5-Methyluridine is Ubiquitous in Pseudomonas aeruginosa tRNA and Modulates Antimicrobial Resistance and Virulence.

Building on decades of work in characterizing the dozens of RNA modifications in the microbial epitranscriptome, recent advances in analytical technology and genetics have revealed systems-level functions for many tRNA modifications. The tRNA (uracil-5-)-methyltransferase TrmA and its product, 5-methyl uridine (mU) at position 54 in the T-loop, however, has not been linked to a specific phenotype. Here, we defined the functional and biological roles of TrmA in Pseudomonas aeruginosa (PA14), a major multidrug-resistant pathogen.

tRNA modification profiling reveals epitranscriptome regulatory networks in .

Transfer RNA (tRNA) modifications have emerged as critical posttranscriptional regulators of gene expression affecting diverse biological and disease processes. While there is extensive knowledge about the enzymes installing the dozens of post-transcriptional tRNA modifications - the tRNA epitranscriptome - very little is known about how metabolic, signaling, and other networks integrate to regulate tRNA modification levels. Here we took a comprehensive first step at understanding epitranscriptome regulatory networks by developing a high-throughput tRNA isolation and mass spectrometry-based modification profiling platform and applying it to a transposon insertion mutant library comprising 5,746 strains.

Candidate prognostic biomarkers and prediction models for high-grade serous ovarian cancer from urinary proteomics.

High-grade serous ovarian cancer (HGSOC) is one of the most common histologic types of ovarian cancer. The purpose of this study was to identify potential prognostic biomarkers in urine specimens from patients with HGSOC. First, 56 urine samples with information on relapse-free survival (RFS) months were collected and classified into good prognosis (RFS ≥ 12 months) and poor prognosis (RFS < 12 months) groups.

The preoperative platelet to neutrophil ratio and lymphocyte to monocyte ratio are superior prognostic indicators compared with other inflammatory biomarkers in ovarian cancer.

Background: Previous studies have suggested that the ratios of immune-inflammatory cells could serve as prognostic indicators in ovarian cancer. However, which of these is the superior prognostic indicator in ovarian cancer remains unknown. In addition, studies on the prognostic value of the platelet to neutrophil ratio (PNR) in ovarian cancer are still limited.

Clinical and prognostic significance of perioperative change in red cell distribution width in patients with esophageal squamous cell carcinoma.

Background: Numerous studies have reported the prognostic significance of the red cell distribution width (RDW) in patients with esophageal squamous cell carcinoma (ESCC), but the relationship between the perioperative change in RDW (delta RDW) and survival in patients with ESCC after surgery has not been evaluated.

Methods: A total of 594 patients with newly diagnosed ESCC after surgery were enrolled in the study. Delta RDW (delta RDW = Postoperative RDW-Preoperative RDW) was counted based on data within one week before surgery and two weeks after surgery.

Thiol oxidative stress-dependent degradation of transglutaminase2 via protein S-glutathionylation sensitizes 5-fluorouracil therapy in 5-fluorouracil-resistant colorectal cancer cells.

5-Fluorouracil (5-Fu) is a first-line drug for colorectal cancer (CRC) therapy. However, the development of 5-Fu resistance limits its chemotherapeutic effectiveness and often leads to poor prognoses of CRC. Transglutaminase 2 (TGM2), a member of the transglutaminase family, is considered to be associated with chemoresistance through apoptotic prevention in various cancers including CRC.

Multimodal Sonographic Appearance and Survival Outcomes of 69 Cases of Primary Thyroid Lymphoma Over 10 Years.

Objectives: To investigate ultrasound appearance and the survival outcomes for patients with primary thyroid lymphoma (PTL).

Methods: Ultrasonic images and clinical characteristics from pathologically confirmed 69 PTL patients (2008-2019) were retrospectively analyzed. The clinical characteristics, ultrasonic characters, and prognostic factors were analyzed.

Depletion of METTL3 alters cellular and extracellular levels of miRNAs containing mA consensus sequences.

Extracellular vesicles (EVs) are capable of transferring cargo from donor to recipient cells, but precisely how cargo content is regulated for export is mostly unknown. For miRNA cargo, we previously showed that when compared to isogenic colorectal cancer (CRC) cells expressing wild-type KRAS, a distinct subset of miRNAs are differentially enriched in EVs from KRAS mutant active CRC cells, with being one of the most enriched. The mechanisms that could explain how and other miRNAs are differentially exported into EVs have not been fully elucidated.

PTP4A3 Is a Prognostic Biomarker Correlated With Immune Infiltrates in Papillary Renal Cell Carcinoma.

PTP4A3 plays an important role in the tumorigenesis and metastasis of multiple tumors, but its prognostic role in renal cancer is not well understood. We utilized the Oncomine and Tumor Immunoassay Resource databases to examine the differential expression of PTP4A3 in tumor tissues and normal tissues in breast, urinary tract, gastrointestinal tract and skin. Using the GEPIA and PrognoScan databases, the independent prognostic role of PTP4A3 was confirmed in clear cell renal cell cancer and papillary renal cell cancer.

Perioperative change in neutrophil count predicts worse survival in esophageal squamous cell carcinoma.

This study aimed to investigate the relationship between perioperative change in neutrophil count and survival of patients with esophageal squamous cell carcinoma. Neutrophil change (Nc) (where Nc = post-surgery neutrophil count - pre-surgery neutrophil count) was counted according to data within 1 week before surgery and 2 weeks after surgery. Patients were divided into two groups, Nc ≥2.

Next-generation DNA damage sequencing.

Cellular DNA is constantly chemically altered by exogenous and endogenous agents. As all processes of life depend on the transmission of the genetic information, multiple biological processes exist to ensure genome integrity. Chemically damaged DNA has been linked to cancer and aging, therefore it is of great interest to map DNA damage formation and repair to elucidate the distribution of damage on a genome-wide scale.

Development of a serum miRNA panel for detection of early stage non-small cell lung cancer.

Minimally invasive testing for early detection of lung cancer to improve patient survival is a major unmet clinical need. This study aimed to develop and validate a serum multi-microRNA (multimiR) panel as a minimally invasive test for early detection of nonsmall cell lung cancer (NSCLC) regardless of smoking status, gender, and ethnicity. Our study included 744 NSCLC cases and 944 matched controls, including smokers and nonsmokers, male and female, with Asian and Caucasian subjects.

The Postoperative Lymphocyte to Monocyte Ratio Change Predicts Poor Clinical Outcome in Patients with Esophageal Squamous Cell Carcinoma Undergoing Curative Resection.

Background: Postoperative lymphocyte to monocyte ratio (post-LMR) change (LMRc) reflects the dynamic change of balance between inflammatory reaction and immune reaction after curative operation. An elevated preoperative LMR (pre-LMR) has been shown to be a prognostic factor in patients with esophageal squamous cell carcinoma (ESCC), but the clinical value of the LMRc remains unknown.

Methods: 674 patients in ESCC undergoing curative operation were enrolled in this study.

The ABO Blood Group is an Independent Prognostic Factor in Patients with Ovarian Cancer.

Previous studies have suggested a relationship between ABO blood group and clinical outcome of various cancers. Nevertheless, little is known about the association between ABO blood group and survival in patients with ovarian carcinoma. This study aimed to investigate the prognostic significance of ABO blood group in patients with ovarian carcinoma.

Kindlin-2 suppresses transcription factor GATA4 through interaction with SUV39H1 to attenuate hypertrophy.

Kindlin-2 plays an important role in the regulation of cardiac structure and function. Depletion of Kindlin-2 contributes to cardiac hypertrophy and progressive heart failure, however, the precise mechanisms involved in this process remain unclear. GATA4 is a critical transcription factor in regulating cardiogenesis.

Identification of predictors of drug sensitivity using patient-derived models of esophageal squamous cell carcinoma.

Previous studies from the Cancer Cell Line Encyclopedia (CCLE) project have adopted commercial pan-cancer cell line models to identify drug sensitivity biomarkers. However, drug sensitivity biomarkers in esophageal squamous cell carcinoma (ESCC) have not been widely explored. Here, eight patient-derived cell lines (PDCs) are successfully established from 123 patients with ESCC.

Elevated preoperative platelet distribution width predicts poor prognosis in Esophageal Squamous Cell Carcinoma.

Activated platelets play a multifaceted role in tumorigenesis and progression. Platelet distribution width (PDW) is generally applied platelet parameters from routine blood test. Preoperative PDW has been considered a prognostic factor in many cancers.

Postoperative Monocyte Count Change Is a Better Predictor of Survival Than Preoperative Monocyte Count in Esophageal Squamous Cell Carcinoma.

In esophageal squamous cell carcinoma, an elevated preoperative absolute monocyte count (Pre-AMC) is reported to be a predictor of survival, but the clinical application of postoperative absolute monocyte count change (AMCc) remains unknown. The present study was designed to investigate the prognostic value of AMCc in ESCC. 686 patients of ESCC after radical surgery without preoperative adjuvant therapy were enrolled.

Perioperative change in lymphocyte count and prognosis in esophageal squamous cell carcinoma.

Background: Preoperative lymphocyte count (pre-LC) predicts the relapse and survival in patients with esophageal squamous cell carcinoma (ESCC), the clinical application of postoperative lymphocyte count (post-LC) change (LCc) remains unclear.

Methods: A retrospective analysis of patients with newly diagnosed ESCC who received curative resection from 2008 to 2015 was conducted. Complete blood counts from preoperative within seven days to postoperative within seven days were analyzed.

Low Preoperative Lymphocyte to Monocyte Ratio Serves as a Worse Prognostic Marker in Patients with Esophageal Squamous Cell Carcinoma Undergoing Curative Tumor Resection.

Preoperative lymphocyte to monocyte ratio (LMR) has been considered a prognostic factor in various cancers. However, the application of LMR in the assessment of patients with esophageal squamous cell carcinoma (ESCC) remains controversial. This study aimed to investigate whether preoperative LMR could serve as a prognostic marker in patients with ESCC undergoing curative tumor resection.

Impact of DNA Oxidation on Toxicology: From Quantification to Genomics.

Understanding the toxicological implications of deoxyribonucleic acid (DNA) oxidation arising from cellular oxidative stress depends on identifying DNA oxidation products, their location in the genome, and their interaction with repair, replication, and gene expression.

Kindlin-2 interacts with and stabilizes DNMT1 to promote breast cancer development.

Integrin-interacting protein Kindlin-2, as a focal adhesion protein, promotes growth and progression of breast cancer. However, the precise mechanism that underlie the role of Kindlin-2 in breast cancer is elusive. Here, we report that the expression of Kindlin-2 positively correlated with DNA methyltransferase 1(DNMT1) in breast cancer patients.

Glutathione reductase-mediated thiol oxidative stress suppresses metastasis of murine melanoma cells.

Malignant melanoma is a highly metastatic and life-threatening cancer. Reactive oxygen species (ROS) play important roles in cancer initiation and progression including metastasis. It has been reported that the oxidative stress spontaneously generated in circulating melanoma cells was able to suppress distant metastasis in vivo.

Nucleotide-Resolution Genome-Wide Mapping of Oxidative DNA Damage by Click-Code-Seq.

Single-nucleotide-resolution sequencing of DNA damage is required to decipher the complex causal link between the identity and location of DNA adducts and their biological impact. However, the low abundance and inability to specifically amplify DNA damage hinders single-nucleotide mapping of adducts within whole genomes. Despite the high biological relevance of guanine oxidation and seminal recent advances in sequencing bulky adducts, single-nucleotide-resolution whole genome mapping of oxidative damage is not yet realized.

Multifocality is associated with central neck lymph node metastases in papillary thyroid microcarcinoma.

Background: This study aimed to assess the predictive factor of multifocality to identify patients at high risk of central lymph node metastasis (CLNM).

Patients And Methods: Papillary thyroid microcarcinoma patients who underwent total or hemi-thyroidectomy with effective unilateral or bilateral central lymph node dissection were enrolled.

Results: Multifocality, age, sex, tumor size, extrathyroidal extension, and nodular goiter were significantly associated with CLNM.