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Background <p>Disrupted RNA processing is increasingly recognized as a key driver of severe neurodevelopmental disorders. Variants in the Integrator catalytic subunit INTS11 and its binding partner BRAT1 lead to clinically overlapping phenotypes, yet only the molecular function of INTS11 has been relatively well characterized. In contrast, the mechanistic contribution of BRAT1 to RNA metabolism and disease has remained unclear, leaving major gaps in variant interpretation and diagnostic classification.</p> Methods <p>We employed an integrated genetic, molecular, and in vivo approach to investigate the impact of <i>INTS11</i> and <i>BRAT1</i> mutations on U small nuclear RNA (U snRNA) processing. Patient-derived fibroblasts and lymphoblastoid cells were analysed by western blotting, RT-qPCR and fluorescence in situ hybridization to assess U1 snRNA 3′-end processing and nuclear retention. To validate the functional consequences of Integrator deficiency in vivo, we generated and characterized an <i>ints11</i> knockout zebrafish model.</p> Results <p>We identified novel biallelic variants in <i>INTS11</i> and <i>BRAT1</i> in individuals with overlapping neurodevelopmental features. While defective snRNA processing is anticipated in INTS11 deficiency, this study provides the first direct demonstration of impaired U1 snRNA processing across multiple <i>INTS11</i>-mutated patient cells. Critically, we show that <i>BRAT1</i> mutations also compromise U1 snRNA 3′-end processing, leading to nuclear accumulation of unprocessed transcripts. These findings provide direct evidence of BRAT1’s role in RNA processing and establish Integrator dysfunction as a primary pathogenic mechanism in BRAT1-associated neurological disease. The magnitude of U1 snRNA misprocessing closely correlates with clinical severity across the BRAT1 cohort, highlighting its potential as a diagnostic biomarker. Consistently, the <i>ints11</i> knockout zebrafish model recapitulates core patient features – including microcephaly, neurodevelopmental defects, and U snRNA processing defects – further validating the causal role of Integrator deficiency in vivo.</p> Conclusions <p>Our results redefine BRAT1-associated neurological disorders as Integrator-related diseases driven by RNA processing defects. Nuclear accumulation of unprocessed U1 snRNAs emerges as a robust biomarker for variant interpretation, disease severity, and patient stratification, particularly in BRAT1 cases. These findings broaden the clinical and molecular spectrum of Integrator dysfunction and provide a foundation for improved diagnostic and translational approaches.</p>

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Unprocessed U1 snRNAs as a biomarker of INTS11- and BRAT1-related neurodevelopmental disorders

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年5月12日

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  • Beatrice Valtorta,
  • Zuzana Polackova,
  • Reza Maroofian,
  • Aveeva Herold,
  • Irem Karagoz,
  • Maha S Zaki,
  • Denisa Bronisova,
  • Meijiang Liao,
  • Mina Zamani,
  • Annarita Scardamaglia,
  • Nine Collomb,
  • Lidia Lopez-Jimenez,
  • Maria J Barrero,
  • Julian Schröter,
  • Steffen Syrbe,
  • Marion Heidi Vallanger,
  • Sofia Douzgou Houge,
  • Yasemin Alanay,
  • Ozlem Akgun-Dogan,
  • Julie Vogt,
  • Michael Muriello,
  • Yvonne M C Hendriks,
  • Alexandra Afenjar,
  • Nadirah Damseh,
  • Rauan Kaiyrzhanov,
  • Marcello Niceta,
  • Marco Tartaglia,
  • Manju A Kurian,
  • Nataliya Di Donato,
  • Grace Yoon,
  • Henry Houlden,
  • Éric Samarut,
  • Hana Hanzlikova

摘要

Background

Disrupted RNA processing is increasingly recognized as a key driver of severe neurodevelopmental disorders. Variants in the Integrator catalytic subunit INTS11 and its binding partner BRAT1 lead to clinically overlapping phenotypes, yet only the molecular function of INTS11 has been relatively well characterized. In contrast, the mechanistic contribution of BRAT1 to RNA metabolism and disease has remained unclear, leaving major gaps in variant interpretation and diagnostic classification.

Methods

We employed an integrated genetic, molecular, and in vivo approach to investigate the impact of INTS11 and BRAT1 mutations on U small nuclear RNA (U snRNA) processing. Patient-derived fibroblasts and lymphoblastoid cells were analysed by western blotting, RT-qPCR and fluorescence in situ hybridization to assess U1 snRNA 3′-end processing and nuclear retention. To validate the functional consequences of Integrator deficiency in vivo, we generated and characterized an ints11 knockout zebrafish model.

Results

We identified novel biallelic variants in INTS11 and BRAT1 in individuals with overlapping neurodevelopmental features. While defective snRNA processing is anticipated in INTS11 deficiency, this study provides the first direct demonstration of impaired U1 snRNA processing across multiple INTS11-mutated patient cells. Critically, we show that BRAT1 mutations also compromise U1 snRNA 3′-end processing, leading to nuclear accumulation of unprocessed transcripts. These findings provide direct evidence of BRAT1’s role in RNA processing and establish Integrator dysfunction as a primary pathogenic mechanism in BRAT1-associated neurological disease. The magnitude of U1 snRNA misprocessing closely correlates with clinical severity across the BRAT1 cohort, highlighting its potential as a diagnostic biomarker. Consistently, the ints11 knockout zebrafish model recapitulates core patient features – including microcephaly, neurodevelopmental defects, and U snRNA processing defects – further validating the causal role of Integrator deficiency in vivo.

Conclusions

Our results redefine BRAT1-associated neurological disorders as Integrator-related diseases driven by RNA processing defects. Nuclear accumulation of unprocessed U1 snRNAs emerges as a robust biomarker for variant interpretation, disease severity, and patient stratification, particularly in BRAT1 cases. These findings broaden the clinical and molecular spectrum of Integrator dysfunction and provide a foundation for improved diagnostic and translational approaches.