Abstract B49: Modeling a pathogenic <i>SAMD9</i> mutation in human induced pluripotent stem cells
Bibliographic record
Abstract
Abstract Germline mutations in SAMD9 are the molecular determinants of some pedigrees with familial monosomy 7 and myelodysplastic syndrome (MDS) (OMIM 252270), MIRAGE syndrome (myelodysplasia, infection, restriction of growth, adrenal hypoplasia, genital phenotypes, enteropathy), and other nonsyndromic pediatric MDS. Mutations identified thus far have been associated with decreased growth of hematopoietic stem and progenitor cells (HSPCs) and bone marrow hypocellularity. Previous studies suggest that the wild-type function of SAMD9 is growth restrictive; therefore, the mutations identified in pediatric MDS have been deemed gain-of-function (GoF), given the exaggerated antiproliferative phenotype demonstrated in overexpression systems within nonhematopoietic cell lines, most commonly HEK-293T. To date, no model systems are available to study the impact of these mutations in their endogenous locus, a locus known to be induced by inflammatory stimuli, namely interferon (IFN). Here we report our development, using CRISPR/Cas9 genomic engineering, of two separate isogenic human induced pluripotent stem cell (iPSC) lines, derived from a non-neoplastic iPSC line (BJFF.6), containing a known pathogenic SAMD9 mutation (c.3406G>C; p.E1136Q), which we previously identified in a family with monosomy 7 and MDS. From this mutated iPSC line we are able to successfully differentiate hematopoietic precursors and myeloid cells that contain a pathogenic SAMD9 mutation. Using our novel pediatric MDS model system, we demonstrate that in the presence of IFN, viability of HSPCs (CD34+) and differentiated myeloid cells (CD13+) is significantly decreased when the SAMD9 p.E1136Q mutation is present (CD34+; WT=16.7% vs Mut=11.5% (p=0.05), CD13+; WT=22.6% vs. Mut=3.5% (p<0.0001)). Furthermore, we show that the genomically engineered SAMD9 locus of our iPSC-derived CD34+ and CD13+ cells remains robustly responsive to IFN stimulation. The basal level of SAMD9 expression is higher in differentiated myeloid cells than in HSPCs, a finding consistent with expression levels within normal hematopoiesis. These data suggest that we have a SAMD9 mutant pediatric MDS model system that provides a plentiful source of cells in which the effect of specific mutations on hematopoietic differentiation, proliferation, and viability may be investigated. Citation Format: Jason R. Schwartz, Jon P. Connelly, Shondra M. Pruett-Miller, Jeffery M. Klco. Modeling a pathogenic SAMD9 mutation in human induced pluripotent stem cells [abstract]. In: Proceedings of the AACR Special Conference on the Advances in Pediatric Cancer Research; 2019 Sep 17-20; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Res 2020;80(14 Suppl):Abstract nr B49.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.003 | 0.001 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".