Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Effect of mitochondrial haplotype on gene expression in inter-species composite cell lines formed through cell fusion

ABSTRACT: Inter-species tetraploid composite cells formed by fusing cells from multiple contributor species are a new model system for disentangling cis from trans gene-regulatory divergence. It is unclear, however, how often mitochondria from one or both contributor species are inherited by these cells. We generated a panel of inter-species composite iPSCs by fusing human, chimpanzee, and bonobo contributor cell lines, labeling the composite cell line of origin using MULTI-seq barcodes. We then performed single cell RNA sequencing and demultiplexed cells using the CellBouncer toolkit. After identifying the species of origin of the mitochondria in all cells, we found that human mitochondria tend to predominate over those of other species in fusions including human contributor lines, and that cells containing two species' mitochondria are rare and show signs of apoptotic signaling, along with abnormal mitochondrial gene regulation.

ORGANISM(S): Pan troglodytes

PROVIDER: GSE329917 | GEO | 2026/07/15

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Mitochondria-selective primate cell fusions reveal functional consequences of mitochondrial divergence

Project description:Interspecies composite cell lines (or hybrid cells) are powerful tools to study genomic divergence between species. However, to date, the only pluripotent composite lines to exist are between human and chimpanzee. In addition, while these human-chimp composite lines contain the nuclear genomes from both species, they only contain the mitochondrial genome from one: human. Here we describe the generation of multiple composite pluripotent stem cell (PSC) lines between human and all other species of great apes (chimpanzee [Pan troglodytes], bonobo [Pan paniscus], gorilla [Gorilla gorilla], and orangutan [Pongo abelii]). In addition, we utilized a strategy based on enforced mitophagy to generate human-great ape composite PSCs that contain either the human or the non-human primate (NHP) mitochondrial genomes.

2025-06-03 | GSE270085 | GEO

Project description:single cell RNA-seq of composite iPSCs from human, chimpanzee, and bonobo contributor lines

| PRJNA1358605 | ENA

Primate cell fusion disentangles gene regulatory divergence in neural development

Project description:Among primates, humans display a unique trajectory of development responsible for the many traits specific to our species. However, the inaccessibility of human and chimpanzee primary tissues has limited our ability to study human evolution. Comparative in vitro approaches using primate-derived induced pluripotent stem cells have begun to reveal species differences on the cellular and molecular levels. In particular, brain organoids have emerged as a promising platform to study primate neural development in vitro, although cross-species comparisons of organoids are complicated by differences in developmental timing and variability of differentiation. Here, we developed a new platform to address these limitations. We first generated a panel of tetraploid hybrid stem cells by fusing human and chimpanzee induced pluripotent stem cells. We next applied this approach to study species divergence in cerebral cortical development by differentiating them into neural organoids. We found that hybrid organoids provide a controlled system for disentangling cis- and trans-acting gene expression divergence across cell types and developmental stages, revealing a signature of selection on astrocyte-related genes. In addition, we identified an up-regulation of human somatostatin receptor 2 (SSTR2), which regulates neuronal calcium signaling and is associated with neuropsychiatric disorders. We discovered a human-specific response to modulation of SSTR2 function in cortical neurons, underscoring the potential of this unique platform to reveal the molecular basis of human evolution.

2020-11-17 | GSE144825 | GEO

Generation and transcriptome profiling of bonobo induced pluripotent stem cells using stealth RNA vectors: a tripartite comparative study with humans and chimpanzees

Project description:Bonobos (Pan paniscus), which share a close evolutionary lineage with chimpanzees (Pan troglodytes) and humans, offer vital insights into the genetic and developmental propensities underlying human evolution. In this study, we established nine integration-free bonobo induced pluripotent stem cell (iPSC) lines from cryopreserved peripheral blood mononuclear cells using Sendai virus-derived RNA vectors. These iPSCs exhibited key pluripotency gene expression, normal karyotypes, and the capacity for differentiation into neural, mesodermal, and endodermal lineages, including the first successful induction of limb bud mesoderm cells from great ape iPSCs. Comprehensive transcriptome comparisons among bonobo, chimpanzee, and human iPSCs uncovered significant gene expression and retrotransposon divergence between Homo and Pan species, while highlighting minimal differences between bonobos and chimpanzees. Nevertheless, variation in the expression of mitochondrial metabolism-related genes was observed between the Pan species, suggesting potential interspecies differences in metabolic activity. This work provides a valuable platform for investigating the molecular and cellular mechanisms underlying species-specific developmental traits in closely related hominids and sheds light on the evolutionary origins of human characteristics.

2025-11-17 | GSE271715 | GEO

Species-specific maturation profiles of human, chimpanzee and bonobo neural cells

Project description:Species-specific maturation profiles of human, chimpanzee and bonobo neural cells

| PRJNA513185 | ENA

Great Ape Copy Number Variation

Project description:Intra-specific polymorphism in copy number is documented in many organisms, including human and chimpanzee, but very little is known for other great apes. This study aims to provide CNVs data for orangutan, gorilla, bonobo and chimpanzee, and compare the CNV patterns among these species, as well as with human CNVs and segmental duplications from public databases.

2011-08-03 | GSE30559 | GEO

Bonobo Fibroblast Data: Hacia Laboratory

Project description:Data from bonobo fibroblast cell lines described in Genome Research paper "Comparative analysis of gene expression patterns in human and African great ape cultured fibroblasts" Keywords = African Great Ape, Human Evolution, Fibroblast, Bonobo, Gorilla, Human Keywords: ordered

2003-05-08 | GSE428 | GEO

CPI-613 and Fluorouracil in Treating Patients With Metastatic Colorectal Cancer That Cannot Be Removed by Surgery

Project description:This pilot phase I trial studies the side effects and best dose of CPI-613 when given together with fluorouracil in treating patients with colorectal cancer that has spread to other parts of the body and cannot be removed by surgery. CPI-613 may kill tumor cells by turning off their mitochondria. Mitochondria are used by tumor cells to produce energy and are the building blocks needed to make more tumor cells. By shutting off these mitochondria, CPI-613 deprives the tumor cells of energy and other supplies that they need to survive and grow in the body. Drugs used in chemotherapy, such as fluorouracil, work in different ways to stop the growth of tumor cells, either by killing the cells, by stopping them from dividing, or by stopping them from spreading. Giving CPI-613 with fluorouracil may kill more tumor cells.

| 2173777 | ecrin-mdr-crc

Genetic studies of human-chimpanzee divergence using stem cell fusions

Project description:Complete genome sequencing has identified millions of DNA changes that differ between humans and chimpanzees. Although a subset of these changes likely underlies important phenotypic differences between humans and chimpanzees, it is currently difficult to distinguish causal from incidental changes and to map specific phenotypes to particular genome locations. To facilitate further genetic study of human-chimpanzee divergence, we have generated human and chimpanzee auto-tetraploids and allo-tetraploids by fusing induced pluripotent stem cells (iPSCs) of each species. The resulting tetraploid iPSCs can be stably maintained and retain the ability to differentiate along ectoderm, mesoderm, and endoderm lineages. RNA sequencing identifies thousands of genes whose expression differs between humans and chimpanzees when assessed in single-species diploid or auto-tetraploid iPSCs. Analysis of gene expression patterns in inter-specific allo-tetraploid iPSCs shows that human-chimpanzee expression differences arise from substantial contributions of both cis-acting changes linked to the genes themselves, and trans-acting changes elsewhere in the genome. To enable further genetic mapping of species differences, we tested chemical treatments for stimulating genome-wide mitotic recombination between human and chimpanzee chromosomes, and CRISPR methods for inducing species-specific changes on particular chromosomes in allo-tetraploid cells. We successfully generated derivative cells with nested deletions or inter-specific recombination on the X chromosome. These studies identify a long distance cis-regulatory domain of the Fragile X-associated gene (FMR1), confirm an important role for the X chromosome in trans-regulation of other expression differences, and illustrate the potential of this system for more detailed mapping of the molecular basis of human and chimpanzee evolution.

2021-11-29 | GSE184768 | GEO

A Proximity Labeling Strategy Enables Spatial Proteomic Analysis of Inter-organelle Membrane Contacts in Living Cells

Project description:Inter-organelle membrane contacts especially mitochondria-endoplasmic reticulum contacts (MERC) conduct important biological functions including exchange of lipids and ions, and modulation of membrane dynamics. Alterations of inter-organelle membrane contacts have been implicated with the pathogenesis of diseases, such as neurodegenerative diseases, cancers and type 2 diabetes. However, the protein compositions of inter-organelle contacts remain largely unknown as no biomarker has been discovered and it’s difficult to purify intact inter-organelle contact proteins. Here, we applied a systematic approach to probe the spatial proteome of MERC in living cells by combining the bimolecular fluorescence complementation assay and a proximity labeling strategy based on APEX2. As a result, we discovered 403 highly confident MERC proteins including many well-known MERC proteins and a variety of novel protein species as well. We further validated that WFS1, BAG2, SPTLC1 and GLUD1 are enriched at MERC with high resolution fluorescent imaging. Our study provides a powerful tool to characterize the spatial proteomes of inter-organelle membrane contacts in living cells.

2023-10-24 | PXD035801 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data