Near-Atomic Fabrication with Nucleic Acids

Nucleic acids hold great promise for bottom-up construction of nanostructures via programmable self-assembly. Especially, the emerging of advanced sequence design principles and the maturation of chemical synthesis of nucleic acids together have led to the rapid development of structural DNA/RNA nanotechnology. Diverse nucleic acids-based nano objects and patterns have been constructed with near-atomic resolutions and with controllable sizes and geometries. The monodispersed distribution of objects, the up-to-submillimeter scalability of patterns, and the excellent feasibility of carrying other materials with spatial and temporal resolutions have made DNA/RNA assemblies extremely unique in molecular engineering. In this review, we summarize recent advances in nucleic acids-based (mainly DNA-based) near-atomic fabrication by focusing on state-of-the-art design techniques, toolkits for DNA/RNA nanoengineering, and related applications in a range of areas.

Engineered DNA nanodrugs alleviate inflammation in inflammatory arthritis

Rheumatoid arthritis (RA) is an autoimmune disease featured with chronic joint inflammation. Suppression of inflammation is critical to RA treatment and joint protection. In this study, DNA nanodrugs are prepared via the conjugation of NF-κB decoy oligodeoxynucleotides (dODNs) and VCAM-1 targeted peptides (P) onto self-assembled DNA tetrahedrons (TDs). Physicochemical properties of DNA nanodrugs are characterized using atomic force microscopy (AFM), gel electrophoresis and Fourier Transform Infrared Spectrometer (FTIR). Cytotoxicity, cellular uptake and anti-inflammatory efficacy of DNA nanodrugs are evaluated in vitro. Clinical arthritis index, inflammatory proteins in serum and joint pathophysiology are also investigated in vivo. TD-P-dODN possesses one dODN and one P and exhibits faster and higher cellular uptake by inflammatory cells compared with free dODNs. TD-P-dODN also significantly reduce inflammatory proteins in cells and adjuvant induced arthritis (AIA) mice. Reduced clinical arthritis index and improved joint rehabilitation are also achieved by TD-P-dODN treatment. This study demonstrates that an engineered DNA nanodrug (TD-P-dODN) enhances the efficacy of nucleic acid drugs and represents a promising strategy for RA treatment.

WHITE STRIPE LEAF8, encoding a deoxyribonucleoside kinase, is involved in chloroplast development in rice

WSL8 encoding a deoxyribonucleoside kinase (dNK) that catalyzes the first step in the salvage pathway of nucleotide synthesis plays an important role in early chloroplast development in rice. The chloroplast is an organelle that converts light energy into chemical energy; therefore, the normal differentiation and development of chloroplast are pivotal for plant survival. Deoxyribonucleoside kinases (dNKs) play an important role in the salvage pathway of nucleotides. However, the relationship between dNKs and chloroplast development remains elusive. Here, we identified a white stripe leaf 8 (wsl8) mutant that exhibited a white stripe leaf phenotype at seedling stage (before the four-leaf stage). The mutant showed a significantly lower chlorophyll content and defective chloroplast morphology, whereas higher reactive oxygen species than the wild type. As the leaf developed, the chlorotic mutant plants gradually turned green, accompanied by the restoration in chlorophyll accumulation and chloroplast ultrastructure. Map-based cloning revealed that WSL8 encodes a dNK on chromosome 5. Compared with the wild type, a C-to-G single base substitution occurred in the wsl8 mutant, which caused a missense mutation (Leu 349 Val) and significantly reduced dNK enzyme activity. A subcellular localization experiment showed the WSL8 protein was targeted in the chloroplast and its transcripts were expressed in various tissues, with more abundance in young leaves and nodes. Ribosome and RNA-sequencing analysis indicated that some components and genes related to ribosome biosynthesis were down-regulated in the mutant. An exogenous feeding experiment suggested that the WSL8 performed the enzymic activity of thymidine kinase, especially functioning in the salvage synthesis of thymidine monophosphate. Our results highlight that the salvage pathway mediated by the dNK is essential for early chloroplast development in rice.

563 Early systolic function is impaired in patients with heart failure and preserved ejection fraction and is a more important predictor of clinical outcomes than diastolic function

Funding Acknowledgements

British Heart Foundation

Aims

First-phase ejection fraction (EF1), the ejection fraction up to the time of maximal ventricular contraction may be impaired in heart failure with preserved ejection fraction (HFpEF), with homeostatic mechanisms preserving the overall ejection fraction. We examined whether EF1 is impaired and whether it predicts adverse outcomes in patients with HFpEF.

Methods and Results

We examined EF1 in patients with HFpEF diagnosed according to European Society of Cardiology guidelines, in subjects with pre-clinical diastolic dysfunction and in control subjects with no evidence of heart failure. The predictive value of EF1 for a combined end-point of re-hospitalisation for heart failure and death from any cause was compared to that of conventional echocardiographic and other indices. There was a progressive impairment of EF1 in patients with diastolic dysfunction and HFpEF compared to those without evidence of heart failure (P < 0.001). In 180 HFpEF patients followed for a median of 14.7 months, 101 patients reached the primary endpoint (61 deaths and 40 hospitalisations). EF1 was the most powerful predictor of events (table 1). A cut-off value of 19.4% gave hazard ratios (for EF1 < 19.4% compared to ≥19.4%) of 3.04 (figure 1), (95% confidence interval 2.014 – 4.604, P < 0.001) unadjusted, and 2.976 (1.887 – 4.695, P < 0.001) adjusted for age, gender, other echocardiographic indices (including EF, E/e’ ratio, stroke volume and left atrial volume index) and N-terminal pro-brain natriuretic peptide.

Conclusion

Early systolic function is impaired in HFpEF and is a powerful predictor of clinical outcomes. Therapies targeted at improving early systolic function may improve outcomes in HFpEF.

Table 1 HR CI (95%) P value Age 1.020 1.001 - 1.039 0.042 Female Gender 1.989 1.254 - 3.156 0.003 ln NT-proBNP 1.354 1.096 - 1.672 0.005 Haemoglobin 0.992 0.980 - 1.005 0.225 eGFR 0.997 0.988 - 1.006 0.568 Structural Heart Disease 0.748 0.439 - 1.274 0.285 Diastolic Dysfunction 0.694 0.445 - 1.082 0.107 Ejection Fraction 1.031 0.996 - 1.068 0.082 Stroke Volume index 0.963 0.940 - 0.986 0.002 TPAVF 0.995 0.980 - 1.005 0.230 EF1 0.900 0.869 - 0.932 <0.001 Multivariate analysis of predictors of events

Abstract 563 Figure 1 Kaplan-Meier Curve

Increased expression of miR-330-3p: a novel independent indicator of poor prognosis in human breast cancer

OBJECTIVE

Previous study has reported that miR-330-3p was highly expressed in breast cancer (BC) patients. However, the effect of miR-330-3p in BC progression remains largely unclear. The purpose of this study was to investigate the clinical significance of miR-330-3p expression in BC.

PATIENTS AND METHODS

The expression of miR-330-3p was detected by quantitative Real-time PCR in BC tissues and matched normal breast tissues. The association of miR-330-3p expression with clinicopathological factors of BC patients was also analyzed by x2-test. Prognosis value of patients with BC was assessed by Kaplan-Meier method and Cox proportional hazards model, respectively.

RESULTS

Quantitative real-time PCR analysis showed that the expression level of miR-330-3p was significantly higher in BC specimens than that in corresponding noncancerous tissues (p < 0.01). The levels of miR-330-3p were positively correlated with the status of TNM stage (p = 0.011) and lymph node metastasis (p = 0.006). Kaplan-Meier analysis revealed that 5-year overall survival of BC patients with high miR-330-3p expression was shorter compared to those patients with low miR-330-3p expression (p < 0.0001). Moreover, univariate and multivariate regression analysis demonstrated that miR-330-3p was an independent prognostic factor in BC.

CONCLUSIONS

Our data suggest that miR-330-3p upregulation maybe concurrently associated with prognosis in patients with BC, suggesting that miR-330-3p may be a potential prognostic biomarker and therapeutic target for patients with BC.

Whole exome sequencing identified a second pathogenic variant in HOMER2 for autosomal dominant non-syndromic deafness

Hearing loss is one of the most common sensory disorders worldwide, and about half of all occurrences are attributable to genetic factors. Here, we have identified a novel pathogenic variant in HOMER2 in a Chinese family with autosomal dominant, non-syndromic hearing loss. This is the second family reported globally with hearing loss caused by a variant in HOMER2. The pathogenic variant c.840_841insC in HOMER2 (NM_199330), segregating with the hearing-loss phenotype in the family, leads to a premature stop codon producing a truncated protein. The coiled-coil domain in the C-terminal of HOMER2 protein is essential for protein multimerization and HOMER2-CDC42 interaction. We compared the phenotypes in the two families and found that hearing impairment in this Chinese family was more severe. Furthermore, we found that the ability of this insertion mutant type HOMER2 (HOMER2_MU ) to multimerize decreased more significantly than wild-type HOMER2 (HOMER2_WT ) and the reported c.554G>C (NM_004839) mutant HOMER2. HOMER2_MU protein tended to be distributed in a diffuse manner, whereas HOMER2_WT and the reported mutant HOMER2 tended to cluster together. Our research provides a validating second family for variants in HOMER2 causing non-syndromic sensorineural hearing loss. HOMER2 homo-/hetero-multimerization might be the first step in exerting its normal function.

Recognizing basal cell carcinoma on smartphone-captured digital histopathology images with a deep neural network

BACKGROUND

Pioneering effort has been made to facilitate the recognition of pathology in malignancies based on whole-slide images (WSIs) through deep learning approaches. It remains unclear whether we can accurately detect and locate basal cell carcinoma (BCC) using smartphone-captured images.

OBJECTIVES

To develop deep neural network frameworks for accurate BCC recognition and segmentation based on smartphone-captured microscopic ocular images (MOIs).

METHODS

We collected a total of 8046 MOIs, 6610 of which had binary classification labels and the other 1436 had pixelwise annotations. Meanwhile, 128 WSIs were collected for comparison. Two deep learning frameworks were created. The 'cascade' framework had a classification model for identifying hard cases (images with low prediction confidence) and a segmentation model for further in-depth analysis of the hard cases. The 'segmentation' framework directly segmented and classified all images. Sensitivity, specificity and area under the curve (AUC) were used to evaluate the overall performance of BCC recognition.

RESULTS

The MOI- and WSI-based models achieved comparable AUCs around 0·95. The 'cascade' framework achieved 0·93 sensitivity and 0·91 specificity. The 'segmentation' framework was more accurate but required more computational resources, achieving 0·97 sensitivity, 0·94 specificity and 0·987 AUC. The runtime of the 'segmentation' framework was 15·3 ± 3·9 s per image, whereas the 'cascade' framework took 4·1 ± 1·4 s. Additionally, the 'segmentation' framework achieved 0·863 mean intersection over union.

CONCLUSIONS

Based on the accessible MOIs via smartphone photography, we developed two deep learning frameworks for recognizing BCC pathology with high sensitivity and specificity. This work opens a new avenue for automatic BCC diagnosis in different clinical scenarios. What's already known about this topic? The diagnosis of basal cell carcinoma (BCC) is labour intensive due to the large number of images to be examined, especially when consecutive slide reading is needed in Mohs surgery. Deep learning approaches have demonstrated promising results on pathological image-related diagnostic tasks. Previous studies have focused on whole-slide images (WSIs) and leveraged classification on image patches for detecting and localizing breast cancer metastases. What does this study add? Instead of WSIs, microscopic ocular images (MOIs) photographed from microscope eyepieces using smartphone cameras were used to develop neural network models for recognizing BCC automatically. The MOI- and WSI-based models achieved comparable areas under the curve around 0·95. Two deep learning frameworks for recognizing BCC pathology were developed with high sensitivity and specificity. Recognizing BCC through a smartphone could be considered a future clinical choice.

[Effect of two kinds of materials on the prevention of early erosive enamel wear]

Objective: To investigate the preventive effect of resin infiltration and adhesive on early erosive enamel wear. Methods: Orthodontic reduction premolars collected from Central Laboratory of Nanjing Stomatological Hospital, Medical School of Nanjing University were used to prepare 70 specimens. Forty samples were divided into eight groups (n=5) and treated with different conditions (pH=1.6, 2.4, 3.2 or 4.0 hydrochloric acid solution, etching time was 30 or 60 s), and the conditions for obtaining early erosive enamel samples were selected. Based on this procedure, thirty early erosive enamel samples were made and divided into three groups: control group, resin infiltration group, and adhesive group. And the treatment of 30 days acid abrasion cycle was carried out. Confocal microscopy was used to measure the thickness changes of enamel or material before and after cycle. Results: Early erosive enamel samples was obtained when pH was 4.0 and etching time was 60 s. After 30 days cycle, the wear of enamel was (29.71±6.72) μm in control group, (5.60±2.24) μm in resin infiltration group and (2.89±1.03) μm in adhesive group. In infiltration group and adhesive group, lower enamel was not affected by the cycle, and the material loss ratios of the infiltration resin group and adhesive group were 0.41±0.14 and 0.29±0.13, respectively. The ratio of material loss was not significantly different (P>0.05). But infiltration group lost (12.95±2.22) μm of enamel during the application of the material. Conclusions: Resin infiltration and adhesive have the same short-term protective effect against early erosive enamel wear. Adhesive has less damage to enamel and better effect.

[Clinical analysis of MRS and DWI in predicting delayed brain edema after spontaneous intracerebral hemorrhage]

Objective: Prediction of delayed brain edema after spontaneous intracerebral hemorrhage by magnetic resonance spectroscopy combined with diffusion weighted imaging, and to explore the causes and treatment of delayed brain edema after intracerebral hemorrhage. Methods: The patients with spontaneous cerebral hemorrhage diagnosed by CT from January 2015 to June 2018 in our hospital were analyzed. Magnetic resonance spectroscopy and diffusion weighted imaging examinations were performed on the third day after hemorrhage. It was diagnosed as delayed brain edema that the edema range enlarged more than 1 cm in CT scan on the 14th day Compare with the 7th Day. The patients were divided into the delayed brain edema group and the control group(n=27 for each). The NAA/Cr value and rADC value of the edema area in the two groups were analyzed by T test. Results: The NAA/Cr value (1.67±0.38) in the edema area of patients with delayed brain edema was significantly decreased Compare with the control group(1.92±0.42), and the rADC value (2.59±0.42) reduced significantly Compare with the control group (2.93±0.51), the differences were statistically significant (P<0.05). Conclusion: MRS and DWI were susceptive in showing delayed brain edema lesions at hyper-early phase. Combination of MRS and DWI can provide a basis for clinical individual treatment programs selection and prognostic evaluation.

[Association of arsenic with unexplained recurrent spontaneous abortion: a case-control study]

Objective: To explore the association of arsenic with unexplained recurrent spontaneous abortion (URSA). Methods: A case-control study was conducted to select URSA patients who were admitted to the Beijing Maternal and Child Health Care Hospital affiliated to Capital Medical University from April to October 2018 as a case group. Women who had a normal pregnancy in the Family Planning Department of the hospital but volunteered to have an abortion were selected as a control group. The case and control group were paired in a 1: 1 ratio. The inclusion criteria of the case group were patients with newly diagnosed recurrent spontaneous abortion who had clinically confirmed more than 2 spontaneous abortions and had 20 weeks prior to pregnancy, excluding patients with recurrent spontaneous abortion caused by abnormal blood coagulation (anti-phospholipid antibody positive), abnormal physiological anatomy (B-ultrasound), abnormal immune factors (anti-nuclear antibody positive, anti-cardiolipin antibody, etc.), genetic chromosomal abnormalities (karyotype analysis) and pathogenic microbial infection. The control group was matched according to the age of the case group (±3 years old) and the gestational age (±2 weeks) to exclude adverse pregnancy outcomes such as stillbirth, congenital malformation, premature delivery and low birth weight infants. A total of 192 subjects were included. Questionnaires were used to collect information of all subjects, and 12 ml of peripheral venous blood was collected to detect blood arsenic levels. Blood arsenic levels were divided into low concentration group (<1.00 μg/L), medium concentration group (1.00-1.50 μg/L) and high concentration group (>1.50 μg/L). The multivariate conditional logistic regression was performed to analyze the relationship between blood arsenic exposure and URSA and explore the influencing factors of blood Arsenic. Results: The geometric mean values of blood arsenic level in the cases group and control group were 1.68 (1.50-1.86) μg/L and 1.26 (1.17-1.37) μg/L, respectively. The blood arsenic level in the case group was significantly higher than that in the control group (P<0.05). The results of multivariate conditional logistic regression analysis showed that after adjusting for tobacco exposure during pregnancy, pre-pregnancy body mass index and the effects of residential decoration in past five years, the risk of URSA was higher in the high-concentration group compared with the low-concentration group (OR=2.56, 95%CI:1.06-6.24). Conclusion: Blood arsenic may increase the risk of URSA in women of childbearing age.

Targeting nucleolin to obstruct vasculature feeding with an intelligent DNA nanorobot

A prototype of DNA nanorobot with the ability to transport molecular payloads was designed to target cancer cells in tissue culture. Moreover, a further step was taken to succeed in the first in vivo application of the DNA nanorobot for cancer therapy. The robot was constructed using aptamer and DNA origami to fold a 90-nm tubular device to carry the blood coagulation protease thrombin inside, shielded from circulating platelets and plasma fibrinogen. The recognition and binding of the aptamer to its tumour-specific target molecule triggered the robot unfolding to expose thrombin to the blood, which in turn activated coagulation at the local tumour site, resulting in tumour necrosis and inhibition of tumour growth. Since all solid-tumour feeding vessels are virtually the same, this strategy could be effective against many types of malignant diseases.

Why hasn't this woman been screened for breast and cervical cancer? - Evidence from a Chinese population-based study

OBJECTIVE

Less than half of eligible Chinese rural women have been screened for breast and cervical cancer. The objective of this study was to describe individual-level reasons for attending or not attending 'two cancers' screening using Andersen's Behavioral Model of Health Services Use.

STUDY DESIGN

Cross-sectional study.

METHODS

The study sample was from the Health Services Survey in 2013 in Jiangsu, China. A total of 6520 rural women aged 36-65 years answered the questions on 'two cancers' screening participation and were included in the final analysis, which consisted of univariate and multivariate logistic regression.

RESULTS

In the results of multivariate logistic regression, factors significantly associated with having 'two cancers' screening included educational level (odds ratio [OR] = 0.78, 95% confidence interval [CI] = 0.65-0.92), per capita household income (OR = 0.65, 95% CI = 0.58-0.73), availability of female medical faculty in township facilities (OR = 0.35, 95% CI = 0.28-0.42), quality of life (OR = 0.72, 95% CI = 0.58-0.90), being nulliparous (OR = 3.21, 95% CI = 1.96-5.26), and multiparous (OR = 1.91, 95% CI = 1.68-2.16).

CONCLUSION

To reduce inadequate screening service utilization of breast and cervical cancer in rural areas, efforts should be made not only to target the vulnerable rural women with lower income, lower educational level, and lower health conditions but also to further improve access to female primary-care providers. Strategies are also urgently needed to focus on nulliparous and multiparous women.

[Analysis of 5 children with congenital thrombotic thrombocytopenic purpura]

Objective: To explore the clinical features and points of diagnosis and treatment for congenital thrombotic thrombocytopenic purpura (TTP) in children. Methods: The clinical manifestations, laboratory tests, genetic analysis and treatments of 5 children with congenital TTP hospitalized in Beijing Children's Hospital, Capital Medical University from February 2015 to July 2017 were analyzed retrospectively. Results: Among the 5 children with congenital TTP diagnosed by genetic monitoring and enzymology, there were 1 male and 4 females, 3 cases had suspicious positive family history, the age of onset was several hours after birth (range several hours after birth to 28 months). The main clinical manifestations were recurrent moderate to severe thrombocytopenia in 5 cases, mild to moderate hemolytic anemia in 4 cases, proteinuria or hematuria in 2 cases, and nervous system involvement in 1 case. The recurrence time was 1.5 (range 1.0 to 5.0) times per year and most of the inducing factors were respiratory and (or) digestive tract infections. Laboratory test showed that ADMATS13 enzyme activity were 0 in 4 cases, the enzyme activity was 100% in 1 case due to plasma infusion before examination. ADMATS13 enzyme antibody detection of all 5 cases were negative. Genetic analysis of all 5 children showed complex heterozygous mutations at different loci of ADAMTS13 gene, among which 8 loci were previously unreported, details are as follows: missense mutations in 4 cases (c.1564T>C(p.522C>R), c.1510G>T(p.504D>Y), c.4154A>C(p.1385Q>P) and c.G3854C (P.R1285P)); frameshift mutations in 3 cases(c.2875_2876insT (p.959Lfs29), c.2362_2363delGG (p.788G>Gfs56) and c.1335delC (p.F445fs)), shear mutation in one case(IVS21+1A>G). The patients in the acute phase were all treated with fresh frozen plasma infusion (10 ml/(kg·d)), continuous application for 7-14 days). Platelets gradually returned to normal and clinical symptoms improved. The follow-up time was 27 months (range 11-35 months). All the children survived, among whom 2 cases were treated with prophylaxis and monitoring platelet stability above 200×10(9)/L, 3 cases were treated on-demand only when platelet decreased and monitoring platelet stability above 100×10(9)/L. Conclusions: The main clinical manifestation of congenital TTP is recurrent thrombocytopenia with or without hemolytic anemia. The key point of treatment is plasma infusion. Genetic testing is helpful for early diagnosis.

DNA Nanostructure-Based Systems for Intelligent Delivery of Therapeutic Oligonucleotides

In the beginning of the 21st century, therapeutic oligonucleotides have shown great potential for the treatment of many life-threatening diseases. However, effective delivery of therapeutic oligonucleotides to the targeted location in vivo remains a major issue. As an emerging field, DNA nanotechnology is applied in many aspects including bioimaging, biosensing, and drug delivery. With sequence programming and optimization, a series of DNA nanostructures can be precisely engineered with defined size, shape, surface chemistry, and function. Simply with hybridization, therapeutic oligonucleotides including unmethylated cytosine-phosphate-guanine dinucleotide oligos, small interfering RNA (siRNA) or antisense RNA, single guide RNA of the regularly interspaced short palindromic repeat-Cas9 system, and aptamers, are successfully loaded on DNA nanostructures for delivery. In this progress report, the development history of DNA nanotechnology is first introduced, and then the mechanisms and means for cellular uptake of DNA nanostructures are discussed. Next, current approaches to deliver therapeutic oligonucleotides with DNA nanovehicles are summarized. In the end, the challenges and opportunities for DNA nanostructure-based systems for the delivery of therapeutic oligonucleotides are discussed.