Strategies for improving the performance of prediction models for response to immune checkpoint blockade therapy in cancer.

Immune checkpoint blockade (ICB) therapy holds promise for bringing long-lasting clinical gains for the treatment of cancer. However, studies show that only a fraction of patients respond to the treatment. In this regard, it is valuable to develop gene expression signatures based on RNA sequencing (RNAseq) data and machine learning methods to predict a patient's response to the ICB therapy, which contributes to more personalized treatment strategy and better management of cancer patients. However, due to the limited sample size of ICB trials with RNAseq data available and the vast number of candidate gene expression features, it is challenging to develop well-performed gene expression signatures. In this study, we used several published melanoma datasets and investigated approaches that can improve the construction of gene expression-based prediction models. We found that merging datasets from multiple studies and incorporating prior biological knowledge yielded prediction models with higher predictive accuracies. Our finding suggests that these two strategies are of high value to identify ICB response biomarkers in future studies.

Tensile-Strained Holey Pd Metallene toward Efficient and Stable Electrocatalysis.

Noble metal-based metallenes are attracting intensive attention in energy catalysis, but it is still very challenging to precisely control the surface structures of metallenes for higher catalytic properties on account of their intrinsic thermodynamic instability. Herein, the synthesis of tensile-strained holey Pd metallene by oxidative etching is reported using hydrogen peroxide, which exhibits highly enhanced catalytic activity and stability in comparison with normal Pd metallene toward both oxygen reduction reaction and formic acid oxidation. The pre-prepared Pd metallene functions as a catalyst to decompose hydrogen peroxide, and the Pd atoms in amorphous regions of Pd metallene are preferentially removed by the introduced hydrogen peroxide during the etching process. The greatly enhanced ORR activity is mainly determined by the strong electrostatic repulsion between intermediate O* and the dopant O, which balances the adsorption strength of O* on Pd sites, ultimately endowing a weakened adsorption energy of O* on TH-Pd metallene. This work creates a facile and economical strategy to precisely shape metallene-based nanoarchitectures with broad applications for energy systems and sensing devices.

Strategies for Improving the Performance of Prediction Models for Response to Immune Checkpoint Blockade Therapy in Cancer.

Immune checkpoint blockade (ICB) therapy holds promise for bringing long-lasting clinical gains for the treatment of cancer. However, studies show that only a fraction of patients respond to the treatment. In this regard, it is valuable to develop gene expression signatures based on RNA sequencing (RNAseq) data and machine learning methods to predict patients' response to the ICB therapy, which contributes to more personalized treatment strategy and better management of cancer patients. However, due to the limited sample size of ICB trials with RNAseq data available and the vast number of candidate gene expression features, it is challenging to develop well-performed gene expression signatures. In this study, we used several published melanoma datasets and investigated approaches that can improve the construction of gene expression-based prediction models. We found that merging datasets from multiple studies and incorporating prior biological knowledge yielded prediction models with higher predictive accuracies. Our finding suggests that these two strategies are of high value to identify ICB response biomarkers in future studies.

Controllable Synthesis of Web-Footed PdCu Nanosheets and Their Electrocatalytic Applications.

Morphological control of noble-metal-based nanocrystals has attracted enormous attention because their catalytic behaviors can be optimized well by adjusting the size and shape. Herein, the controllable synthesis of web-footed PdCu nanosheets via a facile surfactant-free method is reported. It is discovered that the Cu(II) precursor in this synthetic system displays a critical role in growing branches along the lateral of nanosheets. This work demonstrates a Pd-based alloy nanoarchitecture for efficient and stable electrocatalysis of both ethanal and formic acid oxidation reactions.

Knockout of the HCC suppressor gene Lass2 downregulates the expression level of miR-694.

Homo sapiens longevity assurance homolog 2 of yeast LAG (Lass2) catalyzes the synthesis of long-chain ceramide which is an essential element of membranous structures. Deletion of Lass2 is associated with a high risk of spontaneous or DEN-induced hepatocellular carcinoma (HCC), yet the mechanism remains unclear. In the present study, we found extensive vesicles in hepatocytes of one-month-old Lass2-knockout (KO) mice. Hepatic biochemical indices were increased and expression of albumin was attenuated in the one­month Lass2-KO liver. The results indicate that the injuries of the hepatocytes in young Lass2-KO mice, based on the results of Gene Ontology analysis of mRNA microarray of Lass2-KO liver vs. wild-type liver showed 'wounding response' was the mostly possible altered pathway in the Lass2-KO mice. miR-mRNA integrated analysis revealed that miR-694 was downregulated while its target gene tumor necrosis factor α-induced protein 3 (Tnfaip3) was upregulated, as confirmed by qPCR. The expression of NF-κB which is negatively controlled by Tnfaip3 was detected by qPCR and was found to be downregulated. Herein, we first report that Lass2 deficiency caused the downregulation of miR-694 and the upregulation of its target gene Tnfaip3 in vivo in mice, which may be related to a high risk of occurrence of HCC.

Enhancement of DEN-induced liver tumourigenesis in hepatocyte-specific Lass2-knockout mice coincident with upregulation of the TGF-ß1-Smad4-PAI-1 axis.

Longevity assurance homolog 2 of yeast LAG1 (Lass2) gene is capable of suppressing the proliferation and metastasis of several types of tumours including liver cancer. In the present study, hepatocyte-specific Lass2-knockout (Lass2 KO) and wild-type (WT) mice were exposed to the carcinogen, diethylnitrosamine (DEN), to induced liver tumours. At week 23 following DEN injection, tumours were produced in 100% of the Lass2 KO mice and 21.4% of the WT mice. At week 40, 100% of the Lass2 KO mice and 78.6% of the WT mice developed tumours, with no distinct significant difference in tumour occurrences between the two genotypes; yet, tumours in the Lass2 KO mouse livers were more numerous and larger in size. Hepatocellular carcinoma (HCC) was confirmed by α-fetoprotein (AFP). PCNA and EdU assays indicated more active proliferation whereas TUNEL assay revealed decreased apoptosis in Lass2 KO livers, when compared with the WT control. The expression of plasminogen activator inhibitor type-1 (PAI-1), a tumour-promoting gene, in the liver tissues of the 2 genotypes was detected using qPCR and western blotting, showing that PAI-1 levels were significantly elevated in Lass2 KO livers at week 40 following DEN introduction. Moreover, the expression of PAI-1-related TGF-ß1, Smad-4 and -7 was detected, displaying an elevation in TGF-ß1 and Smad-4 (not including Smad-7) in the Lass2 KO livers. Our data demonstrates that i) Lass2 is a protective gene against DEN-induced liver tumourigenesis; and ii) upregulation of the TGF-ß1-Smad4-PAI-1 axis may contribute to the vulnerability of Lass2-knockout mice to DEN.