Feasibility of laser speckle contrast imaging using the bowel perfusion assessment tool Lapvas-Imaging
Ontology highlight
ABSTRACT:
DISEASE(S): Colorectal Cancer
PROVIDER: 2443699 | ecrin-mdr-crc |
REPOSITORIES: ECRIN MDR
Similar Datasets
Project description:<p>The incidence of intestinal diseases increases with age, but the regulators of gut aging and the molecules linking gut aging and diseases remain largely unknown. By profiling the transcriptome, proteome, phosphoproteome and metabolome of 104 <em>Macaca fascicularis</em> large intestinal tissues, we unveiled asynchronous aging within the proximal and distal colon. The levels of many gene products, phosphosites and metabolites changed with age in a location- and sex-dependent manner, and many of these changes occurred at distinct rates or even in opposite directions at different locations. Assessment of 60 age-related molecules (genes, phosphosites, metabolites) across<em> C. elegans</em>, mice, and cell lines identified 32 crucial regulators of gut atrophy and barrier integrity. Notably, we found that tryptophan metabolism via the kynurenine and serotonin (5-HT) pathways was more active in the proximal and distal colon, respectively. In a mouse colitis model, reducing 5-HT production with a Tph1 inhibitor alleviated distal but not proximal colitis, while adding 5-HT aggravated distal symptoms, indicating that distal colitis is more sensitive to 5-HT fluctuations. Moreover, we identified 24 proteins, particularly HPX, that potentially link gut aging to colorectal cancer (CRC). High levels of HPX in CRC predicted poor prognosis in patients older than 50 yr but not in younger patients, suggesting that an age-linked HPX increase in the gut may contribute to CRC progression. Collectively, this work reveals the heterogeneity of large intestinal aging in non-human primates and offers promising targets for preventing gut aging and diseases.</p>
2023-12-14 | MTBLS7612 | MetaboLights
Project description:Goal: Since disease susceptibility of the intestine exhibits an anatomical bias, we propose that the chromatin landscape, especially the site-specific epigenetic differences in histone modification patterns throughout the longitudinal axis, contributes to a differential response to chemoprotective agents. Method: We assessed the chromatin structure associated with gene expression profiles in the rat proximal and distal colon by globally correlating chromatin immunoprecipitation next-generation sequencing analysis (ChIP-Seq) with mRNA transcription (RNA-Seq) data. Crypts were isolated from the proximal and distal colonic regions from rats maintained on a semi-purified diet, and mRNA gene expression profiles were generated using RNA-Seq. The remaining isolated crypts were paraformaldehyde-crosslinked and chromatin immunoprecipitated using antibodies against H3K4me3, H3K9me3, and RNA Polymerase II. Results/Conclusion: Globally, RNA-Seq results indicated that 9,866 genes were actively expressed, of which 540 genes were differentially expressed between the proximal and distal colon. With regard to differentially expressed genes, a high correlation was observed between H3K4me3-Seq and RNA-Seq data, with 96% of the canonical pathways being similarly affected in the H3K4me3-Seq and RNA-Seq data sets. Gene ontology analysis indicated that colonic crypt location significantly impacted both chromatin and transcriptional regulation of genes involved in cell transformation, lipid metabolism, lymphatic development and immune cell trafficking. Gene function analysis indicated that the PI3-Kinase signaling pathway was regulated in a site-specific manner, e.g., pathway proto-oncogenes, c-Jun, c-Fos and ATF, were up-regulated in the distal colon. Middle and long non-coding RNAs (lncRNAs) were also detected in the colon, including select lncRNAs formerly only detected in the rat nervous system. In summary, distinct combinatorial patterns of histone modifications exist in the proximal versus distal colon. These site-specific differences may explain the differential effects of chemoprotective agents on cell transformation in the ascending (proximal) and descending (distal) colon. Examination of mRNA profiles and 2 different histone modifications (H3K4me3 and H3K9me3) in 2 tissue types (proximal and distal colon).
2013-08-01 | E-GEOD-49389 | biostudies-arrayexpress
Project description:It is not known why cancers arising in anatomically distinct locations but within the same tissue type can exhibit stark differences in molecular, pathological and clinical features. Cancers arising in proximal and distal sites of the colon are emblematic of these above differences as the proximal and distal colon cancers harbor differences in key molecular features, with BRAFV600E oncogene predominantly occurring in proximal colon cancers in the context of the increased promoter DNA methylation phenotype (CIMP-high), while distal colon cancers lack these molecular features. We determined the molecular basis of tissue-location specificity of driver mutations using normal mouse derived organoid models for colon cancer initiation. We show that the homeobox transcription factor, Cdx2, which is downregulated by DNA methylation in proximal colon cancers, plays distinct roles in regulating stem cell and differentiation in proximal compared to distal colon stem cells. Loss of Cdx2 altered the differentiation and stem cell programs and result in transformation by BRAFV600E specifically in the proximal but not distal colon stem cells. Analyses of RNA expression and Cdx2-binding to target genomic regions revealed that Cdx2 was a key effector of the transcriptional response to differentiation cues in proximal colon cells. This proximal colon-specific transcriptional program concurrently is tumor suppressive, and its loss sufficiently creates permissive state for oncogenic-BRAF mutations. The transcriptional program associated with Cdx2 loss in mouse proximal organoids matches that of human proximal colon cancers with downregulated CDX2 expression due to epigenetic silencing. Our analyses reveal that developmental and lineage-restricted transcription factors maintain tissue-location specific transcriptional programs which create critical dependencies for tumor initiation.
2023-12-12 | GSE218480 | GEO
Project description:It is not known why cancers arising in anatomically distinct locations but within the same tissue type can exhibit stark differences in molecular, pathological and clinical features. Cancers arising in proximal and distal sites of the colon are emblematic of these above differences as the proximal and distal colon cancers harbor differences in key molecular features, with BRAFV600E oncogene predominantly occurring in proximal colon cancers in the context of the increased promoter DNA methylation phenotype (CIMP-high), while distal colon cancers lack these molecular features. We determined the molecular basis of tissue-location specificity of driver mutations using normal mouse derived organoid models for colon cancer initiation. We show that the homeobox transcription factor, Cdx2, which is downregulated by DNA methylation in proximal colon cancers, plays distinct roles in regulating stem cell and differentiation in proximal compared to distal colon stem cells. Loss of Cdx2 altered the differentiation and stem cell programs and result in transformation by BRAFV600E specifically in the proximal but not distal colon stem cells. Analyses of RNA expression and Cdx2-binding to target genomic regions revealed that Cdx2 was a key effector of the transcriptional response to differentiation cues in proximal colon cells. This proximal colon-specific transcriptional program concurrently is tumor suppressive, and its loss sufficiently creates permissive state for oncogenic-BRAF mutations. The transcriptional program associated with Cdx2 loss in mouse proximal organoids matches that of human proximal colon cancers with downregulated CDX2 expression due to epigenetic silencing. Our analyses reveal that developmental and lineage-restricted transcription factors maintain tissue-location specific transcriptional programs which create critical dependencies for tumor initiation.
2023-12-12 | GSE218479 | GEO
Project description:Goal: Since disease susceptibility of the intestine exhibits an anatomical bias, we propose that the chromatin landscape, especially the site-specific epigenetic differences in histone modification patterns throughout the longitudinal axis, contributes to a differential response to chemoprotective agents. Method: We assessed the chromatin structure associated with gene expression profiles in the rat proximal and distal colon by globally correlating chromatin immunoprecipitation next-generation sequencing analysis (ChIP-Seq) with mRNA transcription (RNA-Seq) data. Crypts were isolated from the proximal and distal colonic regions from rats maintained on a semi-purified diet, and mRNA gene expression profiles were generated using RNA-Seq. The remaining isolated crypts were paraformaldehyde-crosslinked and chromatin immunoprecipitated using antibodies against H3K4me3, H3K9me3, and RNA Polymerase II. Results/Conclusion: Globally, RNA-Seq results indicated that 9,866 genes were actively expressed, of which 540 genes were differentially expressed between the proximal and distal colon. With regard to differentially expressed genes, a high correlation was observed between H3K4me3-Seq and RNA-Seq data, with 96% of the canonical pathways being similarly affected in the H3K4me3-Seq and RNA-Seq data sets. Gene ontology analysis indicated that colonic crypt location significantly impacted both chromatin and transcriptional regulation of genes involved in cell transformation, lipid metabolism, lymphatic development and immune cell trafficking. Gene function analysis indicated that the PI3-Kinase signaling pathway was regulated in a site-specific manner, e.g., pathway proto-oncogenes, c-Jun, c-Fos and ATF, were up-regulated in the distal colon. Middle and long non-coding RNAs (lncRNAs) were also detected in the colon, including select lncRNAs formerly only detected in the rat nervous system. In summary, distinct combinatorial patterns of histone modifications exist in the proximal versus distal colon. These site-specific differences may explain the differential effects of chemoprotective agents on cell transformation in the ascending (proximal) and descending (distal) colon.
2013-08-01 | GSE49389 | GEO
Project description:The biological behavior and clinical outcome of gastric cancers are variable considerably according to anatomic location, such as proximal gastric cancer (PGC) and distal gastric cancer (DGC). Therefore, identification of the biomarkers used for recognizing the biological behavior and predicting clinical outcome has been a major goal in gastric cancer researches.
2013-03-27 | E-MTAB-1307 | biostudies-arrayexpress
Project description:Salamander limb regeneration is an accurate process which gives rise exclusively to the missing structures, irrespective of the amputation level. This suggests that cells in the stump have an awareness of their spatial location, a property termed ‘positional identity’. Little is known about how positional identity is encoded, in salamanders or other biological systems. Through single-cell RNAseq analysis, we identified Tig1/RARRES1 as a potential determinant of proximal identity. Tig1 encodes a conserved cell surface molecule, is regulated by retinoic acid and exhibits a graded expression along the proximo-distal axis of the limb. Its overexpression leads to regeneration defects in the distal elements and elicits proximal displacement of blastema cells, while its neutralisation blocks proximo-distal cell surface interactions. Critically, Tig1 reprogrammes distal cells to a proximal identity, upregulating Prod1 and inhibiting HoxA13 and distal transcriptional networks. Thus, Tig1 is a central cell surface determinant of proximal identity in the salamander limb.
2022-01-30 | GSE184948 | GEO
Project description:Proteomic analysis of injured human peripheral nerves, particularly focusing on events occurring in the proximal and distal nerve ends, remains relatively underexplored. This study aimed to investigate the molecular patterns underlying a digital nerve injury, concentrating on differences in protein expression between the proximal and distal nerve ends. A total of 26 human injured digital nerve samples (24 men; 2 women; median age 47 [30-66] years), harvested during primary nerve repair within 48 hours post-injury from proximal and distal nerve ends, were analyzed using mass spectrometry. A total of 3914 proteins were identified, with 127 proteins showing significant differences in abundance between the proximal and the distal nerve ends. The downregulation of proteins in the distal nerve end was associated with synaptic transmission, autophagy, neurotransmitter regulation, cell adhesion and migration. Conversely, proteins upregulated in the distal nerve end were implicated in cellular stress response, neuromuscular junction stability and muscle contraction, neuronal excitability and neurotransmitter release, synaptic vesicle recycling and axon guidance and angiogenesis. Investigation of proteins, with functional annotations analysis, in proximal and the distal ends of human injured digital nerves, revealed dynamic cellular responses aimed at promoting tissue degeneration and restoration, while suppressing non-essential processes.
2024-07-19 | PXD051266 | Pride
Project description:Intervention 1: Intervention group A: 32 patients randomly select and place in the resection and anastomosis group. Proximal and distal of the intestine within the ileostomy site are resected then hand sewn anastomosis will be done. Intervention 2: Intervention group B : 32 patients randomly select and place in the anterior repair group. Anterior intestinal defect within the ileostomy site will be repaired. Intervention 3: Intervention group C: 32 patients randomly select and place in the resection and anastomosis group. Proximal and distal of the intestine within the ileostomy site are resected then anastomosis will be done by the stapler.
Primary outcome(s): The first day of defecation. Timepoint: daily up to one week. Method of measurement: question from the patient in daily ward visits.;The first day of flatus. Timepoint: daily up to one week. Method of measurement: question from the patient in daily ward visits.;The first day of oral feeding. Timepoint: daily up to one week. Method of measurement: stariting of oral diet based on surgeons decision.;Post operation early complications. Timepoint: daily up to one month. Method of measurement: question from the patient in daily ward visits.;Post operation late complications. Timepoint: monthly up to 6 months. Method of measurement: question from the patient in monthly clinic visits.
Study Design: Randomization: Randomized, Blinding: Double blinded, Placebo: Not used, Assignment: Parallel, Purpose: Treatment, Randomization description: patients were randomly assigned into three groups using randomly permuted blocks method. random allocation sequence was generated by the online platform www.randomization.com, Blinding description: In this double-blind study, participants, Investigator and Outcome assessor , were blind to the study.Before the surgery, the patients are randomly divided into three groups, which the patients and investigators do not know about it, and then the surgeon in the operating room is informed about the type of surgery of each patient, and the surgery is performed, and then the patients are transferred to the surgery ward. The patients are visited by the another surgeon ( investigator and outcome assessor) who is blind with the type of surgery of each patient and the information and data of the patients are collected and then the information is se
| 23569 | ecrin-mdr-crc
Project description:Evaluation of early transcriptional changes in blood brain barrier genes involved in the patogenesis of brain edema associated with ALF. Two different well stablished rat models were analyzed: Portacaval anastomosis plus hepatic artery ligation and portacaval anastomosis plus total hepatectomy.
2016-04-05 | GSE79906 | GEO