Mutation analysis and pathogenicity identification of Mucopolysaccharidosis type IVA in 8 south China families

BACKGROUND

Mucopolysaccharidosis type IVA (MPS IVA) is a rare autosomal recessive lysosomal storage disorder caused by GALNS gene mutation. The aim of our study is to detect pathogenic variants for patients suspected of MPS IVA and set the base for subsequent prenatal diagnosis and preimplantation genetic diagnosis.

METHODS

In our study, 9 MPS IVA patients from south China families were investigated. Urine glycosaminoglycans (GAG_S) screening was used as an initial method. For patients with abnormal result, all 14 exons and intron-exon junctions of the GALNS gene were sequenced after amplification from genomic DNA. The pathogenicity of novel mutations were analyzed with molecular genetics, bioinformatics and structure modeling in light of clinical manifestations and biochemical results.

RESULTS

Among 12 mutations detected, direct sequencing found 3 novel mutations (c.686A>C, p.Y229S; c.1498G>T, p.G500C; c.278T>C, p.I93T). The pathogenicity of these novel mutations was illustrated by correlating clinical symptoms with pedigree analysis and bioinformatics analysis.

CONCLUSION

The detection and variant analysis are essential for accurate diagnosis of MPS IVA patients. Our results enrich GALNS gene mutation spectrum of Chinese population. This information has important clinical value for molecular diagnosis and genetic counseling of patients with this disease.

Increased PD-1 MRNA Expression in Peripheral Blood Cells of ER+ and PR+ Breast Cancer Patients and Its Unfavorable Prognostic Value

Background: The clinical significance of programmed cell death 1 (PD-1) and cytotoxic T lymphocyte-associated protein 4 (CTLA-4) expression on tumor infiltrating lymphocytes in breast cancer patients has been confirmed, while that of peripheral blood cells derived immune molecules remain unclear. Aim: We aimed to investigate the clinical importance of immune molecules, including PD-1 and CTLA-4, expression in peripheral blood cells of breast cancer patients, especially in terms of the relationship between immune molecules and estrogen receptor (ER)/progesterone receptor (PR) status, as well as their prognostic values. Methods: We enrolled 109 breast cancer patients, including 52 cases before surgery and neoadjuvant treatment (PreS group), 18 cases postsurgery and adjuvant chemoradiotherapy (PostS group), 39 metastatic cases presalvage treatment (Met group), and 21 age- and sex-matched healthy volunteers). The mRNA abundance of PD-1, CTLA-4, IL-2 receptor alpha (IL-2Rα), and cluster of differentiation 28 (CD28), forkhead box P3 (FOXP3), transforming growth factor beta (TGF-β), and interleukin-10 (IL-10) in pretreatment peripheral blood were analyzed by quantitative real-time PCR. Results: ER+ breast cancer patients showed significant higher mRNA levels of PD-1, CTLA-4, IL-2Rα, and CD28 with fold changes of 10.8, 2.4, 5.0, and 3.8, respectively ( P < 0.05) than that of ER− cases. Similarly, PR+ patients showed increased levels of PD-1, CTLA-4, and CD28 with fold changes of 6.7, 2.0, and 2.5, respectively ( P < 0.05) comparing to that of PR− cases. Patients in PreS group and Met group showed higher mRNA levels of PD-1, CTLA-4, IL-2Rα, CD28, FOXP3, TGF-β, and IL-10 than PostS group and healthy volunteers. Univariable analysis revealed that high PD-1 expression was associated with poorer progression-free survival (PFS) in metastatic breast cancer patients (5.9 vs 14.6 months, HR: 2.47, 95% CI: 1.22-5.02, P = 0.046). Meanwhile, the prognostic value of PD-1 was remained in multivariate analyses (HR: 2.22, 95% CI: 1.04-4.73, P = 0.039). Conclusion: Increased PD-1, CTLA-4, and CD28 mRNA abundance were showed in breast cancer patients and ER+/PR+ cases, which may provide the rationale for combining checkpoint inhibitors with endocrine therapy for breast cancer treatment. Furthermore, PD-1 is a promising prognostic biomarker for metastatic breast cancer.

Data-Driven Robust M-LS-SVR-Based NARX Modeling for Estimation and Control of Molten Iron Quality Indices in Blast Furnace Ironmaking

Optimal operation of an industrial blast furnace (BF) ironmaking process largely depends on a reliable measurement of molten iron quality (MIQ) indices, which are not feasible using the conventional sensors. This paper proposes a novel data-driven robust modeling method for the online estimation and control of MIQ indices. First, a nonlinear autoregressive exogenous (NARX) model is constructed for the MIQ indices to completely capture the nonlinear dynamics of the BF process. Then, considering that the standard least-squares support vector regression (LS-SVR) cannot directly cope with the multioutput problem, a multitask transfer learning is proposed to design a novel multioutput LS-SVR (M-LS-SVR) for the learning of the NARX model. Furthermore, a novel M-estimator is proposed to reduce the interference of outliers and improve the robustness of the M-LS-SVR model. Since the weights of different outlier data are properly given by the weight function, their corresponding contributions on modeling can properly be distinguished, thus a robust modeling result can be achieved. Finally, a novel multiobjective evaluation index on the modeling performance is developed by comprehensively considering the root-mean-square error of modeling and the correlation coefficient on trend fitting, based on which the nondominated sorting genetic algorithm II is used to globally optimize the model parameters. Both experiments using industrial data and industrial applications illustrate that the proposed method can eliminate the adverse effect caused by the fluctuation of data in BF process efficiently. This indicates its stronger robustness and higher accuracy. Moreover, control testing shows that the developed model can be well applied to realize data-driven control of the BF process.

Evolutionary, structural and expression analysis of core genes involved in starch synthesis

Starch is the main storage carbohydrate in plants and an important natural resource for food, feed and industrial raw materials. However, the details regarding the pathway for starch biosynthesis and the diversity of biosynthetic enzymes involved in this process are poorly understood. This study uses a comprehensive phylogenetic analysis of 74 sequenced plant genomes to revisit the evolutionary history of the genes encoding ADP-glucose pyrophosphorylase (AGPase), starch synthase (SS), starch branching enzyme (SBE) and starch de-branching enzyme (DBE). Additionally, the protein structures and expression patterns of these four core genes in starch biosynthesis were studied to determine their functional differences. The results showed that AGPase, SS, SBE and DBE have undergone complicated evolutionary processes in plants and that gene/genome duplications are responsible for the observed differences in isoform numbers. A structure analysis of these proteins suggested that the deletion/mutation of amino acids in some active sites resulted in not only structural variation but also sub-functionalization or neo-functionalization. Expression profiling indicated that AGPase-, SS-, SBE- and DBE-encoding genes exhibit spatio-temporally divergent expression patterns related to the composition of functional complexes in starch biosynthesis. This study provides a comprehensive atlas of the starch biosynthetic pathway, and these data should support future studies aimed at increasing understanding of starch biosynthesis and the functional evolutionary divergence of AGPase, SS, SBE, and DBE in plants.

Genetic characterization of inbred lines from Shaan A and B groups for identifying loci associated with maize grain yield

BACKGROUND

Increasing grain yield is a primary objective of maize breeding. Dissecting the genetic architecture of grain yield furthers genetic improvements to increase yield. Presented here is an association panel composed of 126 maize inbreds (AM126), which were genotyped by the genotyping-by-sequencing (tGBS) method. We performed genetic characterization and association analysis related to grain yield in the association panel.

RESULTS

In total, 46,046 SNPs with a minor allele frequency (MAF) ≥0.01 were used to assess genetic diversity and kinship in AM126. The results showed that the average MAF and polymorphism information content (PIC) were 0.164 and 0.198, respectively. The Shaan B group, with 11,284 unique SNPs, exhibited greater genetic diversity than did the Shaan A group, with 2644 SNPs. The 61.82% kinship coefficient in AM126 was equal to 0, and only 0.15% of that percentage was greater than 0.7. A total of 31,983 SNPs with MAF ≥0.05 were used to characterize population structure, LD decay and association mapping. Population structure analysis suggested that AM126 can be divided into 6 subgroups, which is consistent with breeding experience and pedigree information. The LD decay distance in AM126 was 150 kb. A total of 51 significant SNPs associated with grain yield were identified at P < 1 × 10- 3 across two environments (Yangling and Yulin). Among those SNPs, two loci displayed overlapping regions in the two environments. Finally, 30 candidate genes were found to be associated with grain yield.

CONCLUSIONS

These results contribute to the genetic characterization of this breeding population, which serves as a reference for hybrid breeding and population improvement, and demonstrate the genetic architecture of maize grain yield, potentially facilitating genetic improvement.

[Diagnosis of obstructive sleep apnea using cardiopulmonary coupling analysis]

Objective: To explore the diagnostic value of cardiopulmonary coupling analysis in the screening of obstructive sleep apnea (OSA). Methods: A total of 44 participants with sleep disorders from Sleep Medicine Center of West China Hospital in May 2016 were included in the study. All participants were monitored with cardiopulmonary coupling while undergoing polysomnography (PSG). The sleep parameters detected by cardiopulmonary coupling and PSG were compared and the correlation between respiratory disturbance index (RDI) of cardiopulmonary coupling and sleep parameters of PSG were analyzed. Using PSG as "golden standard" , the sensitivity, specificity, positive predictive value, negative predictive value and the corresponding areas under the receiver operating characteristic (ROC) curves were calculated for cardiopulmonary coupling. Results: There were 44 participants included in the study (37 males and 7 females) with a mean age of (46.3±12.5) years old and a mean body mass index of (25.6±3.7) kg/m(2). And there were 33 subjects diagnosed with OSA. There were no significant difference between respiratory disturbance index (RDI) derived from cardiopulmonary coupling and apnea-hypopnea index (AHI) derived from PSG. Correlation analysis showed that the RDI, low frequency coupling monitored by cardiopulmonary coupling was positively correlated with AHI detected by PSG (r=0.849, 0.850, both P<0.001); and the high frequency coupling was significantly negatively correlated with AHI (r=-0.767, P<0.001). For AHI ≥5/h, ≥10/h, ≥15/h, ≥20/h and ≥30/h respectively according to PSG, sensitivity was 0.82, 0.93, 0.96, 0.96, 0.77, specificity was 0.50, 0.75 0.72, 0.80, 0.86, positive predictive value was 0.85, 0.87, 0.83, 0.85, 0.85, negative predictive value was 0.55, 0.86, 0.93, 0.94, 0.79 for cardiopulmonary coupling. The corresponding areas under the ROC curves were 0.868, 0.892, 0.915, 0.942, 0.921 respectively. In addition, when the RDI derived from CPC was higher than 20.4/h, the patients were more likely suffering from OSA, and the sensitivity was 0.79 and the specificity was 0.91. Conclusions: The results of cardiopulmonary coupling are consistent with simultaneous PSG parameters. Cardiopulmonary coupling has a highly diagnostic value for sleep respiratory disorder.

Effects of Different Thermal Treatment Methods on Preparation and Physical Properties of High Amylose Maize Starch Based Films

Because of its biodegradable trait, starch has been widely used as the raw material for packaging. Effects of different thermal treatment methods (high temperature-high pressure heating (HH), microwave heating (MH) and alkali heating (AH) with and without glycerol on physical properties of high amylose maize starch films (HASFs) were investigated in this study. HASFs under HH had highest elongation at break (E%), and lowest tensile strength (TS), modulus of elasticity (EM) and opacity (OC). HASFs under MH had highest TS, water holding capacity (WHC) and OC, and lowest thickness (TN), E%, solubility in water (SW) and solubility in oil (SO), while HASFs under AH had highest TN, EM, SW and SO, and lowest WHC. Compared with water, plasticized HASFs with glycerol had higher TN，E%, WHC, SW and OC, and lower TS, EM and SO. XRD results revealed the V-type polymorph and the difference in intensity of diffraction peaks of HASFs under three methods. This study would be helpful to design and prepare HASFs.

A simple and rapid method for preparing the whole section of starchy seed to investigate the morphology and distribution of starch in different regions of seed

BACKGROUND

Storage starch in starchy seed influences the seed weight and texture, and determines its applications in food and nonfood industries. Starch granules from different plant sources have significantly different shapes and sizes, and even more the difference exists in the different regions of the same tissue. Therefore, it is very important to in situ investigate the morphology and distribution of starch in the whole seed. However, a simple and rapid method is deficient to prepare the whole section of starchy seed for investigating the morphology and distribution of starch in the whole seeds for a large number of samples.

RESULTS

A simple and rapid method was established to prepare the whole section of starchy seed, especially for floury seed, in this study. The whole seeds of translucent and chalky rice, vitreous and floury maize, and normal barley and wheat were sectioned successfully using the newly established method. The iodine-stained section clearly exhibited the shapes and size of starch granules in different regions of seed. The starch granules with different morphologies and iodine-staining colors existed regionally in the seeds of high-amylose rice and maize. The sections of lotus and kidney bean seeds also showed the feasibility of this method for starchy non-cereal seeds.

CONCLUSION

The simple and rapid method was proven effective for preparing the whole sections of starchy seeds. The whole section of seed could be used to investigate the morphology and distribution of starch granules in different regions of the whole seed. The method was especially suitable for large sample numbers to investigate the starch morphology in short time.

Quinolinate Phosphoribosyltransferase is an Antiviral Host Factor Against Hepatitis C Virus Infection

HCV infection can decrease NAD⁺/NADH ratio, which could convert lipid metabolism to favor HCV replication. In hepatocytes, quinolinate phosphoribosyl transferase (QPRT) catabolizes quinolinic acid (QA) to nicotinic acid mononucleotide (NAMN) for de novo NAD synthesis. However, whether and how HCV modulates QPRT hence the lipogenesis is unknown. In this work, we found QPRT was reduced significantly in livers of patients or humanized C/O^Tg mice with persistent HCV infection. Mechanistic studies indicated that HCV NS3/4A promoted proteasomal degradation of QPRT through Smurf2, an E3 ubiquitin-protein ligase, in Huh7.5.1 cells. Furthermore, QPRT enzymatic activity involved in suppression of HCV replication in cells. Activation of QPRT with clofibrate (CLO) or addition of QPRT catabolite NAD both inhibited HCV replication in cells, probably through NAD⁺-dependent Sirt1 inhibition of cellular lipogenesis. More importantly, administration of CLO, a hypolipidemic drug used in clinics, could significantly reduce the viral load in HCV infected C/O^Tg mice. Take together, these results suggested that HCV infection triggered proteasomal degradation of QPRT and consequently reduced de novo NAD synthesis and lipogenesis, in favor of HCV replication. Hepatic QPRT thus likely served as a cellular factor that dampened productive HCV replication.

Randomized clinical trial of autologous skin cell suspension for accelerating re-epithelialization of split-thickness donor sites

BACKGROUND

Split-thickness skin graft (STSG) is used frequently, but may result in complications at the donor site. Rapid healing of donor-site wounds is critical to relieving morbidity. This study investigated whether autologous skin cell suspension could improve healing of STSG donor-site wounds.

METHODS

Between September 2014 and February 2016, patients requiring STSGs were randomized to receive autologous skin cell suspension plus hydrocolloid dressings (experimental group) or hydrocolloid dressings alone (control group) for the donor site. The primary outcome was time to complete re-epithelialization. Secondary outcomes included pain and itching scores measured on a visual analogue scale, and adverse events. Patients were followed for 12 weeks to evaluate quality of healing. Analysis was by intention to treat.

RESULTS

Some 106 patients were included, 53 in each group. Median time to complete re-epithelialization was 9·0 (95 per cent c.i. 8·3 to 9·7) days in the experimental group, compared with 13·0 (12·4 to 13·6) days in the control group (P < 0·001). Overall postoperative pain and itching scores were similar in both groups. No between-group differences in treatment-related complications were observed. Both patients and observers were more satisfied with healing quality after autologous skin cell suspension had been used.

CONCLUSION

The use of autologous skin cell suspension with hydrocolloid dressings accelerated epithelialization and improved healing quality of the donor site compared with hydrocolloid dressings alone. Registration number: UMIN000015000 ( http://www.umin.ac.jp/ctr).

Two novel mutations in the PPIB gene cause a rare pedigree of osteogenesis imperfecta type IX

BACKGROUND

Osteogenesis imperfecta (OI) is a rare genetic skeletal disorder characterized by increased bone fragility and vulnerability to fractures. PPIB is identified as a candidate gene for OI-IX, here we detect two pathogenic mutations in PPIB and analyze the genotype-phenotype correlation in a Chinese family with OI.

METHODS

Next-generation sequencing (NGS) was used to screen the whole exome of the parents of proband. Screening of variation frequency, evolutionary conservation comparisons, pathogenicity evaluation, and protein structure prediction were conducted to assess the pathogenicity of the novel mutations. Sanger sequencing was used to confirm the candidate variants. RTQ-PCR was used to analyze the PPIB gene expression.

RESULTS

All mutant genes screened out by NGS were excluded except PPIB. Two novel heterozygous PPIB mutations (father, c.25A>G; mother, c.509G>A) were identified in relation to osteogenesis imperfecta type IX. Both mutations were predicted to be pathogenic by bioinformatics analysis and RTQ-PCR analysis revealed downregulated PPIB expression in the two carriers.

CONCLUSION

We report a rare pedigree with an autosomal recessive osteogenesis imperfecta type IX (OI-IX) caused by two novel PPIB mutations identified for the first time in China. The current study expands our knowledge of PPIB mutations and their associated phenotypes, and provides new information on the genetic defects associated with this disease for clinical diagnosis.

The effect of salt concentration on swelling power, rheological properties and saltiness perception of waxy, normal and high amylose maize starch

The effect of salt concentration on swelling power, rheological properties and saltiness perception of waxy, normal and high amylose maize starch was investigated.