Chromatin accessibility in canine stromal cells and its implications for canine somatic cell reprogramming,STEM CELLS Translational Medicine

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Chromatin accessibility in canine stromal cells and its implications for canine somatic cell reprogramming
STEM CELLS Translational Medicine ( IF 5.4 ) Pub Date : 2020-11-16 , DOI: 10.1002/sctm.20-0278
Maria Questa ₁ , Maryam Moshref ₁ , Robert J Jimenez ₁ , Veronica Lopez-Cervantes ₁ , Charles K Crawford ₁ , Matthew L Settles ₂ , Pablo J Ross ₃ , Amir Kol ₁

Affiliation

Naturally occurring disease in pet dogs is an untapped and unique resource for stem cell‐based regenerative medicine translational research, given the many similarities and complexity such disease shares with their human counterparts. Canine‐specific regulators of somatic cell reprogramming and pluripotency maintenance are poorly understood. While retroviral delivery of the four Yamanaka factors successfully reprogrammed canine embryonic fibroblasts, adult stromal cells remained resistant to reprogramming in spite of effective viral transduction and transgene expression. We hypothesized that adult stromal cells fail to reprogram due to an epigenetic barrier. Here, we performed assay for transposase‐accessible chromatin using sequencing (ATAC‐seq) on canine stromal and pluripotent stem cells, analyzing 51 samples in total, and establishing the global landscape of chromatin accessibility before and after reprogramming to induced pluripotent stem cells (iPSC). We also studied adult stromal cells that do not yield iPSC colonies to identify potential reprogramming barriers. ATAC‐seq analysis identified distinct cell type clustering patterns and chromatin remodeling during embryonic fibroblast reprogramming. Compared with embryonic fibroblasts, adult stromal cells had a chromatin accessibility landscape that reflects phenotypic differentiation and somatic cell‐fate stability. We ultimately identified 76 candidate genes and several transcription factor binding motifs that may be impeding somatic cell reprogramming to iPSC, and could be targeted for inhibition or activation, in order to improve the process in canines. These results provide a vast resource for better understanding of pluripotency regulators in dogs and provide an unbiased rationale for novel canine‐specific reprogramming approaches.

中文翻译：

犬基质细胞的染色质可及性及其对犬体细胞重编程的影响

鉴于宠物狗自然发生的疾病与人类疾病有许多相似之处和复杂性，对于基于干细胞的再生医学转化研究来说，这种疾病是一种尚未开发的独特资源。人们对犬类体细胞重编程和多能性维持的特异性调节剂知之甚少。虽然四种山中因子的逆转录病毒递送成功地重新编程了犬胚胎成纤维细胞，但尽管有效的病毒转导和转基因表达，成体基质细胞仍然对重新编程具有抵抗力。我们假设成体基质细胞由于表观遗传障碍而无法重新编程。在这里，我们使用测序 (ATAC-seq) 对犬基质干细胞和多能干细胞进行转座酶可及染色质分析，总共分析了 51 个样本，并建立了重编程为诱导多能干细胞 (iPSC) 之前和之后染色质可及性的全局图景）。我们还研究了不产生 iPSC 集落的成体基质细胞，以确定潜在的重编程障碍。 ATAC-seq 分析确定了胚胎成纤维细胞重编程过程中不同的细胞类型聚类模式和染色质重塑。与胚胎成纤维细胞相比，成体基质细胞具有反映表型分化和体细胞命运稳定性的染色质可及性景观。我们最终确定了 76 个候选基因和几个可能阻碍体细胞重编程为 iPSC 的转录因子结合基序，并且可以作为抑制或激活的目标，以改善犬科动物的这一过程。这些结果为更好地理解狗的多能性调节因子提供了丰富的资源，并为新型的犬特异性重编程方法提供了公正的理论基础。

更新日期：2020-11-16

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