Integrating Machine Learning in Metabolomics: A Path to Enhanced Diagnostics and Data Interpretation.

Metabolomics, leveraging techniques like NMR and MS, is crucial for understanding biochemical processes in pathophysiological states. This field, however, faces challenges in metabolite sensitivity, data complexity, and omics data integration. Recent machine learning advancements have enhanced data analysis and disease classification in metabolomics. This study explores machine learning integration with metabolomics to improve metabolite identification, data efficiency, and diagnostic methods. Using deep learning and traditional machine learning, it presents advancements in metabolic data analysis, including novel algorithms for accurate peak identification, robust disease classification from metabolic profiles, and improved metabolite annotation. It also highlights multiomics integration, demonstrating machine learning's potential in elucidating biological phenomena and advancing disease diagnostics. This work contributes significantly to metabolomics by merging it with machine learning, offering innovative solutions to analytical challenges and setting new standards for omics data analysis.

Exploration of the effect and mechanism of Scutellaria barbata D. Don in the treatment of ovarian cancer based on network pharmacology and in vitro experimental verification.

The mortality rate of ovarian cancer is the highest among gynecological cancers, posing a serious threat to women health and life. Scutellaria barbata D. Don (SBD) can effectively treat ovarian cancer. However, its mechanism of action is unclear. The aim of this study was to elucidate the mechanism of SBD in the treatment of ovarian cancer using network pharmacology, and to verify the experimental results using human ovarian cancer SKOV3 cells. The Herb and Disease Gene databases were searched to identify common targets of SBD and ovarian cancer. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, and Protein-Protein Interaction (PPI) network analyses were performed to identify the potential molecular mechanisms behind SBD. Finally, the molecular docking and main possible pathways were verified by experimental studies. Cell proliferation, the mRNA expression level of key genes and signaling pathway were all investigated and evaluated in vitro. A total of 29 bioactive ingredients and 137 common targets in SBD were found to inhibit ovarian cancer development. The active ingredients identified include quercetin, luteolin, and wogonin. Analysis of the PPI network showed that AKT1, VEGFA, JUN, TNF, and Caspase-3 shared centrality among all target genes. The results of the KEGG pathway analysis indicated that the cancer pathway, PI3K-Akt signaling pathway, and MAPK signaling pathways mediated the effects of SBD against ovarian cancer progression. Cell experiments showed that quercetin, luteolin, and wogonin inhibited the proliferation and clone formation of SKOV3 cells and regulated mRNA expression of 5 key genes by inhibiting PI3K/Akt signaling pathway. Our results demonstrate that SBD exerted anti-ovarian cancer effects through its key components quercetin, luteolin and wogonin. Mechanistically, its anti-cancer effects were mediated by inhibition of the PI3K/Akt signaling pathways. Therefore, SBD might be a candidate drug for ovarian cancer treatment.

DCLK1 and tuft cells: Immune-related functions and implications for cancer immunotherapy.

DCLK1, a tuft cell marker, is widely expressed in various tumors. Its high expression levels are closely linked to malignant tumor progression, making it a potential tumor-related marker. Recent studies have shed light on the critical roles of DCLK1 and tuft cells in the immune response and the maintenance of epithelial homeostasis, as well as targeted immune escape mechanisms in the tumor microenvironment. This review aims to comprehensively examine the current understanding of immune-related functions mediated by DCLK1 and tuft cells in epithelial tissues, including the roles of relevant cells and important factors involved. Additionally, this review will discuss recent advances in anti-tumor immunity mediated by DCLK1/tuft cells and their potential as immunotherapeutic targets. Furthermore, we will consider the potential impact of DCLK1 targeted therapy in cancer immunotherapy, particularly DCLK1 kinase inhibitors as potential therapeutic drugs in anti-tumor immunity, providing a new perspective and reference for future research.

Clinicopathological analysis of primary thyroid non-Hodgkin lymphoma: a single-center study.

Background: Primary thyroid lymphoma (PTL) is very rare. The aim of this study was to describe the clinical characteristics, pathological features, and survival outcomes of primary thyroid non-Hodgkin lymphoma, including the diagnostic value of clonal immunoglobulin (Ig) gene rearrangements in diagnosing mucosa-associated lymphoid tissue (MALT) lymphoma of the thyroid gland with co-existing Hashimoto thyroiditis (HT). Methods: Paraffin-embedded tissues of patients diagnosed in our institute with PTL between 2007 and 2021 were collected. Clinicopathological features and follow-up data were retrospectively analyzed. Analysis of clonal Ig gene rearrangements were performed in patients with suspected PTL. Results: Of the 22 patients included in our study, 17 were female. The median age at diagnosis was 65.5 years (range, 44-80 years). We detected 11 cases of diffuse large B-cell lymphoma (DLBCL), 10 cases of MALT lymphoma, and 1 case of T-cell lymphoma. A total of 18 patients (81.8%) had early stage (I/II) disease. B-cell lymphoma showed diffuse positivity for CD20 but negative markers for thyroid-origin cells. Double-hit and triple-hit lymphomas were not found in the 8 DLBCL cases, and 2 cases of HT with lymphoid tissue dysplasia were diagnosed with MALT lymphoma with gene rearrangement testing. The median follow-up time was 47 months (range, 4-160 months), and the overall survival was 80% for MALT lymphoma (8 of 10), 72.7% for DLBCL lymphoma (8 of 11), and 100% for T-cell lymphoma (1 of 1). There was no significant difference between the groups. Conclusions: PTL mostly affects middle-aged and older adult females with HT, and its main histological type is non-Hodgkin B-cell lymphoma. For patients with HT along with a histologically benign lymphoepithelial lesion, the identification of clonal Ig gene rearrangements is important for differential diagnosis. The prognosis between DLBCL and MALT is not statistically significant.

Marine-Derived Stichloroside C2 Inhibits Epithelial-Mesenchymal Transition and Induces Apoptosis through the Mitogen-Activated Protein Kinase Signalling Pathway in Triple-Negative Breast Cancer Cells.

Background: Triterpenoid saponins from sea cucumbers exhibit significant antitumour, antifungal, and antibacterial activities. However, the associated molecular mechanisms have yet to be elucidated. In this study, we screened and explored the antitumour activity and underlying mechanisms of triterpenoid saponins isolated from Thelenota ananas. Methods: We isolated and purified sea cucumber saponins, determined their chemical structures, and confirmed their function in vitro. We also screened and explored the antitumour activity and underlying mechanisms of triterpenoid saponins isolated from Thelenota ananas. Results: Four saponins were discovered from sea cucumber Thelenota ananas collected from the South China Sea. We found that stichloroside C2 (STC2) inhibited the proliferation and clonogenesis of the human triple-negative breast cancer (TNBC) cell line MDA-MB-231 and mouse TNBC cell line 4 T1 in a dose-dependent manner and induced apoptosis and cycle arrest in these two TNBC cell lines. STC2 induced DNA damage in two TNBC cell lines and significantly increased the protein expression level of the DNA double-strand break marker γ-H2AX. STC2 downregulated the protein expression levels of phosphorylated cyclin-dependent kinase 1 (CDK1), cyclin B1, CDK2, and cyclin A2 in MDA-MB-231 and 4 T1 cells. STC2 upregulated Bax and cleaved PARP protein expression in two types of breast cancer cells. In addition, STC2 promoted E-cadherin expression; inhibited vimentin expression; upregulated the phosphorylation levels of the mitogen-activated protein kinase (MAPK) signalling pathway-related proteins p38, JNK, and ERK1/2; and downregulated Akt phosphorylation. Conclusions: STC2 exerts anti-TNBC activity, inhibits epithelial-mesenchymal transition (EMT), and induces apoptosis by regulating the cell cycle, EMT-related proteins, and MAPK signalling pathway.

CO2 Laser Moxibustion for Knee Osteoarthritis: Study Protocol for A Multicenter, Double-blind, Randomized Controlled Trial.

BACKGROUND: Knee osteoarthritis (OA) is a major cause of disability among the older adults. Few treatments are safe and effective. Moxibustion is commonly used in treating knee OA in Chinese medicine (CM). CO2 Laser moxibustion device is a substitute for traditional moxibustion, which mimics the effects of traditional moxibustion. More data are needed to support its application in knee OA. OBJECTIVE: ObjectiveThe trial aims to assess the effect and safety of CO2 laser moxibustion in patients with knee osteoarthritis compared with a sham control. METHODS: This is a protocol for a multicenter, randomized, double-blind, placebo-controlled trial. A total of 392 participants were recruited and assigned to the CO2 laser moxibustion group and sham laser moxibustion group with a 1:1 ratio at 6 outpatient clinics in Shanghai, China. Participants in both groups received treatment at the affected knee(s) at the acupuncture point Dubi (ST 35) and an Ashi point. There were 3 sessions per week for 4 weeks, and an additional 20-week follow-up. Primary outcomes were changes in the Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC) pain scores at week 4. Secondary outcomes were WOMAC function score, stiffness score and overall score, VAS pain, Short-Form heath survey (SF-36), and patients' global assessment. The serum levels of cytokines involved in progress of knee OA were explored. Safety was assessed during the whole trial. Masking effectiveness was assessed by both participants and treatment providers.This is a protocol for a multicenter, randomized, double-blind, placebo-controlled trial. A total of 392 participants were recruited and assigned to the CO2 laser moxibustion group and sham laser moxibustion group with a 1:1 ratio at 6 outpatient clinics in Shanghai, China. Participants in both groups received treatment at the affected knee(s) at the acupuncture point Dubi (ST 35) and an Ashi point. There were 3 sessions per week for 4 weeks, and an additional 20-week follow-up. Primary outcomes were changes in the Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC) pain scores at week 4. Secondary outcomes were WOMAC function score, stiffness score and overall score, VAS pain, Short-Form heath survey (SF-36), and patients' global assessment. The serum levels of cytokines involved in progress of knee OA were explored. Safety was assessed during the whole trial. Masking effectiveness was assessed by both participants and treatment providers. DISCUSSION: CO2 laser moxibustion device, designed as a substitute for CM moxibustion, is easy to use and control with no choking smoke and smell, and is a plausible method for double-blind research. This study would provide rigorous evidence for the effect and safety of CO2 laser moxibustion in treating knee OA (Trial registration No.: ISRCTN15030019).

The Effect of Triptolide-Loaded Exosomes on the Proliferation and Apoptosis of Human Ovarian Cancer SKOV3 Cells.

Triptolide has been proven to possess anticancer efficacy; however, its application in the clinical practice was limited by poor water solubility, hepatotoxicity, and nephrotoxicity. In this study, a triptolide-loaded exosomes delivery system (TP-Exos) was constructed and its effects on the proliferation and apoptosis of SKOV3 cells in vitro and in vivo were observed. SKOV3-exosomes (SK-Exos) were collected by ultracentrifugation and ultrafiltration centrifugation. TP-Exos was constructed by sonication and ultrafiltration centrifugation. SK-Exos and TP-Exos were characterized by transmission electron microscopy, western blotting, nanoparticle-tracking analysis, and high-performance liquid chromatography. Cellular uptake of exosomes, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay, bromodeoxyuridine (BrdU) cell proliferation assay, and cell apoptosis experiment were used to study the effect of TP-Exos on ovarian cancer in vitro. Tumor-targeting study of exosomes, monitoring the tumor volume of mice, and TdT-mediated dUTP Nick-End labeling (TUNEL) assay were used to evaluate the effect of TP-Exos on ovarian cancer in vivo. The toxicity of TP-Exos in vivo was evaluated by liver and kidney function and histopathology of major organs (heart, liver, spleen, lung, kidney, and ovary). The results revealed that TP-Exos not only have the general characteristics of exosomes but also have high drug encapsulation efficiency. Besides, PKH26 labeled exosomes (PKH26-Exos) could be uptaken by SKOV3 cells, and Dir labeled exosomes (Dir-Exos) could be enriched to the tumor site of tumor bearing mice. Furthermore, the cytotoxic and apoptotic effects on SKOV3 cells of TP-Exos were weaker than those of free TP, and tumor cell proliferation inhibition and tumor growth inhibition were stronger than that of free TP. Moreover, TP-Exos have toxic effect on liver and spleen. In conclusion, the TP-Exos could be a promising strategy for ovarian cancer, but they need to be further optimized to attenuate the damage to liver and spleen.

pH Sensitive Triptolide-Loaded Liposome Calcium Phosphate Nanoparticles Exhibit Enhanced Anti-Tumor Activities Against Ovarian Cancer Without Damaging the Reproductive System.

Triptolide (TP), a diterpenoid triepoxide purified from the Chinese traditional medicine Tripterygium wilfordii Hook F (TWHF), possesses potent anti-tumor activities against several malignancies, including ovarian cancer. However, its short half-life in circulation and severe reproductive toxicity prohibit the clinical use of TP. In this study, we engineered novel nanoparticles consisting of calcium phosphate conjugated TP-loaded liposomes (TP@Lips-Ca/P), constituted of mPEGDPPE2000, to improve the circulation time, stability and biodistribution of TP. The average particles size was 134.1 nm, and the drug loading efficiency and encapsulation efficiency were 1.31 ± 0.13% and 72.31 ± 3.11% respectively. TP@Lips-Ca/P exhibits greatly enhanced anti-tumor effects on SKOV-3 ovarian cancer cells compared to TP alone. We further demonstrated that apoptosis of SKOV-3 cells induced by TP@Lips-Ca/P resulted from excessive accumulation of reactive oxygen species (ROS). ROS activates the MAPK signal pathway, leading to induction of apoptosis and inhibition of tumor growth. In addition, we found that TP@Lips-Ca/P displays significantly reduced toxicity toward the female reproductive system compared to free TP. In conclusion, TP@Lips-Ca/P nanoparticles are a promising novel chemotherapy approach for ovarian cancer.

Progesterone receptor PROGINS and +331G/A polymorphisms confer susceptibility to ovarian cancer: a meta-analysis based on 17 studies.

Progesterone and its receptor, progesterone receptor (PGR), have been widely studied for their roles in the onset and development of ovarian cancer. Although numerous epidemiological studies have focused on the association of PGR PROGINS and +331G/A polymorphisms with ovarian cancer susceptibility, presently, available results remain controversial, in part due to low sample sizes. Thus, a meta-analysis is required to evaluate this association. A literature search of PubMed, Embase, Web of Science, CNKI, and CBM databases was performed to retrieve eligible studies published before August 15, 2013. Summary odds ratios (ORs) with 95% confidence intervals (CIs) were used to evaluate the strength of this association. All analyses were done using STATA 12.0 software (Stata Corp., College Station, TX, USA). Seventeen case-control studies with a total of 6,365 cases and 9,998 controls were identified. While no statistically significant association between the PROGINS allele and ovarian cancer risk was found in an overall analysis, a stratified analysis revealed that for Caucasians, never-oral contraceptive (OC) users, and serous tumor patients, there were statistically significant ORs for ovarian cancer risk associated with the mutated PROGINS allele. No significant association, however, between the +331G/A polymorphism and ovarian cancer susceptibility was observed in the overall analyses and subgroup analyses based on ethnicity and histological type. This meta-analysis provides evidence that the PROGINS allele occurs more frequently in ovarian cancer patients and especially in non-OC users and serous cancer patients, indicating that PROGINS may be a risk modifier. No significant association between the +331G/A polymorphism and ovarian cancer was found, even in stratified analyses by ethnicity and histological type. More detailed and well-designed studies are still needed to confirm the role of the PROGINS allele in ovarian cancer development.

WITHDRAWN: MicroRNA-200c and microRNA-141 as potential diagnostic and prognostic biomarkers for ovarian cancer.

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