Raman
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB59061 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| ERR10793725_1.fastq.gz | Fastqsanger.gz | |||
| ERR10793725_2.fastq.gz | Fastqsanger.gz | |||
| ERR10793726_1.fastq.gz | Fastqsanger.gz | |||
| ERR10793726_2.fastq.gz | Fastqsanger.gz |
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Project description:Nonlinear optical imaging modalities, such as stimulated Raman scattering (SRS) microscopy, use pulsed-laser excitation with high peak intensity that can perturb the native state of cells. In this study, we used bulk RNA sequencing, quantitative measurement of cell proliferation, and fluorescent measurement of the generation of reactive oxygen species (ROS) to assess phototoxic effects of near-IR pulsed laser radiation, at different time scales, for laser excitation settings relevant to SRS imaging. We define a range of laser excitation settings for which there was no significant change in mouse Neuro2A cells after laser exposure. This study provides guidance for imaging parameters that minimize photo-induced perturbations in SRS microscopy to ensure accurate interpretation of experiments with time-lapse imaging or with paired measurements of imaging and sequencing on the same cells.
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Project description:Primary outcome(s): Identification of enteric nerve system in the gastrointestinal wall using Raman spectroscopy
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Project description:Intestinal failure (IF), following extensive anatomical or functional loss of small intestine (SI), hasdebilitating long-term consequences on children1. Priority of care is to increase the child’s length of functional intestine, jejunum in particular, to promote nutritional independence2. Here we construct autologous jejunal mucosal grafts using primary patient biomaterials. We show that organoids derived from patients can be expanded efficiently in vitro. In parallel, we generate decellularized human intestinal matrix with intact nanotopography, which form optimal biological scaffolds. Remarkably, proteomic and Raman spectroscopy analyses reveal highly analogous biochemical profiles of human SI and colon scaffolds, indicating that both can be used interchangeably as platforms for intestinal engineering. Indeed, seeding jejunal organoids onto either scaffold type reliably reconstructs grafts that exhibit several aspects of physiological jejunal function with potential to survive after transplantation. Our findings provide proof-of-concept data for engineering IF patient-specific jejunal grafts, ultimately aiding in restoration of nutritional autonomy.
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Project description:Alteration in metabolic repertoire is commonly associated with resistance phenotype. Although it’s a common phenotype, not much efforts have been undertaken to design effective strategies to target the metabolic drift in such cancerous cells and especially with drug resistant properties. In our study, we identified that drug resistant AML cell line HL-60/MX2 do not follow classical Warburg effect, instead these cells exhibit drastically low levels of aerobic glycolysis. Biochemical analysis confirms reduced glucose consumption and lactic acid production by resistant population with no differences in glutamine consumption. Raman spectroscopy revealed increased lipid and cytochrome content in resistant cells which were also visualized in the form of lipid droplets by Raman mapping, electron microscopy and lipid specific staining. Gene set enrichment analysis data from both the cell lines revealed significant enrichment of lipid metabolic pathways in HL-60/MX2 cells. Further drug resistant cells possess higher mitochondrial activity and increased OXPHOS suggested the role of fatty acid metabolism as energy source which was confirmed by increased rate of fatty acid oxidation. Pharmacological inhibition of fatty acid oxidation using Etomoxir affected the colony formation ability of resistant cells and inhibition of OXPHOS using Antimycin-A increased the sensitivity of resistant cells to chemotherapeutic drug, demonstrating requirement of fatty acid metabolism and increased dependency on OXPHOS by resistant leukemic cells for tumorigenicity.
2021-01-01 | E-MTAB-8981 | biostudies-arrayexpress
Project description:Early detection and treatment of gastric premalignant lesion and early gastric cancer (EGC) have been proposed to improve outcomes of gastric cancer. Gastric dysplasia is a premalignant lesion and the penultimate stage in gastric carcinogenesis. On white light endoscopy (WLE), it is difficult to distinguish gastric dysplasia and EGC from benign pathology such as gastric intestinal metaplasia (GIM). Image enhanced endoscopy such as narrow-band imaging (NBI) is recommended to improve characterization of suspicious gastric lesions detected on WLE. Magnified-endoscopy with NBI (ME-NBI) have been shown to be superior to HD-WLE for diagnosis of GIM and EGC. Data on gastric dysplasia is less robust. Ultimately, biopsy is required to confirm diagnosis of gastric dysplasia/EGC. Gastric dysplasia can be classified into low-grade dysplasia (LGD) or high-grade dysplasia (HGD). Biopsy sampling may not be representative of the final histopathological grade of resected specimens and may under-stage dysplasia. Thus, endoscopic resection (ER) is recommended for gastric dysplasia and EGC on biopsy for diagnostic and therapeutic purpose. The current gap is to improve concordance of endoscopic and histologic findings of gastric dysplasia and early gastric cancer. Raman spectroscopy based artificial intelligence system (SPECTRA IMDx) was developed to provide an objective method to identify patients with gastric premalignant lesions and EGC. SPECTRA IMDx interrogate tissues at the cellular level and utilizes molecular information to provide actionable information to endoscopist during gastroscopy. Studies on diagnostic performance using Raman spectroscopy analysis devices have shown high sensitivity and specificity in detection of gastric cancer and precancerous lesions compared to WLE. However, these studies included few GIM, gastric dysplasia and gastric carcinoma. It is still unclear if Raman spectroscopy outperforms WLE in diagnosis of gastric HGD and EGC. In addition, the Raman spectroscopy algorithm is only able to characterize lesions into high risk (HGD/EGC) versus low risk (GIM/LGD/Gastritis/Normal). It is also uncertain if this technology is able to differentiate GIM and LGD. We plan to conduct a prospective trial to validate the diagnostic accuracy of SPECTRA for prediction of gastric HGD and EGC prior to gastric ER. Hypothesis: SPECTRA IMDx is able to differentiate higher risk lesions (HGD/EGC) from lower risk tissue/lesion (GIM/LGD/Gastritis/Normal)
| 2376206 | ecrin-mdr-crc