Systems Biology and Multi-Omics Integration: Viewpoints from the Metabolomics Research Community

Metabolites, Год журнала: 2019, Номер 9(4), С. 76 - 76

Опубликована: Апрель 18, 2019

The use of multiple omics techniques (i.e., genomics, transcriptomics, proteomics, and metabolomics) is becoming increasingly popular in all facets life science. Omics provide a more holistic molecular perspective studied biological systems compared to traditional approaches. However, due their inherent data differences, integrating platforms remains an ongoing challenge for many researchers. As metabolites represent the downstream products interactions between genes, transcripts, proteins, metabolomics, tools approaches routinely used this field could assist with integration these complex multi-omics sets. question is, how? Here we some answers (in terms methods, software databases) along variety recommendations list continuing challenges as identified during peer session on that was held at recent ‘Australian New Zealand Metabolomics Conference’ (ANZMET 2018) Auckland, (Sept. 2018). We envisage document will serve guide metabolomics researchers other members community wishing perform studies. also believe ideas may allow full promise integrated research and, ultimately, biology be realized.

Язык: Английский

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Precision Medicine and Radiogenomics in Breast Cancer: New Approaches toward Diagnosis and Treatment

Radiology, Год журнала: 2018, Номер 287(3), С. 732 - 747

Опубликована: Май 21, 2018

Precision medicine is optimized to the genotypic and phenotypic characteristics of an individual and, when present, his or her disease. It has a host targets, including genes their transcripts, proteins, metabolites. Studying precision involves systems biology approach that integrates mathematical modeling genomics, transcriptomics, proteomics, metabolomics. Moreover, must consider not only relatively static genetic codes individuals, but also dynamic heterogeneous cancers. Thus, relies on discovering identifiable targets for treatment surveillance modification, reliable, noninvasive methods identifying changes in these over time. Imaging via radiomics radiogenomics poised central role. Radiomics, which extracts large volumes quantitative data from digital images amalgamates together with clinical patient into searchable shared databases, potentiates radiogenomics, combination radiomic data. Radiogenomics may provide voxel-by-voxel information complete, tumor or, setting metastatic disease, set tumors thereby guide tailored therapy. quantify lesion characteristics, better differentiate between benign malignant entities, stratify patients according risk allowing more precise imaging screening. This report provides overview discusses specifically breast cancer. © RSNA, 2018.

Язык: Английский

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Translational Metabolomics: Current Challenges and Future Opportunities

Metabolites, Год журнала: 2019, Номер 9(6), С. 108 - 108

Опубликована: Июнь 6, 2019

Metabolomics is one of the latest omics technologies that has been applied successfully in many areas life sciences. Despite being relatively new, a plethora publications over years have exploited opportunities provided through this data and question driven approach. Most importantly, metabolomics studies produced great breakthroughs biomarker discovery, identification novel metabolites more detailed characterisation biological pathways organisms. However, translation research outcomes into clinical tests user-friendly interfaces hindered due to factors, some which outlined hereafter. This position paper summary discussion on translational undertaken during peer session Australian New Zealand Conference (ANZMET 2018) held Auckland, Zealand. Here, we discuss key including existing challenges suggested solutions, as well how expand industrial application metabolomics. In addition, share our perspective full capability can be explored.

Язык: Английский

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Current Achievements and Applications of Transcriptomics in Personalized Cancer Medicine

International Journal of Molecular Sciences, Год журнала: 2021, Номер 22(3), С. 1422 - 1422

Опубликована: Янв. 31, 2021

Over the last decades, transcriptome profiling emerged as one of most powerful approaches in oncology, providing prognostic and predictive utility for cancer management. The development novel technologies, such revolutionary next-generation sequencing, enables identification biomarkers, gene signatures, their aberrant expression affecting oncogenesis, well discovery molecular targets anticancer therapies. Transcriptomics contribute to a change holistic understanding cancer, from histopathological organic classifications, opening more personalized perspective tumor diagnostics therapy. further advancement on may allow standardization cost reduction its analysis, which will be next step transcriptomics become canon contemporary medicine.

Язык: Английский

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Navigating Challenges and Opportunities in Multi-Omics Integration for Personalized Healthcare

Biomedicines, Год журнала: 2024, Номер 12(7), С. 1496 - 1496

Опубликована: Июль 5, 2024

The field of multi-omics has witnessed unprecedented growth, converging multiple scientific disciplines and technological advances. This surge is evidenced by a more than doubling in publications within just two years (2022-2023) since its first referenced mention 2002, as indexed the National Library Medicine. emerging demonstrated capability to provide comprehensive insights into complex biological systems, representing transformative force health diagnostics therapeutic strategies. However, several challenges are evident when merging varied omics data sets methodologies, interpreting vast dimensions, streamlining longitudinal sampling analysis, addressing ethical implications managing sensitive information. review evaluates these while spotlighting pivotal milestones: development targeted methods, use artificial intelligence formulating indices, integration sophisticated

Язык: Английский

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Extracellular vesicles in nanomedicine and regenerative medicine: A review over the last decade

Bioactive Materials, Год журнала: 2024, Номер 36, С. 126 - 156

Опубликована: Март 2, 2024

Small extracellular vesicles (sEVs) are known to be secreted by a vast majority of cells. These sEVs, specifically exosomes, induce specific cell-to-cell interactions and can activate signaling pathways in recipient cells through fusion or interaction. nanovesicles possess several desirable properties, making them ideal for regenerative medicine nanomedicine applications. properties include exceptional stability, biocompatibility, wide biodistribution, minimal immunogenicity. However, the practical utilization particularly clinical settings at large scale, is hindered expensive procedures required their isolation, limited circulation lifetime, suboptimal targeting capacity. Despite these challenges, sEVs have demonstrated remarkable ability accommodate various cargoes found extensive applications biomedical sciences. To overcome limitations broaden potential applications, researchers should strive deepen understanding current loading, characterization techniques. Additionally, acquiring fundamental knowledge about origins employing state-of-the-art methodologies expand research scope. This review provides comprehensive overview exosome-based strategies diverse domains, encompassing cancer therapy, immunotherapy, biomarker Furthermore, we emphasize immense exosomes medicine.

Язык: Английский

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Reviving the Transcriptome Studies: An Insight Into the Emergence of Single-Molecule Transcriptome Sequencing

Frontiers in Genetics, Год журнала: 2019, Номер 10

Опубликована: Апрель 26, 2019

Advances in transcriptomics have provided an exceptional opportunity to study functional implications of the genetic variability. Technologies such as RNA-Seq emerged state-of-the-art techniques for transcriptome analysis that take advantage high-throughput next-generation sequencing. However, similar their predecessors, these approaches continue impose major challenges on full-length transcript structure identification, primarily due inherent limitations read length. With development single-molecule sequencing (SMS) from PacBio, a growing number studies different organisms been reported. SMS has advantageous comprehensive genome annotation including identification novel genes/isoforms, long non-coding RNAs and fusion transcripts. This approach can be used across broad spectrum species better interpret coding information genome, facilitate biological function study. We provide overview platform its diverse applications various studies, our perspective associated with studies.

Язык: Английский

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Identification of Novel MicroRNAs and Their Diagnostic and Prognostic Significance in Oral Cancer

Cancers, Год журнала: 2019, Номер 11(5), С. 610 - 610

Опубликована: Апрель 30, 2019

Background: Oral cancer is one of the most prevalent cancers worldwide. Despite that oral cavity easily accessible for clinical examinations, are often not promptly diagnosed. Furthermore, to date no effective biomarkers available cancer. Therefore, there an urgent need identify novel able improve both diagnostic and prognostic strategies. In this context, development innovative high-throughput technologies molecular epigenetics analyses has generated a huge amount data may be used identification new biomarkers. Methods: present study, GEO DataSets TCGA miRNA profiling datasets were analyzed in order miRNAs with significance. several computational approaches adopted establish functional roles these miRNAs. Results: The analysis allowed 11 potential role Additionally, eight associated patients' prognosis also identified; six predictive overall survival (OS) one, hsa-miR-let.7i-3p, tumor recurrence. Conclusion: integrated different expression allows set that, after validation, early detection cancers.

Язык: Английский

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LncRNA BCYRN1 inhibits glioma tumorigenesis by competitively binding with miR-619-5p to regulate CUEDC2 expression and the PTEN/AKT/p21 pathway

Oncogene, Год журнала: 2020, Номер 39(45), С. 6879 - 6892

Опубликована: Сен. 25, 2020

Abstract Glioma is the most common malignant tumor in central nervous system. Altered long noncoding RNAs (lncRNAs) are playing regulatory roles physiological and pathogenic processes cancer. Here, we uncovered a differentially expressed lncRNA called brain cytoplasmic RNA 1 (BCYRN1), elucidated its function molecular mechanism progression development of glioma. Three fresh tissues from glioma patients three normal craniocerebral trauma were prepared for high-throughput sequencing. Differential transcripts BCYRN1 identified by RT-qPCR samples controls. CCK-8, colony formation assays, flow cytometry, TUNEL cell migration wound-healing xenograft model established to investigate biological both vitro vivo. Various bioinformatics analysis, dual-luciferase reporter biotinylated pulldown rescue experiments conducted reveal underlying mechanisms competitive endogenous (ceRNAs). 183 lncRNAs with significant dysregulation randomly selected differential further confirmed RT-qPCR. Among them, was downregulated lncRNA, low expression positively correlated progression. Functionally, overexpression inhibited proliferation, lines, whereas depletion resulted opposite way. MiR-619-5p as direct target BCYRN1. Mechanistically, miR-619-5p specifically targeted CUE domain containing protein 2 (CUEDC2), BCYRN1/miR-619-5p suppressed tumorigenesis inactivating PTEN/AKT/p21 pathway CUEDC2-dependent manner. Overall, our data presented that reduced associated poor patient outcome functioned ceRNA inhibit sponging regulate CUEDC2 pathway. Our results indicated exerted suppressor potential might be candidate diagnosis treatment

Язык: Английский

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RNA Sequencing of the NCI-60: Integration into CellMiner and CellMiner CDB

Cancer Research, Год журнала: 2019, Номер 79(13), С. 3514 - 3524

Опубликована: Май 21, 2019

CellMiner (http://discover.nci.nih.gov/cellminer) and CellMinerCDB (https://discover.nci.nih.gov/cellminercdb/) are web-based applications for mining publicly available genomic, molecular, pharmacologic datasets of human cancer cell lines including the NCI-60, Cancer Cell Line Encyclopedia, Genomics Drug Sensitivity in Cancer, Therapeutics Response Portal, NCI/DTP small lung cancer, NCI Almanac line sets. Here, we introduce our RNA sequencing (RNA-seq) data NCI-60 their access integration with other databases. Correlation to transcript microarray expression levels identical genes across demonstrates high quality these new RNA-seq data. We provide composite isoform demonstrate diversity composition individual cancer- pharmacologically relevant genes, HRAS, PTEN, EGFR, RAD51, ALKBH2, BRCA1, ERBB2, TP53, FGFR2, CTNND1. reveal cell-specific differences overall isoforms show linkage processing splicing as well resultant alterations gene Gene-drug pairings linked by pathways or functions specific correlations compared expression, ALKBH2-benzaldehyde, AKT3-vandetanib, BCR-imatinib, CDK1 20-palbociclib, CASP1-imexon, FGFR3-pazopanib. Loss MUC1 20 amino acid variable number tandem repeats, which is used elicit immune response, presence androgen receptor AR-V4 -V7 all tissue origin types translational relevance. In summary, web applications, allowing exploration both research purposes. SIGNIFICANCE: The current study provides made accessible through an important pharmacogenomics resource field.

Язык: Английский

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