# The microcephaly-associated protein YIPF5 differentially regulates ER export

**Authors:** Francesca Bruno, Mihaela Anitei, Domenico Di Fraia, William Durso, Therese Dau, Emilio Cirri, Mara Sannai, Christina Valkova, Julija Maldutyte, Elizabeth A. Miller, Ignacio Rubio, Vera Garloff, Noortje Kersten, Ginny G. Farias, Alessandro Ori, Iván Mestres, Federico Calegari, Christoph Kaether

PMC · DOI: 10.1016/j.isci.2026.114791 · iScience · 2026-01-27

## TL;DR

This study shows that the YIPF5 protein helps regulate the transport of specific proteins from the endoplasmic reticulum, and its loss disrupts neuronal development, leading to microcephaly.

## Contribution

The study reveals YIPF5's role in ER export and its interaction with SURF4, linking these mechanisms to neurological disorders.

## Key findings

- YIPF5 knockout alters cell surface and secretome profiles, reducing neuronal adhesion molecules.
- YIPF5 depletion causes elongated ERGIC53- and Rab1-positive tubules and enhances cell migration.
- In utero Yipf5 knockdown leads to premature neuronal migration and abnormal morphology in mice.

## Abstract

YIPF5 is an ER-membrane protein implicated in ER-Golgi transport. Mutations in YIPF5 cause MEDS2 (microcephaly, epilepsy, and neonatal diabetes syndrome), a fatal disorder manifesting in early childhood. We demonstrate that YIPF5 is involved in ER export of a subset of proteins, including cargoes of the ER export receptor SURF4, with which it directly interacts. YIPF5 knockout cells display altered cell surface and secretome profiles, with reduced neuronal adhesion molecules and increased secretion of ER chaperones affecting migration. YIPF5 depletion enhances cell migration in a wound-healing assay and alters SURF4 localization, causing elongated ERGIC53- and Rab1-positive tubules from ER exit sites. Kinetic analysis suggests that YIPF5 negatively regulates SURF4-mediated ER export. In utero knockdown of Yipf5 in embryonic mouse brains induces premature neuronal migration and abnormal neuronal morphology. Our findings suggest that YIPF5 and SURF4 coordinate ER export of key proteins and disruption may underlie cortical development defects leading to microcephaly.

•Loss of YIPF5 alters surfaceome and secretome, disrupting neuronal protein balance•YIPF5 interacts with the transport receptor SURF4•YIPF5-loss mislocalizes SURF4, producing elongated ERGIC53/Rab1-positive tubules•Yipf5 knockdown causes early neuronal migration and abnormal morphology

Loss of YIPF5 alters surfaceome and secretome, disrupting neuronal protein balance

YIPF5 interacts with the transport receptor SURF4

YIPF5-loss mislocalizes SURF4, producing elongated ERGIC53/Rab1-positive tubules

Yipf5 knockdown causes early neuronal migration and abnormal morphology

Neuroscience; Cell biology

## Linked entities

- **Genes:** YIPF5 (Yip1 domain family member 5) [NCBI Gene 81555], SURF4 (surfeit 4) [NCBI Gene 6836], LMAN1 (lectin, mannose binding 1) [NCBI Gene 3998], RAB1A (RAB1A, member RAS oncogene family) [NCBI Gene 5861], YIPF5 (Yip1 domain family member 5) [NCBI Gene 81555]
- **Proteins:** YIPF5 (Yip1 domain family member 5), SURF4 (surfeit 4), LMAN1 (lectin, mannose binding 1), RAB1A (RAB1A, member RAS oncogene family)
- **Diseases:** MEDS2 (MONDO:0025690), microcephaly (MONDO:0001149), epilepsy (MONDO:0005027)
- **Species:** Mus musculus (taxon 10090)

## Full-text entities

- **Genes:** Rab1a (RAB1A, member RAS oncogene family) [NCBI Gene 19324] {aka Gtbp, Rab-1, Rab1, Ypt1, mKIAA3012}, EEF1A2 (eukaryotic translation elongation factor 1 alpha 2) [NCBI Gene 1917] {aka DEE33, EEF1AL, EF-1-alpha-2, EF1A, EIEE33, HS1}, SEC24C (SEC24 homolog C, COPII component) [NCBI Gene 9632], CHI3L1 (chitinase 3 like 1) [NCBI Gene 1116] {aka ASRT7, CGP-39, GP-39, GP39, HC-gp39, HCGP-3P}, ERN1 (endoplasmic reticulum to nucleus signaling 1) [NCBI Gene 2081] {aka IRE1, IRE1P, IRE1a, hIRE1p}, KDELR2 (KDEL endoplasmic reticulum protein retention receptor 2) [NCBI Gene 11014] {aka ELP-1, ERD2.2, OI21}, Lman1 (lectin, mannose-binding, 1) [NCBI Gene 70361] {aka 2610020P13Rik, C730041J05, ERGIC53, F5F8D, MCFD1, MR60}, CNPY3 (canopy FGF signaling regulator 3) [NCBI Gene 10695] {aka CAG4A, DEE60, EIEE60, ERDA5, PRAT4A, TNRC5}, SDF4 (stromal cell derived factor 4) [NCBI Gene 51150] {aka Cab45, SDF-4}, Yipf5 (Yip1 domain family, member 5) [NCBI Gene 67180] {aka 2610311I19Rik, Yip1a}, EREG (epiregulin) [NCBI Gene 2069] {aka EPR, ER, Ep}, TENM3 (teneurin transmembrane protein 3) [NCBI Gene 55714] {aka MCOPCB9, MCOPS15, ODZ3, TEN3, TNM3, Ten-m3}, RAB1B (RAB1B, member RAS oncogene family) [NCBI Gene 81876], EPHB2 (EPH receptor B2) [NCBI Gene 2048] {aka BDPLT22, CAPB, DRT, EK5, EPHT3, ERK}, HSPG2 (heparan sulfate proteoglycan 2) [NCBI Gene 3339] {aka HSPG, PLC, PRCAN, SJA, SJS, SJS1}, HSP90B1 (heat shock protein 90 beta family member 1) [NCBI Gene 7184] {aka ECGP, GP96, GRP94, HEL-S-125m, HEL35, TRA1}, NRP1 (neuropilin 1) [NCBI Gene 8829] {aka BDCA4, CD304, NP1, NRP, VEGF165R}, POFUT1 (protein O-fucosyltransferase 1) [NCBI Gene 23509] {aka DDD2, FUT12, O-FUT, O-Fuc-T, O-FucT-1, OFUCT1}, NUCB1 (nucleobindin 1) [NCBI Gene 4924] {aka CALNUC, NUC}, NRCAM (neuronal cell adhesion molecule) [NCBI Gene 4897] {aka NEDNMS}, SLITRK5 (SLIT and NTRK like family member 5) [NCBI Gene 26050] {aka LRRC11, bA364G4.2}, YIF1B (Yip1 interacting factor homolog B, membrane trafficking protein) [NCBI Gene 90522] {aka FinGER8, KABAMAS}, SERPINA1 (serpin family A member 1) [NCBI Gene 5265] {aka A1A, A1AT, AAT, PI, PI1, PRO2275}, SEC31A (SEC31 homolog A, COPII component) [NCBI Gene 22872] {aka ABP125, ABP130, HPBKS, HSPC275, HSPC334, NEDSOSB}, SURF4 (surfeit 4) [NCBI Gene 6836] {aka ERV29}, CRKL (CRK like proto-oncogene, adaptor protein) [NCBI Gene 1399], NCAM1 (neural cell adhesion molecule 1) [NCBI Gene 4684] {aka CD56, MSK39, NCAM}, SAR1A (secretion associated Ras related GTPase 1A) [NCBI Gene 56681] {aka SAR1, SARA1, Sara, masra2}, INS (insulin) [NCBI Gene 3630] {aka IDDM, IDDM1, IDDM2, ILPR, IRDN, MODY10}, LMAN1 (lectin, mannose binding 1) [NCBI Gene 3998] {aka ERGIC-53, ERGIC53, F5F8D, FMFD1, MCFD1, MR60}, ALB (albumin) [NCBI Gene 213] {aka FDAHT, HSA, PRO0883, PRO0903, PRO1341}, PLXND1 (plexin D1) [NCBI Gene 23129] {aka CHTD9, PLEXD1}, BLNK (B cell linker) [NCBI Gene 29760] {aka AGM4, BASH, BLNK-S, LY57, SLP-65, SLP65}, TMED2 (transmembrane p24 trafficking protein 2) [NCBI Gene 10959] {aka P24A, RNP24, p24, p24b1, p24beta1}, EPHB3 (EPH receptor B3) [NCBI Gene 2049] {aka EK2, ETK2, HEK2, TYRO6}, PLXNA2 (plexin A2) [NCBI Gene 5362] {aka OCT, PLXN2}, SEC13 (SEC13 homolog, nuclear pore and COPII component) [NCBI Gene 6396] {aka D3S1231E, SEC13L1, SEC13R, npp-20}, POTEF (POTE ankyrin domain family member F) [NCBI Gene 728378] {aka A26C1B, POTE2alpha, POTEACTIN}, GAPDH (glyceraldehyde-3-phosphate dehydrogenase) [NCBI Gene 2597] {aka G3PD, GAPD, HEL-S-162eP}, L1CAM (L1 cell adhesion molecule) [NCBI Gene 3897] {aka CAML1, CD171, HSAS, HSAS1, HYCX, MASA}, IER3IP1 (immediate early response 3 interacting protein 1) [NCBI Gene 51124] {aka HSPC039, MEDS, PRO2309}, YIF1A (Yip1 interacting factor homolog A, membrane trafficking protein) [NCBI Gene 10897] {aka 54TM, FinGER7, YIF1, YIF1P}, CALU (calumenin) [NCBI Gene 813], GDF10 (growth differentiation factor 10) [NCBI Gene 2662] {aka BIP, BMP-3b, BMP3B}, SULF2 (sulfatase 2) [NCBI Gene 55959] {aka HSULF-2}, EGF (epidermal growth factor) [NCBI Gene 1950] {aka HOMG4, URG}, YIPF5 (Yip1 domain family member 5) [NCBI Gene 81555] {aka FinGER5, MEDS2, SB140, SMAP-5, SMAP5, YIP1A}, ROBO1 (roundabout guidance receptor 1) [NCBI Gene 6091] {aka CPHD8, DUTT1, NORS, NYS8, SAX3}, Surf4 (surfeit gene 4) [NCBI Gene 20932] {aka Surf-4}, KDELR1 (KDEL endoplasmic reticulum protein retention receptor 1) [NCBI Gene 10945] {aka ERD2, ERD2.1, HDEL, PM23}, L1cam (L1 cell adhesion molecule) [NCBI Gene 50687] {aka Hsas, Hyd, N-CAM L1, NCAML1, NgCAM}, PCSK9 (proprotein convertase subtilisin/kexin type 9) [NCBI Gene 255738] {aka FH3, FHCL3, HCHOLA3, LDLCQ1, NARC-1, NARC1}, SEC24B (SEC24 homolog B, COPII component) [NCBI Gene 10427] {aka SEC24}, STING1 (stimulator of interferon response cGAMP interactor 1) [NCBI Gene 340061] {aka ERIS, MITA, MPYS, NET23, SAVI, STING}, GOLGA2 (golgin A2) [NCBI Gene 2801] {aka DEDHMB, GM130}, Ier3ip1 (immediate early response 3 interacting protein 1) [NCBI Gene 66191] {aka 1110057H19Rik}, Yipf5 (Yip1 domain family, member 5) [NCBI Gene 361315] {aka Ac2-256}
- **Diseases:** MEDS2 syndrome (MESH:D013577), death (MESH:D003643), epileptic encephalopathy (MESH:D001927), brain injury (MESH:D001930), epilepsy (MESH:D004827), neuroinflammation (MESH:D000090862), microcephaly, epilepsy, and diabetes syndrome (OMIM:614231), neurodevelopmental defects (MESH:D065886), Microcephaly (MESH:D008831), cortical development defects (MESH:D054220), developmental defects (MESH:D000094602), neonatal diabetes syndrome (MESH:C563322)
- **Chemicals:** HEPES (MESH:D006531), penicillin (MESH:D010406), glycerol (MESH:D005990), formic acid (MESH:C030544), sodium citrate (MESH:D000077559), sugar (MESH:D000073893), NaCl (MESH:D012965), phenol red (MESH:D010637), thapsigargin (MESH:D019284), ManNAz (MESH:C405953), doxycycline (MESH:D004318), DBCO-Sulfo-Biotin (-), MgCl2 (MESH:D015636), Alexa Fluor 488 (MESH:C000711379), polyacrylamide (MESH:C016679), acetone (MESH:D000096), oil (MESH:D009821), Sudan Black B (MESH:C016118), CHAPSO (MESH:C048531), streptomycin (MESH:D013307), TFA (MESH:D014269), agar (MESH:D000362), Triton X-100 (MESH:D017830), TCA (MESH:D014238), sialic acid (MESH:D019158), acetonitrile (MESH:C032159), Fast Green (MESH:C035906), Bromophenol Blue (MESH:D001978), F-12 (MESH:C007782), azide (MESH:D001386), Urea (MESH:D014508), hydrocortisone (MESH:D006854), EDTA (MESH:D004492), Hoechst 33342 (MESH:C017807), Lipofectamine (MESH:C086724), Thiol (MESH:D013438), NP-40 (MESH:C010615), agarose (MESH:D012685), iodoacetamide (MESH:D007460), Methyl-alpha-D-mannopyranoside (MESH:C008466), paraformaldehyde (MESH:C003043), isoflurane (MESH:D007530), bicinchoninic acid (MESH:C047117), Hygromycin B. (MESH:D006921), glutamine (MESH:D005973), SYBR Green (MESH:C098022), citrate (MESH:D019343), CO2 (MESH:D002245), phenol (MESH:D019800), Water (MESH:D014867), calcium (MESH:D002118), argon (MESH:D001128), Reprosil (MESH:C034183), glycine (MESH:D005998), magnesium (MESH:D008274), DAPI (MESH:C007293), glucose (MESH:D005947), GlutaMax (MESH:C054122), formaldehyde (MESH:D005557), ethanol (MESH:D000431)
- **Species:** Homo sapiens (human, species) [taxon 9606], Saccharomyces cerevisiae (baker's yeast, species) [taxon 4932], Spleen focus-forming virus (species) [taxon 11819], Mus musculus (house mouse, species) [taxon 10090], Rattus norvegicus (brown rat, species) [taxon 10116], Oryctolagus cuniculus (domestic rabbit, species) [taxon 9986]
- **Mutations:** p.(Lys106del), P35G, A181V, L108del, G98V, K106del, p.(Gly97Val), W218R
- **Cell lines:** C57BL/6J — Mus musculus (Mouse), Transformed cell line (CVCL_C0MW), B2261-25MG — Homo sapiens (Human), Finite cell line (CVCL_0D98), MCF10A — Homo sapiens (Human), Spontaneously immortalized cell line (CVCL_0598), shRNA2 — Homo sapiens (Human), Ewing sarcoma, Cancer cell line (CVCL_QW73), HEK293T-LentiX — Homo sapiens (Human), Transformed cell line (CVCL_4401), S2 — Drosophila melanogaster (Fruit fly), Spontaneously immortalized cell line (CVCL_Z232), U2OS — Homo sapiens (Human), Osteosarcoma, Cancer cell line (CVCL_0042), NIH3T3 — Mus musculus (Mouse), Spontaneously immortalized cell line (CVCL_0594), C8052-2MG — Mus musculus (Mouse), Mouse erythroid leukemia, Cancer cell line (CVCL_6579), HeLa — Homo sapiens (Human), Human papillomavirus-related endocervical adenocarcinoma, Cancer cell line (CVCL_0030), shRNA3 — Homo sapiens (Human), Breast adenocarcinoma, Cancer cell line (CVCL_A9BB)

## Full text

_Full body text omitted from this summary view._ Fetch the complete paper as Markdown: https://tomesphere.com/paper/PMC12915289/full.md

## Figures

7 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12915289/full.md

## References

93 references — full list in the complete paper: https://tomesphere.com/paper/PMC12915289/full.md

---
Source: https://tomesphere.com/paper/PMC12915289