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1.
Cell ; 187(7): 1651-1665.e21, 2024 Mar 28.
Artigo em Inglês | MEDLINE | ID: mdl-38490195

RESUMO

The immune checkpoint blockade (ICB) response in human cancers is closely linked to the gut microbiota. Here, we report that the abundance of commensal Lactobacillus johnsonii is positively correlated with the responsiveness of ICB. Supplementation with Lactobacillus johnsonii or tryptophan-derived metabolite indole-3-propionic acid (IPA) enhances the efficacy of CD8+ T cell-mediated αPD-1 immunotherapy. Mechanistically, Lactobacillus johnsonii collaborates with Clostridium sporogenes to produce IPA. IPA modulates the stemness program of CD8+ T cells and facilitates the generation of progenitor exhausted CD8+ T cells (Tpex) by increasing H3K27 acetylation at the super-enhancer region of Tcf7. IPA improves ICB responsiveness at the pan-cancer level, including melanoma, breast cancer, and colorectal cancer. Collectively, our findings identify a microbial metabolite-immune regulatory pathway and suggest a potential microbial-based adjuvant approach to improve the responsiveness of immunotherapy.


Assuntos
Linfócitos T CD8-Positivos , Imunoterapia , Lactobacillus , Neoplasias , Humanos , Lactobacillus/metabolismo , Neoplasias/imunologia , Neoplasias/terapia , Indóis/metabolismo , Inibidores de Checkpoint Imunológico/uso terapêutico
2.
Nucleic Acids Res ; 51(W1): W115-W121, 2023 07 05.
Artigo em Inglês | MEDLINE | ID: mdl-37125649

RESUMO

Carbohydrate active enzymes (CAZymes) are made by various organisms for complex carbohydrate metabolism. Genome mining of CAZymes has become a routine data analysis in (meta-)genome projects, owing to the importance of CAZymes in bioenergy, microbiome, nutrition, agriculture, and global carbon recycling. In 2012, dbCAN was provided as an online web server for automated CAZyme annotation. dbCAN2 (https://bcb.unl.edu/dbCAN2) was further developed in 2018 as a meta server to combine multiple tools for improved CAZyme annotation. dbCAN2 also included CGC-Finder, a tool for identifying CAZyme gene clusters (CGCs) in (meta-)genomes. We have updated the meta server to dbCAN3 with the following new functions and components: (i) dbCAN-sub as a profile Hidden Markov Model database (HMMdb) for substrate prediction at the CAZyme subfamily level; (ii) searching against experimentally characterized polysaccharide utilization loci (PULs) with known glycan substates of the dbCAN-PUL database for substrate prediction at the CGC level; (iii) a majority voting method to consider all CAZymes with substrate predicted from dbCAN-sub for substrate prediction at the CGC level; (iv) improved data browsing and visualization of substrate prediction results on the website. In summary, dbCAN3 not only inherits all the functions of dbCAN2, but also integrates three new methods for glycan substrate prediction.


Assuntos
Carboidratos , Microbiota , Metabolismo dos Carboidratos/genética , Polissacarídeos , Bases de Dados Factuais
3.
Nucleic Acids Res ; 51(D1): D557-D563, 2023 01 06.
Artigo em Inglês | MEDLINE | ID: mdl-36399503

RESUMO

Carbohydrate Active EnZymes (CAZymes) are significantly important for microbial communities to thrive in carbohydrate rich environments such as animal guts, agricultural soils, forest floors, and ocean sediments. Since 2017, microbiome sequencing and assembly have produced numerous metagenome assembled genomes (MAGs). We have updated our dbCAN-seq database (https://bcb.unl.edu/dbCAN_seq) to include the following new data and features: (i) ∼498 000 CAZymes and ∼169 000 CAZyme gene clusters (CGCs) from 9421 MAGs of four ecological (human gut, human oral, cow rumen, and marine) environments; (ii) Glycan substrates for 41 447 (24.54%) CGCs inferred by two novel approaches (dbCAN-PUL homology search and eCAMI subfamily majority voting) (the two approaches agreed on 4183 CGCs for substrate assignments); (iii) A redesigned CGC page to include the graphical display of CGC gene compositions, the alignment of query CGC and subject PUL (polysaccharide utilization loci) of dbCAN-PUL, and the eCAMI subfamily table to support the predicted substrates; (iv) A statistics page to organize all the data for easy CGC access according to substrates and taxonomic phyla; and (v) A batch download page. In summary, this updated dbCAN-seq database highlights glycan substrates predicted for CGCs from microbiomes. Future work will implement the substrate prediction function in our dbCAN2 web server.


Assuntos
Microbiota , Animais , Humanos , Carboidratos , Metagenoma/genética , Microbiota/genética , Família Multigênica , Polissacarídeos/metabolismo , Enzimas/genética , Bactérias/enzimologia , Microbiologia Ambiental
4.
BMC Public Health ; 24(1): 2529, 2024 Sep 17.
Artigo em Inglês | MEDLINE | ID: mdl-39289643

RESUMO

BACKGROUND: Both interpregnancy intervals (IPI) and environmental factors might contribute to low birth weight (LBW). However, the extent to which air pollution influences the effect of IPIs on LBW remains unclear. We aimed to investigate whether IPI and air pollution jointly affect LBW. METHODS: A retrospective cohort study was designed in this study. The data of birth records was collected from the Jiangsu Maternal Child Information System, covering January 2020 to June 2021 in Nantong city, China. IPI was defined as the duration between the delivery date for last live birth and date of LMP for the subsequent birth. The maternal exposure to ambient air pollutants during pregnancy-including particulate matter (PM) with an aerodynamic diameter of ≤ 2.5 µm (PM2.5), PM10, ozone (O3), nitrogen dioxide (NO2), sulfur dioxide (SO2) and carbon monoxide (CO)-was estimated using a hybrid kriging-LUR-RF model. A novel air pollution score was proposed, assessing combined exposure to five pollutants (excluding CO) by summing their concentrations, weighted by LBW regression coefficients. Multivariate logistic regression models were used to estimate the effects of IPI, air pollution and their interactions on LBW. Relative excess risk due to interaction (RERI), attributable proportion of interaction (AP) and synergy index (S) were utilized to assess the additive interaction. RESULTS: Among 10, 512 singleton live births, the LBW rate was 3.7%. The IPI-LBW risk curve exhibited an L-shaped pattern. The odds ratios (ORs) for LBW for each interquartile range increase in PM2.5, PM10, O3 and the air pollution score were 1.16 (95% CI: 1.01-1.32), 1.30 (1.06-1.59), 1.22 (1.06-1.41), and 1.32 (1.10-1.60) during the entire pregnancy, respectively. An additive interaction between IPI and PM2.5 was noted during the first trimester. Compared to records with normal IPI and low PM2.5 exposure, those with short IPI and high PM2.5 exposure had the highest risk of LBW (relative risk = 3.53, 95% CI: 1.85-6.49, first trimester). CONCLUSION: The study demonstrates a synergistic effect of interpregnancy interval and air pollution on LBW, indicating that rational birth spacing and air pollution control can jointly improve LBW outcomes.


Assuntos
Poluentes Atmosféricos , Poluição do Ar , Intervalo entre Nascimentos , Recém-Nascido de Baixo Peso , Exposição Materna , Humanos , Estudos Retrospectivos , China/epidemiologia , Feminino , Poluição do Ar/efeitos adversos , Poluição do Ar/análise , Gravidez , Adulto , Recém-Nascido , Intervalo entre Nascimentos/estatística & dados numéricos , Exposição Materna/efeitos adversos , Exposição Materna/estatística & dados numéricos , Poluentes Atmosféricos/análise , Poluentes Atmosféricos/efeitos adversos , Fatores de Risco , Material Particulado/análise , Material Particulado/efeitos adversos , Masculino , Adulto Jovem
5.
AIDS Behav ; 27(8): 2720-2730, 2023 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-36705771

RESUMO

An individual based randomized controlled trial (RCT) was designed to evaluate the impact of a customized short message service (SMS) intervention on HIV-related high-risk behaviors among Men who have sex with men (MSM). In total, 631 HIV-negative MSM were enrolled at baseline and divided into intervention and control groups randomly. Nine months later, the intervention group who received additional customized SMS intervention reported significantly lower rates of multiple partners, unclear partner infection status and condomless anal intercourse compared to the control group who received the routine intervention only. Six months post stopping the SMS intervention, the rates of unclear partner infection status and condomless anal intercourse still remained lower report in the intervention group. Our study shown that the customized SMS interventions can significantly reduce the HIV-related high-risk behaviors among MSM and with sustained effects over a period of time.


Assuntos
Infecções por HIV , Minorias Sexuais e de Gênero , Envio de Mensagens de Texto , Masculino , Humanos , Infecções por HIV/epidemiologia , Infecções por HIV/prevenção & controle , Homossexualidade Masculina , Assunção de Riscos , Comportamento Sexual , China/epidemiologia , Parceiros Sexuais
6.
BMC Geriatr ; 22(1): 20, 2022 01 03.
Artigo em Inglês | MEDLINE | ID: mdl-34979974

RESUMO

BACKGROUND: Obesity is associated with type 2 diabetes mellitus (T2DM). However, the obesity index that is most closely related to type 2 diabetes remains controversial. Therefore, the aim of this study was to compare the associations of five anthropometric indices (body mass index [BMI], body adiposity index, waist circumference [WC], waist-to-hip ratio, and waist-to-height ratio [WHtR]) with T2DM among Chinese adults divided into four groups according to sex and age. METHODS: A total of 4007 adult participants (1669 men and 2338 women) were included in the study. Odds ratios (ORs) and 95% confidence intervals were used with binary logistic regression models to estimate the risk of T2DM for each obesity index. Furthermore, we compared the area under the receiver operating characteristic curve (AUC) of each obesity index for the criterion of T2DM under the influence of risk factors. RESULTS: WC had the highest OR (3.211 and 1.452) and AUC (0.783 and 0.614) in both age groups of men. However, WHtR (OR = 2.366, AUC = 0.771) and BMI (OR = 1.596, AUC = 0.647) were the optimal criteria for predicting T2DM among females in the 18-59 and ≥ 60 years age groups, respectively. CONCLUSIONS: This study suggests that there is a positive association between obesity-related anthropometric indices and T2DM in different sex and age groups. WC appears to be the optimal anthropometric index for predicting T2DM in men. The optimal obesity indices related to T2DM were WHtR and BMI for women aged 18-59 and ≥ 60 years, respectively.


Assuntos
Diabetes Mellitus Tipo 2 , Índice de Massa Corporal , China/epidemiologia , Diabetes Mellitus Tipo 2/diagnóstico , Diabetes Mellitus Tipo 2/epidemiologia , Feminino , Humanos , Masculino , Obesidade/diagnóstico , Obesidade/epidemiologia , Curva ROC , Fatores de Risco , Circunferência da Cintura , Razão Cintura-Estatura , Relação Cintura-Quadril
7.
FASEB J ; 34(2): 2161-2172, 2020 02.
Artigo em Inglês | MEDLINE | ID: mdl-31909528

RESUMO

Gastric cancer (GC) patients with metastasis had limited treatment options and dismal outcome. We have previously reported the aberrant expression of Zic family member 1 (Zic1) in GC. However, the functional roles and underlying mechanism of Zic1 in GC metastasis remain unknown. Here, we demonstrate that lower expression of Zic1 was correlated with more lymph node metastasis and poor outcome of GC patients. Ectopic expression of Zic1 suppressed both lung metastasis and peritoneal tumor dissemination of GC in mice. The metastatic suppressing ability of Zic1 was mediated by regulating the process of cell invasion, adhesion and epithelial-mesenchymal transition (EMT). Mechanistically, Zic1 could downregulate Wnt targets including c-Myc and Cyclin D1 by inhibiting LEF transcriptional activity in GC cells. Notably, Zic1 was inversely related to the expression of Cyclin D1 in GC tissues tested. In addition, Zic1 could physically interact with ß-catenin/transcription factor 4 (TCF4) and disrupt their complex formation, while not affecting ß-catenin nuclear localization. Collectively, our study indicated that Zic1 suppressed GC metastasis through attenuating Wnt/ß-catenin signaling and the EMT process. Our work may provide novel therapeutic strategies for the metastasis of GC.


Assuntos
Transição Epitelial-Mesenquimal , Proteínas de Neoplasias/metabolismo , Neoplasias Gástricas/metabolismo , Fatores de Transcrição/metabolismo , Via de Sinalização Wnt , beta Catenina/metabolismo , Animais , Linhagem Celular Tumoral , Feminino , Células HEK293 , Humanos , Camundongos , Camundongos Endogâmicos BALB C , Camundongos Nus , Metástase Neoplásica , Proteínas de Neoplasias/genética , Neoplasias Gástricas/genética , Neoplasias Gástricas/patologia , Fatores de Transcrição/genética , beta Catenina/genética
8.
FASEB J ; 34(6): 8544-8557, 2020 06.
Artigo em Inglês | MEDLINE | ID: mdl-32356314

RESUMO

MicroRNAs (miRNAs) play important roles in posttranscriptional regulation and may serve as targets for the diagnosis and treatment of cancers. Nevertheless, a comprehensive understanding of miRNAs profiles in gastric cancer progression is still lacking. Here, we report that miR-129-5p is downregulated in gastric cancer by analyzing TCGA database (n = 41) and clinical tumor samples (n = 60). MiR-129-5p transfection suppressed gastric cancer cell proliferation through inducing G1 phase arrest in vitro and inhibit xenograft tumor growth in vivo. MiR-129-5p directly targeted the 3' untranslated regions (3' UTR) of HOXC10 mRNA and downregulated its expression. Importantly, miR-129-5p could reverse the oncogenic effect induced by HOXC10. We systemically screened the downstream target of HOXC10 by ChIP sequencing, and found that HOXC10 could transcriptionally regulate the expression of Cyclin D1 and facilitate G1/S cell cycle transition. Notably, high levels of HOXC10 and Cyclin D1 were related with poor prognosis of gastric cancer patients (n = 90). These findings reveal a novel role of miR-129-5p/HOXC10/Cyclin D1 axis in modulating cell cycle and gastric tumorigenesis, which might provide potential prognostic biomarkers and therapeutic targets for gastric cancer patients.


Assuntos
Pontos de Checagem do Ciclo Celular/genética , Ciclina D1/genética , Proteínas de Homeodomínio/genética , MicroRNAs/genética , Neoplasias Gástricas/genética , Regiões 3' não Traduzidas/genética , Animais , Linhagem Celular , Linhagem Celular Tumoral , Proliferação de Células/genética , Progressão da Doença , Regulação para Baixo/genética , Feminino , Fase G1/genética , Regulação Neoplásica da Expressão Gênica/genética , Células HEK293 , Humanos , Camundongos , Camundongos Endogâmicos BALB C , Oncogenes/genética , Fase S/genética , Estômago/patologia
9.
Nutr Metab Cardiovasc Dis ; 31(3): 793-801, 2021 03 10.
Artigo em Inglês | MEDLINE | ID: mdl-33549448

RESUMO

BACKGROUND AND AIMS: To compare the relationships of five obesity-related routine anthropometric indicators (body mass index (BMI), body adiposity index (BAI), waist circumference (WC), waist-to-hip ratio (WHR), waist-to-height ratio (WHtR)) for hypertension in both sexes and among different age groups of the Chinese population. METHODS AND RESULTS: A total of 12,064 adult participants (5638 males and 6426 females) were included. Odds ratios (OR) and 95% confidence intervals were used with binary logistic regression models to estimate the risk of hypertension for each obesity index. For the males, WHtR had the highest OR value in all age groups. The degrees of correlation between hypertension and the obesity indices for different age groups were different among the females. WC, BMI, and WHtR were the highest in the 18-44, 45-59, and ≥60 years age groups, respectively. Furthermore, we compared the area under the ROC curve (AUC) of each obesity index for the criterion of hypertension under the influence of risk factors. For the males, the AUC of WHtR was the largest (0.814, 0.710, and 0.662). WC (AUC = 0.820), BMI (AUC = 0.765), and WHtR (AUC = 0.668) tended to be the best criteria for hypertension among females in the 18-44, 45-59, and ≥60 years age groups respectively. In addition, BAI, as an obesity indicator proposed in recent years, has a positive association with hypertension except in 18-44 years women, which was not stronger than other obesity indicators. CONCLUSIONS: For males, WHtR appears to be the best obesity index related with hypertension. For young, middle-aged, and elderly women, the best obesity indices related with hypertension are WC, BMI, and WHtR, respectively.


Assuntos
Antropometria , Pressão Sanguínea , Hipertensão/epidemiologia , Obesidade/diagnóstico , Adiposidade , Adolescente , Adulto , Fatores Etários , Idoso , Índice de Massa Corporal , Estudos Transversais , Feminino , Humanos , Hipertensão/diagnóstico , Hipertensão/fisiopatologia , Masculino , Pessoa de Meia-Idade , Obesidade/epidemiologia , Obesidade/fisiopatologia , Valor Preditivo dos Testes , Medição de Risco , Fatores de Risco , Fatores Sexuais , Circunferência da Cintura , Razão Cintura-Estatura , Relação Cintura-Quadril , Adulto Jovem
10.
Artif Intell Med ; 153: 102887, 2024 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-38735156

RESUMO

In the contemporary era, the applications of data mining and machine learning have permeated extensively into medical research, significantly contributing to areas such as HIV studies. By reviewing 38 articles published in the past 15 years, the study presents a roadmap based on seven different aspects, utilizing various machine learning techniques for both novice researchers and experienced researchers seeking to comprehend the current state of the art in this area. While traditional regression modeling techniques have been commonly used, researchers are increasingly adopting more advanced fully supervised machine learning and deep learning techniques, which often outperform the traditional methods in predictive performance. Additionally, the study identifies nine new open research issues and outlines possible future research plans to enhance the outcomes of HIV infection risk research. This review is expected to be an insightful guide for researchers, illuminating current practices and suggesting advancements in the field.


Assuntos
Mineração de Dados , Infecções por HIV , Aprendizado de Máquina , Mineração de Dados/métodos , Humanos , Infecções por HIV/diagnóstico , Pesquisa Biomédica/métodos , Medição de Risco
11.
Cancer Commun (Lond) ; 43(9): 1027-1047, 2023 09.
Artigo em Inglês | MEDLINE | ID: mdl-37533188

RESUMO

BACKGROUND: The interplay between gut microbiota and tumor microenvironment (TME) in the pathogenesis of colorectal cancer (CRC) is not well explored. Here, we elucidated the functional role of Bifidobacterium adolescentis (B.a) on CRC and investigated its possible mechanism on the manipulation of cancer-associated fibroblasts (CAFs) in CRC. METHODS: Different CRC animal models and various cell line models were established to explore the function of B.a on CRC. The single-cell RNA sequencing (scRNA-seq) or flow cytometry was used to detect the cell subsets in the TME of CRC. Western blot, quantitative real-time polymerase chain reaction (qRT-PCR), or immunofluorescence staining were performed to examine the activation of Wnt signaling and growth arrest specific 1 (GAS1) on CD143+ CAFs. Chromatin immunoprecipitation quantitative real-time PCR (CHIP-qPCR) was performed to investigate the regulation of transcription factor 4 (TCF4) on GAS1. Multi-immunofluorescence assay examined the expression level of CD143 and GAS1 on tissue microarray. RESULTS: We found that B.a abundance was significantly reduced in CRC patients from two independent cohorts and the bacteria database of GMrepo. Supplementation with B.a suppressed ApcMin/+ spontaneous or AOM/DSS-induced tumorigenesis in mice. scRNA-seq revealed that B.a facilitated a subset of CD143+ CAFs by inhibiting the infiltration of Th2 cells, while promoting the TNF-alpha+ B cells in TME. CD143+ CAFs highly expressed GAS1 and exhibited tumor suppressive effect. Mechanistically, GAS1 was activated by the Wnt/ß-catenin signaling in CD143+ CAFs. B.a abundance was correlated with the expression level of CD143 and GAS1. The level of CD143+ CAFs predicted the better survival outcome in CRC patients. CONCLUSIONS: These results highlighted that B.a induced a new subset of CD143+ CAFs by Wnt signaling-regulated GAS1 to suppress tumorigenesis and provided a novel therapeutic target for probiotic-based modulation of TME in CRC.


Assuntos
Bifidobacterium adolescentis , Fibroblastos Associados a Câncer , Neoplasias Colorretais , Camundongos , Animais , Fibroblastos Associados a Câncer/metabolismo , Fibroblastos Associados a Câncer/patologia , Via de Sinalização Wnt/genética , Neoplasias Colorretais/patologia , Carcinogênese/genética , Carcinogênese/metabolismo , Microambiente Tumoral
12.
Nat Commun ; 14(1): 6121, 2023 09 30.
Artigo em Inglês | MEDLINE | ID: mdl-37777508

RESUMO

Declined numbers and weakened functions of intestinal stem cells (ISCs) impair the integrity of the intestinal epithelium during aging. However, the impact of intestinal microbiota on ISCs in this process is unclear. Here, using premature aging mice (telomerase RNA component knockout, Terc-/-), natural aging mice, and in vitro colonoid models, we explore how heat-inactivated Bifidobacterium adolescentis (B. adolescentis) affects colon senescence. We find that B. adolescentis could mitigate colonic senescence-related changes by enhancing intestinal integrity and stimulating the regeneration of Lgr5+ ISCs via Wnt/ß-catenin signaling. Furthermore, we uncover the involvement of Paneth-like cells (PLCs) within the colonic stem-cell-supporting niche in the B. adolescentis-induced ISC regeneration. In addition, we identify soluble polysaccharides (SPS) as potential effective components of B. adolescentis. Overall, our findings reveal the role of heat-inactivated B. adolescentis in maintaining the ISCs regeneration and intestinal barrier, and propose a microbiota target for ameliorating colon senescence.


Assuntos
Bifidobacterium adolescentis , Camundongos , Animais , Temperatura Alta , Intestinos , Células-Tronco , Mucosa Intestinal , Colo
13.
Adv Sci (Weinh) ; 10(36): e2303457, 2023 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-37983567

RESUMO

Gut microbiome is integral to the pathogenesis of ulcerative colitis. A novel probiotic Lactobacillus intestinalis (L. intestinalis) exerts a protective effect against dextran sodium sulfate-induced colitis in mice. Based on flow cytometry, colitis-associated Th17 cells are the target of L. intestinalis, which is supported by the lack of protective effects of L. intestinalis in T cell-null Rag1-/- mice or upon anti-IL-17-A antibody-treated mice. Although L. intestinalis exerts no direct effect on T cell differentiation, it decreases C/EBPA-driven gut epithelial SAA1 and SAA2 production, which in turn impairs Th17 cell differentiation. Cometabolism of L. intestinalis ALDH and host ALDH1A2 contributed to elevated biosynthesis of retinoic acid (RA), which accounts for the anti-colitis effect in RAR-α -mediated way. In a cohort of ulcerative colitis patients, it is observed that fecal abundance of L. intestinalis is negatively associated with the C/EBPA-SAA1/2-Th17 axis. Finally, L. intestinalis has a synergistic effect with mesalazine in alleviating murine colitis. In conclusion, L. intestinalis and associated metabolites, RA, have potential therapeutic effects for suppressing colonic inflammation by modulating the crosstalk between intestinal epithelia and immunity.


Assuntos
Colite Ulcerativa , Colite , Humanos , Animais , Camundongos , Colite Ulcerativa/tratamento farmacológico , Células Th17/metabolismo , Colite/induzido quimicamente , Colite/tratamento farmacológico , Células Epiteliais/metabolismo , Tretinoína/metabolismo , Tretinoína/farmacologia , Tretinoína/uso terapêutico
14.
Wiley Interdiscip Rev RNA ; 13(6): e1729, 2022 11.
Artigo em Inglês | MEDLINE | ID: mdl-35413151

RESUMO

Eukaryotic cells contain subcellular organelles with spatiotemporal regulation to coordinate various biochemical reactions. The various organelles perform their essential biological functions by employing specific biomolecules, including nucleic acids. Recent studies have revealed that noncoding RNAs (ncRNAs) are highly compartmentalized in cells and that their spatial distribution is intimately related to their functions. Dysregulation of subcellular ncRNAs can disrupt cellular homeostasis and cause human diseases. Mitochondria are responsible for energy generation to fuel cell growth and proliferation. Therefore, identifying mitochondria-associated ncRNAs helps to reveal new regulatory mechanisms and physiological functions of mitochondria. In this review, we summarize the latest advances in subcellular ncRNAs derived from either the nuclear or mitochondrial genome. We also discuss available biological approaches for investigating organelle-specific ncRNAs. Exploring the distribution and function of subcellular ncRNAs may facilitate the understanding of endomembrane dynamics and provide potential strategies for clinical transformation. This article is categorized under: RNA Export and Localization > RNA Localization Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Methods > RNA Analyses in Cells.


Assuntos
RNA Longo não Codificante , RNA não Traduzido , Humanos , RNA não Traduzido/genética , Interferência de RNA , RNA , Núcleo Celular , Mitocôndrias
15.
Mol Biomed ; 3(1): 38, 2022 Dec 02.
Artigo em Inglês | MEDLINE | ID: mdl-36459282

RESUMO

Extrachromosomal circular DNA (eccDNA) has been shown to play an important role in the amplification of tumor genes and the maintenance of intra-tumor genetic heterogeneity, although its complex functional mechanism still remains to be elucidated. As the top three common malignancies in the world, colorectal cancer (CRC) has been threatening human life and health, whose tumorigenesis and development may have elusive connection with eccDNAs. Here, we described the extensive distribution of eccDNAs in the CRC tissues using Circle-seq, which range in size from hundreds to thousands of base pairs (bp). The distribution in tumor tissues had aggregation and tendency compared with random in tumor-adjacent tissues, accompanied with smaller and more regular circle lengths. After sequencing and restoring, we found that the shedding sites of eccDNAs in CRC had similar tendency in chromosome distribution, and focused on tumor-associated genes. Meanwhile, we combined RNA sequencing to explore the correlation of eccDNA differential expression in the gene transcription and signaling pathways, confirming a connection between eccDNA and RNA somewhere. Subsequently, we validated eccDNAs in CRC cell lines and the potential consistency of the junction sites of eccDNAs in CRC tissues and cell lines. Using fragments of the cationic amino acid transporter SLC7A1 to synthesize eccDNAs, we discovered the role of eccDNAs in different regions within the gene.

16.
J Infect Public Health ; 15(12): 1446-1454, 2022 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-36395669

RESUMO

BACKGROUND: To identify long non-coding RNAs (lncRNAs) that may be used as potential biomarkers of sensitivity to antiretroviral therapy (ART) against human immunodeficiency virus (HIV) infection. METHOD: A two-stage matched case-control study was conducted. First, in the screening stage, peripheral blood lymphocytes (PBLs) of six subjects receiving lamivudine-based ART (3 ART-resistant and 3 ART-sensitive subjects with matching durations of ART) were subjected to comprehensive microarray expression profiling in order to screen out lncRNAs associated with ART sensitivity. Secondly, during the validation stage, promising lncRNAs were evaluated via a 1:4 matched case-control study using 50 subjects (10 ART-resistant and 40 ART-sensitive subjects with matching durations of ART). RESULTS: Seven lncRNAs were screened out (P < 1.06 × 10-3) in the first stage. Among these, two lncRNAs (n341598 and n407911) survived validation conducted at the second stage (n341598: P < 0.001; n407911: P = 0.007), while another lncRNA n406445 showed marginally significant (P = 0.049). All three showed higher expression in ART-resistant subjects compared to that in ART-sensitive subjects. The area under the ROC curve (AUC) for n341598 was 0.867 (95 % CI: 0.796-0.966; P < 0.001), which was better than that for n406445 (0.702) and n407911 (0.780). Meanwhile, the AUC for n341598 was better than that of any combination of the three lncRNAs. CONCLUSION: Our study identified three highly expressed lncRNAs in patients with HIV ART-resistant, among which the lncRNA n341598 may be utilized as an optimal biomarker to distinguish ART-resistant and ART-sensitive patients. Further studies aimed at revealing the molecular mechanisms underlying the regulation of ART sensitivity by n341598 are warranted to complement our findings.


Assuntos
Infecções por HIV , RNA Longo não Codificante , Humanos , RNA Longo não Codificante/genética , Estudos de Casos e Controles , Infecções por HIV/tratamento farmacológico , Área Sob a Curva
17.
Gut Microbes ; 14(1): 2145843, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-36398889

RESUMO

Imbalance of gut microbiota homeostasis is related to the occurrence of ulcerative colitis (UC), and probiotics are thought to modulate immune microenvironment and repair barrier function. Here, in order to reveal the interaction between UC and gut microbiota, we screened a new probiotic strain by 16S rRNA sequencing from Dextran Sulfate Sodium (DSS)-induced colitis mice, and explored the mechanism and clinical relevance. Lactobacillus johnsonii (L. johnsonii), as a potential anti-inflammatory bacterium was decreased colonization in colitis mice. Gavage L. johnsonii could alleviate colitis by specifically increasing the proportion of intestinal macrophages and the secretion of Il-10 with macrophages depleted model and in Il10-/- mice. We identified this subset of immune cells activated by L. johnsonii as CD206+ macrophagesIL-10. Mechanistically, L. johnsonii supplementation enhanced the mobilization of CD206+ macrophagesIL-10 through the activation of STAT3 in vivo and in vitro. In addition, we revealed that TLR1/2 was essential for the activation of STAT3 and the recognition of L. johnsonii by macrophages. Clinically, there was positive correlation between the abundance of L. johnsonii and the expression level of MRC1, IL10 and TLR1/2 in UC tissues. L. johnsonii could activate native macrophages into CD206+ macrophages and release IL-10 through TLR1/2-STAT3 pathway to relieve experimental colitis. L. johnsonii may serve as an immunomodulator and anti-inflammatory therapeutic target for UC.


Assuntos
Colite Ulcerativa , Colite , Microbioma Gastrointestinal , Lactobacillus johnsonii , Receptor 1 Toll-Like , Animais , Camundongos , Anti-Inflamatórios , Colite/genética , Colite/microbiologia , Colite/terapia , Colite Ulcerativa/genética , Colite Ulcerativa/microbiologia , Colite Ulcerativa/terapia , Sulfato de Dextrana/toxicidade , Interleucina-10/genética , Macrófagos , RNA Ribossômico 16S , Receptor 1 Toll-Like/genética , Receptor 1 Toll-Like/metabolismo
18.
Stud Health Technol Inform ; 162: 204-21, 2011.
Artigo em Inglês | MEDLINE | ID: mdl-21685573

RESUMO

Parameter determination is important in modeling and simulating biological pathways including signaling pathways. Parameters are determined according to biological facts obtained from biological experiments and scientific publications. However, such reliable data describing detailed reactions are not reported in most cases. This prompted us to develop a general methodology of determining the parameters of a model in the case of that no information of the underlying biological facts is provided. In this study, we use the Petri net approach for modeling signaling pathways, and propose a method to determine firing delay times of transitions for Petri net models of signaling pathways by introducing stochastic decision rules. Petri net technology provides a powerful approach to modeling and simulating various concurrent systems, and recently have been widely accepted as a description method for biological pathways. Our method enables to determine the range of firing delay time which realizes smooth token flows in the Petri net model of a signaling pathway. The availability of this method has been confirmed by the results of an application to the interleukin-1 induced signaling pathway.


Assuntos
Modelos Biológicos , Transdução de Sinais , Algoritmos , Simulação por Computador , Humanos , Modelos Teóricos , Fatores de Tempo
19.
Biosystems ; 210: 104526, 2021 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-34509580

RESUMO

Acupuncture and moxibustion treatment has been widely spread all over the world because it has few side effects and is effective for ahead sick and incurable disease. However, the treatment is often performed empirically and clinically, and the mechanism and process of the treatment are not yet scientifically elucidated. Therefore, it is required to establish objective and unified research methods and evaluation criteria that incorporate modern Western medicine and scientific and technological viewpoints. In this paper, a human body model is constructed, which includes the internal organs and the meridians for acupuncture and moxibustion treatment based on traditional Chinese medicine using colored Petri nets. This model aims at expressing the relationship between acupoints and internal organs realistically and accurately in acupuncture and moxibustion treatment, and leading to realization of an objective analysis method of the mechanism and process of acupuncture and moxibustion treatment. Firstly, the calculation of the acupoints' efficacy on internal organs is discussed, and measurement equations and model construction methods are proposed. Next, an interface is established as a bridge to connect the internal organs and the meridians with acupoints. By Java language, a simulation system is developed based on the proposed Petri net model. Finally, simulations of acupuncture and moxibustion treatment are performed to verify the validity of model.


Assuntos
Pontos de Acupuntura , Terapia por Acupuntura/métodos , Medicina Tradicional Chinesa/métodos , Modelos Anatômicos , Moxibustão/métodos , Nomogramas , Corpo Humano , Humanos , Meridianos
20.
Adv Mater ; 33(49): e2104037, 2021 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-34622500

RESUMO

Although immunotherapy such as immune checkpoint inhibitors has shown promising efficacy in cancer treatment, the responsiveness among patients is relatively limited. Activation of the cyclic guanosine monophosphate-adenosine monophosphate synthase/interferon gene stimulator (cGAS/STING) signaling pathway to upregulate innate immunity has become an emerging strategy for enhancing tumor immunotherapy. Herein, ZnS@BSA (bovine serum albumin) nanoclusters synthesized via a self-assembly approach are reported, where the released zinc ions under acidic tumor microenvironment significantly enhance cGAS/STING signals. Meanwhile, intracellular zinc ions can produce reactive oxygen species, which is further facilitated by the generated H2 S gas from ZnS@BSA via specifically inhibiting catalase in hepatocellular carcinoma cells. It is found that the nanoclusters activate the cGAS/STING signals in mice, which promotes the infiltration of CD8+ T cells at the tumor site and cross-presentation of dendritic cells, leading to an improved immunotherapy efficacy against hepatocellular carcinoma.


Assuntos
Carcinoma Hepatocelular , Neoplasias Hepáticas , Compostos de Zinco , Animais , Linfócitos T CD8-Positivos , Carcinoma Hepatocelular/terapia , Humanos , Imunoterapia , Neoplasias Hepáticas/terapia , Proteínas de Membrana/metabolismo , Nanopartículas Metálicas , Camundongos , Nucleotidiltransferases/genética , Nucleotidiltransferases/metabolismo , Sulfetos , Microambiente Tumoral , Compostos de Zinco/farmacologia
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