# PFKM governs metabolic shifts throughout skeletal muscle differentiation

**Authors:** Melissa Campos, Steven T. Nguyen, Xiangduo Kong, Ying Yang, Richard L. Watson, Anastasia Gromova, Catherine R. Livelo, Carolina N. Franco, Julia E. Cabral, Laurence J. Seabrook, Shengqi Dai, Yingzi Liu, Mingqi Zhou, Eric A. Hanse, Kaelyn Sumigray, Albert R. La Spada, Marcus M. Seldin, Maksim V. Plikus, Dequina A. Nicholas, Reginald McNulty, Mei Kong, Kyoko Yokomori, Lauren V. Albrecht

PMC · DOI: 10.1038/s42255-026-01457-4 · Nature Metabolism · 2026-02-24

## TL;DR

This study shows how the enzyme PFKM controls metabolic changes during muscle cell development, influencing cell fate through its regulation by Wnt signaling and lysosomal degradation.

## Contribution

The study reveals a novel mechanism by which PFKM degradation via Wnt signaling and microautophagy regulates metabolic shifts and muscle cell differentiation.

## Key findings

- PFKM expression increases during skeletal muscle differentiation and is degraded via Wnt signaling and microautophagy.
- PFKM degradation shifts metabolism from glycolysis to the pentose phosphate pathway, affecting cell fate.
- PFKM overexpression promotes differentiation, while its knockdown inhibits it, but can be rescued by 3-phosphoglycerate.

## Abstract

Metabolism is known to influence cell identity, but the underlying mechanisms remain unclear. Here we reveal spatiotemporal dynamics of phosphofructokinase 1 (PFK1), a key glycolytic enzyme, within the skeletal muscle lineage. The expression of PFKM (the muscle isoform of PFK1) is low in muscle stem cells and increases during differentiation. Mechanistically, Wnt signalling rapidly induces lysosomal degradation of PFKM through a methyl arginine degron motif, which gets selectively methylated by the protein arginine methyltransferase (PRMT1) and delivered to lysosomes through microautophagy. PFKM degradation shifts glucose metabolism from glycolysis to the pentose phosphate pathway. PFKM overexpression increases glycolysis and promotes differentiation into terminally differentiated myofibres. On the other hand, PFKM knockdown blunts differentiation, which can be rescued by supplementation with the downstream glycolytic intermediate 3-phosphoglycerate. In sum, our findings highlight the importance of compartmentalized metabolism in cell fate decisions.

Subcellular compartmentalization of the glycolytic enzyme PFKM regulates cell fate and metabolic switch during skeletal muscle differentiation.

## Linked entities

- **Genes:** PFKM (phosphofructokinase, muscle) [NCBI Gene 5213], PRMT1 (protein arginine methyltransferase 1) [NCBI Gene 3276]
- **Proteins:** PFKM (phosphofructokinase, muscle), Wnt (protein Wnt-2), PRMT1 (protein arginine methyltransferase 1)
- **Chemicals:** 3-phosphoglycerate (PubChem CID 724)

## Full-text entities

- **Genes:** GPI (glucose-6-phosphate isomerase) [NCBI Gene 2821] {aka AMF, CNSHA4, GNPI, NLK, PGI, PHI}, ACO2 (aconitase 2) [NCBI Gene 50] {aka ACONM, HEL-S-284, ICRD, OCA8, OPA9}, VCL (vinculin) [NCBI Gene 7414] {aka CMD1W, CMH15, HEL114, MV, MVCL, VINC}, G6PD (glucose-6-phosphate dehydrogenase) [NCBI Gene 2539] {aka CNSHA1, G6PD1}, OGDH (oxoglutarate dehydrogenase) [NCBI Gene 4967] {aka AKGDH, E1k, E1o, HsOGDH, KGD1, OGDC}, HK2 (hexokinase 2) [NCBI Gene 3099] {aka HKII, HXK2}, MYH3 (myosin heavy chain 3) [NCBI Gene 4621] {aka CPSFS1A, CPSFS1B, CPSKF1A, CPSKF1B, DA2A, DA2B}, ALDOC (aldolase, fructose-bisphosphate C) [NCBI Gene 230] {aka ALDC}, IDH2 (isocitrate dehydrogenase (NADP(+)) 2) [NCBI Gene 3418] {aka D2HGA2, ICD-M, IDH, IDH-2, IDHM, IDP}, CHMP4B (charged multivesicular body protein 4B) [NCBI Gene 128866] {aka C20orf178, CHMP4A, CTPP3, CTRCT31, SNF7, SNF7-2}, GAPDH (glyceraldehyde-3-phosphate dehydrogenase) [NCBI Gene 2597] {aka G3PD, GAPD, HEL-S-162eP}, GSK3B (glycogen synthase kinase 3 beta) [NCBI Gene 2932], MCOLN1 (mucolipin TRP cation channel 1) [NCBI Gene 57192] {aka LECD, MG-2, ML1, ML4, MLIV, MST080}, LRP6 (LDL receptor related protein 6) [NCBI Gene 4040] {aka ADCAD2, EVR8, OPTA4, STHAG7}, MYH14 (myosin heavy chain 14) [NCBI Gene 79784] {aka DFNA4, DFNA4A, FP17425, MHC16, MYH17, NMHC II-C}, PRMT1 (protein arginine methyltransferase 1) [NCBI Gene 3276] {aka ANM1, HCP1, HRMT1L2, IR1B4}, PFKP (phosphofructokinase, platelet) [NCBI Gene 5214] {aka ATP-PFK, PFK-C, PFK-P, PFKF}, AXIN1 (axin 1) [NCBI Gene 8312] {aka AXIN, CMDOH, PPP1R49}, PGM2 (phosphoglucomutase 2) [NCBI Gene 55276] {aka MSTP006}, ACSS2 (acyl-CoA synthetase short chain family member 2) [NCBI Gene 55902] {aka ACAS2, ACECS, ACS, ACSA, AceCS1, dJ1161H23.1}, ATP6V1B2 (ATPase H+ transporting V1 subunit B2) [NCBI Gene 526] {aka ATP6B1B2, ATP6B2, DOOD, HO57, VATB, VPP3}, PAX7 (paired box 7) [NCBI Gene 5081] {aka CMYO19, CMYP19, HUP1, MYOSCO, PAX7B, RMS2}, MYOG (myogenin) [NCBI Gene 4656] {aka MYF4, bHLHc3, myf-4}, CTNNB1 (catenin beta 1) [NCBI Gene 1499] {aka CTNNB, EVR7, MRD19, NEDSDV, armadillo}, CTSB (cathepsin B) [NCBI Gene 1508] {aka APPS, CPSB, KWE, RECEUP}, TTN (titin) [NCBI Gene 7273] {aka CMD1G, CMH9, CMPD4, CMYO5, CMYP5, EOMFC}, SLC11A1 (solute carrier family 11 member 1) [NCBI Gene 6556] {aka LSH, NRAMP, NRAMP1}, MYOD1 (myogenic differentiation 1) [NCBI Gene 4654] {aka CMYO17, CMYP17, MYF3, MYOD, MYODRIF, PUM}, SUCLA2 (succinate-CoA ligase ADP-forming subunit beta) [NCBI Gene 8803] {aka A-BETA, A-SCS, LINC00444, MTDPS5, SCS-betaA}, ITGAV (integrin subunit alpha V) [NCBI Gene 3685] {aka CD51, IDNDC, MSK8, VNRA, VTNR}, PRPS2 (phosphoribosyl pyrophosphate synthetase 2) [NCBI Gene 5634] {aka PRSII}, PRPS1 (phosphoribosyl pyrophosphate synthetase 1) [NCBI Gene 5631] {aka ARTS, CMTX5, DFN2, DFNX1, PPRibP, PRS-I}, RPL13A (ribosomal protein L13a) [NCBI Gene 23521] {aka L13A, TSTA1, uL13}, PGLS (6-phosphogluconolactonase) [NCBI Gene 25796] {aka 6PGL, HEL-S-304}, ENO3 (enolase 3) [NCBI Gene 2027] {aka GSD13, MSE}, CHMP2A (charged multivesicular body protein 2A) [NCBI Gene 27243] {aka BC-2, BC2, CHMP2, VPS2, VPS2A}, ALDOA (aldolase, fructose-bisphosphate A) [NCBI Gene 226] {aka ALDA, GSD12, HEL-S-87p}, PGAM2 (phosphoglycerate mutase 2) [NCBI Gene 5224] {aka GSD10, PGAM-M, PGAMM}, ALDH1B1 (aldehyde dehydrogenase 1 family member B1) [NCBI Gene 219] {aka ALDH5, ALDHX}, LAMP1 (lysosome associated membrane protein 1) [NCBI Gene 3916] {aka CD107a, LAMPA, LGP120}, PGK1 (phosphoglycerate kinase 1) [NCBI Gene 5230] {aka HEL-S-68p, MIG10, PGKA}, CDK1 (cyclin dependent kinase 1) [NCBI Gene 983] {aka CDC2, CDC28A, P34CDC2}, TFE3 (transcription factor binding to IGHM enhancer 3) [NCBI Gene 7030] {aka MRXSPF, RCCP2, RCCX1, TFEA, bHLHe33}, TKT (transketolase) [NCBI Gene 7086] {aka HEL-S-48, HEL107, SDDHD, TK, TKT1}, ACTA1 (actin alpha 1, skeletal muscle) [NCBI Gene 58] {aka ACTA, ASMA, CFTD, CFTD1, CFTDM, CMYO2A}, CS (citrate synthase) [NCBI Gene 1431], TFEB (transcription factor EB) [NCBI Gene 7942] {aka ALPHATFEB, BHLHE35, TCFEB}, ID3 (inhibitor of DNA binding 3) [NCBI Gene 3399] {aka HEIR-1, bHLHb25}, CHKA (choline kinase alpha) [NCBI Gene 1119] {aka CHK, CK, CKI, EK, NEDMIMS}, APC (APC regulator of Wnt signaling pathway) [NCBI Gene 324] {aka BTPS2, DESMD, DP2, DP2.5, DP3, GS}, MYF5 (myogenic factor 5) [NCBI Gene 4617] {aka EORVA, bHLHc2}, PFKM (phosphofructokinase, muscle) [NCBI Gene 5213] {aka ATP-PFK, GSD7, PFK-1, PFK-A, PFK1, PFKA}, IDH3A (isocitrate dehydrogenase (NAD(+)) 3 catalytic subunit alpha) [NCBI Gene 3419] {aka RP90}, CTSD (cathepsin D) [NCBI Gene 1509] {aka CLN10, CPSD, HEL-S-130P}, WNT3A (Wnt family member 3A) [NCBI Gene 89780], DICER1 (dicer 1, ribonuclease III) [NCBI Gene 23405] {aka DCR1, Dicer, Dicer1e, GLOW, HERNA, K12H4.8-LIKE}, MYH1 (myosin heavy chain 1) [NCBI Gene 4619] {aka HEL71, MYHSA1, MYHa, MyHC-2X/D, MyHC-2x}, PKM (pyruvate kinase M1/2) [NCBI Gene 5315] {aka CTHBP, HEL-S-30, OIP3, PK3, PKM2, TCB}, PGD (phosphogluconate dehydrogenase) [NCBI Gene 5226] {aka 6PGD}, MYH6 (myosin heavy chain 6) [NCBI Gene 4624] {aka ASD3, CMD1EE, CMH14, MYHC, MYHCA, SSS3}
- **Diseases:** muscular dystrophy (MESH:D009136), Breast cancers (MESH:D001943), PPP (MESH:D007015), Stills (MESH:D001171), metastasis (MESH:D009362), deficiency of PFKM (MESH:D007153), MuSC (MESH:D000092423), diabetes (MESH:D003920), cancer (MESH:D009369), Tarui disease (MESH:D006014)
- **Chemicals:** CHX (MESH:D003513), PVDF (MESH:C024865), vitamin B6 (MESH:D025101), PBS (MESH:D007854), Oligomycin (MESH:D009840), hexosamine (MESH:D006595), GlcN (MESH:D005944), N-acetylglucosamine-6-phosphate (MESH:C010004), hexose-phosphate (MESH:D006600), glucose (MESH:D005947), 4',6-diamidino-2-phenylindole (MESH:C007293), ADMA (MESH:C018524), CO2 (MESH:D002245), EGTA (MESH:D004533), Rotenone (MESH:D012402), GSH (MESH:D005978), citrate (MESH:D019343), SYBR Green (MESH:C098022), L-glutamine (MESH:D005973), ATP (MESH:D000255), Antimycin A (MESH:D000968), ammonium acetate (MESH:C018824), paraformaldehyde (MESH:C003043), lipid (MESH:D008055), cysteine (MESH:D003545), Ultroser G (MESH:C044609), NADPH (MESH:D009249), Lipofectamine 2000 (MESH:C086724), fatty acid (MESH:D005227), AEBSF (MESH:C002010), arginine (MESH:D001120), oil (MESH:D009821), GlcNAc (MESH:D000117), GSSG (MESH:D019803), R5P (MESH:C031626), TCA (MESH:D014238), Helium (MESH:D006371), H2O2 (MESH:D006861), BAM15 (-), Lysotracker (MESH:C493330), penicillin (MESH:D010406), Plasmocin (MESH:C554844), F6P (MESH:C027618), FBP (MESH:C029063), pyridine (MESH:C023666), G418 (MESH:C010680), SDS (MESH:D012967), Bafilomycin A1 (MESH:C040929), M + 1 (MESH:C400939), DTT (MESH:D004229), Laemmli buffer (MESH:C088816), norvaline (MESH:C005313), S7P (MESH:C020495), cholesterol (MESH:D002784), Hoechst 33258 (MESH:D006690), water (MESH:D014867), iodoacetamide (MESH:D007460), S-adenosyl-methionine (MESH:D012436), MG132 (MESH:C072553), 3-PG (MESH:C005156)
- **Species:** Oryctolagus cuniculus (domestic rabbit, species) [taxon 9986], Homo sapiens (human, species) [taxon 9606], Mycoplasma (genus) [taxon 2093], Mus musculus (house mouse, species) [taxon 10090]
- **Mutations:** C at 10, R5P, G6P, S7P, R3189S, arginine-to-lysine, 6P, R3136S, R0176S, R774, R774K
- **Cell lines:** HeLa — Homo sapiens (Human), Human papillomavirus-related endocervical adenocarcinoma, Cancer cell line (CVCL_0030), CRL-2647 — Homo sapiens (Human), Finite cell line (CVCL_A2LP), C2C12 — Mus musculus (Mouse), Spontaneously immortalized cell line (CVCL_0188), HEK293 — Homo sapiens (Human), Transformed cell line (CVCL_0045), B0-41 — Homo sapiens (Human), Ovarian mucinous cystadenocarcinoma, Cancer cell line (CVCL_C6VI), CRL-1772 — Homo sapiens (Human), 5' 10' methylenetetrahydrofolate reductase deficiency, Finite cell line (CVCL_B3VW), CCL-2 — Mus musculus (Mouse), Undefined cell line type (CVCL_M023), CRL-1573 — Sigmodon hispidus (Hispid cotton rat), Spontaneously immortalized cell line (CVCL_YD58), L — Mus musculus (Mouse), Spontaneously immortalized cell line (CVCL_0462)

## Full text

_Full body text omitted from this summary view._ Fetch the complete paper as Markdown: https://tomesphere.com/paper/PMC12945692/full.md

## Figures

13 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12945692/full.md

## References

1 references — full list in the complete paper: https://tomesphere.com/paper/PMC12945692/full.md

---
Source: https://tomesphere.com/paper/PMC12945692