Clinical application of whole-genome low-coverage next-generation sequencing to detect and characterize balanced chromosomal translocations

Individuals carrying balanced translocations have a high risk of birth defects, recurrent spontaneous abortions and infertility. Thus, the detection and characterization of balanced translocations is important to reveal the genetic background of the carriers and to provide proper genetic counseling. Next-generation sequencing (NGS), which has great advantages over other methods such as karyotyping and fluorescence in situ hybridization (FISH), has been used to detect disease-associated breakpoints. Herein, to evaluate the application of this technology to detect balanced translocations in the clinic, we performed a parental study for prenatal cases with unbalanced translocations. Eight candidate families with potential balanced translocations were investigated using two strategies in parallel, low-coverage whole-genome sequencing (WGS) followed-up by Sanger sequencing and G-banding karyotype coupled with FISH. G-banding analysis revealed three balanced translocations, and FISH detected two cryptic submicroscopic balanced translocations. Consistently, WGS detected five balanced translocations and mapped all the breakpoints by Sanger sequencing. Analysis of the breakpoints revealed that six genes were disrupted in the four apparently healthy carriers. In summary, our result suggested low-coverage WGS can detect balanced translocations reliably and can map breakpoints precisely compared with conventional procedures. WGS may replace cytogenetic methods in the diagnosis of balanced translocation carriers in the clinic.

Subjective well-being amongst migrant children in China: unravelling the roles of social support and identity integration

BACKGROUND

Migrant children refer to rural children who accompany one or both parents to urban area. Empirical evidence showed that compared with their urban counterparts, migrant children had poorer developmental, emotional and psychological health.

METHOD

A sample of 1306 migrant children were recruited to examine the characteristics of migrant children and investigate the effects of identity integration, support and socioeconomic factors (e.g. age, gender, type of school, family socioeconomic status, city type) on their subjective wellbeing.

RESULTS

Children with higher levels of identity integration, social support, family socioeconomic status, who attended public school and who lived in the third-tiered city of Weihai demonstrated better subjective wellbeing. Social support remained a strong predictor for subjective wellbeing, despite a significant mediating effect of identity integration.

CONCLUSIONS

These results highlight the need for policymakers and practitioners alike to address individual factors pertaining to psychological adjustments, as well as social determinants of subjective wellbeing in the context of migration.

Identification of a novel HLA-C*03 variant, C*03:303, by sequence-based typing in a Dai Chinese individual

HLA-C*03:303 has one nonsynonymous nucleotide change from HLA-C*03:04:01:01 in codon 194, exon 4 (GTC>GCC).

Identification of a novel HLA-C allele, HLA-C*07:477 in a Drung Chinese individual

HLA-C*07:477 has one nonsynonymous nucleotide change from HLA-C*07:02:01:01 in codon 176, exon 3 (AAG>GAG).

HLA-B*46:40:02, a novel HLA-B*46 allele identified in a Chinese individual by sequence-based typing

HLA-B*46:40:02 has one synonymous nucleotide change from HLA-B*46:40:01 in codon 23, exon 2 (ATT>ATC).

Comparison of intramedullary fibular allograft with locking compression plate versus shoulder hemi-arthroplasty for repair of osteoporotic four-part proximal humerus fracture: Consecutive, prospective, controlled, and comparative study

OBJECTIVES

To compare the outcomes of intramedullary fibular allograft (IFA) with locking compression plates (LCPs) versus shoulder hemi-arthroplasty (HA) in osteoporotic four-part proximal humeral fracture (PHF).

METHODS

Between January 2010 and December 2012, totally 60 cases with osteoporotic four-part PHF were enrolled in this study and were randomly separated into IFA and LCPs group and HA group (n=30). Additionally, surgery indexes for patients in the two groups, such as Constant-Murley score (CMS), the Disability of Arm, Shoulder and Hand (DASH) score, individual subject evaluation of the outcomes, plain X-ray, and computer tomography (CT) scanning were evaluated and compared.

RESULTS

CMS, DASH score, activities of daily living (ADL), and range of motion (ROM) were statistically higher in the IFA and LCPs group than those in the HA group at the last follow-up, whereas the pain were obviously lower than that in the HA group. Besides, patients in the IFA and LCPs group had higher abduction, external rotation with elbow, strength, and satisfactory rating compared with HA group at the last follow-up. However, one case developed avascular necrosis (AVN), one case encountered screw perforation, and one case experienced varus displacement in the IFA and LCPs group, while there were 2, 4, and 2 cases suffered from superficial infection, shoulder stiffness, tuberosity migration in the HA group, respectively.

CONCLUSION

IFA with LCP have an advantage in functional outcomes than shoulder HA.

LEVEL OF EVIDENCE

Level II. Prospective cohort study.

Molecular mechanism of the susceptibility difference between HLA-B*27:02/04/05 and HLA-B*27:06/09 to ankylosing spondylitis: substitution analysis, MD simulation, QSAR modelling, and in vitro assay

The human leukocyte antigen HLA-B27 is directly involved in the disease pathogenesis of ankylosing spondylitis (AS). HLA-B27 has a high degree of genetic polymorphism, with 105 currently known subtypes; the presence of aspartic acid at residue 116 (Asp116) has been found to play an essential role in AS susceptibility. Here, we systematically investigated the molecular mechanism of the susceptibility difference between the AS-associated subtypes HLA-B*27:02/04/05 and AS-unassociated subtypes HLA-B*27:06/09 to AS at sequence, structure, energetic and dynamic levels. In total seven variable residues were identified among the five studied HLA-B27 subtypes, in which Asp116 can be largely stabilized by a spatially vicinal, positively charged His114 through a salt bridge, while five other variable residues seem to have only a marginal effect on AS susceptibility. We also employed a quantitative structure-activity relationship approach to model the statistical correlation between peptide structure and affinity to HLA-B*27:05, a genetic ancestor of all other HLA-B27 subtypes and associated strongly with AS. The built regression predictor was verified rigorously through both internal cross-validation and external blind validation, and was then employed to identify potential HLA-B*27:05 binders from >20,000 cartilage-derived self-peptides. Subsequently, the binding potency of the top five antigenic peptides to HLA-B*27:05 was assayed in vitro using a FACS-based MHC stabilization experiment. Consequently, two (QRVGSDEFK and LRGAGTNEK) out of the five peptides were determined to have high affinity (BL50 = 5.5 and 15.8 nM, respectively) and, as expected, both of them possess positively charged Lys at the C-terminus.

Identification of a novel HLA-A allele, A*11:209 by sequence-based high-resolution typing in an HIV-infected individual

The novel allele A*11:209 shows three nucleotides difference from A*11:27 in exon 3.

Misdiagnosis of primary hepatic marginal zone B cell lymphoma of mucosa-associated lymphoid tissue type, a case report

Background

Extra-nodal marginal zone B cell lymphoma of mucosa-associated lymphoid tissue originating in the liver is less common.

Case presentation

We described the clinical presentation, immunohistochemistry, and immunophenotypes of this lymphoma, which was misdiagnosed with tiny hepatic carcinoma in a 44-year-old woman with hepatitis C; the patient underwent left lateral sectionectomy. The immunophenotype identified the most of the lymphoid cells as positive CD20, CD34, Ki67, CD3, CD4, CD79a, CD45RO, MUM-1, and CD5 and negative CD10, CD15, CD30, ACT, CK, CRO, DES, and HMB45. The diagnosis of primary hepatic mucosa-associated lymphoid tissue (MALT) was made by histology after surgery; the patient went through the excellent recovery with no chemotherapy and is disease free for 27 months.

Conclusions

Primary hepatic MALT is less common with incidental finding; local resection is beneficial due to its oncological indolence.

Multicenter Prospective Trial of Stent Placement in Patients with Symptomatic High-Grade Intracranial Stenosis

BACKGROUND AND PURPOSE

On the basis of the high 1-month stroke and/or death (14.7%) rates associated with stent placement in the Stenting versus Aggressive Medical Management for Preventing Recurrent Stroke in Intracranial Stenosis trial, modifications in patient selection and procedural aspects for intracranial stent placement have been recommended. We performed a multicenter prospective single-arm trial to determine whether such modifications would result in lower rates of periprocedural stroke and/or death.

MATERIALS AND METHODS

The study enrolled patients with recent transient ischemic attack or ischemic stroke (excluding perforator ischemic events) related to high-grade (70%-99% in severity) stenosis of a major intracranial artery. Patients were treated by using angioplasty and self-expanding stents 3 weeks after the index ischemic event at 1 of the 10 high-volume centers in China. An independent neurologist ascertained the occurrence of any stroke and/or death within 1 month after the procedure.

RESULTS

A total of 100 consecutive patients were recruited. The target lesions were located in the middle cerebral artery (M1) (n = 38, 38%), intracranial internal carotid artery (n = 17, 17%), intradural vertebral artery (n = 18, 18%), and basilar artery (n = 27, 27%). The technical success rate of stent deployment with residual stenosis of <50% was 100%. The overall 1-month stroke and/or death rate was 2% (95% confidence interval, 0.2%-7.0%). Two ischemic strokes occurred in the pontine region (perforator distribution) in patients following angioplasty and stent placement for basilar artery stenosis.

CONCLUSIONS

The results of this prospective multicenter study demonstrated that modifications in patient selection and procedural aspects can substantially reduce the 1-month stroke and/or death rate following intracranial stent placement.

Adjuvant therapies using normobaric oxygen with hypothermia or ethanol for reducing hyperglycolysis in thromboembolic cerebral ischemia

BACKGROUND AND PURPOSE

Normobaric oxygen (NBO), ethanol (EtOH), and therapeutic hypothermia (TH) delivered alone or in combination have neuroprotective properties after acute stroke. We used an autologous thromboembolic rat stroke model to assess the additive effects of these treatments for reducing the deleterious effects of hyperglycolysis post-stroke in which reperfusion is induced with recombinant tissue plasminogen activator (rt-PA).

METHODS

Sprague-Dawley rats were subjected to middle cerebral artery (MCA) occlusion with an autologous embolus. One hour after occlusion, rt-PA was administered alone or with NBO (60%), EtOH (1.0 g/kg), TH (33 °C), either singly or in combination. Infarct volume and neurological deficit were assessed at 24h after rt-PA-induced reperfusion with or without other treatments. The extent of hyperglycolysis, as determined by cerebral glucose and lactate levels was evaluated at 3 and 24h after rt-PA administration. At the same time points, expressions of glucose transporter 1 (Glut1), glucose transporter 3 (Glut3), phosphofructokinase1 (PFK-1), and lactate dehydrogenase were (LDH) measured by Western blotting.

RESULTS

Following rt-PA in rats with thromboembolic stroke, NBO combined with TH or EtOH most effectively decreased infarct volume and neurological deficit. As compared to rt-PA alone, EtOH or TH but not NBO monotherapies significantly reduced post-stroke hyperglycolysis. The increased utilization of glucose and production of lactate post-stroke was prevented most effectively when NBO was combined with either EtOH or TH after reperfusion with rt-PA, as shown by the significantly decreased Glut1, Glut3, PFK-1, and LDH levels.

CONCLUSIONS

In a rat thromboembolic stroke model, both EtOH and TH used individually offer neuroprotection after the administration of rt-PA. While NBO monotherapy does not appear to be effective, it significantly potentiates the efficacy of EtOH and TH. The similar neuroprotection and underlying mechanisms pertaining to the attenuation of hyperglycolysis provided by EtOH or TH in combination with NBO suggest a possibility of substituting EtOH for TH. Thus a combination of NBO and EtOH, which are widely available and easily used, could become a novel and effective neuroprotective strategy in the clinical setting.

The chemistry, morphology, crystal structure and hydrophilicity properties of wood fibers treated by a magnetic immobilized laccase–mediator system

The chemistry, morphology, crystal structure and hydrophilicity properties of wood fibers treated by magnetic immobilized laccase–mediator system (ILMS) which had never previously been examined were investigated.

Characterization of complementary determinant region 3δ in human MutS homologue 2-specific γδ T cells

γδT cells function as sentinels in early host responses to infections and malignancies. Previously, we found ectopically expressed human MutS homologue 2 (hMSH2), recognized by γδT cells, triggered a γδT cell-mediated cytolysis to tumor cells. However, the characteristics of hMSH2-specific γδ Τ cells are not fully understood. In this study, we investigated the complementary determinant region (CDR) 3δ diversity of hMSH2-specific γδ T cells. We found that the CDR3δ sequences of hMSH2-specific γδ T cells displayed limited diversity, while the length and germline gene usage showed no differences compared with whole CDR3δ immune repertoire. There are more hydrophilic amino acids in P/N insert of hMSH2-specific γδ T cells including the more conserved amino acid at the position 97. Our results offer clues to understanding antigen recognition pattern of γδ T cells to stress-induced hMSH2 of tumor cells and also the mechanism of γδT cell-mediated tumor immune surveillance.

Prognostic value of metastatic lymph node ratio as an additional tool to the TNM stage system in gastric cancer

BACKGROUND

Gastric cancer is one of most common malignancies in the world. Currently the prognostic prediction is entirely based on the TNM staging system. In this study, we evaluated whether metastatic lymph node ratio (rN) at the time of surgery would improve the prognostic prediction in conjunction with the TNM staging system.

METHODS

This retrospective study includes 745 patients, who had been referred for surgery due to gastric cancer between 1995 and 2007 and had at least 15 lymph nodes examined at the time of surgery without preoperative treatment. Clinicopathologic features and overall survival were analyzed using univariate and multivariate modes to identify the risk factors for overall survival.

RESULTS

Median overall survival of all patients analyzed is 57.8 months and 5-year overall survival is 49.5%. Tumor site, macroscopic type, pTNM stage, and rN stage are identified as independent prognostic factors. Increased positive lymph node ratio correlates with shorter survival in all patients and in each T and N stage. In stage III gastric cancer patients, rN stage shows additional prognostic value on overall survival (p < 0.001).

CONCLUSIONS

rN stage is a simple and promising prognostic factor of gastric cancer after surgery in addition to the TNM stage system especially in stage III patients. But the independent prognostic value of rN stage in stage I, II and IV gastric cancer is yet to be determined.

Interleukin 8 enhances the immune response of ducks to avian influenza vaccine

Interleukins are reported to be valuable immunostimulants in enhancing the immune efficiency of conventional vaccines. In this study, the effect of expression of interleukin 8 (IL-8) on the immune response of ducks to avian influenza vaccine was investigated. The results showed that the serum antibody titer, lymphocyte transformation efficiency and serum interferon gamma (IFN-γ) level of ducks injected with avian influenza vaccine along with a plasmid expressing duck IL-8 were higher than those of ducks injected with conventional immunostimulant Astragalus polysaccharide (APS) or empty plasmid. Therefore, the duck IL-8 may be used as a good immunostimulant to enhance the immune efficiency of avian influenza vaccine in ducks.

Annexin A5 promotes macrophage activation and contributes to pulmonary fibrosis induced by silica particles

OBJECTIVE

To investigate the contributions and underlying molecular mechanisms of annexin A5 toward silica-induced pulmonary fibrosis.

METHODS

Male C57BL/6 mice were randomly divided into three groups and instilled intratracheally with silica, saline, or air. Mice were euthanized at 3, 7, 14, or 28 days following treatment. Annexin A5 levels in serum and lung tissues were detected by enzyme-linked immunosorbant assay (ELISA) assays or Western blots. The association of annexin A5 levels with silica-induced lung fibrosis was further investigated in the macrophage cell line, RAW264.7. Following exposure of these cells to silica at a concentration of 200 μg/ml for 6 or 12 h, the expression levels of transforming growth factor β1 (TGF-β1), interleukin 1α (IL-1α), Fas ligand (FasL), and their downstream targets were evaluated by Western blots. Furthermore, annexin A5 and FasL were knocked down by small interfering ribonucleic acid (siRNA) and TGF-β1 secretion into the cell culture medium was measured by ELISA assays or Western blots.

RESULTS

Mice treated with silica demonstrated lung fibrosis at 28 days following exposure, whereas, in controls, only mild and transient inflammation was evident at day 3 and day 7 postinstillation and was not present at day 14. Furthermore, silica-exposed mice exhibited significantly (p < 0.05) elevated levels of annexin A5 in serum and lung tissues, relative to control groups. Consistent with these findings, silica exposure of RAW264.7 cells for 6 or 12 h, led to an annexin A5-dependent increase in the expression levels of TGF-β1, IL-1α, FasL, and their downstream target molecules. These silica-induced changes were reversed by siRNA-mediated knockdown of annexin A5, but downregulation of FasL led to increased annexin A5 expression and reduced levels of TGF-β1, IL-1α, and FasL downstream target molecules.

CONCLUSIONS

These findings define a role of annexin A5 in promoting macrophage activation via Fas/FasL pathways in silica-induced lung fibrosis.

The new allele HLA-DPB1*363:01 identified by sequence-based typing in a donor from the Chinese Marrow Donor Program

The new allele HLA-DPB1*363:01 most closely resembles DPB1*92:01, differing at a single position 191 (exon 2, codon 35).

HLA-B*58:63, a novel allele identified by sequence-based typing in a Chinese bone marrow voluntary donor

HLA-B*58:63 differs from HLA-B*58:01:01 by one nucleotide at position 248 resulting in a single amino acid change.

Preoperative chemotherapy with a trastuzumab-containing regimen for a patient with gastric cancer and hepatic metastases

Gastric cancer is the fourth most common cancer worldwide and the leading cause of tumor-related death in China. Gastric cancer is a heterogeneous disease and therefore requires different treatments based on the subtype. We describe a patient who had gastric cancer with liver metastases. Biopsy and tumor analysis using the HercepTest revealed a human epidermal growth factor receptor 2 (HER2)-positive adenocarcinoma as confirmed by fluorescence in situ hybridization. The patient was treated with a regimen of trastuzumab, oxaliplatin, and S-1 (six cycles). When positron emission tomography findings suggested that the metastases had resolved, the patient underwent surgery. Histopathologically, no cancer cells were observed in the resected hepatic tissue. The patient underwent tumor resection surgery, during which the tumor and gastric lymph nodes with lesions were removed. The patient has remained disease-free for 3 months. Therefore, trastuzumab may be an effective agent in the chemotherapeutic treatment of liver metastases in patients with HER2-positive gastric adenocarcinoma.

Identification of a novel HLA-A*24 allele, A*24:289, in a Chinese individual

The new allele, A*24:289 is different to A*24:03:01 at codons 151, 152 and 156 at exon 3.