Role of Ulk1b-regulated autophagy in zebrafish definitive hematopoiesis

Abstract

Autophagy is a dynamic and evolutionary conserved lysosomal degradation pathway for cellular remodeling, development and homeostasis, yet its function in definitive hematopoiesis is elusive. Taking advantage of the optically clear and externally fertilized zebrafish (Danio rerio) embryos together with the genetic tractability and the availability of pharmacological approaches, here we inhibited autophagy by knocking out uncoordinated-51-like autophagy activating kinases 1a (ulk1a) and 1b (ulk1b) to investigate the role of autophagy in definitive hematopoiesis. The overall autophagy processes were monitored by western blot analysis, high-resolution microscopy with zebrafish Lc3 fluorescent transgenic embryo Tg(GFP-Lc3), lysosome dye (Lysotracker red) and autophagy detection dye (CYTO-ID®). Furthermore, hematopoietic phenotypes were examined by whole-mount in situ hybridization (WISH) and flow cytometry-based lineage-specific cell population counts. Zebrafish deleting ulk1b resulted in the inhibition of autophagy activation, but not autophagy flux at the whole embryo protein level. However, both autophagy activation and flux were significantly impaired in neurons, suggesting the tissue-specific requirement of ulk1b in zebrafish autophagy during embryonic development. Further investigation revealed that both chimeric and stable ulk1b knock-out significantly decreased the number of hematopoietic stem cells (HSCs) while increased myeloid progenitors, leukocytes and neutrophils in the caudal hematopoietic tissue (CHT). In contrast, both autophagy and hematopoiesis were unaffected upon somatically targated ulk1aTAL. CYTO-ID® green staining indicated that ulk1b knock-out did not affect coro1a:DsRed positive leukocyte's autophagy activation but inhibited autophagy flux upon CQ treatment. Chemical inhibition of autophagy using 3-MA treatment recapitulated the hematopoietic phenotypes observed in ulk1b mutants, suggesting that the increase in CMPs, leukocytes and neutrophils in the ulk1b mutants was likely autophagy-dependent. However, treatment with the autophagy inducer, calpeptin, can only rescue the increased neutrophil population in ulk1b mutants. Though calpeptin treatment significantly induced autophagy activation in leukocytes of wild-type and ulk1b mutant, the effects of calpeptin treatment on autophagy flux were not examined. It is possible that calpeptin cannot rescue the autophagy defects, particularly the suppressed autophagy flux in all hematopoietic lineages and thus cannot rescue all the hematopoietic phenotypes. Also, maintenance of normal hematopoiesis might require a specific autophagy level under tight regulation. In this project, we demonstrated that zebrafish is a valuable in vivo model for studying autophagy. Our results showed that ulk1b knock-out affects zebrafish autophagy in a tissue-specific manner, which is consistent with the current understanding that multiple canonical and non-canonical autophagy pathways involving different subsets of autophagy components are ongoing in different tissues. While our ulk1b knock-out models demonstrated the role of ulk1b-dependent autophagy in hematopoiesis, further investigation targeting other autophagy components in a lineage-specific manner is warranted to reveal the complete autophagy network in hematopoiesis.