RNA methyltransferase SPOUT1/CENP-32 links mitotic spindle organization with the neurodevelopmental disorder SpADMiSS

Avinash V. Dharmadhikari; Maria Alba Abad; Sheraz Khan; Reza Maroofian; Tristan T. Sands; Farid Ullah; Itaru Samejima; Yanwen Shen; Martin A. Wear; Kiara E. Moore; Elena Kondakova; Natalia Mitina; Theres Schaub; Grace K. Lee; Christine H. Umandap; Sara M. Berger; Alejandro D. Iglesias; Bernt Popp; Rami Abou jamra; Heinz Gabriel; Stefan Rentas; Alyssa L. Rippert; Christopher Gray; Kosuke Izumi; Laura K. Conlin; Daniel C. Koboldt; Theresa Mihalic Mosher; Scott E. Hickey; Dara V. F. Albert; Haley Norwood; Amy feldman Lewanda; Hongzheng Dai; Pengfei Liu; Tadahiro Mitani; Dana Marafi; Hatice Koçak Eker; Davut Pehlivan; Jennifer E. Posey; Natalie C. Lippa; Natalie Vena; Erin L. Heinzen; David B. Goldstein; Cyril Mignot; Jean-Madeleine De sainte agathe; Nouriya Abbas Al-Sannaa; Mina Zamani; Saeid Sadeghian; Reza Azizimalamiri; Tahere Seifia; Maha S. Zaki; Ghada M. H. Abdel-Salam; Mohamed S. Abdel-Hamid; Lama Alabdi; Fowzan sami Alkuraya; Heba Dawoud; Aya Lofty; Peter Bauer; Giovanni Zifarelli; Erum Afzal; Faisal Zafar; Stephanie Efthymiou; Daniel Gossett; Meghan C. Towne; Raey Yeneabat; Belen Perez-Duenas; Ana Cazurro-Gutierrez; Edgard Verdura; Veronica Cantarin-Extremera; Ana do Vale Marques; Aleksandra Helwak; David Tollervey; Sandeep N. Wontakal; Vimla S. Aggarwal; Jill A. Rosenfeld; Victor Tarabykin; Shinya Ohta; James R. Lupski; Henry Houlden; William C. Earnshaw; Erica E. Davis; A. Arockia Jeyaprakash; Jun Liao

doi:10.1038/s41467-025-56876-w

RNA methyltransferase SPOUT1/CENP-32 links mitotic spindle organization with the neurodevelopmental disorder SpADMiSS

Avinash V. Dharmadhikari, Maria Alba Abad, Sheraz Khan, Reza Maroofian, Tristan T. Sands, Farid Ullah, Itaru Samejima, Yanwen Shen, Martin A. Wear, Kiara E. Moore, Elena Kondakova, Natalia Mitina, Theres Schaub, Grace K. Lee, Christine H. Umandap, Sara M. Berger, Alejandro D. Iglesias, Bernt Popp, Rami Abou jamra, Heinz GabrielStefan Rentas, Alyssa L. Rippert, Christopher Gray, Kosuke Izumi, Laura K. Conlin, Daniel C. Koboldt, Theresa Mihalic Mosher, Scott E. Hickey, Dara V. F. Albert, Haley Norwood, Amy feldman Lewanda, Hongzheng Dai, Pengfei Liu, Tadahiro Mitani, Dana Marafi, Hatice Koçak Eker, Davut Pehlivan, Jennifer E. Posey, Natalie C. Lippa, Natalie Vena, Erin L. Heinzen, David B. Goldstein, Cyril Mignot, Jean-Madeleine De sainte agathe, Nouriya Abbas Al-Sannaa, Mina Zamani, Saeid Sadeghian, Reza Azizimalamiri, Tahere Seifia, Maha S. Zaki, Ghada M. H. Abdel-Salam, Mohamed S. Abdel-Hamid, Lama Alabdi, Fowzan sami Alkuraya, Heba Dawoud, Aya Lofty, Peter Bauer, Giovanni Zifarelli, Erum Afzal, Faisal Zafar, Stephanie Efthymiou, Daniel Gossett, Meghan C. Towne, Raey Yeneabat, Belen Perez-Duenas, Ana Cazurro-Gutierrez, Edgard Verdura, Veronica Cantarin-Extremera, Ana do Vale Marques, Aleksandra Helwak, David Tollervey, Sandeep N. Wontakal, Vimla S. Aggarwal, Jill A. Rosenfeld, Victor Tarabykin, Shinya Ohta, James R. Lupski, Henry Houlden, William C. Earnshaw, Erica E. Davis^*, A. Arockia Jeyaprakash^*, Jun Liao^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

Abstract

SPOUT1/CENP-32 encodes a putative SPOUT RNA methyltransferase previously identified as a mitotic chromosome associated protein. SPOUT1/CENP-32 depletion leads to centrosome detachment from the spindle poles and chromosome misalignment. Aided by gene matching platforms, here we identify 28 individuals with neurodevelopmental delays from 21 families with bi-allelic variants in SPOUT1/CENP-32 detected by exome/genome sequencing. Zebrafish spout1/cenp-32 mutants show reduction in larval head size with concomitant apoptosis likely associated with altered cell cycle progression. In vivo complementation assays in zebrafish indicate that SPOUT1/CENP-32 missense variants identified in humans are pathogenic. Crystal structure analysis of SPOUT1/CENP-32 reveals that most disease-associated missense variants are located within the catalytic domain. Additionally, SPOUT1/CENP-32 recurrent missense variants show reduced methyltransferase activity in vitro and compromised centrosome tethering to the spindle poles in human cells. Thus, SPOUT1/CENP-32 pathogenic variants cause an autosomal recessive neurodevelopmental disorder: SpADMiSS (SPOUT1 Associated Development delay Microcephaly Seizures Short stature) underpinned by mitotic spindle organization defects and consequent chromosome segregation errors.

Original language	English
Article number	1703
Number of pages	24
Journal	Nature Communications
Volume	16
Issue number	1
DOIs	https://doi.org/10.1038/s41467-025-56876-w
Publication status	Published - 17 Feb 2025

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Dharmadhikari, A. V., Abad, M. A., Khan, S., Maroofian, R., Sands, T. T., Ullah, F., Samejima, I., Shen, Y., Wear, M. A., Moore, K. E., Kondakova, E., Mitina, N., Schaub, T., Lee, G. K., Umandap, C. H., Berger, S. M., Iglesias, A. D., Popp, B., Abou jamra, R., ... Liao, J. (2025). RNA methyltransferase SPOUT1/CENP-32 links mitotic spindle organization with the neurodevelopmental disorder SpADMiSS. Nature Communications, 16(1), Article 1703. https://doi.org/10.1038/s41467-025-56876-w

@article{660b1d7f3e25410db5af121a14e5a59d,

title = "RNA methyltransferase SPOUT1/CENP-32 links mitotic spindle organization with the neurodevelopmental disorder SpADMiSS",

abstract = "SPOUT1/CENP-32 encodes a putative SPOUT RNA methyltransferase previously identified as a mitotic chromosome associated protein. SPOUT1/CENP-32 depletion leads to centrosome detachment from the spindle poles and chromosome misalignment. Aided by gene matching platforms, here we identify 28 individuals with neurodevelopmental delays from 21 families with bi-allelic variants in SPOUT1/CENP-32 detected by exome/genome sequencing. Zebrafish spout1/cenp-32 mutants show reduction in larval head size with concomitant apoptosis likely associated with altered cell cycle progression. In vivo complementation assays in zebrafish indicate that SPOUT1/CENP-32 missense variants identified in humans are pathogenic. Crystal structure analysis of SPOUT1/CENP-32 reveals that most disease-associated missense variants are located within the catalytic domain. Additionally, SPOUT1/CENP-32 recurrent missense variants show reduced methyltransferase activity in vitro and compromised centrosome tethering to the spindle poles in human cells. Thus, SPOUT1/CENP-32 pathogenic variants cause an autosomal recessive neurodevelopmental disorder: SpADMiSS (SPOUT1 Associated Development delay Microcephaly Seizures Short stature) underpinned by mitotic spindle organization defects and consequent chromosome segregation errors.",

author = "Dharmadhikari, {Avinash V.} and Abad, {Maria Alba} and Sheraz Khan and Reza Maroofian and Sands, {Tristan T.} and Farid Ullah and Itaru Samejima and Yanwen Shen and Wear, {Martin A.} and Moore, {Kiara E.} and Elena Kondakova and Natalia Mitina and Theres Schaub and Lee, {Grace K.} and Umandap, {Christine H.} and Berger, {Sara M.} and Iglesias, {Alejandro D.} and Bernt Popp and {Abou jamra}, Rami and Heinz Gabriel and Stefan Rentas and Rippert, {Alyssa L.} and Christopher Gray and Kosuke Izumi and Conlin, {Laura K.} and Koboldt, {Daniel C.} and Mosher, {Theresa Mihalic} and Hickey, {Scott E.} and Albert, {Dara V. F.} and Haley Norwood and Lewanda, {Amy feldman} and Hongzheng Dai and Pengfei Liu and Tadahiro Mitani and Dana Marafi and Eker, {Hatice Ko{\c c}ak} and Davut Pehlivan and Posey, {Jennifer E.} and Lippa, {Natalie C.} and Natalie Vena and Heinzen, {Erin L.} and Goldstein, {David B.} and Cyril Mignot and {De sainte agathe}, Jean-Madeleine and Al-Sannaa, {Nouriya Abbas} and Mina Zamani and Saeid Sadeghian and Reza Azizimalamiri and Tahere Seifia and Zaki, {Maha S.} and Abdel-Salam, {Ghada M. H.} and Abdel-Hamid, {Mohamed S.} and Lama Alabdi and Alkuraya, {Fowzan sami} and Heba Dawoud and Aya Lofty and Peter Bauer and Giovanni Zifarelli and Erum Afzal and Faisal Zafar and Stephanie Efthymiou and Daniel Gossett and Towne, {Meghan C.} and Raey Yeneabat and Belen Perez-Duenas and Ana Cazurro-Gutierrez and Edgard Verdura and Veronica Cantarin-Extremera and Marques, {Ana do Vale} and Aleksandra Helwak and David Tollervey and Wontakal, {Sandeep N.} and Aggarwal, {Vimla S.} and Rosenfeld, {Jill A.} and Victor Tarabykin and Shinya Ohta and Lupski, {James R.} and Henry Houlden and Earnshaw, {William C.} and Davis, {Erica E.} and Jeyaprakash, {A. Arockia} and Jun Liao",

note = "We thank the families for consenting to participate in this study. We thank Elizabeth LeClair for assistance on statistical analyses of zebrafish data; and Jaewon Lee for help with illustrations in Figure 9.",

year = "2025",

month = feb,

day = "17",

doi = "10.1038/s41467-025-56876-w",

language = "English",

volume = "16",

journal = "Nature Communications",

issn = "2041-1723",

publisher = "Nature Publishing Group",

number = "1",

}

Dharmadhikari, AV, Abad, MA, Khan, S, Maroofian, R, Sands, TT, Ullah, F, Samejima, I, Shen, Y, Wear, MA, Moore, KE, Kondakova, E, Mitina, N, Schaub, T, Lee, GK, Umandap, CH, Berger, SM, Iglesias, AD, Popp, B, Abou jamra, R, Gabriel, H, Rentas, S, Rippert, AL, Gray, C, Izumi, K, Conlin, LK, Koboldt, DC, Mosher, TM, Hickey, SE, Albert, DVF, Norwood, H, Lewanda, AF, Dai, H, Liu, P, Mitani, T, Marafi, D, Eker, HK, Pehlivan, D, Posey, JE, Lippa, NC, Vena, N, Heinzen, EL, Goldstein, DB, Mignot, C, De sainte agathe, J-M, Al-Sannaa, NA, Zamani, M, Sadeghian, S, Azizimalamiri, R, Seifia, T, Zaki, MS, Abdel-Salam, GMH, Abdel-Hamid, MS, Alabdi, L, Alkuraya, FS, Dawoud, H, Lofty, A, Bauer, P, Zifarelli, G, Afzal, E, Zafar, F, Efthymiou, S, Gossett, D, Towne, MC, Yeneabat, R, Perez-Duenas, B, Cazurro-Gutierrez, A, Verdura, E, Cantarin-Extremera, V, Marques, ADV, Helwak, A , Tollervey, D, Wontakal, SN, Aggarwal, VS, Rosenfeld, JA, Tarabykin, V, Ohta, S, Lupski, JR, Houlden, H, Earnshaw, WC, Davis, EE, Jeyaprakash, AA & Liao, J 2025, 'RNA methyltransferase SPOUT1/CENP-32 links mitotic spindle organization with the neurodevelopmental disorder SpADMiSS', Nature Communications, vol. 16, no. 1, 1703. https://doi.org/10.1038/s41467-025-56876-w

TY - JOUR

T1 - RNA methyltransferase SPOUT1/CENP-32 links mitotic spindle organization with the neurodevelopmental disorder SpADMiSS

AU - Dharmadhikari, Avinash V.

AU - Abad, Maria Alba

AU - Khan, Sheraz

AU - Maroofian, Reza

AU - Sands, Tristan T.

AU - Ullah, Farid

AU - Samejima, Itaru

AU - Shen, Yanwen

AU - Wear, Martin A.

AU - Moore, Kiara E.

AU - Kondakova, Elena

AU - Mitina, Natalia

AU - Schaub, Theres

AU - Lee, Grace K.

AU - Umandap, Christine H.

AU - Berger, Sara M.

AU - Iglesias, Alejandro D.

AU - Popp, Bernt

AU - Abou jamra, Rami

AU - Gabriel, Heinz

AU - Rentas, Stefan

AU - Rippert, Alyssa L.

AU - Gray, Christopher

AU - Izumi, Kosuke

AU - Conlin, Laura K.

AU - Koboldt, Daniel C.

AU - Mosher, Theresa Mihalic

AU - Hickey, Scott E.

AU - Albert, Dara V. F.

AU - Norwood, Haley

AU - Lewanda, Amy feldman

AU - Dai, Hongzheng

AU - Liu, Pengfei

AU - Mitani, Tadahiro

AU - Marafi, Dana

AU - Eker, Hatice Koçak

AU - Pehlivan, Davut

AU - Posey, Jennifer E.

AU - Lippa, Natalie C.

AU - Vena, Natalie

AU - Heinzen, Erin L.

AU - Goldstein, David B.

AU - Mignot, Cyril

AU - De sainte agathe, Jean-Madeleine

AU - Al-Sannaa, Nouriya Abbas

AU - Zamani, Mina

AU - Sadeghian, Saeid

AU - Azizimalamiri, Reza

AU - Seifia, Tahere

AU - Zaki, Maha S.

AU - Abdel-Salam, Ghada M. H.

AU - Abdel-Hamid, Mohamed S.

AU - Alabdi, Lama

AU - Alkuraya, Fowzan sami

AU - Dawoud, Heba

AU - Lofty, Aya

AU - Bauer, Peter

AU - Zifarelli, Giovanni

AU - Afzal, Erum

AU - Zafar, Faisal

AU - Efthymiou, Stephanie

AU - Gossett, Daniel

AU - Towne, Meghan C.

AU - Yeneabat, Raey

AU - Perez-Duenas, Belen

AU - Cazurro-Gutierrez, Ana

AU - Verdura, Edgard

AU - Cantarin-Extremera, Veronica

AU - Marques, Ana do Vale

AU - Helwak, Aleksandra

AU - Tollervey, David

AU - Wontakal, Sandeep N.

AU - Aggarwal, Vimla S.

AU - Rosenfeld, Jill A.

AU - Tarabykin, Victor

AU - Ohta, Shinya

AU - Lupski, James R.

AU - Houlden, Henry

AU - Earnshaw, William C.

AU - Davis, Erica E.

AU - Jeyaprakash, A. Arockia

AU - Liao, Jun

N1 - We thank the families for consenting to participate in this study. We thank Elizabeth LeClair for assistance on statistical analyses of zebrafish data; and Jaewon Lee for help with illustrations in Figure 9.

PY - 2025/2/17

Y1 - 2025/2/17

N2 - SPOUT1/CENP-32 encodes a putative SPOUT RNA methyltransferase previously identified as a mitotic chromosome associated protein. SPOUT1/CENP-32 depletion leads to centrosome detachment from the spindle poles and chromosome misalignment. Aided by gene matching platforms, here we identify 28 individuals with neurodevelopmental delays from 21 families with bi-allelic variants in SPOUT1/CENP-32 detected by exome/genome sequencing. Zebrafish spout1/cenp-32 mutants show reduction in larval head size with concomitant apoptosis likely associated with altered cell cycle progression. In vivo complementation assays in zebrafish indicate that SPOUT1/CENP-32 missense variants identified in humans are pathogenic. Crystal structure analysis of SPOUT1/CENP-32 reveals that most disease-associated missense variants are located within the catalytic domain. Additionally, SPOUT1/CENP-32 recurrent missense variants show reduced methyltransferase activity in vitro and compromised centrosome tethering to the spindle poles in human cells. Thus, SPOUT1/CENP-32 pathogenic variants cause an autosomal recessive neurodevelopmental disorder: SpADMiSS (SPOUT1 Associated Development delay Microcephaly Seizures Short stature) underpinned by mitotic spindle organization defects and consequent chromosome segregation errors.

AB - SPOUT1/CENP-32 encodes a putative SPOUT RNA methyltransferase previously identified as a mitotic chromosome associated protein. SPOUT1/CENP-32 depletion leads to centrosome detachment from the spindle poles and chromosome misalignment. Aided by gene matching platforms, here we identify 28 individuals with neurodevelopmental delays from 21 families with bi-allelic variants in SPOUT1/CENP-32 detected by exome/genome sequencing. Zebrafish spout1/cenp-32 mutants show reduction in larval head size with concomitant apoptosis likely associated with altered cell cycle progression. In vivo complementation assays in zebrafish indicate that SPOUT1/CENP-32 missense variants identified in humans are pathogenic. Crystal structure analysis of SPOUT1/CENP-32 reveals that most disease-associated missense variants are located within the catalytic domain. Additionally, SPOUT1/CENP-32 recurrent missense variants show reduced methyltransferase activity in vitro and compromised centrosome tethering to the spindle poles in human cells. Thus, SPOUT1/CENP-32 pathogenic variants cause an autosomal recessive neurodevelopmental disorder: SpADMiSS (SPOUT1 Associated Development delay Microcephaly Seizures Short stature) underpinned by mitotic spindle organization defects and consequent chromosome segregation errors.

UR - https://www.ncbi.nlm.nih.gov/clinvar/

U2 - 10.1038/s41467-025-56876-w

DO - 10.1038/s41467-025-56876-w

M3 - Article

SN - 2041-1723

VL - 16

JO - Nature Communications

JF - Nature Communications

IS - 1

M1 - 1703

ER -

RNA methyltransferase SPOUT1/CENP-32 links mitotic spindle organization with the neurodevelopmental disorder SpADMiSS

Abstract

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Structural Basis for Centromere-Mediated Control of Error-free Chromosome Segregation

Mechanistic Basis for CENP-32 Mediated Regulation of Cell Division

The role of non-histone proteins in chromosome structure and function during mitosis

PDB ID 8QSU: Crystal structure of SPOUT1/CENP-32 bound to SAH

PDB ID 8QSW: Crystal structure of SPOUT1/CENP-32 | A356N catalytic site mutant

Fig.S13 SDS-PAGE analysis of SPOUT1/CENP-32 71

Cite this

RNA methyltransferase SPOUT1/CENP-32 links mitotic spindle organization with the neurodevelopmental disorder SpADMiSS

Abstract

Access to Document

Other files and links

Fingerprint

Projects

Structural Basis for Centromere-Mediated Control of Error-free Chromosome Segregation

Mechanistic Basis for CENP-32 Mediated Regulation of Cell Division

The role of non-histone proteins in chromosome structure and function during mitosis

Datasets

PDB ID 8QSU: Crystal structure of SPOUT1/CENP-32 bound to SAH

PDB ID 8QSW: Crystal structure of SPOUT1/CENP-32 | A356N catalytic site mutant

Fig.S13 SDS-PAGE analysis of SPOUT1/CENP-32 71

Cite this