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Three-dimensional cell-cell interactions promote direct reprogramming of patient fibroblasts into functional and transplantable neurons

ABSTRACT: Three-dimensional cell-cell interactions promote direct reprogramming of patient fibroblasts into functional and transplantable neurons

PROVIDER: PRJNA1211502 | ENA |

REPOSITORIES: ENA

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Three-dimensional cell-cell interactions promote direct reprogramming of patient fibroblasts into functional and transplantable neurons

Project description:Direct reprogramming of somatic cells into induced neurons (iNs) has become an attractive strategy for the generation of patient-specific neurons for disease modeling and regenerative neuroscience. To this end, adult human dermal fibroblasts (hDFs) present one of the most relevant cell sources. However, iNs generated from adult hDFs using traditional two-dimensional (2D) cultures are difficult to maintain long-term in vitro and face challenges in survival upon transplantation into the adult brain. These limitations impose considerable constraints on the biomedical applications and translational potential of iN technology. Here, we present a platform for direct in vitro reprogramming of adult hDFs inside three-dimensional suspension microcultures (3D-iNs) that eliminates some of the major bottlenecks in the direct neuronal reprogramming field. We show that the 3D environment favors neuronal over fibroblast cellular identity to yield more robust conversion into functional neurons with extended culturing span. The 3D reprogramming approach also provides a platform for fusion of different neuronal populations into induced assembloids. Importantly, unlike conventional iNs, 3D-iNs can be gently harvested and transplanted into the adult rodent brain to reproducibly generate functionally integrated neuron-rich grafts. Due to its simplicity, versatility, and robustness, our approach could readily be adapted as a culturing platform used for a broad range of in vitro and in vivo studies to improve disease modeling, drug screening, and other biomedical applications.

2025-04-10 | GSE287155 | GEO

Three-dimensional brain-like microenvironments facilitate the direct reprogramming of fibroblasts into therapeutic neurons

Project description:Three-dimensional brain-like microenvironments facilitate the direct reprogramming of fibroblasts into therapeutic neurons

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HNF1B induced three-dimensional genome analysis of patient-derived pancreas neoplasm organoids [HiC]

Project description:Three-dimensional (3D) genome structures are organized in a hierarchy of various module layers, including chromosome compartment, topologically associating domain, and enhancer-promoter loop. These modules are important in regulating cell type specific gene expression. Here, we aimed to elucidate how 3D genome organization is related to regulating subtype specific genes in pancreatic neoplasms.

2022-12-27 | GSE202021 | GEO

Gene expression analysis of MCF7 breast cancer cells cultured as xenografts, in two dimensional cultures, in polyHEMA anchorage independent three dimansional cell culture models and in Matrigel three dimensional cultures.

Project description:The traditional method for studying cancer in vitro is to grow immortalized cancer cells in two-dimensional (2D) monolayers on plastic. However, many cellular features are impaired in these unnatural conditions and big alterations in gene expression in comparison to tumors have been reported. Three-dimensional (3D) cell culture models have become increasingly popular and are suggested to be better models than 2D monolayers due to improved cell-to-cell contacts and structures that resemble in vivo architecture. The aim of this study was to compare gene expression patterns of MCF7 breast cancer cells when grown as xenografts, in 2D, in polyHEMA coated anchorage independent 3D models and in Matrigel on-top 3D cell culture models. Surprisingly small variations in gene expression patterns were observed between the models indicating that 3D and xenograft are not always that different from 2D cell cultures. Gene expression analysis of MCF7 breast cancer cells cultured as xenografts for 43 days, in two dimensional cultures for seven days (2D7d), in polyHEMA three dimensional cell culture models for four and seven days (PH7d and PH7d), and in Matrigel three dimensional cultures for four and seven days (MG4d and MG7d). Two biological replicates was included for each sample.

2013-10-30 | E-GEOD-47583 | biostudies-arrayexpress

HNF1B induced three-dimensional genome analysis of patient-derived pancreas neoplasm organoids [RNA-seq]

2022-12-27 | GSE202022 | GEO

HNF1B induced three-dimensional genome analysis of patient-derived pancreas neoplasm organoids [ChIP-seq]

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Gene expression profiles of colorectal cancer cells under the three dimensional culture

Project description:Colorectal cancer (CRC) shows the high mortality and morbidity. The mortal number of patients and the morbid number of patients with CRC is also increasing. However, the genes which relate to promote tumorigenesis in CRC remain unclear. In order to investigate specific genes and pathways involved in CRC tumorigenesis, we compared genes expressed between three dimensional cultures and control two-dimensional cultures. Total RNA was prepared from the CRC cell lines under the condition of two-dimensional culture and three dimensional culture.

2014-04-12 | E-GEOD-56738 | biostudies-arrayexpress

Three-dimensional chromatin re-organization during muscle stem cell aging

Project description:Three-dimensional chromatin re-organization during muscle stem cell aging

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Three-Dimensional Tumor Profiling Reveals Minimal mRNA Heterogeneity in Esophageal Squamous Cell Carcinoma

Project description:We microdissected discrete sub-regions of esophageal squamous cell carcinoma (ESCC) and analyzed the transcriptomes throughout three-dimensional (3D) tumor space. Nine cases were used for TP/TC comparison, five cases were used for 3D analysis, one normal case was set as a control.

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CD200-based cell sorting for transplantable postmitotic striatal progenitors

Project description:CD200-based cell sorting results in homogeneous subpopulations of transplantable postmitotic striatal progenitors

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