# Deficient de-S-acylation in aging and CLN1 contributes to lyso-mitochondrial dysfunction, lipid dyshomeostasis, and resultant lipofuscin biogenesis

**Authors:** Sofia Massaro Tieze, Alexander Esqueda, Rachel McAllister, Matija Lagator, Betül Yücel, Eric Sun, TuKiet T. Lam, Nicholas Lockyer, Kallol Gupta, Sreeganga S. Chandra

PMC · DOI: 10.21203/rs.3.rs-8770768/v1 · Research Square · 2026-02-09

## TL;DR

This study explores how aging and a neurodegenerative disease called NCL lead to the buildup of lipofuscin in the brain, linking it to mitochondrial and lysosomal dysfunction.

## Contribution

The study identifies protein S-acylation and lipid homeostasis as key processes in lipofuscin formation during aging and NCL.

## Key findings

- Lipofuscin accumulates in brain tissues with age and in NCL, linked to lysosomal-mitochondrial dysfunction.
- Protein S-acylation and unsaturated lipid homeostasis are central to lipofuscin deposition.
- Multimodal analyses reveal spatiotemporal dynamics of lipofuscin in aging and NCL.

## Abstract

Lipofuscin is an autofluorescent material that accrues in brain tissues with age and in Neuronal Ceroid Lipofuscinosis (NCL), a neurodegenerative disease with pediatric onset. The distribution, composition, and organellar origin of lipofuscin have remained unclear despite its widespread presence in aged tissues and involvement in neurodegeneration. Here, we elucidate lipofuscin composition in mouse and human brain and report the spatiotemporal dynamics of lipofuscin accumulation in aging and NCL in a murine neuroanatomical atlas. Multimodal mass spectrometry, ultrastructural analyses, and assays of metabolic flux identify a primary role of the lysosomal-mitochondrial axis in the formation of lipofuscin pathology. Dissection of implicated molecular pathways reveals protein S-acylation and unsaturated lipid homeostasis as central processes involved in lipofuscin deposition during aging and NCL.

## Linked entities

- **Diseases:** Neuronal Ceroid Lipofuscinosis (MONDO:0016295), NCL (MONDO:0016295)
- **Species:** Mus musculus (taxon 10090), Homo sapiens (taxon 9606)

## Full-text entities

- **Genes:** CALM1 (calmodulin 1) [NCBI Gene 801] {aka CALML2, CAM2, CAM3, CAMB, CAMC, CAMI}, PPT1 (palmitoyl-protein thioesterase 1) [NCBI Gene 5538] {aka CLN1, INCL, PPT}, Map1lc3a (microtubule-associated protein 1 light chain 3 alpha) [NCBI Gene 66734] {aka 1010001H21Rik, 4922501H04Rik, LC3, LC3a}, Asah1 (N-acylsphingosine amidohydrolase 1) [NCBI Gene 11886] {aka 2310081N20Rik, AC, Asah}, CLN5 (CLN5 lysosomal BMP synthase) [NCBI Gene 1203], COX5B (cytochrome c oxidase subunit 5B) [NCBI Gene 1329] {aka COXVB}, MOG (myelin oligodendrocyte glycoprotein) [NCBI Gene 4340] {aka BTN6, BTNL11, MOGIG2, NRCLP7}, HPT (hypoparathyroidism) [NCBI Gene 3258] {aka HPTX, HYPX}, Gba2 (glucosidase beta 2) [NCBI Gene 230101] {aka F630034E04}, Blnk (B cell linker) [NCBI Gene 17060] {aka BASH, Bca, Ly-57, Ly57, Lyw-57, SLP-65}, Gba1 (glucosylceramidase beta 1) [NCBI Gene 14466] {aka GC, GCase, GLUC, Gba, betaGC}, CTSD (cathepsin D) [NCBI Gene 1509] {aka CLN10, CPSD, HEL-S-130P}, Sod1 (superoxide dismutase 1, soluble) [NCBI Gene 20655] {aka B430204E11Rik, Cu/Zn-SOD, CuZnSOD, Ipo-1, Ipo1, SODC}, UQCRH (ubiquinol-cytochrome c reductase hinge protein) [NCBI Gene 7388] {aka MC3DN11, QCR6, UQCR8}, Vdac1 (voltage-dependent anion channel 1) [NCBI Gene 22333] {aka Vdac5, mVDAC1, mVDAC5}, IGHA1 (immunoglobulin heavy constant alpha 1) [NCBI Gene 3493] {aka IgA1}, TPP1 (tripeptidyl peptidase 1) [NCBI Gene 1200] {aka CLN2, GIG1, LPIC, SCAR7, TPP-1}, Ngly1 (N-glycanase 1) [NCBI Gene 59007] {aka 1110002C09Rik, PNGase, Png1}, MAG (myelin associated glycoprotein) [NCBI Gene 4099] {aka GMA, S-MAG, SIGLEC-4A, SIGLEC4, SIGLEC4A, SPG75}, Ctsd (cathepsin D) [NCBI Gene 13033] {aka CD, CatD}, PLLP (plasmolipin) [NCBI Gene 51090] {aka PMLP, TM4SF11}, SDHAF4 (succinate dehydrogenase complex assembly factor 4) [NCBI Gene 135154] {aka C6orf57, Sdh8}, Psap (prosaposin) [NCBI Gene 19156] {aka SGP-1}, Trap1 (TNF receptor-associated protein 1) [NCBI Gene 68015] {aka 2410002K23Rik, HSP75}, BMP1 (bone morphogenetic protein 1) [NCBI Gene 649] {aka OI13, PCOLC, PCP, TLD}, H2AZ1 (H2A.Z variant histone 1) [NCBI Gene 3015] {aka H2A.Z-1, H2A.z, H2A/z, H2AFZ, H2AZ}, Lamp1 (lysosomal-associated membrane protein 1) [NCBI Gene 16783] {aka CD107a, LGP-120, LGP-A, Lamp-1, P2B, Perk}, Aldh2 (aldehyde dehydrogenase 2, mitochondrial) [NCBI Gene 11669] {aka AHD-M1, ALDH-E2, ALDHI, Ahd-5, Ahd5}, Apcs (amyloid P component, serum) [NCBI Gene 20219] {aka Sap}, COX6B1 (cytochrome c oxidase subunit 6B1) [NCBI Gene 1340] {aka COX6B, COXG, COXVIb1, MC4DN7}, Tpp1 (tripeptidyl peptidase I) [NCBI Gene 12751] {aka Cln2, LPIC, TPP-1, TPP-I}, TIMM8A (translocase of inner mitochondrial membrane 8A) [NCBI Gene 1678] {aka DDP, DDP1, DFN1, MTS, TIM8}, Nup62 (nucleoporin 62) [NCBI Gene 18226] {aka D7Ertd649e, Nupc1, p62}, NDUFAB1 (NADH:ubiquinone oxidoreductase subunit AB1) [NCBI Gene 4706] {aka ACP, ACP1, FASN2A, SDAP}, Ppt1 (palmitoyl-protein thioesterase 1) [NCBI Gene 19063] {aka 9530043G02Rik, CLN1, D4Ertd184e, INCL, PPT}, Atp1b1 (ATPase, Na+/K+ transporting, beta 1 polypeptide) [NCBI Gene 11931] {aka Atp4b, Atpb, Atpb-1, NKbeta1}, APCS (amyloid P component, serum) [NCBI Gene 325] {aka HEL-S-92n, PTX2, SAP}
- **Diseases:** Farber Disease (MESH:D055577), CLN14 (OMIM:611726), lipofuscinatlas.yale.edu (MESH:C536205), neuronal and metabolic dysfunction (MESH:D008659), Gaucher Disease (MESH:D005776), atrophy (MESH:D001284), lysosomal storage disorder (MESH:D016464), Huntington's Disease (MESH:D006816), mitochondrial deficits (MESH:D028361), Parkinson's Disease (MESH:D010300), neurodegeneration (MESH:D019636), myoclonic epilepsy (MESH:D004831), Batten Disease (MESH:D009472), leak (MESH:D019559), spine dislocation (MESH:D016135)
- **Chemicals:** FCCP (MESH:D002259), Cer (MESH:D002518), bis(monoacylglycero)phosphate (MESH:C012786), E-64 (MESH:C024974), 4-methylumbelliferone (MESH:D006923), glycine (MESH:D005998), EPON (MESH:C004875), NaOH (MESH:D012972), asparagine (MESH:D001216), ethanol (MESH:D000431), LPG (MESH:C026223), Copper (MESH:D003300), ACN (MESH:C084683), SDS (MESH:D012967), DTT (MESH:D004229), phosphatidylglycerol (MESH:D010715), iodoacetamide (MESH:D007460), arachidonic acid (MESH:D016718), stearic acid (MESH:C031183), isoflurane (MESH:D007530), peptides (MESH:D010455), CL (MESH:D002308), H2O (MESH:D014867), EPA (MESH:D015118), Schiff base (MESH:D012545), LPI (MESH:C025449), SB3 (MESH:C016118), carbon (MESH:D002244), streptomycin (MESH:D013307), Triton X-100 (MESH:D017830), agar (MESH:D000362), TG (MESH:D014280), acetonitrile (MESH:C032159), carbonyl cyanide-4 (trifluoromethoxy) phenylhydrazone (MESH:C108897), EDTA (MESH:D004492), glycosphingolipids (MESH:D006028), ammonium (MESH:D064751), omega-3 fatty acids (MESH:D015525), FITC (MESH:D016650), osmium tetroxide (MESH:D009993), N-butyldeoxynojirimycin (MESH:C059896), O2 (MESH:D010100), phosphate (MESH:D010710), PI (MESH:D010716), Formic Acid (MESH:C030544), acids (MESH:D000143), NaCL (MESH:D012965), methanol (MESH:D000432), leupeptin (MESH:C032854), DPA (MESH:C026219), OCT (MESH:C051883), methionine (MESH:D008715), ROS (MESH:D017382), FA (MESH:D005492), oligomycin (MESH:D009840), DAPI (MESH:C007293), ether (MESH:D004986), glucose (MESH:D005947), pepstatin A (MESH:C031375), H (MESH:D006859)
- **Species:** Mus musculus (house mouse, species) [taxon 10090], Homo sapiens (human, species) [taxon 9606]
- **Mutations:** Ala-Phe-7
- **Cell lines:** WT-12 — Megaptera novaeangliae (Humpback whale), Finite cell line (CVCL_4U66), HEK293T — Homo sapiens (Human), Transformed cell line (CVCL_0063), -7 — Cricetulus griseus (Chinese hamster), Spontaneously immortalized cell line (CVCL_H340)

## Full text

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## Figures

6 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12919294/full.md

## References

107 references — full list in the complete paper: https://tomesphere.com/paper/PMC12919294/full.md

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Source: https://tomesphere.com/paper/PMC12919294