Loss-of-function variants in SAT1 cause X-linked childhood-onset systemic lupus erythematosus

OBJECTIVES

Families that contain multiple siblings affected with childhood onset of systemic lupus erythematosus (SLE) likely have strong genetic predispositions. We performed whole exome sequencing (WES) to identify familial rare risk variants and to assess their effects in lupus.

METHODS

Sanger sequencing validated the two ultra-rare, predicted pathogenic risk variants discovered by WES and identified additional variants in 562 additional patients with SLE. Effects of a splice site variant and a frameshift variant were assessed using a Minigene assay and CRISPR/Cas9-mediated knock-in (KI) mice, respectively.

RESULTS

The two familial ultra-rare, predicted loss-of-function (LOF) SAT1 variants exhibited X-linked recessive Mendelian inheritance in two unrelated African-American families. Each LOF variant was transmitted from the heterozygous unaffected mother to her two sons with childhood-onset SLE. The p.Asp40Tyr variant affected a splice donor site causing deleterious transcripts. The young hemizygous male and homozygous female Sat1 p.Glu92Leufs*6 KI mice spontaneously developed splenomegaly, enlarged glomeruli with leucocyte infiltration, proteinuria and elevated expression of type I interferon-inducible genes. SAT1 is highly expressed in neutrophils and encodes spermidine/spermine-N1-acetyltransferase 1 (SSAT1), a rate-limiting enzyme in polyamine catabolism. Young male KI mice exhibited neutrophil defects and decreased proportions of Foxp3 +CD4+ T-cell subsets. Circulating neutrophil counts and proportions of Foxp3 +CD4+ T cells correlated with decreased plasma levels of spermine in treatment-naive, incipient SLE patients.

CONCLUSIONS

We identified two novel SAT1 LOF variants, showed the ability of the frameshift variant to confer murine lupus, highlighted the pathogenic role of dysregulated polyamine catabolism and identified SAT1 LOF variants as new monogenic causes for SLE.

[An interpretation of the British Association for the Study of the Liver practice guideline for the evaluation and treatment of hepatolenticular degeneration]

Hepatolenticular degeneration is common among rare diseases. China has a higher incidence rate than Western countries, and it is increasing year by year. The disease is easy to overlook and misdiagnose due to its complexity and non-specific clinical manifestations. Therefore, the British Association for the Study of the Liver has recently issued practice guidelines for the evaluation and treatment of hepatolenticular degeneration in order to aid clinicians in improving the clinical decision-making process regarding diagnosis, treatment, and long-term follow-up management. Herein is a brief introduction and interpretation of the content of the guideline, with aim of facilitating its application in clinical practice.

Genetic diversity and phylogeography of the endemic species Chimonobambusa utilis growing in southwest China: Chloroplast DNA sequence and microsatellite marker analyses

Chimonobambusa utilis (Keng) Keng F is an endemic species distributed only in the Daluoshan Mountains, southwest China. Ch. utilis is popular due to its unique flavor and deliciousness and plays an important role in the industrial revolution in many counties in China. A total of 20 natural populations were sampled from the entire distribution range of Ch. utilis. In the present study, we used five EST-SSR molecular markers, three chloroplast DNA (trnH-psbA, atpF-atpH, and psbK-psbI), and one ITS molecular marker to elucidate the genetic diversity and phylogeography analyses of these Ch. utilis populations. The results exhibited that Ch. utilis populations showed lower genetic diversity than other angiosperms (H_T = 0.752, H_S = 0.364, and F_ST = 0.05021 for EST-SSR; H_T = 0.956, Hs = 0.507, and F_ST = 0.70121 for cpDNA; H_T = 0.868, Hs = 0.495, and F_ST = 0.70121 for nrDNA). A total of 40 alleles were detected for five polymorphic loci. We detected 20 polymorphic sites and 11 haplotypes within 1,398 bp of cpDNA and 59 polymorphic sites and 32 haplotypes within the 589 bp of the ITS sequence. Based on the haplotype distribution, we infer that there were at least two glacial refuges of Ch. utilis populations during the Quaternary Ice Age. The genetic and geographic distance were correlated (p < 0.05), indicating that narrow distribution might be the primary cause of the low genetic differentiation of Ch. utilis populations. Based on the genetic diversity of Ch. utilis populations, we recommend implementing effective genetic resource management and sustainable utilization.

Influence of verapamil on pressure overload-induced ventricular arrhythmias by regulating gene-expression profiles

BACKGROUND

Life-threatening ventricular arrhythmias can lead to sudden cardiac death in patients. This study aimed to investigate the changes in gene profiles involved when verapamil (VRP) affects increased wall stress (pressure overload)-induced ventricular arrhythmias, thus revealing the potential causative molecular mechanisms and therapeutic targets through gene-expression identification and functional analysis.

METHODS

Animal models with wall stress-induced ventricular arrhythmias were established. Low (0.5 mg/kg) and high (1 mg/kg) doses of VRP were administered intravenously 10 minutes before transverse aortic constriction, and average ventricular arrhythmia scores were calculated. Next, we evaluated the molecular role of VRP by characterising differential gene-expression profiles between VRP-pretreated (1 mg/kg) and control groups using RNA-sequencing technology. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were used to reveal molecular function. A protein-protein interaction (PPI) network was then developed.

RESULTS

VRP exerted its anti-arrhythmic effects in response to increases in left ventricular (LV) afterload. We detected differentially expressed genes (DEGs), of which 36 were upregulated and 1 397 downregulated, between the VRP-pretreated and model groups during acute increases in LV wall stress. GO analysis demonstrated that the DEGs were associated with cytoskeletal protein binding. KEGG analysis showed that enriched pathways were mainly distributed in adherens junctions, actin cytoskeleton regulation and the MAPK signalling pathway. Centralities analysis of the PPI identified Rac1, Grb2, Rbm8a and Mapk1 as hub genes.

CONCLUSIONS

VRP prevented acute pressure overload-induced ventricular arrhythmias, possibly through the hub genes Rac1, Grb2, Rbm8a and Mapk1 as potential targets of VRP.

Clinical feasibility of deep learning-based automatic head CBCT image segmentation and landmark detection in computer-aided surgical simulation for orthognathic surgery

The purpose of this ambispective study was to investigate whether deep learning-based automatic segmentation and landmark detection, the SkullEngine, could be used for orthognathic surgical planning. Sixty-one sets of cone beam computed tomography (CBCT) images were automatically inferred for midface, mandible, upper and lower teeth, and 68 landmarks. The experimental group included automatic segmentation and landmarks, while the control group included manual ones that were previously used to plan orthognathic surgery. The qualitative analysis of segmentation showed that all of the automatic results could be used for computer-aided surgical simulation. Among these, 98.4% of midface, 70.5% of mandible, 98.4% of upper teeth, and 93.4% of lower teeth could be directly used without manual revision. The Dice similarity coefficient was 96% and the average symmetric surface distance was 0.1 mm for all four structures. With SkullEngine, it took 4 minutes to complete the automatic segmentation and an additional 10 minutes for a manual touchup. The results also showed the overall mean difference between the two groups was 2.3 mm for the midface and 2.4 mm for the mandible. In summary, the authors believe that automatic segmentation using SkullEngine is ready for daily practice. However, the accuracy of automatic landmark digitization needs to be improved.

Lower-dose corticosteroid therapy in severe immune thrombocytopenia during pregnancy: The comparable efficacy and lower incidence of maternal complications

Background: This study assessed the clinical efficacy of oral prednisone at low dose (LD) versus the previous high-dose (HD) study in patients with severe immune thrombocytopenia during pregnancy and its side effects on maternal and neonatal outcomes.

Study design: Pregnant patients with ITP were enrolled in the study (platelet count &lt;30×109/L) between January 2015 and 2019. A total of 43 patients received LD oral prednisone (0.25–0.5 mg/kg) as the initial treatment and were compared retrospectively with the 31 patients in the HD (1 mg/kg) study. The primary clinical endpoint was the response rate, and the secondary endpoint was maternal hemorrhagic events, complications, and neonatal outcomes.

Results: In total, 35% of patients responded (15/43) to the LD cortico-therapy, including four patients with a complete response which was no less than HD therapy (35.5%). The bleeding symptoms of 10 (30%) patients were ameliorated after 14 days of LD prednisone treatment. Preeclampsia occurred in three cases (7% of total) of which the incidence was obviously lower than that of the previous study at HD (18%). No stillbirth or miscarriage occurred in the LD group, and neonatal outcomes had no significant differences between the two studies.

Conclusion: LD prednisone therapy for severe ITP patients during pregnancy had equal efficacy to HD treatment. In addition, the decrease in dosage significantly reduced the incidence of hypertension.

[Recent progress of aptasensors for tumor exosome-associated protein detection]

Exosomes are phospholipid bilayer membrane-enclosed vesicles released from cells with diameters of 30-150 nm, exosomes can directly reflect the physiological and functional state of secretory cells, participate in material transport and information communication between cells, which are of great significance as biomarkers for early tumor diagnosis and treatment evaluation. There are many detection methods for exosomes, among which aptasensor technology with the properties of low price and easy operation, fast response, high sensitivity, remarkable specificity helps tumor patients to find, diagnose and treat early, improve the survival rate, and provide important basis for the evaluation of the prognosis. There are seven types of common aptasensors: fluorescent, electrochemical, colorimetric, luminescence, lateral flow strips, surface-enhanced Raman scattering and surface plasmon resonance sensors. Different aptasensors have different characteristics, this article focuses on the research progress of several common aptasensor for tumor exosomes detection.

Demethylation and reactivation of the fibrosis-suppressor gene Rasal1 is initiated by R-loop formation which facilitates recruitment of TET3 and GADD45g

Background

Silencing of fibrosis suppressor genes through DNA methylation has been shown to contribute to fibrosis progression in the heart and in other organs. Growth Arrest and DNA Damage 45-(GADD45) and Ten-Eleven-Translocation (TET) proteins are involved in active DNA demethylation, but how they are recruited to the promoter of fibrosis suppressor genes has not yet been understood.

Purpose

To identify the mechanisms involved in site-specific demethylation of the promoter region of the cardiac fibrosis suppressor gene Rasal1.

Methods

We previously identified lncRNA Gm15749 located within the Rasal1 promoter region. Using DRIP qRT-PCR, we demonstrated an enrichment of R-loops at the Rasal1 promoter in non-fibrotic mouse cardiac fibroblasts. Such enrichment of R-loops was lost upon TGF-beta-treatment in activated “fibrotic” fibroblasts, and also upon Gm15749 knockdown in untreated non-fibrotic fibroblasts. ChIP qRT-PCR further revealed binding of GADD45g to the Rasal1 promoter and Co-IP experiments confirmed a physical interaction of TET3 and GADD45g.

Results

Studying the RAS Protein Activator Like 1 (Rasal1), which has been shown to be silenced in fibrosis of the heart due to promoter hypermethylation, we find that the lncRNA Gm15749 within the promoter region of Rasal1 is protective by forming an R-loop at the Rasal1 promoter. Gm15749 mediates the recruitment and binding of GADD45g, which then triggers the demethylation process by recruiting TET3 specifically to the Rasal1 promoter region. During cardiac fibrosis, all three factors; Gm15749, TET3, and GADD45g are significantly downregulated and the protection of Rasal1 is lost due to the failure of the formation of the demethylation complex.

Conclusions

Our results suggest a complex involving an R-loop forming lncRNA termed Gm15749, which interacts with the demethylation complex consisting of GADD45g and TET3 to perform site-specific demethylation at the Rasal1 promoter. Such R-loop formation may counteract fibrogenesis through reactivation of fibrosis-suppressor genes silenced by hypermethylation.

Funding Acknowledgement

Type of funding sources: None.

Validation of a highly sensitive Sanger sequencing in detecting EGFR mutations from circulating tumor DNA in patients with lung cancers

BACKGROUND

The novel method, named blocker displacement amplification (BDA) Sanger, was applied to detect low variant allele frequency mutations in the circulating tumor DNA (ctDNA). This study aimed to evaluate the performance of the BDA Sanger method for the EGFR mutation detection in the ctDNA from lung cancer patients.

METHODS

A total of 195 plasma samples of lung cancer patients were included. The EGFR mutation status in the ctDNA was detected by the BDA Sanger and Super-ARMS assays. Next-generation sequencing (NGS) was further used to verify the mutant of EGFR with inconsistencies.

RESULTS

BDA Sanger assay was capable of detecting EGFR mutations with a 0.20% VAF from plasma samples. Among treatment-naive patients with paired tissue and plasma samples, the EGFR positive percent agreement (PPA) was 79% by BDA sanger. EGFR mutation was detected in 34.4% (67/195) ctDNA samples by the Super-ARMS and in 41.0% (80/195) ctDNA samples by the BDA Sanger assay. The overall concordance rate between the BDA Sanger and Super-ARMS assays was 82% (160/195). The BDA Sanger also enabled the detection of rare EGFR mutations, which were not discovered by the Super-ARMS.

CONCLUSION

The results supported the validity and efficiency of the BDA Sanger method for EGFR detection in patients with lung cancer, indicating that BDA Sanger has a great potential for application in detecting mutations in the ctDNA.

[Association of nutritional status with clinical outcomes of stroke patients with acute anterior circulation large vessel occlusion after emergency endovascular treatment]

OBJECTIVE

To explore the influence of nutritional status on 90-day functional outcomes of stroke patients with acute large vessel occlusion in the anterior circulation after endovascular treatment (EVT).

METHODS

We retrospectively analyzed the baseline, laboratory, surgical and 90-day follow-up data of patients with stroke resulting from acute large vessel occlusion in the anterior circulation, who underwent emergency endovascular treatment in our hospital from July, 2015 to December, 2020. A favorable outcome was defined as a modified Rankin scale score ≤2 at 90 days. Univariate and multivariate regression analyses were performed to explore the relationship between nutritional status and 90-day functional outcomes of the patients.

RESULTS

A total of 459 patients (mean age of 68.29±11.21 years, including 260 males) were enrolled in this study. According to their prognostic nutritional index (PNI), the patients were divided into normal nutrition group (392 cases, 85.4%), moderate malnutrition group (44 cases, 9.6%), and severe malnutrition group (23 cases, 5.0%). Univariate analysis showed that the patients with good clinical outcomes had a lower proportion of malnutrition with a younger age, a lower rate of diabetes, lower baseline blood pressure, lower baseline NIHSS score, higher baseline ASPECT score, and higher rates of good collateral circulation and complete vascular recanalization. Multivariate analysis showed that in addition to age, diabetes, baseline systolic blood pressure, successful recanalization, baseline ASPECT score, baseline NIHSS score and collateral circulation, a greater PNI was a protective factor for a good 90-day outcome of patients after EVT (moderate vs severe: OR=0.245, 95% CI: 0.066-0.908, P=0.035; normal vs severe: OR=0.185, 95% CI: 0.059-0.581, P=0.004).

CONCLUSION

Nutritional status an important factor affecting the 90-day outcomes after EVT of stroke patients with acute large vessel occlusion in the anterior circulation.

[Clinicopathological features and HER2 expression of metaplastic squamous cell carcinoma of the breast]

Objective: To investigate the clinicopathological features and HER2 expression of metaplastic squamous cell carcinoma (MSCC) of the breast. Methods: A total of 47 MSCC cases diagnosed in the Wuhan Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China from January 2010 to December 2021 were reviewed. The clinical information (including the follow-up data of HER2 positive patients) and pathological features were collected and analyzed. Results: All of the patients were female. Among the 47 cases, 25 were pure squamous cell carcinoma (PSCC) and 22 were mixed metaplastic carcinoma with squamous cell component (MMSC). The median age of the patients was 54 years (range, 29-84 years). The maximum diameter of the mass ranged from 0.8 to 10.0 cm, with a mean value of 3.3 cm, 85.7% (24/28) of the cases were smaller than 5 cm, and only 4 cases were larger than or equal to 5 cm. 89.5% of the MMSC presented with a solid mass. Cystic changes were more commonly found in the PSCC group (50%, P<0.05) than the MMSC group. 36.7% (11/30) of the patients had lymph node metastasis at the time of diagnosis. The squamous cell carcinoma component in all cases showed diffuse or patchy expression of p63, p40 and CK5/6. 55.3% (26/47) of the cases showed triple-negative phenotype. Among the 7 HER2-positive patients, 6 were MMSC group, which had a significantly higher rate of HER2-positivity than that in the PSCC group (1 case). In 1 MMSC case, immunohistochemistry showed HER2 2+in the invasive ductal carcinoma component and HER2 negativity (0) in the squamous cell carcinoma component, but HER2 FISH was negative in invasive ductal carcinoma and positive in squamous cell carcinoma component. Six HER2-positive MSCC patients received anti-HER2-targeted therapy, including two patients who received neoadjuvant chemotherapy combined with anti-HER2-targeted therapy before surgery. One patient achieved pathological complete remission, while the other achieved partial remission (the residual tumors were squamous cell carcinoma components). After 9-26 months of follow-up, four patients had no disease progression, two patients developed pulmonary metastases, and one patient showed local recurrence. Conclusions: MSCC is a group of heterogeneous diseases. PSCC and MMSC may be two different entities. Most of the MSCC are triple-negative and HER2 positivity is more commonly seen in MMSC with invasive ductal carcinoma component. Some HER2-positive MSCC patients can achieve complete remission or long-term progression-free survival after receiving anti-HER2 targeted therapy, but the squamous cell carcinoma component may be less sensitive to targeted therapy than the invasive ductal carcinoma component.

TAIGET: A small-molecule target identification and annotation web server

Background: Accurate target identification of small molecules and downstream target annotation are important in pharmaceutical research and drug development.

Methods: We present TAIGET, a friendly and easy to operate graphical web interface, which consists of a docking module based on AutoDock Vina and LeDock, a target screen module based on a Bayesian–Gaussian mixture model (BGMM), and a target annotation module derived from >14,000 cancer-related literature works.

Results: TAIGET produces binding poses by selecting ≤5 proteins at a time from the UniProt ID-PDB network and submitting ≤3 ligands at a time with the SMILES format. Once the identification process of binding poses is complete, TAIGET then screens potential targets based on the BGMM. In addition, three medical experts and 10 medical students curated associations among drugs, genes, gene regulation, cancer outcome phenotype, 2,170 cancer cell types, and 73 cancer types from the PubMed literature, with the aim to construct a target annotation module. A target-related PPI network can be visualized by an interactive interface.

Conclusion: This online tool significantly lowers the entry barrier of virtual identification of targets for users who are not experts in the technical aspects of virtual drug discovery. The web server is available free of charge at http://www.taiget.cn/.

Thrombocytopenia in the first trimester predicts adverse pregnancy outcomes in obstetric antiphospholipid syndrome

Background

Thrombocytopenia is a common manifestation of antiphospholipid syndrome (APS), and is a main concern for bleeding on the standard treatment of low dose aspirin (LDA) and low molecular weight heparin (LMWH) in obstetric APS (OAPS).

Objective

This study assesses the possible relationship between thrombocytopenia during the first trimester and adverse pregnancy outcomes (APOs) in OAPS patients.

Methods

A case-control study was conducted at Peking University People’s Hospital, Beijing, China. The clinical, immunologic, and pregnancy outcomes of the OAPS patients were collected. Univariate and multivariate logistic regression analyses were applied to assess the relationship between APOs and thrombocytopenia in the first trimester.

Results

A total of 115 participants were included in the analysis. There were no difference on antepartum and postpartum hemorrhage between the two groups. The gestational age in the thrombocytopenia group was less than that in the control group (34.12 ± 8.44 vs. 37.44 ± 3.81 weeks, p = 0.002). Hypocomplementemia, double aPL positive, and high titers of anti-β2 glycoprotein I were more frequent in APS patients with thrombocytopenia (p < 0.05). Compared to the control group, thrombocytopenia in the first trimester was correlated with SGA (12.12% vs. 31.25%, p = 0.043), premature birth <37 weeks (16.16% vs 43.75%, p = 0.010) and intrauterine fetal death (2.02% vs 12.50%, p = 0.033). Thrombocytopenia in first-trimester independently increased the risk of preterm birth <37 weeks (OR = 5.40, 95% CI: 1.35-21.53, p = 0.02) after adjusting for demographic and laboratory factors. After adding medication adjustments, these factors above become insignificant (p > 0.05). Of note, the number of platelets increased after delivery in 14 thrombocytopenia patients with live fetuses (p = 0.03).

Conclusion

This study demonstrates that thrombocytopenia in the first trimester increases the risks of preterm birth in women with APS. The effective OAPS treatments may improve pregnancy outcomes and not increase the risk of antepartum and postpartum hemorrhage.

Evaluation of commonly used cardiovascular drugs in inhibiting vonoprazan metabolism in vitro and in vivo

As a novel acid-suppressing drug, vonoprazan shows the potential to replace traditional proton-pump inhibitors. With its widespread use, some adverse effects that require further study have emerged due to drug–drug interactions. Our study is the first experiment that evaluated the drug–drug interactions of eleven common cardiovascular drugs that inhibit vonoprazan metabolism in vitro and in vivo. Rat liver microsome incubation and molecular simulation docking were applied to explore the inhibition mechanism. Amlodipine and nifedipine showed inhibitory effects on vonoprazan metabolism in both rat and human liver microsomes in the first evaluation part in vitro. The inhibition mechanism analysis results demonstrated that amlodipine and nifedipine might inhibit the metabolism of vonoprazan by a mixed type of competitive and non-competitive inhibition. However, the pharmacokinetic data of the vonoprazan prototype revealed that amlodipine affected vonoprazan in vivo while nifedipine did not. Thus, more attention should be paid when amlodipine is prescribed with vonoprazan. Furthermore, the changes in its carboxylic acid metabolites MI hinted at a complex situation. Molecular simulation suggested the CYP2B6 enzyme may contribute more to this than CYP3A4, and further inhibitory experiments preliminarily verified this speculation. In conclusion, the use of vonoprazan with cardiovascular drugs, especially amlodipine, should receive particular attention in clinical prescriptions.

[Association between metabolic risk factors and the hepatitis B reactivation of inactive HBsAg carriers in Jiangsu province: a cohort study]

Objective: To analyze the impact of metabolic risk factors on the epidemiological characteristics of the reactivation of inactive HBsAg carriers (IHC) and provide effective intervention measures to standardize the management of chronic hepatitis B infections. Methods: Based on the chronic hepatitis B infection cohort established in 2010 in Jiangsu province, six follow-up visits from 2012 to 2020 were conducted to analyze the characteristics and influencing factors of the hepatitis B reactivation of IHC and the impact of metabolic risk factors, including obesity, high blood pressure, diabetes and hyperglycemia. Results: From 2012 to 2020, 2 527 IHC and 17 730 person-years were observed during a median follow-up period of 7.0 person-years. Ninety-eight cases of hepatitis B reactivation, with a cumulative reaction rate, was 3.9%, and the incidence density was 5.53/1 000 person-years. Multivariate Cox proportional risk regression analysis showed that age and baseline HBV DNA were independent risk factors of HBV reactivation. Compared with the patients ≥60 years, 40-49 age group (aHR=2.16, 95%CI:1.20-3.90) and 20-29 age group (aHR=5.48, 95%CI:2.07-14.48) were significantly associated with hepatitis B reactivation. Compared with the HBV DNA negative patients at baseline, the risk of hepatitis B reactivation was higher in the group with low HBV DNA level 100-1 999 IU/ml (aHR=1.67, 95%CI:1.11-2.52). Stratification analysis results showed that compared with those without metabolic risk factors, in the ≥50 age group, patients with ≥2 metabolic risk factors showed adjusted HR of 2.73 (95%CI:1.08-6.96). Conclusions: The risk of hepatitis B being reactive is the persistent existence of IHC in communities in Jiangsu province, especially young adults, low-level HBV DNA carriers, and IHC with ≥2 metabolic risk factors. Follow-up for these IHC should be strengthened to reduce the risk of disease progression by antiviral treatment at the right time.