Introduction
Osteoporosis is a major problem in our aging population, with significant health and economic burden associated with fragility fractures (Harvey et al., 2010). Bone mass is determined by the balance between bone formation by osteoblasts and bone resorption by osteoclasts (Zaidi, 2007). Osteocytes, terminally differentiated cells of the osteoblast lineage buried deep within mineralized bone matrix, sense hormonal and mechanical cues to bone and in turn regulate the activity of cells on bone surfaces (Dallas et al., 2013). The majority of current osteoporosis therapeutics act by slowing down bone resorption, a strategy that most often fails to fully reverse the effects of this disease (Compston et al., 2019). Currently, bone anabolic treatment strategies are limited; development of orally available small molecules that stimulate bone formation represents a major unmet medical need (Estell and Rosen, 2021). Notably, efficacy of parathyroid hormone-based subcutaneous administration of osteoanabolic agents (teriparatide and abaloparatide) may be blunted by concomitant stimulation of bone resorption (Bilezikian, 2008). As such, orally available agents that stimulate bone formation without inducing bone resorption represent the ‘holy grail’ in osteoporosis drug development.
Parathyroid hormone (PTH) signaling in osteocytes stimulates new bone formation by osteoblasts (Wein, 2018). Salt inducible kinases (SIKs) are broadly expressed AMPK family serine/threonine kinases (Sakamoto et al., 2018) whose activity is regulated by cAMP signaling (Wein et al., 2018). In osteocytes, PTH signaling leads to protein kinase A-mediated phosphorylation of SIK2 and SIK3, a signaling event that suppresses cellular SIK activity (Wein et al., 2016). Genetic deletion of SIK2 and SIK3 in osteoblasts and osteocytes dramatically increases trabecular bone mass and causes phenotypic and molecular changes in bone similar to those observed with constitutive PTH receptor action (Nishimori et al., 2019). PTH signaling inhibits cellular SIK2/3 function; therefore, small molecule SIK inhibitors such as YKL-05–099 (Sundberg et al., 2016) mimic many of the actions of PTH, both in vitro and in vivo in initial studies in young, eugonadal mice (Wein et al., 2016).
Despite these advances, major unanswered questions remain regarding small molecule SIK inhibitors as potential therapeutic agents for osteoporosis. First, initial in vivo studies with YKL-05–099 showed increased bone formation (via a PTH-like mechanism) and, surprisingly,
Here, we tested YKL-05–099 in female mice rendered hypogonadal by surgical oophorectomy and observed increased trabecular bone mass, increased bone formation, and reduced bone resorption. Despite these beneficial effects, toxicities of hyperglycemia and nephrotoxicity were noted. Inducible, post-natal SIK2/3 gene deletion caused dramatic bone anabolism without hyperglycemia or BUN elevation, indicating that these side effects were due to inhibition of SIK1 or other targets of YKL-05–099. Notably, inducible, global SIK2/3 gene deletion
Results
YKL-05–099 increases trabecular bone mass in hypogonadal female mice
We previously showed that the SIK inhibitor YKL-05–099 increased bone formation and bone mass in young, eugonadal mice while simultaneously suppressing osteoclastic bone resorption (Wein et al., 2016). Based on these findings, we tested the efficacy of this compound in female mice rendered hypogonadal by surgical removal of the ovaries (OVX, Figure 1A), a common preclinical model for post-menopausal osteoporosis. In this study, 12-week-old female C57Bl/6J mice were subjected to sham or OVX surgery. 8 weeks later, mice from each surgical group were randomly divided into three treatment groups for 4 weeks total treatment. We performed side-by-side comparison of YKL-05–099 (18 mg/kg) with human PTH 1–34 (100 mcg/kg). As shown in Figure 1B–E and Supplementary file 1, YKL-05–099 treatment increased trabecular bone mass in the femur and L5 vertebral body of hypogonadal female mice. Compared to once daily PTH (100 mcg/kg) treatment, YKL-05–099 (18 mg/kg) led to comparable gains in trabecular bone mass. In contrast, this dose of PTH increased cortical bone mass and bone strength. The relationship between cortical bone mass and bone strength was preserved in response to YKL-05–099, indicating that this agent does not cause obvious defects in cortical bone quality (Figure 1F, Supplementary file 1, Figure 1—figure supplement 1A,B, Supplementary file 2).
Figure 1.
YKL-05–099 increases cancellous bone mass in hypogonadal female mice.
(A) Overview of ovariectomy (OVX) study design. N = 48 C57B/6 mice were subjected to sham or OVX surgery at 12 weeks of age. Eight weeks later, mice were randomly divided into the six indicated treatment groups, with n = 8 mice per group. Animals were treated over the course of 4 weeks and then sacrificed for skeletal analyses. (B) Representative femur micro-CT images from each treatment group. Scale bar = 1 mm. (C–D) Trabecular parameters in the distal femur. BV/TV = bone vol fraction. tBMD = trabecular bone mineral density. p Values between groups were calculated by two way ANOVA followed by Dunnett’s multiple comparisons test. All p values less than 0.1 are shown. OVX surgery reduces trabecular bone mineral density, and this is rescued by YKL-05–099 treatment. (E) Trabecular bone mass in L5. OVX surgery reduces vertebral trabecular bone mass, and this is rescued by YKL-05–099 treatment. (F) Cortical thickness in the femur midshaft. OVX surgery reduces cortical thickness. PTH (100 mcg/kg/d), but not YKL-05–099, increases cortical thickness. Also see Supplementary file 1 for all micro-CT data from both skeletal sites. All graphs show mean ± SD with each data point representing an individual experimental animal. See Source Data File for additional information.
Figure 1—figure supplement 1.
Results of biomechanical testing (A,B) and quantitative backscattered electron imaging (qBEI, C–H) from OVX study.
(A) Bending rigidity results. Consistent with cortical bone micro-CT data, only PTH treatment increases femur mechanical strength. p Values between groups were calculated by two way ANOVA followed by Dunnett’s multiple comparisons test. All p values less than 0.05 are shown. See Supplementary file 3 for additional parameters obtained from three point bending testing. (B) The relationship between cortical bone mass (x-axis, Cortical Area) and bone strength (y-axis, Bending rigidity) was plotted for individual mice in the indicated surgical and drug treatment groups. No obvious changes in the bone mass/strength relationship were noted in response to PTH or YKL-05–099 compared to vehicle-treated animals. (C) qBEI was performed on distal femur from OVX study mice (n = 8 per each group) to determine the effects of OVX and drug treatments on bone mineralization in metaphyseal spongiosa (MS) and midshaft cortical bone (Ct). (D) BMDD from a representative SHAM-VEH mouse in the cortical midshaft region. The BMDD parameters are depicted: CaMean (mean Ca content), CaPeak (mode Ca content), CaWidth (the full width at half maximum of the distribution), CaLow (the percentage of mineralized bone with a calcium concentration less than 23.84 weight % corresponding to CaYoung), and CaHigh (the percentage of bone areas with a calcium concentration beyond the 95th percentile of the SHAM-VEH group BMDD, which was 29.81 weight % Ca in cortex and 28.25 weight % Ca in the metaphysis). (E) For the evaluation of CaLow, the mean calcium concentration between the two fluorescence labels CaYoung (corresponding to a mineralized tissue age of 2–7 days) was determined. For this purpose, the (a) qBEI image was overlaid with a matched confocal scanning laser microscope image (fluorescence mode) from the identical sample surface, and (b) CaYoung was measured in the bone areas between the double labels (areas enclosed by dotted lines). (c) Example of mineralization of a line profile through an area of new bone formation as indicated in (b), showing the rapid primary increase and second slower increase in bone matrix mineralization. CaYoung represents the calcium level at the beginning of the second phase. Graphs in (F–H) show the effects of surgery and drug treatment on cortical bone CaMean, CaWidth and CaLow (for cortical bone CaPeak and CaHigh as well as metaphyseal BMDD results, see Supplementary file 4). In sham-operated mice, PTH treatment increases CaWidth. In general, minimal effects of surgery or drug (PTH or YKL-05–099) were observed as assessed by qBEI. See Source Data File for additional information.
YKL-05–099 uncouples bone formation and bone resorption in OVX mice
Having established that YKL-05–099 increases trabecular bone mass in OVX mice, we next sought to define the underlying cellular mechanisms. First, fasting serum was collected just prior to sacrifice to measure P1NP (a marker of bone formation) and CTX (a marker of bone resorption). Like once daily PTH treatment, YKL-05–099 treatment increased serum P1NP in both surgical groups (Figure 2A). As predicted, PTH treatment also increased bone resorption as measured by serum CTX; however, unlike PTH, YKL-05–099 treatment did not lead to statistically-significant increases in serum CTX (Figure 2B).
Figure 2.
YKL-05–099 increases bone formation without increasing bone resorption in OVX mice.
(A, B) Fasting serum was obtained just prior to sacrifice, following 4 weeks of treatment as indicated. p Values between groups were calculated by two way ANOVA followed by Dunnett’s multiple comparisons test. All p values less than 0.05 are shown. Both PTH and YKL-05–099 increase levels of the bone formation marker P1NP. In contrast, only PTH treatment increases levels of the bone resorption marker CTX. P1NP levels (mean ± SD) in the different treatment groups are as follows: SHAM/VEH 27.05 (ng/ml)±4.07, SHAM/PTH 44.97 ± 12.9, SHAM/YKL 36.73 ± 7.33, OVX/VEH 27.53 ± 4.64, OVX/PTH 68.29 ± 9.0, OVX/YKL 44.97 ± 10.01. CTX levels (mean ± SD) in the different treatment groups are as follows: SHAM/VEH 17.69 (ng/ml)±5.26, SHAM/PTH 24.97 ± 4.78, SHAM/YKL 21.88 ± 5.18, OVX/VEH 16.75 ± 3.67, OVX/PTH 28.61 ± 3.4, OVX/YKL 19.04 ± 3.9. (C, D) Static histomorphometry was performed on the tibia in the proximal metaphysis to measure cancellous osteoblast surface (Ob.S/BS), eroded surface (ES/BS), and osteoclast number per bone perimeter (Oc.N/B.Pm). Both PTH and YKL-05–099 treatment increases osteoblast surfaces, only PTH tends to increase osteoclast numbers and eroded surface while YKL-05–099 shows the opposite effect. (E) Representative fluorescent images showing dual calcein (green) and demeclocycline (red) labeling on trabecular surfaces. (F–H) Quantification of dynamic histomorphometry parameters: MAR = matrix apposition rate. MS/BS = mineralizing surface per total bone surface. BFR/BS = bone formation rate. Also see Supplementary file 2 for all histomorphometry data. See Source Data File for additional information.
Figure 2—figure supplement 1.
Effects of YKL-05–099 on marrow adipocytes in the proximal tibia.
(A) Trichrome stained tibia sections for histomorphometry are shown. In 24-week-old mice, many cells with adipocyte morphology are seen in the proximal tibial metaphysis. Qualitative reductions in adipocytes at this skeletal site are seen in YKL-05–099-treated mice. (B) Marrow adipocytes were quantified in a blinded manner. p Values between groups were calculated by two-way ANOVA followed by Dunnett’s multiple comparisons test. All p values less than 0.1 are shown. OVX surgery increases tissue space occupied by marrow adipocytes, and YKL-05–099 treatment tends to reduce this parameter. See Source Data File for additional information.
Figure 2—figure supplement 2.
Effects of YKL-05–099 treatment on basic hematologic and serum parameters.
Three hr fasting blood was collected prior to sacrifice and analyzed for complete blood counts (A, WBC = white blood cells, Hgb = hemoglobin) and the indicated serum parameters (B, BUN = blood urea nitrogen, ALT = alanine transaminase, AlkP = alkaline phosphatase). For (B), the normal mouse reference ranges are shown in dotted horizontal lines. p Values between groups were calculated by one way ANOVA followed by Dunnett’s correction. All p values less than 0.05 are shown. For these analyses, no effects of surgical intervention (sham versus ovariectomy) were noted. Therefore, mice are grouped based on drug treatment alone. No significant changes in hematologic parameters were noted. YKL-05–099 treatment led to statistically significant increases in serum glucose and BUN. See Source Data File for additional information.
Next, static and dynamic histomorphometry was performed to investigate the effects of PTH and YKL-05–099 on bone cell numbers and activity at the tissue level on trabecular bone surfaces in the metaphysis of the proximal tibia. Like PTH, YKL-05–099 increased osteoblast numbers and activity (Figure 2C,E,F–H, Supplementary file 3). In contrast, unlike PTH (which, as expected, tended to increase osteoclast numbers, eroded surface, and serum CTX levels), YKL-05–099 treatment reduced both osteoclast numbers and eroded surface in OVX mice (Figure 2D, Supplementary file 3). Taken together, these findings demonstrate that systemic YKL-05–099 treatment boosts trabecular bone mass and bone formation as PTH does. However, unlike PTH which predictably tends to stimulate both bone formation and bone resorption, YKL-05–099 treatment only increases bone formation.
An intriguing difference between the effects of PTH and YKL-05–099oc curred at the level of osteoid surface (Supplementary file 3). As expected, intermittent PTH treatment in OVX mice led to exuberant new bone formation leading to increased accumulation of unmineralized (osteoid) matrix on trabecular surfaces. Although YKL-05–099 increased osteoblast numbers and bone formation rate (as assessed by dual calcein/demeclocycline labeling), osteoid surface was
A second, provocative effect of YKL-05–099 occurred at the level of bone marrow adipocytes (de Paula and Rosen, 2020). PTH signaling in mesenchymal lineage precursors may shift cellular differentiation from adipocyte to osteoblast lineages (Fan et al., 2017; Balani et al., 2017; Yang et al., 2019; Maridas et al., 2019). As previously reported (Yang et al., 2019), acquired hypogonadism in response to OVX surgery led to increased marrow adipocytes in the metaphyseal region. YKL-05–099 treatment (Figure 2—figure supplement 1A–C) reduced marrow adipocyte volume as assessed by semi-automated histology (Tratwal et al., 2020). Future studies are needed to define a potential cell intrinsic role for salt inducible kinases (or other intracellular targets of YKL-05–099) in bone marrow adipocyte differentiation and survival.
Given the clear effects observed in trabecular bone in response to YKL-05–099 treatment, we next turned our attention to the safety profile of this agent over the course of 4 weeks of treatment. Surgical treatment group (sham versus OVX) had no impact on parameters measured in vehicle-treated mice; for this reason, data are presented by drug (vehicle, PTH, or YKL-05–099) treatment. YKL-05–099 treatment had no effect on peripheral white blood cell numbers, hemoglobin, platelet counts, or absolute monocyte count (Figure 2—figure supplement 2A). Prior to sacrifice, standard toxicology profiling was performed on fasting serum. While most parameters were unaffected by YKL-05–099 treatment, we did note mild but significant increases in blood urea nitrogen (BUN) and glucose (Figure 2—figure supplement 2B). Hyperglycemia may be related to a potential role of salt-inducible kinases downstream of hepatic glucagon signaling (Patel et al., 2014). In contrast, current genetic models do not necessarily predict nephrotoxicity from in vivo SIK inhibition. Taken together, these results largely demonstrate an appealing therapeutic action in bone in response to YKL-05–099 treatment. However, the potential tolerability issues observed with YKL-05–099 and key differences from the pharmacologic actions of PTH (with respect to bone resorption) prompted us to develop genetic models of adult-onset SIK isoform deletion to gain insight into whether some effects of YKL-05–099 may be related to non-SIK targets of this multi-kinase inhibitor (Sundberg et al., 2016).
Inducible, global SIK2/3 deletion increases trabecular bone mass and increases bone turnover
Similar to YKL-05–099 treatment, deletion of SIK2 and SIK3 in mesenchymal lineage bone cells with Dmp1-Cre increases trabecular bone area and mass (Nishimori et al., 2019). However, unlike YKL-05–099 treatment, deletion of SIK2/3 selective in mesenchymal-lineage bone cells dramatically stimulates bone resorption. To mimic the pharmacologic effects of systemic SIK inhibitor treatment, we bred animals with ‘floxed’ SIK alleles to ubiquitin-CreERt2 mice (Ruzankina et al., 2007) to allow global, tamoxifen-dependent SIK isoform deletion (Figure 3—figure supplement 1A). Here, SIK3 ablation had to be postnatal to circumvent early perinatal lethality due to the key role of this kinase in PTHrP-mediated growth plate hypertrophy (Nishimori et al., 2019; Sasagawa et al., 2012). For these studies, 6-week-old control (
Figure 3.
Postnatal onset global Sik2/3 deletion increases trabecular bone mass.
(A) 6 week old
Figure 3—figure supplement 1.
Efficacy and safety of global inducible
(A) Ubiquitin-CreERt2 mice were crossed to tdTomato reporter (Ai14) animals. Six-week-old male mice were treated with tamoxifen (1 mg by intraperitoneal injection, every other day, three doses total) and then sacrificed 7 days after the first tamoxifen injection. Cryosections of the kidney and liver were analyzed for tdTomato fluorescence. Bottom panels show kidney and liver sections from ubiquitin-CreERt2 mice that are negative for the Ai14 reporter allele. (B)
Figure 3—figure supplement 2.
Growth plate defect induced by post-natal SIK2/3 deletion.
6 week old female Sik2f/f; Sik3f/f (WT) or Sik2f/f; Sik3f/f; ubiquitin-CreERt2 (DKO) mice were treated with tamoxifen (1 mg by intraperitoneal injection, every other day, three doses total) and then sacrificed 21 days after the first tamoxifen injection. Non-decalcified sections were obtained from the tibia which were stained with von Kossa (black) and safranin O (red). Dramatic growth plate expansion and disorganization is noted with inducible
Figure 3—figure supplement 3.
Adult-onset global
(A) Twelve-week-old female
Figure 3—figure supplement 4.
In vivo
(A) Ubiquitin-CreERt2; Ai14 reporter mice (tdTomatoLSL) were treated with tamoxifen (1 mg by intraperitoneal injection, every other day, three doses total) starting at 6 weeks of age. Mice were sacrificed 2 weeks after the first tamoxifen dose and bone marrow cells were analyzed by flow cytometry. The majority (>90%) of myeloid lineage cells, as marked by CD11B (left) or LY6C (right), show evidence of CreERt2 activity as assessed by tdTomato protein. 97% of CD11B+ cells are tdTomato+, and 96% of LY6C+ cells are tdTomato+. (B) Bone marrow macrophages were grown in the presence of M-CSF plus RANKL for the indicated times. Culture supernatants were collected and secreted TRAP activity was measured over time. Robust osteoclast differentiation is noted after 10–14 days in these culture conditions. (C) Bone marrow cells were isolated from mice 2 weeks after in vivo tamoxifen administration as in (A). Bone marrow macrophages were isolated and grown in the presence of M-CSF alone (top) or M-CSF plus RANKL (M + R, bottom) followed by TRAP staining (purple). Cells isolated from DKO mice treated with tamoxifen in vivo show increased osteoclast differentiation. Scale bar = 50 µm (D) Culture supernatants from (C) were assessed for secreted TRAP activity. (E) TRAP-positive multinucleated cells from (C) treated with RANKL 50 ng/mL were quantified. See Source Data File for additional information.
Histology and histomorphometry from control and SIK2/3 DKO mice confirmed a dramatic increase in trabecular bone mass and an accumulation of marrow stromal cells (Figure 4A, all findings consistent with previously reported phenotypes seen when
Figure 4.
Postnatal onset global Sik2/3 deletion increases bone remodeling.
(A) 6 week old
Prompted by the observations that YKL-05–099 treatment caused mild hyperglycemia and increased BUN (Figure 2—figure supplement 2), similar serum toxicology profiling was performed in control and postnatal-onset ubiquitous SIK2/3 DKO mice. Animals were treated with tamoxifen at 6 weeks of age and then serum profiling was performed 2 weeks later. In these studies, BUN and fasting glucose levels were unaffected by global SIK2/3 ablation (Figure 3—figure supplement 1B). Therefore, these YKL-05–099-associated toxicities are likely due to either SIK1 inhibition or off-target effects of this pharmacologic agent. These reassuring results suggest a favorable initial safety profile associated with whole body SIK2/3 gene deletion, and further support the idea of this target combination for osteoporosis drug development.
Since 6-week-old mice are rapidly growing, we performed additional experiments with postnatal Sik2/3 gene deletion in older (12-week-old) mice in order to facilitate better comparison between our OVX pharmacologic studies. Notably, similar changes were observed 4 weeks after
No cell-autonomous effects of SIK gene deletion on osteoclast differentiation and function
Discordant effects at the level of bone resorption between
Previous studies in murine RAW264.7 pre-osteoclastic cells suggested a potential cell intrinsic role for salt-inducible kinases in osteoclast differentiation (Lombardi et al., 2017). Given our apparently discordant observations that (Harvey et al., 2010) YKL-05–099 treatment has anti-resorptive effects and (Zaidi, 2007) SIK2/3 gene deletion increases bone resorption in vivo, we established a system in which SIK isoforms could be deleted ex vivo to test the cell-intrinsic function of SIKs in osteoclast differentiation and function. For this, bone marrow macrophages from control (
Figure 5.
Deletion of SIK2 and SIK3 does not affect cell-autonomous osteoclast differentiation or function.
(A) Bone marrow macrophages from ubiquitin-CreERt2; Ai14 mice were treated with vehicle (red) or 4-hydroxytamoxifen (blue, 4-OHT, 300 nM) for 72 hr followed by flow cytometry. 4-OHT treatment induces in vitro ubiquitin-CreERt2 activity as measured by this sensitive reporter allele. (C) Bone marrow macrophages from control or DKO mice were treated as indicated followed by immunoblotting. 4-OHT treatment leads to robust deletion of SIK2 and SIK3 protein in DKO cells. (D, E, F) BMMs from control or DKO mice were treated with vehicle or 4-OHT and then subjected to in vitro osteoclast differentiation with M-CSF plus RANKL (M + R). 4-OHT treatment in DKO cells did not cause significant changes in osteoclast differentiation as assessed by morphology (D, scale bar = 50 µm), quantifying TRAP secretion (E), or counting TRAP-positive multi-nucleated cells (F). (G, H) Osteoclasts as in (D) were grown on hydroxyapatite-coated plates in the presence of M-CSF plus RANKL. After 7 days, resorption was measured by von Kossa staining. 4-OHT treatment of DKO cells did not affect resorbed surface. M-CSF treatment alone serves as a negative control to demonstrate that pit resorption in this assay is RANKL-dependent. All in vitro experiments were repeated three times. See Source Data File for additional information.
Since YKL-05–099 inhibits all three SIK isoforms (Sundberg et al., 2016), the possibility remained that the inhibitory effects of this compound on osteoclast differentiation were due to SIK1 blockade. Therefore, we crossed
Figure 6.
Deletion of SIK1, SIK2, and SIK3 does not affect cell-autonomous osteoclast differentiation or function.
(A) Bone marrow macrophages from ubiquitin-CreERt2; SIK1/2/3 floxed mice were treated with vehicle (blue) or 4-hydroxytamoxifen (red, 4-OHT, 300 nM) for 72 hr. Genomic DNA was isolated for qPCR-based assessment of SIK isoform deletion. (B, C, D) BMMs from control or TKO mice were treated with vehicle or 4-OHT and then subjected to in vitro osteoclast differentiation with M-CSF plus RANKL. 4-OHT treatment in TKO cells did not cause significant changes in osteoclast differentiation as assessed by morphology (B), quantifying TRAP secretion (C, scale bar = 50 µm), or counting TRAP-positive multi-nucleated cells (D). (E, F) Osteoclasts as in (B) were grown on hydroxyapatite-coated plates in the presence of M-CSF plus RANKL. After 7 days, resorption was measured by von Kossa staining. 4-OHT treatment of DKO cells did not affect resorbed surface. M-CSF treatment alone serves as a negative control to demonstrate that pit resorption in this assay is RANKL-dependent. All in vitro experiments were repeated three times. See Source Data File for additional information.
Figure 6—figure supplement 1.
Parallel reporter assay (TF-seq) was used to determine the effects of YKL-05–099 on 58 reporter synthetic reporter elements.
(A) Ocy454 cells were infected with TF-seq lentiviral particles which co-express GFP using spin infection in the presence of polybrene (2 µg/ml). Infected cells were expanded and then subjected to flow cytometry. GFP + cells were sorted for subsequent experiments. (B) Sorted GFP +TF seq Ocy454 cells were treated with the indicated dose of YKL-05–099 or DMSO (vehicle) control for the indicated times. Cells were lysed and reporter element (RE) for each of the 58 elements was measured as detailed in the methods. Of the 58 elements tested, only CRE activity was significantly regulated by YKL-05–099 treatment. Panel B shows the effects of YKL-05–099 on CRE activity. (C) Heat map showing activity of all 58 reporter elements in response to vehicle or 10 µM YKL-05–099. Each row represents a distinct reporter element. Arrowhead (left) shows the row that corresponds to the CRE element. Color code shows log2 fold change relative to time zero. This TF-seq experiment was performed twice. See Source Data File for additional information.
Modeling reveals conformation-selective preference of YKL-05–099 for SIK2 and CSF1R
Differences between YKL-05–099 treatment and
TF-seq profiling of YKL-05–099 in osteocytic Ocy454 cells failed to inform our thinking about the anti-resorptive effects of this compound in vivo. However, an important clue came from review of previous data profiling YKL-05–099 binding to a panel of 468 recombinant human kinases (Sundberg et al., 2016). While this compound binds the active site of SIKs, it also engages a number of tyrosine kinases including the receptor tyrosine kinase CSF1R (FMS, the M-CSF receptor) (Figure 7A). Given the essential role of M-CSF action in osteoclast development (Mun et al., 2020; Ross and Teitelbaum, 2005), this raised the possibility that YKL-05–099 might block osteoclast differentiation via effects on CSF1R.
Figure 7.
Modeling reveals
(A) Dendrogram representation of previously published (Sundberg et al., 2016) kinome profiling data for YKL-05–099 tested at 1.0 µM. Red circles indicate kinases with active site binding to this compound. The position of CSF1R (green) and SIK2 (blue) are noted. (B) Docking scores for YKL-05–099 binding to the active site of four kinase conformation defined by the αC-helix and DFG-motif for CSF1R (left) and SIK2 (right). (C) Preferential docked pose of YKL-05–099 in the modeled αC-out/DFG-in (CODI) conformation of CSF1R (FMS) (left) and SIK2 (QIK) (right).
Most proteins within the human kinome share a highly conserved catalytic domain (Manning et al., 2002). This core domain is highly dynamic adopting a range of conformational states that are associated with catalytic activity (Ung and Schlessinger, 2015; Roskoski, 2016; Ung et al., 2018). However, due to the limited number of atomic structures available, most kinases have only been structurally characterized in one or two conformational states (Ung et al., 2018). CSF1R (FMS) and SIK2 (QIK) represent two distinct branches of the human kinome (Figure 7A): CSF1R belongs to the receptor tyrosine kinase (TK) family, while SIKs are in the CAMK family. Although atomic structures of CSF1R have been solved in two conformational states, structure of SIKs have not been determined. Therefore, to evaluate the putative mode(s) of binding of YKL-05–099, we constructed homology models of CSF1R and SIK2 in the pharmacologically relevant conformational states.
DFGmodel (Ung and Schlessinger, 2015) in combination with Kinformation (Ung et al., 2018; Rahman et al., 2019), can model four commonly-observed kinase conformations defined by two critical structural elements of the kinase domain, the αC-helix and the DFG-motif. The four states are αC-in/DFG-in (CIDI), αC-in/DFG-out (CIDO), αC-out/DFG-in (CODI), and αC-out/DFG-out (CODO) conformations. Kinase inhibitors can also be classified by the kinase conformation they bind (Dar and Shokat, 2011). For example, type-I inhibitors target the active CIDI conformation, whereas the type-II inhibitor sorafenib and type-I1/2 inhibitor erlotinib prefer the inactive CIDO and CODI conformations, respectively (Ung et al., 2018). Therefore, to model potential binding modes of a kinase inhibitor, different conformations of the kinase should be explored.
Docking of YKL-05–099 to all four modeled conformations of CSF1R and SIK2 suggested that, across both kinases, this compound shows preferences for the CODI conformation (Figure 7B). Therefore, we explored docking modes in the CODI conformation for both kinases. Three common features were noted between how YKL-05–099 engages the CODI conformation of both kinases (Figure 7C): (i) the core pyrimidine scaffold interacts with the hinge region of the kinase; (ii) the 2-chloro-6-methylphenyl moiety is buried deep in the binding pocket toward the αC-helix; and (iii) the 5-methoxypridin-2-yl moiety resides in the ribose binding site and the 2-methoxy-4-methylpiperdinylphenyl moiety extends outside the binding site. These modeling data demonstrate how a single kinase inhibitor can show promiscuity across unrelated kinases, and provide further support for the model that YKL-05–099 might block bone resorption via effects on CSF1R.
YKL-05–099 blocks M-CSF action in myeloid cells
Consistent with active site binding data and modeling results, we observed that YKL-05–099 potently blocks CSF1R kinase function in vitro (Figure 8A, IC50 = 1.17 nM). Bone marrow macrophages were treated with YKL-05–099 during M-CSF/RANKL-stimulated osteoclast differentiation. In these assays, we noted potent inhibition of osteoclast differentiation in response to this compound (Figure 8B–D), with cytotoxicity noted at doses above 312 nM (Figure 8B). To more directly assess whether YKL-05–099 might block M-CSF action in pre-osteoclasts, we serum-starved cells and then re-challenged with M-CSF. M-CSF-induced receptor Y723 autophosphorylation (Bourette et al., 1997) and ERK1/2 phosphorylation were completely blocked by pre-treatment with YKL-05–099 (Figure 8E). Consistent with these biochemical effects of YKL-05–099 on M-CSF receptor signaling, we also noted that YKL-05–099 pre-treatment blocked M-CSF-induced upregulation of immediate early genes
Figure 8.
YKL-05–099 blocks M-CSF action.
(A) CSF1R in vitro kinase assays were performed in the presence of increasing doses of YKL-05–099. This compound blocks CSF1R activity with an IC50 of 1.17 nM. (B) Murine bone-marrow-derived macrophages were grown in the presence of M-CSF, RANKL, and the indicated doses of YKL-05–099. After 3 days of differentiation, TRAP staining (purple) was performed. YKL-05–099 blocks osteoclast differentiation and causes cytotoxicity in these cultures (scale bar = 50 µm). (C) After three days of differentiation in the presence of M-CSF and RANKL, conditioned medium was collected and secreted TRAP assays were performed. YKL-05–099 treatment causes a dose-dependent reduction in TRAP secretion. Values indicate mean ± SD of n = 3 wells per condition. (D) After three days of differentiation in the presence of M-CSF and RANKL, TRAP staining was performed. The number of TRAP positive multinucleated cells (MNCs) per well of a 96-well plate (n = 3 wells/condition) is shown. (E) Murine bone marrow macrophages were grown in the presence of M-CSF for 5 days. Cells were then deprived of M-CSF for 6 hr, then pre-treated plus/minus YKL-05–099 (15 µM) for 60 min. Cells were then re-challenged with M-CSF (50 ng/ml) for the indicated times followed by immunoblotting. YKL-05–099 pre-treatment blocks M-CSF-induced M-CSFR autophosphorylation and ERK1/2 phosphorylation. (F, G) Cells as in (E) were challenged with M-CSF (50 ng/ml) for the indicated times, followed by RT-qPCR for the M-CSF target genes Ets2 and Egr1. YKL-05–099 pre-treatment blocks M-CSF-induced Ets2 and Egr1 up-regulation. (H, I) Bone marrow macrophages from ubiquitin-CreERt2; SIK2/3 (DKO) or ubiquitin-CreERt2; SIK1/2/3 (TKO) floxed mice were treated plus/minus 4-OHT as in Figures 5 and 6, then plated in M-CSF/RANKL plus the indicated doses of PLX-5622 (H) or YKL-05–099 (I) for 12 days followed by secreted TRAP assays (n = 6 wells from two independent experiments were assayed). In these plots, ‘control’ cells include BMMs from both DKO and TKO mice treated with vehicle prior to M-CSF/RANKL and inhibitor dose response. Irrespective of the cellular genotype, CSF1R inhibitor (PLX-5622 or YKL-05–099) treatment potently blocked osteoclast differentiation. All in vitro experiments were repeated three times. See Source Data File for additional information.
Figure 8—figure supplement 1.
The dose response relationship of YKL-05–099 on M-CSF action in bone marrow macrophages.
Murine bone marrow macrophages were grown in the presence of M-CSF for 5 days. Cells were then deprived of M-CSF for 6 hr, then pre-treated ±the indicated doses of YKL-05–099 for 60 min. Cells were then re-challenged with M-CSF (50 ng/ml) followed by immunoblotting (A, 5 min M-CSF treatment) or RT-qPCR (B, 90 min M-CSF treatment). YKL-05–099 inhibits M-CSF action at sub-µM doses in both of these assays. All in vitro experiments were repeated twice. See Source Data File for additional information.
Figure 8—figure supplement 2.
PLX-5622 blocks osteoclast differentiation in SIK mutant cells.
Bone marrow macrophages from ubiquitin-CreERt2; SIK2/3 (DKO) or ubiquitin-CreERt2; SIK1/2/3 (TKO) floxed mice were treated plus/minus 4-OHT and then were grown in the presence of M-CSF/RANKL plus the indicated doses of PLX-5622 for 12 days followed by TRAP staining. Representative photomicrographs from the indicated cells and drug concentration are shown. Scale bar = 50 µm. Bottom, quantification of TRAP +multinucleated cells. For each condition, n = 3 wells (96 well plate) were analyzed, error bars represent mean ± SD. PLX-5622 reduced numbers of TRAP +multinucleated cells irrespective of SIK genotype. All in vitro experiments shown here were performed three times. See Source Data File for additional information.
Figure 8—figure supplement 3.
Bone marrow macrophages from ubiquitin-CreERt2; SIK2/3 (DKO) or ubiquitin-CreERt2; SIK1/2/3 (TKO) floxed mice were treated plus/minus 4-OHT and then were grown in the presence of M-CSF/RANKL plus the indicated doses of YKL-05–099 for 12 days followed by TRAP staining. Representative photomicrographs from the indicated cells and drug concentration are shown. Scale bar = 50 µm. Bottom, quantification of TRAP +multinucleated cells. For each condition, n = 3 wells (96 well plate) were analyzed, error bars represent mean ± SD. YKL-05–099 reduced numbers of TRAP +multinucleated cells irrespective of SIK genotype. All in vitro experiments shown here were performed three times. See Source Data File for additional information.
Discussion
Anti-resorptive therapies (bisphosphonates and the anti-RANKL antibody denosumab) have long represented first line treatment for patients with osteoporosis. These agents boost bone mass and reduce fractures (Bone et al., 2017), yet are linked to rare but serious side effects (osteonecrosis of the jaw and atypical femur fractures) which are related to excessive suppression of both bone resorption and bone formation (Black et al., 2020). New bone anabolic therapies for osteoporosis are desperately needed in order to provide more effective treatment options for this common and debilitating disease. Currently, analogs of parathyroid hormone (teriparatide and abaloparatide) represent the most commonlyused class of bone anabolic osteoporosis treatment agents. While effective in increasing spine bone density, efficacy of such agents may be limited by concomitant stimulation of bone resorption (Estell and Rosen, 2021). For this reason, novel strategies that stimulate bone formation without simultaneous induction of bone resorption are highly desired (Leder, 2018). Here, we show that the small molecule kinase inhibitor YKL-05–099 boosts bone formation and trabecular bone mass in a commonly used preclinical model of post-menopausal osteoporosis. In addition to stimulating bone formation, YKL-05–099 treatment inhibits bone resorption. This appealing combination of anabolic and anti-resorptive effects is, to date, only seen with the biologic agent romosozumab (McClung et al., 2014), an anti-sclerostin antibody whose widespread use is limited due to risk of increased cardiovascular events (Fixen and Tunoa, 2021).
In this study, we investigated mechanisms underlying the in vivo effects of YKL-05–099 treatment, and compared these results with those obtained following post-natal, ubiquitous
Second, YKL-05–099 caused mild hyperglycemia and increased BUN, changes not observed following
Detailed analysis of bones from OVX mice treated with YKL-05–099 for 4 weeks revealed unanticipated findings including trends toward reduced bone marrow adipocytes and potential effects on matrix mineralization. First, there may be a direct role of PTH signaling in differentiation of bone marrow adipocyte precursors (Fan et al., 2017; Balani et al., 2017; Yang et al., 2019; Maridas et al., 2019). In addition, activation of other cAMP-linked GPCR signaling systems, such as ß3-adrenergic receptors, can also inhibit SIK cellular function (Berggreen et al., 2012; Henriksson et al., 2012) and regulate bone marrow adipocyte size and numbers (Scheller et al., 2019). Future studies are needed to determine whether a cell-intrinsic role exists for SIKs in bone marrow adipocyte differentiation or response to catecholamines. Second, we were surprised to note that YKL-05–099 treatment accelerated bone formation (Figure 2A,H) without increasing osteoid surface (Supplementary file 3). These findings are in stark contrast with the effects of PTH treatment which, as expected, increased bone formation and accumulation of under-mineralized bone matrix. These results suggest that YKL-05–099 somehow accelerates both matrix deposition and decreases osteoid maturation time. The assessment of CaYoung (the mean calcium concentration between the double labels) which represents the calcium level at a well-defined young tissue age, did not show large differences among selected samples from all study groups. However, future studies are needed to investigate how this compound might stimulate mineralization of newly formed bone matrix in more detail (Murshed and McKee, 2010). Our previous studies indicated that YKL-05–099 treatment stimulates bone formation via PTH-like effects in osteocytes, including suppressing expression of the osteoblast inhibitor sclerostin (Wein et al., 2016). Whether YKL-05–099 has direct effects on osteoblast activity remains to be determined.
Our OVX study demonstrated that YKL-05–099 treatment increased trabecular, but not cortical, bone mass (Figure 1). In contrast, sclerostin antibody treatment increases both trabecular and cortical bone mass (Li et al., 2009). At this point, we do not understand the mechanistic basis of this compartment-selective effect of this small molecule. Analysis of cortical bone at multiple time points after YKL-05–099 treatment is needed to conclusively demonstrate the absence of a cortical bone effect of this compound. However,
Our current claim that YKL-05–099 ‘uncouples’ bone formation and bone resorption is based upon our histomorphometry and serum bone turnover marker data which clearly show that this agent increases bone formation without increasing the measured resorption-related parameters. Future study is needed using dynamic histomorphometry in association with cement line visualization (Langdahl et al., 2016) to see if this compound can stimulate modeling-based bone formation independent of bone resorption. While both
Achieving specificity in active site kinase inhibitors is challenging due to the conserved nature of the ATP-binding pocket across protein kinases (Zhang et al., 2009). It is plausible that due to small threonine residues (CSF1R: Thr663; SIK2: Thr96) at the so-called gatekeeper position (Liu et al., 1998; Azam et al., 2008), the active sites of both CSF1R and SIK2 can accommodate multiple inhibitors (Klaeger et al., 2017; Hanson et al., 2019). Our modeling here further demonstrates that YKL-05–099 preferentially engages the CODI conformation of both kinases in a common binding mode. As such, multi-target binding of kinase inhibitors represents both a challenge and an opportunity as such agents are developed for chronic, non-oncologic indications (Ferguson and Gray, 2018). While avoiding undesired off-target effects will be necessary to avoid unacceptable toxicities, it remains possible that targeting precise combinations of kinases may lead to synergistic therapeutic benefits.
In summary, these findings demonstrate that a single kinase inhibitor can uncouple bone formation and bone resorption via concurrent effects on distinct kinases in distinct cell types. This work provides a framework for development of ‘next generation’ inhibitors with improved selectivity toward relevant SIK isoforms (likely SIK2 and SIK3) and CSF1R versus the remainder of the kinome. Furthermore, this work highlights the power of combining complementary genetic and pharmacologic approaches to explore the target biology and therapeutic mode of action of a small molecule kinase inhibitor.
Materials and methods
Key resources table
| Reagent type | Designation | Source or | Identifiers | Additional |
|---|---|---|---|---|
| Strain, strain background ( | EUCOMM | RRID:MGI_6712189 | Both males and females were used | |
| Strain, strain background ( | EUCOMM | RRID:MGI_ 6712188 | Both males and females were used | |
| Strain, strain background ( | EUCOMM | RRID:MGI_5085429 | Both males and females were used | |
| Strain, strain background ( | PGK1-FLPo | The Jackson Laboratory | IMSR Cat# JAX:011065, RRID:IMSR_JAX:011065 | Both males and females were used |
| Strain, strain background ( | Ubc-CreERt2 | The Jackson Laboratory | IMSR Cat# JAX:008085, RRID:IMSR_JAX:008085 | Both males and females were used |
| Strain, strain background ( | Ai14 LSL-tdTomato reporter, Gt(ROSA)26Sor | The Jackson Laboratory | IMSR Cat# JAX:007914, RRID:IMSR_JAX:007914 | Both males and females were used |
| Strain, strain background ( | OVX-operated female C57BL/6 | The Jackson Laboratory | IMSR Cat# JAX:000664, RRID:IMSR_JAX:000664 | |
| Antibody | SIK2 (Rabbit monoclonal) | Cell Signaling Technology | Cat# 6919, RRID:AB_10830063 | WB (1:1000) |
| Antibody | Anti-SIK3 (Rabbit | Abcam | Cat# ab88495, RRID:AB_2042747 | WB (1:1000) |
| Antibody | Phospho-M-CSF Receptor Tyr723 (Rabbit monoclonal) | Cell Signaling Technology | Cat# 3155, RRID:AB_2085229 | WB (1:1000) |
| Antibody | CSF1R (Rabbit monoclonal) | Cell Signaling Technology | Cat# 67455, RRID:AB_2799725 | WB (1:1000) |
| Antibody | Phospho-ERK1/2 | Cell Signaling Technology | Cat# 4376, RRID:AB_331772 | WB (1:1000) |
| Antibody | ERK1/2 | Cell Signaling Technology | Cat# 4695, RRID:AB_390779 | WB (1:2000) |
| Antibody | Tubulin | Cell Signaling Technology | Cat# 2128, RRID:AB_823664 | WB (1:1000) |
| Antibody | APC anti-mouse/human CD11b antibody | BioLegend | Cat# 101211, RRID:AB_312794 | FC (1:50) |
| Antibody | FITC anti-mouse CD3 antibody | BioLegend | Cat# 100305, RRID:AB_312670 | FC (1:33) |
| Antibody | PE/Cy7 anti-mouse Ly-6C antibody | BioLegend | Cat# 128017, RRID:AB_1732093 | FC (1:75) |
| Antibody | Anti-rabbit IgG, HRP-linked antibody | Cell Signaling Technology | Cat# 7074, RRID:AB_2099233 | WB (1:2500) |
| Commercial assay or kit | pro-collagen type 1 N-terminal peptide (P1NP) | IDS Immunodiagnostic Systems | Cat# AC-33F1, RRID:AB_2801263 | |
| Commercial assay or kit | carboxy-terminal telopeptide of type I collagen (CTX) | IDS Immunodiagnostic Systems | Cat# AC-06F1, RRID:AB_2801265 | |
| Commercial assay or kit | Acid phosphatase leukocyte kit | Sigma-Aldrich | Cat# 387A-1KT | |
| Commercial assay or kit | DNeasy Blood and Tissue Kit | Qiagen | Cat# 69504 | |
| Chemical compound, drug | (Z)−4-Hydroxytamoxifen | Sigma-Aldrich | Cat# H7904-5MG | |
| Chemical compound, drug | Tamoxifen | Sigma-Aldrich | Cat# T5648 | |
| Chemical compound, drug | Methanol BioReagent | Sigma-Aldrich | Cat# 494437–1L | |
| Chemical compound, drug | Dimethyl sulfoxide | Sigma-Aldrich | Cat# D8418-100ML | |
| Chemical compound, drug | Sodium L-tartrate dibasic dihydrate | Sigma-Aldrich | Cat# 228729–100G | |
| Chemical compound, drug | Phosphatase substrate | Sigma-Aldrich | Cat# SRE0026 | |
| Chemical compound, drug | Acetone | VWR | Cat# E6460500mL | |
| Chemical compound, drug | 140 Proof Pure Ethanol | Koptec | Cat# UN1170 | |
| Chemical compound, drug | Formaldehyde 37% by weight with preservative | Fisher Chemical | Cat# F79-500 | |
| Chemical compound, drug | phosphatase inhibitor cocktail | Thermo Fisher Scientific | Cat# 78440 | |
| Chemical compound, drug | PLX5622 | MCE MedChemExpress | Cat# HY-114153 | |
| Chemical compound, drug | Calcein | Sigma-Aldrich | Cat# C0875-5G | |
| Chemical compound, drug | Demeclocycline hydrochloride | Sigma-Aldrich | Cat# D6140-1G | |
| Peptide, recombinant protein | Recombinant mouse RANKL | R and D systems | Cat# 462-TEC-010 | |
| Peptide, recombinant protein | Recombinant mouse M-CSF | R and D systems | Cat# 416 ML-050 | |
| Peptide, recombinant protein | Recombinant CSFR1 | Invitrogen | Cat# PV3249 | |
| Software, algorithm | HeskaView Integrated software | Heska | ||
| Software, algorithm | FlowJo | BD Biosciences | RRID:SCR_008520 | |
| Software, algorithm | ImageJ | PMID:22930834 | NIH Image, RRID:SCR_003073 | |
| Software, algorithm | Prism 8.0 | GraphPad Software | RRID:SCR_002798 | |
| Other | Bio-Rad Protein Assay Dye Reagent Concentrate | Bio-Rad | Cat# 5000006 | |
| Other | Pierce ECL Plus Western Blotting Substrate | Thermo Scientific | Cat# 32132 | |
| Other | Maxima reverse transcriptase | Thermo Fisher Scientific | Cat# EP0742 | |
| Other | Sunflower oil | Sigma-Aldrich | Cat# 88921–250 ML-F | |
| Other | Red blood cell lysis buffer | Sigma-Aldrich | Cat# R7757-100mL | |
| Other | 0.05% Trypsin-EDTA (1x) | Gibco | Cat# 25300–062 |
Mice
All animals were housed in the Center for Comparative Medicine at the Massachusetts General Hospital and all experiments were approved by the hospital’s Subcommittee on Research Animal Care. The following published genetically modified strains were used:
Both males and females were included in this study, except for the OVX studies where only female mice were used. All procedures involving animals were performed in accordance with guidelines issued by the Institutional Animal Care and Use Committees (IACUC) in the Center for Comparative Medicine at the Massachusetts General Hospital and Harvard Medical School under approved Animal Use Protocols (2019N000201). All animals were housed in the Center for Comparative Medicine at the Massachusetts General Hospital (21.9 ± 0.8°C, 45 ± 15% humidity, and 12 hr light cycle 7 am–7 pm).
For OVX studies, 12-week-old sham- and OVX-operated female C57Bl/6J mice were obtained from a commercial vendor (JAX #000664). Mice from each surgical group were randomly allocated into three drug treatment groups. Drug treatments started 8 weeks after OVX surgery for a total of 4 weeks. YKL-05–099 was dissolved in PBS + 25 mM HCl and injected IP once daily five times per week for a total of 20 injections. PTH was dissolved in buffer (10 mM citric acid, 150 mM NaCl, 0.05% Tween-80, pH 5.0) and injected SC once daily five times per week for a total of 20 injections. Power calculations were performed based on previous data where eugonadal mice were treated with YKL-05–099 for 2 weeks (Wein et al., 2016), detailed below. For experiments in which mice were treated with either vehicle or PTH (or YKL-05–099), mice were assigned to alternating treatment groups in consecutive order. Tamoxifen (Sigma-Aldrich, St. Louis, MO, catalog #T5648) was dissolved in 100% ethanol at a concentration of 10 mg/mL. Thereafter, equal volume of sunflower oil (Sigma, catalog #88921–250 ML-F) was added, the solution was vortexed and placed un-capped in a 65°C incubator overnight in order to evaporate ethanol. This working solution of tamoxifen dissolved in sunflower oil at a concentration of 10 mg/mL was used for intraperitoneal injections.
The sample size for this study was determined using the following power calculation. Grassi et al., 2016 performed a similar study design to assess the effects of the small molecule H2S donor GYY4137 on OVX-induced bone loss. In these studies, femoral BV/TV (%± SD) fell from 7.8 ± 2 to 4.2 ± 1 following OVX. From these studies, a sample size of n = 5/group would be required to reach 95% power to detect a ‘p’ value of 0.05. In our published studies (Wein et al., 2016) with YKL-05–099 (6 mg/kg/d) treatment caused BV/TV to increase from 10.6 ± 1.0 to 12.5 ± 1.0. In these studies, a sample size of n = 7/group would be required to reach 95% power to detect a ‘p’ value of 0.05. In our preliminary data using YKL-05–099 18 mg/kg/d caused BV/TV to increase from 10.3 ± 2.0 to 16.3 ± 2.0. In these studies, a sample size of n = 3/group would be required to reach 95% power to detect a ‘p’ value of 0.05. In designing these experiments, a conservative estimate will be used of n = 8/group, as this number reflects one additional mouse per group beyond the minimum number needed from the aforementioned scenarios. In addition, since more stringent ANOVA analysis will be required to test for an interaction between surgery and drug treatment, a larger size will be necessary. For studies investigating the effects of
Antibodies and compounds
YKL-05–099 was synthesized as previously described (Sundberg et al., 2016), PLX-5622 was obtained from MedChem Express (Monmouth Junction, NJ). Antibody sources and dilutions are listed below under the immunoblotting section. See Key Resources Table.
Micro-CT
Assessment of bone morphology and microarchitecture was performed with high-resolution micro-computed tomography (μCT40; Scanco Medical, Brüttisellen, Switzerland) in 8-week-old male mice. Femora and vertebrae were dissected, fixed overnight in neutral buffered formalin, then stored in 70% EtOH until the time of scanning. In brief, the distal femoral metaphysis and mid-diaphysis were scanned using 70 kVp peak X-ray tube potential, 113 mAs X-ray tube current, 200 ms integration time, and 10 μm isotropic voxel size. Cancellous (trabecular) bone was assessed in the distal metaphysis and cortical bone was assessed in the mid-diaphysis. The femoral metaphysis region began 1700 μm proximal to the distal growth plate and extended 1500 μm distally. Cancellous bone was separated from cortical bone with a semiautomated contouring program. For the cancellous bone region, we assessed trabecular bone volume fraction (Tb.BV/TV, %), trabecular thickness (Tb.Th, mm), trabecular separation (Tb.Sp, mm), trabecular number (Tb.N, 1/mm), connectivity density (Conn.D, 1/mm3), and structure model index. Transverse µCT slices were also acquired in a 500 μm long region at the femoral mid-diaphysis to assess total cross-sectional area, cortical bone area, and medullary area (Tt.Ar, Ct.Ar and Ma.Ar, respectively, all mm2); cortical bone area fraction (Ct.Ar/Tt.Ar, %), cortical thickness (Ct.Th, mm), porosity (Ct.Po, %) and minimum (
Mechanical testing
Femora were mechanically tested in three-point bending using a materials testing machine (Electroforce 3230, Bose Corporation, Eden Prairie, MN). The bending fixture had a bottom span length of 8 mm. The test was performed in displacement control moving at a rate of 0.03 mm/s with force and displacement data collected at 50 Hz. All bones were positioned in the same orientation during testing with the cranial surface resting on the supports and being loaded in tension. Bending rigidity (EI, N-mm2), apparent modulus of elasticity (Eapp, MPa), and ultimate moment (Mult, N-mm) were calculated based on the force and displacement data from the tests and the mid-diaphysis bone geometry measured with μCT. Bending rigidity was calculated using the linear portion of the force-displacement curve. The minimum moment of inertia (Imin) was used when calculating the apparent modulus of elasticity.
Histomorphometry
Femora were subjected to bone histomorphometric analysis. The mice were given calcein (20 mg/kg by intraperitoneal injection) and demeclocycline (40 mg/kg by intraperitoneal injection) on 7 and 2 days before necropsy, respectively. The femur was dissected and fixed in 70% ethanol for 3 days. Fixed bones were dehydrated in graded ethanol, then infiltrated and embedded in methylmethacrylate without demineralization. Undecalcified 5 μm and 10-μm-thick longitudinal sections were obtained using a microtome (RM2255, Leica Biosystems., IL, USA). Five μm sections were stained with Goldner Trichome and at least two nonconsecutive sections per sample were examined for measurement of cellular parameters. The 10 μm sections were left unstained for measurement of dynamic parameters, and only double-labels were measured, avoiding nonspecific fluorochrome labeling. A standard dynamic bone histomorphometric analysis of the tibial metaphysis was done using the Osteomeasure analyzing system (Osteometrics Inc, Decatur, GA, USA). Measurements were performed in the area of secondary spongiosa, 200 μm below the proximal growth plate. The observer was blinded to the experimental genotype at the time of measurement. The structural, dynamic, and cellular parameters were calculated and expressed according to the standardized nomenclature (Dempster et al., 2013).
For the adipocyte parameters, we used sections of the proximal tibia with H and E staining at ×20 magnification. The following MAT outcome parameters were measured and calculated: [1] MAT volume as a percentage of the tissue volume (total adipose tissue volume: Ad.V/TV; %), [2] MAT volume as a percentage of the marrow volume (marrow adipose tissue volume: Ad.V/Ma.V; %), [3] adipocyte density (Ad.Dn; cells/mm2 marrow area) representing adipocyte number. These measurements were performed by semi-automatically tracing out individual adipocytes ‘ghosts’ in all the fields analyzed. Adipocyte ghosts appear as distinct, translucent, yellow ellipsoids in the marrow space. The total proximal tibia area below the secondary spongiosa was measured in 1–4 sections per biopsy. Adipocyte analysis was performed using a semi-automated measurement program on ImageJ (Schneider et al., 2012) based image analysis software adapted from the OsteoidHisto package (van 't Hof et al., 2017). All assessments of the sections were performed together by examiners (YV and AV-V) who were blinded to the intervention assignment.
Serum analysis
Three hr fasting serum was collected at ZT3 from mice just prior to sacrifice by retro-orbital bleed. Serum was isolated and analyte levels were determined using the following commercially available detection kits: P1NP (IDS Immunodiagnostic Systems, #AC-33F1), CTX from IDS (#AC-06F1). All absolute concentrations were determined based on interpolation from standard curves provided by the manufacturer. DRI-CHEM 700 veterinary chemistry analyzer (Heska, Loveland, CO) was used for measurement of serum analytes: albumin, alkaline phosphatase, ALT, BUN, calcium, cholesterol, globulin, glucose, phosphorus, total bilirubin, triglycerides, and total protein. For complete blood counts, whole blood was collected into heparin-coated tubes and kept on ice. CBCs were measured on a 2015 Heska Element HT5 Veterinary Hematology Analyzer. HeskaView Integrated software was used for data analysis.
Quantitative Backscattered Electron Imaging (qBEI)
Distal femora from six study groups were analyzed (n = 8 each group): SHAM VEH, SHAM PTH, SHAM YKL, OVX VEH, OVX PTH, and OVX YKL. These bones were embedded undecalcified in polymethylmethacrylate (PMMA) and measured for bone mineralization density distribution (BMDD) using qBEI. The surfaces of the sample blocks were flattened by grinding and polishing (Logitech PM5, Glasgow, Scotland) and carbon coated so as to facilitate qBEI. A scanning electron microscope equipped with a four quadrant semiconductor backscatter electron detector (Zeiss Supra 40, Oberkochen, Germany) was used. Areas of metaphyseal (MS) and cortical midshaft bone (Ct) were imaged with a spatial resolution of 0.88 µm/pixel. The gray levels, reflecting the calcium content, were calibrated by the material contrast of pure Carbon and Aluminum. Thus, the resulting gray level histograms could be transformed into calcium weight percent (wt% Ca) histograms (Figure 1—figure supplement 1) as described previously (Roschger et al., 1998). Five parameters were derived to characterize the BMDD (Roschger et al., 2008). For information about CaYoung, which is the mean calcium concentration of the bone area between the double fluorescence labels, the identical bone surface measured with qBEI was additionally imaged in a Confocal Laser Scanning Microscope (Leica TCS SP5, Leica Microsystems CMS GmbH, Wetzlar, Germany) using a laser light of 405 nm for fluorescence excitation and a 20x object lens (pixel resolution of 0.76 µm). By matching the CLSM with the qBEI images, the sites of the fluorescence labels were overlaid exactly onto the qBEI images (Figure 1—figure supplement 1E). CaYoung was obtained from a total of 39 areas from a subgroup of nine samples and was subsequently used to calculate CaLow, which reflects the percentage of newly formed bone area (Figure 1—figure supplement 1H).
Flow cytometry
Ubiquitin-CreERt2; tdTomatoLSL mice were treated with tamoxifen (1 mg IP Q48H, three injections total). Two weeks after the first tamoxifen injection, mice were sacrificed and bone marrow cells were isolated by flushing with ice cold PBS using a 25G needle. 106 bone marrow cells were protected from light and stained on ice for 30 min with the following primary antibodies in a 10 µL staining volume. APC anti-mouse/human CD 11b antibody (Biolegend, San Diego, CA), FITC anti-mouse CD3 antibody (Biolegend, San Diego, CA), and PE/Cy7 anti-mouse Ly-6C antibody (Biolegend, San Diego, CA). After staining, cells were washed twice with FACS buffer (PBS plus 2% heat inactivated fetal bovine serum) and analyzed on a SORP 8 Laser BD LSR flow cytometer (Becton, Dickinson and Company, Franklin Lakes, NJ).
Bone marrow macrophages and osteoclast differentiation
Bone marrow cells were harvested from 4 week-old C57BL/6J mice. Femur and tibia were removed and the marrow cavity was flushed out with 10 mL 1x phosphate-buffered saline per mouse (GE Healthcare Life Sciences, MA) with a 25 G needle (Becton, Dickinson and Company, (Franklin Lakes, NJ)) which was then centrifuged at 1,000 rpm for 10 min. Supernatant was removed, and cell pellet was resuspended in 1 mL red blood cell lysis buffer (Sigma-Aldrich, St. Louis, MO) and incubated for 2 min followed by centrifugation at 1000 rpm for 5 min to collect cells. Bone marrow cells were plated on 100 mm non-treated tissue culture dishes (Corning Inc, Corning, NY) and maintained in alpha minimum essential medium eagle (MEM) (Sigma-Aldrich, St. Louis, MO) containing 15% fetal bovine serum FBS (Gemini Bio, West Sacramento, CA), 1x penicillin-streptomycin (Gibco, Waltham, MA), 1x GlutaMAX supplement (Gibco, Waltham, MA) and in the presence of 30 ng/mL recombinant mouse M-CSF (R and D systems, Minneapolis, MN). These cells were maintained at 37°C in a humidified 5% CO2 incubator for 3 days, then collected by trypsinization. Primary osteoclast precursors were then seeded in 96 well plates at 2,000 cells/well (20,000 cells/mL), and differentiation was induced with 50 ng/mL of recombinant mouse RANKL (R and D systems, Minneapolis, MN) and 30 ng/mL recombinant mouse M-CSF (R and D systems, Minneapolis, MN). Fresh medium was replenished every 3 days.
For experiments with 4-hydroxytamoxifen treatment, primary osteoclast precursors were seeded after initial culture on non-treated plates into six-well plates in the presence of 30 ng/mL recombinant mouse M-CSF (R and D systems, Minneapolis, MN) for 3 days. Cells were then treated with 300 nM of 4-hydroxytamoxifen (Sigma-Aldrich, St. Louis, MO) or vehicle (methanol, Sigma-Aldrich, St. Louis, MO) for 3 days. Fresh medium with 30 ng/mL recombinant mouse M-CSF (R and D systems, MN) was then added for another 3 days prior to collecting cells for subsequent osteoclast differentiation.
For osteoclast differentiation assays, primary osteoclast precursors were seeded in 96-well plates, and differentiation was induced with 50 ng/mL of recombinant mouse RANKL (R and D systems, Minneapolis, MN) and 30 ng/mL recombinant mouse M-CSF (R and D systems, Minneapolis, MN). Fresh medium was replenished every 3 days. sTRAP assay was measured with acetate buffer from acid phosphatase leukocyte kit (Sigma-Aldrich, St. Louis, MO), 1M sodium L-tartrate dibasic dihydrate (Sigma-Aldrich, St. Louis, MO) and pNPP substrate (Sigma-Aldrich, St. Louis, MO). Fifty µL of cell culture supernatant was transferred to a new 96-well plate and 150 µL of substrate mix was added. Plate was then incubated 37°C for an hour. Reaction was terminated by adding 3N NaOH (Sigma-Aldrich, St. Louis, MO), which results in an intense yellow color. Absorbance was measured at 405 nm.
TRAP staining was performed using acid phosphatase leukocyte kit (Sigma-Aldrich, St. Louis, MO) to visualize osteoclasts. TRAP buffer was prepared freshly on the day of experiment by mixing acetate buffer containing sodium acetate and acetic acid with sodium tartrate and naphthol AS-BI phosphate disodium salt (Sigma-Aldrich, St. Louis, MO). TRAP staining solution was prepared by mixing Fast Garnet GBC Base with sodium nitrite. For TRAP staining, culture medium was removed from cells, and cells were fixed with fixative solution for 5 min at room temperature. Fixative solution was prepared fresh on the day of experiment by mixing citrate solution, acetone with 37% formaldehyde. Cells were then washed twice with deionized water and stained with TRAP staining solution for 60 min at 37°C.
For pit resorption assays, primary osteoclast precursors were seeded in 96-well resorption plates at 2000 cells/well (Corning, Inc, Corning, NY), and differentiation was induced with 50 ng/mL of recombinant mouse RANKL and 30 ng/mL recombinant mouse M-CSF. Fresh medium with M-CSF and RANKL was replenished every 3 days. Culture was aspirated and cells were washed three times with 1x PBS. A total of 100 µL of 10% bleach was added to each well and incubated for 30 min at room temperature. Bleach solution was removed and cells were washed twice with deionized water. Plates were air-dried at 4°C overnight and osteoclast resorption pits were visualized the next day. Pit resorption was quantified using ImageJ.
gDNA deletion analysis
Genomic DNA was isolated from cultured bone marrow macrophages or cortical bone using DNeasy Blood and Tissue Kit (Qiagen, Hilden, Germany) according to the instructions of the manufacturer. For cultured bone marrow macrophages, cell were treated with vehicle (methanol) or 4-hydroxytamoxifen (0.3 µM) for 72 hr prior to gDNA isolation. For cortical bone, mice were treated with tamoxifen (three 1 mg IP injection every 48 hr) and then sacrificed 7 days after the first tamoxifen injection. Epiphyses were removed and bone marrow cells were flushed using ice cold PBS. Remaining cortical bone fragments were flash frozen in liquid nitrogen and then pulverized using a mortar and pestle. Bone tissue was then subjected to gDNA isolation and quantified using a spectrophotometer (Nanodrop 2000, Thermo Fisher Scientific, Waltham, MA). 15 ng gDNA was used for each qPCR reaction. For each gene, one primer pair was used that was internal to the targeted loxP sites and a second external primer pair was used to normalize to input gDNA amount. See PCR primer Appendix for primer sequences used. Relative abundance of the targeted gene was calculated by the 2(-Delta Delta C(T)) method using the external primer pair as control (Livak and Schmittgen, 2001).
TF-seq
Ocy454 cells were infected with lentiviral particles expressing TF-seq library (O'Connell et al., 2016) and eGFP. Infected cells were isolated by sorting for GFP expression. The cell line was confirmed to be mycoplasma-free by PCR. Thereafter, cells were plated at a density of 50,000/ml in 96 well plates (5000 cells/well) and allowed to expand at 33°C for 48 hr. Cells were then moved to 37°C for 24 hr, then treated with vehicle (DMSO) or YKL-05–099 for time points ranging from zero minutes to 4 hr with n = 3 wells per condition. Cells were washed with ice cold PBS and then lysed with RLT buffer (Qiagen, supplemented with ß-mercaptoethanol) and stored at −80°C. RNA was purified using Agentcourt RNA Clean XP to precipitate the nucleic acids in 1.25 M NaCl and 10% PEG-8000. Maxima reverse transcriptase (Thermo Fisher Scientific) was run according to the manufacturer’s instructions using a multiplexed primed reverse transcriptase reaction. The biotinylated 96-well sequence tagged TF-seq-specific reverse transcriptase primers, and the biotinylated 96-well degenerate sequence-tagged polydT reverse transcriptase primers were used at 750 and 250 nM final concentrations, respectively, with 50 units of Maxima. After sequencing-tagging all cDNA during reverse transcriptase, each 96-well plate was pooled and the unincorporated primers were washed away from the cDNA by precipitating with 10% PEG-8000 and 1.25 M NaCl. Amplification of the TF-seq gene reporter amplicon was performed on 50% of the cDNA using primers with full Illumina-compatible sequencing adapters in a 600 µl PCR reaction for 28 cycles. The 422 bp amplicon was then gel extracted for sequencing. TF-seq is a 50 bp single-end read, well-tag, RNA UMI, followed by a 17 bp constant sequence, then the reporter tag UMI, and ultimately the reporter tag. We counted the number of unique RNA molecules for every well and reporter element, requiring a perfect match for the respective tags. UMI tag counts for each reporter element were obtained. Reporter element activity was expressed as fold change versus baseline (time 0) for each drug treatment.
Generation of models of kinases in various conformational states
Models of CSF1R (FMS), SIK1, and SIK2 (QIK) in four conformations, the CIDI, CIDO, CODI, and CODO states, were generated using DFGmodel (Ung and Schlessinger, 2015). DFGmodel uses a multi-template homology modeling approach to construct composite homology models in various kinase conformations. The models are based on an augmented version of a structurally validated sequence alignment of human kinome (Modi and Dunbrack, 2019). For the CIDO, CODI, and CODO states, DFGmodel uses multi-template approach, where manually curated sets of determined structures, covering a unique range of conformations for each state are used as template structures. For the CIDI, DFGmodel uses a single-template approach to construct the models; DFGmodel searches a library of kinase structures annotated by Kinformation (Ung et al., 2018; Rahman et al., 2019; Camacho et al., 2009; http://www.kinametrix.com) to identify a best-matched kinase in CIDI state as template. DFGmodel then uses MODELLER (Sali and Blundell, 1993) v9.21 to generate homology models for each kinase. For CIDI, CIDO, and CODO states, 50 models were generated; POVME (Durrant et al., 2014) v2.1 was used to estimate the binding site volume of each model, where 10 models with the largest volume were selected. For CODI, four sets of templates are required to cover the observed conformation, thus 40 models were generated for each of these sets; eight models with the largest volume in each of the sets were selected. Lastly, CSF1R crystal structures are also included for examination.
Molecular docking
Molecular docking was performed using Glide (Friesner et al., 2004) (Schrödinger 2019–3). Default settings and Standard Precision (SP) model, with the addition of aromatic hydrogen and halogen bonds, were used for Glide protein grid generation and docking of inhibitor into the active site of protein kinase models in CIDI, CIDO, CODI, and CODO conformations. OPLS3e force field (Harder et al., 2016) was used to parameterize both protein and ligands. Scaling of van der Waals (vdW) radius for receptor atoms was set to 0.75. The docking results were averaged for 10 models, as described by Ung and Schlessinger, 2015. The small molecule YKL-05–099 was prepared with Schrödinger’s LigPrep program. Docking pose of this molecule in each of the models was examined; poses that do not possess the critical hydrogen-bonds with the hinge residues or have docking score higher than −7.0 were rejected.
CSF1R kinase assay
Assays were performed in base reaction buffer (20 mM Hepes (pH 7.5), 10 mM MgCl2, 1 mM EGTA, 0.02% Brij35, 0.02 mg/ml BSA, 0.1 mM Na3VO4, 2 mM DTT, 1% DMSO). YKL-05–099 was dissolved in 100% DMSO in a 10 mM stock. Serial dilution was conducted by Integra Viaflo Assist in DMSO. Recombinant CSF1R (Invitrogen, Carlsbad, CA) was used at a concentration of 2.5 nM. The substrate used was pEY (Sigma-Aldrich, St. Louis, MO) at a concentration of 0.2 mg/ml. Kinase assays were supplemented with 2 mM Mn2+, and 1 µM ATP was added. Assays were performed for 20 min at room temperature, after which time 33P-ATP (10 µCi/µl) was added followed by incubation for another 120 min at room temperature. Thereafter, radioactivity incorporated into the pEY peptide substrate was detected by filter-binding method. Kinase activity data were expressed as the percent remaining kinase activity in test samples compared to DMSO reactions. IC50 values and curve fits were obtained using Prism 8.0 GraphPad Software (GraphPad Software, San Diego, CA).
Immunoblotting
Immunoblotting was performed in lysates derived from primary bone marrow macrophages. Cells were scraped into ice cold PBS and cell pellets were lysed in TNT (200 mM NaCl, 20 mM Tris HCl pH 8, 0.5% Triton X-100 supplemented with protease and phosphatase inhibitor cocktail (Thermo Fisher Scientific, Waltham, MA)). Cells were vortexed twice in lysis buffer for 30 s followed by centrifugation at top speed at 4°C for 5 min. Protein concentration in cell lysates was quantified using Bradford assay (Thermo Fisher Scientific, Waltham, MA). Equal amounts of protein were then separated by SDS-PAGE under reducing conditions. Proteins were then transferred to nitrocellulose membranes. Membranes were blocked in TBST plus 5% milk for 30 min at room temperature. Thereafter, membranes were incubated overnight at 4°C in TBST with 5% BSA plus primary antibodies (source and dilutions below). Membranes were then washed three times with TBST for 5 min, followed by secondary antibody incubation (1:2000 goat anti-rabbit) for 30 min at room temperature. Next, membranes were washed again for three times with TBST for five minutes followed by detection with Pierce ECL Plus Western Blotting Substrate (Thermo Fisher Scientific, Waltham, MA) and imaging by Azure c600. The primary antibodies were: SIK2 (1:1000), CSF1R phospho-Y723 (1:1000), CSF1R (1:1000), phospho-ERK1/2 (1:1000), ERK1/2 (1:2000), Tubulin (1:1000) were obtained from Cell Signaling Technology (Danvers, MA). Anti-SIK3 rabbit polyclonal antibodies (1:1000) were obtained from Abcam (Cambridge, United Kingdom).
Statistical analysis
When two groups were compared, statistical analyses were performed using unpaired two-tailed Student’s t-test. Population samples were shown to be normally distributed. For OVX studies (Figures 1 and 2), two-way ANOVA was performed followed by Dunnett’s multiple comparisons test (GraphPad Prism 9.1.1). p Values less than 0.05 were considered to be significant. The numbers of mice studied in all experiments are described in figure legends, and in all figures data points represent individual mice. All data points indicate individual biologic replicates (independent experimental samples) and not technical replicates (the same sample re-analyzed using the same method). A Source Data File is presented for all figures.
2 Center for Advanced Orthopaedic Studies, Department of Orthopedic Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School Boston United States
3 Dana Farber Cancer Institute, Harvard Medical School Boston United States
4 Ludwig Boltzmann Institute of Osteology at Hanusch Hospital of OEGK and AUVA Trauma Centre, Meidling, 1st Medical Department Hanusch Hospital Vienna Austria
5 Center for Bone Quality, Leiden University Medical Center Leiden Netherlands
6 Center for Clinical and Translational Research, Maine Medical Center Research Institute Scarborough Canada
7 Department of Endocrinology and Metabolism, Academic Medical Center Amsterdam Netherlands
8 Broad Institute of MIT and Harvard Cambridge United States
9 Center for Computational and Integrative Biology, Massachusetts General Hospital Boston United States
10 Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai New York United States
11 Department of Integrative Biology and Pharmacology, McGovern Medical School at The University of Texas Health Science Center at Houston (UTHealth) Houston United States
12 Université de Paris, Institut Cochin, CNRS Paris France
13 Harvard Stem Cell Institute Cambridge United States
University of Pennsylvania United States
Icahn School of Medicine at Mount Sinai United States
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