Nat Commun. 2025 Jan 8;16(1):498. doi: 10.1038/s41467-024-55660-6.

ABSTRACT

Tumor initiation represents the first step in tumorigenesis during which normal progenitor cells undergo cell fate transition to cancer. Capturing this process as it occurs in vivo, however, remains elusive. Here we employ spatiotemporally controlled oncogene activation and tumor suppressor inhibition together with multiomics to unveil the processes underlying oral epithelial progenitor cell reprogramming into tumor initiating cells at single cell resolution. Tumor initiating cells displayed a distinct stem-like state, defined by aberrant proliferative, hypoxic, squamous differentiation, and partial epithelial to mesenchymal invasive gene programs. YAP-mediated tumor initiating cell programs included activation of oncogenic transcriptional networks and mTOR signaling, and recruitment of myeloid cells to the invasive front contributing to tumor infiltration. Tumor initiating cell transcriptional programs are conserved in human head and neck cancer and associated with poor patient survival. These findings illuminate processes underlying cancer initiation at single cell resolution, and identify candidate targets for early cancer detection and prevention.

PMID:39779672 | DOI:10.1038/s41467-024-55660-6

Med Oncol. 2025 Jan 8;42(2):41. doi: 10.1007/s12032-024-02560-w.

ABSTRACT

CRC has the third-highest cancer incidence and death. Many human cancers, including colorectal cancer, are connected to abnormal signaling pathway gene expression. Many human malignancies include Hippo and Rap1 signaling. This research examined curcumin's therapeutic effects on colorectal cancer cell lines' Hippo and Rap1 signaling pathway genes. The role of the above signaling pathways is considered in colorectal cancer development. No research has examined curcumin's influence on key genes in these pathways; thus, this work is meant to uncover its more precise mechanism. First, the gene expression omnibus database is queried to discover GSE8671, a dataset that contains differentially expressed genes associated in CRC formation. DAVID was used to discover the corporation of these genes and signaling pathways (Hippo and Rap1), and the cancer genome atlas (TCGA) database was utilized to select genes and assess their expression and biomarker potential. MTT, apoptosis, and quantitative PCR were used to assess whether curcumin is therapeutic for colorectal cancer cell lines. An in-silico analysis identified the dysregulation of several critical genes AXIN2, MYC, TEAD4, MET, LPAR1, and ADCY9 in colorectal cancer, highlighting their involvement in the Hippo and Rap1 signaling pathways. Experimental assessments, including MTT assays, apoptosis assays, and quantitative PCR (qPCR) analysis, demonstrated that the targeted modulation of these genes effectively inhibits cancer cell proliferation. Specifically, treatment with curcumin resulted in a significant reduction in cell viability in HT-29 and HCT-116 colorectal cancer cell lines, thereby facilitating apoptotic cell death. Furthermore, curcumin administration was associated with the upregulation of LPAR1 and ADCY9 gene expression, while concurrently downregulating AXIN2, MYC, TEAD4, and MET in both cell lines. This study reveals compelling evidence of curcumin's potent anticancer properties, highlighting its transformative influence on the Hippo and Rap1 signaling pathways within colorectal cancer cells. These findings not only underscore curcumin's potential as a therapeutic agent but also pave the way for innovative strategies in the fight against colorectal cancer.

PMID:39779534 | DOI:10.1007/s12032-024-02560-w

Nucleic Acids Res. 2025 Jan 7;53(1):gkae1235. doi: 10.1093/nar/gkae1235.

ABSTRACT

Dinucleases of the DEDD superfamily, such as oligoribonuclease, Rexo2 and nanoRNase C, catalyze the essential final step of RNA degradation, the conversion of di- to mononucleotides. The active sites of these enzymes are optimized for substrates that are two nucleotides long, and do not discriminate between RNA and DNA. Here, we identified a novel DEDD subfamily, members of which function as dedicated deoxydinucleases (diDNases) that specifically hydrolyze single-stranded DNA dinucleotides in a sequence-independent manner. Crystal structures of enzyme-substrate complexes reveal that specificity for DNA stems from a combination of conserved structural elements that exclude diribonucleotides as substrates. Consistently, diDNases fail to complement the loss of enzymes that act on diribonucleotides, indicating that these two groups of enzymes support distinct cellular functions. The genes encoding diDNases are found predominantly in genomic islands of Actinomycetes and Clostridia, which, together with their association with phage-defense systems, suggest potential roles in bacterial immunity.

PMID:39778863 | DOI:10.1093/nar/gkae1235

Planta Med. 2025 Jan 8. doi: 10.1055/a-2512-8928. Online ahead of print.

ABSTRACT

In recent years, the incidence of neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, Huntington's disease, and amyotrophic lateral sclerosis, has shown a steadily rising trend, which has posed a major challenge to the global public health. Traditional Chinese Medicine (TCM), with its multi-component and multi-target characteristics, offers a promising approach for the treatment of neurodegenerative diseases. However, it is difficult to comprehensively elucidate the complex mechanisms underlying TCM formulations. As an emerging systems biology approach, network pharmacology has provided a crucial tool for uncovering the multi-target mechanisms of TCM through high-throughput technologies, molecular docking, and network analysis. This paper reviews the advancements in the application of network pharmacology in treating neurodegenerative diseases with TCM, analyzes the current status of relevant databases and technological methods, discusses the limitations in the research, and proposes future directions to promote the modernization of TCM and the development of precision medicine. Keywords: Neurodegenerative diseases, Traditional Chinese Medicine, Network pharmacology, Therapeutic targets.

PMID:39778593 | DOI:10.1055/a-2512-8928

Cell Syst. 2024 Dec 31:101163. doi: 10.1016/j.cels.2024.12.004. Online ahead of print.

ABSTRACT

Deep learning is a promising strategy for modeling cis-regulatory elements. However, models trained on genomic sequences often fail to explain why the same transcription factor can activate or repress transcription in different contexts. To address this limitation, we developed an active learning approach to train models that distinguish between enhancers and silencers composed of binding sites for the photoreceptor transcription factor cone-rod homeobox (CRX). After training the model on nearly all bound CRX sites from the genome, we coupled synthetic biology with uncertainty sampling to generate additional rounds of informative training data. This allowed us to iteratively train models on data from multiple rounds of massively parallel reporter assays. The ability of the resulting models to discriminate between CRX sites with identical sequence but opposite functions establishes active learning as an effective strategy to train models of regulatory DNA. A record of this paper's transparent peer review process is included in the supplemental information.

PMID:39778579 | DOI:10.1016/j.cels.2024.12.004

PLoS Pathog. 2025 Jan 8;21(1):e1012823. doi: 10.1371/journal.ppat.1012823. Online ahead of print.

ABSTRACT

Malaria parasites must respond quickly to environmental changes, including during their transmission between mammalian and mosquito hosts. Therefore, female gametocytes proactively produce and translationally repress mRNAs that encode essential proteins that the zygote requires to establish a new infection. While the release of translational repression of individual mRNAs has been documented, the details of the global release of translational repression have not. Moreover, changes in the spatial arrangement and composition of the DOZI/CITH/ALBA complex that contribute to translational control are also not known. Therefore, we have conducted the first quantitative, comparative transcriptomics and DIA-MS proteomics of Plasmodium parasites across the host-to-vector transmission event to document the global release of translational repression. Using female gametocytes and zygotes of P. yoelii, we found that ~200 transcripts are released for translation soon after fertilization, including those encoding essential functions. Moreover, we identified that many transcripts remain repressed beyond this point. TurboID-based proximity proteomics of the DOZI/CITH/ALBA regulatory complex revealed substantial spatial and/or compositional changes across this transmission event, which are consistent with recent, paradigm-shifting models of translational control. Together, these data provide a model for the essential translational control mechanisms that promote Plasmodium's efficient transmission from mammalian host to mosquito vector.

PMID:39777415 | DOI:10.1371/journal.ppat.1012823

Synth Syst Biotechnol. 2024 Jul 30;9(4):861-870. doi: 10.1016/j.synbio.2024.07.006. eCollection 2024 Dec.

ABSTRACT

Saccharomyces cerevisiae, a widely utilized model organism, has seen continuous updates to its genome-scale metabolic model (GEM) to enhance the prediction performance for metabolic engineering and systems biology. This study presents an auxotrophy-based curation of the yeast GEM, enabling facile upgrades to yeast GEMs in future endeavors. We illustrated that the curation bolstered the predictive capability of the yeast GEM particularly in predicting auxotrophs without compromising accuracy in other simulations, and thus could be an effective manner for GEM refinement. Last, we leveraged the curated yeast GEM to systematically predict auxotrophs, thereby furnishing a valuable reference for the design of nutrient-dependent cell factories and synthetic yeast consortia.

PMID:39777162 | PMC:PMC11704421 | DOI:10.1016/j.synbio.2024.07.006

BMJ Case Rep. 2025 Jan 8;18(1):e263129. doi: 10.1136/bcr-2024-263129.

ABSTRACT

Denosumab, an anti-RANKL antibody, induces bone metabolism to a low-turnover bone status by arresting osteoclast activity. Frequent adverse events include infusion reactions, fever and hypocalcaemia but not hypophosphataemia. We report a case of severe hypophosphataemia associated with secondary hyperparathyroidism following denosumab administration in a young boy with recurrent osteosarcoma who was successfully treated with evocalcet. He developed hypocalcaemia and severe refractory hypophosphataemia after receiving denosumab for bone metastases despite calcium, cholecalciferol and phosphorus supplementation. Laboratory data revealed secondary hyperparathyroidism due to denosumab-induced hypocalcaemia as the cause of hypophosphataemia. Evocalcet contributed to the normalised parathyroid hormone and phosphorus levels, allowing the discontinuation of phosphorus supplementation. This case highlights the complexity of managing electrolyte imbalances induced by bone-modifying agents, such as denosumab, underscoring the importance of monitoring bone metabolism markers and the potential effectiveness of evocalcet in managing drug-induced secondary hyperparathyroidism and hypophosphataemia.

PMID:39778963 | DOI:10.1136/bcr-2024-263129

Adv Clin Exp Med. 2025 Jan 8. doi: 10.17219/acem/193023. Online ahead of print.

ABSTRACT

BACKGROUND: Turmeric and boswellia supplements have gained popularity for their anti-inflammatory and antioxidant properties. It is important to critically assess the safety of such supplements for prolonged use.

OBJECTIVES: To assess the safety and tolerability of turmeric-boswellia-sesame oil formulation (TBSF) in healthy human volunteers.

MATERIAL AND METHODS: Forty participants were supplemented with TBSF at a dose of 2,000 mg daily for 90 days. Safety assessments were performed at baseline, as well as on day 30, 60 and 90. Adverse events were monitored throughout the study period. Any evidence of hepatotoxicity injury or drug induced liver injury (DILI) was assessed using R value (R ratio/R factor), which is a relative pattern of liver enzymes. Additionally, Hy's law criteria, based on liver enzymes and bilirubin levels, were employed, along with an evaluation of drug-induced serious hepatotoxicity (eDISH) plot. The neutrophil-to-lymphocyte ratio (NLR) and platelet-to-lymphocyte ratio (PLR) were calculated, as these values are relevant to the safety of the intervention.

RESULTS: The study found that TBSF supplementation did not cause any adverse effects or clinically significant variations in vital signs, hematological parameters, lipid profile, liver function enzymes, and renal function markers, and all were within the normal range after 90 days of TBSF supplementation. Platelet-to-lymphocyte ratio and NLR did not change significantly and were within the normal range. All the participants when plotted were in the normal range quadrant of the eDISH plot throughout the study period. No abnormal findings were observed in R value and Hy's law criteria, indicating that TBSF does not induce any hepatotoxicity. The present study showed a normal estimated glomerular filtration rate (eGFR), blood urea nitrogen (BUN), creatinine (Cr), Cr clearance, and BUN/Cr ratio throughout the study period. There was no significant change between these values at 4 abovementioned time points.

CONCLUSIONS: The study findings suggest that TBSF is a safe supplement for regular and long-term consumption.

PMID:39778015 | DOI:10.17219/acem/193023

Aust Prescr. 2024 Dec;47(6):186-191. doi: 10.18773/austprescr.2024.056.

ABSTRACT

Reporting adverse events (adverse drug reactions) associated with medicines and vaccines assists with identifying previously unrecognised side effects and other safety concerns. Reporting adverse events to the Therapeutic Goods Administration is mandatory for sponsors (pharmaceutical companies), and strongly encouraged but voluntary for healthcare professionals and consumers. Adverse events should be reported even when causality is uncertain, as reports may contribute to identification of a safety signal for new or uncommon events. Suspected adverse events associated with new medicines and vaccines (registered in the last 5 years), and medicines included in the Black Triangle Scheme, should be prioritised for reporting. For other medicines, serious adverse events and unexpected adverse events should be prioritised. The Therapeutic Goods Administration analyses adverse event reporting data and uses signal detection methods to identify and evaluate emerging safety signals, which may lead to regulatory actions and communication to address safety issues.

PMID:39777041 | PMC:PMC11703569 | DOI:10.18773/austprescr.2024.056

Front Immunol. 2024 Dec 24;15:1503316. doi: 10.3389/fimmu.2024.1503316. eCollection 2024.

ABSTRACT

BACKGROUND: The occurrence of immune-related adverse events (irAEs) seemed to be associated with better outcomes in advanced gastric cancer (AGC) patients. However, research focusing on the impact of the single-organ irAE (uni-irAE) or multi-organ irAEs (multi-irAEs) on the AGC outcome is relatively limited. In this study, we investigated individually the impact of the different irAEs on AGC survival as well as the co-occurrence patterns of multi-irAEs.

METHODS: The uni-irAE, multi-irAEs, and non-irAE were identified based on National Comprehensive Cancer Network (NCCN) guidelines. ICI efficacy for the disease control rate (DCR) and the objective response rate (ORR) was assessed based on the Response Evaluation Criteria in Solid Tumors (RECIST) Version 1.1. The association for the irAEs with progression-free survival (PFS) or overall survival (OS) was analyzed using the Kaplan-Meier method and Cox regression model. We also performed pairwise correlation analysis to identify co-occurrence patterns of multi-organ irAEs.

RESULTS: A total of 288 patients including 175 non-irAE, 73 uni-irAE, and 40 multi-irAE patients were evaluated for their association with AGC outcome. The irAEs patients displayed higher DCR (78.8% vs. 67.4%, p=0.037) when compared with those of non-irAE patients, and both uni-irAE patients (82.2% vs. 67.4%, p=0.019) and multi-irAE patients (72.5% vs. 67.4%, p=0.534) showed higher DCR than that of non-irAE patients. The multivariate analyses revealed that multi-irAEs was an independent risk factor for PFS (hazard ratio [HR] of 0.63, 95% confidence interval [CI] 0.41~0.96, p=0.031) and OS (HR 0.47, 95% CI 0.29~0.76, p=0.002), whereas the survival association for uni-irAE was not obtained. The analysis of the co-occurrence patterns for multi-irAEs revealed that the thyroid, adrenal gland, heart, skin, and lung irAEs exhibited a high risk of co-occurrence of multi-irAEs. The multivariate Cox regression analysis for organ-specific irAEs revealed that patients experiencing thyroid, adrenal gland, and skin irAEs had favorable survival outcomes compared with those without these irAEs.

CONCLUSION: Multi-irAEs and some organ-specific irAEs can be used as predictive indicators for ICI treatment efficacy in AGC patients. The thyroid, adrenal gland, heart, skin, and lung irAEs are often accompanied by multi-irAE occurrence.

PMID:39776906 | PMC:PMC11703953 | DOI:10.3389/fimmu.2024.1503316

Pharmacoepidemiol Drug Saf. 2025 Jan;34(1):e70084. doi: 10.1002/pds.70084.

ABSTRACT

BACKGROUND AND OBJECTIVES: Based on the Adverse Event Reporting System (FAERS) data from the US FDA, this study mined the adverse drug reactions of obeticholic acid (OCA) in the real world and provided reference for clinical safe drug use.

METHODS: Adverse event reports for OCA from the second quarter of 2016 to the third quarter of 2023 were extracted. The analysis for adverse reaction signal detection was conducted using reporting odds ratio, proportional reporting ratio, Bayesian confidence propagation neural network, and multi-item gamma Poisson shrinker methods.

RESULTS: A total of 5661 OCA-related adverse event reports were collected, and 105 OCA-related adverse reaction signals were obtained, involving 14 systems, among which 46 new signals were not previously mentioned in the product labeling. Severe adverse event of OCA accounted for a relatively high proportion (1445 cases, 25.53%), among which the number of hospitalization reports was the largest (1042 cases, 18.41%). The top five adverse events were pruritus, fatigue, constipation, elevated blood alkaline phosphatase, and abdominal distention. The top five adverse reaction signals intensity were abnormal blood alkaline phosphatase, abnormal ratio of albumin globulin, spider nevus, combined with abnormal bilirubin, and γ-abnormal glutamyl transferase.

DISCUSSION: Based on the pharmacovigilance study of the FAERS database, it is necessary to strengthen the clinical medication monitoring of OCA, so as to provide reference for effective pharmaceutical monitoring and rational clinical medication.

PMID:39776053 | DOI:10.1002/pds.70084

Age Ageing. 2025 Jan 6;54(1):afae276. doi: 10.1093/ageing/afae276.

ABSTRACT

INTRODUCTION: Drug-related hospital admissions (DRAs) can account for 5%-40% of total hospital admissions in older adults, with a significant proportion deemed preventable. To increase the detection of DRAs, in 2021, a revised trigger tool listing 21 frequent causes of admissions and medications at risk was proposed. This study aimed to describe DRAs using this trigger tool in a French acute geriatric ward and to assess the performance of the tool.

METHODS: This was a retrospective cohort study in a 20-bed geriatric unit including all patients hospitalised in 2023. During the first quarter of 2024, each patient's chart was adjudicated by using a two-step standardised review procedure to assess whether the admission was a DRA. The potentially at cause medications and reasons for admission were also assessed.

RESULTS: During the study period, 483 patients were hospitalised in the acute-care geriatric ward (mean age 86.7 ± 6.15 years). After adjudication, 207 admissions (43%) were identified as DRAs; 70% were considered preventable. The main causes of DRAs were falls/fractures (33%), bleeding (23%) and delirium (14%). The drugs most frequently responsible were diuretics (21%), renin-angiotensin system inhibitors (20%) and direct oral anticoagulants (15%). The overall sensitivity and specificity of the tool for detecting DRAs was 90% (95% CI 88-93) and 72% (68-76), respectively. After adjudication, the trigger tool helped detect 83% more DRAs as compared with the attending geriatrician.

CONCLUSION: DRAs are frequent in a geriatric population and often preventable. Their detection may be improved by the use of a trigger tool.

PMID:39775781 | DOI:10.1093/ageing/afae276

Theranostics. 2025 Jan 1;15(3):1122-1134. doi: 10.7150/thno.101358. eCollection 2025.

ABSTRACT

Rationale: Acute liver failure (ALF) is characterized by rapid hepatic dysfunction, primarily caused by drug-induced hepatotoxicity. Due to the lack of satisfactory treatment options, ALF remains a fatal clinical disease, representing a grand challenge in global health. Methods: For the drug repositioning to ALF of mesalamine, which is clinically approved for the treatment of inflammatory bowel disease (IBD), we propose a supramolecular prodrug nanoassembly (SPNs). Mesalamine is modified with a functional peptide of the FRRG sequence. The resulting mesalamine prodrugs form nanoassemblies solely through intermolecular interactions, ensuring high drug loading capacity and reducing the potential toxicity associated with the carrier materials of conventional nanoparticle systems. Results: In acetaminophen (APAP)-induced ALF mouse models, the SPNs predominantly accumulate in injured target tissues owing to the nanoparticles' propensity to target the liver. Subsequently, cathepsin B overexpressed in hepatocytes by drug-induced inflammation triggers the release of mesalamine from the nanoassemblies via enzymatic cleavage, resulting in remarkable therapeutic efficacy. Meanwhile, nonspecific drug release in healthy cells is inhibited due to their relatively lower cathepsin B expression, which helps prevent the exacerbation of the ALF by minimizing adverse events related to drug exposure. Conclusions: This study provides valuable insights into designing rational nanomedicine for repurposing mesalamine in ALF treatment, potentially inspiring further research to discover effective and safe therapeutic options for patients.

PMID:39776792 | PMC:PMC11700871 | DOI:10.7150/thno.101358

Fundam Clin Pharmacol. 2025 Feb;39(1):e13046. doi: 10.1111/fcp.13046.

NO ABSTRACT

PMID:39775992 | DOI:10.1111/fcp.13046

Pharm Res. 2025 Jan 7. doi: 10.1007/s11095-024-03811-1. Online ahead of print.

ABSTRACT

Metabolic alterations are commonly associated with various cancers and are recognized as contributing factors to cancer progression, invasion, and metastasis. Drug repurposing, a strategy in drug discovery, utilizes existing knowledge to recommend established drugs for new indications based on clinical data or biological evidence. This approach is considered a less risky alternative to traditional drug development. Metformin, a biguanide, is a product of Galega officinalis (French lilac) primarily prescribed for managing type 2 diabetes, is recognized for its ability to reduce hepatic glucose production and enhance insulin sensitivity, particularly in peripheral tissues such as muscle. It also improves glucose uptake and utilization while decreasing intestinal glucose absorption. Statins, first isolated from the fungus Penicillium citrinum is another class of medication mainly used to lower cholesterol levels in individuals at risk for cardiovascular diseases, work by inhibiting the enzyme 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase, which is essential for cholesterol biosynthesis in the liver. Metformin is frequently used in conjunction with statins to investigate their potential synergistic effects. Combination of metformin and simvastatin has gathered much attention in cancer research because of its potential advantages for cancer prevention and treatment. In this review, we analyze the effects of metformin and simvastatin, both individually and in combination, on key cancer hallmarks, and how this combination affects the expression of biomolecules and associated signaling pathways. We also summarize preclinical research, including clinical trials, on the efficacy, safety, and potential applications of repurposing metformin and simvastatin for cancer therapy.

PMID:39775614 | DOI:10.1007/s11095-024-03811-1

Elife. 2025 Jan 8;12:RP92491. doi: 10.7554/eLife.92491.

ABSTRACT

There are thousands of Mendelian diseases with more being discovered weekly and the majority have no approved treatments. To address this need, we require scalable approaches that are relatively inexpensive compared to traditional drug development. In the absence of a validated drug target, phenotypic screening in model organisms provides a route for identifying candidate treatments. Success requires a screenable phenotype. However, the right phenotype and assay may not be obvious for pleiotropic neuromuscular disorders. Here, we show that high-throughput imaging and quantitative phenotyping can be conducted systematically on a panel of C. elegans disease model strains. We used CRISPR genome-editing to create 25 worm models of human Mendelian diseases and phenotyped them using a single standardised assay. All but two strains were significantly different from wild-type controls in at least one feature. The observed phenotypes were diverse, but mutations of genes predicted to have related functions led to similar behavioural differences in worms. As a proof-of-concept, we performed a drug repurposing screen of an FDA-approved compound library, and identified two compounds that rescued the behavioural phenotype of a model of UNC80 deficiency. Our results show that a single assay to measure multiple phenotypes can be applied systematically to diverse Mendelian disease models. The relatively short time and low cost associated with creating and phenotyping multiple strains suggest that high-throughput worm tracking could provide a scalable approach to drug repurposing commensurate with the number of Mendelian diseases.

PMID:39773880 | DOI:10.7554/eLife.92491

BMC Bioinformatics. 2025 Jan 7;26(1):5. doi: 10.1186/s12859-024-06032-w.

ABSTRACT

The process of new drug development is complex, whereas drug-disease association (DDA) prediction aims to identify new therapeutic uses for existing medications. However, existing graph contrastive learning approaches typically rely on single-view contrastive learning, which struggle to fully capture drug-disease relationships. Subsequently, we introduce a novel multi-view contrastive learning framework, named CDPMF-DDA, which enhances the model's ability to capture drug-disease associations by incorporating diverse information representations from different views. First, we decompose the original drug-disease association matrix into drug and disease feature matrices, which are then used to reconstruct the drug-disease association network, as well as the drug-drug and disease-disease similarity networks. This process effectively reduces noise in the data, establishing a reliable foundation for the networks produced. Next, we generate multiple contrastive views from both the original and generated networks. These views effectively capture hidden feature associations, significantly enhancing the model's ability to represent complex relationships. Extensive cross-validation experiments on three standard datasets show that CDPMF-DDA achieves an average AUC of 0.9475 and an AUPR of 0.5009, outperforming existing models. Additionally, case studies on Alzheimer's disease and epilepsy further validate the model's effectiveness, demonstrating its high accuracy and robustness in drug-disease association prediction. Based on a multi-view contrastive learning framework, CDPMF-DDA is capable of integrating multi-source information and effectively capturing complex drug-disease associations, making it a powerful tool for drug repositioning and the discovery of new therapeutic strategies.

PMID:39773275 | DOI:10.1186/s12859-024-06032-w

J Transl Med. 2025 Jan 7;23(1):25. doi: 10.1186/s12967-024-06046-1.

ABSTRACT

BACKGROUND: Glioblastoma (GBM) is a rare brain cancer with an exceptionally high mortality rate, which illustrates the pressing demand for more effective therapeutic options. Despite considerable research efforts on GBM, its underlying biological mechanisms remain unclear. Furthermore, none of the United States Food and Drug Administration (FDA) approved drugs used for GBM deliver satisfactory survival improvement.

METHODS: This study presents a novel computational pipeline by utilizing gene expression data analysis for GBM for drug repurposing to address the challenges in rare disease drug development, particularly focusing on GBM. The GBM Gene Expression Profile (GGEP) was constructed with multi-omics data to identify drugs with reversal gene expression to GGEP from the Integrated Network-Based Cellular Signatures (iLINCS) database.

RESULTS: We prioritized the candidates via hierarchical clustering of their expression signatures and quantification of their reversal strength by calculating two self-defined indices based on the GGEP genes' log2 foldchange (LFC) that the drug candidates could induce. Among five prioritized candidates, in-vitro experiments validated Clofarabine and Ciclopirox as highly efficacious in selectively targeting GBM cancer cells.

CONCLUSIONS: The success of this study illustrated a promising avenue for accelerating drug development by uncovering underlying gene expression effect between drugs and diseases, which can be extended to other rare diseases and non-rare diseases.

PMID:39773231 | DOI:10.1186/s12967-024-06046-1

BMC Cancer. 2025 Jan 7;25(1):22. doi: 10.1186/s12885-024-13369-1.

ABSTRACT

BACKGROUND: Small Bowel Adenocarcinoma (SBA) is a rare gastrointestinal cancer with a limited understanding of the molecular pathology. This study aims to bridge the knowledge gap, providing a robust molecular foundation for SBA and addressing the clinical challenges inherent in treating this orphan disease. The study proposes to redefine the clinical management for SBA patients through advanced molecular profiling techniques to improve potential precision medicine.

METHODS/DESIGN: This National multicenter, observational cohort study combines retrospective and prospective analyses across Danish University Hospitals. The study enrolls patients diagnosed with SBA, retrospectively from 2009 and prospectively from 2022 onwards. Molecular profiling, including DNA, RNA, and T-cell receptor sequencing, will be conducted on SBA tissue samples. The primary outcome is to categorize SBA into consensus molecular-guided subgroups. Secondary outcomes include correlating these subgroups with clinical features, treatment responses, and patient outcomes. Machine learning algorithms will be employed for bioinformatic analyses to interpret molecular data. Ethical approval has been obtained, and patient consent will be secured for the retrospective study component.

DISCUSSION: The molecular and clinical characterization of SBA is expected to add novel insights into the heterogeneity of this rare disease. By identifying molecular subgroups, the research could enable the development of personalized treatment strategies, a paradigm shift within SBA. The study acknowledges the challenges of working with orphan diseases, including limited patient numbers and diverse clinical presentations. However, its findings will have the potential to substantially impact future clinical practices and guide targeted therapies for SBA patients.

TRIAL REGISTRATION: ClinicalTrials.gov NCT06234306.

PMID:39773121 | DOI:10.1186/s12885-024-13369-1