Gene expression profile of colorectal carcinoma HT29 PARP13 KO cells cultivated in 2D or 3D cell culture models
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1177863 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Among the key players in the DDR networks are members of the 17 PARP (poly-ADP-ribose polymerase) protein family. Beyond their involvement in various biological processes - such as transcription control, cell death, and inflammation – some PARPs specifically contribute to attracting repair proteins to sites of DNA damage. PARP1 and PARP2, the most well-studied members, act as DNA damage sensors and signal transducers synthesizing poly-ADP-ribose chains that recruits DNA repair factors and can remodel chromatin structure around damaged DNA. In addition to the well-characterized PARPs, other members of this family hold promise for cancer therapeutic applications as they are also involved in the DNA damage response. In the present study, we investigated PARP13-dependent changes in gene expression in colorectal carcinoma HT29 cell lines. Agilent microarray technology was used to analyze gene expression levels in cells cultured under 2D and 3D culture conditions. The results of our study demonstrate the pivotal role of PARP13 in the immune response and the potential for using this target for therapeutic purposes. The profile of differentially expressed genes identified in the present study could be used for further development of diagnostic and therapeutic applications in CRC.
2025-07-16 | GSE280332 | GEO
Project description:Livestock farming and conventional meat production pose significant environmental, health, and animal welfare challenges. In seeking sustainable alternative solutions, cultivated meat technology typically utilizes differentiation of myogenic progenitor cells (MPCs) into muscle cells for in vitro meat production. However, understanding the molecular determinants governing MPC differentiation into muscle cells, and the potential enhancement of this process through modulation of signaling pathways, remains limited. Herein, we characterized the molecular landscape associated with bovine MPC differentiation in vitro by employing multiomics, and explored its augmentation by small molecules, together leading to identification of media that enhanced myogenic differentiation compared with conventional methods in both 2D cultures and tissue‐engineered 3D skeletal muscle constructs. Through bulk and single‐cell transcriptomics and proteomics, we compared conventional and enhanced differentiation media, demonstrating that the enhanced media gave rise to unique progenitor‐like cell populations, while simultaneously promoting differentiation into myocytes and contractile myotubes expressing a wide array of myogenic markers that more closely resemble bovine muscle cells in vivo. The improved method for promoting myogenic differentiation in 2D and 3D formats, together with the corresponding molecular roadmap, may prove valuable for cultivated meat applications.
2025-07-25 | GSE262675 | GEO
Project description:Livestock farming and conventional meat production pose significant environmental, health, and animal welfare challenges. In seeking sustainable alternative solutions, cultivated meat technology typically utilizes differentiation of myogenic progenitor cells (MPCs) into muscle cells for in vitro meat production. However, understanding the molecular determinants governing MPC differentiation into muscle cells, and the potential enhancement of this process through modulation of signaling pathways, remains limited. Herein, we characterized the molecular landscape associated with bovine MPC differentiation in vitro by employing multiomics, and explored its augmentation by small molecules, together leading to identification of media that enhanced myogenic differentiation compared with conventional methods in both 2D cultures and tissue‐engineered 3D skeletal muscle constructs. Through bulk and single‐cell transcriptomics and proteomics, we compared conventional and enhanced differentiation media, demonstrating that the enhanced media gave rise to unique progenitor‐like cell populations, while simultaneously promoting differentiation into myocytes and contractile myotubes expressing a wide array of myogenic markers that more closely resemble bovine muscle cells in vivo. The improved method for promoting myogenic differentiation in 2D and 3D formats, together with the corresponding molecular roadmap, may prove valuable for cultivated meat applications.
2025-07-24 | PXD051019 | Pride
Project description:Livestock farming and conventional meat production pose significant environmental, health, and animal welfare challenges. In seeking sustainable alternative solutions, cultivated meat technology typically utilizes differentiation of myogenic progenitor cells (MPCs) into muscle cells for in vitro meat production. However, understanding the molecular determinants governing MPC differentiation into muscle cells, and the potential enhancement of this process through modulation of signaling pathways, remains limited. Herein, we characterized the molecular landscape associated with bovine MPC differentiation in vitro by employing multiomics, and explored its augmentation by small molecules, together leading to identification of media that enhanced myogenic differentiation compared with conventional methods in both 2D cultures and tissue‐engineered 3D skeletal muscle constructs. Through bulk and single‐cell transcriptomics and proteomics, we compared conventional and enhanced differentiation media, demonstrating that the enhanced media gave rise to unique progenitor‐like cell populations, while simultaneously promoting differentiation into myocytes and contractile myotubes expressing a wide array of myogenic markers that more closely resemble bovine muscle cells in vivo. The improved method for promoting myogenic differentiation in 2D and 3D formats, together with the corresponding molecular roadmap, may prove valuable for cultivated meat applications.
2025-07-25 | GSE290556 | GEO
Project description:Livestock farming and conventional meat production pose significant environmental, health, and animal welfare challenges. In seeking sustainable alternative solutions, cultivated meat technology typically utilizes differentiation of myogenic progenitor cells (MPCs) into muscle cells for in vitro meat production. However, understanding the molecular determinants governing MPC differentiation into muscle cells, and the potential enhancement of this process through modulation of signaling pathways, remains limited. Herein, we characterized the molecular landscape associated with bovine MPC differentiation in vitro by employing multiomics, and explored its augmentation by small molecules, together leading to identification of media that enhanced myogenic differentiation compared with conventional methods in both 2D cultures and tissue‐engineered 3D skeletal muscle constructs. Through bulk and single‐cell transcriptomics and proteomics, we compared conventional and enhanced differentiation media, demonstrating that the enhanced media gave rise to unique progenitor‐like cell populations, while simultaneously promoting differentiation into myocytes and contractile myotubes expressing a wide array of myogenic markers that more closely resemble bovine muscle cells in vivo. The improved method for promoting myogenic differentiation in 2D and 3D formats, together with the corresponding molecular roadmap, may prove valuable for cultivated meat applications.
2025-07-25 | GSE262757 | GEO
Project description:Radiotherapy is one of the most common treatments for cancer. The effects of IR are dose-dependent and different cell types have different sensitivities to IR. To reduce the damage of IR to the most sensitive cells of normal tissue, radiotherapy is administered as a fractionated dose treatment, delivering radiation in 2 Gy fractions every 24 hours, 5 times a week. However, during the course of therapy, intrinsic and acquired radioresistance of the tumor can lead to treatment failure. Therefore, there is a need for combination therapy including radiotherapy and targeted anticancer treatment. In the present study, we investigated global gene expression changes in colorectal cancer HT29 PARP13 KO cells after X-ray irradiation with a fractionated dose of 5 x 2 Gy. Agilent microarray technology was used to analyze gene expression levels in cells cultured under 2D and 3D culture conditions.
2025-07-16 | GSE280331 | GEO
Project description:* To compare surgical and oncological outcomes in patients underwent to colorectal resection with 3D vs 2D laparoscopic technique.
* To evaluate the visual overload in surgeons using 3D laparoscopic technique.
| 2220465 | ecrin-mdr-crc
Project description:In the present study we investigated the microenvironment-dependent changes of miRNA expression in colorectal carcinoma DLD1 and HT29 cell lines. Next-generation sequencing technology was employed for the analysis of miRNA expression levels in cells cultivated under 3D multicellular spheroid and 2D culture conditions. The results of our study support the previous observations regarding the role of the tumor microenvironment in the regulation of gene expression. Furthermore, the profile of differentially expressed miRNAs, determined in the present study, could be applied for a further development of diagnostic and therapeutic applications in CRC.
2018-03-30 | GSE112492 | GEO
Project description:Enhanced Media Optimize Bovine Myogenesis in 2D and 3D Models for Cultivated Meat Applications
| PRJNA1093120 | ENA
Project description:Interventions: 2D group:2D laparoscopic surgery;3D group:3D laparoscopic surgery
Primary outcome(s): operation time;The amount of bleeding;Number of lymph nodes;Postoperative gastrointestinal function recovery time;Postoperative complications
Study Design: Randomized parallel controlled trial
| 2663755 | ecrin-mdr-crc