SUPPLEMENTARY INFORMATION

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SUPPLEMENTARY INFORMATION DOI: 10.1038/ncb3575 In the format provided by the authors and unedited.

1 SUPPLEMENTARY INFORMATION DOI: /ncb3575 In the format provided by the authors and unedited. Supplementary Figure 1 Validation of key reagents and assays a, top, IHC with antibody recognizing specifically Ldha (same as used in Fig 1a). bottom, IHC with antibody recognizing multiple isoforms of Ldh protein. Scale bars indicate 20 micrometers. b, the sorting strategy employed to isolate two populations of cells from the bulge. This particular sort was used to isolate the protein samples shown by western blot in Fig 1b. c, Validation of colorimetric Ldh enzyme activity assay. The highest Ldh enzyme activity was observed in HFSC bulge and in the muscle. Activity indicated by purple stain; pink color is nuclear fast red counterstain. In absence of substrate lactate there was no detectable activity (purple stain). right, Additional validation of colorimetric Ldh enzyme activity assay. Enzyme activity inhibited by treating skin with HCl before addition of staining solution with substrate lactate. No Ldh activity (purple stain) detected. Skin in which enzyme activity is not inhibited by Hydrochloric Acid (HCl) shows highest Ldh enzyme activity in HFSC bulge and in the muscle. Scale bars indicate 50 micrometers. 1

S U P P L E M E N TA R Y I N F O R M AT I O N Supplementary Figure 2 Validation of hair cycle stage a, Analysis of RNAseq data to validate that HFSCs in telogen-anagen transition were in fact in such

2 S U P P L E M E N TA R Y I N F O R M AT I O N Supplementary Figure 2 Validation of hair cycle stage a, Analysis of RNAseq data to validate that HFSCs in telogen-anagen transition were in fact in such a transition. The telogen-anagen transition is known to be driven by Shh (Gli factors are targets) and Wnt (Lef1, Axin, Ccnd1 are targets) signaling, and correlate with increased proliferation (Ki67 and Pcna). In addition, Sox4 was previously identified as a regulator of the telogen-anagen transition. n=3 mice per timepoint. Shown as mean ± SEM. Paired t-test was performed, p < b, staining for Ki-67 marks dividing cells during various stages of the hair cycle. Brackets indicate the HFSC niche. Scale bars indicate 100 micrometers. 2

S U P P L E M E N TA R Y I N F O R M AT I O N Supplementary Figure 3 Long term deletion of Ldha in HFSCs a, K15CrePR;Ldhafl/fl animals treated with Mifepristone during telogen (day 50) were allowed

3 S U P P L E M E N TA R Y I N F O R M AT I O N Supplementary Figure 3 Long term deletion of Ldha in HFSCs a, K15CrePR;Ldhafl/fl animals treated with Mifepristone during telogen (day 50) were allowed to develop for 6 months. None of the K15CrePR;Ldhafl/ fl mice showed complete hair regrowth, compared to control animals that all grew their hair coats back completely. Images are representative of at least 12 animals per genotype. b, Histological examination of the long term K15CrePR;Ldhafl/fl mice showed that Ldha-null HFSCs remained in telogen while WT HFSCs went through anagen and then returned to telogen. This is apparent from thick sections (50 micron, right) that show an increased number of club hairs in the WT relative to Ldha-null follicles. Scale bars indicate 100 micrometers (left), and 20 micrometers (middle and right). c, IHC for HFSC marker Sox9 showed that deletion of Ldha from HFSCs does not affect their presence in the bulge even after 6 months. In addition, IHC and Ldh activity assay demonstrate that the deletion of Ldha was sustained. Because of the mosaicism of the deletion, in some portions of K15CrePR;Ldhafl/fl skin Ldha was not deleted. Shown on the bottom row is tissue from hair bearing skin in the K15CrePR;Ldhafl/fl mice where Ldha was still expressed, showing that new hair growth in K15CrePR;Ldhafl/fl mice was due to lack of deletion of Ldha caused by the mosaic approach used to mediate Cre recombination. Scale bars indicate 20 micrometers. d, To determine how various signaling pathways previously linked to the hair cycle are affected by loss of Ldha in HFSCs, we performed IHC for markers that indicate activity of these pathways in telogen and telogen-anagen transition. Note that pstat5 appears to be suppressed in normal telogen-anagen transition, and this does not seem to occur in Ldha-null HFSCs. pstat1 and pstat3 did not seem to be affected by loss of Ldha. Expression of Gli3, a target of Shh signaling, is typically induced in an activated hair germ derived from HFSCs, but Ldha-null HFSCs do not make an active hair germ. Activation of the Wnt pathway is indicated by nuclear localization of β-catenin, and very little nuclear β-catenin was detected in Ldha-null HFSCs. Scale bars indicate 6 micrometers. 3

SUPPLEMENTARY INFORMATION Supplementary Figure 4 Long term deletion of Mpc1 in HFSCs a, Six months after initiation of deletion of Mpc1 in HFSCs (K15CrePR;Mpc1fl/ fl), mice lacking Mpc1 show no

4 SUPPLEMENTARY INFORMATION Supplementary Figure 4 Long term deletion of Mpc1 in HFSCs a, Six months after initiation of deletion of Mpc1 in HFSCs (K15CrePR;Mpc1fl/ fl), mice lacking Mpc1 show no deleterious effects as measured by the hair cycle (left), pathology (middle, H and E), or staining for HFSCs (right, Sox9). Scale bars indicate 100 micrometers in middle panel, and 50 micrometers in right panel. Images are representative of at least 12 animals per genotype. b, To demonstrate that the deletion of Mpc1 promotes proliferation specifically in HFSCs, we used K15CrePR;Ldha fl/fl mice bearing a lox-stoplox-tomato allele to look at K15+ HFSCs and proliferation with and without Mpc1 deletion (left). In addition, we took advantage of the ires-gfp within the Lgr5CreER allele to stain for Ki-67 and GFP and look for co-localization with and without Mpc1 deletion (right). White brackets denote bulge area. Scale bars represent 20 micrometers. c, Deletion of Mpc1 in mice bearing the Lgr6CreER allele shows no premature induction of the hair cycle. d, Ldh activity assay on sorted HFSCs from either control or Lgr6CreER mediated Mpc1 deletion mice showed increased activity in cells lacking Mpc1. n=6 mice per genotype pooled from 2 independent experiments. Shown as mean ± SEM. Paired t-test was performed, p <

SUPPLEMENTARY INFORMATION Supplementary Figure 5 Stimulation of Jak-Stat signaling and the hair cycle. RCGD423 was applied topically to shaved mice at day 50.

5 SUPPLEMENTARY INFORMATION Supplementary Figure 5 Stimulation of Jak-Stat signaling and the hair cycle. RCGD423 was applied topically to shaved mice at day hours after treatment, the skin was harvested and prepared for IHC. IHC with the indicated antibodies demonstrates relative activity of Stat signaling in vehicle vs RCGD423 treated skin. Scale bars indicate 20 micrometers. 5

6 S U P P L E M E N TA R Y I N F O R M AT I O N Fig1 Fig 4 Fig 6 Supplementary Figure 6 Unprocessed Blots. Unprocessed scans of the blots shown in Figures 1, 4, 6 are shown. 6

7 SUPPLEMENTARY INFORMATION Supplementary Table Legend Supplementary Table 1 Presented is an inventory of mice that are described in Figures 1-6 (and Supplementary Figures 1-5), including age, sex, and genotype. 7

8 Life Sciences Reporting Summary Corresponding Author: Date: William Lowry Heather Christofk Nature Research wishes to improve the reproducibility of the work we publish. This form is published with all life science papers and is intended to promote consistency and transparency in reporting. All life sciences submissions use this form; while some list items might not apply to an individual manuscript, all fields must be completed for clarity. For further information on the points included in this form, see Reporting Life Sciences Research. For further information on Nature Research policies, including our data availability policy, see Authors & Referees and the Editorial Policy Checklist. Experimental design 1. Sample size Describe how sample size was determined. 2. Data exclusions Describe any data exclusions. 3. Replication Describe whether the experimental findings were reliably reproduced. 4. Randomization Describe how samples/organisms/participants were allocated into experimental groups. 5. Blinding Describe whether the investigators were blinded to group allocation during data collection and/or analysis. no a priori power analysis was performed. We performed at least three biologically independent experiments for all data presented, and each experiments included multiple technical replicates. no data were excluded all data presented reflect findings that were highly reproducible There was no justification for randomization into experimental groups. Blinding was not necessary because each experiment was performed with unbiased methods, measured by instruments. There were no subjective measurements made. Note: all studies involving animals and/or human research participants must disclose whether blinding and randomization were used. 6. Statistical parameters n/a For all figures and tables that use statistical methods, confirm that the following items are present in relevant figure legends (or the Methods section if additional space is needed). Confirmed The exact sample size (n) for each experimental group/condition, given as a discrete number and unit of measurement (animals, litters, cultures, etc.) A description of how samples were collected, noting whether measurements were taken from distinct samples or whether the same sample was measured repeatedly. A statement indicating how many times each experiment was replicated The statistical test(s) used and whether they are one- or two-sided (note: only common tests should be described solely by name; more complex techniques should be described in the Methods section) A description of any assumptions or corrections, such as an adjustment for multiple comparisons The test results (e.g. p values) given as exact values whenever possible and with confidence intervals noted A summary of the descriptive statistics, including central tendency (e.g. median, mean) and variation (e.g. standard deviation, interquartile range) Clearly defined error bars See the web collection on statistics for biologists for further resources and guidance. nature research life sciences reporting summary June

9 Software Policy information about availability of computer code 7. Software Describe the software used to analyze the data in this study. no new code were generated in this study. software used for analyses are standard such as excel. For all studies, we encourage code deposition in a community repository (e.g. GitHub). Authors must make computer code available to editors and reviewers upon request. The Nature Methods guidance for providing algorithms and software for publication may be useful for any submission. Materials and reagents Policy information about availability of materials 8. Materials availability Indicate whether there are restrictions on availability of unique materials or if these materials are only available for distribution by a for-profit company. 9. Antibodies Describe the antibodies used and how they were validated for use in the system under study (i.e. assay and species). 10. Eukaryotic cell lines a. State the source of each eukaryotic cell line used. no cell lines were used in this study b. Describe the method of cell line authentication used. no cell lines were used in this study c. Report whether the cell lines were tested for mycoplasma contamination. d. If any of the cell lines used in the paper are listed in the database of commonly misidentified cell lines maintained by ICLAC, provide a scientific rationale for their use. All transgenic animals described in the study will be made available upon request. All but Mpc1-flox and Ldha-flox are available from Jackson Labs. CD34 Monoclonal Antibody (RAM34), FITC, ebioscience (Catalog #: ) and CD49d (Integrin alpha 4) Monoclonal Antibody (R1-2), PE, ebioscience (Catalog #: ). β-actin (Abcam ab8227; 1:1000), β-actin (Santa Cruz sc-47778; 1:1000), C-Myc (Abcam ab32072; 1:1000), N- Myc (Santa Cruz sc-53993; 1:200), H3K27Ac (Abcam ab177178; 1:200), Mpc1(Sigma HPA045119). Ki67 (Abcam ab16667, 1:50), p-s6 (Cell Signaling CST2215, 1:50), Sox9 (Abcam ab185230, 1:1000), Ldha (Abcam ab47010, 1:100), Ldh (Abcam ab125683, 1:100), p-stat3 (Abcam ab68153, 1:200), p-stat1 (Abcam ab109461, 1:200), p-stat5 (Abcam ab32364; 1:50), Gli3 (Abcam ab6050; 1:100), β-catenin (Abcam ab32572; 1:500). no cell lines were used in this study no cell lines were used in this study nature research life sciences reporting summary June

10 Animals and human research participants Policy information about studies involving animals; when reporting animal research, follow the ARRIVE guidelines 11. Description of research animals Provide details on animals and/or animal-derived materials used in the study. Policy information about studies involving human research participants 12. Description of human research participants Describe the covariate-relevant population characteristics of the human research participants. K15-Cre-PR strain: C57bl6 The mice express Cre-ER recombinase under control of the Keratin 15 promoter and thus strictly in the stem cells of the epidermis. The Cre-ER transgene efficiently recognizes and cleaves DNA between recognition sites known as LoxP sites. When these mice are crossed to generate homozygous floxed animals with the Cre-ER transgene, the gene flanked by LoxP sites is deleted upon treatment with progesterone, allowing for an inducible conditional ablation of the gene over any kind of timecourse. In this case we can eliminate a gene of interest specifically in the stem cells of the epidermis. Floxed Ldha STrain: C57Bl6 These mice harbor genetically modified alleles of the Ldha gene. These mice are normal, but any offspring that also express an allele of Cre recombinase will have the floxed allele of Ldha deleted. We are using these mice to study the effect of deleting this metabolic gene in stem and transit-amplifying cells of the epidermis. Floxed MPC1 STrain: C57Bl6 These mice harbor genetically modified alleles of the MPC1 gene. These mice are normal, but any offspring that also express an allele of Cre recombinase will have the floxed allele of MPC1 deleted. We are using these mice to study the effect of deleting this gene in stem and transitamplifying cells of the epidermis. Lgr5-CreER-IresGFP These mice are transgenic for a knockin allele of CreER-IresGFP into the Lgr5 locus. Lgr5 is only expressed in Hair follicle stem cells, so this transgenic mouse allows for inducible Cre activity to be delivered just to the stem cells. We use these mice to induce or delete genes specifically in the stem cells. Lgr6-CreER-IresGFP These mice are transgenic for a knockin allele of CreER-IresGFP into the Lgr6 locus. Lgr6 is only expressed in Hair follicle cells of the infundibulum, so this transgenic mouse allows for inducible Cre activity to be delivered just to the infundibulum of the follice. We use these mice to induce or delete genes specifically in the infundibular cells. A full inventory of the animals used, including age, sex and genotype, can be found in Supplementary Table 1. this study did not involve human subjects nature research life sciences reporting summary June

Supplementary Figure 1. Isolation of GFPHigh cells.

Supplementary Figure 1. Isolation of GFP High cells. (A) Schematic diagram of cell isolation based on Wnt signaling activity. Colorectal cancer (CRC) cell lines were stably transduced with lentivirus encoding