keyword
https://read.qxmd.com/read/38495503/identification-of-t-cell-exhaustion-related-genes-and-prediction-of-their-immunotherapeutic-role-in-lung-adenocarcinoma
#21
JOURNAL ARTICLE
Chaoqun Lian, Feifan Li, Yiluo Xie, Linxiang Zhang, Huili Chen, Ziqiang Wang, Xinyu Pan, Xiaojing Wang, Jing Zhang
Background: Lung adenocarcinoma ranks as the second most widespread form of cancer globally, accompanied by a significant mortality rate. Several studies have shown that T cell exhaustion is associated with immunotherapy of tumours. Consequently, it is essential to comprehend the possible impact of T cell exhaustion on the tumor microenvironment. The purpose of this research was to create a TEX-based model that would use single-cell RNA-seq (scRNA-seq) and bulk-RNA sequencing to explore new possibilities for assessing the prognosis and immunotherapeutic response of LUAD patients...
2024: Journal of Cancer
https://read.qxmd.com/read/38495492/uncovering-microbial-composition-of-the-tissue-microenvironment-in-bladder-cancer-using-rna-sequencing-data
#22
JOURNAL ARTICLE
Ruiqian Yao, Bin Ai, Zeyi Wang, Bing Shen, Geng Xue, Dong Yu
Purpose: Bladder cancer (BC) is one of the top 10 common tumors in the world. It has been reported that microbiota can colonize tissues and play important roles in tumorigenesis and progression. However, the current understanding of microorganisms in the BC tissue microenvironment remains unclear. Methods: In this study, we integrated the RNA-seq data of 479 BC tissue samples from seven datasets combined with a range of bioinformatics tools to explore the landscape of microbiome in the BC tissue microenvironment...
2024: Journal of Cancer
https://read.qxmd.com/read/38495440/studying-temporal-dynamics-of-single-cells-expression-lineage-and-regulatory-networks
#23
REVIEW
Xinhai Pan, Xiuwei Zhang
UNLABELLED: Learning how multicellular organs are developed from single cells to different cell types is a fundamental problem in biology. With the high-throughput scRNA-seq technology, computational methods have been developed to reveal the temporal dynamics of single cells from transcriptomic data, from phenomena on cell trajectories to the underlying mechanism that formed the trajectory. There are several distinct families of computational methods including Trajectory Inference (TI), Lineage Tracing (LT), and Gene Regulatory Network (GRN) Inference which are involved in such studies...
February 2024: Biophysical Reviews
https://read.qxmd.com/read/38495181/holistic-exploration-of-chga-and-hsa-mir-137-in-colorectal-cancer-via-multi-omic-data-integration
#24
JOURNAL ARTICLE
Hossein Safarpour, Javad Ranjbaran, Nafiseh Erfanian, Samira Nomiri, Afshin Derakhshani, Casimiro Gerarduzzi, Adib Miraki Feriz, Edris HosseiniGol, Samira Saghafi, Nicola Silvestris
Colorectal cancer (CRC) ranks among the most widespread malignancies globally, with early detection significantly influencing prognosis. Employing a systems biology approach, we aimed to unravel the intricate mRNA-miRNA network linked to CRC pathogenesis, potentially yielding diagnostic biomarkers. Through an integrative analysis of microarray, Bulk RNA-seq, and single-cell RNA-seq data, we explored CRC-related transcriptomes comprehensively. Differential gene expression analysis uncovered crucial genes, while Weighted Gene Co-expression Network Analysis (WGCNA) identified key modules closely linked to CRC...
March 15, 2024: Heliyon
https://read.qxmd.com/read/38495121/mir-21-responsive-nanocarrier-targeting-ovarian-cancer-cells
#25
JOURNAL ARTICLE
Liting Han, Tao Song, Xinyu Wang, Yan Luo, Chuanqi Gu, Xin Li, Jinda Wen, Zhibin Wen, Xiaolong Shi
In recent years, DNA origami-based nanocarriers have been extensively utilized for efficient cancer therapy. However, developing a nanocarrier capable of effectively protecting cargos such as RNA remains a challenge. In this study, we designed a compact and controllable DNA tubular origami (DTO) measuring 120 nm in length and 18 nm in width. The DTO exhibited appropriate structural characteristics for encapsulating and safeguarding cargo. Inside the DTO, we incorporated 20 connecting points to facilitate the delivery of cargoes to various ovarian and normal epithelial cell lines...
December 2024: Computational and Structural Biotechnology Journal
https://read.qxmd.com/read/38494946/novel-aminocoumarin-derivatives-against-phytopathogenic-fungi-design-synthesis-and-structure-activity-relationships
#26
JOURNAL ARTICLE
Pengzhi Sun, Jiangping Pu, Dongyu Lei, Jiashan Li, Xingyu Ren, Lu Jin, le Pan
Phytopathogenic fungi is the most devastating reason for the decrease of the agricultural production and food safety. To develop new fungicidal agents for resistance concerning, a novel series of aminocoumarin derivatives were synthesized and their fungicidal activity were investigated both in vitro and in vivo. Transmission electron microscope (TEM), scanning electron microscope (SEM), RNA-Seq, 3D-QSAR and molecular docking were applied to reveal the underlying anti-fungal mechanisms. Most of the compounds exhibited significant fungicidal activity...
March 18, 2024: Chemistry & Biodiversity
https://read.qxmd.com/read/38494904/lung-gene-expression-suggests-roles-for-interferon-stimulated-genes-and-adenosine-deaminase-acting-against-rna-1-in-pathologic-responses-to-diisocyanate
#27
JOURNAL ARTICLE
Adam V Wisnewski, Jian Liu
Mechanisms underlying methylene diphenyl diisocyanate (MDI) and other low molecular weight chemical-induced asthma are unclear and appear distinct from those of high molecular weight (HMW) allergen-induced asthma. We sought to elucidate molecular pathways that differentiate asthma-like pathogenic vs nonpathogenic responses to respiratory tract MDI exposure in a murine model. Lung gene expression differences in MDI exposed immune-sensitized and nonsensitized mice vs unexposed controls were measured by microarrays, and associated molecular pathways were identified through bioinformatic analyses and further compared with published studies of a prototypic HMW asthmagen (ovalbumin)...
March 18, 2024: Chemical Research in Toxicology
https://read.qxmd.com/read/38494878/prognostic-value-of-an-immune-long-noncoding-rna-signature-in-liver-hepatocellular-carcinoma
#28
JOURNAL ARTICLE
Rui Kong, Nan Wang, Chun Li Zhou, Jie Lu
In recent years, there has been a growing recognition of the important role that long non-coding RNAs (lncRNAs) play in the immunological process of hepatocellular carcinoma (LIHC). An increasing number of studies have shown that certain lncRNAs hold great potential as viable options for diagnosis and treatment in clinical practice. The primary objective of our investigation was to devise an immune lncRNA profile to explore the significance of immune-associated lncRNAs in the accurate diagnosis and prognosis of LIHC...
January 30, 2024: Journal of Microbiology and Biotechnology
https://read.qxmd.com/read/38494861/exploring-the-current-landscape-of-single-cell-rna-sequencing-applications-in-gastric-cancer-research
#29
REVIEW
Wireko Andrew Awuah, Sakshi Roy, Joecelyn Kirani Tan, Favour Tope Adebusoye, Zekai Qiang, Tomas Ferreira, Arjun Ahluwalia, Vallabh Shet, Amanda Leong Weng Yee, Toufik Abdul-Rahman, Marios Papadakis
Gastric cancer (GC) represents a major global health burden and is responsible for a significant number of cancer-related fatalities. Its complex nature, characterized by heterogeneity and aggressive behaviour, poses considerable challenges for effective diagnosis and treatment. Single-cell RNA sequencing (scRNA-seq) has emerged as an important technique, offering unprecedented precision and depth in gene expression profiling at the cellular level. By facilitating the identification of distinct cell populations, rare cells and dynamic transcriptional changes within GC, scRNA-seq has yielded valuable insights into tumour progression and potential therapeutic targets...
April 2024: Journal of Cellular and Molecular Medicine
https://read.qxmd.com/read/38494844/microglia-orchestrate-synaptic-and-neuronal-stripping-implication-in-neuropsychiatric-lupus
#30
JOURNAL ARTICLE
Yishan Zhou, Liang Chen, Xiulan Zheng, Qijun Fang, Yunzhi Qian, Tianshu Xu, Jun Liang, Huajun Zhang, Xiaojuan Han, Lingyun Sun
Systemic lupus erythematosus (SLE), a multifactorial autoimmune disease, can affect the brain and cause neuropsychiatric dysfunction, also named neuropsychiatric lupus (NPSLE). Microglial activation is observed in NPSLE patients. However, the mechanisms regulating microglia-mediated neurotoxicity in NPSLE remain elusive. Here, we showed that M1-like proinflammatory cytokine levels were increased in the cerebrospinal fluid (CSF) of SLE patients, especially those with neuropsychiatric symptoms. We also demonstrated that MRL/lpr lupus mice developed anxiety-like behaviours and cognitive deficits in the early and active phases of lupus, respectively...
April 2024: Journal of Cellular and Molecular Medicine
https://read.qxmd.com/read/38494830/impact-of-translational-regulation-on-diel-expression-revealed-by-time-series-ribosome-profiling-in-arabidopsis
#31
JOURNAL ARTICLE
Haruka Aoyama, Toshihiro Arae, Yui Yamashita, Atsushi Toyoda, Satoshi Naito, Naoyuki Sotta, Yukako Chiba
Plants have developed the ability to adjust to the day/night cycle through the expression of diel genes, which allow them to effectively respond to environmental changes and optimise their growth and development. Diel oscillations also have substantial implications in many physiological processes, including photosynthesis, floral development, and environmental stress responses. The expression of diel genes is regulated by a combination of the circadian clock and responses to environmental cues, such as light and temperature...
March 17, 2024: Plant Journal
https://read.qxmd.com/read/38494660/yinxieling-decoction-ameliorates-psoriasis-by-regulating-the-differentiation-and-functions-of-langerhans-cells-via-the-tgf-%C3%AE-1-pu-1-il-23-signal-axis
#32
JOURNAL ARTICLE
Ning Li, Jiagu Ke, Qihua Yu, Xiong Li, Lipeng Tang, Miaomiao Zhang, Xiaoshu Chai, Qiaoling Wu, Chuanjian Lu, Dinghong Wu
Langerhans cells (LCs) play a critical role in skin immune responses and the development of psoriasis. Yinxieling (YXL) is a representative Chinese herbal medicine for the treatment of psoriasis in South China. It was found to improve psoriasis without obvious side effects in the clinic. Here we attempted to clarify whether and how YXL regulates the differentiation and functions of LCs in Imiquimod (IMQ)-induced psoriasis in vivo and induced LCs in vitro. The Psoriasis Area Severity Index (PASI) score was used to evaluate the efficacy of YXL for IMQ-induced psoriasis-like mice...
March 2024: Cell Biochemistry and Function
https://read.qxmd.com/read/38494545/chalkiness-and-premature-controlled-by-energy-homeostasis-in-osnac02-ko-mutant-during-vegetative-endosperm-development
#33
JOURNAL ARTICLE
Mei Yan, Guiai Jiao, Gaoneng Shao, Ying Chen, Maodi Zhu, Lingwei Yang, Lihong Xie, Peisong Hu, Shaoqing Tang
BACKGROUND: Chalkiness is a common phenotype induced by various reasons, such as abiotic stress or the imbalance of starch synthesis and metabolism during the development period. However, the reason mainly for one gene losing its function such as NAC (TFs has a large family in rice) which may cause premature is rarely known to us. RESULTS: The Ko-Osnac02 mutant demonstrated an obviously early maturation stage compared to the wild type (WT) with 15 days earlier...
March 18, 2024: BMC Plant Biology
https://read.qxmd.com/read/38494503/pdcl3-is-a-prognostic-biomarker-associated-with-immune-infiltration-in-hepatocellular-carcinoma
#34
JOURNAL ARTICLE
Wenzhi Jin, Ganggang Wang, Meiyuan Dong, Xiaoliang Wang
BACKGROUND: Phosducin-like 3 (PDCL3) is a member of the photoreceptor family, characterized by a thioredoxin-like structural domain and evolutionary conservation. It plays roles in angiogenesis and apoptosis. Despite its significance, research on the biological role of PDCL3 in liver hepatocellular carcinoma (LIHC) remains limited. This study aims to explore the prognostic value and potential mechanisms of PDCL3 in cancer, particularly in LIHC, through bioinformatics analysis. METHODS: RNA-seq data and corresponding clinical information for pan-cancer and LIHC were extracted from the TCGA database to analyze PDCL3 expression and survival prognosis...
March 17, 2024: European Journal of Medical Research
https://read.qxmd.com/read/38494474/integrative-genomic-analyses-identify-candidate-causal-genes-for-calcific-aortic-valve-stenosis-involving-tissue-specific-regulation
#35
JOURNAL ARTICLE
Sébastien Thériault, Zhonglin Li, Erik Abner, Jian'an Luan, Hasanga D Manikpurage, Ursula Houessou, Pardis Zamani, Mewen Briend, Dominique K Boudreau, Nathalie Gaudreault, Lily Frenette, Déborah Argaud, Manel Dahmene, François Dagenais, Marie-Annick Clavel, Philippe Pibarot, Benoit J Arsenault, S Matthijs Boekholdt, Nicholas J Wareham, Tõnu Esko, Patrick Mathieu, Yohan Bossé
There is currently no medical therapy to prevent calcific aortic valve stenosis (CAVS). Multi-omics approaches could lead to the identification of novel molecular targets. Here, we perform a genome-wide association study (GWAS) meta-analysis including 14,819 cases among 941,863 participants of European ancestry. We report 32 genomic loci, among which 20 are novel. RNA sequencing of 500 human aortic valves highlights an enrichment in expression regulation at these loci and prioritizes candidate causal genes...
March 18, 2024: Nature Communications
https://read.qxmd.com/read/38494386/suppressor-t-helper-type-17-cell-responses-in-intestinal-transplant-recipients-with-allograft-rejection
#36
JOURNAL ARTICLE
Leonid Belyayev, Jiman Kang, Mohammed Sadat, Katrina Loh, Digvijay Patil, Vinona Muralidaran, Khalid Khan, Stuart Kaufman, Sukanya Subramanian, Yuriy Gusev, Krithika Bhuvaneshwar, Habtom Ressom, Rency Varghese, Udeme Ekong, Cal S Matsumoto, Simon C Robson, Thomas M Fishbein, Alexander Kroemer
BACKGROUND: Intestinal transplant (ITx) rejection is associated with memory T helper type 17 cell (Th17) infiltration of grafted tissues. Modulation of Th17 effector cell response is facilitated by T regulatory (Treg) cells, but a phenotypic characterization of this process is lacking in the context of allograft rejection. METHODS: Flow cytometry was performed to examine the expression of surface receptors, cytokines, and transcription factors in Th17 and Treg cells in ITx control (n = 34) and rejection patients (n = 23)...
March 16, 2024: Human Immunology
https://read.qxmd.com/read/38494152/rna-therapies-for-cns-diseases
#37
REVIEW
Valentina Di Francesco, Andy J Chua, Di Huang, Anisha D'Souza, Alicia Yang, Benjamin S Bleier, Mansoor M Amiji
Neurological disorders are a diverse group of conditions that pose an increasing health burden worldwide. There is a general lack of effective therapies due to multiple reasons, of which a key obstacle is the presence of the blood-brain barrier, which limits drug delivery to the central nervous system, and generally restricts the pool of candidate drugs to small, lipophilic molecules. However, in many cases, these are unable to target key pathways in the pathogenesis of neurological disorders. As a group, RNA therapies have shown tremendous promise in treating various conditions because they offer unique opportunities for specific targeting by leveraging Watson-Crick base pairing systems, opening up possibilities to modulate pathological mechanisms that previously could not be addressed by small molecules or antibody-protein interactions...
March 15, 2024: Advanced Drug Delivery Reviews
https://read.qxmd.com/read/38494090/comparing-dna-isolation-and-sequencing-strategies-for-16s-rrna-gene-amplicon-analysis-in-biofilm-containing-environments
#38
JOURNAL ARTICLE
Ilgaz Cakin, Barbara Morrissey, Matthew Gordon, Paul P J Gaffney, Lucio Marcello, Kenneth Macgregor, Mark A Taggart
Bacteria are primarily responsible for biological water treatment processes in constructed wetland systems. Gravel in constructed wetlands serves as an essential substrate onto which complex bacterial biofilms may successfully grow and evolve. To fully understand the bacterial community in these systems it is crucial to properly isolate biofilms and process DNA from such substrates. This study looked at how best to isolate bacterial biofilms from gravel substrates in terms of bacterial richness. It considered factors including the duration of agitation during extraction, extraction temperature, and enzyme usage...
March 15, 2024: Journal of Microbiological Methods
https://read.qxmd.com/read/38494075/exploring-the-ire1-interactome-from-canonical-signaling-functions-to-unexpected-roles
#39
REVIEW
Simon Le Goupil, Hadrien Laprade, Marc Aubry, Eric Chevet
The unfolded protein response (UPR) is a mechanism aiming at restoring endoplasmic reticulum (ER) homeostasis and is likely involved in other adaptive pathways. The UPR is transduced by three proteins acting as sensors and triggering downstream signaling pathways. Among them, IRE1α (referred to as IRE1 hereafter), an ER-resident type I transmembrane protein, exerts its function through both kinase and endoribonuclease activities, resulting in both XBP1 mRNA splicing and RNA degradation (Regulated IRE1 Dependent Decay, RIDD)...
March 15, 2024: Journal of Biological Chemistry
https://read.qxmd.com/read/38494067/regulation-of-the-ages-induced-inflammatory-response-in-human-periodontal-ligament-cells-via-the-ampk-nf-%C3%AE%C2%BAb-nlrp3-signaling-pathway
#40
JOURNAL ARTICLE
Zhu-Ling Guo, Jie Zhou, Xue-Jing Lin, Qing Yuan, Yu-Lei Dong, Qi-Bing Liu, Tao Wang
The heightened prevalence and accelerated progression of periodontitis in individuals with diabetes is primarily attributed to inflammatory responses in human periodontal ligament cells (HPDLCs). This study is aimed at delineating the regulatory mechanism of nucleotide-binding oligomerization domain-like receptors (NLRs) in mediating inflammation incited by muramyl dipeptide (MDP) in HPDLCs, under the influence of advanced glycation end products (AGEs), metabolic by-products associated with diabetes. We performed RNA-seq in HPDLCs induced by AGEs treatment and delineated activation markers for the receptor of AGEs (RAGE)...
March 15, 2024: Experimental Cell Research
keyword
keyword
101437
2
3
Fetch more papers »
Fetching more papers... Fetching...
Remove bar
Read by QxMD icon Read
×

Save your favorite articles in one place with a free QxMD account.

×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"

We want to hear from doctors like you!

Take a second to answer a survey question.