A systematic review of computational approaches to understand cancer biology for informed drug repurposing

Journal of Biomedical Informatics, Год журнала: 2023, Номер 142, С. 104373 - 104373

Опубликована: Апрель 27, 2023

Cancer is the second leading cause of death globally, trailing only heart disease. In United States alone, 1.9 million new cancer cases and 609,360 deaths were recorded for 2022. Unfortunately, success rate drug development remains less than 10%, making disease particularly challenging. This low largely attributed to complex poorly understood nature etiology. Therefore, it critical find alternative approaches understanding biology developing effective treatments. One such approach repurposing, which offers a shorter timeline lower costs while increasing likelihood success. this review, we provide comprehensive analysis computational biology, including systems multi-omics, pathway analysis. Additionally, examine use these methods repurposing in cancer, databases tools that are used research. Finally, present case studies discussing their limitations offering recommendations future research area.

Язык: Английский

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A systematic review of biologically-informed deep learning models for cancer: fundamental trends for encoding and interpreting oncology data

BMC Bioinformatics, Год журнала: 2023, Номер 24(1)

Опубликована: Май 15, 2023

There is an increasing interest in the use of Deep Learning (DL) based methods as a supporting analytical framework oncology. However, most direct applications DL will deliver models with limited transparency and explainability, which constrain their deployment biomedical settings.

Язык: Английский

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The Role of Selected Adipocytokines in Ovarian Cancer and Endometrial Cancer

Cells, Год журнала: 2023, Номер 12(8), С. 1118 - 1118

Опубликована: Апрель 9, 2023

Due to their multidirectional influence, adipocytokines are currently the subject of numerous intensive studies. Significant impact applies many processes, both physiological and pathological. Moreover, role in carcinogenesis seems particularly interesting not fully understood. For this reason, ongoing research focuses on these compounds network interactions tumor microenvironment. Particular attention should be drawn cancers that remain challenging for modern gynecological oncology—ovarian endometrial cancer. This paper presents selected adipocytokines, including leptin, adiponectin, visfatin, resistin, apelin, chemerin, omentin vaspin cancer, with a particular focus ovarian potential clinical relevance.

Язык: Английский

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Biomarkers for Early Cancer Detection: A Landscape View of Recent Advancements, Spotlighting Pancreatic and Liver Cancers

ACS Pharmacology & Translational Science, Год журнала: 2024, Номер 7(3), С. 586 - 613

Опубликована: Фев. 14, 2024

Cancer is one of the leading causes death worldwide. Early cancer detection critical because it can significantly improve treatment outcomes, thus saving lives, reducing suffering, and lessening psychological economic burdens. biomarkers provide varied information about cancer, from early malignancy to decisions on subsequent monitoring. A large variety molecular, histologic, radiographic, or physiological entities features are among common types biomarkers. Sizeable recent methodological progress insights have promoted significant developments in field Here we an overview advances knowledge related biomolecules cellular used for detection. We examine data CAS Content Collection, largest human-curated collection published scientific information, as well biomarker datasets at Excelra, analyze publication landscape research. also discuss evolution key concepts development pipelines, with a particular focus pancreatic liver cancers, which known be remarkably difficult detect particularly high morbidity mortality. The objective paper broad evolving current outline challenges evaluate growth opportunities, order further efforts solving problems that remain. merit this review stems extensive, wide-ranging coverage most up-to-date allowing unique, unmatched breadth analysis in-depth insights.

Язык: Английский

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Folate-targeted nanoparticles for glutamine metabolism inhibition enhance anti-tumor immunity and suppress tumor growth in ovarian cancer

Journal of Controlled Release, Год журнала: 2025, Номер 379, С. 89 - 104

Опубликована: Янв. 8, 2025

Язык: Английский

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5-Hydroxymethylcytosine modifications in circulating cell-free DNA: frontiers of cancer detection, monitoring, and prognostic evaluation

Biomarker Research, Год журнала: 2025, Номер 13(1)

Опубликована: Март 7, 2025

Abstract Developing accurate, clinically convenient, and non-invasive methods for early cancer detection, monitoring, prognosis assessment is essential improving patient survival rates, enhancing quality of life, reducing the socioeconomic burden associated with cancer. This goal critical in precision oncology. Genetic epigenetic alterations circulating cell-free DNA (cfDNA) have emerged as transformative tools advancing outcomes. Among these, 5-hydroxymethylcytosine (5hmC) modifications cfDNA stand out promising markers, offering insights into initiation, progression, metastasis, across various types, such lung cancer, colorectal hepatocellular carcinoma. review comprehensively explores biology sequencing methodologies 5hmC, emphasizing their potential screening, diagnosis, treatment prognostic assessment. It highlights recent advancements cfDNA-derived 5hmC signatures’ applications, addressing strengths limitations context clinical translation. Furthermore, this outlines key challenges future directions integrating routine practice, facilitating personalized management.

Язык: Английский

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Ameliorating microalgal OMEGA production using omics platforms

Trends in Plant Science, Год журнала: 2024, Номер 29(7), С. 799 - 813

Опубликована: Фев. 12, 2024

Over the past decade, focus on omega (ω)-3 fatty acids from microalgae has intensified due to their diverse health benefits. Bioprocess optimization notably increased ω-3 acid yields, yet understanding of genetic architecture and metabolic pathways high-yielding strains remains limited. Leveraging genomics, transcriptomics, proteomics, metabolomics tools can provide vital system-level insights into native acid-producing microalgae, further boosting production. In this review, we explore 'omics' studies uncovering alternative for synthesis genome-wide regulation in response cultivation parameters. We also emphasize potential targets fine-tune order enhance yield. Despite progress, an integrated omics platform is essential overcome current bottlenecks optimizing process production advancing crucial field.

Язык: Английский

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Knockdown of CENPM activates cGAS-STING pathway to inhibit ovarian cancer by promoting pyroptosis

BMC Cancer, Год журнала: 2024, Номер 24(1)

Опубликована: Май 1, 2024

Abstract Objective We aimed to screen novel gene signatures for ovarian cancer (OC) and explore the role of biomarkers in OC via regulating pyroptosis using bioinformatics analysis. Methods Differentially expressed genes (DEGs) were screened from GSE12470 GSE16709 datasets. Hub determined protein–protein interaction networks after The Centromeric protein M (CENPM) was assessed by subcutaneous tumor experiment hematoxylin–eosin immunohistochemical staining. Tumor metastasis evaluated detecting epithelial-mesenchymal transition-related proteins. proliferation, migration, invasion cell counting kit transwell assay. Enzyme-linked immunosorbent assay applied measure inflammatory factors. mRNA expression detected real-time quantitative PCR western blot. Results 9 hub (KIFC1, PCLAF, CDCA5, KNTC1, MCM3, OIP5, CENPM, KIF15, ASF1B) with high prediction value OC. In SKOV3 A2780 cells, levels significantly up-regulated, compared normal cells. CENPM selected as a key gene. Knockdown suppressed Subcutaneous revealed that knockdown growth metastasis. Additionally, promoted cells xenograft tumors knockdown. Furthermore, activated cGAS-STING pathway inhibitor reversed inhibitory effect on viability, Conclusion biomarker OC, inhibited progression promoting activating pathway.

Язык: Английский

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Multi‑omics identification of a novel signature for serous ovarian carcinoma in the context of 3P medicine and based on twelve programmed cell death patterns: a multi-cohort machine learning study

Molecular Medicine, Год журнала: 2025, Номер 31(1)

Опубликована: Янв. 8, 2025

Abstract Background Predictive, preventive, and personalized medicine (PPPM/3PM) is a strategy aimed at improving the prognosis of cancer, programmed cell death (PCD) increasingly recognized as potential target in cancer therapy prognosis. However, PCD-based predictive model for serous ovarian carcinoma (SOC) lacking. In present study, we to establish index (CDI)–based using PCD-related genes. Methods We included 1254 genes from 12 PCD patterns our analysis. Differentially expressed (DEGs) Cancer Genome Atlas (TCGA) Genotype-Tissue Expression (GTEx) were screened. Subsequently, 14 PCD-gene-based CDI model. Genomics, single-cell transcriptomes, bulk spatial clinical information TCGA-OV, GSE26193, GSE63885, GSE140082 collected analyzed verify prediction Results The was an independent prognostic risk factor patients with SOC. Patients SOC high had lower survival rates poorer prognoses than those low CDI. Specific parameters combined nomogram that accurately assessed patient survival. used PCD-genes observe differences between groups. results showed immunosuppression hardly benefited immunotherapy; therefore, trametinib_1372 BMS-754807 may be therapeutic agents these patients. Conclusions CDI-based model, which established genes, predicted tumor microenvironment, immunotherapy response, drug sensitivity Thus this help improve diagnostic efficacy PPPM.

Язык: Английский

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Clinical Peptidomics: Advances in Instrumentation, Analyses, and Applications

BME Frontiers, Год журнала: 2023, Номер 4

Опубликована: Янв. 1, 2023

Extensive effort has been devoted to the discovery, development, and validation of biomarkers for early disease diagnosis prognosis as well rapid evaluation response therapeutic interventions. Genomic transcriptomic profiling are well-established means identify disease-associated biomarkers. However, analysis peptidomes can also novel peptide or signatures that provide sensitive specific diagnostic prognostic information malignant, chronic, infectious diseases. Growing evidence suggests peptidomic changes in liquid biopsies may more effectively detect pathophysiology than other molecular methods. Knowledge gained from peptide-based diagnostic, therapeutic, imaging approaches led promising new theranostic applications increase their bioavailability target tissues at reduced doses decrease side effects improve treatment responses. despite major advances, multiple factors still affect utility data. This review summarizes several remaining challenges biomarker discovery use diagnostics, with a focus on technological advances detection, identification, monitoring personalized medicine.

Язык: Английский

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