Extended Data Fig. 1: Additional evaluation of the effects of CSF1R inhibitors and irradiation dose.

a, Experimental design. The last injection of busulfan was applied one day before transplantation, and PLX5622 diet was withdrawn on the day of transplantation. 200 ×10³ B6.UBC-GFP graft cells were transplanted per recipient animal. iv, intravenous. b, Representative flow cytometry plots and gating strategy. c, Quantification of donor derived GFP⁺ chimerism in the peripheral blood and myeloid compartment of the contralateral brain hemisphere based on flow cytometry. n = 4, 4, 3, and 4 animals per group, respectively (from left to right). Two-sided Welch t-test. d, Evaluation of microglia depletion. Representative flow cytometry plots and gating strategy are shown for two female animals. e, Flow cytometric quantification. The brain was analyzed one day after the last PLX5622 injection. The drug was administered daily over 4 days. n = 3 animals per group. Two-sided Welch t-test. f, Flow cytometric quantification. The brain was analyzed one day after the last PLX3397 injection. The drug was administered daily over 3 days. n = 3 animals per group. Two-sided Welch t-test. g, Experimental design. 200 ×10³ B6.UBC-GFP HSPC were transplanted per recipient animal. Numbers (n) represent assigned and survived animals per group. ip, intraperitoneal. h, Representative flow cytometry plots and gating strategy per experimental group. i, Flow cytometric quantification (contralateral brain hemisphere). n = 5, 4, and 1 animals per group, respectively (from left to right). Two-sided Welch t-test. j, Experimental outline. 200 ×10³ B6.UBC-GFP HSPC were transplanted per recipient animal. n = 3 animals per group. k, Flow cytometric quantification (contralateral brain hemisphere). l, Immunofluorescent staining for GFP of sagittal brain sections of the ipsilateral hemisphere of two animals with irradiation+PLX3397 treatment. Shown are cortical areas of reduced donor cell engraftment density. Purple square illustrates magnified area of panel m. Scale bar = 200 µm. m, Immunofluorescent stain shows repopulated endogenous GFP⁻ microglia and grafted GFP⁺ cells. Demonstrated is the border between high-density donor cell repopulated brain and an area with low chimerism. Scale bar = 50 µm. n, Experimental outline. 200 ×10³ B6.UBC-GFP HSPC were transplanted per recipient animal. n = 3 animals per group. o, Flow cytometric quantification (contralateral brain hemisphere). Two-sided Welch t-test. p, Flow cytometric quantification of myeloid donor chimerism in the brain and blood 33 weeks after ICV transplantation and preconditioning with PLX3397 and 10 Gy head irradiation. n = 4 animals. Box-plot elements in Extended Data Fig. 1 represent median (center line), first and third quartiles (lower and upper hinges) and smallest/highest value with at most 1.5*IQR (inter-quartile range) from the hinge (whiskers).

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