Deep learning framework for comprehensive molecular and prognostic stratifications of triple-negative breast cancer.

Triple-negative breast cancer (TNBC) is the most challenging breast cancer subtype. Molecular stratification and target therapy bring clinical benefit for TNBC patients, but it is difficult to implement comprehensive molecular testing in clinical practice. Here, using our multi-omics TNBC cohort (N = 425), a deep learning-based framework was devised and validated for comprehensive predictions of molecular features, subtypes and prognosis from pathological whole slide images. The framework first incorporated a neural network to decompose the tissue on WSIs, followed by a second one which was trained based on certain tissue types for predicting different targets. Multi-omics molecular features were analyzed including somatic mutations, copy number alterations, germline mutations, biological pathway activities, metabolomics features and immunotherapy biomarkers. It was shown that the molecular features with therapeutic implications can be predicted including the somatic PIK3CA mutation, germline BRCA2 mutation and PD-L1 protein expression (area under the curve [AUC]: 0.78, 0.79 and 0.74 respectively). The molecular subtypes of TNBC can be identified (AUC: 0.84, 0.85, 0.93 and 0.73 for the basal-like immune-suppressed, immunomodulatory, luminal androgen receptor, and mesenchymal-like subtypes respectively) and their distinctive morphological patterns were revealed, which provided novel insights into the heterogeneity of TNBC. A neural network integrating image features and clinical covariates stratified patients into groups with different survival outcomes (log-rank P < 0.001). Our prediction framework and neural network models were externally validated on the TNBC cases from TCGA (N = 143) and appeared robust to the changes in patient population. For potential clinical translation, we built a novel online platform, where we modularized and deployed our framework along with the validated models. It can realize real-time one-stop prediction for new cases. In summary, using only pathological WSIs, our proposed framework can enable comprehensive stratifications of TNBC patients and provide valuable information for therapeutic decision-making. It had the potential to be clinically implemented and promote the personalized management of TNBC.

miR-29a-5p rescues depressive-like behaviors in a CUMS-induced mouse model by facilitating microglia M2-polarization in the prefrontal cortex via TMEM33 suppression.

BACKGROUND: Depression accounts for a high proportion of neuropsychiatric disorders and is associated with abnormal states of neurons in specific brain regions. Microglia play a pivotal role in the inflammatory state during depression development; however, the exact mechanism underlying chronic mood states remains unknown. Thus, the present study aimed to determine whether microRNAs (miRNAs) alleviate stress-induced depression-like behavior in mice by regulating the expression levels of their target genes, explore the role of neuroinflammation induced by microglial activation in the pathogenesis and progression of depression, and determine whether the role of the miR-29a-5p/transmembrane protein 33 (TMEM33) axis. METHODS: In this study, chronic unpredictable mild stress (CUMS) mouse depression model, various behavioral tests, western blotting, dual-luciferase reporter assay, enzyme-linked immunosorbent assay, real-time quantitative reverse transcription PCR, immunofluorescence and lentivirus-mediated gene transfer were used. RESULTS: After exposure to the CUMS paradigm, miR-29a-5p was significantly down-regulated. This downregulation subsequently promoted the polarization of microglia M1 by upregulating the expression of TMEM33, resulting in enhanced inflammatory chemokines affecting neurons. Conversely, the upregulation of miR-29a-5p within the prefrontal cortex (PFC) suppressed TMEM33 expression, facilitated microglia M2-polarization, and ameliorated depressive-like behavior. LIMITATIONS: Only rodent models of depression were used, and human samples were not included. CONCLUSIONS: The results of this study suggest that miR-29a-5p deficits within the PFC mediate microglial anomalies and contribute to depressive-like behaviors. miR-29a-5p and TMEM33 may, therefore, serve as potential therapeutic targets for the treatment of depression.

Repurposing fluphenazine as an autophagy modulator for treating liver cancer.

Hepatocellular carcinoma (HCC) is a common malignant tumor of the digestive system with a low early diagnosis rate. Owing to the side effects, tolerance, and patient contraindications of existing therapies, effective drug treatments for HCC remain a major clinical challenge. However, using approved or investigational drugs not initially intended for cancer therapy is a promising strategy for resolving this problem because their safety have been tested in clinic. Therefore, this study evaluated differentially expressed genes between liver cancer and normal tissues in a cohort of patients with HCC from The Cancer Genome Atlas and applied them to query a connectivity map to identify candidate anti-HCC drugs. As a result, fluphenazine was identified as a candidate for anti-HCC therapy in vitro and in vivo. Fluphenazine suppressed HCC cell proliferation and migration and induced cell cycle arrest and apoptosis, possibly owing to disrupted lysosomal function, blocking autophagy flux. Additionally, in vivo studies demonstrated that fluphenazine suppresses HCC subcutaneous xenografts growth without causing severe side effects. Strikingly, fluphenazine could be used as an analgesic to alleviate oxaliplatin-induced pain as well as pain related anxiety-like behavior. Therefore, fluphenazine could be a novel liver cancer treatment candidate.

Single-cell morphological and topological atlas reveals the ecosystem diversity of human breast cancer.

Digital pathology allows computerized analysis of tumor ecosystem using whole slide images (WSIs). Here, we present single-cell morphological and topological profiling (sc-MTOP) to characterize tumor ecosystem by extracting the features of nuclear morphology and intercellular spatial relationship for individual cells. We construct a single-cell atlas comprising 410 million cells from 637 breast cancer WSIs and dissect the phenotypic diversity within tumor, inflammatory and stroma cells respectively. Spatially-resolved analysis identifies recurrent micro-ecological modules representing locoregional multicellular structures and reveals four breast cancer ecotypes correlating with distinct molecular features and patient prognosis. Further analysis with multiomics data uncovers clinically relevant ecosystem features. High abundance of locally-aggregated inflammatory cells indicates immune-activated tumor microenvironment and favorable immunotherapy response in triple-negative breast cancers. Morphological intratumor heterogeneity of tumor nuclei correlates with cell cycle pathway activation and CDK inhibitors responsiveness in hormone receptor-positive cases. sc-MTOP enables using WSIs to characterize tumor ecosystems at the single-cell level.

Identification of CCDC115 as an adverse prognostic biomarker in liver cancer based on bioinformatics and experimental analyses.

Liver hepatocellular carcinoma (LIHC) is a major malignant tumor of the digestive system with a high incidence rate and poor early diagnosis. Coiled-coil domain-containing protein 115 (CCDC115), an accessory component of vacuolar-ATPase with dramatically abnormal expression, is associated with survival outcomes of cancer patients. However, the role of CCDC115 in LIHC remains unclear. In this study, we aimed to determine the functional role of CCDC115 in LIHC by examining CCDC115 expression, and its influence on LIHC prognosis. Through extensive statistical analyses, using LIHC patient databases, we observed that CCDC115 expression significantly increased in tumor tissues of LIHC patients. In addition, CCDC115 expression correlated with the poor prognosis. Additionally, CCDC115 was found to be involved in several cancer-related pathways, specifically the PI3K-Akt pathway. The expression of CCDC115 was positively correlated with human leukocyte antigen molecules as well as with immune checkpoint molecules in LIHC patients. We performed in vitro experiments and confirmed that the expression of CCDC115 significantly affects the proliferation potential, metastasis and sorafenib resistance of liver cancer cells, as well as some key protein expression in PI3K-Akt pathway. These results indicate that CCDC115 could serve as a diagnostic and prognostic biomarker of LIHC, and targeting CCDC115 may provide a potential strategy to enhance the efficacy of liver cancer therapy.

Caffeine ameliorates the metabolic syndrome in diet-induced obese mice through regulating the gut microbiota and serum metabolism.

OBJECTIVE: Obesity is associated with gut microbiota disorders, which has been related to developing metabolic syndromes. The research aims to investigate the effects of caffeine treatment on insulin resistance, intestinal microbiota composition and serum metabolomic changes in high-fat diet (HFD)-induced obesity mice. METHODS: Eight-week-old male C57BL/6 J mice were fed a normal chow diet (NCD) or HFD with or without different concentrations of caffeine. After 12 weeks of treatment, body weight, insulin resistance, serum lipid profiles, gut microbiota and serum metabolomic profiles were assessed. RESULTS: Caffeine intervention improved the metabolic syndrome in HFD-fed mice, such as serum lipid disorders and insulin resistance. 16S rRNA Sequencing analysis revealed that caffeine increased the relative abundance of Dubosiella, Bifidobacterium and Desulfovibrio and decreased that of Bacteroides, Lactobacillus and Lactococcus to reverse HFD-fed obesity in mice. Additionally, Caffeine Supplementation also altered serum metabolomics, mainly focusing on lipid metabolism, bile acid metabolism and energy metabolism. Caffeine increased its metabolite 1,7-Dimethylxanthine, which was positively correlated with Dubosiella. CONCLUSIONS: Caffeine exerts a beneficial effect on insulin resistance in HFD-mice, and the underlying mechanism may be partly related to altered gut microbiota and bile acid metabolism.

Thrombocytopenia in 737 adult intensive care unit patients: A real-world study of associated factors, drugs, platelet transfusion, and clinical outcome.

OBJECTIVE: We aimed to identify and represent factors associated with thrombocytopenia in intensive care unit, especially the pathogens and drugs related to severe and extremely thrombocytopenia. Then, we aim to compare the mortality of platelet transfusion and non-transfusion in patients with different degrees of thrombocytopenia. METHODS: We identified all thrombocytopenic patients in intensive care unit by using platelet-specific values and then extracted electronic health records from our Hospital Information System. Data were statistically analyzed with t test, chi-square test, and logistic regression. RESULTS: We found that infections (32.7%) were the most frequent cause associated with thrombocytopenia, followed by sepsis shock (3.93%) and blood loss (2.99%). Meanwhile, antifungals (p = 0.002) and bacterial infection (p = 0.037) were associated with severe and extremely severe thrombocytopenia. Finally, we found that the mortality of platelet transfusion and non-transfusion in patients was statistically significant for patients with platelet counts between 30 and 49/nL (χ2 = 9.719, p = 0.002). CONCLUSION: Infection and sepsis emerged as two primary factors associated with thrombocytopenia in intensive care unit. Meanwhile, antifungals and bacterial infection were associated with platelet counts less than 49/nL. Finally, platelet transfusion may be associated with reduced mortality in patients with platelet counts between 30 and 49/nL.

Water translocation between ramets of strawberry during soil drying and its effects on photosynthetic performance.

To explore the mechanisms underlying water regulation in clonal plants and its effects on carbon assimilation under water stress, we studied the responses of water status, gas exchange and abscisic acid (ABA) contents to water stress in leaves of pairs of strawberry ramets that consist of mother and daughter ramets. There was a greater decrease in photosynthetic rates (P(n)) and stomatal conductance (G(s)) in the disconnected mother ramets than the connected mother ramets upon exposure to water stress, indicating that water stress in mother ramets was alleviated by water translocation from the well-watered daughter ramets. Conversely, the connected mother ramets displayed enhanced symptoms of water stress when the connected daughter ramets were exposed to water deficit. The mother ramets had lower water potential (psi(w)) due to their stronger osmotic adjustment than in well-watered daughter ramets; this resulted in water flow from the connected daughter ramets to mother ramets, thus alleviating water stress of mother ramets. During soil drying, there was a striking increase in ABA concentrations in leaves of the disconnected mother ramets, whereas leaf bulk ABA was much lower in the connected and water-stressed mother ramets than that in the drought-affected mother ramets in the disconnected group. In this study, though G(s) was linearly correlated with leaf bulk ABA and psi(w), G(s) in water-stressed mother ramets in disconnected group exhibited less sensitivity to the variation in leaf bulk ABA and psi(w) than that in connected and water-stressed mother ramets. Taken together, these results indicate that: (1) the flux of water translocation between the connected ramets is determined by a water potential gradient; (2) water translocation between connected ramets helps to keep sensitivity of G(s) to ABA and psi(w) in drought-affected ramets, thereby benefit to effectively maintain the homeostasis of leaf water status and (3) the improvements in P(n) in water-stressed ramets due to water translocation from well-watered ramets suggest the advantages of physiological integration in clonal plants in environments with heterogeneous water distribution.

Long-term impacts of land-use change on dynamics of tropical soil carbon and nitrogen pools.

Land-use changes, especially the conversion of native forest vegetation to cropland and plantations in tropical region, can alter soil C and N pools and N availability for plant uptake. Deforestation, followed by shifting cultivation and establishment of rubber tree plantation, is a common land-use change in Xishuangbanna, southwest China. However the influence of this kind of land-use change on soil C and N dynamics in this region remains poorly understood. This study was conducted to assess the effects of land-use change on soil C and N pools. Soil samples were collected on five adjacent plots, which belong to three land-use types including secondary forest-an acuminate banana (Musa itinerans) secondary forest and a male bamboo (Dendrocalamus membranaceae) secondary forest, shifting cultivation, and rubber tree (Hevea brasiliensis (H. B. K.) Muell. Arg.) plantation (one plot is 3-year-old, and another is 7-year-old). We measured soil bulk density (BD), pH value, moisture content and concentrations of soil organic carbon (SOC), total soil nitrogen (TSN), and inorganic N (NO3- -N and NH4+ -N) at 0-3, 3-20, 20-40 and 40-60 cm depths, and calculated C and N pools in 0-20, 20-40, 40-60, and 0-60 cm soil layers. Compared with the adjacent secondary forests, shifting cultivation and establishment of rubber tree plantations resulted in significant decline in concentrations and stocks of SOC and TSN in 0-20 and 0-60 cm soil layers, and increase in pH and bulk density at 0-3, 3-20, and 20-40 cm depths. Soil moisture content decreased only in 0-20 cm surface soils in shifting cultivation and plantations. The dynamics of mineral N was much more complex, which had different trends among depths and ecosystems. Compared with the secondary forests, SOC stocks in 0-20 cm surface soils in shifting cultivation and rubber tree plantations (3-year-old plantation and 7-year-old plantation) decreased by 34.0%, 33%, and 23%; and TSN stocks decreased by 32.2%, 20.4%, and 20.4%, respectively, whereas the decreases of SOC and TSN stocks in 0-60 cm soil layers were much less. The results indicated that C and N losses were mainly occurred in 0-20 cm surface soil, followed by 20-40 cm layer.