scholarly journals Systematic analysis of the role of SLC52A2 in multiple human cancers

2022 ◽  
Vol 22 (1) ◽  
Author(s):  
Lilong Zhang ◽  
Man Li ◽  
Zhoujun Cui ◽  
Dongqi Chai ◽  
Yongjun Guan ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Ribosome Biogenesis ◽  
Enrichment Analysis ◽  
The Body ◽  
Systematic Analysis ◽  
Regulatory Pathways ◽  
Transporter Protein ◽  
Oocyte Meiosis ◽  
Tumor Mutational Burden ◽  
Almost All

Abstract Background In humans, riboflavin must be obtained through intestinal absorption because it cannot be synthesized by the body. SLC52A2 encodes a membrane protein belonging to the riboflavin transporter protein family and is associated with a variety of diseases. Here, we systematically explore its relevance to multiple human tumors. Methods We analyzed the association of SLC52A2 with 33 tumors using publicly available databases such as TCGA and GEO. We verified the SLC52A2 expression in hepatocellular carcinoma, gastric cancer, colon cancer, and rectal cancer using immunohistochemistry. Results We report that SLC52A2 was highly expressed in almost all tumors, and the immunohistochemical results in the hepatocellular, gastric, colon, and rectal cancers were consistent with the above. SLC52A2 expression was linked to patient overall survival, disease-specific survival, progression-free interval, diagnosis, mutations, tumor mutational burden, microsatellite instability, common immune checkpoint genes, and immune cells infiltration. Enrichment analysis showed that SLC52A2 was mainly enriched in oocyte meiosis, eukaryotic ribosome biogenesis, and cell cycle. In hepatocellular carcinoma, the SLC52A2 expression is an independent prognostic factor. The SNHG3 and THUMPD3-AS1/hsa-miR-139-5p-SLC52A2 axis were identified as potential regulatory pathways in hepatocellular carcinoma. Conclusion In conclusion, we have systematically described for the first time that SLC52A2 is closely associated with a variety of tumors, especially hepatocellular carcinoma.

scholarly journals Identification and Validation of a Novel Six-Gene Expression Signature for Predicting Hepatocellular Carcinoma Prognosis

2021 ◽  
Vol 12 ◽  
Author(s):  
Zongcai Yan ◽  
Meiling He ◽  
Lifeng He ◽  
Liuxia Wei ◽  
Yumei Zhang
Keyword(s):  
Gene Expression ◽  
Hepatocellular Carcinoma ◽  
Prognostic Model ◽  
Gene Expression Signature ◽  
Enrichment Analysis ◽  
Risk Groups ◽  
Expression Signature ◽  
Free Interval ◽  
Mutational Burden ◽  
Tumor Mutational Burden

BackgroundHepatocellular carcinoma (HCC) is a highly lethal disease. Effective prognostic tools to guide clinical decision-making for HCC patients are lacking.ObjectiveWe aimed to establish a robust prognostic model based on differentially expressed genes (DEGs) in HCC.MethodsUsing datasets from The Cancer Genome Atlas (TCGA), the Gene Expression Omnibus (GEO), and the International Genome Consortium (ICGC), DEGs between HCC tissues and adjacent normal tissues were identified. Using TCGA dataset as the training cohort, we applied the least absolute shrinkage and selection operator (LASSO) algorithm and multivariate Cox regression analyses to identify a multi-gene expression signature. Proportional hazard assumptions and multicollinearity among covariates were evaluated while building the model. The ICGC cohort was used for validation. The Pearson test was used to evaluate the correlation between tumor mutational burden and risk score. Through single-sample gene set enrichment analysis, we investigated the role of signature genes in the HCC microenvironment.ResultsA total of 274 DEGs were identified, and a six-DEG prognostic model was developed. Patients were stratified into low- or high-risk groups based on risk scoring by the model. Kaplan–Meier analysis revealed significant differences in overall survival and progression-free interval. Through univariate and multivariate Cox analyses, the model proved to be an independent prognostic factor compared to other clinic-pathological parameters. Time-dependent receiver operating characteristic curve analysis revealed satisfactory prediction of overall survival, but not progression-free interval. Functional enrichment analysis showed that cancer-related pathways were enriched, while immune infiltration analyses differed between the two risk groups. The risk score did not correlate with levels of PD-1, PD-L1, CTLA4, or tumor mutational burden.ConclusionsWe propose a six-gene expression signature that could help to determine HCC patient prognosis. These genes may serve as biomarkers in HCC and support personalized disease management.

scholarly journals Proteome-Wide Analysis of Lysine 2-Hydroxyisobutyrylated Proteins in Fusarium oxysporum

2021 ◽  
Vol 12 ◽  
Author(s):  
Hengwei Qian ◽  
Lulu Wang ◽  
Xianliang Ma ◽  
Xingling Yi ◽  
Baoshan Wang ◽  
...  
Keyword(s):  
Fusarium Oxysporum ◽  
Protein Complexes ◽  
Pathogenic Fungus ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Pathogenic Fungi ◽  
Post Translational Modification ◽  
Systematic Analysis ◽  
Plant Pathogenic Fungus ◽  
Almost All

Protein lysine 2-hydroxyisobutyrylation (Khib), a new type of post-translational modification, occurs in histones and non-histone proteins and plays an important role in almost all aspects of both eukaryotic and prokaryotic living cells. Fusarium oxysporum, a soil-borne fungal pathogen, can cause disease in more than 150 plants. However, little is currently known about the functions of Khib in this plant pathogenic fungus. Here, we report a systematic analysis of 2-hydroxyisobutyrylated proteins in F. oxysporum. In this study, 3782 Khib sites in 1299 proteins were identified in F. oxysporum. The bioinformatics analysis showed that 2-hydroxyisobutyrylated proteins are involved in different biological processes and functions and are located in diverse subcellular localizations. The enrichment analysis revealed that Khib participates in a variety of pathways, including the ribosome, oxidative phosphorylation, and proteasome pathways. The protein interaction network analysis showed that 2-hydroxyisobutyrylated protein complexes are involved in diverse interactions. Notably, several 2-hydroxyisobutyrylated proteins, including three kinds of protein kinases, were involved in the virulence or conidiation of F. oxysporum, suggesting that Khib plays regulatory roles in pathogenesis. Moreover, our study shows that there are different Khib levels of F. oxysporum in conidial and mycelial stages. These findings provide evidence of Khib in F. oxysporum, an important filamentous plant pathogenic fungus, and serve as a resource for further exploration of the potential functions of Khib in Fusarium species and other filamentous pathogenic fungi.

scholarly journals A novel panel based on Immune infiltration and tumor mutational burden for prognostic prediction in hepatocellular carcinoma

2020 ◽  
Author(s):  
Hewei Wu ◽  
Xingrong Zheng ◽  
Tao Pan ◽  
Xiaoan Yang ◽  
Genglin Zhang ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
T Cell Activation ◽  
Cell Activation ◽  
Gene Mutations ◽  
Enrichment Analysis ◽  
The Cancer Genome Atlas ◽  
Matrix Composition ◽  
Immune Infiltration ◽  
Tumor Mutational Burden ◽  
Worse Prognosis

Abstract Background : Tumor mutation burden (TMB) was associated with prognosis in various malignancies, but it remains to be elucidated in hepatocellular carcinoma (HCC). We aimed to investigate the prognostic effects of TMB and its relationship with immune infiltration so as to establish a panel model capable of predicting prognosis. Methods : TMB was calculated in all 374 HCC patients from the Cancer Genome Atlas, and high TMB and low TMB groups were determined based on propensity score matching and X-tile analysis. WCGNA was utilized to screen out genes related to immune cells and TMB, followed by multivariate analysis to generated the final TMB-Infiltration (TMB-IF) panel. 453 HCC patients from ICGC-LIRI-JP, GSE76427 and GSE20017 verified the robustness and extensibility of TMB-IF. Additionally, whole-exome sequencing (WES) was performed in 8 follow-up patients to investigate the relationship between HCC recurrence and TMB. Results : Patients in high TMB group had worse prognosis than those in low TMB group, with a cutoff TMB value of 4.9. Enrichment analysis demonstrated that differentially expressed genes were mainly related to T cell activation, cell membrane localization and matrix composition. Tumor immune infiltration analysis revealed the infiltrations of Th2, Th17, and Tgd were up-regulated in high TMB group, while those of Tr1, MAIT, and DC were up-regulated in low TMB group. And TMB-IF fit well with the actual survival observation, with a C-index 0.785 (0.700-0.870), which verified in ICGC-LIRI-JP was 0.670 (0.573-0.767), and 0.774 (0.670-0.877) in GSE76427. In addition, TMB-IF showed a good performance in predicting tumor vascular invasion with a C-index of 0.847 (0.778-0.916). Conclusions : Higher TMB means worse prognosis in HCC patients. Patients with higher frequency of immune-related gene mutations and TMB are prone to relapse after radical treatment.

Digestibility of nutrients and milk productivity of cows when using the concentrate mixture with the inclusion of rapeseed presscake

2020 ◽  
pp. 48-53
Author(s):  
L. Yarmots ◽  
G. Yarmots ◽  
A. Belenkaya
Keyword(s):  
Protein Digestibility ◽  
High Energy ◽  
Negative Influence ◽  
The Body ◽  
Milk Productivity ◽  
Lactating Cows ◽  
Low Protein ◽  
Concentrate Mixture ◽  
Almost All ◽  
Experimental Group

For ruminants, especially high-yielding animals in addition to the complete supply of animals with protein, its digestibility in the rumen is important. With low protein digestibility in the rumen, the released ammonia will be more effectively used by the rumen microflora, and the undigestible protein in the subsequent sections of the digestive tract can serve as a source of amino acids for the body. The use of concentrate mixtures with the inclusion of local, affordable and cheaper grain feeds, in particular a high-energy and protein ingredient- rapeseed presscake makes it possible to increase the milk productivity of cows throughout lactation. These presscakes are well balanced in their amino acid composition and belong to feeds whose protein has a low degree of digestibility in the rumen. The purpose of the researches was to study the digestibility of nutrients and milk productivity of cows when using the concentrate mixture with the inclusion of rapeseed presscake. In the scientific and economic experiment has been carried out on lactating cows, where the cows of the experimental group in the concentrate mixture of peas has been replaced with rapeseed presscake the digestibility of nutrients in the ration, energy metabolism and milk productivity have been studied. Studies have shown that almost all the nutrients were significantly better digested by the animals of the experimental group. Energy in milk was more allocated by cows of the experimental group by 6,29 MJ. From cows of the experimental group for 100 and 305 days of lactation has been obtained more milk by 6,27 and 7,06 %, respectively, than from control herdmates. The biochemical parameters of blood were within the limits of the physiological norm in animals of both groups. Thus, the replacement of peas with rapeseed presscake in the concentrate mixture did not have a negative influence on the metabolic processes and helped to increase the milk productivity of cows.

scholarly journals Cyclin B1 acts as a tumor microenvironment-related cancer promoter and prognostic biomarker in hepatocellular carcinoma

2021 ◽  
Vol 49 (5) ◽  
pp. 030006052110162
Author(s):  
Yangming Hou ◽  
Xin Wang ◽  
Junwei Wang ◽  
Xuemei Sun ◽  
Xinbo Liu ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Tumor Microenvironment ◽  
Proportional Hazards ◽  
Enrichment Analysis ◽  
Gene Signature ◽  
Cyclin B1 ◽  
Cox Proportional Hazards ◽  
Gene Set Enrichment Analysis ◽  
Tumor Promoter ◽  
Protein Protein Interaction

Objectives The present study aimed to develop a gene signature based on the ESTIMATE algorithm in hepatocellular carcinoma (HCC) and explore possible cancer promoters. Methods The ESTIMATE and CIBERSORT algorithms were applied to calculate the immune/stromal scores and the proportion of tumor-infiltrating immune cells (TICs) in a cohort of HCC patients. The differentially expressed genes (DEGs) were screened by Cox proportional hazards regression analysis and protein–protein interaction (PPI) network construction. Cyclin B1 (CCNB1) function was verified using experiments. Results The stromal and immune scores were associated with clinicopathological factors and recurrence-free survival (RFS) in HCC patients. In total, 546 DEGs were up-regulated in low score groups, 127 of which were associated with RFS. CCNB1 was regarded as the most predictive factor closely related to prognosis of HCC and could be a cancer promoter. Gene Set Enrichment Analysis (GSEA) and CIBERSORT analyses indicated that CCNB1 levels influenced HCC tumor microenvironment (TME) immune activity. Conclusions The ESTIMATE signature can be used as a prognosis tool in HCC. CCNB1 is a tumor promoter and contributes to TME status conversion.

scholarly journals In Silico Identification of Contradictory Role of ADAMTS5 in Hepatocellular Carcinoma

2021 ◽  
Vol 20 ◽  
pp. 153303382098682
Author(s):  
Zhipeng Zhu ◽  
Jiuhua Xu ◽  
Xiaofang Wu ◽  
Sihao Lin ◽  
Lulu Li ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Subgroup Analysis ◽  
Prognostic Value ◽  
Molecular Mechanisms ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
Clinicopathological Parameters ◽  
Free Survival ◽  
Cox Regression Analysis ◽  
The Impact

Background: ADAMTS5 has different roles in multiple types of cancers and participates in various molecular mechanisms. However, the prognostic value of ADAMTS5 in patients with hepatocellular carcinoma (HCC) still remains unclear. We carried the study to evaluate the prognostic value and identified underlying molecular mechanisms in HCC. Methods: Firstly, the association of ADAMTS5 expression and clinicopathological parameters was evaluated by in GSE14520. Next, ADAMTS5 expression in HCC was performed using GSE14520, GSE36376, GSE76427 and The Cancer Genome Atlas (TCGA) profile. Furthermore, Kaplan-Meier analysis, Univariate and Multivariate Cox regression analysis, subgroup analysis was performed to evaluate the prognostic value of ADAMTS5 in HCC. Finally, GO enrichment analysis, gene set enrichment analysis (GSEA) and weighted gene co-expression network analysis (WGCNA) were performed to revealed underlying molecular mechanisms. Result: The expression of ADAMTS5 was positively correlated with the development of HCC. Next, high ADAMTS5 expression was significantly associated with poorer survival (all P < 0.05) and the impact of ADAMTS5 on all overall survival (OS), disease-free survival (DFS), relapse-free survival (RFS), disease specific survival (DSS) and progression free interval (PFI) was specific for HCC among other 29 cancer types. Subgroup analysis showed that ADAMTS5 overexpression was significantly associated with poorer OS in patients with HCC. Finally, ADAMTS5 might participate in the status conversion from metabolic-dominant to extracellular matrix-dominant, and the activation of ECM-related biological process might contribute to high higher mortality risk for patients with HCC. Conclusion: ADAMTS5 may play an important role in the progression of HCC, and may be considered as a novel and effective biomarker for predicting prognosis for patients with HCC.

Blood, joy and tears: menarche narratives of undergraduate females in a selected in Nigeria Private University

2017 ◽  
Vol 31 (4) ◽  
Author(s):  
Adenike Adegbayi
Keyword(s):  
Adolescent Health ◽  
Qualitative Methodology ◽  
Private University ◽  
The Body ◽  
Female Adolescent ◽  
Menstrual Period ◽  
Future Health ◽  
Female Relative ◽  
Undergraduate Females ◽  
Almost All

Abstract The aim of the study is to add to the body of knowledge on less researched aspects of female adolescent health in Nigeria. It specifically explored the menarche or first period narratives of 136 young women, focusing on the contents of the discussion that ensued with whom they told when they first got their period using qualitative methodology. It also explores sources of premenstrual information and how the menstrual period is managed. The sample consisted of 136 undergraduate females in Redeemer’s University, Ede, Nigeria. Almost all of the respondents (95%) received information about menstruation from mothers, female relatives and school lessons prior to menarche. The majority of the respondents first told either their mother or a female relative when they first got their period and viewed menarche as a crisis. Two salient themes emerged from the contents of the narratives; celebration and advice. The advice theme was further explored and three advice patterns were identified: being a woman, hygiene and changed dynamics in relationships with males. Data from the present study suggests that only certain aspects of the menstruation discourse have evolved. All respondents reported using sanitary towels during their menstrual period with the majority experiencing cramps regularly and (61%) using pharmalogical agents for remedy. It is envisaged that findings from the study will be useful in future health intervention programmes and research on female adolescent health in Nigeria and elsewhere.

scholarly journals Children’s Greenness Exposure and IQ-Associated DNA Methylation: A Prospective Cohort Study

2021 ◽  
Vol 18 (14) ◽  
pp. 7429
Author(s):  
Kyung-Shin Lee ◽  
Yoon-Jung Choi ◽  
Jin-Woo Cho ◽  
Sung-Ji Moon ◽  
Youn-Hee Lim ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Cohort Study ◽  
Literature Review ◽  
Cognitive Ability ◽  
Prospective Cohort Study ◽  
Prospective Cohort ◽  
Association Studies ◽  
The Body ◽  
Genome Wide Association Studies ◽  
Regulatory Pathways

Epigenetics is known to be involved in regulatory pathways through which greenness exposure influences child development and health. We aimed to investigate the associations between residential surrounding greenness and DNA methylation changes in children, and further assessed the association between DNA methylation and children’s intelligence quotient (IQ) in a prospective cohort study. We identified cytosine-guanine dinucleotide sites (CpGs) associated with cognitive abilities from epigenome- and genome-wide association studies through a systematic literature review for candidate gene analysis. We estimated the residential surrounding greenness at age 2 using a geographic information system. DNA methylation was analyzed from whole blood using the HumanMethylationEPIC array in 59 children at age 2. We analyzed the association between greenness exposure and DNA methylation at age 2 at the selected CpGs using multivariable linear regression. We further investigated the relationship between DNA methylation and children’s IQ. We identified 8743 CpGs associated with cognitive ability based on the literature review. Among these CpGs, we found that 25 CpGs were significantly associated with greenness exposure at age 2, including cg26269038 (Bonferroni-corrected p ≤ 0.05) located in the body of SLC6A3, which encodes a dopamine transporter. DNA methylation at cg26269038 at age 2 was significantly associated with children’s performance IQ at age 6. Exposure to surrounding greenness was associated with cognitive ability-related DNA methylation changes, which was also associated with children’s IQ. Further studies are warranted to clarify the epigenetic pathways linking greenness exposure and neurocognitive function.

scholarly journals Clinical Characterisation and Management of the Main Treatment-Induced Toxicities in Patients with Hepatocellular Carcinoma and Cirrhosis

Cancers ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 584
Author(s):  
Fausto Meriggi ◽  
Massimo Graffeo
Keyword(s):  
Hepatocellular Carcinoma ◽  
Hepatic Impairment ◽  
Hepatic Cirrhosis ◽  
Disease Stage ◽  
The Past ◽  
Systemic Treatments ◽  
Key Points ◽  
Locoregional Therapies ◽  
Almost All ◽  
Selection Of

The incidence of hepatocellular carcinoma (HCC) continues to increase worldwide, particularly in Western countries. In almost all cases, HCC develops in subjects with hepatic cirrhosis, often as the result of hepatitis B or C virus infection, alcohol abuse or metabolic forms secondary to non-alcoholic steatohepatitis. Patients with HCC and hepatic symptoms can therefore present symptoms that are attributable to both conditions. These patients require multidisciplinary management, calling for close interaction between the hepatologist and the oncologist. Indeed, the treatment of HCC requires, depending on the disease stage and the degree of hepatic impairment, locoregional therapies that can in turn be broken down into surgical and nonsurgical treatments and systemic treatments used in the event of progression after the administration of locoregional treatments. The past decade has seen the publication of countless papers of great interest that have radically changed the scenario of treatment for HCC. Novel therapies with biological agents and immunotherapy have come to be standard options in the approach to treatment of this cancer, obtaining very promising results where in the past chemotherapy was almost never able to have an impact on the course of the disease. However, in addition to being costly, these drugs are not devoid of adverse effects and their management cannot forgo the consideration of the underlying hepatic impairment. Patients with HCC and cirrhosis therefore require special attention, starting from the initial characterisation needed for an appropriate selection of those to be referred for treatment, as these patients are almost never fit. In this chapter, we will attempt to investigate and clarify the key points of the management of the main toxicities induced by locoregional and systemic treatments for HCC secondary to cirrhosis.

Demonstration of the relationship between MSD and online learning during the COVID-19 pandemic

2021 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Kochu Therisa Karingada ◽  
Michael Sony
Keyword(s):  
Online Learning ◽  
Undergraduate Students ◽  
Online Survey ◽  
Cross Sectional Study ◽  
The Body ◽  
Body Parts ◽  
Cross Sectional ◽  
Content Type ◽  
The Right ◽  
Almost All

PurposeThe COVID-19 pandemic lockdown has caught many educational institutions by surprise and warranted an abrupt migration from offline to online learning. This has resulted in an education change, without any time for due consideration, as regards its impact on musculoskeletal disorders (MSD) on students. The purpose of this study is to investigate MSD related to online learning during the COVID-19 pandemic lockdown.Design/methodology/approachA cross-sectional study was conducted on undergraduate students in India. In total, 261 students participated in this online survey.FindingsThe study finds that around 80% of students have reported some symptom in the head, neck and eyes since they started online learning. In total, 58% have reported MSD symptom in the right shoulder and 56% in the right hand fingers. Besides, more than 40 % of students experienced some MSD symptoms, in almost all the body parts studied, due to online learning. Correlation analysis is conducted between time spent on online learning per day and MSD symptoms.Originality/valueThis is the first study conducted on MSD and online learning during COVID-19 pandemic.

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