Search bioRxiv⌕ Search

bioRxiv · 10.1101/114611

Early biomarker discovery in urine of Walker 256 subcutaneous rat model

Abstract

Despite advances in cancer treatments, early detection of cancer is still the most promising way to improve outcomes. Without homeostatic control, urine reflects early changes in the body and can potentially be used for early cancer diagnosis. In this study, a Walker 256 tumor rat model was established by subcutaneous injection of Walker 256 tumor cells. To identify urinary proteome changes during cancer development, urine samples from Walker 256 tumor-bearing rats were collected at five time points corresponding to before cancer cell implantation, before tumor mass palpability, at tumor mass appearance, during rapid tumor growth, and at cachexia. The urinary protein patterns changed significantly as the tumors progressed, as measured using sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). The urinary proteome of tumor-bearing rats was identified using Fusion Lumos mass spectrometry with label-free quantification. Then, 30 dynamically changed urinary proteins during cancer progression were selected as more reliable cancer biomarkers, and they were validated by targeted proteomics. Combined with the results of label-free and targeted proteome quantification, a total of 10 urinary proteins (HPT, APOA4, CO4, B2MG, A1AG, CATC, VCAM1, CALB1, CSPG4, and VTDB) changed significantly even before a tumor mass was palpable, and these early changes in urine could also be identified with differential abundance at late stages of cancer. Our study indicated that urine is a sensitive biomarker source for early detection of cancer.

Explore related subjects

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Wu, J., Guo, Z., Gao, Y.. 2017-03-07. Early biomarker discovery in urine of Walker 256 subcutaneous rat model. https://doi.org/10.1101/114611

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

The intrinsically disordered N-terminal region of eIF5B nucleates RNA-driven phase separation

Recently, we found that eukaryotic Initiation Factor 5B (eIF5B) forms cytoplasmic puncta under conditions of cellular stress and that the puncta formation drives an increase in alternative translation initiation. The formation of these puncta depends on the intrinsically disordered N-terminal region of eIF5B (eIF5B-NTR). To address the driving force behind this observation, we reconstituted a purified, binary, in vitro system to study the phase separation potential of the eIF5B-NTR. Utilizing this system, we show that eIF5B-NTR forms RNA-driven condensates at physiological concentrations. Furthermore, we defined the properties of the eIF5B condensates and the amino acid sequence requirements of this polypeptide to form complex liquid-liquid condensates. Truncation mapping identified a central arginine-rich core (residues ~200-400) that drives condensation but forms nearly static droplets in the absence of the rest of the polypeptide. Finally, we tested this model in cells to determine if the in vitro observations apply to the complex cellular environment.

biochemistry↗

Structural basis of ribosomal RNA repair by RtcB2

Ribotoxins disable ribosomes by cleaving ribosomal RNA, but how repair enzymes recognize and restore these damaged machines remains unclear. Here, we report three cryo-electron microscopy structures of the RNA ligase RtcB2 bound to damaged Escherichia coli 30S subunits. An extended interface stabilizes the ribosomal head and decoding-center scaffold while positioning the cleaved 3'-phosphate end within the catalytic pocket. Two structures contain enzyme-linked guanosine monophosphate, whereas the third captures its transfer to the RNA. RNA activation accompanies RtcB2 reorientation and entry of the 5'-hydroxyl-containing segment into an adjacent cleft. Comparisons with assembled ribosomes reveal structural barriers to substrate access. These structures connect recognition of a damaged ribosome to chemical activation of its RNA for repair.

biochemistry↗

Enhancers Silence Coupled-coding RNAs in Animals

The exact working mechanism and biogenesis of regulatory non-coding RNAs (rncRNAs), including enhancer RNAs (eRNAs), microRNAs (miRNAs), piRNAs, small interfering RNAs (siRNAs), transposons, and other non-coding RNAs, remain enigmatic. Conversely, the unique transcriptional regulation mechanism that differentiates animals from simple unicellular organisms remains elusive in life sciences. We find that regulatory non-coding genes are independent transcription units marked with arginine methylation of nucleosomes within their gene bodies, which is regulated by JMJD5. Enhancer RNAs are similar to those of other regulatory RNAs in targeting the 3-prime UTRs of coupled coding RNAs. All regulatory RNA genes share transcription factors with their target coding genes, both of which are regulated by promoter-proximal RNA Polymerase II pausing and may control the development of animals. Temporal and spatial coding genes and regulatory non-coding genes are intrinsically coupled in animals.

biochemistry↗