for 20.98 [95% Uncertainty Interval, 9.15-46.16] globally, which was a 51% decrease from 1990. SIDS was most prevalent in Western sub-Saharan Africa, High-income North America and Oceania in 2019. The burden of SIDS was higher in males than females consistently from 1990 to 2019. Higher SDI and income level was associated with lower burden of SIDS; furthermore, countries with higher SDI and income had greater decreases in SIDS burden from 1990 to 2019.

CONCLUSIONS

The burden of SIDS has decreased drastically from 1990 to 2019. However, the improvements have occurred disproportionately between regions and SDI levels. Focused preventive efforts in under-resourced populations are needed.

Analysis of synthetic electron cyclotron emission from the high field side of HL-2M tokamak plasmas

A synthetic electron cyclotron emission (ECE) diagnostic is used to interpret ECE signals from preset plasma equilibrium profiles, including magnetic field, electron density, and electron temperature. According to the simulation results, the electron temperature (T_e) profile covering the harmonic overlap region can be obtained by receiving ECE signals at the high field side (HFS) of the HL-2M plasma. The third harmonic ECE at the low field side (LFS) cannot pass through the second harmonic resonance layer at the HFS unless the optical thickness (τ) of the second harmonic becomes gray (τ ≤ 2). In addition, the impact of the relativistic frequency down-shift has been evaluated and corrected. The measurable range of the HFS ECE has been calculated by scanning different parameters (electron density, temperature, and magnetic field). Higher plasma parameters allow a wider radial range of electron temperature measurements. The minimum inner measurable position can reach R = 120 cm (r/a = -0.89) when the product of core temperature (T_e0) and density (n_e0) is greater than 35 × 10¹⁹ keV m^-3, which is extended by more than 30 cm inward compared with that of the LFS measurement. The HFS ECE will greatly improve the diagnostic ability of ECE systems on the HL-2M tokamak.

Mutations in the ribosome biogenesis factor gene LTV1 are linked to LIPHAK syndrome, a novel poikiloderma-like disorder

In the framework of the UK 100 000 Genomes Project, we investigated the genetic origin of a previously undescribed recessive dermatological condition, which we named LIPHAK (LTV1-associated Inflammatory Poikiloderma with Hair abnormalities and Acral Keratoses), in four affected individuals from two UK families of Pakistani and Indian origins, respectively. Our analysis showed that only one gene, LTV1, carried rare biallelic variants that were shared in all affected individuals, and specifically they bore the NM_032860.5:c.503A > G, p.(Asn168Ser) change, found homozygously in all of them. In addition, high-resolution homozygosity mapping revealed the presence of a small 652-kb stretch on chromosome 6, encompassing LTV1, that was haploidentical and common to all affected individuals. The c.503A > G variant was predicted by in silico tools to affect the correct splicing of LTV1's exon 5. Minigene-driven splicing assays in HEK293T cells and in a skin sample from one of the patients confirmed that this variant was indeed responsible for the creation of a new donor splice site, resulting in aberrant splicing and in a premature termination codon in exon 6 of this gene. LTV1 encodes one of the ribosome biogenesis factors that promote the assembly of the small (40S) ribosomal subunit. In yeast, defects in LTV1 alter the export of nascent ribosomal subunits to the cytoplasm; however, the role of this gene in human pathology is unknown to date. Our data suggest that LIPHAK could be a previously unrecognized ribosomopathy.

Effectiveness and safety of acupotomy on lumbar spinal stenosis: A pragmatic randomized, controlled, pilot clinical trial: A study protocol

INTRODUCTION

Lumbar spinal stenosis (LSS) is a pathological condition that causes a variety of neurological symptoms due to narrowing of the anatomical structures; usually, conservative treatment is recommended, rather than surgical treatment. Acupotomy combines conventional acupuncture with small scalpels; the procedure can be considered minimally invasive, and has recently received considerable attention in clinical practice. Still, there is a lack of data and randomized controlled trials regarding acupotomy related to LSS. Additional studies are necessary, considering the low methodological quality and small size of the study.

METHODS AND ANALYSIS

This is a pragmatic, pilot, randomized controlled trial. The trial comprises 8 weeks of treatment, with 16 visits and a 4-week follow-up period. Forty participants diagnosed with LSS will be randomly assigned to either the experimental or control groups; both groups will receive acupuncture and interferential current therapy twice a week for 8 weeks, while the experimental group will receive an additional acupotomy intervention once a week for 8 weeks. The primary outcome will be assessed using the visual analog scale; the secondary outcome will be measured by self-rated walking distance, Oswestry Disability Index, and short-form McGill Pain Questionnaire. Measurements will be obtained prior to the start of the clinical trial, 4 weeks after the interventional procedure, 8 weeks after the procedure, and 4 weeks after the end of the interventional procedure. Blood tests and adverse reactions will be performed to ensure safety of the treatments.

CONCLUSION

We expect that this study will provide basic data for future large-scale acupotomy studies regarding LSS.

3D wide-field multispectral photoacoustic imaging of human melanomas in vivo: a pilot study

BACKGROUND

The Breslow depth is an important parameter to determine the excision margin and prognosis of melanoma. However, it is difficult to accurately determine the actual Breslow depth before surgery using the existing ocular micrometer and biopsy technique.

OBJECTIVES

To evaluate the use of 3D wide-field multispectral photoacoustic imaging to non-invasively measure depth and outline the boundary of melanomas for optimal surgical margin selection.

METHODS

Six melanoma patients were examined in vivo using the 3D multispectral photoacoustic imaging system. For five cases of melanomas (one in situ, three nodular, and one acral lentiginous type melanoma), the spectrally unmixed photoacoustic depths were calculated and compared against histopathological depths.

RESULTS

Spectrally unmixed photoacoustic depths and histopathological depths match well within a mean absolute error of 0.36 mm. In particular, the measured minimum and maximum depths in the in situ and nodular type of melanoma were 0.6 and 9.1 mm, respectively. In the 3D photoacoustic image of one metastatic melanoma, feeding vessels were visualized in the melanoma, suggesting the neovascularization around the tumour.

CONCLUSIONS

The 3D multispectral photoacoustic imaging not only provides well-measured depth and sizes of various types of melanomas, it also visualizes the metastatic type of melanoma. Obtaining accurate depth and boundary information of melanoma before surgery would play a useful role in the complete excision of melanoma during surgery.

Binding Properties of Various Cationic Porphyrins to DNA in the Molecular Crowding Condition Induced by Poly(ethylene glycol)

The binding modes of various cationic porphyrins to DNA in an aqueous solution and under the molecular crowding condition induced by poly(ethylene glycol) (PEG) were compared by normal absorption, circular dichroism (CD), and linear dichroism (LD) spectroscopy techniques. Large negative CD and LD signals in the Soret absorption regions of the meta- and para-TMPyP [meso-tetrakis (n-N-methylpyridiniumyl) porphyrin (meta, n = 3) and (para, n = 4)] were apparent in the aqueous solution, indicating an intercalative-binding mode, while a positive CD spectrum and a less intense negative LD spectrum for the ortho-TMPyP (n = 2)-complexed DNA suggested a major-groove-binding mode. These binding modes are retained under a molecular crowding condition, suggesting that the PEG cluster cannot access the TMPyPs that are intercalated between the DNA base pairs or that bind at the major groove. The spectral properties of the ortho-, meta-, and para-trans-BMPyP [trans-bis(N-methylpyrodinium-n-yl)diphenyl porphyrin, n = 2,3,4]-bound DNA in an aqueous solution correspond to neither the intercalative-binding nor the groove-binding mode, which is in contrast with the TMPyP cases. The spectral properties under the molecular crowding condition are altered considerably for all of the three trans-BMPyPs compared to those in an aqueous solution, suggesting that the matted PEG cluster is in contact with the cationic trans-BMPyPs, causing a change in the polarity of the porphyrin environment. Consequently, trans-BMPyPs bind to the external side of the DNA.

Effect of periphery cationic substituents of porphyrin on the B-Z transition of poly[d(A-T)2], poly[d(G-C)2] and their binding modes

The binding mode of cationic porphyrin (trans-BMPyP) with poly[d(G-C)₂] and poly[d(A-T)₂] was examined according to the site of the periphery cationic methyl pyridine ion of the cationic porphyrin (o-, m-, p-) as well as the possibility of a B-Z transition depending on the binding modes by measuring the absorption spectrum and circular dichroism (CD). The negative band found in the soret region showed the intercalation mode of m- and p-trans-BMPyP-poly[d(G-C)₂] to the DNA base pairs, but no B-Z transition was induced. On the other hand, the distinctive bisignate band found in the soret region of the CD spectrum for m- and p-trans-BMPyP-poly[d(A-T)₂] suggests that m- and p-trans-BMPyP have an effective extensive stacking-based binding mode along with the skeleton of poly[d(A-T)₂], wherein the B-Z transition was induced through extensive stacking. The difference in binding mode was attributed to the difference in the molecular structure depending on the site of the periphery cationic methyl pyridine ion in the cationic porphyrin. In other words, o-trans-BMPyP is nonplanar because of the steric hindrance of the cationic methyl pyridine ion at the o-site. In contrast, m- and p-trans-BMPyP are planar, but not all porphyrins with a planar structure undergo the B-Z transition. In conclusion, a B-Z transition is induced if the structure of a porphyrin is planar and the binding mode allows the porphyrins to be stacked effectively along the DNA skeleton, not in a binding mode where the porphyrin is intercalated to the DNA.Communicated by Ramaswamy H. Sarma.

Fate of the micropenis and constitutional small penis: do they grow to normalcy in puberty?

INTRODUCTION

Penile length is an important indicator of male sexual development. Scarce data were reported on penile length measurements in children comparing changes between prepuberty and puberty for the small penile issue with long-term follow-up.

OBJECTIVE

The purpose of this study was to investigate the possibility of catch-up growth of the penile length of boys with a small penis in the long-term follow-up.

STUDY DESIGN

From April 2001 to December 2016, 27 boys who visited the outpatient clinic owing to a small penis, without any chromosomal anomalies and other genital disorder, were investigated retrospectively. Micropenis is defined as 2.5 standard deviations less than the mean stretched penile length (SPL) of age. Periodic penile length, testicular volume, hormonal levels (serum testosterone, luteinizing hormone (LH), and follicle-stimulating hormone (FSH)), and bone age were measured. Pubertal development was recorded by using the Tanner scale. The effect of hormonal therapy and the factors attributable to the increment of the penile length were evaluated.

RESULTS

The mean age at the first visit was 9.8 years (5-12 years) and that at puberty was 12.6 years (10-16 years). The length of the penis at the initial visit was 4.0 ± 0.8 cm (2.5-6.0) and at puberty, 7.3 ± 1.8 cm (4.0-12.0). Nine patients diagnosed with micropenis no longer had a micropenis in puberty. The less the age-matched SPL, the more the increment of SPL that was observed (rho = - 0.548, P = 0.003). The mean increment of SPL in the hormonal therapy group (11 boys) and the non-hormonal therapy group (16 boys) was not statistically different (43.5 ± 22. 9% vs 41.5 ± 21.6%, respectively, P = 0.497).

DISCUSSION

This study explains how much the growth of a small penis catches up in puberty. From the point of view of the increment of SPL, the increment was higher in boys who belonged to the smaller penis group. Hormonal therapy does not attribute to an increase in the length after long-term follow-up. Limitations of this study were its retrospective origin with a small number of patients in a single center.

CONCLUSION

Catch-up growth of the small penis at puberty was accomplished in most children with a small penis before puberty. Hormonal treatment was not significantly correlated with the penile length increment in the long-term follow-up.

Conformational change of a G-quadruplex under molecular crowding conditions

This study examined the influence of the molecular crowding condition induced by polyethylene glycol (PEG) on the G-quadruplex structure of the thrombin-binding aptamer sequence, 5'-GGGTTGGGTGTGGGTTGGG (G3), in a solution containing a sufficient concentration of mono cations (K⁺ and Na⁺). Although the G3 sequence preferably formed the antiparallel type G-quadruplex structure in a Na⁺ solution, conversion to the parallel type occurred when PEG was added. The antiparallel type was maintained at low PEG concentrations. When the PEG concentration reached 30%, the antiparallel type and parallel type coexist. At PEG concentrations above 40%, the G-quadruplex structure adopted the parallel type completely. In the presence of K⁺ ions, G3 showed a parallel conformation and remained as a parallel conformation with increasing PEG concentration. The dissociation temperature increased with increasing PEG concentration in all cases, suggesting that the G-quadruplex conformation is more stable under molecular crowding conditions.Communicated by Ramaswamy H. Sarma.

Highly sensitive and selective mercury sensor based on mismatched base pairing with dioxT

A highly selective and sensitive sensor for mercury was designed based on a new fluorescent nucleobase, dioxT. Its metal-sensing ability was investigated using mismatched dioxT-T and dioxT-C base pairing. The sensor exhibited a high sensitivity (quenching efficiency, 80%, 1 : 1 binding mode) and selectivity upon the addition of mercury ions.

Association between 18F-FDG uptake in PET/CT, Nrf2, and NQO1 expression and their prognostic significance in non-small cell lung cancer

Two pentose phosphate pathway-related proteins, NF-E2-related factor 2 (Nrf2)/ NAD(P)H dehydrogenase (Quinone) 1 (NQO1) regulate the expression of glucose metabolism and antioxidant genes. We evaluated the prognostic significance of NRF2, NQO1 and 18F-fluorodeoxyglucose positron emission tomography (18F-FDG PET) parameter and their relationship with non-small cell lung cancer (NSCLC) histology. A total of 241 patients, who underwent surgical resection for NSCLC, were reviewed retrospectively. Preoperative 18F-FDG PET and immunohistochemical results of Nrf2 and NQO1 were evaluated. In SQCC, the maximum standardized uptake value (SUVmax) was significantly higher in NQO1-high than in NQO1-low expression (p=0.023). In adenocarcinoma, SUVmax was not correlated with NQO1 expression. Patients with a high NQO1 expression showed poor recurrence-free survival (RFS) and overall survival (OS) than patients with a low NQO1 expression in squamous cell carcinoma (SQCC) (p=0.002 and p=0.014, respectively). NQO1 expression was not associated with clinical outcome in adenocarcinoma. Nrf2 expression was not correlated with prognosis in two types of NSCLC. High SUVmax was associated with poor RFS (p=0.03) but is not related to poor OS (p=0.569) in SQCC. In multivariate analyses, NQO1 expression and SUVmax were not independent prognostic factors in SQCC. However, in multivariate analysis combining NQO1 and SUVmax values, both low SUVmax and low NQO1 was independent prognostic factor for RFS and OS (HR= 3.790, p = 0.033 and HR= 2.961, p = 0.045, respectively). In conclusion, both low SUVmax and low NQO1 was an independent prognostic factor in SQCC alone. The sample size was small but there was a positive correlation between NQO1 expression and SUVmax in SQCC.

Sequence preference and structural heterogeneity of BZ junctions

BZ junctions, which connect B-DNA to Z-DNA, are necessary for local transformation of B-DNA to Z-DNA in the genome. However, the limited information on the junction-forming sequences and junction structures has led to a lack of understanding of the structural diversity and sequence preferences of BZ junctions. We determined three crystal structures of BZ junctions with diverse sequences followed by spectroscopic validation of DNA conformation. The structural features of the BZ junctions were well conserved regardless of sequences via the continuous base stacking through B-to-Z DNA with A-T base extrusion. However, the sequence-dependent structural heterogeneity of the junctions was also observed in base step parameters that are correlated with steric constraints imposed during Z-DNA formation. Further, circular dichroism and fluorescence-based analysis of BZ junctions revealed that a base extrusion was only found at the A-T base pair present next to a stable dinucleotide Z-DNA unit. Our findings suggest that Z-DNA formation in the genome is influenced by the sequence preference for BZ junctions.

A chloroplast-targeted pentatricopeptide repeat protein PPR287 is crucial for chloroplast function and Arabidopsis development

BACKGROUND

Even though the roles of pentatricopeptide repeat (PPR) proteins are essential in plant organelles, the function of many chloroplast-targeted PPR proteins remains unknown. Here, we characterized the function of a chloroplast-localized PPR protein (At3g59040), which is classified as the 287th PPR protein among the 450 PPR proteins in Arabidopsis ( http://ppr.plantenergy.uwa.edu.au ).

RESULTS

The homozygous ppr287 mutant with the T-DNA inserted into the last exon displayed pale-green and yellowish phenotypes. The microRNA-mediated knockdown mutants were generated to further confirm the developmental defect phenotypes of ppr287 mutants. All mutants had yellowish leaves, shorter roots and height, and less seed yield, indicating that PPR287 is crucial for normal Arabidopsis growth and development. The photosynthetic activity and chlorophyll content of ppr287 mutants were markedly reduced, and the chloroplast structures of the mutants were abnormal. The levels of chloroplast rRNAs were decreased in ppr287 mutants.

CONCLUSIONS

These results suggest that PPR287 plays an essential role in chloroplast biogenesis and function, which is crucial for the normal growth and development of Arabidopsis.

Abstract P3-03-05: Not presented

This abstract was not presented at the conference.

Citation Format: Jung S-Y, Han JH, Park SJ, Lee E-G, Lee MH, Lee ES, Kang H-S, Lee KS, Park IH, Sim SH, Jeong HJ, Kwon Y, Lee D-E, Joo J, Kim S-K, Lee S. Not presented [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P3-03-05.

The overexpression of cucumber (Cucumis sativus L.) genes that encode the branched-chain amino acid transferase modulate flowering time in Arabidopsis thaliana

The overexpression of CsBCATs promotes flowering in Arabidopsis by regulating the expression of flowering time genes. The branched-chain amino acid transferases (BCATs) play an important role in the metabolism of branched-chain amino acids (BCAAs), such as isoleucine, leucine, and valine. They function in both the synthesis and the degradation of this class of amino acids. We identified and characterized the three BCAT genes in cucumber (Cucumis sativus L.). The tissue-specific expression profiling in cucumber plants revealed that CsBCAT2 and CsBCAT7 were highly expressed in the reproductive tissues, whereas CsBCAT3 expression was highly detected in the vegetative tissues. The subcellular localization patterns of three CsBCATs were observed in the mitochondria. The functional analyses of CsBCATs showed that CsBCAT2 and CsBCAT3 restored the growth of bat1Δ/bat2Δ double knockout yeast (Saccharomyces cerevisiae), and CsBCAT3 and CsBCAT7 with different substrate preferences acted in a reverse reaction. The transgenic approach demonstrated that the overexpression of the three CsBCATs resulted in early flowering phenotypes, which were associated with the upregulation of FLOWERING LOCUS T (FT) and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1) in a manner in which they were dependent on GIGANTEA (GI)/CONSTANS (CO) and SHORT VEGETATIVE PHASE (SVP)/FLOWERING LOCUS C (FLC) modules. Our results, which are observed in conjunction, suggest that there is an interconnection between BCAT genes that function in BCAA metabolism and the flowering time in plants.

Inhibition of Cannabinoid Receptor 1 Can Influence the Lipid Metabolism in Mice with Diet-Induced Obesity

A growing number of evidences accumulated about critical metabolic role of cannabinoid type 1 receptor (CB1), carnitine palmitoyltransferase-1 (CPT1) and peroxisome proliferator-activated receptors (PPARs) in some peripheral tissues, including adipose tissue, liver, skeletal muscle and heart. To better understand the interactions of CB1, CPT1 and PPARs in these tissues, 30 diet-induced obese (DIO) C57BL/6J male mice were obtained, weight-matched and divided into two groups (15 in each group): (i) DIO/vehicle mice (D-Veh) and (ii) DIO/SR141716 mice (D-SR) treated with SR141716 (or rimonabant, a selective CB1 receptor blocker) administered orally (10 mg/kg daily). Another 15 mice fed standard diet (STD) formed the STD/vehicle group (S-Veh). At the end of 3-week treatment, mean body weight was 28.4 ± 0.5, 36.5 ± 0.8, and 30.3 ± 1.2 g for the S-Veh, D-Veh, and D-SR group, respectively (p < 0.05; D-Veh vs. D-SR). Liver weight in the D-SR group was also decreased significantly compared to the D-Veh group (p < 0.05). Serum levels of total cholesterol, high-density lipoprotein cholesterol, leptin and adiponectin in the D-SR group were ameliorated compared to the D-Veh group (p < 0.05). Both qRT-PCR and Western blot assay revealed that CB1 expression levels were efficiently blocked by SR141716 in subcutaneous adipose tissue (SAT), visceral adipose tissue (VAT), skeletal muscles and liver (D-SR vs. D-Veh; p < 0.05), whereas there was no significant difference between S-Veh and D-Veh mice (p > 0.05). Simultaneously with the reduction of CB1 expression in the D-SR group, the expression levels of CPT1A isoform (protein) in the liver and heart and CPT1B isoform (protein) in the SAT, VAT, liver and skeletal muscles were significantly increased (p < 0.05; D-SR vs. D-Veh). Interestingly, the CPT1A and CPT1B expression levels in heart were detected slightly. The expression levels of PPARα in the SAT, VAT, liver and skeletal muscles and PPARγ in the SAT and skeletal muscles in the D-SR group were significantly increased compared to the D-Veh mice (p < 0.05). However, the PPARβ expression level differed from that of PPARα and PPARγ. Taken together, these data indicate that the inhibition of CB1 could ameliorate lipid metabolism via the stimulation of the CPT1A and CPT1B expression in vivo. Simultaneously, the PPARα and PPARγ expression levels significantly differed compared to that of PPARβ in obesity and lipid metabolism-related disorders under blockade of CB1. Both the mechanism of the influence of CB1 inhibition on lipid metabolism in the examined tissues and the specific mechanism of PPARα, PPARγ and PPARβ involvement in lipid exchange under these conditions remain to be further elucidated.

Evidence of acclimatization or adaptation in Hawaiian corals to higher ocean temperatures

Ocean temperatures have been accelerating at an alarming rate mainly due to anthropogenic fossil fuel emissions. This has led to an increase in the severity and duration of coral bleaching events. Predicted projections for the state of reefs do not take into account the rates of adaptation or acclimatization of corals as these have not as yet been fully documented. To determine any possible changes in thermal tolerances, manipulative experiments were conducted to precisely replicate the initial, pivotal research defining threshold temperatures of corals nearly five decades ago. Statistically higher calcification rates, survivorship, and lower mortality were observed in Montipora capitata, Pocillopora damicornis, and Lobactis scutaria in the present study at 31 °C compared to the original 1970 findings. First whole colony mortality was also observed to occur sooner in 1970 than in 2017 in M. capitata (3 d vs. 15 d respectively), L. scutaria (3 d vs. 17 d), and in P. damicornis (3 d vs. 13 d). Additionally, bleaching occurred sooner in 1970 compared to the 2017 experiment across species. Irradiance was an important factor during the recovery period for mortality but did not significantly alter calcification. Mortality was decreased by 17% with a 50% reduction in irradiance during the recovery period. These findings provide the first evidence of coral acclimatization or adaptation to increasing ocean temperatures for corals collected from the same location and using close replication of the experiment conducted nearly 50 years earlier. An important factor in this increased resistance to elevated temperature may be related to removal of the discharge of treated sewage into Kāne'ohe Bay and resulting decrease in nitrification and eutrophication. However, this level of increased temperature tolerance may not be occurring rapidly enough to escape the projected increased intensity of bleaching events, as evidenced by the recent 2014 and 2015 high coral mortality in Hawai'i (34%) and in the tropics worldwide.

Abstract P4-06-12: Different patterns of risk reducing decisions in affected or unaffected BRCA mutation carriers

BACKGROUND

Risk-reducing (RR) management decreases the risk of breast cancer and BRCA related gynecologic cancer. However, there are fewer reports on the RR management in Asia compared to Western countries.The aim of this study is to identify risk reducing management patterns with BRCA1 or BRCA2 mutation carriers.

METHODS

The study group consisted of all consecutive 1104 breast cancer, ovarian patients and their families of high-risk patients who underwent BRCA gene testing in National Cancer Center, Korea from 2008 to 2016. A total 220 BRCA mutations (19.9%) were detected with 125(11.3%) of BRCA1 gene and 95 (8.6%) of BRCA2 gene.

RESULTS

Out of 220 BRCA mutations carriers, they were consisted of 83 breast cancers, 10 ovarian cancers, 7 both cancers, and 120 unaffected carriers. Among them, 42 were men and 178 were women. About 90 % (198/ 220) had the familial history of breast, ovarian or both malignancies (113 in BRCA1 and 85 in BRCA2 mutation (p=0.821)).

All 42 men chose surveillance. Among 178 female BRCA mutation carriers, 98(55.1%) underwent risk reducing management including 18(10.1%) of chemoprevention, and 80(49.9%) had risk-reducing surgeries (RRSs) (1 case of risk-reducing mastectomy, 76 of risk reducing bilateral salphingo-oophorectomy (RRSO), and 3 of both) and 80 (54.9%) chose only intensive surveillance for both of breast and ovary cancer.

In affected carriers with breast cancer, 59 (71.1%) underwent RR management (1 case of risk reducing mastectomy, 53 of RRSO, 3 of both surgery, and 2 of chemoprevention). There was no risk reducing management in affected carrier with ovarian cancer patients. In 78 unaffected women carriers, 39(50.0%) women received RR management (23(29.5%) cases of RRSO and 16(20.5%) cases of chemoprevention). The rates of RRSs have increased annually since the 2013 year, (prior to 2013 vs. since 2013, RRSs 28.6% (6 cases/21 carriers) vs. 37.2% (74/199), p&lt;0.01).

CONCLUSION

This study was conducted on the largest numbers of BRCA mutation carriers in Asian countries. RRSO is the more preferred management for affected carriers with breast cancer or unaffected carriers. The results might be explained by the severity of the illness and that RRSO was only reimbursed RR strategy from the Korean Government Insurance. Tailored genetic counseling and insurance policy may enhance overall levels of RR management.

Citation Format: Lee EG, Kang H, Park SJ, Han JH, Jung S-Y, Lee S, Kang H-S, Park B, Kong S-Y, Lim MC, Park S-Y, Lee ES. Different patterns of risk reducing decisions in affected or unaffected BRCA mutation carriers [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P4-06-12.

Relationship between the photoinduced electron transfer and binding modes of a pyrene-porphyrin dyad to DNA

The binding modes of a pyrene-porphyrin dyad, (1-pyrenyl)-tris(N-methyl-p-pyridino)porphyrin (PyTMpyP), to DNA and its photophysical properties have been investigated using various spectroscopic techniques. The circular dichroism (CD) spectrum of PyTMpyP bound to DNA (PyTMpyP-DNA) showed one negative and two positive bands in the Soret region. The CD signal in the pyrene absorption region was positive. The shape of the CD spectrum does not support an intercalative binding mode of TMpyP, which would typically afford a negative CD band in the absence of the pyrene moiety. Linear dichroism (LD) experiments revealed a very small signal in the Soret region, which also challenges the intercalation of TMpyP into DNA. Upon excitation of the pyrene moiety, the emission intensity of porphyrin in aqueous solution was quenched due to a photoinduced electron transfer (PET) process between the pyrenyl and porphyrin moieties. On the other hand, the emission of porphyrin was markedly enhanced upon binding to DNA, as the PET process from the excited pyrene moiety to TMpyP was suppressed when bound to DNA. The PET process occurs in the timescale of 65 ps, and could be detected by femtosecond transient absorption spectroscopic methods. Two fluorescence decay times were observed for PyTMpyP in aqueous solution (0.78 and 4.8 ns). Both decay times increased upon binding to DNA owing to environment and/or conformational changes in PyTMpyP. The driving force (ΔG) of the PET process was evaluated under conditions of minor and major groove binding. The PET process and photophysical properties of the PyTMpyP dyad were concluded to be influenced by the binding mode.

[Analysis of curative effect of transoral radiofrequency ablation microsurgery on glottic carcinoma with anterior commissure involvement at the early stage]

Objective: To explore the key technique and outcome of transoral radiofrequency ablation microsurgery for early stage of glottic carcinoma with anterior commissure involvement (ACI). Methods: A retrospective analysis was conducted on 31 patients, who were diagnosed as early stage glottic carcinoma during January 2010 to March 2016 in ENT Department. According to whether the anterior commissure was involved or not, two groups were divided. There were eleven cases with ACI (stages T1a, T1b, and T2). Twenty cases without ACI (stages Tis, T1a, and T2). All the patients received transoral radiofrequency ablation microsurgery and followed up closely.Only one case received radiotheraphy after surgery. SPSS19.0 software was used to analyze data. Results: The follow-up time was 12-67 months, and the median follow-up time was 30 months. Nine among 11 cases with ACI obtained good oncologic outcomes, initial local recurrence was identified in 2/11 cases, including 2 cases of T2. Two cases ultimately required salvage total laryngectomy. Meanwhile, initial local recurrence was identified in 2/20 cases without ACI, including 1 case of T1a and 1 case of T2. One case underwent elective neck dissection, and another one received salvage total laryngectomy.Compared to the patients without ACI, it seemed that the cases with ACI always accomponied with a little higher initial local recurrence and lower overall laryngealpreservation, but the difference had no significance (P>0.05). Conclusions: Transoral radiofrequency ablation microsurgery is an effective treatment for glottic carcinoma with ACI. Its advantages, such as more flexibility and deformability, make it more feasible to operate at the narrow space of anterior commissure assisted with laryngeal endoscopy.Good oncologic outcomes can be obtained by this technique with lower initial local recurrence as well as higher overall laryngeal preservation rate.

UVA irradiation of BrU-substituted DNA in the presence of Hoechst 33258

Given that our knowledge of DNA repair is limited because of the complexity of the DNA system, a technique called UVA micro-irradiation has been developed that can be used to visualize the recruitment of DNA repair proteins at double-strand break (DSB) sites. Interestingly, Hoechst 33258 was used under micro-irradiation to sensitize 5-bromouracil (^BrU)-labelled DNA, causing efficient DSBs. However, the molecular basis of DSB formation under UVA micro-irradiation remains unknown. Herein, we investigated the mechanism of DSB formation under UVA micro-irradiation conditions. Our results suggest that the generation of a uracil-5-yl radical through electron transfer from Hoechst 33258 to ^BrU caused DNA cleavage preferentially at self-complementary 5'-AA^BrU^BrU-3' sequences to induce DSB. We also investigated the DNA cleavage in the context of the nucleosome to gain a better understanding of UVA micro-irradiation in a cell-like model. We found that DNA cleavage occurred in both core and linker DNA regions although its efficiency reduced in core DNA.

[Complications analysis of adenoidectomy and tonsillectomy assisted with ablation on children]

Objective:To analyze the complications of adenotonsilectomy assisted with coblation in children. Method:Complications of 2 089 cases of children with adenoid and tonsil surgery assisted with coblation, in our hospital nearly 10 years, were analyzed by epidemiological methods through the method of retrospective analysis. Result:①the sex ratio of male to female was 2.08：1, average age (5.87±3.12) years old, and most of 2 089 cases 76.35% (1 595/2 089) were 3-7 years old; ②all cases underwent adenoidectomy. Different surgery methods of tonsil consisted of three groups as partial resection associated with ablation was 69.17% (1 445/2 089), ablation (channeling) alone was 22.26% (465/2 089) and total resection was 8.57% (179/208). The amount of bleeding in operation was (8.52±3.18)ml, average operation time was (30.15±8.26) minutes, the postoperative pain score was (3.77±1.61); ③The incidence of postoperative complications: postoperative bleeding (all were secondary bleeding cases) rate was 0.24% (5/2 089), recurrence rate was 0.14% (3/2 089), prevertebral lymphadenitis was 0.96% (20/2 089), the other was 0.29% (torus hyperplasia in 2 cases, dyspnea in 2 cases, 1 cases of angle of mouth burned, nasopharyngeal adhesion in 1 cases). Postoperative fever rate was 9.81% (205/2 089). Conclusion:coblation technique is a good method for the treatment of children's adenoids and tonsil diseases with high efficiency and low complications. But improving the operation procedure proficiency level and skills of operation is an important link to reduce complications.

[The images of osteoarthrosis associated with anterior disc displacement without reduction detected by cone-beam CT]

Objective: To analyze the radiological characteristics of the condylar bone in patients with anterior disc displacement without reduction of temporomandibular joint using cone-beam CT (CBCT), and to further investigate the clinical factors possibly associated with the early-stage osteoarthritic changes. Methods: Two hundred and four individuals (≤30 years old) diagnosed as unilateral anterior disc displacement without reduction (disease duration≤1 year) were recruited. CBCT images of bilateral condyles were independently evaluated by two assessors and documented. Correlation between the early-stage osteoarthritic (OA) changes and gender, age, disease duration and mouth opening were analyzed using SPSS 21.0 software. Results: About sixty percent were presented with OA changes in the symptomatic joints, and most of them (47.1%) (96/204) were early-stage OA changes characterized by loss of continuity of articular cortex (Ⅰ) and/or surface erosion (Ⅱ). Logistics regression analyses indicated that disease duration (P =0.000) and mouth opening (P =0.002) were correlated significantly with early-stage OA changes. Conclusions: Disc displacement without reduction was closely related to OA occurrence. OA changes occurred in more than half of the patients after one month of the joint locked and more possibly in patients with increased mouth opening.

The mitochondrial pentatricopeptide repeat protein PPR19 is involved in the stabilization of NADH dehydrogenase 1 transcripts and is crucial for mitochondrial function and Arabidopsis thaliana development

Despite the importance of pentatricopeptide repeat (PPR) proteins in organellar RNA metabolism and plant development, the functions of many PPR proteins remain unknown. Here, we determined the role of a mitochondrial PPR protein (At1g52620) comprising 19 PPR motifs, thus named PPR19, in Arabidopsis thaliana. The ppr19 mutant displayed abnormal seed development, reduced seed yield, delayed seed germination, and retarded growth, indicating that PPR19 is indispensable for normal growth and development of Arabidopsis thaliana. Splicing pattern analysis of mitochondrial genes revealed that PPR19 specifically binds to the specific sequence in the 3'-terminus of the NADH dehydrogenase 1 (nad1) transcript and stabilizes transcripts containing the second and third exons of nad1. Loss of these transcripts in ppr19 leads to multiple secondary effects on accumulation and splicing of other nad1 transcripts, from which we can infer the order in which cis- and trans-spliced nad1 transcripts are normally processed. Improper splicing of nad1 transcripts leads to the absence of mitochondrial complex I and alteration of the nuclear transcriptome, notably influencing the alternative splicing of a variety of nuclear genes. Our results indicate that the mitochondrial PPR19 is an essential component in the splicing of nad1 transcripts, which is crucial for mitochondrial function and plant development.

Development of a Vivid FRET System Based on a Highly Emissive dG-dC Analogue Pair

A new type of Förster Resonance Energy Transfer (FRET) system using highly emissive isomorphic nucleobase analogues is reported. The FRET pair consists of 2-aminothieno[3,4-d]pyrimidine G-mimic deoxyribonucleoside (^th dG) as an energy donor and 1,3-diaza-2-oxophenothiazine (tC) as an energy acceptor. The distance and orientation between donor and acceptor was controlled by systematic incorporation of ^th dG and tC into DNA sequences to investigate the FRET efficiencies. This is the first Watson-Crick base-pairable FRET pair to produce vivid colors. In addition, this nucleic acid-based FRET pair was used to monitor DNA conformation and achieved visualization of the B-Z transition.

[Study on the contribution rate of follow-up formula to the nutrient intake of infants and young children aged 7-24 months in China]

Objective: To determine the contribution of follow-up formula (FUF) to the nutrient intake of 7-24-month-old infants and young children. Methods: The cluster random sampling method and the convenience sampling method were used in combination, and geographic and economic factors were taken into consideration. Four areas of China (Beijing, Hebei, Guangxi, Guangdong) were selected, with 120 infants chosen from each of these areas (half of which were 7-12 months old, and half were 13-24 months old). A dietary survey was completed by a continuous 24-hour weighing method over two days. Questionnaires were completed by their caregivers which included weighing the FUF and supplementary food given to the infant, and recording the frequency of breast feeding and any supplementary nutrients. A total of 518 questionnaires were distributed, and 472 questionnaires qualified for inclusion. Nutrient intake was calculated using the China food composition, infant formula food nutrient content and infant nutrition supplement brand-label information databases, and then the nutrient intake proportion (the percentage of estimated energy requirement (EER%), recommended nutrient intake (RNI%) or adequate intake (AI%)), and the contribution rate of FUF were analyzed. Results: A total of 472 infants were investigated (227 infants aged 7-12 months old, 245 infants aged 13-24 months old). The findings revealed that the median energy intake of 7- 12-month-old and 13- 24-month-old infants were 2 530.08 kJ and 3 445.48 kJ, respectively, which accounted for 85.18% and 94.14% of EER, respectively; and the median intake of protein reached 91.50% and 105.88% of their RNI/AI, respectively. For micronutrients, the median intake of vitamin B₁, vitamin B₂, niacin, vitamin E, potassium, zinc and manganese in 7- 12-month-old infants and vitamin B₂, vitamin E, potassium, magnesium, iron and manganese in 13-24-month-old children accounted for 82.00% and 114.29% of RNI/AI (RNI%/AI%), respectively. The intake of vitamin B₆, iron and selenium in 7-12-month-old infants and vitamin B₁, vitamin B₆, vitamin C, calcium and selenium in 13-24-month-old children was less than 80% RNI/AI. Furthermore, some nutrients showed higher intake levels, such as vitamin A, calcium, phosphorus and magnesium in 7-12-month-old infants and vitamin A and phosphorus in 13-24-month-old children, which were higher than 130% RNI/AI. In total, 40.53% (92) of infants aged 7-12 months and 52.65% (129) of children aged 13- 24 months were fed FUF as part of their diet, and its contribution rate to macronutrients was 29.69% for carbohydrates and 51.77% for fats, and to micronutrients was 2.04% for manganese and 74.24% for vitamin C. Conclusion: FUF contributes to the nutrient intake of infants and young children aged from 7-24 months old at different rates depending on the macronutrient or micronutrient analyzed.

[Photodynamic therapy by topical drup for the treatment of juvenile onset laryngeal papillomatosis]

Objective:To observe the therapeutic effect of photodynamic therapy(PDT) on the treatment of juvenile onset laryngeal papillomatosis. Method:Twenty-eight cases of children with laryngeal papilloma were treated,only 2 cases for the first time, and the rest were repeatedly treated outside our hospital, the average hospital surgery were more than 4 times. Under self retaining laryngoscope and microscope and endoscope assisted by semiconductor laser and plasma and cold instrument method，visible tumor resection and local affixed deposited 20% 5-aminolevulinic acid(photosensitizer) 3 hours later, with 635 nm semiconductor laser photodynamic,200-280 mW and can volume density of 80 to 120 J/cm², 20 min irradiation. PDT should be repeated after 25 days until no visible tumor.Then,2 times PDT must be done. Result:In 28 cases, 24 cases were followed up for more than 1 years(12 cases were followed up for 3 years),19 had no recurrence, the cure rate was 79.2%(19/24)；5 cases recurrence, and the recurrence rate was 20.8%(5/24)，among them,2 cases were abandoned because of the relapse，the other 3 cases were cure after 3 times of PDT.The main complications were adhesion of larynx. Conclusion:The preliminary effect of PDT by topical drug for the treatment of juvenile onset laryngeal papillomatosis is encouraging. The principle of PDT and the principle of the recurrence of laryngeal papilloma in children were also introduced in this paper.

Effects of pH and Salts on Physical and Mechanical Properties of Pea Starch Films

To identify the significant contribution of intermolecular hydrogen bonds of starch molecules to the film structure formation, pH of film-forming solutions was adjusted and also various salts (NaCl, CaCl2 , CaSO4 , and K2 SO4 ) were mixed into the glycerol-plasticized pea starch film. The film made from pH 7 possessed the highest tensile strength-at-break (2 times) and elastic modulus (4 to 15 times) and the lowest elongation-at-break compared with those of the films made from acid and alkali environments. The pH 7 film also has the highest film density and the lowest total soluble matter. At the level of 0.01 to 0.1 M of CaSO4 and 0.1 M of K2 SO4 in a kilogram of starch, the water solubility of the film increased, while chloride salts slightly lowered the solubility. NaCl and CaSO4 reduced water vapor permeability (WVP), while CaCl2 slightly increased WVP at 0.01 and 0.06 M concentrations, and K2 SO4 significantly increased WVP at 0.03 and 0.15 M. Presence of salts increased tensile strength (5 to 14 times than the control films) and elastic modulus (35 to 180 times) of starch film at 0.01 to 0.03 M of CaSO4 and K2 SO4 . Elongation-at-break increased significantly as salt concentration increases to an optimal level. However, when the concentration exceeded above the optimal level, the E of starch films decreased and showed no significant difference from the control film. Overall, the addition of salts modified physical and mechanical properties of pea starch films more than pH adjustment without any salt addition.

Effects of dietary supplementation of bacteriophages against enterotoxigenic Escherichia coli (ETEC) K88 on clinical symptoms of post-weaning pigs challenged with the ETEC pathogen

The present study was performed to investigate the effects of dietary supplementation of bacteriophages (phages) against enterotoxigenic Escherichia coli (ETEC) K88 as a therapy against the ETEC infection in post-weaning pigs. Two groups of post-weaning pigs aged 35 days, eight animals per group, were challenged with 3.0 × 10¹⁰ colony forming units of ETEC K88, a third group given the vehicle. The unchallenged group and one challenged group were fed a basal nursery diet for 14 days while the remaining challenged group was fed the basal diet supplemented with 1.0 × 10⁷ plaque forming units of the phage per kg. Average daily gain (ADG), goblet cell density and villous height:crypt depth (VH:CD) ratio in the intestine were less in the challenged group than in the unchallenged group within the animals fed the basal diet (p < 0.05); the reverse was true for rectal temperature, faecal consistency score (FCS), E. coli adhesion score (EAS) in the intestine, serum interleukin-8 (IL-8) and tumour necrosis factor-α (TNF-α) concentrations and digesta pH in the stomach, caecum and colon. The ETEC infection symptom within the challenged animals was alleviated by the dietary phage supplementation (p < 0.05) in ADG, FCS, EAS in the jejunum, serum TNF-α concentration, digesta pH in the colon, goblet cell density in the ileum and colon and VH:CD ratio in the ileum. Moreover, the infection symptom tended to be alleviated (p < 0.10) by the phage supplementation in rectal temperature, EAS in the ileum and caecum, and VH:CD ratio in the duodenum and jejunum. However, EAS in the colon, digesta pH in the stomach and caecum, and goblet cell density in the jejunum did not change due to the dietary phage. Overall, results indicate that the phage therapy is effective for alleviation of acute ETEC K88 infection in post-weaning pigs.

[Clinical effect analysis of adenoidectomy and tonsillectomy assisted with ablation on children]

Objective:This study aims to explore the clinical effect of adenoidectomy and tonsillectomy assisted with ablation on children.Method:The investigation took the form of retrospective review of 2 089 cases of children applied with adenoidectomy and tonsillectomy assisted with ablation in our hospital in recent 10 years. We obtained data of these children with epidemiological methods based on analyzing the status of general information and operation selections, and then analyzing the scores of snoring and breath preoperation and postoperation.Result:①General information of 2 089 cases followed with: the ratio of male and female was 2.08∶1，the average onset age was（5.87±3.12）years old, mostly ranged from 3 to 7 years old, which consists of 76.35%（1595/2089）of the group.②Different surgery methods of tonsil consisted of three groups as: partial resection associate with ablation was 69.17%(1445/2089), ablation alone was 22.26%(465/2089) and partial resection alone was 8.57%(179/2089) of the group.③A high level scores of snoring and breath more frequently found in preoperative cases than in postoperative cases(P <0.01).There are no differentiation among the scores of above three groups(P >0.05).The postoperative effect evaluation were related to allergic rhinitis, recurrent of tonsillitis, obesity, circular occipital hyperplasia and nasopharyngeal adhesion.Conclusion:The results suggested that surgery assisted with ablation has its advantage in adenoidectomy and tonsillectomy. Individual therapy for different children will improve the curative effect and relieve the pain of operation, thus is worth a wide application.

Abstract P5-08-23: Ki-67 expression is not a valuable predictive prognostic factor when progesterone receptor expression is high in estrogen receptor-positive breast cancer

Background

Immunohistochemistry markers are recognized as a predictive prognostic factor for women with breast cancer. Ki-67 and progesterone receptor (PgR) expression are reported to be independently associated with breast cancer prognosis. Some studies report high Ki-67 expression as a negative predictive marker. Whereas other studies report tendency of similar survival between high and low Ki67 cancers when PgR expression is high. In this study, we examined the prognostic significance of Ki-67 expression under PgR expression status.

Methods

The records of 2,366 patients were retrospectively reviewed. The patients underwent surgery for primary breast cancer from July 2009 to December 2012 at a single institution. We studied the prognostic significance of Ki-67 expression under PgR expression. We used 20% and 10% as the cut-off value for PgR and Ki-67, respectively. The end point was recurrence-free survival (RFS) evaluated by use of Kaplan-Meier analysis.

Result

Of the 2,366 analyzed patients, the median follow-up time was 43 months. During follow-up, 44 patients had recurrence, loco-regional recurrence developed in 23 patients and distant recurrence developed in 21 patients. In patients with low PgR expression, high Ki-67 expression group showed significantly worse prognosis compared to low Ki-67 expression group (p=0.005). On the other hand, no significant difference was shown between low and high Ki-67 expression group when PgR expression was high (p=0.637). Also multivariate analysis demonstrated that high Ki-67 expression was an independent prognostic factor only when PgR expression was low. (95% confidence interval [CI], 1.35-10.48; p=0.011)

Conclusion

This is the largest reported study that prognostic significance of Ki-67 expression is defined by PgR expression. Our study presents that high Ki-67 expression is inversely correlated with recurrence risk in early breast cancer patients only under low PgR expression. At high PgR expression, Ki-67 expression has no influence on breast cancer prognosis. Therefore, attention should be paid to correlation between PgR and Ki-67 expression.

Citation Format: Han JH, Kang YJ, Han W, Lee H-B, Kim Y, Yoo T-K, Moon H-G, Noh D-Y. Ki-67 expression is not a valuable predictive prognostic factor when progesterone receptor expression is high in estrogen receptor-positive breast cancer. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P5-08-23.

Abstract P6-04-02: Identification of ESR1 splice variants associated with prognosis in estrogen receptor positive breast cancer

Background: Splice variants play a major role in carcinogenesis and disease progression. It is well known that androgen receptor splice variants are associated with resistance to prostate cancer treatment. Estrogen receptor (ER)-positive breast cancers constitute about 70% of all breast cancers and have better prognosis compared to ER-negative cancers. However, there are ER-positive breast cancers that acquire resistance to anti-estrogen therapy, and 12-55% of those tumors were shown to possess ESR1 mutations. The aim of this study was to identify common splice variants in the ESR1 gene and investigate their association with disease outcome.

Methods: Whole transcriptome sequencing was performed on breast cancer specimens from 120 invasive breast cancer patients who underwent operation at Seoul National University Hospital (SNUH) and data from SNUH, GEO, and The Cancer Genome Atlas (TCGA) was used for normal breast tissue sequencing. Exon-exon junctions were identified on aligned RNA sequencing data and was used to construct exon graphs. Splice variant candidates were selected from exon graphs and were merged according to variant subtypes of samples. Subtypes were accessed differentially in relation to how frequent the junctions appear in tumor samples and common exon skipping types with frequent junctions were identified. TCGA RNA sequencing data was then used to search for the common exon skipping subtypes detected from SNUH RNA sequencing data.

Results: Of the 120 tumor samples, 50 were clinically ER-positive by immunohistochemistry. Among exon paths logically possible, 125 paths were not observed in normal breast tissues. Exon 4-5 junction was the most commonly observed junction in the tumor samples. In a search for exon skipping type that results in missing ligand-binding domain of ER, three exon skipping types were identified. Exon skipping with exon 5-10 junction (type 1), exon 9-12 junction (type 2), and exon 10-12 (type 3) was seen in 4 (8%), 4 (8%), and 10 (20%) ER-positive samples, respectively. Retrospective medical chart review of the 18 patients showed recurrence in 4 (100%), 2 (50%), and 4 (40%) patients with type 1, 2, and 3 exon skipping, respectively. Evaluation of TCGA RNA sequencing data of 872 ER-positive samples suggested exon 4-5 junction as the most common junction. A search for exon skipping types in TCGA revealed 1 (0.1%), 9 (1.0%), and 454 (52.1%) samples with type 1, 2, and 3 exon skipping, respectively. However, none of the patients with type 1 or 2 had metastasis or had expired. Of the 454 patients with type 3 exon skipping, 54 patients had died, constituting 61.4% of 88 mortalities in the whole ER-positive population.

Conclusion: Certain splice variants of ESR1 gene yields exon skipping subtypes commonly observed in the ER-positive breast cancer. Estrogen receptor-positive breast cancer with these exon skipping types resulting in a missing ligand-binding domain of ER may be associated with poorer disease outcome. Further investigation is warranted to validate the role of ESR1 exon skipping subtypes in the disease progression of breast cancer.

Citation Format: Lee H-B, Han W, Ko S, Kim M-S, Lim S, Lee K-M, Kang YJ, Han JH, Kim Y, Yoo T-K, Moon H-G, Noh D-Y, Kim S, Han W. Identification of ESR1 splice variants associated with prognosis in estrogen receptor positive breast cancer. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P6-04-02.

Abstract P2-02-15: Discovery of putative circulating tumor cells through somatic mutation profile of epithelial cell adhesion molecule positive single cells from blood of metastatic breast cancer patients

Background: Circulating tumor cell (CTC) enumeration provides prognostic information for chemotherapy in metastatic breast cancer. However, due to its rarity and heterogeneity, it is difficult to distinguish true CTCs from normal blood cells and perform genomic analysis on them for use in therapeutic strategies. The main application of most currently available CTC detection systems consists of an enumeration of putative CTCs without further analysis. The aim of this study was to evaluate the feasibility of single cell picking and target sequencing of epithelial cell adhesion molecule (EpCAM)-positive cells for detecting CTCs.

Methods: Whole blood sampled from metastatic breast cancer patients who were newly diagnosed with metastasis or who had disease progression during palliative treatment were used for this study. After applying IsoFlux Circulating Tumor Cell Enrichment Kit (Fluxion, South San Francisco, CA, USA), single CTC candidates were picked from a pool of EpCAM-positive cells. Genomic DNA from the picked cells was whole genome amplified and target sequencing was performed using Ion AmpliSeq™ Cancer Hotspot Panel (Life Technologies, Carlsbad, CA, USA). Target sequencing reads were mapped to human genome reference (hg19) using BWA-MEM (0.7.10). Single nucleotide variants (SNVs) were annotated using dbSNP, Variome Data 0.2, and COSMIC databases.

Results: A total of 172 EpCAM-positive cells were selected according to size and EpCAM status from whole blood of 11 patients. The remaining cells were grouped into a pooled sample for each patient. The mean read depth of the target genes was 13455×. A mean 7.82 mutations as determined by SNVs listed in the COSMIC database but not in dbSNP and Variome Data 0.2 were detected in each patient. Cells with multiple mutated genes, or those with a mutated gene repeatedly observed in another cell from the same patient were judged to be putative CTCs. At least 2 putative CTCs were detected in 7 patients while no CTCs were detected in 2 patients. Mutated genes observed in the putative CTCs were ABL1, AKT1, APC, CDH1, CDKN2A, ERBB2, FGFR3, HRAS, IDH1, JAK2, KDR, NPM1, RB1, RET, SMARCB1, STK11, and TP53.

Conclusions: Potential CTCs were successfully identified by single cell picking and target sequencing of EpCAM-positive cells from whole blood of metastatic breast cancer patients. Unique mutations not detected in other single cells and pooled samples can be used to distinguish putative CTCs from normal cells. Genomic profiling of corresponding primary tumor and metastatic site biopsy is warranted to verify the CTCs and investigate their role in disease progression.

Citation Format: Lee H-B, Jeon S, Kim BC, Jho S, Kim J, Kang YJ, Yoo T-K, Han JH, Kim Y, Im S-A, Moon H-G, Noh D-Y, Han W. Discovery of putative circulating tumor cells through somatic mutation profile of epithelial cell adhesion molecule positive single cells from blood of metastatic breast cancer patients. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P2-02-15.

Poor physical fitness is independently associated with mild cognitive impairment in elderly Koreans

The purpose of this study was to investigate the association between physical fitness and mild cognitive impairment (MCI) in elderly Koreans. This was a cross-sectional study that involved 134 men and 299 women aged 65 to 88 years. Six senior fitness tests were used as independent variables: 30 s chair stand for lower body strength, arm curl for upper body strength, chair-sit-and-reach for lower body flexibility, back scratch for upper body flexibility, 8-ft up-and-go for agility/dynamic balance, and 2-min walk for aerobic endurance. Global cognitive function was assessed using the Korean version of the Mini-Mental State Examination (MMSE). Potential covariates such as age, education levels, blood lipids, and insulin resistance (IR) markers were also assessed. Compared to individuals without MMSE-based MCI, individuals with MMSE-based MCI had poor physical fitness based on the senior fitness test (SFT). There were significant positive trends observed for education level (p=0.001) and MMSE score (p<0.001) across incremental levels of physical fitness in this study population. Individuals with moderate (OR=0.341, p=0.006) and high (OR=0.271, p=0.007) physical fitness based on a composite score of the SFT measures were less likely to have MMSE-based MCI than individuals with low physical fitness (referent, OR=1). The strength of the association between moderate (OR=0.377, p=0.038) or high (OR=0.282, p=0.050) physical fitness and MMSE-based MCI was somewhat attenuated but remained statistically significant even after adjustment for the measured compounding factors. We found that poor physical fitness was independently associated with MMSE-based MCI in elderly Koreans.