# Mutations in VPS18 lead to a neutrophil maturation defect associated with disturbed vesicle homeostasis

**Authors:** Jincheng Gao, Almke Bader, Monika I. Linder, Jingyuan Cheng, Mathis Richter, Raul da Costa, Annette Zehrer, Karl Mitt, Bastian Popper, Felix Meissner, Xiang Wei, Enrique de Vega Gómez, Megumi Tatematsu, Meino Rohlfs, Stephanie Frenz-Wiessner, Mehmet Kiziltug, Ido Somekh, Joanne Yacobovich, Orna Steinberg-Shemer, Raz Somech, Oliver Soehnlein, Bettina Schmid, Christoph Klein, Barbara Walzog, Daniela Maier-Begandt

PMC · DOI: 10.1038/s41419-025-08338-w · Cell Death & Disease · 2026-01-12

## TL;DR

This study shows that mutations in VPS18 disrupt neutrophil development by impairing vesicle trafficking and causing autophagy issues.

## Contribution

The study identifies VPS18 as a key gene for neutrophil maturation and vesicle homeostasis in humans and model organisms.

## Key findings

- VPS18 deficiency causes instability in tethering complexes and impaired vesicle dynamics in neutrophil progenitors.
- VPS18 mutations lead to autophagosome accumulation and premature apoptosis in neutrophil development.
- Human iPSCs and zebrafish with VPS18 mutations show significantly reduced neutrophil numbers.

## Abstract

Neutrophils, the first cells to arrive at the site of inflammation, are rather short-lived cells and thus have to be constantly replenished. During neutrophil development, vesicle dynamics need to be fine-tuned and impaired vesicle trafficking has been linked to failure in neutrophil maturation. Here, we characterized the role of VPS18 as a central core component of CORVET & HOPS tethering complexes for neutrophil development. Using CRISPR/Cas9-engineered Hoxb8 cells with heterozygous mutations in Vps18, we found that VPS18 deficiency interfered with neutrophil development due to tethering complex instability. As a result, vesicle dynamics were impaired with a strong increase in LC3B-II and p62 levels, indicating autophagosome accumulation and reduced autophagic flux. With transmission electron microscopy, we verified the increase in autophagosomes and also found irregularly shaped vesicular structures in Vps18 mutants. Subsequently, Vps18 mutant neutrophil progenitors underwent premature apoptosis. We described a novel patient with a heterozygous stop-gain mutation in VPS18 suffering from neutropenia and recurrent infections. To verify our findings in the human system, we used human induced pluripotent stem cells (iPSCs). Upon differentiation into neutrophils, loss of VPS18 resulted in an almost complete absence of iPSC-derived developing neutrophils. Heterozygous VPS18 mutant and patient mutation-harboring iPSCs were characterized by strongly reduced numbers of developing neutrophils. Zebrafish larvae with heterozygous mutations in vps18 were also characterized by significantly reduced neutrophil numbers. This study shows the pivotal impact of VPS18 for adequate vesicle dynamics during neutrophil development which might be relevant in the context of vesicle trafficking during granulopoiesis and congenital neutropenia.

## Linked entities

- **Genes:** VPS18 (VPS18 core subunit of CORVET and HOPS complexes) [NCBI Gene 57617], VPS18 (VPS18 core subunit of CORVET and HOPS complexes) [NCBI Gene 57617], VPS18 (VPS18 core subunit of CORVET and HOPS complexes) [NCBI Gene 57617]
- **Proteins:** GTF2H1 (general transcription factor IIH subunit 1)
- **Diseases:** neutropenia (MONDO:0001475), congenital neutropenia (MONDO:0015134)
- **Species:** Homo sapiens (taxon 9606), Mus musculus (taxon 10090), Danio rerio (taxon 7955)

## Full-text entities

- **Genes:** ERN1 (endoplasmic reticulum to nucleus signaling 1) [NCBI Gene 2081] {aka IRE1, IRE1P, IRE1a, hIRE1p}, SIGLEC8 (sialic acid binding Ig like lectin 8) [NCBI Gene 27181] {aka SAF2, SIGLEC-8, SIGLEC8L}, VCAM1 (vascular cell adhesion molecule 1) [NCBI Gene 7412] {aka CD106, INCAM-100}, VPS41 (VPS41 subunit of HOPS complex) [NCBI Gene 27072] {aka HVPS41, HVSP41, SCAR29, hVps41p}, VPS45 (vacuolar protein sorting 45 homolog) [NCBI Gene 11311] {aka H1, H1VPS45, SCN5, VPS45A, VPS45B, VPS54A}, CTRL (chymotrypsin like) [NCBI Gene 1506] {aka CTRL1}, ATF6 (activating transcription factor 6) [NCBI Gene 22926] {aka ACHM7, ATF6A, ATP6alpha}, ELANE (elastase, neutrophil expressed) [NCBI Gene 1991] {aka ELA2, GE, HLE, HNE, NE, PMN-E}, ATF4 (activating transcription factor 4) [NCBI Gene 468] {aka CREB-2, CREB2, TAXREB67, TXREB}, PTPRC (protein tyrosine phosphatase receptor type C) [NCBI Gene 5788] {aka B220, CD45, CD45R, GP180, IMD105, L-CA}, XBP1 (X-box binding protein 1) [NCBI Gene 7494] {aka TREB-5, TREB5, XBP-1, XBP2}, EIF2AK3 (eukaryotic translation initiation factor 2 alpha kinase 3) [NCBI Gene 9451] {aka PEK, PERK, WRS}, CSF3 (colony stimulating factor 3) [NCBI Gene 1440] {aka C17orf33, CSF3OS, GCSF}, FLI1 (Fli-1 proto-oncogene, ETS transcription factor) [NCBI Gene 2313] {aka BDPLT21, EWSR2, FLI-1, SIC-1}, GAPDH (glyceraldehyde-3-phosphate dehydrogenase) [NCBI Gene 2597] {aka G3PD, GAPD, HEL-S-162eP}, CD14 (CD14 molecule) [NCBI Gene 929], RAB5A (RAB5A, member RAS oncogene family) [NCBI Gene 5868] {aka RAB5}, EEA1 (early endosome antigen 1) [NCBI Gene 8411] {aka MST105, MSTP105, ZFYVE2}, EIF2A (eukaryotic translation initiation factor 2A) [NCBI Gene 83939] {aka CDA02, EIF-2A, MST089, MSTP004, MSTP089}, CASP3 (caspase 3) [NCBI Gene 836] {aka CPP32, CPP32B, SCA-1}, MAP1LC3B (microtubule associated protein 1 light chain 3 beta) [NCBI Gene 81631] {aka ATG8F, LC3B, MAP1A/1BLC3, MAP1LC3B-a}, VPS16 (VPS16 core subunit of CORVET and HOPS complexes) [NCBI Gene 64601] {aka DYT30, hVPS16}, KIT (KIT proto-oncogene, receptor tyrosine kinase) [NCBI Gene 3815] {aka C-Kit, CD117, MASTC, PBT, SCFR}, RAB7B (RAB7B, member RAS oncogene family) [NCBI Gene 338382] {aka RAB7}, VPS13B (vacuolar protein sorting 13 homolog B) [NCBI Gene 157680] {aka BLTP5B, CHS1, COH1}, DDIT3 (DNA damage inducible transcript 3) [NCBI Gene 1649] {aka AltDDIT3, C/EBPzeta, CEBPZ, CHOP, CHOP-10, CHOP10}, LAMP1 (lysosome associated membrane protein 1) [NCBI Gene 3916] {aka CD107a, LAMPA, LGP120}, POTEF (POTE ankyrin domain family member F) [NCBI Gene 728378] {aka A26C1B, POTE2alpha, POTEACTIN}, MME (membrane metalloendopeptidase) [NCBI Gene 4311] {aka CALLA, CD10, CMT2T, NEP, SCA43, SFE}, HOXB8 (homeobox B8) [NCBI Gene 3218] {aka HOX2, HOX2D, Hox-2.4}, VPS18 (VPS18 core subunit of CORVET and HOPS complexes) [NCBI Gene 57617] {aka PEP3}, ITGA4 (integrin subunit alpha 4) [NCBI Gene 3676] {aka CD49D, IA4}, TGFBRAP1 (transforming growth factor beta receptor associated protein 1) [NCBI Gene 9392] {aka TRAP-1, TRAP1, VPS3}, vps18 (VPS18 core subunit of CORVET and HOPS complexes) [NCBI Gene 100005887] {aka chunp6929, hm:zehl0587, wu:fj35h10}, ANXA5 (annexin A5) [NCBI Gene 308] {aka ANX5, CPB-I, ENX2, HEL-S-7, PP4, RPRGL3}, FCGR3A (Fc gamma receptor IIIa) [NCBI Gene 2214] {aka CD16-II, CD16A, FCG3, FCGR3, FCRIIIA, FcGRIIIA}, SELL (selectin L) [NCBI Gene 6402] {aka CD62L, LAM1, LECAM1, LEU8, LNHR, LSEL}, CD101 (CD101 molecule) [NCBI Gene 9398] {aka EWI-101, IGSF2, V7}, VPS11 (VPS11 core subunit of CORVET and HOPS complexes) [NCBI Gene 55823] {aka DYT32, END1, HLD12, HLD12; DYT32, PEP5, RNF108}, CR1 (complement C3b/C4b receptor 1 (Knops blood group)) [NCBI Gene 1378] {aka C3BR, C4BR, CD35, KN}, CSF1R (colony stimulating factor 1 receptor) [NCBI Gene 1436] {aka BANDDOS, C-FMS, CD115, CSF-1R, CSFR, FIM2}, VPS33A (VPS33A core subunit of CORVET and HOPS complexes) [NCBI Gene 65082] {aka MPSPS}, fli1 (Fli-1 proto-oncogene, ETS transcription factor) [NCBI Gene 30619] {aka cb855, fli, fli-1, fli1a, wu:fc45b11}, CEACAM8 (CEA cell adhesion molecule 8) [NCBI Gene 1088] {aka CD66b, CD67, CGM6, NCA-95}, VPS39 (VPS39 subunit of HOPS complex) [NCBI Gene 23339] {aka TLP, VAM6, hVam6p}, SRP54 (signal recognition particle 54) [NCBI Gene 6729] {aka SCN8}, ITGAM (integrin subunit alpha M) [NCBI Gene 3684] {aka CD11B, CR3A, HNA-4, MAC-1, MAC1A, MO1A}, KITLG (KIT ligand) [NCBI Gene 4254] {aka DCUA, DFNA69, FPH2, FPHH, KL-1, Kitl}, CXCR2 (C-X-C motif chemokine receptor 2) [NCBI Gene 3579] {aka CD182, CDw128b, CMKAR2, IL8R2, IL8RA, IL8RB}, VPS8 (VPS8 subunit of CORVET complex) [NCBI Gene 23355] {aka KIAA0804}, NUP62 (nucleoporin 62) [NCBI Gene 23636] {aka IBSN, SNDI, p62}, EIF2S1 (eukaryotic translation initiation factor 2 subunit alpha) [NCBI Gene 1965] {aka EIF-2, EIF-2A, EIF-2alpha, EIF2, EIF2A}, CXCR4 (C-X-C motif chemokine receptor 4) [NCBI Gene 7852] {aka CD184, D2S201E, FB22, HM89, HSY3RR, LCR1}
- **Diseases:** albinism (MESH:D000417), developmental delay (MESH:D002658), genetic defect (MESH:D030342), leukoencephalopathy disorder (MESH:D056784), neurodegeneration (MESH:D019636), dystonia (MESH:D004421), aphthous ulcers (MESH:D013281), neutropenia (MESH:D009503), MPS (MESH:D008059), liver defects (MESH:D017093), diaper rash (MESH:D003963), infections (MESH:D007239), inflammation (MESH:D007249), congenital neutropenia (MESH:C537592), Deficiency of (MESH:D007153), primary dystonia (MESH:D020821), respiratory infections (MESH:D012141)
- **Chemicals:** Puromycin (MESH:D011691), Peptides (MESH:D010455), free fatty acids (MESH:D005230), LysoTrackerTM Red (-), isopropanol (MESH:D019840), MgSO4 (MESH:D008278), 1-Phenyl 2-thiourea (MESH:D010670), acetonitrile (MESH:C032159), formic acid (MESH:C030544), sodium deoxycholate (MESH:D003840), Lipid (MESH:D008055), glutaraldehyde (MESH:D005976), TFA (MESH:D014269), TMRM (MESH:C401833), SDS (MESH:D012967), Epon (MESH:C004875), methylene blue (MESH:D008751), 2-chloroacetamide (MESH:C013874), KCl (MESH:D011189), NaCl (MESH:D012965), Bodipy (MESH:C095489), Trypan Blue (MESH:D014343), Lipofectamine (MESH:C086724), PBS (MESH:D007854), CO2 (MESH:D002245), tricaine (MESH:C003636), BODIPY  493/503 (MESH:C527198), LysoTracker (MESH:C493330), Laemmli buffer (MESH:C088816), copper (MESH:D003300), ATP (MESH:D000255), Nile red (MESH:C044808), FITC (MESH:D016650), tris(2-carboxyethyl)phosphine (MESH:C080938), paraformaldehyde (MESH:C003043), osmium tetroxide (MESH:D009993), penicillin (MESH:D010406), streptomycin (MESH:D013307), ethanol (MESH:D000431), polystyrene (MESH:D011137), CaCl2 (MESH:D002122), Giemsa (MESH:D001399), DMSO (MESH:D004121)
- **Species:** Danio rerio (leopard danio, species) [taxon 7955], Adenoviridae (family) [taxon 10508], Haemophilus influenzae (species) [taxon 727], Homo sapiens (human, species) [taxon 9606], Mus musculus (house mouse, species) [taxon 10090]
- **Mutations:** c.2536T>G, c.2272-18C>A, c.1492C>T, c.700C>T, p.Arg234Ter, c.156C>A
- **Cell lines:** HL-60 — Homo sapiens (Human), Adult acute myeloid leukemia with maturation, Cancer cell line (CVCL_0002), ATCCCRL-11268 — Homo sapiens (Human), Frontotemporal dementia, Transformed cell line (CVCL_HR73), dHoxb8 — Xenopus laevis (African clawed frog), Spontaneously immortalized cell line (CVCL_4564), 293T — Homo sapiens (Human), Transformed cell line (CVCL_0063), CHO — Cricetulus griseus (Chinese hamster), Spontaneously immortalized cell line (CVCL_0213), HeLa — Homo sapiens (Human), Human papillomavirus-related endocervical adenocarcinoma, Cancer cell line (CVCL_0030), HEK — Homo sapiens (Human), Human papillomavirus-related endocervical adenocarcinoma, Cancer cell line (CVCL_M624)

## Full text

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## Figures

7 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12876832/full.md

## References

1 references — full list in the complete paper: https://tomesphere.com/paper/PMC12876832/full.md

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Source: https://tomesphere.com/paper/PMC12876832