bluuebunny/crossref_metadata_2025 huggingface dataset:
Genetic diversity using biochemical, physiological, karyological and molecular markers of Sesamum indicum L
Authors: Mesfer ALshamrani Salha , Safhi Fatmah Ahmed , Alshaya Dalal Sulaiman , Ibrahim Amira A. , Mansour Hassan , Abd El Moneim Diaa
Published: October 2022

The genetic diversity and the relationships among sesame cultivars were investigated using physiological and cyto/molecular analysis. To our information, no studies have yet been conducted on the genetic evaluation of sesame genotypes based on cyto/molecular analysis in Saudi Arabia. This study showed that genotype Bah-312 had the highest values from physiological and biochemical traits (plant height, harvest index, total plant dry matter, seed yield, oil content, and fatty acids content). Using 20 ISSR and 25 SCoT primers, the studied genotypes amplified 233 and 275 alleles, while the average polymorphism percentage (P%) was 65.32% (ISSR) and 77.8% (SCoT) across all the studied genotypes, respectively. To assess the markers efficiency analysis the polymorphism information contents (PIC), Marker Index (MI), Effective Multiplex Ratio (EMR), Resolving Power (Rp) were estimated. In general, primers (ISSR 2 & SCoT 21) and (ISSR 4 & SCoT 3) revealed the highest and lowest values for P %, PIC, MI, and EMR%. Furthermore, 188 positive and negative unique bands were detected, out of which ISSR generated 84, while 104 were amplified by SCoT analysis. In this regard, genotype Bah-312 generated 41 unique amplicons, and Jiz-511 genotype 23 unique amplicons. In the same context, the population genetics parameters, number of different alleles (Na), number of effective alleles (Ne), Shannon’s index (I), expected heterozygosity (He), and Unbiased Expected Heterozygosity (uHe), were calculated. ISSR marker showed the highest values for all the estimated parameters. In this regard, genotype Bah-312 exhibited the highest values (1.35, 1.37, 0.31, 0.21, 0.29) & (1.31, 1.35, 0.30, 0.20, 0.27) while, genotype Ahs-670 revealed the least values (1.29, 1.31, 0.26, 0.16, 0.23) &(1.14, 1.26, 0.22, 0.15, 0.20) for ISSR and SCoT markers respectively. For cytological data, according to the highest asymmetry index (AsK%) and lowest total form percentage (TF%) values, genotype Ahs-670 was the most advanced cultivar, and genotype Bah-312 was the most primitive one. According to the degree of asymmetry of karyotype (A) and intrachromosomal asymmetry index (A1), sesame genotype Ahs-670 was the most asymmetrical, and Bah-312 was the most symmetrical genotype. This study gives some helpful information about the genetic diversity of six sesame landraces. The variation harbored by these landraces could be used in sesame breeding programs.
Advances in the functions of CTRP6 in the development and progression of the malignancy
Authors: Hu Bo , Qian Xiaolan , Qian Ping , Xu Guangtao , Jin Xin , Chen Deqing , Xu Long , Tang Jie , Wu Wenjing , Li Wanlu , Zhang Jin
Published: October 2022

CTRP6, a member of the C1q/TNF-related protein (CTRP) family, has gained increasing scientific interest because of its regulatory role in tumor progression. Previous studies have shown that CTRP6 is closely involved in regulating various pathophysiological processes, including glucose and lipid metabolism, cell proliferation, apoptosis, and inflammation. To date, CTRP6 has been identified as related to eight different malignancies, including lung cancer, oral cancer, gastric cancer, colon cancer, liver cancer, bladder cancer, renal cancer, and ovarian cancer. CTRP6 is reported to be associated with tumor progression by activating a series of related signal networks. This review article mainly discusses the biochemistry and pleiotropic pathophysiological functions of CTRP6 as a new molecular mediator in carcinogenesis, hoping that the information summarized herein could make a modest contribution to the development of novel cancer treatments in the future.
Genotypic spectrum underlying tetrahydrobiopterin metabolism defects: Experience in a single Mexican reference center
Authors: Vela-Amieva M. , Alcántara-Ortigoza M. A. , Ibarra-González I. , González-del Angel A. , Fernández-Hernández L. , Guillén-López S. , López-Mejía L. , Carrillo-Nieto R. I. , Fiesco-Roa M. O. , Fernández-Lainez C.
Published: October 2022

Background: Pterin profiles or molecular analyses of hyperphenylalaninemia (HPA) caused by phenylalanine hydroxylase (PAH) deficiency or tetrahydrobiopterin deficiency (BH4D) are not always available in low- or middle-income countries, including Mexico, limiting information regarding the phenotypic and genotypic characteristics of patients exhibiting BH4D.

Objective: To report the genotypes underlying BH4D and the clinical presentation in unrelated Mexican HPA pediatric patients with normal PAH genotypes who attended a single metabolic reference center in Mexico.

Methods: Automated Sanger sequencing of the PTS, QDPR, and PCBD1 genes of 14 HPA patients was performed. Predicted effects on protein structure caused by missense variants were assessed by in silico protein modeling.

Results and discussion: A high prevalence of BH4D was noted in our HPA cohort (9.8%, N = 14/142). Clinically relevant biallelic genotypes were identified in the PTS (N = 7/14 patients), QDPR (N = 6/14 patients), and PCBD1 (N = 1/14 patients) genes. Four novel QDPR variants [c.714dup or p.(Leu239Thrfs*44), c.106-1G>T or p.(?), c.214G>T or p.(Gly72*), and c.187_189dup or p.(Gln63dup)] were identified. In silico protein modeling of six missense variants of PTS [p.(Thr67Met), p.(Glu81Ala), and p.(Tyr113Cys)], QDPR [p.(Cys161Phe) and p.(Pro172Leu)], and PCBD1 [p.(Glu97Lys)] supports their pathogenicity. Progressive neurological symptoms (mainly intellectual and motor impairment and even death in three patients) were noted in all patients with biallelic QDPR genotypes and in 5/7 patients bearing biallelic PTS genotypes. The single homozygous PCBD1 p.(Glu97Lys) patient remains asymptomatic.

Conclusion: A higher proportion of BH4D (9.8 vs. 1%–2% worldwide), attributable to a heterogeneous mutational spectrum and wide clinical presentation, was noted in our Mexican HPA cohort, with the PTS-related HPA disorder being the most frequent. Sequencing-based assays could be a reliable approach for diagnosing BH4D in our population.
Case Report: Interventional therapy for portal venous stenosis caused by systemic vasculitis
Authors: Cai Qiuyu , Wei Bo , Tai Yang , Wu Hao
Published: October 2022

Systemic vasculitis are multisystem blood vessel disorders. However, Portal venous involvement is extremely rare, which represents a diagnostic and therapeutic challenge due to the heterogeneous nature, a lack of diagnostic criteria and limited effective therapy of vasculitis. We have reported a 48-year-old woman who was previously diagnosed with systemic vasculitis and was treated with prednisone, presented with gastrointestinal (GI) bleeding on admission. Further abdominal contrast-enhanced computed tomography (CT) with three-dimensional reconstruction suggested atrophic left hepatic lobe, enlarged spleen, and severe stenosis of main portal vein. Liver biopsy showed no evidence of fibrosis/cirrhosis. To prevent rebleeding, portal venous angioplasty by balloon dilation with collateral varices embolization was performed, and the GI hemorrhage was resolved completely. However, refractory ascites presented 8 months postoperatively. Abdominal CT angiography confirmed the recurrence of portal venous stenosis. Portal venous angioplasty by stent implantation was then performed to treat the portal hypertension (PHT)-related complications. After the intervention, the patient received anticoagulation therapy and continued immunosuppressive therapy. During the 5-year follow-up, the patient did not experience any onset of GI bleeding or ascites. Therefore, portal venous angioplasty with stent placement could be an effective treatment to prevent PHT-related complications when immunosuppression therapy failed.
Immune-infiltrating signature-based classification reveals CD103+CD39+ T cells associate with colorectal cancer prognosis and response to immunotherapy
Authors: Luo Yang , Zong Yunfeng , Hua Hanju , Gong Meiting , Peng Qiao , Li Chen , Neculai Dante , Zeng Xun
Published: October 2022

Background

Current stratification systems for tumor prognostic prediction and immunotherapeutic efficacy evaluation are less satisfying in colorectal cancer (CRC). As infiltrating immune cells in tumor microenvironment (TME) played a key role in tumor progression and responses to immune checkpoint blockade (ICB) therapy, we want to construct an immune-related scoring system with detailed immune profiles to stratify CRC patients.

Methods

We developed a scoring system based on immune-related signatures and validated its ability to predict prognosis and immunotherapeutic outcomes in CRC. CD45+ cells from CRC patients were sorted to investigate detailed immune profiles of the stratification system using mass cytometry. A single-cell RNA sequencing dataset was used to analyze transcriptomic profiles.

Results

We constructed an immune-related signature score (IRScore) based on 54 recurrence-free survival (RFS)-related immune signatures to stratify CRC patients. We revealed that IRScore was positively correlated with RFS and favorable outcomes in ICB treatment. Moreover, we depicted a detailed immune profile in TME using mass cytometry and identified that CD103+CD39+ T cells, characterized by an exhaustive, cytotoxic and proliferative phenotype, were enriched in CRC patients with high IRScore. As a beneficial immune signature, CD103+CD39+ T cells could predict prognosis and responses to ICB therapy in CRC.

Conclusions

All the analyses above revealed that IRScore could be a valuable tool for predicting prognosis and facilitating the development of new therapeutic strategies in CRC, and CD103+CD39+ T cells were one of defined immune signatures in IRScore, which might be a key factor for antitumor immunity.
SARS-CoV-2 specific antibody trajectories in mothers and infants over two months following maternal infection
Authors: Martin Melanie A. , Keith Monica , Pace Ryan M. , Williams Janet E. , Ley Sylvia H. , Barbosa-Leiker Celestina , Caffé Beatrice , Smith Caroline B. , Kunkle Amanda , Lackey Kimberly A. , Navarrete Alexandra D. , Pace Christina D. W. , Gogel Alexandra C. , Eisenberg Dan T.A. , Fehrenkamp Bethaney D. , McGuire Mark A. , McGuire Michelle K. , Meehan Courtney L. , Brindle Eleanor
Published: October 2022

Infants exposed to caregivers infected with SARS-CoV-2 may have heightened infection risks relative to older children due to their more intensive care and feeding needs. However, there has been limited research on COVID-19 outcomes in exposed infants beyond the neonatal period. Between June 2020 – March 2021, we conducted interviews and collected capillary dried blood spots from 46 SARS-CoV-2 infected mothers and their infants (aged 1-36 months) for up to two months following maternal infection onset (COVID+ group, 87% breastfeeding). Comparative data were also collected from 26 breastfeeding mothers with no known SARS-CoV-2 infection or exposures (breastfeeding control group), and 11 mothers who tested SARS-CoV-2 negative after experiencing symptoms or close contact exposure (COVID- group, 73% breastfeeding). Dried blood spots were assayed for anti-SARS-CoV-2 S-RBD IgG and IgA positivity and anti-SARS-CoV-2 S1 + S2 IgG concentrations. Within the COVID+ group, the mean probability of seropositivity among infant samples was lower than that of corresponding maternal samples (0.54 and 0.87, respectively, for IgG; 0.33 and 0.85, respectively, for IgA), with likelihood of infant infection positively associated with the number of maternal symptoms and other household infections reported. COVID+ mothers reported a lower incidence of COVID-19 symptoms among their infants as compared to themselves and other household adults, and infants had similar PCR positivity rates as other household children. No samples returned by COVID- mothers or their infants tested antibody positive. Among the breastfeeding control group, 44% of mothers but none of their infants tested antibody positive in at least one sample. Results support previous research demonstrating minimal risks to infants following maternal COVID-19 infection, including for breastfeeding infants.
Identification of hub genes and their correlation with infiltration of immune cells in MYCN positive neuroblastoma based on WGCNA and LASSO algorithm
Authors: Chen Ji , Sun Mengjiao , Chen Chuqin , Jiang Bin , Fang Yongjun
Published: October 2022

Background

The prognosis of MYCN positive NB is poor, and there is no targeted drug for N-myc at present. This study aims to screen out hub genes closely related to MYCN, analyze the relationship between hub genes and NB microenvironment, and provide basis for molecular targeted therapy of MYCN positive NB.

Methods

We combined the microarray data of GSE45547 (n=649) and GSE49710 (n=498), screened the DEGs between MYCN positive (n=185) and MYCN negative NB (n=951), performed WGCNA, Lasso regression and Roc analyses on the merged matrix, and obtained the hub genes related to MYCN in the training group. We performed ssGSEA on the experimental group to calculate the infiltration level of 28 kinds of immune cells in each sample, compared the differences of immune cell infiltration between MYCN positive and MYCN negative group. The influences of hub genes on the distribution of each immune cell were also analyzed by ssGSEA. The expression differences of the three hub genes were verified in the E-MTAB-8248 cohort (n=223), and the correlation between hub genes and prognosis of NB was calculated by Kaplan-Meier method in GSE62564 (n=498) and the validation group. We also verified the expression differences of hub genes by qRT-PCR in SK-N-BE(2), SKNDZ, Kelly and SH-SY5Y cell lines.

Results

Here were 880 DEGs including 420 upregulated and 460 downregulated genes in MYCN positive NB in the training group. Overlap of the DEGs and WGCNA networks identified four shared genes, namely, ZNF695, CHEK1, C15ORF42 and EXO1, as candidate hub genes in MYCN positive NB. Three core genes, ZNF695, CHEK1 and C15ORF42, were finally identified by Lasso regression and Roc analyses. ZNF695, CHEK1 and C15ORF42 were highly expressed in MYCN positive NB tissues and cell lines. These three genes were closely related to the prognosis of children with NB. Except that Activated CD4 T cell and Type2 T helper cell increased, the infiltration levels of the other 26 cells decreased significantly in MYCN positive NB tissues. The infiltration levels of Type2 T helper cell and Activated CD4 T cell were also significantly positively correlated with the expression levels of the three hub genes.

Conclusion

ZNF695, CHEK1 and C15ORF42 are highly expressed in MYCN positive NB, and their expression levels are negatively correlated with the prognosis of children with NB. The infiltration levels of Activated CD4 T cell and Type2 T helper cell increased in the microenvironment of MYCN positive NB and were significantly positively correlated with the expression levels of the three hub genes. The results of this study provide that ZNF695, CHEK1 and C15ORF42 may be potential prognostic markers and immunotherapy targets for MYCN positive NB.
Reshaping the tumor microenvironment: The versatility of immunomodulatory drugs in B-cell neoplasms
Authors: Guo Hao , Yang Jingyi , Wang Haoran , Liu Xingchen , Liu Yanyan , Zhou Keshu
Published: October 2022

Immunomodulatory drugs (IMiDs) such as thalidomide, lenalidomide and pomalidomide are antitumor compounds that have direct tumoricidal activity and indirect effects mediated by multiple types of immune cells in the tumor microenvironment (TME). IMiDs have shown remarkable therapeutic efficacy in a set of B-cell neoplasms including multiple myeloma, B-cell lymphomas and chronic lymphocytic leukemia. More recently, the advent of immunotherapy has revolutionized the treatment of these B-cell neoplasms. However, the success of immunotherapy is restrained by immunosuppressive signals and dysfunctional immune cells in the TME. Due to the pleiotropic immunobiological properties, IMiDs have shown to generate synergetic effects in preclinical models when combined with monoclonal antibodies, immune checkpoint inhibitors or CAR-T cell therapy, some of which were successfully translated to the clinic and lead to improved responses for both first-line and relapsed/refractory settings. Mechanistically, despite cereblon (CRBN), an E3 ubiquitin ligase, is considered as considered as the major molecular target responsible for the antineoplastic activities of IMiDs, the exact mechanisms of action for IMiDs-based TME re-education remain largely unknown. This review presents an overview of IMiDs in regulation of immune cell function and their utilization in potentiating efficacy of immunotherapies across multiple types of B-cell neoplasms.
CXCR6 expressing T cells: Functions and role in the control of tumors
Authors: Mabrouk Nesrine , Tran Thi , Sam Ikuan , Pourmir Ivan , Gruel Nadège , Granier Clémence , Pineau Joséphine , Gey Alain , Kobold Sebastian , Fabre Elizabeth , Tartour Eric
Published: October 2022

CXCR6 is a receptor for the chemokine CXCL16, which exists as a membrane or soluble form. CXCR6 is a marker for resident memory T (TRM) cells that plays a role in immunosurveillance through their interaction with epithelial cells. The interaction of CXCR6 with CXCL16 expressed at the membrane of certain subpopulations of intratumor dendritic cells (DC) called DC3, ideally positions these CXCR6+ T cells to receive a proliferation signal from IL-15 also presented by DC3. Mice deficient in cxcr6 or blocking the interaction of CXCR6 with its ligand, experience a poorer control of tumor proliferation by CD8+ T cells, but also by NKT cells especially in the liver. Intranasal vaccination induces CXCL16 production in the lungs and is associated with infiltration by TRM expressing CXCR6, which are then required for the efficacy of anti-tumor vaccination. Therapeutically, the addition of CXCR6 to specific CAR-T cells enhances their intratumoral accumulation and prolongs survival in animal models of pancreatic, ovarian and lung cancer. Finally, CXCR6 is part of immunological signatures that predict response to immunotherapy based on anti-PD-(L)1 in various cancers. In contrast, a protumoral role of CXCR6+T cells has also been reported mainly in Non-alcoholic steatohepatitis (NASH) due to a non-antigen specific mechanism. The targeting and amplification of antigen-specific TRM expressing CXCR6 and its potential use as a biomarker of response to immunotherapy opens new perspectives in cancer treatment.
Dysregulation of B7 family and its association with tumor microenvironment in uveal melanoma
Authors: Chen Yao , Zheng Anfu , Zhang Yao , Xiao Mintao , Zhao Yueshui , Wu Xu , Li Mingxing , Du Fukuan , Chen Yu , Chen Meijuan , Li Wanping , Li Xiaobing , Sun Yuhong , Gu Li , Xiao Zhangang , Shen Jing
Published: October 2022

Background

Uveal melanoma (UVM) is the most common primary intraocular malignancy in adults with a poor prognosis. B7 family is an important modulator of the immune response. However, its dysregulation and underlying molecular mechanism in UVM still remains unclear.

Methods

Data were derived from TCGA and GEO databases. The prognosis was analyzed by Kaplan-Meier curve. The ESTIMATE algorithm, CIBERSORT algorithm, and TIMER database were used to demonstrate the correlation between B7 family and tumor immune microenvironment in UVM. Single-cell RNA sequencing was used to detect the expression levels of the B7 family in different cell types of UVM. UVM was classified into different types by consistent clustering. Enrichment analysis revealed downstream signaling pathways of the B7 family. The interaction between different cell types was visualized by cell chat.

Results

The expression level of B7 family in UVM was significantly dysregulated and negatively correlated with methylation level. The expression of B7 family was associated with prognosis and immune infiltration, and B7 family plays an important role in the tumor microenvironment (TME). B7 family members were highly expressed in monocytes/macrophages of UVM compared with other cell types. Immune response and visual perception were the main functions affected by B7 family. The result of cell chat showed that the interaction between photoreceptor cells and immune-related cells was mainly generated by HLA-C-CD8A. CABP4, KCNJ10 and RORB had the strongest correlation with HLA-C-CD8A, and their high expression was significantly correlated with poor prognosis. CABP4 and RORB were specifically expressed in photoreceptor cells.

Conclusions

Dysregulation of the B7 family in UVM is associated with poor prognosis and affects the tumor immune microenvironment. CABP4 and RORB can serve as potential therapeutic targets for UVM, which can be regulated by the B7 family to affect the visual perception and immune response function of the eye, thus influencing the prognosis of UVM.
Significance of macrophage infiltration in the prognosis of lung adenocarcinoma patients evaluated by scRNA and bulkRNA analysis
Authors: Zhu Huaiyang , Zheng Chunning , Liu Hongtao , Kong Fanhua , Kong Shuai , Chen Feng , Tian Yuan
Published: October 2022

Purpose

To investigate the significance of macrophage infiltration to the prognosis of lung adenocarcinoma.

Methods

R language bioinformatics analysis technology, was used to obtain macrophage infiltration-related module genes through WGCNA (Weighted Gene Co-Expression Network Analysis). Marker genes of macrophage subtypes were identified using single-cell sequencing of lung adenocarcinoma tissue. Risk score models were constructed and validated using external data cohorts and clinical samples.

Results

Analysis of cohorts TCGA-LUAD, GSE11969, GSE31210, GSE50081, GSE72094 and GSE8894, revealed a negative correlation between macrophage infiltration and survival. Immunohistochemical analyses of clinical samples were consistent with these data. Based on cell-cluster-markers and TAMs-related-genes, TOP8 genes were obtained (C1QTNF6, CCNB1, FSCN1, HMMR, KPNA2, PRC1, RRM2, and TK1) with a significant association to prognosis. Risk score models including 9 factors (C1QTNF6, FSCN1, KPNA2, GLI2, TYMS, BIRC3, RBBP7, KRT8, GPR65) for prognosis were constructed. The efficacy, stability and generalizability of the risk score models were validated using multiple data cohorts (GSE19188, GSE26939, GSE31210, GSE50081, GSE42127, and GSE72094).

Conclusions

Macrophage infiltration negatively correlates with prognosis in patients with lung adenocarcinoma. Based on cell-cluster-markers and TAMs-related-genes, both TOP8 genes (C1QTNF6, CCNB1, FSCN1, HMMR, KPNA2, PRC1, RRM2, TK1) and risk score models using C1QTNF6, FSCN1, KPNA2, GLI2, TYMS, BIRC3, RBBP7, KRT8, GPR65 could predict disease prognosis.
Sorting nexin 17 increases low-density lipoprotein receptor-related protein 4 membrane expression: A novel mechanism of acetylcholine receptor aggregation in myasthenia gravis
Authors: He Xiaoxiao , Zhou Shuxian , Ji Ying , Zhang Yingna , Lv Jie , Quan Shangkun , Zhang Jing , Zhao Xue , Cui Weike , Li Wenbo , Liu Peipei , Zhang Linyuan , Shen Tong , Fang Hua , Yang Junhong , Zhang Yunke , Cui Xinzheng , Zhang Qingyong , Gao Feng
Published: October 2022

Myasthenia gravis (MG) is characterized by autoimmune damage to the postsynaptic membrane of the neuromuscular junction (NMJ) with impaired postsynaptic acetylcholine receptor (AChR) aggregation. Low-density lipoprotein receptor-related protein 4 (LRP4) plays an important role in AChR aggregation at endplate membranes via the Agrin–LRP4–muscle-specific receptor tyrosine kinase (MuSK) cascade. Sorting nexin 17 (SNX17) regulates the degradation and recycling of various internalized membrane proteins. However, whether SNX17 regulates LRP4 remains unclear. Therefore, we examined the regulatory effects of SNX17 on LRP4 and its influence on AChR aggregation in MG. We selected C2C12 myotubes and induced LRP4 internalization via stimulation with anti-LRP4 antibody and confirmed intracellular interaction between SNX17 and LRP4. SNX17 knockdown and overexpression confirmed that SNX17 promoted MuSK phosphorylation and AChR aggregation by increasing cell surface LRP4 expression. By establishing experimental autoimmune MG (EAMG) mouse models, we identified that SNX17 upregulation improved fragmentation of the AChR structure at the NMJ and alleviated leg weakness in EAMG mice. Thus, these results reveal that SNX17 may be a novel target for future MG therapy.
Bovine delta papillomavirus E5 oncoprotein negatively regulates the cGAS-STING signaling pathway in cattle in a spontaneous model of viral disease
Authors: De Falco Francesca , Cutarelli Anna , Catoi Adriana Florinela , Uberti Barbara Degli , Cuccaro Bianca , Roperto Sante
Published: October 2022

Persistent infection and tumorigenesis by papillomaviruses (PVs) require viral manipulation of various cellular processes, including those involved in innate immune responses. The cyclic guanosine monophosphate-adenosine monophosphate synthase-stimulator of interferon genes (cGAS-STING) pathway has emerged as an essential innate immune sensing system, that recognizes DNA and trigger potent antiviral effector responses. In this study, we found that bovine PV (BPV) E5 protein, the major oncoprotein of bovine delta PVs, interacts with STING but not with cGAS in a spontaneous BPV infection of neoplastic urothelial cells of cattle. Real-time RT-PCR revealed a significant reduction in both cGAS and STING transcripts in E5-expressing cells. Furthermore, western blot (WB) analysis failed to detect any variation in the expression of interferon-inducible protein 16 (IFI16), an upstream effector of the STING pathway. A ternary complex composed of E5/STING/IFI16 was also observed. Co-immunoprecipitation studies showed that STING interacts with a protein network composed of total and phosphorylated TANK-binding kinase 1 (TBK1), total and phosphorylated interferon regulatory factor 3 (IRF3), IRF7, IKKα, IKKβ, IKKϵ, ELKS, MEKK3, and TAK1. RT-qPCR revealed a significant reduction in TBK1 mRNA levels in BPV-infected cells. WB analysis revealed significantly reduced expression levels of pTBK1, which is essential for the activation and phosphorylation of IRF3, a prerequisite for the latter to enter the nucleus to activate type 1 IFN genes. WB also revealed significantly down-expression of IKKα, IKKβ, IKKϵ, and overexpression of IRF7, ELKS, MEKK3, and TAK1in BPV-positive urothelial cells compared with that in uninfected healthy cells. Phosphorylated p65 (p-p65) was significantly reduced in both the nuclear and cytosolic compartments of BPV-infected cells compared with that in uninfected urothelial cells. Our results suggest that the innate immune signaling pathway mediated by cGAS-STING is impaired in cells infected with BPV. Therefore, effective immune responses are not elicited against these viruses, which facilitates persistent viral infection and subsequent tumorigenesis.
Advances in immunotherapy for glioblastoma multiforme
Authors: Mahmoud Ahmad Bakur , Ajina Reham , Aref Sarah , Darwish Manar , Alsayb May , Taher Mustafa , AlSharif Shaker A. , Hashem Anwar M. , Alkayyal Almohanad A.
Published: October 2022

Glioblastoma multiforme (GBM) is the most common and aggressive malignant brain tumor of the central nervous system and has a very poor prognosis. The current standard of care for patients with GBM involves surgical resection, radiotherapy, and chemotherapy. Unfortunately, conventional therapies have not resulted in significant improvements in the survival outcomes of patients with GBM; therefore, the overall mortality rate remains high. Immunotherapy is a type of cancer treatment that helps the immune system to fight cancer and has shown success in different types of aggressive cancers. Recently, healthcare providers have been actively investigating various immunotherapeutic approaches to treat GBM. We reviewed the most promising immunotherapy candidates for glioblastoma that have achieved encouraging results in clinical trials, focusing on immune checkpoint inhibitors, oncolytic viruses, nonreplicating viral vectors, and chimeric antigen receptor (CAR) immunotherapies.
Microglial exosomal miR-466i-5p induces brain injury via promoting hippocampal neuron apoptosis in heatstroke
Authors: Zhu Jie , Chen Yahong , Ji Jingjing , Wang Longyan , Xie Guoqiang , Tang Zhen , Qu Xiangmeng , Liu Zhifeng , Ren Guangli
Published: October 2022

Background

Brain injury is the main cause of poor prognosis in heatstroke (HS) patients due to heat-stress-induced neuronal apoptosis. However, as a new cross-talk way among cells, whether microglial exosomal-microRNAs (miRNAs) are involved in HS-induced neuron apoptosis has not been elucidated.

Methods

We established a heatstroke mouse model and a heat-stressed neuronal cellular model on HT22 cell line. Then, we detected neuron apoptosis by histopathology and flow cytometry. The microglial exosomes are isolated by standard differential ultracentrifugation and characterized. Recipient neurons are treated with the control and HS exosomes, whereas in vivo, the exosomes were injected into the mice tail vein. The internalization of HS microglial exosomes by neurons was tracked. Apoptosis of HT22 was evaluated by flow cytometry and Western blot in vitro, TUNEL assay, and immunohistochemistry in vivo. We screened miR-466i-5p as the mostly upregulated microRNAs in HS exosomes by high-throughput sequencing and further conducted gene ontology (GO) pathway analysis. The effect and mechanism of HS exosomal miR-466i-5p on the induction of neuron apoptosis are demonstrated by nasal delivery of miR-466i-5p antagomir in vivo and transfecting miR-466i-5p mimics to HT22 in vitro.

Results

HS induced an increase in neurons apoptosis. Microglial exosomes are identified and taken up by neurons, which induced HT22 apoptosis in vivo and vitro. HS significantly changed the miRNA profiles of microglial exosomes based on high-throughput sequencing. We selected miR-466i-5p as a target, and upregulated miR-466i-5p induced neurons apoptosis in vivo and vitro experiments. The effects are exerted by targeting Bcl-2, activating caspase-3 to induce neurons apoptosis.

Conclusions

We demonstrate the effect of microglial exosomal miR-466i-5p on neurons apoptosis and reveal potentially Bcl-2/caspase-3 pathway in heatstroke.
Specific location of galactosylation in an afucosylated antiviral monoclonal antibody affects its FcγRIIIA binding affinity
Authors: Hatfield Grayson , Tepliakova Lioudmila , Gingras Genevieve , Stalker Andrew , Li Xuguang , Aubin Yves , Tam Roger Y.
Published: October 2022

Monoclonal antibodies (mAbs) comprise an essential type of biologic therapeutics and are used to treat diseases because of their anti-cancer and anti-inflammatory properties, and their ability to protect against respiratory infections. Its production involves post-translational glycosylation, a biosynthetic process that conjugates glycans to proteins, which plays crucial roles in mAb bioactivities including effector functions and pharmacokinetics. These glycans are heterogeneous and have diverse chemical structures whose composition is sensitive to manufacturing conditions, rendering the understanding of how specific glycan structures affect mAb bioactivity challenging. There is a need to delineate the effects of specific glycans on mAb bioactivity to determine whether changes in certain glycosylation profiles (that can occur during manufacturing) will significantly affect product quality. Using enzymatic transglycosylation with chemically-defined N-glycans, we show that galactosylation at a specific location of N-glycans in an afucosylated anti-viral mAb is responsible for FcγRIIIA binding and antibody-dependent cell-mediated cytotoxicity (ADCC) activity. We report a facile method to obtain purified asymmetric mono-galactosylated biantennary complex N-glycans, and their influence on bioactivity upon incorporation into an afucosylated mAb. Using ELISA, surface plasmon resonance and flow cytometry, we show that galactosylation of the α6 antenna, but not the α3 antenna, consistently increases FcγRIIIA binding affinity. We confirm its relevance in an anti-viral model of respiratory syncytial virus (RSV) using an adapted ADCC reporter assay. We further correlate this structure-function relationship to the interaction of the galactose residue of the α6 antenna with the protein backbone using 2D-1H-15N-NMR, which showed that galactosylation of at this location exhibited chemical shift perturbations compared to glycoforms lacking this galactose residue. Our results highlight the importance of identifying and quantifying specific glycan isomers to ensure adequate quality control in batch-to-batch and biosimilar comparisons.
Dental pulp stem cells retain mesenchymal phenotype despite differentiation toward retinal neuronal fate in vitro
Authors: Balasankar Aishwarya , Chan Shu-Yi Claire , Babu Venkata Pakala Sudheer , Yam Gary , Tin Goh Bee , Singhal Shweta
Published: October 2022

Dental pulp stem cells (DPSCs) are an easily accessible, heterogenous source of mesenchymal stem cells (MSCs) that are derived from the neural crest. Evidence suggests that they have neurotrophic qualities in their undifferentiated state and can also be differentiated into neuronal and retinal cell types. There is growing interest in using DPSCs in cell-based therapies to treat glaucoma and blinding retinal diseases. However, careful characterization of these cells is necessary as direct intravitreal and subretinal MSC transplantation is known to lead to deleterious glial reaction and fibrosis. In this study, we provide evidence for the mesenchymal-predominant nature of DPSCs and show that DPSCs maintain their mesenchymal phenotype despite upregulating mature retinal markers under retinal differentiation conditions. CD56, which was previously thought to be a specific marker of neural crest lineage, is robustly co-expressed with mesenchymal markers and may not be adequate for isolating a subpopulation of neural crest cells in DPSCs. Therefore, identification of more specific markers is required to elucidate the heterogeneity of the population and to successfully isolate a putative neural stem cell population before DPSCs can be used for retinal therapy.
Limited permissibility of ENL-R and Mv-1-Lu mink cell lines to SARS-CoV-2
Authors: Le Bideau Marion , Pires de Souza Gabriel Augusto , Boschi Celine , Baudoin Jean-Pierre , Penant Gwilherm , Jardot Priscilla , Fenollar Florence , Colson Philippe , Lenk Matthias , La Scola Bernard
Published: October 2022

The SARS-CoV-2 pandemic started in the end of 2019 in Wuhan, China, which highlighted the scenario of frequent cross-species transmission events. From the outbreak possibly initiated by viral spill-over into humans from an animal reservoir, now we face the human host moving globally while interacting with domesticated and peridomestic animals. The emergence of a new virus into the ecosystem leads to selecting forces and species-specific adaptations. The adaptation of SARS-CoV-2 to other animals represents a risk to controlling the dissemination of this coronavirus and the emergence of new variants. Since 2020, several mink farms in Europe and the United States have had SARS-CoV-2 outbreaks with human–mink and mink–human transmission, where the mink-selected variants possibly hold evolutionary concerning advantages. Here we investigated the permissibility of mink lung-derived cells using two cell lines, Mv-1-Lu and ENL-R, against several lineages of SARS-CoV-2, including some classified as variants of concern. The viral release rate and the infectious titers indicate that these cells support infections by different SARS-CoV-2 lineages. The viral production occurs in the first few days after infection with the low viral release by these mink cells, which is often absent for the omicron variant for lung cells. The electron microscopy reveals that during the viral replication cycle, the endomembrane system of the mink-host cell undergoes typical changes while the viral particles are produced, especially in the first days of infection. Therefore, even if limited, mink lung cells may represent a selecting source for SARS-CoV-2 variants, impacting their transmissibility and pathogenicity and making it difficult to control this new coronavirus.
Mirror proteases of Ac-Trypsin and Ac-LysargiNase precisely improve novel event identifications in Mycolicibacterium smegmatis MC2 155 by proteogenomic analysis
Authors: Jiang Songhao , Shi Jiahui , Li Yanchang , Zhang Zhenpeng , Chang Lei , Wang Guibin , Wu Wenhui , Yu Liyan , Dai Erhei , Zhang Lixia , Lyu Zhitang , Xu Ping , Zhang Yao
Published: October 2022

Accurate identification of novel peptides remains challenging because of the lack of evaluation criteria in large-scale proteogenomic studies. Mirror proteases of trypsin and lysargiNase can generate complementary b/y ion series, providing the opportunity to efficiently assess authentic novel peptides in experiments other than filter potential targets by different false discovery rates (FDRs) ranking. In this study, a pair of in-house developed acetylated mirror proteases, Ac-Trypsin and Ac-LysargiNase, were used in Mycolicibacterium smegmatis MC2 155 for proteogenomic analysis. The mirror proteases accurately identified 368 novel peptides, exhibiting 75–80% b and y ion coverages against 65–68% y or b ion coverages of Ac-Trypsin (38.9% b and 68.3% y) or Ac-LysargiNase (65.5% b and 39.6% y) as annotated peptides from M. smegmatis MC2 155. The complementary b and y ion series largely increased the reliability of overlapped sequences derived from novel peptides. Among these novel peptides, 311 peptides were annotated in other public M. smegmatis strains, and 57 novel peptides with more continuous b and y pairs were obtained for further analysis after spectral quality assessment. This enabled mirror proteases to successfully correct six annotated proteins' N-termini and detect 17 new coding open reading frames (ORFs). We believe that mirror proteases will be an effective strategy for novel peptide detection in both prokaryotic and eukaryotic proteogenomics.
Christensenella regulated by Huang-Qi-Ling-Hua-San is a key factor by which to improve type 2 diabetes
Authors: Pan Tong , Zheng Shujun , Zheng Weiwei , Shi Chao , Ning Ke , Zhang Qinghui , Xie Yanbo , Xiang Hongyu , Xie Qiuhong
Published: October 2022

There is a lot of evidence that oral hypoglycemic drugs work by affecting gut microbes, but the key strains responsible for this effect are not well known. Huang-Qi-Ling-Hua-San (HQLHS), composed of Astragalus Membranaceus, Ganoderma lucidum, Inonotus obliquus, and Momordica charantia L., is a specially designed Chinese medicine formula to treat type 2 diabetes (T2D). In this study, a mouse model of T2D induced by high-fat diet and streptozotocin was used to explore the mechanism of HQLHS in improving hyperglycemia and hyperlipidemia through multiple rounds of animal experiments, such as HQLHS feeding, fecal microbiota transplantation (FMT), and live bacteria feeding, so as to explore the potential target intestinal flora in its hypoglycemic effect. Results show that such specific taxa as Bifidobacterium, Turicibacter, Alistipes, Romboutsia, and Christensenella were identified to be preferably enriched by HQLHS and then assumed to be the target microbes. Herein, FMT was used to test if the upregulated beneficial bacteria by HQLHS play a therapeutic role. The strain Christensenella minuta DSM 22607 and the strain Christensenella timonensis DSM 102800 were selected to test the beneficial effect of Christensenella taxa on T2D. Diabetic animals supplemented with these strains showed the improvement in blood glucose and lipid metabolism, the promotion of GLP-1 secretion, the increase in antioxidant capacity, the inhibition of hepatic gluconeogenesis, the suppression of intestinal glucose absorption, the enhancement of intestinal barrier, reduced LPS-induced inflammation, and the reduction of branched amino acids (BCAAs) content in the liver. Overall, these data demonstrate that Christensenella plays a beneficial role in T2D and is a target for the action of HQLHS therapy.
Contribution of the EnvZ/OmpR two-component system to growth, virulence and stress tolerance of colistin-resistant Aeromonas hydrophila
Authors: Xiao Gang , Zheng Xiaofeng , Li Jiyun , Yang Yang , Yang Jie , Xiao Ning , Liu Junqi , Sun Zhiliang
Published: October 2022

Aeromonas hydrophila is an important zoonotic pathogen responsible for septicemia, diarrhea and gastroenteritis, and has attracted considerable attention. The EnvZ/OmpR two-component system (TCS) mediates environmental stress responses in gram-negative bacteria. We investigated the role of the TCS in A. hydrophila by comparing the characteristics of the parental (23-C-23), EnvZ/OmpR knockout (23-C-23:ΔEnvZ/OmpR), and complemented strains (23-C-23:CΔEnvZ/OmpR). Under non-stress conditions, the 23-C-23:ΔEnvZ/OmpR strain showed a significant decrease in growth rate compared to that of 23-C-23. Transcriptome and metabonomic analysis indicated that many metabolic pathways were remarkably affected in the ΔEnvZ/OmpR strain, including the TCA cycle and arginine biosynthesis. In addition, the virulence of the ΔEnvZ/OmpR strain was attenuated in a Kunming mouse model. The ΔEnvZ/OmpR strain exhibited notably reduced tolerance to environmental stresses, including high temperature, different pH conditions, oxidative stress, and high osmotic stress. The downregulated expression of genes related to cell metabolism, motility, and virulence in the ΔEnvZ/OmpR mutant strain was further validated by real-time quantitative PCR. Consequently, our data suggest that the EnvZ/OmpR TCS is required for growth, motility, virulence, and stress response in A. hydrophila, which has significant implications in the development of novel antibacterial and vaccine therapies targeting EnvZ/OmpR against A. hydrophila.
Better under stress: Improving bacterial cellulose production by Komagataeibacter xylinus K2G30 (UMCC 2756) using adaptive laboratory evolution
Authors: Anguluri Kavitha , La China Salvatore , Brugnoli Marcello , Cassanelli Stefano , Gullo Maria
Published: October 2022

Among naturally produced polymers, bacterial cellulose is receiving enormous attention due to remarkable properties, making it suitable for a wide range of industrial applications. However, the low yield, the instability of microbial strains and the limited knowledge of the mechanisms regulating the metabolism of producer strains, limit the large-scale production of bacterial cellulose. In this study, Komagataeibacter xylinus K2G30 was adapted in mannitol based medium, a carbon source that is also available in agri-food wastes. K. xylinus K2G30 was continuously cultured by replacing glucose with mannitol (2% w/v) for 210 days. After a starting lag-phase, in which no changes were observed in the utilization of mannitol and in bacterial cellulose production (cycles 1–25), a constant improvement of the phenotypic performances was observed from cycle 26 to cycle 30, accompanied by an increase in mannitol consumption. At cycle 30, the end-point of the experiment, bacterial cellulose yield increased by 38% in comparision compared to cycle 1. Furthermore, considering the mannitol metabolic pathway, D-fructose is an intermediate in the bioconversion of mannitol to glucose. Based on this consideration, K. xylinus K2G30 was tested in fructose-based medium, obtaining the same trend of bacterial cellulose production observed in mannitol medium. The adaptive laboratory evolution approach used in this study was suitable for the phenotypic improvement of K. xylinus K2G30 in bacterial cellulose production. Metabolic versatility of the strain was confirmed by the increase in bacterial cellulose production from D-fructose-based medium. Moreover, the adaptation on mannitol did not occur at the expense of glucose, confirming the versatility of K2G30 in producing bacterial cellulose from different carbon sources. Results of this study contribute to the knowledge for designing new strategies, as an alternative to the genetic engineering approach, for bacterial cellulose production.
Prediction and analysis of periprocedural complications associated with endovascular treatment for unruptured intracranial aneurysms using machine learning
Authors: Tian Zhongbin , Li Wenqiang , Feng Xin , Sun Kaijian , Duan Chuanzhi
Published: October 2022

Background

The management of unruptured intracranial aneurysm (UIA) remains controversial. Recently, machine learning has been widely applied in the field of medicine. This study developed predictive models using machine learning to investigate periprocedural complications associated with endovascular procedures for UIA.

Methods

We enrolled patients with solitary UIA who underwent endovascular procedures. Periprocedural complications were defined as neurological adverse events resulting from endovascular procedures. We incorporated three machine learning algorithms into our prediction models: artificial neural networks (ANN), random forest (RF), and logistic regression (LR). The Shapley Additive Explanations (SHAP) approach and feature importance analysis were used to identify and prioritize significant features associated with periprocedural complications.

Results

In total, 443 patients were included. Forty-eight (10.83%) procedure-related complications occurred. In the testing set, the ANN model produced the largest value (0.761) for area under the curve (AUC). The RF model also achieved an acceptable AUC value of 0.735, while the AUC value of the LR model was 0.668. SHAP and feature importance analysis identified distal aneurysm, aneurysm size and treatment modality as most significant features for the prediction of periprocedural complications following endovascular treatment for UIA.

Conclusion

Periprocedural complications after endovascular treatment for UIA are not negligible. Prediction of periprocedural complications via machine learning is feasible and effective. Machine learning can serve as a promising tool in the decision-making process for UIA treatment.
Efficacy of twice-daily high-frequency repetitive transcranial magnetic stimulation on associative memory
Authors: Hua Qiang , Zhang Yuanyuan , Li Qianqian , Gao Xiaoran , Du Rongrong , Wang Yingru , Zhou Qian , Zhang Ting , Sun Jinmei , Zhang Lei , Ji Gong-jun , Wang Kai
Published: October 2022

Objectives

Several studies have examined the effects of repetitive transcranial magnetic stimulation (rTMS) on associative memory (AM) but findings were inconsistent. Here, we aimed to test whether twice-daily rTMS could significantly improve AM.

Methods

In this single-blind, sham-controlled experiment, 40 participants were randomized to receive twice-daily sham or real rTMS sessions for five consecutive days (a total of 16,000 pulses). The stimulation target in left inferior parietal lobule (IPL) exhibiting peak functional connectivity to the left hippocampus was individually defined for each participant. Participants completed both a picture-cued word association task and Stroop test at baseline and 1 day after the final real or sham rTMS session. Effects of twice-daily rTMS on AM and Stroop test performance were compared using two-way repeated measures analysis of variance with main factors Group (real vs. sham) and Time (baseline vs. post-rTMS).

Results

There was a significant Group × Time interaction effect. AM score was significantly enhanced in the twice-daily real group after rTMS, but this difference could not survive the post hoc analysis after multiple comparison correction. Further, AM improvement in the twice-daily real group was not superior to a previously reported once-daily rTMS group receiving 8,000 pulses. Then, we combined the twice- and once-daily real groups, and found a significant Group × Time interaction effect. Post hoc analysis indicated that the AM score was significantly enhanced in the real group after multiple comparisons correction.

Conclusion

Our prospective experiment did not show significant rTMS effect on AM, but this effect may become significant if more participants could be recruited as revealed by our retrospective analysis.