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A computational method to identify cell types within a complex tissue, based on analysis of gene expression profiles, is described in this paper. We introduce CIBERSORT, a method for characterizing cell composition of complex tissues from their gene expression profiles. When applied to enumeration of hematopoietic subsets in RNA mixtures from fresh, frozen and fixed tissues, including solid tumors, CIBERSORT outperformed other methods with respect to noise, unknown mixture content and closely related cell types. CIBERSORT should enable large-scale analysis of RNA mixtures for cellular biomarkers and therapeutic targets ( http://cibersort.stanford.edu/ ).

A searchable pan-cancer resource generated using data from nearly 18,000 human tumors reveals links between tumor infiltration by particular leukocyte subsets, tumor expression of particular gene signatures, and patient prognosis. Molecular profiles of tumors and tumor-associated cells hold great promise as biomarkers of clinical outcomes. However, existing data sets are fragmented and difficult to analyze systematically. Here we present a pan-cancer resource and meta-analysis of expression signatures from ∼18,000 human tumors with overall survival outcomes across 39 malignancies. By using this resource, we identified a forkhead box MI ( FOXM1 ) regulatory network as a major predictor of adverse outcomes, and we found that expression of favorably prognostic genes, including KLRB1 (encoding CD161), largely reflect tumor-associated leukocytes. By applying CIBERSORT, a computational approach for inferring leukocyte representation in bulk tumor transcriptomes, we identified complex associations between 22 distinct leukocyte subsets and cancer survival. For example, tumor-associated neutrophil and plasma cell signatures emerged as significant but opposite predictors of survival for diverse solid tumors, including breast and lung adenocarcinomas. This resource and associated analytical tools ( http://precog.stanford.edu ) may help delineate prognostic genes and leukocyte subsets within and across cancers, shed light on the impact of tumor heterogeneity on cancer outcomes, and facilitate the discovery of biomarkers and therapeutic targets.

Background Mycoplasma pneumoniae (MP) is a prevalent respiratory pathogen in children, with diagnosis typically relying on detecting MP DNA in nasal swabs or antibodies in blood samples. The relationship between MP DNA positivity and age in children is not well understood. We aimed to explore trends in MP DNA and antibody detection rates with age in a pediatric population. Methods This retrospective study analyzed data from 1,161 children under 14 years old hospitalized with suspected MP infection. The study included clinical presentations and laboratory tests, and all participants underwent chemiluminescence and nucleic acid detection for MP antibodies and DNA, respectively. We analyzed the relationship between age and MP DNA and antibodies in our study. Results The mean age of the children was 49.7 ± 32.6 months. Laboratory data showed mild elevations in inflammatory markers and normal liver function tests, reflecting the generally moderate severity of MP infections. The study revealed that the positive rate of MP DNA was 9.0%, and it was negatively correlated with children’s age ( r = -0.21, P  < 0.001). The positive rate of MP IgM antibody was 7.1%, and it was positively correlated with children’s age ( r  = 0.18, P  < 0.001). The positive rate of MP IgG antibody was 6.3%, and it was not correlated with children’s age ( r  = 0.03, P  = 0.36). Conclusion These results suggest that MP DNA detection identifies the MP infection earlier and more accurately than antibody detection and that younger children are more susceptible to MP infection than older children. Given the sensitivity and specificity of MP DNA found in young children in this study, it is recommended that it should be considered in routine clinical practice for early diagnosis and intervention.

Background ABCB1 overexpression is a key factor in causing multidrug resistance (MDR). As a result, it is crucial to discover effective medications against ABCB1 to overcome MDR. Falnidamol, a tyrosine kinase inhibitor (TKI) targeting the epidermal growth factor receptor (EGFR), is currently in phase 1 clinical trials for the treatment of solid tumors. In this work, we assessed whether falnidamol could act as an inhibitor of ABCB1 to reverse ABCB1-mediated MDR. Methods The reversal effect of falnidamol on MDR was assessed by MTT, colony formation, 3D microsphere, and xenograft model assays. The protein expression or cellular localization was tested by western blot and immunofluorescence analysis. The intracellular doxorubicin accumulation and efflux were assessed by flow cytometry. The ATPase activity of ABCB1 was detected by a microplate reader. The interaction between falnidamol and ABCB1 was evaluated by docking analysis and cellular thermal shift assay. Results Our data showed that falnidamol specifically reversed ABCB1-mediated MDR but not ABCG2-mediated MDR in vitro and in vivo. Mechanistic studies suggested falnidamol had no effect on ABCB1 expression or cellular localization, nor on the AKT or ERK pathways. Further studies found that falnidamol reduced ABCB1’s efflux function, resulting in enhanced intracellular agent accumulation and thus overcoming MDR. ATPase assay showed that falnidamol suppressed the ABCB1 ATPase activity. Furthermore, docking analysis and cellular thermal shift assay indicated that falnidamol bound directly to the drug-binding site of ABCB1 transporter. Conclusion The present study proves that falnidamol acts as a highly potent and specific active ABCB1 transporter inhibitor, and can reverse ABCB1-mediated MDR, implying that combining falnidamol with ABCB1 substrate chemotherapeutic agents has the potential to overcome ABCB1-mediated MDR.

Prostate cancer (PCa) is one of the most common malignancies in men worldwide. This study was designed to investigate the potential of Ribosomal Protein L22-like1 (RPL22L1) and Ribosomal Protein S21 (RPS21) as diagnostic and prognostic biomarkers for PCa. First, RPL22L1 and RPS21 were screened as the key molecular of PCa by bioinformatics analysis. Subsequently, the prostate tissue samples were stained for antibodies against RPL22L1 and RPS21. The unbiased signal quantification was performed by ImageJ software, and the results showed that the expression of RPL22L1 and RPS21 exhibited significant differences between the PCa tissues and the normal prostate tissues. Receiver-operating characteristics (ROC) curves were prepared, and then the area under the curve (AUC) values of RPL22L1 and RPS21 were calculated as 0.798 and 0.768, and the likelihood ratio (LR) values of RPL22L1 and RPS21 were calculated as 2.86 and 2.53. These data implied that the over-expression of RPL22L1 and RPS21 is associated with the presence of PCa. The further analysis suggested that the expression of RPL22L1 and RPS21 were significantly higher in high Gleason grade than they were in low Gleason grade. In addition, in vitro studies were undertaken to evaluate the roles of RPL22L1 and RPS21 in PCa. The results revealed that these genes promote PCa cell proliferation, migration and invasion, and inhibit PCa cell apoptosis. Taken together, these data showed that RPL22L1 and RPS21 exhibited higher expression in human prostate cancer tissue, and involved in PCa cell proliferation and invasion. This research provided a novel insight into diagnostic and prognostic biomarkers for PCa.

Background Tumors comprise a complex microenvironment of interacting malignant and stromal cell types. Much of our understanding of the tumor microenvironment comes from in vitro studies isolating the interactions between malignant cells and a single stromal cell type, often along a single pathway. Result To develop a deeper understanding of the interactions between cells within human lung tumors, we perform RNA-seq profiling of flow-sorted malignant cells, endothelial cells, immune cells, fibroblasts, and bulk cells from freshly resected human primary non-small-cell lung tumors. We map the cell-specific differential expression of prognostically associated secreted factors and cell surface genes, and computationally reconstruct cross-talk between these cell types to generate a novel resource called the Lung Tumor Microenvironment Interactome (LTMI). Using this resource, we identify and validate a prognostically unfavorable influence of Gremlin-1 production by fibroblasts on proliferation of malignant lung adenocarcinoma cells. We also find a prognostically favorable association between infiltration of mast cells and less aggressive tumor cell behavior. Conclusion These results illustrate the utility of the LTMI as a resource for generating hypotheses concerning tumor-microenvironment interactions that may have prognostic and therapeutic relevance.

Preeclampsia (PE) is one of the leading causes of maternal and perinatal mortality and morbidity. One of the main hallmarks observed in PE is impaired inflammation state. In the current study, we found that miR-125b was deregulated in placental tissues and plasma derived from PE patients, which suggest a potential association between this miRNA and the pathogenesis of PE. Overexpression of miR-125b significantly reduced SGPL1 expression, and luciferase assays confirmed that SGPL1 is a direct target of miR-125b. We also found that miR-125b enhanced IL-8 production by directly targeting sphingosine-1-phosphate lyase 1 (SGPL1), and this effect could be reversed by SGPL1 overexpression. In placentas derived from PE patients, a negative correlation of miR-125b and SGPL1 was observed, and IL-8 was validated to be increased in the circulation of PE patients. Our data demonstrated a critical role of miR-125b in IL-8 production and the development of PE.

Preeclampsia (PE) is a life-threatening disorder of human pregnancy affecting 5–8% of all pregnancies. Currently, PE remains an elusive complicated and heterogenous medical condition with no early marker or symptoms is recognized for this serious pregnancy complications. Here, we profiled the plasma miRNA expression patterns associated with preeclampsia and found 16 miRNAs were deregulated (p < 0.01) in patients who later developed PE. Circulating hsa-miR-125b was aberrantly upregulated in early pregnancy and significantly reduced after delivery in preeclampsia. We then investigated the underlying molecular mechanisms between miR-125b and PE in vitro. We found that upregulated miR-125b can target KCNA1 to inhibit trophoblast invasion in human trophoblast cells. Moreover, overexpression of miR-125b in HUVECs impaired endothelial cell function through GPC1. The findings indicated that upregulated miR-125b leads to impaired placentation, and an increased risk of preeclampsia, Our studies provide novel insights into the underlying mechanisms on the association of miR-125b in early pregnancy and risk of PE, miR-125b might be a more specific predictive marker and a safe therapeutic target for treating patients with PE.

Harlequin Ichthyosis is a severe skin disease caused by mutations in the human gene encoding ABCA12. Here, we characterize a novel mutation in intron 29 of the mouse Abca12 gene that leads to the loss of a 5' splice donor site and truncation of the Abca12 RNA transcript. Homozygous mutants of this smooth skin or smsk allele die perinatally with shiny translucent skin, typical of animal models of Harlequin Ichthyosis. Characterization of smsk mutant skin showed that the delivery of glucosylceramides and CORNEODESMOSIN was defective, while ultrastructural analysis revealed abnormal lamellar bodies and the absence of lipid lamellae in smsk epidermis. Unexpectedly, mutant stratum corneum remained intact when subjected to harsh chemical dissociation procedures. Moreover, both KALLIKREIN 5 and -7 were drastically decreased, with retention of desmoplakin in mutant SC. In cultured wild type keratinocytes, both KALLIKREIN 5 and -7 colocalized with ceramide metabolites following calcium-induced differentiation. Reducing the intracellular levels of glucosylceramide with a glucosylceramide synthase inhibitor resulted in decreased secretion of KALLIKREIN proteases by wild type keratinocytes, but not by smsk mutant keratinocytes. Together, these findings suggest an essential role for ABCA12 in transferring not only lipids, which are required for the formation of multilamellar structures in the stratum corneum, but also proteolytic enzymes that are required for normal desquamation. Smsk mutant mice recapitulate many of the pathological features of HI and can be used to explore novel topical therapies against a potentially lethal and debilitating neonatal disease.

Microcystin-leucine arginine (MC-LR) is a potent tumor initiator that can induce malignant cell transformation. Cellular mechanical characteristics are pivotal parameters that are closely related to cell invasion. The aim of this study is to determine the effect of MC-LR on mechanical parameters, microfilament, and cell invasion in DU145 and WPMY cells. Firstly, 10 μM MC-LR was selected as the appropriate concentration cell viability assay. Subsequently, after MC-LR treatment, the cellular deformability and viscoelastic parameters were tested using the micropipette aspiration technique. The results showed that MC-LR increased the cellular deformability, reduced the cellular viscoelastic parameter values, and caused the cells to become softer. Furthermore, microfilament and microfilament-associated proteins were examined by immunofluorescence and Western blot, respectively. Our results showed that MC-LR induced microfilament reorganization and increased the expression of p-VASP and p-ezrin. Finally, the impact of MC-LR on cell invasion was evaluated. The results revealed that MC-LR promoted cell invasion. Taken together, our results suggested that mechanical changes and microfilament reorganization were involved in MC-LR-promoted cell invasion in DU145 and WPMY cells. Our data provide novel information to explain the toxicological mechanism of MC-LR.