Protocol for using Multiomics2Targets to identify targets and driver kinases for cancer cohorts profiled with multi-omics assays.

The availability of multi-omics data applied to profile cancer cohorts is rapidly increasing. Here, we present a protocol for Multiomics2Targets, a computational pipeline that can identify driver cell signaling pathways, protein kinases, and cell-surface targets for immunotherapy. We describe steps for preparing the data, uploading files, and tuning parameters.

Prediction of hepatocellular carcinoma response to radiation segmentectomy using an MRI-based machine learning approach.

Purpose: To evaluate the value of pre-treatment MRI-based radiomics in patients with hepatocellular carcinoma (HCC) for the prediction of response to Yttrium 90 radiation segmentectomy.

Methods: This retrospective study included 154 patients (38 female; mean age 66.8 years) who underwent contrast-enhanced MRI prior to radiation segmentectomy.

Multiomics2Targets identifies targets from cancer cohorts profiled with transcriptomics, proteomics, and phosphoproteomics.

The availability of data from profiling of cancer patients with multiomics is rapidly increasing. However, integrative analysis of such data for personalized target identification is not trivial. Multiomics2Targets is a platform that enables users to upload transcriptomics, proteomics, and phosphoproteomics data matrices collected from the same cohort of cancer patients.

Multiomic foundations of human prefrontal cortex tissue function.

The prefrontal cortex (PFC) is a region of the brain that in humans is involved in the production of higher-order functions such as cognition, emotion, perception, and behavior. Neurotransmission in the PFC produces higher-order functions by integrating information from other areas of the brain. At the foundation of neurotransmission, and by extension at the foundation of higher-order brain functions, are an untold number of coordinated molecular processes involving the DNA sequence variants in the genome, RNA transcripts in the transcriptome, and proteins in the proteome.

Pan-cancer proteogenomics characterization of tumor immunity.

Despite the successes of immunotherapy in cancer treatment over recent decades, less than <10%-20% cancer cases have demonstrated durable responses from immune checkpoint blockade. To enhance the efficacy of immunotherapies, combination therapies suppressing multiple immune evasion mechanisms are increasingly contemplated. To better understand immune cell surveillance and diverse immune evasion responses in tumor tissues, we comprehensively characterized the immune landscape of more than 1,000 tumors across ten different cancers using CPTAC pan-cancer proteogenomic data.

RECCIPE: A new framework assessing localized cell-cell interaction on gene expression in multicellular ST data.

Cell-cell interaction (CCI) plays a pivotal role in cellular communication within the tissue microenvironment. The recent development of spatial transcriptomics (ST) technology and associated data analysis methods has empowered researchers to systematically investigate CCI. However, existing methods are tailored to single-cell resolution datasets, whereas the majority of ST platforms lack such resolution.

Design, Synthesis, and Biological Evaluation of Marine Lissodendrins B Analogues as Modulators of ABCB1-Mediated Multidrug Resistance.

Multidrug resistance (MDR) caused by ATP-Binding Cassette Subfamily B Member 1 (ABCB1, P-glycoprotein, P-gp) is a major barrier for the success of chemotherapy in clinics. In this study, we designed and synthesized a total of 19 Lissodendrins B analogues and tested their ABCB1-mediated MDR reversal activity in doxorubicin (DOX)-resistant K562/ADR and MCF-7/ADR cells. Among all derivatives, compounds , , and with a dimethoxy-substituted tetrahydroisoquinoline fragment possessed potent synergistic effects with DOX and reversed ABCB1-mediated drug resistance.

Histopathologic and proteogenomic heterogeneity reveals features of clear cell renal cell carcinoma aggressiveness.

Clear cell renal cell carcinomas (ccRCCs) represent ∼75% of RCC cases and account for most RCC-associated deaths. Inter- and intratumoral heterogeneity (ITH) results in varying prognosis and treatment outcomes. To obtain the most comprehensive profile of ccRCC, we perform integrative histopathologic, proteogenomic, and metabolomic analyses on 305 ccRCC tumor segments and 166 paired adjacent normal tissues from 213 cases.

Chinese physical fitness standard for campus football players: A pilot study of 765 children aged 9 to 11.

In 2022, 55 million Chinese children participate in campus football; however, there is no physical fitness standard, making it a priority task to enhance the current national program. This study aimed to explore a pilot method for the development of a reliable physical fitness standard. This study examined 765 male football players aged 9 to 11 in 2020 and 2022.

Antiperspirant effects and mechanism investigation of Mulisan decoction in rats based on plasma metabolomics.

Context: Mulisan decoction (MLS) is a classic formula of traditional Chinese medicine for treating hyperhidrosis. The mechanism remains unclear.

Objective: To investigate the antiperspirant effect and underlying mechanisms of MLS.

Cell division control 42 elevates during infliximab therapy, and its increment relates to treatment response in ulcerative colitis patients.

Background: Cell division control 42 (CDC42) regulates multiple processes of inflammation and/or immunity in autoimmune diseases and also relates to the treatment efficacy of biologic regimens clinically. This study aimed to explore the longitudinal change in CDC42 during infliximab (IFX) treatment and its correlation with IFX response in ulcerative colitis (UC) patients.

Methods: Active UC patients (N = 48) who received IFX were recruited, and their CDC42 expressions in peripheral blood mononuclear cells (PBMCs) were detected before treatment (W0) and at 12 weeks after treatment (W12) using RT-qPCR.

Stimulating the Hematopoietic Effect of Simulated Digestive Product of Fucoidan from on Cyclophosphamide-Induced Hematopoietic Damage in Mice and Its Protective Mechanisms Based on Serum Lipidomics.

Hematopoietic damage is a serious side effect of cytotoxic drugs, and agents promoting hematopoiesis are quite important for decreasing the death rate in cancer patients. In our previous work, we prepared the simulated digestive product of fucoidan from , DSFF, and found that DSFF could activate macrophages. However, more investigations are needed to further evaluate whether DSFF could promote hematopoiesis in the chemotherapy process.

Semisynthesis and biological evaluation of (+)-sclerotiorin derivatives as antitumor agents for the treatment of hepatocellular carcinoma.

Hepatocellular carcinoma is one of the most common primary hepatic malignancy. Herein, a series of semisynthesized derivatives (2-30) of the natural product (+)-sclerotiorin (1) was prepared and evaluated the cytotoxic activities against six cancer cell lines. Among them, 3 and 5 were the most effective compounds against human hepatocellular carcinoma Bel-7402 cell line with IC values of 1.

Comparative assessment of standard and immune response criteria for evaluation of response to PD-1 monotherapy in unresectable HCC.

Purpose: To assess response to programmed death-1 (PD-1) monotherapy (nivolumab) in hepatocellular carcinoma (HCC) patients using RECIST1.1, modified RECIST (mRECIST), and immune RECIST (iRECIST). A secondary objective was to identify clinicolaboratory and imaging variables predictive of progressive disease (PD) and overall survival (OS).

Importance of applying Mixed Generalized Additive Model (MGAM) as a method for assessing the environmental health impacts: Ambient temperature and Acute Myocardial Infarction (AMI), among elderly in Shanghai, China.

Association between acute myocardial infarction (AMI) morbidity and ambient temperature has been examined with generalized linear model (GLM) or generalized additive model (GAM). However, the effect size by these two methods might be biased due to the autocorrelation of time series data and arbitrary selection of degree of freedom of natural cubic splines. The present study analyzed how the climatic factors affected AMI morbidity for older adults in Shanghai with Mixed generalized additive model (MGAM) that addressed these shortcomings mentioned.

Menopausal Women's Health Care Method Based on Computer Nursing Diagnosis Intelligent System.

Taking into account the current feature extraction speed and recognition effect of intelligent diagnosis of menopausal women's health care behavior, this paper proposes to use a cross-layer convolutional neural network to extract behavior features autonomously and use support vector machine multiclass behavior classifier to classify behavior. Compared with the feature images extracted by traditional methods, the behavioral features extracted in this paper are related to the individual menopausal women and have better semantic information, and the feature description ability in the time domain and the space domain has been enhanced. Through Matlab software, using the database established in this paper to compare its feature extraction time, test classification time, and final recognition accuracy with ordinary convolutional neural networks, it is concluded that the cross-layer CNN-SVM model can ensure the speed of feature extraction.

A community effort to identify and correct mislabeled samples in proteogenomic studies.

Sample mislabeling or misannotation has been a long-standing problem in scientific research, particularly prevalent in large-scale, multi-omic studies due to the complexity of multi-omic workflows. There exists an urgent need for implementing quality controls to automatically screen for and correct sample mislabels or misannotations in multi-omic studies. Here, we describe a crowdsourced precisionFDA NCI-CPTAC Multi-omics Enabled Sample Mislabeling Correction Challenge, which provides a framework for systematic benchmarking and evaluation of mislabel identification and correction methods for integrative proteogenomic studies.

Determination of 13 antidepressants in blood by UPLC-MS/MS with supported liquid extraction pretreatment.

Antidepressants are widely used nowadays. Due to the potential detrimental consequences and involvement in forensic cases, therapeutic drug monitoring of antidepressants is desired. Herein we report a method for sensitive determination of 13 commonly used antidepressants in blood.