Applications of multi‐omics analysis in human diseases

MedComm, Год журнала: 2023, Номер 4(4)

Опубликована: Июль 31, 2023

Multi-omics usually refers to the crossover application of multiple high-throughput screening technologies represented by genomics, transcriptomics, single-cell proteomics and metabolomics, spatial so on, which play a great role in promoting study human diseases. Most current reviews focus on describing development multi-omics technologies, data integration, particular disease; however, few them provide comprehensive systematic introduction multi-omics. This review outlines existing technical categories multi-omics, cautions for experimental design, focuses integrated analysis methods especially approach machine learning deep integration corresponding tools, medical researches (e.g., cancer, neurodegenerative diseases, aging, drug target discovery) as well open-source tools databases, finally, discusses challenges future directions precision medicine. With algorithms, important disease research, also provided detailed introduction. will guidance researchers, who are just entering into research.

Язык: Английский

---

Comprehensive peripheral blood immunoprofiling reveals five immunotypes with immunotherapy response characteristics in patients with cancer

Cancer Cell, Год журнала: 2024, Номер 42(5), С. 759 - 779.e12

Опубликована: Май 1, 2024

The lack of comprehensive diagnostics and consensus analytical models for evaluating the status a patient's immune system has hindered wider adoption immunoprofiling treatment monitoring response prediction in cancer patients. To address this unmet need, we developed an platform that uses multiparameter flow cytometry to characterize cell heterogeneity peripheral blood healthy donors patients with advanced cancers. Using unsupervised clustering, identified five immunotypes unique distributions different types gene expression profiles. An independent analysis 17,800 open-source transcriptomes same approach corroborated these findings. Continuous immunotype-based signature scores were correlate systemic immunity patient responses treatments, including immunotherapy, prognostically predictively. Our findings illustrate potential utility simple test as flexible tool stratifying into therapy groups based on immunoprofiling.

Язык: Английский

---

The Circulating Biomarkers League: Combining miRNAs with Cell-Free DNAs and Proteins

International Journal of Molecular Sciences, Год журнала: 2024, Номер 25(6), С. 3403 - 3403

Опубликована: Март 17, 2024

The potential of liquid biopsy for the prognosis and diagnosis diseases is unquestionable. Within evolving landscape disease diagnostics personalized medicine, circulating microRNAs (c-miRNAs) stand out among biomarkers found in blood circulation other biological fluids due to their stability, specificity, non-invasive detection biofluids. However, complexity human limitations inherent single-marker highlight need a more integrative approach. It has been recently suggested that multi-analyte approach offers advantages over single-analyte diseases. In this review, we explore combining three well-studied classes biofluids—miRNAs, DNAs, proteins—to enhance accuracy efficacy monitoring. Initially, provide an overview each biomarker class discuss main disadvantages highlighting superiority c-miRNAs biomarkers. Additionally, challenges future directions integrating these into clinical practice, emphasizing standardized protocols further validation studies. This integrated revolutionize precision medicine by offering insights mechanisms, facilitating early detection, guiding therapeutic strategies. collaborative power with represents promising frontier comprehensive understanding management complex Nevertheless, several must be addressed before can translated practice.

Язык: Английский

---

DeepKEGG: a multi-omics data integration framework with biological insights for cancer recurrence prediction and biomarker discovery

Briefings in Bioinformatics, Год журнала: 2024, Номер 25(3)

Опубликована: Март 27, 2024

Abstract Deep learning-based multi-omics data integration methods have the capability to reveal mechanisms of cancer development, discover biomarkers and identify pathogenic targets. However, current ignore potential correlations between samples in integrating data. In addition, providing accurate biological explanations still poses significant challenges due complexity deep learning models. Therefore, there is an urgent need for a method explore provide model interpretability. Herein, we propose novel interpretable (DeepKEGG) recurrence prediction biomarker discovery. DeepKEGG, hierarchical module designed local connections neuron nodes interpretability based on relationship genes/miRNAs pathways. pathway self-attention constructed correlation different generate feature representation enhancing performance model. Lastly, attribution-based importance calculation utilized related interpretation Experimental results demonstrate that DeepKEGG outperforms other state-of-the-art 5-fold cross validation. Furthermore, case studies also indicate serves as effective tool The code available at https://github.com/lanbiolab/DeepKEGG.

Язык: Английский

---

Therapeutic targeting of obesity-induced neuroinflammation and neurodegeneration

Frontiers in Endocrinology, Год журнала: 2025, Номер 15

Опубликована: Янв. 17, 2025

Obesity is a major modifiable risk factor leading to neuroinflammation and neurodegeneration. Excessive fat storage in obesity promotes the progressive infiltration of immune cells into adipose tissue, resulting release pro-inflammatory factors such as cytokines adipokines. These inflammatory mediators circulate through bloodstream, propagating inflammation both periphery central nervous system. Gut dysbiosis, which results leaky intestinal barrier, exacerbates plays significant role linking pathogenesis neurodegeneration gut-brain/gut-brain-liver axis. Inflammatory states within brain can lead insulin resistance, mitochondrial dysfunction, autolysosomal increased oxidative stress. disruptions impair normal neuronal function subsequently cognitive decline motor deficits, similar pathologies observed neurodegenerative diseases, including Alzheimer's disease, multiple sclerosis, Parkinson's disease. Understanding underlying disease mechanisms crucial for developing therapeutic strategies address defects these metabolic pathways. In this review, we summarize provide insights different strategies, methods alter gut lifestyle changes, dietary supplementation, well pharmacological agents derived from natural sources, that target obesity-induced

Язык: Английский

---

Artificial intelligence for omics data analysis

Deleted Journal, Год журнала: 2024, Номер 1(1)

Опубликована: Май 3, 2024

Abstract Recent technological advancements have vastly improved access to high-throughput biological instrumentation, sparking an unparalleled surge in omics data generation. The implementation of artificial intelligence techniques is revolutionizing interpretation. BMC Methods Collection "Artificial for analysis" will feature novel approaches leveraging multi-omics accelerate discoveries personalized medicine, disease diagnostics, drug development, and pathway elucidation.

Язык: Английский

---

Extracellular Vesicles as Delivery Vehicles for Non-Coding RNAs: Potential Biomarkers for Chronic Liver Diseases

Biomolecules, Год журнала: 2024, Номер 14(3), С. 277 - 277

Опубликована: Фев. 26, 2024

In recent years, EVs have emerged as promising vehicles for coding and non-coding RNAs (ncRNAs), which demonstrated remarkable potential biomarkers various diseases, including chronic liver diseases (CLDs). are small, membrane-bound particles released by cells, carrying an arsenal of ncRNAs, microRNAs (miRNAs), long (lncRNAs), other ncRNA species, such piRNAs, circRNAs, tsRNAs. These ncRNAs act key regulators gene expression, splicing, translation, providing a comprehensive molecular snapshot the cells origin. The non-invasive nature EV sampling, typically via blood or serum collection, makes them highly attractive candidates clinical biomarker applications. Moreover, EV-encapsulated offer unique advantages over traditional cell-free due to their enhanced stability within EVs, hence allowing detection in circulation extended periods enabling more sensitive reliable measurements. Numerous studies investigated EV-enclosed CLD. MiRNAs, particular, gained significant attention ability rapidly respond changes cellular stress inflammation, hallmarks CLD pathogenesis. Elevated levels specific miRNAs been consistently associated with subtypes, metabolic dysfunction-associated steatotic disease (MASLD), steatohepatitis (MASH), hepatitis B C. LncRNAs also transcripts involved wide range processes, regeneration, fibrosis, cancer progression. Studies shown that lncRNA expression profiles can distinguish between different valuable insights into progression therapeutic response. Promising included miR-122 (elevated MASLD fibrosis), miR-21 (increased is linked inflammation fibrosis patients), miR-192 advanced stages CLD, cirrhosis HCC), LncRNA HOTAIR MASH development), H19 (dysregulation HCC progression). present review, we focus on tools diagnosis monitoring etiologies.

Язык: Английский

---

Spatial multi-omics: deciphering technological landscape of integration of multi-omics and its applications

Journal of Hematology & Oncology, Год журнала: 2024, Номер 17(1)

Опубликована: Авг. 24, 2024

The emergence of spatial multi-omics has helped address the limitations single-cell sequencing, which often leads to loss context among cell populations. Integrated analysis genome, transcriptome, proteome, metabolome, and epigenome enhanced our understanding biology molecular basis human diseases. Moreover, this approach offers profound insights into interactions between intracellular intercellular mechanisms involved in development, physiology, pathogenesis In comprehensive review, we examine current advancements technologies, focusing on their evolution refinement over past decade, including improvements throughput resolution, modality integration, accuracy. We also discuss pivotal contributions revealing heterogeneity, constructing detailed atlases, deciphering crosstalk tumor immunology, advancing translational research cancer therapy through precise mapping.

Язык: Английский

---

Latest insights into the global epidemiological features, screening, early diagnosis and prognosis prediction of esophageal squamous cell carcinoma

World Journal of Gastroenterology, Год журнала: 2024, Номер 30(20), С. 2638 - 2656

Опубликована: Май 27, 2024

As a highly invasive carcinoma, esophageal cancer (EC) was the eighth most prevalent malignancy and sixth leading cause of cancer-related death worldwide in 2020. Esophageal squamous cell carcinoma (ESCC) is major histological subtype EC, its incidence mortality rates are decreasing globally. Due to lack specific early symptoms, ESCC patients usually diagnosed with advanced-stage disease poor prognosis, still high many countries, especially China. Therefore, enormous challenges exist management ESCC, novel strategies urgently needed further decrease ESCC. Although key molecular mechanisms underlying pathogenesis have not been fully elucidated, certain promising biomarkers being investigated facilitate clinical decision-making. With advent advancement high-throughput technologies, such as genomics, proteomics metabolomics, valuable sensitivity, specificity stability could be identified for Herein, we aimed determine epidemiological features different regions world, China, focused on associated screening, diagnosis prognosis prediction.

Язык: Английский

---

Exploring the Ancient Wisdom and Modern Relevance of Chinese Medicine: A Comprehensive Review

Pharmacological Research - Modern Chinese Medicine, Год журнала: 2024, Номер 11, С. 100448 - 100448

Опубликована: Май 21, 2024

Chinese medicine, rooted in a rich history dating back thousands of years, offers holistic approach to healthcare that has endured the test time. This comprehensive review explores ancient wisdom and modern relevance shedding light on its principles, practices, adaptability contemporary healthcare. employs multidisciplinary approach, drawing upon texts, scientific research, clinical studies elucidate core tenets medicine. A literature search was conducted various databases, including PubMed, Web Science, traditional medical identify relevant articles, books, historical documents. The synthesizes fundamental concepts such as Qi, Yin-Yang, five elements, meridian system, while examining their physiological significance context It also delves into integration Medicine mainstream systems worldwide, highlighting growing acceptance utilization treatment conditions, chronic pain, mental health disorders, complementary cancer care. discussion section synergy between medicine emphasizing potential for bridges gap Eastern Western addresses challenges opportunities integrating evidence-based importance rigorous research standardization. In conclusion, this underscores enduring showcasing landscape. advocates continued collaboration conventional systems, fostering more patient-centered By embracing alongside advancements, we can pave way healthier balanced future.

Язык: Английский

---