# Loss of function variants in HPDL impair human cortical development via alterations of mitochondrial function

**Authors:** Matteo Baggiani, Maria Andrea Desbats, Valentina Naef, Michela Giacich, Daniele Galatolo, Serena Mero, Sara Zampieri, Valentina Cappello, Agata Valentino, Leonardo Salviati, Filippo Maria Santorelli, Devid Damiani

PMC · DOI: 10.1038/s41419-026-08476-9 · Cell Death & Disease · 2026-02-20

## TL;DR

This study shows that mutations in the HPDL gene disrupt brain development by affecting mitochondrial function and neurogenesis, leading to neurological disorders.

## Contribution

The study reveals a novel role for HPDL in cortical development and mitochondrial function, linking genetic mutations to specific neurodevelopmental outcomes.

## Key findings

- HPDL mutations impair respiratory chain supercomplex assembly and redox balance in neuroblastoma cells.
- HPDL patient-derived neurons show premature neurogenesis and cortical organoid growth defects resembling microcephaly.
- Mitochondrial dysfunction in HPDL mutants is associated with increased ROS and respirasome assembly defects.

## Abstract

Human brain development is highly regulated by several spatiotemporal processes, which disruption can result in severe neurological disorders. Emerging evidence highlights the pivotal role of mitochondrial function as one of these fundamental pathways involved in neurodevelopment. Our study investigates the role of 4-hydroxyphenylpyruvate dioxygenase-like (HPDL) protein in cortical neurogenesis and mitochondrial activity, since mutations in the HPDL gene are associated with a childhood-onset form of hereditary spastic paraplegia characterized by corticospinal tract degeneration and cortical abnormalities. Starting from mutant neuroblastoma cells, we demonstrated that HPDL is important to respiratory chain supercomplex assembly and cellular redox balance. Moreover, RNA-seq studies revealed dysregulated pathways related to brain development. Generation of cortical neurons and organoids from HPDL patient-derived induced pluripotent stem cells exhibited premature neurogenesis at early differentiation stages, likely leading to depletion of cortical progenitors, as evidenced by decreased proliferation, slight increase of apoptosis, and unbalanced cortical type composition at later stages. Cortical organoids showed failure to grow at a normal rate, a feature highly reminiscent of the “microcephaly” observed in severe HPDL children. Mitochondrial morpho-functional characterization in mutant neurons confirmed disruption of OxPhos chain functionality in neuroblastoma knock-out model cells and HPDL mutant cortical progenitors also displayed defects in respirasome assembly and increased ROS generation rate. Treatment of mutant cortical cells with antioxidants and CoQ10 intermediates partially rescued premature neurogenesis depending on the mutational context, suggesting potential future personalized therapeutic strategies. Our findings reveal a critical role for HPDL in coordinating cortical progenitor proliferation, neurogenesis, and mitochondrial function, shedding light on a better understanding of the related clinical presentations.

## Linked entities

- **Genes:** HPDL (4-hydroxyphenylpyruvate dioxygenase like) [NCBI Gene 84842]
- **Proteins:** HPDL (4-hydroxyphenylpyruvate dioxygenase like)
- **Chemicals:** CoQ10 (PubChem CID 5281915)
- **Diseases:** hereditary spastic paraplegia (MONDO:0019064), microcephaly (MONDO:0001149)

## Full-text entities

- **Genes:** OTX1 (orthodenticle homeobox 1) [NCBI Gene 5013], Uqcrc2 (ubiquinol cytochrome c reductase core protein 2) [NCBI Gene 67003] {aka 1500004O06Rik}, HPDL (4-hydroxyphenylpyruvate dioxygenase like) [NCBI Gene 84842] {aka 4-HPPD-L, GLOXD1, NEDSWMA, SPG83}, FOXP2 (forkhead box P2) [NCBI Gene 93986] {aka CAGH44, SPCH1, TNRC10}, BCL11B (BCL11 transcription factor B) [NCBI Gene 64919] {aka ATL1, ATL1-alpha, ATL1-beta, ATL1-delta, ATL1-gamma, CTIP-2}, BCL6 (BCL6 transcription repressor) [NCBI Gene 604] {aka BCL5, BCL6A, LAZ3, ZBTB27, ZNF51}, UQCRC2 (ubiquinol-cytochrome c reductase core protein 2) [NCBI Gene 7385] {aka MC3DN5, QCR2, UQCR2}, FGF2 (fibroblast growth factor 2) [NCBI Gene 2247] {aka BFGF, FGF-2, FGFB, HBGF-2}, CAT (catalase) [NCBI Gene 847], SPG11 (SPG11 vesicle trafficking associated, spatacsin) [NCBI Gene 80208] {aka ALS5, CMT2X, KIAA1840}, TUBB3 (tubulin beta 3 class III) [NCBI Gene 10381] {aka CDCBM, CDCBM1, CFEOM3, CFEOM3A, FEOM3, TUBB4}, WNT11 (Wnt family member 11) [NCBI Gene 7481] {aka HWNT11}, DNAH8 (dynein axonemal heavy chain 8) [NCBI Gene 1769] {aka ATPase, SPGF46, hdhc9}, NFE2L2 (NFE2 like bZIP transcription factor 2) [NCBI Gene 4780] {aka IMDDHH, NRF2, Nrf-2}, AXIN2 (axin 2) [NCBI Gene 8313] {aka AXIL, ODCRCS}, NDUFB8 (NADH:ubiquinone oxidoreductase subunit B8) [NCBI Gene 4714] {aka ASHI, CI-ASHI, MC1DN32}, CTRL (chymotrypsin like) [NCBI Gene 1506] {aka CTRL1}, COX8A (cytochrome c oxidase subunit 8A) [NCBI Gene 1351] {aka COX, COX8, COX8-2, COX8L, MC4DN15, VIII}, FOXO3 (forkhead box O3) [NCBI Gene 2309] {aka AF6q21, FKHRL1, FKHRL1P2, FOXO2, FOXO3A}, Ndufb8 (NADH:ubiquinone oxidoreductase subunit B8) [NCBI Gene 67264] {aka 2900010I05Rik, CI-ASHI}, TBR1 (T-box brain transcription factor 1) [NCBI Gene 10716] {aka AUTS5, IDDAS, TBR-1, TES-56}, COQ9 (coenzyme Q9) [NCBI Gene 57017] {aka C16orf49, COQ10D5}, SCAF1 (SR-related CTD associated factor 1) [NCBI Gene 58506] {aka SRA1}, COQ2 (coenzyme Q2, polyprenyltransferase) [NCBI Gene 27235] {aka CL640, COQ10D1, MSA1, PHB:PPT}, GSTT2B (glutathione S-transferase theta 2B) [NCBI Gene 653689] {aka GSTT2P}, SQOR (sulfide quinone oxidoreductase) [NCBI Gene 58472] {aka CGI-44, PRO1975, SQR, SQRDL}, PRDX2 (peroxiredoxin 2) [NCBI Gene 7001] {aka HEL-S-2a, NKEF-B, NKEFB, PRP, PRX2, PRXII}, VDAC1 (voltage dependent anion channel 1) [NCBI Gene 7416] {aka PORIN, VDAC-1}, Sdha (succinate dehydrogenase complex, subunit A, flavoprotein (Fp)) [NCBI Gene 66945] {aka 1500032O14Rik, 2310034D06Rik, 4921513A11, FP, SDH2, SDHF}, SDHB (succinate dehydrogenase complex iron sulfur subunit B) [NCBI Gene 6390] {aka CWS2, IP, MC2DN4, PGL4, PPGL4, SDH}, LEF1 (lymphoid enhancer binding factor 1) [NCBI Gene 51176] {aka ECTD1, ECTD17, LEF-1, TCF10, TCF1ALPHA, TCF7L3}, SDHA (succinate dehydrogenase complex flavoprotein subunit A) [NCBI Gene 6389] {aka CMD1GG, FP, MC2DN1, NDAXOA, PGL5, PPGL5}, SURF1 (SURF1 cytochrome c oxidase assembly factor) [NCBI Gene 6834] {aka CMT4K, MC4DN1, SHY1}, WNT7A (Wnt family member 7A) [NCBI Gene 7476] {aka SANTOS, Wnt-7a}, WNT3A (Wnt family member 3A) [NCBI Gene 89780], NEUROG3 (neurogenin 3) [NCBI Gene 50674] {aka Atoh5, Math4B, NGN-3, bHLHa7, ngn3}, CASP3 (caspase 3) [NCBI Gene 836] {aka CPP32, CPP32B, SCA-1}, NEUROG2 (neurogenin 2) [NCBI Gene 63973] {aka Atoh4, Math4A, NGN2, bHLHa8, ngn-2}, CS (citrate synthase) [NCBI Gene 1431], MCUB (mitochondrial calcium uniporter dominant negative subunit beta) [NCBI Gene 55013] {aka CCDC109B}, ATP5MC1 (ATP synthase membrane subunit c locus 1) [NCBI Gene 516] {aka ATP5A, ATP5G, ATP5G1}, BDNF (brain derived neurotrophic factor) [NCBI Gene 627] {aka ANON2, BULN2}, FZD7 (frizzled class receptor 7) [NCBI Gene 8324] {aka FzE3}, HSP90B2P (heat shock protein 90 beta family member 2, pseudogene) [NCBI Gene 7190] {aka GRP94P1, GRP94b, HSP, HSPCP2, TRA1P1, TRAP1}, EGF (epidermal growth factor) [NCBI Gene 1950] {aka HOMG4, URG}
- **Diseases:** epilepsy (MESH:D004827), CoQ10 deficiencies (MESH:C564403), corticospinal tract degeneration (MESH:D009410), cortical abnormalities (MESH:D054220), OxPhos (MESH:C535470), Leigh syndrome (MESH:D007888), HSPs (MESH:D015419), complex II (MESH:C565375), functional impairment (MESH:D003072), neurodegenerative processes (MESH:D019636), spasticity (MESH:D009128), mitochondrial dysfunction (MESH:D028361), DD (MESH:C536170), microcephalic (MESH:C537533), neurological disease (MESH:D020271), HPDL disease (MESH:D020176), microcephaly (MESH:D008831), Neuroblastoma (MESH:D009447), neurological disorders (MESH:D009461)
- **Chemicals:** Y-27632 (MESH:C108830), DMEM (-), HEPES (MESH:D006531), proton (MESH:D011522), MitoTEMPO (MESH:C555916), XAV939 (MESH:C544261), Hoechst 33342 (MESH:C017807), idebenone (MESH:C036619), 2-mercaptoethanol (MESH:D008623), L-glutamine (MESH:D005973), glutathione (MESH:D005978), CO2 (MESH:D002245), ATP (MESH:D000255), SB431542 (MESH:C459179), paraformaldehyde (MESH:C003043), Lipid (MESH:D008055), PVDF (MESH:C024865), NAD (MESH:D009243), PBS (MESH:D007854), PEN (MESH:C058388), ROS (MESH:D017382), Oligomycin (MESH:D009840), DAPI (MESH:C007293), D-Glucose (MESH:D005947), Pyruvate (MESH:D019289), oxygen (MESH:D010100), phosphate (MESH:D010710), N2 (MESH:D009584), Digitonin (MESH:D004072), CoQ10 (MESH:C024989), 4-hydroxyphenylpyruvate (MESH:C010590), Bis-Tris (MESH:C026272), glutathione monoethyl ester (MESH:C042431), LDN193189 (MESH:C554430), tyrosine (MESH:D014443), DCFDA (MESH:C029569), 4-HB (MESH:C038193)
- **Species:** Danio rerio (leopard danio, species) [taxon 7955], Homo sapiens (human, species) [taxon 9606], Mus musculus (house mouse, species) [taxon 10090]
- **Mutations:** p.Gly50Asp, c.318delC
- **Cell lines:** E.V. — Homo sapiens (Human), Transformed cell line (CVCL_E860), SH-SY5Y — Homo sapiens (Human), Neuroblastoma, Cancer cell line (CVCL_0019), ACS1019 — Homo sapiens (Human), Transformed cell line (CVCL_U479), SPG83 — Trachinotus blochii (Snubnose pompano), Spontaneously immortalized cell line (CVCL_B5P6)

## Full text

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## Figures

6 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12948981/full.md

## References

13 references — full list in the complete paper: https://tomesphere.com/paper/PMC12948981/full.md

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Source: https://tomesphere.com/paper/PMC12948981