Comprehensive analysis of circulating cell-free RNAs in blood for diagnosing non-small cell lung cancer.

Early screening and detection of non-small cell lung cancer (NSCLC) is crucial due to the significantly low survival rate in advanced stages. Blood-based liquid biopsy is non-invasive test to assistant disease diagnosis, while cell-free RNA is one of the promising biomarkers in blood. However, the disease related signatures have not been explored completely for most cell-free RNA transcriptome sequencing (cfRNA-Seq) datasets.

Giant liposarcoma of esophagus: a rare case report.

Background: Liposarcoma is a malignant mesenchymal tumor that most commonly involves the retroperitoneum and lower extremities. However, liposarcoma of esophagus has been rarely reported in the literature.

Case Presentation: We report a case of a 46-year-old man with complaint of intermittent dysphagia for 6 years, accompanied with paroxysmal vomiting of pedicled tumor to the mouth.

Awareness of intratumoral bacteria and their potential application in cancer treatment.

Hitherto, the recognition of the microbiota role in tumorigenesis and clinical studies mostly focused on the intestinal flora. In contrast to the gut microbiome, microorganisms resident in tumor tissue are in close contact with cancer cells and therefore have the potential to have similar or even different functional patterns to the gut flora. Some investigations have shown intratumoral bacteria, which might come from commensal microbiota in mucosal areas including the gastrointestinal tract and oral cavity, or from nearby normal tissues.

Toxicity Analysis of Mesoporous Polydopamine on Intestinal Tissue and Microflora.

As a promising therapy, photothermal therapy (PTT) converts near-infrared (NIR) light into heat through efficient photothermal agents (PTAs), causing a rapid increase in local temperature. Considering the importance of PTAs in the clinical application of PTT, the safety of PTAs should be carefully evaluated before their widespread use. As a promising PTA, mesoporous polydopamine (MPDA) was studied for its clinical applications for tumor photothermal therapy and drug delivery.

Case Report: Intravascular Large B-Cell Lymphoma: A Clinicopathologic Study of Four Cases With Review of Additional 331 Cases in the Literature.

Intravascular large B-cell lymphoma (IVLBCL) is a rare and highly malignant non-Hodgkin B-cell lymphoma with uncommon clinical presentation and poor prognosis. The diagnostic pitfall of IVLBCL is mainly due to the fact that subtle histological changes could be easily overlooked, in addition to its rare occurrence, non-specific and variable clinical presentations, and the absence of significant mass lesions. The purpose of this study is to further explore the clinicopathologic and molecular features of IVLBCL to ensure an accurate diagnosis of this entity.

RNA-Seq Based Toxicity Analysis of Mesoporous Polydopamine Nanoparticles in Mice Following Different Exposure Routes.

Mesoporous polydopamine nanoparticles (MPDA NPs) are promising nanomaterials that have the prospect of clinical application for multi-strategy antitumor therapy, while the biosecurity of MPDA NPs remains indistinct. Here, transcriptome sequencing (RNA-Seq) was performed to systematically reveal the toxicity of MPDA NPs to five categories of organs after three different exposure routes, including intravenous injection, intramuscular injection, and intragastric administration. Our results uncovered that MPDA NPs could be deposited in various organs in small amounts after intravenous administration, not for the other two exposure routes.

Triggering Immune System With Nanomaterials for Cancer Immunotherapy.

Cancer is a major cause of incidence rate and mortality worldwide. In recent years, cancer immunotherapy has made great progress in the preclinical and clinical treatment of advanced malignant tumors. However, cancer patients will have transient cancer suppression reaction and serious immune related adverse reactions when receiving immunotherapy.

Discovery of a Series of Theophylline Derivatives Containing 1,2,3-Triazole for Treatment of Non-Small Cell Lung Cancer.

Chemotherapy is the most common clinical treatment for non-small cell lung cancer (NSCLC), but low efficiency and high toxicity of current chemotherapy drugs limit their clinical application. Therefore, it is urgent to develop hypotoxic and efficient chemotherapy drugs. Theophylline, a natural compound, is safe and easy to get, and it can be used as a modified scaffold structure and hold huge potential for developing safe and efficient antitumor drugs.

Desmoplastic Small Round Cell Tumor of the Submandibular Gland: A Case Report and Literature Review.

Desmoplastic small round cell tumor (DSRCT) is a rare and aggressively malignant tumor mostly occurring in the abdominal and pelvic cavity of young patients. However, few cases had been reported concerning DSRCT occurring in the head and neck region. We presented a rare case of DSRCT of the right submandibular in a 25-year-old man.

p53 coordinates glucose and choline metabolism during the mesendoderm differentiation of human embryonic stem cells.

Metabolism plays crucial roles in the fate decision of human embryonic stem cells (hESCs). Here, we show that the depletion of p53 in hESCs enhances glycolysis and reduces oxidative phosphorylation, and delays mesendoderm differentiation of hESCs. More intriguingly, the disruption of p53 in hESCs leads to dramatic upregulation of phosphatidylcholine and decrease of total choline in both pluripotent and differentiated state of hESCs, suggesting abnormal choline metabolism in the absence of p53.

Cell-free DNA Methylation and Transcriptomic Signature Prediction of Pregnancies with Adverse Outcomes.

Although analysis of maternal plasma cell-free content has been employed for screening of genetic abnormalities within a pregnancy, limited attention has been paid to its use for the detection of adverse pregnancy outcomes (APOs) based on placental function. Here we investigated cell-free DNA and RNA content of 102 maternal and 25 cord plasma samples. Employing a novel deconvolution methodology, we found that during the first trimester, placenta-specific DNA increased prior to the subsequent development of gestational diabetes with no change in patients with preeclampsia while decreasing with maternal obesity.

The Role of Nutrition in the Prevention and Intervention of Type 2 Diabetes.

Type 2 diabetes (T2D) is a rapidly growing epidemic, which leads to increased mortality rates and health care costs. Nutrients (namely, carbohydrates, fat, protein, mineral substances, and vitamin), sensing, and management are central to metabolic homeostasis, therefore presenting a leading factor contributing to T2D. Understanding the comprehensive effects and the underlying mechanisms of nutrition in regulating glucose metabolism and the interactions of diet with genetics, epigenetics, and gut microbiota is helpful for developing new strategies to prevent and treat T2D.

A novel neoantigen discovery approach based on chromatin high order conformation.

Background: High-throughput sequencing technology has yielded reliable and ultra-fast sequencing for DNA and RNA. For tumor cells of cancer patients, when combining the results of DNA and RNA sequencing, one can identify potential neoantigens that stimulate the immune response of the T cell. However, when the somatic mutations are abundant, it is computationally challenging to efficiently prioritize the identified neoantigen candidates according to their ability of activating the T cell immuno-response.

EBV-positive intravascular large B-cell lymphoma of the liver: a case report and literature review.

Background: Intravascular large B-cell lymphoma (IVLBCL) is an extremely rare subtype of diffuse large B-cell lymphoma that most commonly involves the central nervous system, skin, and bone marrow. To our knowledge, Epstein-Barr virus (EBV)-positive IVLBCL in the liver has never been reported in the literature.

Case Presentation: We report a case of a 65-year-old Chinese man with complaint of fever for 18 days.

MTR4 drives liver tumorigenesis by promoting cancer metabolic switch through alternative splicing.

The metabolic switch from oxidative phosphorylation to glycolysis is required for tumorigenesis in order to provide cancer cells with energy and substrates of biosynthesis. Therefore, it is important to elucidate mechanisms controlling the cancer metabolic switch. MTR4 is a RNA helicase associated with a nuclear exosome that plays key roles in RNA processing and surveillance.

Nobiletin Triggers Reactive Oxygen Species-Mediated Pyroptosis through Regulating Autophagy in Ovarian Cancer Cells.

Ovarian cancer is one of the most serious female malignancies worldwide. Despite intensive efforts being made to overcome ovarian cancer, there still remain limited optional treatments for this disease. Nobiletin, a prospective food-derived phytochemical extracted from citrus fruits, has recently been reported to suppress ovarian cancer cells, but the role of pyroptosis in ovarian carcinoma with nobiletin still remains unknown.

The size of cell-free mitochondrial DNA in blood is inversely correlated with tumor burden in cancer patients.

Circulating cell-free DNAs (cfDNAs) are fragmented DNA molecules released into the blood by cells. Previous studies have suggested that mitochondria-originated cfDNA fragments (mt-cfDNAs) in cancer patients are more fragmented than those from healthy controls. However, it is still unknown where these short mt-cfDNAs originate, and whether the length of mt-cfDNAs can be correlated with tumor burden and cancer progression.

CancerDetector: ultrasensitive and non-invasive cancer detection at the resolution of individual reads using cell-free DNA methylation sequencing data.

The detection of tumor-derived cell-free DNA in plasma is one of the most promising directions in cancer diagnosis. The major challenge in such an approach is how to identify the tiny amount of tumor DNAs out of total cell-free DNAs in blood. Here we propose an ultrasensitive cancer detection method, termed 'CancerDetector', using the DNA methylation profiles of cell-free DNAs.

The three-dimensional genome organization of Drosophila melanogaster through data integration.

Background: Genome structures are dynamic and non-randomly organized in the nucleus of higher eukaryotes. To maximize the accuracy and coverage of three-dimensional genome structural models, it is important to integrate all available sources of experimental information about a genome's organization. It remains a major challenge to integrate such data from various complementary experimental methods.

CancerLocator: non-invasive cancer diagnosis and tissue-of-origin prediction using methylation profiles of cell-free DNA.

We propose a probabilistic method, CancerLocator, which exploits the diagnostic potential of cell-free DNA by determining not only the presence but also the location of tumors. CancerLocator simultaneously infers the proportions and the tissue-of-origin of tumor-derived cell-free DNA in a blood sample using genome-wide DNA methylation data. CancerLocator outperforms two established multi-class classification methods on simulations and real data, even with the low proportion of tumor-derived DNA in the cell-free DNA scenarios.

Mining 3D genome structure populations identifies major factors governing the stability of regulatory communities.

Three-dimensional (3D) genome structures vary from cell to cell even in an isogenic sample. Unlike protein structures, genome structures are highly plastic, posing a significant challenge for structure-function mapping. Here we report an approach to comprehensively identify 3D chromatin clusters that each occurs frequently across a population of genome structures, either deconvoluted from ensemble-averaged Hi-C data or from a collection of single-cell Hi-C data.

Hi-Corrector: a fast, scalable and memory-efficient package for normalizing large-scale Hi-C data.

Unlabelled: Genome-wide proximity ligation assays, e.g. Hi-C and its variant TCC, have recently become important tools to study spatial genome organization.

Predicting linear B-cell epitopes by using sequence-derived structural and physicochemical features.

The identification of linear B-cell epitopes is important for developing epitope-based vaccines. Recently, machine learning techniques have been used in the epitope prediction, but the existing encoding schemes usually neglected valuable discriminative information. In this paper, we proposed a novel encoding scheme which combines several groups of sequence-derived structural and physicochemical features, and support vector machine was used to construct the prediction models.