Deep learning for digital pathology is hindered by the extremely high spatial resolution of whole-slide images (WSIs). Most studies have employed patch-based methods, which often require detailed ...annotation of image patches. This typically involves laborious free-hand contouring on WSIs. To alleviate the burden of such contouring and obtain benefits from scaling up training with numerous WSIs, we develop a method for training neural networks on entire WSIs using only slide-level diagnoses. Our method leverages the unified memory mechanism to overcome the memory constraint of compute accelerators. Experiments conducted on a data set of 9662 lung cancer WSIs reveal that the proposed method achieves areas under the receiver operating characteristic curve of 0.9594 and 0.9414 for adenocarcinoma and squamous cell carcinoma classification on the testing set, respectively. Furthermore, the method demonstrates higher classification performance than multiple-instance learning as well as strong localization results for small lesions through class activation mapping.
Fetal bovine serum (FBS) is depended upon by investigators as an indispensable supplement in cell and tissue culture systems. Due to increased demand and limited availability, the price of FBS has ...increased by greater than 300% in the past few years. In addition, there are ethical and scientific controversies about the collection and use of FBS in culture systems. In response to the shortage of FBS, many FBS alternative serum products have been developed. Although many have claimed comparable performance to FBS, their support of long-term cell growth and effects on cell phenotype have not been revealed. In this study, we examined the performances of six bovine calf serum-based FBS alternatives in six head and neck cell lines and compared them with FBS. The results indicate that some of these sera had growth promoting capabilities comparable or superior to that of FBS. Additionally, these alternative sera supported long-term (30 passages) growth of tested cells and exhibited plating efficiencies comparable to that of FBS. Cells cultured in alternative sera also exhibited comparable anchorage-independent growth and similar drug inhibition responses in FBS. Still, caution should be taken in choosing suitable sera given that changes in cell morphology and variations in chemotactic responses were noted for cells maintained in certain sera. These FBS alternatives are more readily available, cost less, and are associated with less ethical concerns, thus making them attractive alternatives to FBS in cell culture systems.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Plants may affect the performance of neighboring plants either positively or negatively through interspecific and intraspecific interactions. Productivity of mixed-species systems is ultimately the ...net result of positive and negative interactions among the component species. Despite increasing knowledge of positive interactions occurring in mixed-species tree systems, relatively little is known about the mechanisms underlying such interactions. Based on data from 25-year-old experimental stands in situ and a series of controlled experiments, we test the hypothesis that a broadleaf, non-N fixing species, Michelia macclurei, facilitates the performance of an autotoxic conifer Chinese fir (Cunninghamia lanceolata) through belowground chemical interactions. Chinese fir roots released the allelochemical cyclic dipeptide (6-hydroxy-1,3-dimethyl-8-nonadecyl-1,4-diazocane-2,5-diketone) into the soil environment, resulting in self-growth inhibition, and deterioration of soil microorganisms that improve P availability. However, when grown with M. macclurei the growth of Chinese fir was consistently enhanced. In particular, Chinese fir enhanced root growth and distribution in deep soil layers. When compared with monocultures of Chinese fir, the presence of M. macclurei reduced release and increased degradation of cyclic dipeptide in the soil, resulting in a shift from selfinhibition to chemical facilitation. This association also improved the soil microbial community by increasing arbuscular mycorrhizal fungi, and induced the production of Chinese fir roots. We conclude that interspecific interactions are less negative than intraspecific ones between non-N fixing broadleaf and autotoxic conifer species. The impacts are generated by reducing allelochemical levels, enhancing belowground mutualisms, improving soil properties, and changing root distributions as well as the net effects of all the processes within the soil. In particular, allelochemical context alters the consequences of the belowground ecological interactions with a novel mechanism: reduction of self-inhibition through reduced release and increased degradation of an autotoxic compound in the mixed-species plantations. Such a mechanism would be useful in reforestation programs undertaken to rehabilitate forest plantations that suffer from problems associated with autotoxicity.
The globo-series glycosphingolipids (GSLs) SSEA3, SSEA4, and Globo-H specifically expressed on cancer cells are found to correlate with tumor progression and metastasis, but the functional roles of ...these GSLs and the key enzyme β1,3-galactosyltransferase V (β3GalT5) that converts Gb4 to SSEA3 remain largely unclear. Here we show that the expression of β3GalT5 significantly correlates with tumor progression and poor survival in patients, and the globoseries GSLs in breast cancer cells form a complex in membrane lipid raft with caveolin-1 (CAV1) and focal adhesion kinase (FAK) which then interact with AKT and receptor-interacting protein kinase (RIP), respectively. Knockdown of β3GalT5 disrupts the complex and induces apoptosis through dissociation of RIP from the complex to interact with the Fas death domain (FADD) and trigger the Fas-dependent pathway. This finding provides a link between SSEA3/SSEA4/Globo-H and the FAK/CAV1/AKT/RIP complex in tumor progression and apoptosis and suggests a direction for the treatment of breast cancer, as demonstrated by the combined use of antibodies against Globo-H and SSEA4.
Rab GTPase 3C (RAB3C) is a peripheral membrane protein that is involved in membrane trafficking (vesicle formation) and cell movement. Recently, researchers have noted the exocytosis of RAB proteins, ...and their dysregulation is correlated with drug resistance and the altered tumor microenvironment in tumorigenesis. However, the molecular mechanisms of exocytotic RABs in the carcinogenicity of colorectal cancer (CRC) remain unknown. Researchers have used various in silico datasets to evaluate the expression profiles of RAB family members. We confirmed that RAB3C plays a key role in CRC progression. Its overexpression promotes exocytosis and is related to the resistance to several chemotherapeutic drugs. We established a proteomic dataset based on RAB3C, and found that dystrophin is one of the proteins that is upregulated with the overexpression of RAB3C. According to our results, RAB3C‐induced dystrophin expression promotes vesicle formation and packaging. A connectivity map predicted that the cannabinoid receptor 2 (CB2) agonists reverse RAB3C‐associated drug resistance, and that these agonists have synergistic effects when combined with standard chemotherapy regimens. Moreover, we found high dystrophin expression levels in CRC patients with poor survival outcomes. A combination of the dystrophin and RAB3C expression profiles can serve as an independent prognostic factor in CRC and is associated with several clinicopathological parameters. In addition, the RAB3C–dystrophin axis is positively correlated with the phosphatidylinositol 4,5‐bisphosphate 3‐kinase catalytic subunit alpha isoform (PIK3CA) genetic alterations in CRC patients. These findings can be used to provide novel combined therapeutic options for the treatment of CRC.
The authors found that RAB3C overexpression induces dystrophin expression to promote vesicle formation and packaging for increased exocytosis, is related to drug resistance and is correlated with PIK3CA/KRAS mutation status in colon cancer. RAB3C‐based omics profiles identified inhibitors that directly interact with dystrophin and found synergy with existing chemotherapy regimens.
Follistatin‐like (FSTL) family members are associated with cancer progression. However, differences between FSTL members with identical cancer types have not been systematically investigated. Among ...the most malignant tumours worldwide, colorectal cancer (CRC) has high metastatic potential and chemoresistance, which makes it challenging to treat. A systematic examination of the relationship between the expression of FSTL family members in CRC will provide valuable information for prognosis and therapeutic development. Based on large cohort survival analyses, we determined that FSTL3 was associated with a significantly worse prognosis in CRC at the RNA and protein levels. Immunohistochemistry staining of CRC specimens revealed that FSTL3 expression levels in the cytosol were significantly associated with a poor prognosis in terms of overall and disease‐free survival. Molecular simulation analysis showed that FSTL3 participated in multiple cell motility signalling pathways via the TGF‐β1/TWIST1 axis to control CRC metastasis. The findings provide evidence of the significance of FSTL3 in the oncogenesis and metastasis of CRC. FSTL3 may be useful as a diagnostic or prognostic biomarker, and as a potential therapeutic target.
Monoamine oxidases (MAOs) including MAOA and MAOB are enzymes located on the outer membranes of mitochondria, which are responsible for catalyzing monoamine oxidation. Recently, increased level of ...MAOs were shown in several cancer types. However, possible roles of MAOs have not yet been elucidated in the progression and prognosis of colorectal carcinoma (CRC). We therefore analyzed the importance of MAOs in CRC by an in silico analysis and tissue microarrays. Several independent cohorts indicated that high expression of MAOB, but not MAOA, was correlated with a worse disease stage and poorer survival. In total, 203 colorectal adenocarcinoma cases underwent immunohistochemical staining of MAOs, and associations with clinicopathological parameters and patient outcomes were evaluated. We found that MAOB is highly expressed in CRC tissues compared to normal colorectal tissues, and its expression was significantly correlated with a higher recurrence rate and a poor prognosis. Moreover, according to the univariate and multivariate analyses, we found that MAOB could be an independent prognostic factor for overall survival and disease-free survival, and its prognostic value was better than T and N stage. Furthermore, significant positive and negative correlations of MAOB with mesenchymal-type and epithelial-type gene expressions were observed in CRC tissues. According to the highlighted characteristics of MAOB in CRC, MAOB can be used as a novel indicator to predict the progression and prognosis of CRC patients.
Adipocytes are the most abundant stromal partners in breast tissue. However, the crosstalk between breast cancer cells and adipocytes has been given less attention compared to cancer-associated ...fibroblasts. Here we find, through systematic screening, that primary mammary gland-derived adipocytes (MGDAs) promote growth of breast cancer cells that express monocarboxylate transporter 2 (MCT2) both in vitro and in vivo. We show that β-hydroxybutyrate is secreted by MGDAs and is required to enhance breast cancer cells malignancy in vitro. Consistently, β-hydroxybutyrate is sufficient to promote tumorigenesis of a mouse xenograft model of MCT2-expressing breast cancer cells. Mechanistically we observe that upon co-culturing with MGDAs or treatment with β-hydroxybutyrate, breast cancer cells expressing MCT2 increase the global histone H3K9 acetylation and upregulate several tumour-promoting genes. These results suggest that adipocytes promote malignancy of MCT2-expressing breast cancer via β-hydroxybutyrate potentially by inducing the epigenetic upregulation of tumour-promoting genes.
Background
Aldo‐keto reductase family 1 member B10 (AKR1B10) is an enzyme implicated in physiological xenobiotic detoxification and also in pathological carcinogenesis. Overexpression of AKR1B10 has ...been reported in oral squamous cell carcinoma (OSCC), but its correlation with clinical prognosis is controversial. The aim of this study was to investigate and clarify the role of AKR1B10 in OSCC carcinogenesis.
Methods
Tumor tissue specimens were surgically obtained from 107 patients with OSCC. The expression of AKR1B10 was analyzed by immunohistochemistry to explore the relationship between the level of AKR1B10 and clinicopathological features of OSCC patients. Kaplan‐Meier survival and Cox proportional hazard analysis were used to determine the prognostic value of AKR1B10 in OSCC.
Results
High expression of AKR1B10 was found to be associated with tumor size (P = 0.043), perineural invasion (P = 0.012), and recurrence (P = 0.001) in OSCC. Cox model analysis revealed that high expression of AKR1B10 is significantly associated with poor overall and disease‐free survival in OSCC patients. With the combination of clinicopathological factors in analysis, we found that the expression level of AKR1B10 was a practical indicator that could categorize OSCC patients into different risk groups. High expression of AKR1B10 was associated with a reduced survival in patients with well and moderately differentiated OSCC and even a high incidence of tumor recurrence in the patients with late‐stage (III and IV) disease.
Conclusion
We validated and expanded data on the expression of AKR1B10 in OSCC, suggesting that it is a valuable biomarker for prognostic prediction of recurrence and survival in OSCC.
Glioblastoma (GBM) is a type of brain cancer categorized as a high-grade glioma. GBM is characterized by limited treatment options, low patient survival rates, and abnormal serotonin metabolism. ...Previous studies have investigated the tumor suppressor function of aldolase C (ALDOC), a glycolytic enzyme in GBM. However, it is unclear how ALDOC regulates production of serotonin and its associated receptors, HTRs. In this study, we analyzed ALDOC mRNA levels and methylation status using sequencing data and in silico datasets. Furthermore, we investigated pathways, phenotypes, and drug effects using cell and mouse models. Our results suggest that loss of ALDOC function in GBM promotes tumor cell invasion and migration. We observed that hypermethylation, which results in loss of ALDOC expression, is associated with serotonin hypersecretion and the inhibition of PPAR-γ signaling. Using several omics datasets, we present evidence that ALDOC regulates serotonin levels and safeguards PPAR-γ against serotonin metabolism mediated by 5-HT, which leads to a reduction in PPAR-γ expression. PPAR-γ activation inhibits serotonin release by HTR and diminishes GBM tumor growth in our cellular and animal models. Importantly, research has demonstrated that PPAR-γ agonists prolong animal survival rates and increase the efficacy of temozolomide in an orthotopic brain model of GBM. The relationship and function of the ALDOC-PPAR-γ axis could serve as a potential prognostic indicator. Furthermore, PPAR-γ agonists offer a new treatment alternative for glioblastoma multiforme (GBM).
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