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JOURNAL ARTICLE
Beiru Wang, Chengyu Hou, Xiang Yu, Jiaxin Liu, Jiyong Wang
There has been increasing interest in the role of epigenetic modification in cancers recently. Among the various modifications, sialylation has emerged as a dominant subtype implicated in tumor progression, metastasis, immune evasion, and chemoresistance. The prognostic significance of sialylation-related molecules has been demonstrated in colorectal cancer. However, the potential roles and regulatory mechanisms of sialylation in lung adenocarcinoma (LUAD) have not been thoroughly investigated. Through Pearson correlation, univariate Cox hazards proportional regression, and random survival forest model analyses, we identified several prognostic long non-coding RNAs (lncRNAs) associated with aberrant sialylation and tumor progression, including LINC00857, LINC00968, LINC00663, and ITGA9-AS1...
April 17, 2024: Scientific Reports
#22
JOURNAL ARTICLE
Nicola J Wyatt, Hannah Watson, Carl A Anderson, Nicholas A Kennedy, Tim Raine, Tariq Ahmad, Dean Allerton, Michelle Bardgett, Emma Clark, Dawn Clewes, Cristina Cotobal Martin, Mary Doona, Jennifer A Doyle, Katherine Frith, Helen C Hancock, Ailsa L Hart, Victoria Hildreth, Peter M Irving, Sameena Iqbal, Ciara Kennedy, Andrew King, Sarah Lawrence, Charlie W Lees, Robert Lees, Laura Letchford, Trevor Liddle, James O Lindsay, Rebecca H Maier, John C Mansfield, Julian R Marchesi, Naomi McGregor, Rebecca E McIntyre, Jasmin Ostermayer, Tolulope Osunnuyi, Nick Powell, Natalie J Prescott, Jack Satsangi, Shriya Sharma, Tara Shrestha, Ally Speight, Michelle Strickland, James Ms Wason, Kevin Whelan, Ruth Wood, Gregory R Young, Xinyue Zhang, Miles Parkes, Christopher J Stewart, Luke Jostins-Dean, Christopher A Lamb
INTRODUCTION: Characterised by chronic inflammation of the gastrointestinal tract, inflammatory bowel disease (IBD) symptoms including diarrhoea, abdominal pain and fatigue can significantly impact patient's quality of life. Therapeutic developments in the last 20 years have revolutionised treatment. However, clinical trials and real-world data show primary non-response rates up to 40%. A significant challenge is an inability to predict which treatment will benefit individual patients...
April 17, 2024: BMJ Open
#23
REVIEW
Claudia Christowitz, Daniel W Olivier, Johann W Schneider, Maritha J Kotze, Anna-Mart Engelbrecht
A pathology-supported genetic testing (PSGT) framework was established in South Africa to improve access to precision medicine for patients with breast carcinomas. Nevertheless, the frequent identification of variants of uncertain significance (VUSs) with the use of genome-scale next-generation sequencing has created a bottleneck in the return of results to patients. This review highlights the importance of incorporating functional genomics into the PSGT framework as a proposed initiative. Here, we explore various model systems and experimental methods available for conducting functional studies in South Africa to enhance both variant classification and clinical interpretation...
April 15, 2024: Mutation Research. Reviews in Mutation Research
#24
JOURNAL ARTICLE
Daniela Kocher, Lei Cao, Romain Guiho, Melanie Langhammer, Yun-Lu Lai, Pauline Becker, Hiba Hamdi, Dennis Friedel, Florian Selt, David Vonhören, Julia Zaman, Gintvile Valinciute, Sonja Herter, Daniel Picard, Johanna Rettenmeier, Kendra K Maass, Kristian W Pajtler, Marc Remke, Andreas von Deimling, Stefan Pusch, Stefan M Pfister, Ina Oehme, David T W Jones, Sebastian Halbach, Tilman Brummer, Juan Pedro Martinez-Barbera, Olaf Witt, Till Milde, Romain Sigaud
INTRODUCTION: Patients with pediatric low-grade gliomas (pLGGs), the most common primary brain tumors in children, can often benefit from MAPK inhibitor (MAPKi) treatment. However, rapid tumor regrowth, also referred to as rebound growth, may occur once treatment is stopped, constituting a significant clinical challenge. METHODS: Four patient-derived pediatric glioma models were investigated to model rebound growth in vitro based on viable cell counts in response to MAPKi treatment and withdrawal...
April 17, 2024: Journal of Neuro-oncology
#25
JOURNAL ARTICLE
Zhishang Meng, Yanzhu Chen, Haoyu Li, Yue Zhang, Xiaoxi Yao, Yongan Meng, Wen Shi, Youling Liang, Yuqian Hu, Dan Liu, Manyun Xie, Bin Yan, Jing Luo
BACKGROUND: Diabetic macular edema (DME) is a leading cause of vision loss in patients with diabetes. This study aimed to develop and evaluate an OCT-omics prediction model for assessing anti-vascular endothelial growth factor (VEGF) treatment response in patients with DME. METHODS: A retrospective analysis of 113 eyes from 82 patients with DME was conducted. Comprehensive feature engineering was applied to clinical and optical coherence tomography (OCT) data. Logistic regression, support vector machine (SVM), and backpropagation neural network (BPNN) classifiers were trained using a training set of 79 eyes, and evaluated on a test set of 34 eyes...
April 16, 2024: Journal of Translational Medicine
#26
JOURNAL ARTICLE
Nuria Olvera, Jon Sánchez-Valle, Iker Núñez-Carpintero, Joselyn Rojas-Quintero, Guillaume Noell, Sandra Casas-Recasens, Alen Faiz, Philip Hansbro, Angela Guirao, Rosalba Lepore, Davide Cirillo, Alvar Agustí, Francesca Polverino, Alfonso Valencia, Rosa Faner
BACKGROUND: Chronic Obstructive Pulmonary Disease (COPD) is a heterogeneous condition. We hypothesized that the unbiased integration of different COPD lung omics using a novel multi-layer approach may unravel mechanisms associated with clinical characteristics. METHODS: We profiled mRNA, miRNA and methylome in lung tissue samples from 135 former smokers with COPD. For each omic (layer) we built a patient network based on molecular similarity. The three networks were used to build a multi-layer network, and optimization of multiplex-modularity was employed to identify patient communities across the three distinct layers...
April 16, 2024: American Journal of Respiratory and Critical Care Medicine
#27
REVIEW
Christina R Ferreira, Paulo Clairmont F de Lima Gomes, Kiley Marie Robison, Bruce R Cooper, Jonathan H Shannahan
Omics analyses collectively refer to the possibility of profiling genetic variants, RNA, epigenetic markers, proteins, lipids, and metabolites. The most common analytical approaches used for detecting molecules present within biofluids related to metabolism are vibrational spectroscopy techniques, represented by infrared, Raman, and nuclear magnetic resonance (NMR) spectroscopies and mass spectrometry (MS). Omics-based assessments utilizing MS are rapidly expanding and being applied to various scientific disciplines and clinical settings...
April 16, 2024: Molecular Omics
#28
JOURNAL ARTICLE
Aishani Chakraborty, Leila Alsharqi, Markus Kostrzewa, Darius Armstrong-James, Gerald Larrouy-Maumus
Glycosyl-inositol-phospho-ceramides (GIPCs) or glycosylphosphatidylinositol-anchored fungal polysaccharides are major lipids in plant and fungal plasma membranes and play an important role in stress adaption. However, their analysis remains challenging due to the multiple steps involved in their extraction and purification prior to mass spectrometry analysis. To address this challenge, we report here a novel simplified method to identify GIPCs from Aspergillus fumigatus using the new Bruker MBT lipid Xtract assay...
April 16, 2024: Molecular Omics
#29
REVIEW
Ali Doostmohammadi, Hossein Jooya, Kimia Ghorbanian, Sargol Gohari, Mehdi Dadashpour
Cancer is a major public health problem worldwide with more than an estimated 19.3 million new cases in 2020. The occurrence rises dramatically with age, and the overall risk accumulation is combined with the tendency for cellular repair mechanisms to be less effective in older individuals. Conventional cancer treatments, such as radiotherapy, surgery, and chemotherapy, have been used for decades to combat cancer. However, the emergence of novel fields of cancer research has led to the exploration of innovative treatment approaches focused on immunotherapy, epigenetic therapy, targeted therapy, multi-omics, and also multi-target therapy...
April 15, 2024: Cell Communication and Signaling: CCS
#30
JOURNAL ARTICLE
Zhongwen Lu, Yongsheng Pan, Songbo Wang, Jiajin Wu, Chenkui Miao, Zengjun Wang
Glycolysis-related metabolic reprogramming is a central hallmark of human cancers, especially in renal cell carcinoma. However, the regulatory function of glycolytic signature in papillary RCC has not been well elucidated. In the present study, the glycolysis-immune predictive signature was constructed and validated using WGCNA, glycolysis-immune clustering analysis. PPI network of DEGs was constructed and visualized. Functional enrichments and patients' overall survival were analyzed. QRT-PCR experiments were performed to detect hub genes' expression and distribution, siRNA technology was used to silence targeted genes; cell proliferation and migration assays were applied to evaluate the biological function...
April 15, 2024: European Journal of Medical Research
#31
JOURNAL ARTICLE
Safoora Masoumi, Hossein Amirkhani, Najmeh Sadeghian, Saeid Shahraz
BACKGROUND: Abstract review is a time and labor-consuming step in the systematic and scoping literature review in medicine. Text mining methods, typically natural language processing (NLP), may efficiently replace manual abstract screening. This study applies NLP to a deliberately selected literature review problem, the trend of using NLP in medical research, to demonstrate the performance of this automated abstract review model. METHODS: Scanning PubMed, Embase, PsycINFO, and CINAHL databases, we identified 22,294 with a final selection of 12,817 English abstracts published between 2000 and 2021...
April 15, 2024: Systematic Reviews
#32
JOURNAL ARTICLE
Shao-Song Liu, Qin-Si Wan, Cong Lv, Jin-Ke Wang, Song Jiang, Dan Cai, Mao-Sheng Liu, Ting Wang, Kun-He Zhang
BACKGROUND: Gastric cancer (GC) lacks serum biomarkers with clinical diagnostic value. Multi-omics analysis is an important approach to discovering cancer biomarkers. This study aimed to identify and validate serum biomarkers for GC diagnosis by cross-analysis of proteomics and transcriptomics datasets. METHODS: A cross-omics analysis was performed to identify overlapping differentially expressed genes (DEGs) between our previous aptamer-based GC serum proteomics dataset and the GC tissue RNA-Seq dataset in The Cancer Genome Atlas (TCGA) database, followed by lasso regression and random forest analysis to select key overlapping DEGs as candidate biomarkers for GC...
April 15, 2024: BMC Cancer
#33
JOURNAL ARTICLE
Yong-Yan Wang, Zhong Wang
The development of modern omics technology has facilitated in-depth research on many disciplines in the field of medicine. For instance, the introduction of omics-related technology has facilitated research on the mechanism of formula's action and led to the innovative development of sophisticated pharmacological analysis methods. However, in general, the previous ideas are only limited to the application level, failing to integrate with the discipline connotation of formulaology. Furthermore, they are unable to fulfill their potential role in the future evolution of formulaology and steer comprehensive research on the clinical efficacy and safety of formulas...
February 2024: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
#34
JOURNAL ARTICLE
Haigang Geng, Chen Huang, Lei Xu, Yangyang Zhou, Zhongyi Dong, Yiqing Zhong, Qian Li, Chen Yang, Shaozhuo Huang, Weixin Liao, Yuxuan Lin, Zhicheng Liu, Qing Li, Zizhen Zhang, Chunchao Zhu
AIMS: Cellular senescence (CS) represents an intracellular defense mechanism responding to stress signals and can be leveraged as a "vulnerability" in cancer treatment. This study aims to construct a CS atlas for gastric cancer (GC) and uncover potential therapeutics for GC patients. MATERIALS AND METHODS: 38 senescence-associated regulators with prognostic significance in GC were obtained from the CellAge database to construct Gastric cancer-specific Senescence Score (GSS)...
April 13, 2024: Life Sciences
#35
JOURNAL ARTICLE
Kun Tu, Wenhui Zhou, Shubing Kong
Alzheimer's disease (AD) is a progressive and irreversible neurodegenerative disorder. Its etiology may be associated with genetic, environmental, and lifestyle factors. With the advancement of technology, the integration of genomics, transcriptomics, and imaging data related to AD allows simultaneous exploration of molecular information at different levels and their interaction within the organism. This paper proposes a hypergraph-regularized joint deep semi-non-negative matrix factorization (HR-JDSNMF) algorithm to integrate positron emission tomography (PET), single-nucleotide polymorphism (SNP), and gene expression data for AD...
April 15, 2024: Journal of Molecular Neuroscience: MN
#36
JOURNAL ARTICLE
Shi-Ju Chen, Da-Ya Zhang, Xia Wu, Fa-Ming Zhang, Bo-Ta Cui, Yi-Hao Huang, Zu-Lun Zhang, Rui Wang, Fei-Hu Bai
BACKGROUND: Fecal microbiota transplantation (FMT) is a promising therapeutic approach for treating Crohn's disease (CD). The new method of FMT, based on the automatic washing process, was named as washed microbiota transplantation (WMT). Most existing studies have focused on observing the clinical phenomena. However, the mechanism of action of FMT for the effective management of CD-particularly in-depth multi-omics analysis involving the metagenome, metatranscriptome, and metabolome-has not yet been reported...
March 21, 2024: World Journal of Gastroenterology: WJG
#37
Tongwu Zhang, Jian Sang, Phuc H Hoang, Wei Zhao, Jennifer Rosenbaum, Kofi Ennu Johnson, Leszek J Klimczak, John McElderry, Alyssa Klein, Christopher Wirth, Erik N Bergstrom, Marcos Díaz-Gay, Raviteja Vangara, Frank Colon-Matos, Amy Hutchinson, Scott M Lawrence, Nathan Cole, Bin Zhu, Teresa M Przytycka, Jianxin Shi, Neil E Caporaso, Robert Homer, Angela C Pesatori, Dario Consonni, Marcin Imielinski, Stephen J Chanock, David C Wedge, Dmitry A Gordenin, Ludmil B Alexandrov, Reuben S Harris, Maria Teresa Landi
APOBEC enzymes are part of the innate immunity and are responsible for restricting viruses and retroelements by deaminating cytosine residues 1,2 . Most solid tumors harbor different levels of somatic mutations attributed to the off-target activities of APOBEC3A (A3A) and/or APOBEC3B (A3B) 3-6 . However, how APOBEC3A/B enzymes shape the tumor evolution in the presence of exogenous mutagenic processes is largely unknown. Here, by combining deep whole-genome sequencing with multi-omics profiling of 309 lung cancers from smokers with detailed tobacco smoking information, we identify two subtypes defined by low ( LAS ) and high ( HAS ) APOBEC mutagenesis...
April 3, 2024: bioRxiv
#38
JOURNAL ARTICLE
Luo-Dan Qian, Zi-Ang Zhou, Si-Qi Li, Jun Liu, Shu-Xin Zhang, Jia-Liang Ren, Wei Wang, Jigang Yang
BACKGROUND: The MYCN copy number category is closely related to the prognosis of neuroblastoma (NB). Therefore, this study aimed to assess the predictive ability of 18 F-fluorodeoxyglucose (18 F-FDG) positron emission tomography/computed tomography (PET/CT) radiomic features for MYCN copy number in NB. METHODS: A retrospective analysis was performed on 104 pediatric patients with NB that had been confirmed by pathology. To develop the Bio-omics model (B-model), which incorporated clinical and biological aspects, PET/CT radiographic features, PET quantitative parameters, and significant features with multivariable stepwise logistic regression were preserved...
April 3, 2024: Quantitative Imaging in Medicine and Surgery
#39
JOURNAL ARTICLE
Leyang Xiao, Ruifeng He, Kaibo Hu, Gelin Song, Shengye Han, Jitao Lin, Yixuan Chen, Deju Zhang, Wuming Wang, Yating Peng, Jing Zhang, Peng Yu
The mortality and therapeutic failure in cutaneous melanoma (CM) are mainly caused by wide metastasis and chemotherapy resistance. Meanwhile, immunotherapy is considered a crucial therapy strategy for CM patients. However, the efficiency of currently available methods and biomarkers in predicting the response of immunotherapy and prognosis of CM is limited. Programmed cell death (PCD) plays a significant role in the occurrence, development, and therapy of various malignant tumors. In this research, we integrated fourteen types of PCD, multi-omics data from TCGA-SKCM and other cohorts in GEO, and clinical CM patients to develop our analysis...
April 14, 2024: Apoptosis: An International Journal on Programmed Cell Death
#40
REVIEW
Roland Madadjim, Thuy An, Juan Cui
Pancreatic cancer remains a formidable malignancy characterized by high mortality rates, primarily attributable to late-stage diagnosis and a dearth of effective therapeutic interventions. The identification of reliable biomarkers holds paramount importance in enhancing early detection, prognostic evaluation, and targeted treatment modalities. Small non-coding RNAs, particularly microRNAs, have emerged as promising candidates for pancreatic cancer biomarkers in recent years. In this review, we delve into the evolving role of cellular and circulating miRNAs, including exosomal miRNAs, in the diagnosis, prognosis, and therapeutic targeting of pancreatic cancer...
March 31, 2024: International Journal of Molecular Sciences
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