Alterations in membrane proteins (MPs) and their regulated pathways have been established as cancer hallmarks and extensively targeted in clinical applications. However, the analysis of ...MP-interacting proteins and downstream pathways across human malignancies remains challenging. Here, we present a systematically integrated method to generate a resource of cancer membrane protein-regulated networks (CaMPNets), containing 63,746 high-confidence protein-protein interactions (PPIs) for 1962 MPs, using expression profiles from 5922 tumors with overall survival outcomes across 15 human cancers. Comprehensive analysis of CaMPNets links MP partner communities and regulated pathways to provide MP-based gene sets for identifying prognostic biomarkers and druggable targets. For example, we identify CHRNA9 with 12 PPIs (e.g., ERBB2) can be a therapeutic target and find its anti-metastasis agent, bupropion, for treatment in nicotine-induced breast cancer. This resource is a study to systematically integrate MP interactions, genomics, and clinical outcomes for helping illuminate cancer-wide atlas and prognostic landscapes in tumor homo/heterogeneity.
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•Digital design framework for continuous cooling crystallization is presented.•Batch-to-continuous crystallization translation of kinetic parameters was studied.•Novel continuous ...setup with full recycle-loop was developed to minimize material use.•Model-prediction uncertainties were compared with the measurement uncertainties.
A systematic digital design framework for the development of a digital twin of a continuous crystallization process was presented using the model compound, diphenhydramine hydrochloride (DPH). The key features of the framework include operating space investigations, kinetic parameter estimation using population balance modeling, and systematic batch-to-continuous crystallization translation of the estimated parameters. An approach that compares experimental uncertainties with model-prediction uncertainties was used to justify the robustness of the parameter estimation procedure. For continuous crystallization development, a continuous configuration with full recycle and dissolution was developed, which enabled rapid process design with minimal material use. The results demonstrated successful model development for both batch and mixed-suspension-mixed-product-removal (MSMPR) crystallization configurations. This experimentally validated model, along with quantified uncertainty space of the kinetic parameters, serves as a digital twin of the process, which was later used to optimize the multistage MSMPR process to produce larger crystals with narrower distributions.
Considering the importance of microRNAs (miRNAs) in regulating cellular processes, we performed microarray analysis and revealed miR‐4324 as one of the most differentially expressed miRNAs in bladder ...cancer (BCa). Then, we discovered that miR‐4324 was a negative regulator of Rac GTPase activating protein 1 (RACGAP1) and that RACGAP1 functioned as an oncogenic protein in BCa. Our studies indicated that ectopic overexpression of miR‐4324 in BCa cells significantly suppressed cell proliferation and metastasis and enhanced chemotherapy sensitivity to doxorubicin by repressing RACGAP1 expression. Further studies showed that estrogen receptor 1 (ESR1) increased the expression of miR‐4324 by binding to its promoter, while the downregulation of ESR1 in BCa was caused by hypermethylation of its promoter. p‐STAT3 induced the enrichment of DNMT3B by binding to the ESR1 promoter and then induced methylation of the ESR1 promoter. In turn, RACGAP1 induced STAT3 phosphorylation, increasing p‐STAT3 expression and promoting its translocation to the nucleus. Therefore, the miR‐4324‐RACGAP1‐STAT3‐ESR1 feedback loop could be a critical regulator of BCa progression.
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MicroRNAs have been reported to play important roles in bladder cancer (BCa) carcinogenesis, but mechanisms of action remain to be fully elucidated. This study reveals that miR‐4324 is one of the most significantly downregulated miRNAs in BCa tissues. miR‐4324 suppresses cell proliferation and metastasis and enhances chemotherapy sensitivity to doxorubicin by repressing RACGAP1 expression. ESR1 can increase the expression of miR‐4324 by binding to its promoter. p‐STAT3 can induce the enrichment of DNMT3B by binding to ESR1 promoter and induce methylation of ESR1 promoter. miR‐4324‐RACGAP1‐STAT3‐ESR1 feedback loop may thus be a critical regulator of BCa progression and potential therapeutic target.
The signaling pathways imposing hormonal control over adipocyte differentiation are poorly understood. While insulin and Akt signaling have been found previously to be essential for adipogenesis, the ...relative importance of their many downstream branches have not been defined. One direct substrate that is inhibited by Akt-mediated phosphorylation is the tuberous sclerosis complex 2 (TSC2) protein, which associates with TSC1 and acts as a critical negative regulator of the mammalian target of rapamycin (mTOR) complex 1 (mTORC1). Loss of function of the TSC1-TSC2 complex results in constitutive mTORC1 signaling and, through mTORC1-dependent feedback mechanisms and loss of mTORC2 activity, leads to a concomitant block of Akt signaling to its other downstream targets.
We find that, despite severe insulin resistance and the absence of Akt signaling, TSC2-deficient mouse embryo fibroblasts and 3T3-L1 pre-adipocytes display enhanced adipocyte differentiation that is dependent on the elevated mTORC1 activity in these cells. Activation of mTORC1 causes a robust increase in the mRNA and protein expression of peroxisome proliferator-activated receptor gamma (PPARgamma), which is the master transcriptional regulator of adipocyte differentiation. In examining the requirements for different Akt-mediated phosphorylation sites on TSC2, we find that only TSC2 mutants lacking all five previously identified Akt sites fully block insulin-stimulated mTORC1 signaling in reconstituted Tsc2 null cells, and this mutant also inhibits adipogenesis. Finally, renal angiomyolipomas from patients with tuberous sclerosis complex contain both adipose and smooth muscle-like components with activated mTORC1 signaling and elevated PPARgamma expression.
This study demonstrates that activation of mTORC1 signaling is a critical step in adipocyte differentiation and identifies TSC2 as a primary target of Akt driving this process. Therefore, the TSC1-TSC2 complex regulates the differentiation of mesenchymal cell lineages, at least in part, through its control of mTORC1 activity and PPARgamma expression.
Renal cell carcinoma (RCC) is the most common type of renal tumor, and the clear cell renal cell carcinoma (ccRCC) is the most frequent subtype. In this study, our aim is to identify potential ...biomarkers that could effectively predict the prognosis and progression of ccRCC. First, we used The Cancer Genome Atlas (TCGA) RNA‐sequencing (RNA‐seq) data of ccRCC to identify 2370 differentially expressed genes (DEGs). Second, the DEGs were used to construct a coexpression network by weighted gene coexpression network analysis (WGCNA). Moreover, we identified the yellow module, which was strongly related to the histologic grade and pathological stage of ccRCC. Then, the functional annotation of the yellow module and single‐samples gene‐set enrichment analysis of DEGs were performed and mainly enriched in cell cycle. Subsequently, 18 candidate hub genes were screened through WGCNA and protein–protein interaction (PPI) network analysis. After verification of TCGA’s ccRCC data set, Gene Expression Omnibus (GEO) data set (GSE73731) and tissue validation, we finally identified 15 hub genes that can actually predict the progression of ccRCC. In addition, by using survival analysis, we found that patients of ccRCC with high expression of each hub gene were more likely to have poor prognosis than those with low expression. The receiver operating characteristic curve showed that each hub gene could effectively distinguish between localized and advanced ccRCC. In summary, our study indicates that 15 hub genes have great predictive value for the prognosis and progression of ccRCC, and may contribute to the exploration of the pathogenesis of ccRCC.
We constructed a scale‐free weighted gene coexpression network analysis coexpression network, after a series of rigorous analysis and verification, we finally selected 15 hub genes, which are significantly related to the progress and prognosis of clear cell renal cell carcinoma (ccRCC), as well as could also significantly differentiate between localized and advanced ccRCC. Our study providing new research objects for studying the pathogenesis of ccRCC, they are also new potential therapeutic targets for ccRCC.
Prostate cancer is initially responsive to androgen deprivation, but the effectiveness of androgen receptor (AR) inhibitors in recurrent disease is variable. Biopsy of bone metastases is challenging; ...hence, sampling circulating tumor cells (CTCs) may reveal drug-resistance mechanisms. We established single-cell RNA-sequencing (RNA-Seq) profiles of 77 intact CTCs isolated from 13 patients (mean six CTCs per patient), by using microfluidic enrichment. Single CTCs from each individual display considerable heterogeneity, including expression of AR gene mutations and splicing variants. Retrospective analysis of CTCs from patients progressing under treatment with an AR inhibitor, compared with untreated cases, indicates activation of noncanonical Wnt signaling (P = 0.0064). Ectopic expression of Wnt5a in prostate cancer cells attenuates the antiproliferative effect of AR inhibition, whereas its suppression in drug-resistant cells restores partial sensitivity, a correlation also evident in an established mouse model. Thus, single-cell analysis of prostate CTCs reveals heterogeneity in signaling pathways that could contribute to treatment failure.
This study aimed to describe the timing and patterns of pubertal maturation of girls living in rural Bangladesh. Starting in September 2015, a total of 15,320 girls from a birth cohort, aged 9 to 15 ...years at initial encounter, were visited twice at about a one year interval, typically in their birth month. Participants were asked to self-report extent of pubertal maturation, including breast development, pubic hair growth and age at menarche, if applicable. Pubertal stage (abbreviated as B2 and B3-4 for breast development and PH2 and PH3-4 for pubic hair growth) was assigned. Data from both visits were pooled, yielding a total of 29,377 age-related observations per pubertal characteristic. Probit regression models were used to estimate distributions of age at which each stage of pubertal development was attained. Before age 8, <3% of the study population initiated pubertal maturation as indicated by onset of breast development (B2). The median (95% confidence interval) age of B2 and B3-4 was 11.02 (11.00-11.04) and 12.82 (12.80-12.83) years, respectively; and 12.93 (12.91-12.94) and 14.29 (14.27-14.31) years for the onset (PH2) and advanced stage (PH3-4) of pubic hair growth, respectively. Median age at menarche was 13.17 (13.15-13.19) years, with 2.15 years of timespan from B2 to menarche. Girls in rural Bangladesh progressed through puberty following a well-documented sequence of sexual maturation stages. The age at which each pubertal milestone took place was somewhat later, but the tempo from breast development to menarche was comparable to that observed elsewhere. Our findings present a current norm of pubertal maturation in a typical, rural adolescent population in South Asia, which could help inform future studies and interventions to preserve or improve early adolescent health and development.
To compare the efficacy and safety of ultrasound (US) and computed tomography (CT) in the guidance of radiofrequency ablation (RFA) for hepatocellular carcinoma (HCC).
We retrospectively analyzed ...consecutive treatment-naïve patients who received curative RFA for HCC from January 2008 to July 2013. Patients were divided into the US group or the CT group according to their RFA guidance instruments. Patients who were only suitable for US- or CT-guided RFA were excluded. Cumulative incidences of and hazard ratios for HCC recurrence were analyzed after adjusting for competing mortality risk.
We recruited a total of 101 patients in the US group and 51 patients in the CT group. The baseline demographic characteristics were not significantly different in both groups. Initial response rates were similar between the two groups (US vs. CT: 89.1% vs. 92.2%, p = 0.54), and complete tumor ablation was finally achieved for all patients. However, more ablations per session were performed in US group (median 2.0 1.0-3.0 vs. 1.0 1.0-2.0; p<0.01). The 1-, 2- and 3-year local tumor recurrence rates (US vs. CT: 13.0%, 20.9%, and 29.2% vs. 11.2%, 29.8% and 29.8%, respectively) and overall mortality rates (US vs. CT: 5.2%, 9.6% and 16.5% vs. 0%, 3.1% and 23.8%, respectively) were not significantly different. In multivariate analysis, tumor characteristics and underlying liver function, but not US or CT guidance, were independent prognostic factors. The complication rates were similar between the two groups (US vs. CT: 10.9% vs. 9.8%; p = 0.71), and there was no procedure-related mortality.
With comparable major outcomes, either US or CT can be used in the guidance of RFA in experience hands.
Cook Inlet, Alaska, is home to an endangered and declining population of 279 belugas (Delphinapterus leucas). Recovery efforts highlight a paucity of basic ecological knowledge, impeding the correct ...assessment of threats and the development of recovery actions. In particular, information on diet and foraging habitat is very limited for this population. Passive acoustic monitoring has proven to be an efficient approach to monitor beluga distribution and seasonal occurrence. Identifying acoustic foraging behavior could help address the current gap in information on diet and foraging habitat. To address this conservation challenge, eight belugas from a comparative, healthy population in Bristol Bay, Alaska, were instrumented with a multi-sensor tag (DTAG), a satellite tag, and a stomach temperature transmitter in August 2014 and May 2016. DTAG deployments provided 129.6 hours of data including foraging and social behavioral states. A total of 68 echolocation click trains ending in terminal buzzes were identified during successful prey chasing and capture, as well as during social interactions. Of these, 37 click trains were successfully processed to measure inter-click intervals (ICI) and ICI trend in their buzzing section. Terminal buzzes with short ICI (minimum ICI <8.98 ms) and consistently decreasing ICI trend (ICI increment range <1.49 ms) were exclusively associated with feeding behavior. This dual metric was applied to acoustic data from one acoustic mooring within the Cook Inlet beluga critical habitat as an example of the application of detecting feeding in long-term passive acoustic monitoring data. This approach allowed description of the relationship between beluga presence, feeding occurrence, and the timing of spawning runs by different species of anadromous fish. Results reflected a clear preference for the Susitna River delta during eulachon (Thaleichthys pacificus), Chinook (Oncorhynchus tshawytscha), pink (Oncorhynchus gorbuscha), and coho (Oncorhynchus kisutch) salmon spawning run periods, with increased feeding occurrence at the peak of the Chinook and pink salmon runs.
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