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Derivation of elephant induced pluripotent stem cells [ATAC-seq]

ABSTRACT: The crisis of biodiversity loss in the present era requires new tools for studying non-model organisms. Elephants are both an endangered species and excellent models for studying complex phenotypes including body size, social behavior, and longevity. Here we report here the first derivation of (Elephas maximus) induced pluripotent stem cells (emiPSCs). We achieved emiPSCs using two approaches: (1) a two-step process of chemical-media induction and colony selection followed by overexpression of elephant transcription factors; and (2) a one-step process with the same transgenes but without the chemical induction step and including an additional HRAS mutant transgene, HRASG12V. For both protocols, we inhibited TP53 expansion genes, which are hypothesized to confer unique cancer resistance in elephants. To confirm their reprogrammed state, we generated a functional genomics catalog of the modified cells with RNA-seq, ATAC-seq, and single-molecule direct RNA-sequencing. While these emiPSCs are transgene-dependent, we inactivated them to differentiate emiPSCs into all three germ layers via tri-lineage differentiation, embryoid body generation, and direct differentiation into putative cell types from all three layers. These methods will open new frontiers for cellular models of non-model organisms, including for genetic rescue and conservation.

ORGANISM(S): Elephas maximus

PROVIDER: GSE283467 | GEO | 2026/03/03

REPOSITORIES: GEO

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Project description:We used morphological, ancient DNA and high throughput ancient proteomic analyses to demonstrate that a widely-discussed syntype specimen of E. maximus, a complete foetus preserved in ethanol, is actually an African elephant, genus Loxodonta. Nano-liquid chromatography (nanoLC) coupled with high resolution tandem mass spectrometry (MS/MS) was used to generate a spectra dataset from tryptic peptides and identify, as genus-diagnostic markers, the non-identical homologous ones present in publicly available protein lists for both the two elephant genera. A small, approximately 5×5×3 mm, oesophagus fragment and the terminal portion of a cartilaginous rib of similar size, of 64 and 39 mg respectively (wet weight), were removed from the well preserved, near complete, body of an elephant foetus in a spirit jar, held today at the Swedish Museum of Natural History (NRM) in Stockholm and referred to by Linnaeus (1764) in his description of the Swedish King Adolf Fredrik’s collection. Tryptic peptides were generated using a filter-aided sample preparation (FASP) protocol (Wisniewski et al., 2009). The LC-MS system consisted of an EASY-nLC™system (Thermo Scientific, Odense, Denmark) connected to the Q Exactive (Thermo Scientific, Bremen, Germany) through a nano electrospray ion source. Five uL of each peptide sample were auto-sampled onto and directly separated in a 15 cm analytical column (75 um inner diameter) in-house packed with 3 μm C18 beads (Reprosil-AQ Pur, Dr. Maisch). The settings used were as described for the ‘sensitive’ acquisition by Kelstrup et al. (JPR 11: 3487-3497). Raw files of the two processed samples, generated during spectra acquisition, were merged and searched on a workstation using the MaxQuant algorithm v. 1.2.2.5 and the Andromeda peptide search engine. Trypsin was selected as the proteolytic enzyme and two missed cleavages were allowed. Oxidation (Met and Pro), deamidation (Asn and Gln), acetylation (K), Gln->pyro-Glu (N-term Q), and Glu->pyro-Glu (N-term E) were selected as variable amino-acid modifications. Carbamidomethylation was selected as fixed modification. Default values were used for precursor and fragment ions mass tolerance. False discovery rate was set at 1%, fragment score cut-off was set at 60 and minimum peptide length was set to 6 amino acids.

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Derivation of elephant induced pluripotent stem cells [ATAC-seq]

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