AnFiSA: An open-source computational platform for the analysis of sequencing data for rare genetic disease

Despite genomic sequencing rapidly transforming from being a bench-side tool to a routine procedure in a hospital, there is a noticeable lack of genomic analysis software that supports both clinical and research workflows as well as crowdsourcing. Furthermore, most existing software packages are not forward-compatible in regards to supporting ever-changing diagnostic rules adopted by the genetics community. Regular updates of genomics databases pose challenges for reproducible and traceable automated genetic diagnostics tools. Lastly, most of the software tools score low on explainability amongst clinicians. We have created a fully open-source variant curation tool, AnFiSA, with the intention to invite and accept contributions from clinicians, researchers, and professional software developers. The design of AnFiSA addresses the aforementioned issues via the following architectural principles: using a multidimensional database management system (DBMS) for genomic data to address reproducibility, curated decision trees adaptable to changing clinical rules, and a crowdsourcing-friendly interface to address difficult-to-diagnose cases. We discuss how we have chosen our technology stack and describe the design and implementation of the software. Finally, we show in detail how selected workflows can be implemented using the current version of AnFiSA by a medical geneticist.

The role of ferroptosis in esophageal cancer

Esophageal cancer is one of the most common cancers with high mortality rate around the world. Although the treatment strategy of this disease has made great progress, the prognosis of advanced patients is not ideal. Ferroptosis, a novel regulatory cell death model, that is different from traditional apoptosis and characterized by increased Fenton reaction mediated by intracellular free iron and lipid peroxidation of cell membrane. Ferroptosis has been proved to be closely linked to a variety of diseases, especially cancer. This review aims to summarize the core mechanism of ferroptosis in esophageal cancer, the regulation of ferroptosis signaling pathway and its current application. At the same time, we emphasize the potential and prospect of ferroptosis in the treatment of esophageal cancer. Collectively, targeting ferroptosis pathway may provide new insights into the diagnosis, treatment and prognosis of esophageal cancer.

Relationship of explicit/implicit self-esteem discrepancies, suicide ideation, and suicide risk in patients with major depressive disorder

The present study was conducted to explore the associations between explicit self-esteem (ESE), implicit self-esteem (ISE), ESE/ISE discrepancies, depression severity, suicidal ideation (SI), and suicide risk among patients with major depressive disorder (MDD). To this end, 36 MDD patients with SI, 35 MDD patients without SI, and 32 healthy controls were recruited. All participants were interviewed using the Mini International Neuropsychiatric Interview (MINI), and they also completed the Beck Depression Inventory (BDI). The Beck Scale for Suicide Ideation-Chinese Version (BSI-CV) and the Rosenberg Self-Esteem Scale (SES) were used for the analysis. Further, the Implicit Association Test (IAT) was conducted to assess participants' ISE. The study revealed significant differences in ESE among the three groups, F(2, 90) = 44.88, p < .001. In particular, the group of MDD patients with SI had the lowest score. The interaction between the size and direction of ESE/ISE discrepancy was associated with depression severity, β = -.50, p = .004, and SI, β = -.39, p = .045. Among the four types of self-esteem, individuals with diminished self-esteem had the highest SI score whereas individuals with low congruent self-esteem had the highest suicide risk score. Based on these findings, the study suggested that diminished self-esteem could help in the early detection of depression and SI. Low-congruent self-esteem may also be considered a screening factor for suicide risk.

Concrete damage analysis based on higher-order beam theories using fracture energy regularization

This paper presents the numerical damage analysis of concrete structures using higher-order beam theories based on Carrera Unified Formulation (CUF). The concrete constitutive relation is modeled using continuum damage mechanics based on a modified Mazars concrete damage model, in which both the tensile and compressive softening behaviors are regularized with classical fracture energy methodology. An expression is proposed to estimate the characteristic length in higher-order beam theories, to prevent mesh dependency. Both softening constitutive laws and fracture energy calculations are obtained according to Model Code 2010. To assess the efficiency of the proposed model, three classical benchmark quasi-static experiments are taken for validation. From the comparison between numerical and experimental results, the proposed CUF model using continuum damage mechanics can present 3D accuracy with low computational costs and reduce the mesh dependency.

Prognosis of patients with esophageal squamous cell carcinoma undergoing surgery versus no surgery after neoadjuvant chemoradiotherapy: a retrospective cohort study

Background

Esophageal surgery is an invasive surgical method with high surgical risk, and seriously affects postoperative quality of life. This study compared the prognosis of patients with locally advanced esophageal squamous cell carcinoma (ESCC) treated with neoadjuvant chemoradiotherapy (Neo-CRT) plus surgery and Neo-CRT alone, in order to explore the necessity of continuing operation after Neo-CRT.

Methods

We retrospectively analyzed 223 patients who received Neo-CRT in Taizhou Hospital Affiliated to Wenzhou Medical University from June 2007 to December 2014. According to the treatment, the patients were divided into Neo-CRT plus surgery group (operation group, n=185) and single Neo-CRT group (non-operation group, n=38). Patients in both groups were followed up for a long time until death or deadline. The overall survival (OS), adverse reactions, recurrence and death results of the two groups were evaluated. The risk factors of poor prognosis were analyzed.

Results

The two groups were comparable. The median follow-up time was 23.5 months in non-operation group and 112.9 months in operation group. The 1-year survival rate, 2-year survival rate and 5-year survival rate in non-operation group were 69.9%, 47.7% and 31.8%, respectively. The rates in operation group were 94.0%, 79.3% and 65.0%, respectively. The incidence of low hemoglobin was 73.7% (non-operation group) and 53.0% (operation group). The infection rates were 15.8% and 2.7%, respectively. There was no significant difference in the incidence of leukopenia, neutropenia and thrombocytopenia between the two groups. Multivariate analysis showed that recurrence and treatment were independent risk factors affecting the prognosis of patients.

Conclusions

To sum up, no matter in terms of recurrence rate or OS rate, the prognosis of patients in the operation group was better than that in the non-operation group. Therefore, Neo-CRT combined with esophagectomy is recommended for locally advanced ESCC with acceptable surgical risk.

H2O2 activation over Co substitution in Fe1-xS for tetracycline degradation: Effect of Co substitution

In this work, the effect of Co substitution in the Fe_1-xS (CSP) on the activation of H₂O₂ to degrade tetracycline (TC) is investigated. A series of CSP samples with different Co content are synthesized via a high-temperature sulfidation method and characterized by XRD, XPS, SEM, and electrochemical analysis. The result showed that low Co content (≤1%) promotes the catalytic activity of Fe_1-xS, while excessive Co (1%﹤x ≤ 3%) inhibits its catalytic activity. The investigation of Behnajady-Modirshahla-Ghanbery kinetic model (BMG) showed that the maximum initial degradation rate of TC over 1.0% CSP/H₂O₂ was 1.6 times than that of in CSP/H₂O₂ system. The Box-Behnken with Response Surface Methodology was employed to verify optimum condition for TC degradation. The quenching experiments and ESR determined that ·OH, ·O₂^- and ¹O₂ were involved in TC degradation with the treatment of 1.0% CSP/H₂O₂ system. Electrochemical analysis, ·OH quantification, and metal ion concentrations measure reveal that Co substitution accelerates electron transfer efficiency and Fe²⁺ regeneration. Furthermore, nine intermediates are identified and the possible degradation pathway of TC is proposed. The unique effect of Co provides novel insight and efficient strategies for improving the reactivity of iron sulfide.

Lymph node micrometastasis in non-small cell lung cancer

Lung cancer has some of the highest morbidity and mortality rates of all cancers, and an important risk factor for mortality in patients with lung cancer is tumor metastasis. Even if a tumor is completely removed at an early stage of the disease, quite a number of patients still have the risk of recurrence. With the advent of molecular diagnostic and therapeutics, more and more studies have found that a poor prognosis may be related to lymph node micrometastasis. However, clinicians still find that predicting the prognosis and choosing the type of surgery and postoperative adjuvant chemotherapy are still challenging. Thus, this article reviews the current research status of lymph node micrometastasis in non-small cell lung cancer, envision to provide some updates and insights in this area.

Anion gap predicts the long-term neurological and cognitive outcomes of spontaneous intracerebral hemorrhage

OBJECTIVE

To investigate whether anion gap (AG) can act as a potentially predictive biomarker in recoveries of neurological and cognitive functions.

PATIENTS AND METHODS

A total of 89 patients with intracerebral hemorrhage (ICH) were recruited. Of these, 68 and 21 patients were categorized into screening cohort and validation cohort, respectively. In the screening cohort, patients were categorized into three groups, according to the serum AG levels at admission. We dynamically recorded AG levels. Neurological and cognitive functions were assessed using Glasgow coma scale (GCS), Glasgow outcome scale (GOS) and mini-mental state examination (MMSE) scale at different time points. Furthermore, in the validation cohort, 9 patients with increased AG level underwent interventions to rectify the electrolyte imbalance.

RESULTS

In the screening cohort, statistical differences were observed for respiratory diseases (p=0.029) among the three groups. The number of patients in the ≥16 mmol/L group (59.3%) was higher than that in the other groups. The mean scores of GCS in the ≥16 mmol/L group were lower than those in the other groups. The AG levels at admission had significant associations with 180-day GOS (p=0.043) and 180-day MMSE (p=0.001). Among them, the mean scores of the 180-day GOS and 180-day MMSE were lower in the ≥16 mmol/L group than in the other groups. In the validation cohort, AG intervention promoted recoveries of neurological and cognitive functions when compared to those without AG interventions.

CONCLUSIONS

AG is a potentially predictive biomarker for the long-term outcomes of ICH patients, and rectifying AG at admission improves the outcomes.

Trabecular bone score and its association with Cobb angle kyphosis in older men: a cross-sectional study for the Osteoporotic Fractures in Men (MrOS) Study

Hyperkyphosis (HK), or accentuated forward spinal curvature, commonly affects older people, although its causes are not completely understood. We tested whether a measure of bone quality, trabecular bone score (TBS), is associated with HK in 1997 older men, and determined that men with degraded TBS were more likely to have HK.

INTRODUCTION

While vertebral fractures and low bone mineral density (BMD) contribute to kyphosis progression, it is unknown whether the trabecular bone score (TBS) may provide additional information on bone quality that could influence the degree of kyphosis. We hypothesized that degraded TBS would be associated with hyperkyphosis (HK) defined as a Cobb angle > 50°.

METHODS

Using data from 1997 participants of the Osteoporotic Fractures in Men (MrOS) Study who had baseline TBS and Cobb angle kyphosis measured, we investigated whether men with degraded TBS were more likely to be hyperkyphotic, even after adjustment for BMD and prevalent vertebral fractures.

RESULTS

Men were an average age of 74 ± 6 (mean ± SD) years with a mean kyphosis angle of 38.6 ± 11.5°, 295 (15%) were classified as hyperkyphotic, and 416 (21%) had degraded TBS. Compared with men with TBS > 1.2, men with degraded TBS were more likely to have HK (OR: 1.47, 95% CI: 1.06-2.06, p = 0.02) after adjusting for age, clinic, race, BMI, hip BMD, and prevalent vertebral fracture. If spine instead of hip BMD was included in the model, the odds ratio decreased to 1.35 (95% CI: 0.97-1.89, p = 0.08).

CONCLUSIONS

Older men with degraded TBS are more likely to have HK not explained by underlying vertebral fractures.

[miR-20a-5p inhibits proliferation of lung cancer A549 cells by down-regulating HOXB13]

OBJECTIVE

To investigate the molecular mechanism by which miR-20a-5p regulates HOXB13 gene expression and inhibits lung cancer cell proliferation.

METHODS

The expression levels of HOXB13 mRNA and protein in lung cancer A549 cells transfected with HOXB13 overexpression plasmid or HOXB13 siRNA were detected with real-time fluorescence quantitative PCR (qRT-PCR) and Western blotting. CCK-8 and EdU assays were used to examine the effect of modulation of HOXB13 expression on cell proliferation. We screened possible binding miRNAs of HOXB13 by bioinformatics analysis. In A549 cells transfected with miR-20a-5p mimic or miR-20a-5p inhibitor, the expression level of miR-20a-5p was detected by qRT-PCR and the protein expression of HOXB13 was determined with Western blotting. CCK-8 and EdU assays were used to assess the effect of miR-20a-5p overexpression on the proliferation of A549 cells. miR-20a-5p mimic and HOXB13 overexpression plasmids were co-transfected into A549 cells, and the changes in cell proliferation were evaluated with CCK-8 and EdU assays.

RESULTS

HOXB13 overexpression obviously promoted the proliferation of A549 cells (P < 0.05). miR-20a-5p was identified as the potential binding miRNA of HOXB13. Overexpression of miR-20a-5p in A549 cells significantly decreased the expression of HOXB13 protein (P < 0.05), while interference of miR-20a-5p obviously increased HOXB13 expression (P < 0.05). The results of cell proliferation experiment showed that miR-20a-5p and HOXB13 had opposite effects on cell proliferation, and the cells overexpressing both miR-20a-5p and HOXB13 showed a lower proliferation activity than the cells overexpressing HOXB13 but higher than the cells overexpressing miR-20a-5p alone (P < 0.05).

CONCLUSION

miR-20a-5p inhibits proliferation of lung cancer cells by down-regulating the expression of HOXB13.

Cannabis suppresses antitumor immunity by inhibiting JAK/STAT signaling in T cells through CNR2

The combination of immune checkpoint blockade (ICB) with chemotherapy significantly improves clinical benefit of cancer treatment. Since chemotherapy is often associated with adverse events, concomitant treatment with drugs managing side effects of chemotherapy is frequently used in the combination therapy. However, whether these ancillary drugs could impede immunotherapy remains unknown. Here, we showed that ^∆9-tetrahydrocannabinol (THC), the key ingredient of drugs approved for the treatment of chemotherapy-caused nausea, reduced the therapeutic effect of PD-1 blockade. The endogenous cannabinoid anandamide (AEA) also impeded antitumor immunity, indicating an immunosuppressive role of the endogenous cannabinoid system (ECS). Consistently, high levels of AEA in the sera were associated with poor overall survival in cancer patients. We further found that cannabinoids impaired the function of tumor-specific T cells through CNR2. Using a knock-in mouse model expressing a FLAG-tagged Cnr2 gene, we discovered that CNR2 binds to JAK1 and inhibits the downstream STAT signaling in T cells. Taken together, our results unveiled a novel mechanism of the ECS-mediated suppression on T-cell immunity against cancer, and suggest that cannabis and cannabinoid drugs should be avoided during immunotherapy.

Integrin α6 overexpression promotes lymphangiogenesis and lymphatic metastasis via activating the NF-κB signaling pathway in lung adenocarcinoma

OBJECTIVE

It has been reported that tumor-associated lymphangiogenesis plays an important role in lymph node metastasis and contributes to the poor survival of lung adenocarcinoma (LUAD) patients. As yet, however, the molecular mechanism underlying LUAD-associated lymphangiogenesis has remained elusive.

METHODS

Immunohistochemistry (IHC) was used to determine the expression of integrin subunit alpha 6 (ITGA6) and the lymphatic vessel endothelial hyaluronan receptor 1 (Lyve1) in clinicopathologically characterized LUAD specimens. The effect of ITGA6 overexpression on lymphangiogenesis and lymphatic metastasis was examined by tube formation, scratch wound-healing, and cell migration assays in vitro and a popliteal lymph node metastasis model in vivo. Mechanistically, overexpression of ITGA6 and activation of NF-κB signaling were examined by real-time PCR, ubiquitination and dual-luciferase reporter assays. Finally, high ITGA6 expression in LUAD tissue samples was related to copy number variation (CNV) using the TCGA database.

RESULTS

We found that ITGA6 overexpression correlated with microlymphatic vessel density in LUAD specimens (p < 0.01). Importantly, by using a popliteal lymph node metastasis model, we found that ITGA6 upregulation significantly enhanced lymphangiogenesis and lymphatic metastasis in vivo (p < 0.05). In addition, we found that ITGA6 overexpression enhanced the capability of A549 and H1299 LUAD cells to induce tube formation and migration in human lymphatic endothelial cells (HLECs). Mechanistically, we found that ITGA6 sustained NF-κB activity via binding and promoting K63 polyubiquitination of TNF receptor-associated factor 2 (TRAF2). Finally, CNV analysis revealed ITGA6 amplification of 27.5% in the LUAD tissue samples in the TCGA database.

CONCLUSIONS

Taken together, our results uncover a plausible role for ITGA6 in mediating lymphangiogenesis and lymphatic metastasis and may provide a basis for targeting ITGA6 to treat LUAD lymphatic metastasis.

Efficacy and Benefit of Postoperative Chemotherapy in Micropapillray or Solid Predominant Pattern in Stage IB Lung Adenocarcinoma: A Systematic Review and Meta-Analysis

Background: The benefit of postoperative chemotherapy remains controversial for patients with either a micropapillary or solid pattern in stage IB non-small cell lung cancer. This study is designed to explore the significance of postoperative chemotherapy in patients with either a micropapillary or solid pattern in stage IB lung adenocarcinoma.

Method: To conduct the meta-analysis, PubMed, Cochrane Library, Embase and Medline were used to collect literature on long-term follow-up studies published before March, 2021, involving postoperative chemotherapy for patients with both a micropapillary or solid pattern in stage IB lung adenocarcinoma as compared to non-postoperative chemotherapy. Survival data was extracted from the literature, including the overall survival and disease-free survival. Based on overall survival and disease-free survival, hazard ratios and their 95% of confidence intervals were applied to assess the prognostic effect of postoperative chemotherapy. Review Manager software was used to merge the effect size for the meta-analysis.

Result: In total, 6 papers with 956 patients were included. In terms of the prognosis of patients suffering from lung cancer when receiving postoperative chemotherapy, this study comprehensively reviews and evaluates the available evidence of micropapillary or solid patterns. After excluding the heterogeneity between the studies, we found that the pooled results from 6 studies report that postoperative chemotherapy was associated with a better overall survival rate when compared with non-postoperative chemotherapy (hazard ratio = 0.58, 95% confidence interval, 0.44–0.77; P = 0.0002). Postoperative chemotherapy also significantly improved the disease-free survival in patients with either a micropapillary or a solid pattern in stage IB lung adenocarcinoma (postoperative chemotherapy vs. non-postoperative chemotherapy, hazard ratio = 0.51, 95% confidence interval, 0.40–0.64; P < 0.001). However, a subgroup analysis showed that compared with non-postoperative chemotherapy, tumor size was unrelated to the prognosis of patients in stage IB undergoing postoperative chemotherapy (hazard ratio = 0.98, 95% confidence interval, 0.94–1.02; P = 0.27).

Conclusion: Postoperative chemotherapy results in a better long-term survival rate for patients with either a solid or a micropapillary pattern in stage IB lung adenocarcinoma. Multi-center, prospective, clinical trials are needed to validate our findings.

Effects of Atomoxetine Hydrochloride on Regulation of Lifespan in Drosophila Model

Nootropics (smart drugs) are used by students to enhance cognitive performance which have been reported times in recent years. However, some of the nootropics are central nervous system stimulants which are very likely to lead to addiction or complications such as vomiting and dizziness. Are there nootropics that can improve learning behavior while having potential positive effect on health? Here, we reported that Atomoxetine (ATX) has sex-specific effect on prolonging the life span of female Drosophila melanogaster. Further study indicated that ATX enhanced female resistance to heat stress and their vertical climbing ability, but it did decrease the number of eggs laid. ATX increased food-intake and sleep time both of females and males, and significantly reduced the 24h spontaneous activity of females and males. Our results present the sex dimorphic effect of ATX on life span regulation in Drosophila, and support further research on the beneficial role of ATX and the mechanisms in other animal models.

Targeting TRIM54/Axin1/β-Catenin Axis Prohibits Proliferation and Metastasis in Hepatocellular Carcinoma

Accumulating evidence demonstrates that dysregulation of ubiquitin-mediated degradation of oncogene or suppressors plays an important role in several diseases. However, the function and molecular mechanisms of ubiquitin ligases underlying hepatocellular carcinoma (HCC) remain elusive. In the current study, we show that overexpression of TRIM54 was associated with HCC progression. TRIM54 overexpression facilitates proliferation and lung metastasis; however, inhibition of TRIM54 significantly suppressed HCC progression both in vitro and in vivo. Mechanically, we demonstrated that TRIM54 directly interacts with Axis inhibition proteins 1 (Axin1) and induces E3 ligase-dependent proteasomal turnover of Axin1 and substantially induces sustained activation of wnt/β-catenin in HCC cell lines. Furthermore, we showed that inhibition of the wnt/β-catenin signaling pathway via small molecule inhibitors significantly suppressed TRIM54-induced proliferation. Our data suggest that TRIM54 might function as an oncogenic gene and targeting the TRIM54/Axin1/β-catenin axis signaling may be a promising prognostic factor and a valuable therapeutic target for HCC.

DEEP Study: Modeling Outcomes and Costs of Persistent Orofacial Pain

KNOWLEDGE OF TRANSFER STATEMENT

Despite a substantial number of consultations, individuals experiencing the care pathways in this study continued to have far from perfect health over their life course. The modeling suggests they would only experience 18 y in "perfect health." There is considerable scope to improve current care/outcomes and patient experience.