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Abstract Background WRKY transcription factors (TFs) regulate plant responses to environmental stimuli and development, including flowering. Despite extensive research on different species, their role in the invasive plant Mikania micrantha remains to be explored. The aim of this study was to identify and analyze WRKY genes in M. micrantha to understand their function in flowering and adaptation mechanisms. Results By analysing the whole genome of M. micrantha, a total of 77 M. micrantha WRKY (MmWRKY) genes were identified. Based on phylogenetic relationships, sequence alignment, and structural domain diversity, the MmWRKY gene family was preliminarily classified into three major groups and five subgroups: Group I, Group II (II-a, II-b, II-c, II-d, II-e), and Group III. Expression profiles showed tissue-specific expression patterns, with many WRKY genes highly expressed in flowers, indicating potential roles in floral development. Real-time quantitative PCR confirmed that the selected 11 genes were highly expressed in floral tissues, supporting their functional significance in flowering. Conclusion In this study, 77 WRKY genes were identified in M micrantha, and their phylogenetic relationships, structural domains, and expression patterns across various tissues and organs were comprehensively analyzed. This work provides a foundation for future functional characterization of WRKY genes in M. micrantha, which may contribute to the development of more effective strategies to control its rapid spread.

Abstract Objective To identify white matter fiber injury and network changes that may lead to mild cognitive impairment (MCI) progression, then a joint model was constructed based on neuropsychological scales to predict high-risk individuals for Alzheimer's disease (AD) progression among older adults with MCI. Methods A total of 173 MCI patients were included from the Alzheimer's Disease Neuroimaging Initiative(ADNI) database and randomly divided into training and testing cohorts. Forty-five progressed to AD during a 4-year follow-up period. Diffusion tensor imaging (DTI) techniques extracted relevant DTI quantitative features for each patient. In addition, brain networks were constructed based on white matter fiber bundles to extract network property features. Ensemble dimensionality reduction was applied to reduce both DTI quantitative features and network features from the training cohort, and machine learning algorithms were added to construct white matter signature. In addition, 52 patients from the National Alzheimer's Coordinating Center (NACC) database were used for external validation of white matter signature. A joint model was subsequently generated by combining with scale scores, and its performance was evaluated using data from the testing cohort. Results Based on multivariate logistic regression, clinical dementia rating and Alzheimer’s disease assessment scales (CDRS and ADAS, respectively) were selected as independent predictive factors. A joint model was constructed in combination with the white matter signature. The AUC, sensitivity, and specificity in the training cohort were 0.938, 0.937, and 0.91, respectively, and the AUC, sensitivity, and specificity in the test cohort were 0.905, 0.923, and 0.872, respectively. The Delong test showed a statistically significant difference between the joint model and CDRS or ADAS scores (P

Abstract Background Townes-Brocks syndrome (TBS) is a rare genetic disorder characterized by imperforate anus, dysplastic ears, thumb malformations, and other abnormalities. Previous studies have revealed that mutations in the SALL1 gene can disrupt normal development, resulting in the characteristic features of Townes-Brocks syndrome. Spalt-like transcription factors (SALLs) are highly conserved proteins that play important roles in various cellular processes, including embryonic development, cell differentiation, and cell survival. Over 400 different variants or mutations have been reported in the SALL1 gene in individuals with TBS. Most of these variants lead to the formation of premature termination codons (PTCs), also known as nonsense mutations. The majority of these PTCs occur in a specific region of the SALL1 gene called the “hotspot region”, which is particularly susceptible to mutation. Methods In this study, we conducted whole-exome sequencing on a three-generation Chinese family with anorectal malformations. Results We identified a novel heterozygous mutation (chr16:51175376:c.757 C > T p.Gln253*) in the SALL1 gene. Molecular analysis revealed a heterozygous C to T transition at nucleotide position 757 in exon 2 of the SALL1 (NM_002968) gene. This mutation is predicted to result in the substitution of the Gln253 codon with a premature stop codon (p.Gln253*). The glutamine-rich domain forms a long alpha helix, enabling the mutant protein to interact with the wild-type SALL1 protein. This interaction may result in steric hindrance effects on the wild-type SALL1 protein. Conclusions Our findings have expanded the mutation database of the SALL1 gene, which is significant for genetic counseling and clinical surveillance in the affected family. Furthermore, our study enhances the understanding of Townes-Brocks syndrome and has the potential to improve its diagnosis and treatment.

Abstract Background Psoriasis is a chronic immune-mediated skin condition. Although biologic treatments are effective in controlling psoriasis, some patients do not respond or lose response to these therapies. Thus, new strategies for psoriasis treatment are still urgently needed. Double-negative T cells (DNT) play a significant immunoregulatory role in autoimmune diseases. In this study, we aimed to evaluate the protective effect of DNT in psoriasis and explore the underlying mechanism. Methods We conducted a single adoptive transfer of DNT into an imiquimod (IMQ)-induced psoriasis mouse model through tail vein injection. The skin inflammation and IL-17A producing γδ T cells were evaluated. Results DNT administration significantly reduced the inflammatory response in mouse skin, characterized by decreased skin folds, scales, and red patches. After DNT treatment, the secretion of IL-17A by RORc+ γδlow T cells in the skin was selectively suppressed, resulting in an amelioration of skin inflammation. Transcriptomic data suggested heightened expression of NKG2D ligands in γδlow T cells within the mouse model of psoriasis induced by IMQ. When blocking the NKG2D ligand and NKG2D (expressed by DNT) interaction, the cytotoxic efficacy of DNT against RORc+IL17A+ γδlow T cells was attenuated. Using Ccr5 −/− DNT for treatment yielded evidence that DNT migrates into inflamed skin tissue and fails to protect IMQ-induced skin lesions. Conclusions DNT could migrate to inflamed skin tissue through CCR5, selectively inhibit IL-17-producing γδlow T cells and finally ameliorate mouse psoriasis. Our study provides feasibility for using immune cell therapy for the prevention and treatment of psoriasis in the clinic.

Abstract Background Ovarian cancer is one of the most common gynecological malignancies due to the lack of early symptoms, early diagnosis and limited screening. Therefore, it is necessary to understand the molecular mechanism underlying the occurrence and progression of ovarian cancer and to identify a basic biomarker for the early diagnosis and clinical treatment of ovarian cancer. Methods The association between FBXO28 and ovarian cancer prognosis was analyzed using Kaplan‒Meier survival analysis. The difference in FBXO28 mRNA expression between normal ovarian tissues and ovarian tumor tissues was obtained from The Cancer Genome Atlas (TCGA), and Genotype-Tissue Expression (GTEx) cohorts. The expression levels of the FBXO28 protein in ovarian cancer tissues and normal ovarian tissues were measured via immunohistochemical staining. Western blotting was used to determine the level of FBXO28 expression in ovarian cancer cells. The CCK-8, the colony formation, Transwell migration and invasion assays were performed to evaluate cell proliferation and motility. Results We found that a higher expression level of FBXO28 was associated with poor prognosis in ovarian cancer patients. Analysis of the TCGA and GTEx cohorts showed that the FBXO28 mRNA level was lower in normal ovarian tissue samples than in ovarian cancer tissue samples. Compared with that in normal ovarian tissues or cell lines, the expression of FBXO28 was greater in ovarian tumor tissues or tumor cells. The upregulation of FBXO28 promoted the viability, proliferation, migration and invasion of ovarian cancer cells. Finally, we demonstrated that FBXO28 activated the TGF-beta1/Smad2/3 signaling pathway in ovarian cancer. Conclusions In conclusion, FBXO28 enhanced oncogenic function via upregulation of the TGF-beta1/Smad2/3 signaling pathway in ovarian cancer.

Abstract Background and aim Epstein-Barr virus-associated hemophagocytic lymphohistiocytosis (EBV-HLH) and infectious mononucleosis (EBV-IM) share mimic symptoms in the early stages of childhood development. We aimed to examine the clinical features and laboratory indices of these two diseases in children and uncover unique indicators to assist pediatricians in identifying these diseases early. Methods We collected clinical data from 791 pediatric patients diagnosed with EBV-IM or EBV-HLH, compared the clinical traits and laboratory biomarkers presented in the two groups, and constructed predictive models based on them. Results Patients with EBV-IM had greater ratios of cervical lymphadenopathy, eyelid edema, and tonsillitis, whereas individuals with EBV-HLH were more likely to have hepatomegaly and splenomegaly. When using the criteria of interleukin (IL)-10 > 89.6 pg/mL, interferon (IFN)-γ > 45.6 pg/mL, ferritin > 429 μg/L, D-dimer > 3.15 mg/L and triglycerides > 2.1 mmol/L, the sensitivity was 87.9%, 90.7%, 98.1%, 91.1% and 81.5% to predict EBV-HLH, while the specificity was 98.4%, 96.3%, 96.5%, 94.1% and 80.6%, respectively. A logistic regression model based on four parameters (IL-10, ferritin, D-dimer, and triglycerides) was established to distinguish EBV-HLH patients from EBV-IM patients, with a sensitivity of 98.0% and a specificity of 98.2%. Conclusions IL-10, IFN-γ, ferritin and D-dimer levels are significantly different between EBV-HLH and EBV-IM. Predictive models based on clinical signs and laboratory findings provide simple tools to distinguish the two situations.

Abstract Introduction Gastroesophageal varices (GOV) bleeding is a common and serious complication of advanced liver cirrhosis with a median survival of less than 2 years. Multiple guidelines have pointed out that transjugular intrahepatic portosystemic shunt (TIPS) is the rescue treatment of acute variceal hemorrhage (AVB) after failure of standard therapy and an effective second-line treatment for preventing patients with high risks from rebleeding of GOV. The safety and stability of TIPS have been greatly improved due to the improvements of related technologies and the emergence of various novel devices, but the incidence of hepatic encephalopathy (HE) after shunting (10–50%) hindered the widespread use of TIPS. The target portal vein branch might affect the incidence of HE after TIPS. The aim of this study is to compare the rate of HE in patients with hepatitis B virus (HBV) related cirrhosis receiving TIPS either the left or right branch of the portal vein with 8mm Viatorr stent for preventing rebleeding from GOV. Methods and analysis This study is a multicenter randomized controlled trial comparing the influence of shunting left or right portal vein branch on post-TIPS hepatic encephalopathy for preventing rebleeding from GOV in patients with HBV-related cirrhosis. A total of 130 patients will be recruited over a period of 24 months across 5 centers in China. Eligible patients will be stratified 1:1 to constructing either a left or right portal vein shunt with an 8-mm Viatorr stent. The primary objective was to compare the incidence of post-TIPS hepatic encephalopathy between the two groups. The secondary objectives were to compare the grade and duration of hepatic encephalopathy, the rate of shunt dysfunction, the rate of variceal rebleeding, the HE-free survival, the cumulative patency rate of the stent, and the overall survival at 12 months and 24 months between two groups. Ethics and dissemination This study was approved by the ethics committee of Zhongshan Hospital of Fudan University (No. B2018-292R) and was registered at ClinicalTrials.gov (NCT03825848). All participants give written informed consent. Trial registration ClinicalTrials.gov NCT03825848. Registered on January 31, 2019 Trial status The first patient was recruited into our study on June 19, 2019. A total of 55 patients were recruited till May 27, 2021 (27 and 28 patients assigned to shunting the left (L Group) and right (R Group) branches of the portal vein, respectively).

Abstract Background Cushing’s syndrome is known as an important cause of secondary osteoporosis, characterized by reduction of bone mineral density and potential occurrence of fragility fractures before diagnosis in young population. Therefore, for young patients with fragility fractures, especially in young women, more attention should be paid on glucocorticoid excess caused by Cushing’s syndrome, due to relatively higher rate of misdiagnosis, distinct pathological characteristics and different treatment strategies compared with violent fractures and primary osteoporosis related fractures. Case presentation We presented an unusual case of a 26-year-old woman with multiple vertebral compression fractures and pelvis fractures, subsequently diagnosed as Cushing’s syndrome. On admission, the radiographic results showed fresh second lumbar vertebra fracture, and old fourth lumbar vertebra and pelvic fractures. The dual energy X-ray absorptiometry of lumbar spine revealed marked osteoporosis, and her plasm cortisol was extremely high. Then, Cushing’s syndrome, caused by left adrenal adenoma, was diagnosed by further endocrinological and radiographic examinations. After receiving left adrenalectomy, her plasma ACTH and cortisol values returned to normal level. In term of OVCF, we adopted conservative treatments, including pain management, brace treatment, and anti-osteoporosis measures. Three months after discharge, the patient’s low back pain was in complete remission without new onset of pain, and returned to normal life and work. Furthermore, we reviewed the literatures on advancements in the treatment of OVCF caused by Cushing’s syndrome, and based on our experiences, proposed some additional perspectives to guide treatment. Conclusion In term of OVCF secondary to Cushing’s syndrome without neurological damage, we prefer systematic conservative treatments, including pain management, brace treatment, and anti-osteoporosis measures, to surgical treatment. Among them, anti-osteoporosis treatment has the highest priority because of the reversibility of osteoporosis caused by Cushing’s syndrome.

Abstract Background To evaluate the prognostic value of the pre-treatment aspartate transaminase (AST)/alanine transaminase (ALT) ratio in hepatocellular carcinoma (HCC) patients receiving radiofrequency ablation (RFA)/microwave ablation (MWA) combined with simultaneous TACE. Methods The data for 117 patients were retrospectively analyzed in this study. The endpoint of prognosis was overall survival (OS). The Youden index was used to choose the optimal cut-off value of the pre-treatment AST/ALT ratio for OS prediction. Univariate and multivariate analyses were used to identify independent risk factors, then integrated to establish the nomogram. Results The AST/ALT ratio cut-off value for OS prediction was 0.89, and patients with a higher AST/ALT ratio had poorer OS. The median OS for the high-value AST/ALT group was not reached, while the median OS for the low-value AST/ALT group was 48.5 months (P = 0.0047). The univariate and multivariate analysis showed that AST/ALT ratio, AFP, and tumor numbers were independent prognostic indicators for OS. The integrated nomogram showed higher predictive accuracy for OS (C-index 0.674, 95%CI: 0.600–0.748). Conclusions The preoperative AST/ALT ratio could be a prognostic indicator for HCC patients receiving thermal ablation combined with simultaneous TACE.

Abstract Background The TetR (tetracycline repressor) family is one of the major transcription factor families that regulate expression of genes involved in bacterial antimicrobial resistance systems. NCgl0886 protein, designated as AtsR, is a member of the TetR family identified in Corynebacterium glutamicum, which is conserved in several species of the genera Corynebacterium, also including the well-known pathogen C. diphtheriae. AtsR is located at no far upstream of the identically oriented ncgl0884 gene, encoding a putative multidrug efflux pump protein, and in the same operon with ncgl0887, encoding a resistance, nodulation and cell division (RND) superfamily drug exporter. However, the role of AtsR is not clearly understood. Results Here we showed that dimeric AtsR directly repressed the expression of the ncgl0887-atsR operon, as well as indirectly controlled the ncgl0884 transcription. Antibiotics and toxic compounds induced the expression of ncgl0887-atsR operon. A perfect palindromic motif (5΄-TGCAA-N2-TTGCA-3΄; 12 bp) was identified in the upstream region of ncgl0887-atsR operon. Electrophoretic mobility shift assays (EMSAs) demonstrated specific binding of AtsR to this motif, and hydrogen peroxide (H2O2) blocked binding. H2O2 oxidized cysteine residues to form Cys123-Cys187 intermolecular disulfide bonds between two subunits in AtsR dimer, which altered its DNA-binding characteristics and caused its dissociation, thereby leading to derepression of the drug efflux protein. Deletion of ncgl0884 and ncgl0887 increased the susceptibilities of C. glutamicum for several toxic compounds, but overexpression of atsR decreased the drug tolerance of C. glutamicum. Conclusions Our study revealed that AtsR was a redox regulator that sensed oxidative stress via thiol modification. The results obtained here will contribute to our understanding of the drug response mechanism not only in C. glutamicum but also in the related bacteria C. diphtheriae.

Abstract Background Cardiomyopathy is a complex type of myocardial disease, and its incidence has increased significantly in recent years. Dilated cardiomyopathy (DCM) and ischemic cardiomyopathy (ICM) are two common and indistinguishable types of cardiomyopathy. Results Here, a systematic multi-omics integration approach was proposed to identify cardiomyopathy-related core genes that could distinguish normal, DCM and ICM samples using cardiomyopathy expression profile data based on a human metabolic network. First, according to the differentially expressed genes between different states (DCM/ICM and normal, or DCM and ICM) of samples, three sets of initial modules were obtained from the human metabolic network. Two permutation tests were used to evaluate the significance of the Pearson correlation coefficient difference score of the initial modules, and three candidate modules were screened out. Then, a cardiomyopathy risk module that was significantly related to DCM and ICM was determined according to the significance of the module score based on Markov random field. Finally, based on the shortest path between cardiomyopathy known genes, 13 core genes related to cardiomyopathy were identified. These core genes were enriched in pathways and functions significantly related to cardiomyopathy and could distinguish between samples of different states. Conclusion The identified core genes might serve as potential biomarkers of cardiomyopathy. This research will contribute to identifying potential biomarkers of cardiomyopathy and to distinguishing different types of cardiomyopathy.

Abstract Background Ground-level ozone (O3) pollution is currently the one of the severe environmental problems in China. Although existing studies have quantified the O3-related health impact and economic loss, few have focused on the acute health effects of short-term exposure to O3 and have been limited to a single temporal and spatial dimension. Methods Based on the O3 concentration obtained from ground monitoring networks in 334 Chinese cities in 2015–2018, this study used a two-stage exposure parameter weighted Log-linear exposure-response function to estimate the cause-specific mortality for short-term exposure to O3. Results The value of statistical life (VSL) method that were used to calculate the economic loss at the city-level. Our results show that in China, the national all-cause mortality attributed to O3 was 0.27(95% CI: 0.14–0.55) to 0.39 (95% CI: 0.20–0.67) million across 2015–2018. The estimated economic loss caused by O3 was 387.76 (95% CI: 195.99–904.50) to 594.08 (95% CI: 303.34–1140.65) billion CNY, accounting for 0.52 to 0.69% of total reported GDP. Overall, the O3 attributed health and economic burden has begun to decline in China since 2017. However, highly polluted areas still face severe burden, and undeveloped areas suffer from high GDP losses. Conclusions There are substantial health impacts and economic losses related to short-term O3 exposure in China. The government should pay attention to the emerging ozone pollution, and continue to strengthen the intervention in traditional priority areas while solving the pollution problem in non-priority areas.

Abstract Ovarian carcinoma is the deadliest type of gynecological cancer. The unique tumor microenvironment enables specific and efficient metastasis, weakens immunological monitoring, and mediates drug resistance. Tumor associated macrophages (TAMs) are a crucial part of the TME and are involved in various aspects of tumor behavior. Lysophosphatidic acid (LPA) is elevated in the blood of ovarian carcinoma patients, as well as in the tumor tissues and ascites, which make it a useful biomarker and a potential therapeutic target. Recent studies have shown that LPA transforms monocytes into macrophages and regulates the formation of macrophages through the AKT/mTOR pathway, and PPAR γ is a major regulator of LPA-derived macrophages. In addition, TAMs synthesize and secrete LPA and express LPA receptor (LPAR) on the surface. With these data in mind, we hypothesize that LPA can convert monocytes directly into TAMs in the microenvironment of ovarian cancer. LPA may mediate TAM formation by activating the PI3K/AKT/mTOR signaling pathway through LPAR on the cell surface, which may also affect the function of PPAR γ, leading to increased LPA production by TAMs. Thus, LPA and TAMs form a vicious circle that affects the malignant behavior of ovarian cancer.

Abstract Background The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function. Results Here, we report on the results of the third CAFA challenge, CAFA3, that featured an expanded analysis over the previous CAFA rounds, both in terms of volume of data analyzed and the types of analysis performed. In a novel and major new development, computational predictions and assessment goals drove some of the experimental assays, resulting in new functional annotations for more than 1000 genes. Specifically, we performed experimental whole-genome mutation screening in Candida albicans and Pseudomonas aureginosa genomes, which provided us with genome-wide experimental data for genes associated with biofilm formation and motility. We further performed targeted assays on selected genes in Drosophila melanogaster, which we suspected of being involved in long-term memory. Conclusion We conclude that while predictions of the molecular function and biological process annotations have slightly improved over time, those of the cellular component have not. Term-centric prediction of experimental annotations remains equally challenging; although the performance of the top methods is significantly better than the expectations set by baseline methods in C. albicans and D. melanogaster, it leaves considerable room and need for improvement. Finally, we report that the CAFA community now involves a broad range of participants with expertise in bioinformatics, biological experimentation, biocuration, and bio-ontologies, working together to improve functional annotation, computational function prediction, and our ability to manage big data in the era of large experimental screens.

Abstract Background Cell therapy remains the most promising approach against ischemic heart injury. However, poor survival of engrafted cells in ischemic sites diminishes its therapeutic efficacy. Follistatin-like 1 (Fstl1) is documented as a novel pro-survival cardiokine for cardiomyocytes, and it is protective during ischemic heart injury. In the present study, we characterize the potential of Fstl1 as an effective strategy to enhance hypoxia resistance of donor cells and optimize stem cell-based therapy. Methods Murine bone marrow-derived mesenchymal stem cells (MSCs) were expanded in monolayer culture and characterized by flow cytometry. MSCs were subjected to hypoxia to mimic cardiac ischemic environment. Expression of Fstl1 was monitored 0, 24, and 48 h following hypoxia. Constitutive expression of Fstl1 in MSCs was achieved by lentivirus-mediated Fstl1 overexpression. Genetically modified MSCs were further collected for cell death and proliferation assay following 48 h of hypoxic treatment. Acute myocardial infarction (MI) model was created by ligating the left anterior descending coronary artery, while control MSCs (MSCs-mCherry) or Fstl1-overexpressing MSCs (MSCs-Fstl1) were injected into the peri-infarct zone simultaneously. Subsequently, retention of the donor cells was evaluated on post-therapy 1, 3, & 7 days. Finally, myocardial function, infarct size, inflammation, and neovascularization of the infarcted hearts were calculated thereafter. Results Expression of Fstl1 in hypoxic MSCs declines dramatically in a time-dependent manner. In vitro study further demonstrated that Fstl1 promotes survival and proliferation of hypoxic MSCs. Moreover, Fstl1 significantly prolongs MSC survival/retention after implantation. Finally, transplantation with Fstl1-overexpressing MSCs significantly improves post-MI cardiac function by limiting scar formation, reducing inflammatory response, and enhancing neovascularization. Conclusions Our results suggest Fstl1 is an intrinsic cardiokine promoting survival and proliferation of MSCs, thereby optimizing their engraftment and therapeutic efficacy during cell therapy.