The antibodies, primers, kits, and chemicals used in this study are in extended tables 3–6.
Fyn -/- animal model
Fyn-/- mice (B6.129S7-Fyntm1Sor/J) were purchased from The Jackson laboratory35 and bred, propagated, and maintained at The Hormel Institute, University of Minnesota. Mice were maintained under conditions based on the guidelines established by the University of Minnesota Institutional Animal Care and Use Committee. Genotyping was performed using a standard protocol and Agilent Taq polymerase. Representative genotyping is presented in Extended Fig. 2A. Age matched (± 4 days) wildtype and Fyn-/- mice (n = 12 males + 12 females) were maintained for 97 weeks. Some mice were euthanized based on veterinary advice and the study ended with 13 mice (6 males + 7 females).
Generation of mouse embryonic stem cells (mESCs) from WT and Fyn-/- mice
mESCs were generated from the inner cell mass of blastocysts isolated from 3.5 days post coitum mice36. Briefly, a feeder layer of mouse embryonic fibroblasts (MEFs, 1x106) was plated two days before blastocyst isolation. MEFs were then treated with mitomycin C (10 µg/ml) for 2 h. Isolated blastocysts were washed once with KnockOut™ Dulbecco's Modified Eagle Medium (DMEM) and transferred aseptically on a feeder layer with KnockOut™ DMEM supplemented with 20% knockout serum replacement and 1000 U/mL Leukemia Inhibitory Factor (LIF). After 48 h the medium was changed and blastocysts were left to hatch for 7–10 days. Cells from hatched blastocysts were transferred to a new feeder layer. Colonies generated from the previous step were transferred onto a new feeder layer. Stem cells were confirmed by alkaline phosphatase (AP) staining and Western blotting for Sox2 and KLF4 (Extended Fig. 1D and E).
Cell culture
mESCs (E14Tg2a) were maintained in DMEM supplemented with 15% heat-inactivated ESC-qualified fetal bovine serum (FBS), 0.055 mM β-mercaptoethanol, 2 mM L-glutamine, 0.1 mM minimum essential medium non-essential amino acids, and 1,000 U/mL LIF.
Generation of TIN2-DC conditional mice and PP2 treatment
TIN2-DC conditional mice (B6(Cg)-Tinf2tm2.1Tdl/J) and Cre-recombinase expression [Tg(CMV-cre)1Cgn] were purchased from The Jackson laboratory. TIN2+/DC mice were generated by crossing TIN2+/DC-COND mice with Cre-recombinase expressing mice. TIN2+/DC-COND mice were also bred with Fyn-/- mice and subsequently crossed with Cre-recombinase expressing mice to obtain TIN2+/DC- Fyn-/- double knockout mice. TIN2+/DC- Fyn-/- mice were not obtained possibly due to embryonic lethality of Fyn double knockout in TIN2+/DC mice. Nonetheless, TIN2+/DC- Fyn+/- mice were generated (Extended Fig. 7B). The third generation TIN2+/DC mice were used for experiments. Representative images of genotyping of these mice are shown (Extended Fig. 7A).
TIN2-Fyn double knockout age matched-female mice (± 4 days) were divided into 4 groups: experimental groups TIN2+/DC- Fyn-/+ (n = 8) and TIN2+/DC-Fyn+/+ (n = 8) and negative controls TIN2+/+-Fyn+/+ (n = 4) and TIN2+/+- Fyn+/- (n = 4). A sufficient number of male mice appropriate for statistical analysis was not generated, and thus, only females were included in the study. These mice were maintained for 24 weeks before euthanization.
PP2 (3-(4-chlorophenyl)-1-(1,1-dimethylethyl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine) is a potent SFK inhibitor that blocks Fyn activity (IC50 = 5 nM)37. We used PP2 as a Fyn inhibitor in mice at a dose of 3 mg/kg. This dose of PP2 was safe for mice and did not lead to toxicity or death. Age-matched TIN2+/DC mice (± 4 days) were divided into 2 groups (n = 12, 6 males + 6 females) and treated with vehicle or PP2 for 60 days i.p. TIN2+/+mice (n = 6, females) were also divided into 2 groups and treated similarly with vehicle or PP2 and served as controls.
Mouse embryonic fibroblast (MEF) collection from TIN2+/DC mouse embryos
MEFs were collected from freshly harvested 13.5 dpc TIN2+/DC embryos following a published protocol38. Briefly, harvested embryos were washed with PBS and placental and maternal tissues removed. Embryo heads were saved for genotyping. Embryos were placed in a separate 10 cm2 dish and minced with 1 mL trypsin with sterile surgical blade. Isolated cells were incubated at 37°C for 45 min, and then maintained in MEF media (DMEM with 10% FBS). Suspended cells were transferred into a new flask with complete media and MEFs were grown to 80% confluence. Only MEFs having mutations in TIN2 and Cre transgene were used for further experiments.
Generation of DC-iPSCs from fibroblasts
DC fibroblasts were purchased from The Coriell Cell Repositories and maintained in MEM medium supplemented with 15% FBS and 1% non-essential amino acids. Induced pluripotent stem cells (iPSCs) were generated from DC fibroblasts by ectopic expression of Yamanaka transcription factors, Oct4, Klf4, Sox2, and c-Myc (OKSM), with the help of a STEMCCA Constitutive Polycistronic (OKSM) Lentivirus according to the manufacturer’s protocol (MilliporeSigma). Briefly, 1 x106 DC fibroblasts were seeded onto gelatin-coated plates and infected with STEMCCA virus. Infected cells were then transferred to a plate containing 1 x 105 feeder cells. iPSC colonies were picked 25–30 days’ post-infection and maintained in feeder-free E8 media (StemCell Technologies) on a Matrigel (Corning). Pluripotency was confirmed by Immunofluorescence and Western blotting with human iPSC specific markers.
Alkaline phosphatase (AP) staining
To perform AP staining, mESCs were cultured in the appropriate medium, fixed with 4% paraformaldehyde in phosphate buffered saline (PBS) for 2 min at room temperature. AP staining was performed using the Alkaline Phosphatase Detection Kit following the manufacturer’s protocol (MilliporeSigma).
RNA interference of Fyn
To generate knockdown Fyn cells, pLKO.1-sh-Fyn, or pLKO.1-mock lentivirus plasmids were co-transfected with psPAX2 and pMD2.0G into HEK 293T cells by using the iMFectin transfection reagents (GenDepot). The mouse lentiviral vector sequences for Fyn were purchased from the University of Minnesota Genomic Center. Viral particles containing 4 μg/mL polybrene were infected twice into E14TG2a cells at 24 h and 48 h of culture. After 48 h E14TG2a cells were selected with 1 μg/mL puromycin. Selected cells were maintained in complete media until reaching 80% confluence.
Telomeric repeat amplification protocol (TRAP) assay
TRAP assay was used to determine telomerase activity according to the manufacturer’s recommendation (MilliporeSigma). Briefly, whole-cell lysates were prepared from wildtype, Fyn-/- mESCs, mock-, and sh-Fyn-transfected E14TG2a cells, and colon tissues of wildtype and Fyn-/- mice by using CHAPS lysis buffer. CHAPS-containing cell lysates (500 ng/µL) were used for the TRAP assay. Relative telomerase activity was determined from a TSR8 standard curve according to the manufacturer’s protocol.
Quantitative fluorescent in situ hybridization (Q-FISH) and flow cytometry-FISH (Flow-FISH) assays
Q-FISH of metaphase chromosomes, interphase nuclei, and mouse tissue was performed as previously described39. Briefly, 1 µg/mL Colcemid (Cayman Chemicals) -treated and untreated cells were permeabilized with 75 mM KCl hypotonic solution followed by fixation using Carnoy's fixative. For tissue samples, deparaffinization of 5 µM sections of paraffin-embedded mouse organ specimens were conducted using standard protocols. Telomere Q-FISH staining was performed using TelC-Alexa-488 or TelG-Cy3 PNA telomere probes (PNA Bio Inc). Slides were counterstained with DAPI (Electron Microscopy Sci.) and visualized using Nikon or Zeiss LSM 900 confocal microscopes. Telomeres were analysed by using open-source software (Telometer; http://demarzolab.pathology.jhmi.edu/telometer/), as previously described40.
Flow-FISH analysis was performed 41 with slight modifications. Briefly, cells (0.5 x 106) were washed in PBS containing 0.1% BSA and suspended in 300 µL hybridization buffer (70% formamide, 20 mM Tris-HCl, pH 7.0, 1% blocking reagent, 1 µg/mL PNA probe) and incubated for 2 h at RT. Cells were then washed twice with fixation buffer (60% formamide, 10 mM Tris-HCl, pH 7.0, 0.1% blocking reagent, 0.1% Tween 20) at 40°C, resuspended in PBS containing 0.1% BSA with 0.05 ug/mL of propidium iodide (PI) and analyzed by BD-FACS (BD Aria III). TelC-Alexa-488 PNA probe and PI nuclear stain was used in all flow-FISH analysis, except CRISPR-Cas9 transfected cells, where TelG-Cy3 PNA probe and DAPI were used instead.
q-PCR assay for telomere measurement in cells
Average telomere length was measured from genomic DNA of mouse or human stem cells by using a qPCR method previously described42. The single-copy genes m36B4 and h36B4 and the multicopy gene hAlu were used as references. 10 μL of 2×SYBR Green mix, 0.5 μL each of 10 μM forward and reverse primers, 4 μL DNase/RNase free water, and 5 μL genomic DNA (8 ng/μL) were mixed to obtain a 20 μL reaction. The qPCR was carried out in a Bio-Rad thermocycler (CFX96) with reaction conditions of 95°C for 10 min followed by 40 cycles of denaturation at 95°C for 15 s, 60°C annealing for 30 s, and 72°C extension and data collection for 30 sec. The CFX manager software was used to generate standard curves. The average telomere length is termed as the telomere to single copy gene (T/S) ratio.
Protein extraction, Western blotting, and Immunohistochemistry (IHC)
Cells were lysed withNP-40 lysis buffer (50 mM Tris-HCl, pH 7.6, 150 mM NaCl, 5 mM EDTA, 1% Nonidet P-40 with a protease inhibitor cocktail). Nuclear and Cytoplasmic fractions were obtained using the NE-PER cytoplasmic and nuclear protein extraction kit (ThermoFisher Scientific). A phosphatase inhibitor cocktail was used for phosphoprotein analysis, and N-ethylmaleimide (NEM) was used for SUMO-protein analysis. The proteins were resolved in SDS-PAGE and transferred to polyvinylidene difluoride (PVDF) membranes. The membranes were blocked with 5% milk, and target proteins were detected with specific antibodies and visualized by chemiluminescence.
IHC was performed using a standard protocol. Paraffin-embedded tissues were subjected to deparaffination and antibody retrieval. Tissue sections were blocked with 10% goat-serum followed by overnight incubation with a primary antibody at 4°C. Slides were incubated with a secondary antibody and stained with 3,3′-Diaminobenzidine (DAB). For IF, a fluorochrome-conjugated secondary antibody was used instead. Images were quantified using ImageJ2 software43.
Immunoprecipitation
A total amount of 1 mg of cell lysates in a volume of 500 µL were immunoprecipitated with 2 µg of each respective antibody and samples were rotated overnight at 4°C. 40 µL of protein A/G Sepharose beads (GenDepot) were added to each sample and rotated for 1 h at 4°C. Beads were washed 3 times with lysis buffer, and the supernatant fraction was analyzed by Western blotting.
Chromatin immunoprecipitation assay
Stable sh-mock and sh-Fyn E14 cells were seeded in 10 cm2 plates. Chromatin immunoprecipitation (ChIP) was performed using the One-Day Chromatin Immunoprecipitation Kit (Magna ChIP G, MilliporeSigma) according to the manufacturer's protocol. Chromatin samples were immunoprecipitated with anti-menin antibody overnight at 4℃. The DNA fractions for TERT promoter was analyzed by qPCR.
Protein expression, purification and in vitro kinase assay
WT and mutant MEN1 (Y603F) were cloned into pGEX-5X1 vector upstream a C-terminal 6×His tag. Menin WT and mutant (Y603F) proteins were expressed in E. coli BL21(DE3) pLysS cells (Promega). Cells were grown in Lysogeny broth to an OD 600 of 0.5-0.7 and protein expression was induced with 0.5 mM IPTG for 20 h at 16°C. Cells (200 mL) were pelleted at 7,000 rpm and resuspended in 10 mL lysis buffer (50 mM HEPES pH 8.0, 500 mM NaCl, 20 mM imidazole, 10% glycerol, 2 mM TCEP, 1% Tween-20, 1X protease inhibitor). Cell suspensions were incubated with lysozyme for 30 min and disrupted by sonication for 10 min. Cells were centrifuged for 30 min at 13,000 rpm, and lysates were equilibrated with Ni-NTA agarose beads (ThermoFisher Scientific) for 2 h at 4°C. Samples were centrifuged at 1,000 rpm for 3 min to remove the supernatant fraction. Beads were washed with 10 mL buffer 1 (50 mM HEPES pH 8.0, 500 mM NaCl, 30 mM imidazole, 10% glycerol, 0.5% Tween-20, 2 mM DTT), and 2X with 10 mL buffer 2 (50 mM HEPES pH 8.0, 500 mM NaCl, 40 mM imidazole, 10% glycerol, 0.5% Tween-20, 2 mM DTT). Proteins were eluted 3X with 0.1 mL elution buffer (50 mM HEPES pH 8.0, 150 mM NaCl, 300 mM imidazole) and transferred to kinase buffer (50 mM Tris pH 8.0, 100 mM NaCl) using Zeba Spin Desalting columns (ThermoFisher Scientific). Proteins were separated by SDS-PAGE and stained with Coomassie blue. The protein concentrations were quantified using a Nanodrop at A280 (ThermoFisher Scientific).
Fyn protein with or without Menin recombinant protein (WT and mutant) was incubated for 30 min in a 30°C water bath. Proteins were incubated with 10 μCi [γ32P] ATP and isotope-unlabelled ATP in kinase buffer (20 mM HEPES (pH 7.4), 1 mM dithiothreitol, 10 mM MgCl2, and 10 mM MnCl2). The incorporated radioactivity was measured by autoradiography. For the non-radioactive kinase assay the phosphorylated substrate was detected by Western blotting. Recombinant β-catenin was used as a positive control substrate for Fyn.
Identification of phosphorylation sites on Fyn-phosphorylated Menin
An in vitro kinase assay was performed as discussed above, replacing [γ32P]ATP with unlabelled ATP. The ABSciex TripleTOF 5600 system (SCIEX) coupled with Eksigent 1D+ Nano LC system (SCIEX) was used to identify Menin's phosphorylated sites. Nano LC of enzymatic peptides was performed with the Eksigent 1D+ Nano LC equipped with the cHiPLC nanoflex system (SCIEX). Peptides were loaded onto the column and then eluted with a linear gradient of 5–40% binary solvent B1 for 30 min at a flow rate of 0.3 mL/min. Mass spectrometry analysis of peptides was performed using the ABSciex TripleTOF 5600 system. Analysis was performed using the NanoSpray III source (SCIEX). The mass spectrometry was calibrated by the acquisition of [Glu1] fibrinopeptide (25 pmol/ml). The raw data were processed and searched with ProteinPilotTM software (version 4.0) using the Paragon algorithm. Proteins were identified by searching the UniProtKB human database and filtered at an R95% confidence cut-off. Peptides for phosphorylated Men1 were identified at a 1% false discovery rate.
Small ubiquitin-like modifier (SUMOylation) assay
We performed the in vitro SUMOylation assay with endogenously-expressed or overexpressed proteins. Briefly, HEK 293T cells were transfected with pcDNA3.1-Xpress-MEN1 (WT or Y603F, Y603D, K493R, K609R mutants) and pcDNA3-HA-SUMO-1 using iMFectin. 24 h after transfection, cells were lyzed in NP-40 buffer. SUMOylated-Menin proteins were visualized by immunoprecipitation with an Xpress tag or anti-Menin antibody and immunoblotted for HA or SUMO-1 antibodies. We also analyzed SUMOylation of menin by using the EpiQuikTM In Vivo Universal Protein Sumoylation Assay Kit (EPIGENTEK). Briefly, nuclear lysates from transfected HEK 293T cells and mESCs were prepared using NE-PER cytoplasmic and nuclear protein extraction kit (ThermoFisher Scientific). Nuclear lysates (10 µg) were used for the assay. SUMOylation intensity was calculated against a standard curve prepared from recombinant SUMO proteins according to the manufacturer’s protocol.
Establishing stable transfectants of mESCs by electroporation
E14TG2a cells (2 x108) were co-electroporated with pcDNA3.1-Xpress-MEN1 (mock, WT or Y603F, Y603D, K609R mutants) and pcDNA3.1-HA-SUMO-1. A total of 20 µg of DNA was used at 230 V and 500 mF by the Gene Pulser X (Bio-Rad). Cells were plated onto 60-mm dishes and selected with 1 mg/mL G418 two days after electroporation. Stable cells were confirmed by immunoblotting with Xpress and HA antibodies. Cells were maintained 12 passages before telomere analysis.
RNA-immunoprecipitation (RNA-IP) and RNP-immunoprecipitation (RNP-IP)
RNA-IP was performed according to Tang et al., 201844 with minor modifications. Briefly, cDNA was used as a template to amplify hTERC or mTERC. All 5′ primers contained the T7 promoter sequence 5′-CCAAGCTTCTAATACGACTCACTATAGGGAGA-3′. PCR-amplified DNA was used as a template to transcribe biotinylated RNA using T7 RNA polymerase and biotin-UTP. One µg of purified biotinylated transcripts was incubated with 200 μg of nuclear extracts for 60 min at 4°C. Complexes were isolated with streptavidin-conjugated agarose beads (MilliporeSigma), and the pull-down material was analyzed by Western blotting.
For RNP IP assays, cells were exposed to UVC (400 mJ/cm2), and lysates were prepared in IP buffer (10 mM Hepes, pH 7.4, 50 mM β-glycerophosphate, 1% Triton X-100, 10% glycerol, 2 mM EDTA, 2 mM EGTA, 10 mM NaF, 1 mM DTT, protease inhibitor cocktail, NEM, RNase inhibitor) and immunoprecipitated with anti-Menin or anti-Xpress overnight. The complexes were washed twice with stringent buffer (100 mM Tris-HCl, pH 7.4, 500 mM LiCl, 0.1% Triton X-100, and 1 mM DTT, protease inhibitor cocktail, N-ethylmaleimide, RNase inhibitor) and twice with IP buffer. The RNA in RNP IP was assessed by qRT-PCR analysis and normalized to the U6 gene44.
Identification of unknown proteins recruited by Menin on TERC
A proteome-based approach was used for determining the protein targets interacting with SUMOylated-menin and TERC binding. First, HEK 293T cells were transfected with MEN1 mutants (Y603F, Y603D) with HA-tagged SUMO-1 for 24 h, and nuclear lysates were subjected to RNA-IP. Differential protein expression across the samples was screened by conducting MS/MSALL with SWATHTM acquisition. The raw data were collected through Information Dependent Acquisition (IDA) and SWATHTM acquisition using ABSciex TripleTOFTM 5600 with Eksigent 1D+ nano LC (nanoLC-MS/MS instrument). Protein identification, MS peak extraction, and statistical analysis were performed with ProeinPilotTM (version 4.5), PeakViewTM (version 2.2) and MarkerViewTM (version 1.2), respectively. Bioinformatics analyses were conducted with the BioVenn program 45 45 and displayed in a Venn-diagram of differential expressed proteins. Protein classification was performed using the String software (https://string-db.org) and GraphPad prism 8.0 was used to make the pie diagram.
Bone marrow isolation and hematoxylin and eosin staining
Bone marrow specimens were fixed in acetic acid–zinc–formalin fixative, decalcified in 10% formic acid–5% formaldehyde, and processed for paraffin embedding. The 1.5 µM paraffin-embedded sections were stained with H&E and the morphology visualized by Nikon light microscopy.
Generation of Fyn knockout DC-iPS cells using CRISPR-Cas9
CRISPR-Cas9-mediated genome editing was performed transfecting DC fibroblasts with Fyn and control Double Nickase human Plasmids (Santa Cruz Biotechnology). according to the manufacturer’s protocol. Immunoblots confirmed gene knockout efficiency.
pY603-menin antibody validation
The specificity of custom purified pTyr603-menin (pY603-menin) rabbit polyclonal antibody (Abclonal) was confirmed by using phospho-blocking peptides. Further validation was performed by using in vitro kinase assays.
Immunofluorescence-FISH (IF-FISH) assay
Metaphase spreads were prepared as described above. Slides were fixed in 4% paraformaldehyde at room temperature for 10 min, followed by permeabilization with 0.05% Triton-x100 for 10 min. Slides were blocked in 5% serum for 1 h, incubated overnight with a primary antibody, and incubated with a fluorochrome-tagged secondary antibody for 1 h. The same slides were subjected to FISH assay using telomeric PNA probes as described above.
Statistical analysis
Data were analyzed either by student’s t-test or by one-way analysis of variance (ANOVA) followed by Tukey multiple comparisons test using the GraphPad Prism software. A probability of p < 0.05 was considered statistically significant. Each experiment was performed at least 3 times unless otherwise indicated. ∗p ≤ 0.05, ∗∗p ≤ 0.01, and ∗∗∗p ≤ 0.001.