Editors: Donna E. Hansel, MD, PhD, division head of pathology and laboratory medicine, MD Anderson Cancer Center, Houston; James Solomon, MD, PhD, assistant professor, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York; Erica Reinig, MD, assistant professor and medical director of molecular diagnostics, University of Wisconsin-Madison; Marcela Riveros Angel, MD, molecular genetic pathology fellow, Department of Pathology, Oregon Health and Science University, Portland; Maedeh Mohebnasab, MD, assistant professor of pathology, University of Pittsburgh; Alicia Dillard, MD, clinical pathology chief resident, New York-Presbyterian/Weill Cornell Medical Center; and Richard Wong, MD, PhD, assistant professor of pathology, University of California San Diego.
Mutations in the RNU4-2 gene: cause of a prevalent monogenic neurodevelopmental disorder
November 2024—Many people with an intellectual disability do not receive a molecular diagnosis following genetic testing. While 1,427 genes have been confidently identified as etiological for an intellectual disability (ID), all but nine of them are protein coding. To identify noncoding etiologies of ID, the authors conducted a genetic association analysis using whole genome sequencing data on 77,539 participants in the 100,000 Genomes Project. The study included 29,741 probands and 4,782 affected relatives assigned by expert clinicians to one or more of 220 specific disease classes encompassing a wide range of pathologies. The authors built a database of genotypes and phenotypes and compared rare variant genotypes in 41,132 noncoding genes between 5,529 unrelated cases assigned to the specific disease class “ID” and 46,401 unrelated participants outside of that class. They identified an extremely strong dominant association between rare variants in the RNU4-2 gene and risk of ID. (RNU4-2 is one of the genes that encodes the U4 small nuclear RNA [snRNA] component of the small nuclear ribonucleoprotein U4, which is a key component of the major spliceosome involved in splicing introns from mRNA.) The association was much stronger than that for any other noncoding gene. Three variants in RNU4-2, observed among 34 cases of ID, were computationally determined to have a posterior probability of pathogenicity (PPP) greater than 0.5. None of these 34 cases had other explanatory pathogenic or likely pathogenic variants. Based on Human Phenotype Ontology (HPO) terms assigned to the 100,000 Genomes Project study participants, these 34 ID cases were phenotypically more homogeneous than expected by chance (P = 2.33 × 10−5, one-sided permutation test), further suggesting that the association was causal. An additional eight participants outside the specific disease class ID were also found to carry one of the three variants in RNU4-2 with a PPP greater than 0.5. Seven of these additional participants had the HPO term “neurodevelopmental abnormality” (NDA) and one had related ICD-10 codes, such as “unspecified intellectual disabilities.” No unaffected participants were found to carry the identified rare RNU4-2 variants. Analysis of published secondary structure data of the U4 snRNA revealed that some variants mapped to a quasi-pseudoknot interaction between U4 and U6 and others mapped to an interaction between U4 and U6 called stem III. The authors next examined data sets from the National Institutes of Health and Care Research BioResource for Rare Diseases, the 100,000 Genomes Project pilot project, and the United Kingdom’s Genomic Medicine Service. From these data, a further 27 probands with a rare RNU4-2 variant were identified, 26 of which had neurodevelopmental abnormality. According to the authors, none of the five snRNAs of the major spliceosome were implicated in a human disorder before this study. The study has revealed an underlying etiological mechanism of a newly described ID syndrome driven by RNU4-2.
Greene D, Thys C, Berry IR, et al. Mutations in the U4 snRNA gene RNU4-2 cause one of the most prevalent monogenic neurodevelopmental disorders. Nat Med. 2024;30(8):2165–2169.
Correspondence: Dr. Ernest Turro at ernest.turro@mssm.edu
Rapid tumor DNA analysis of CSF to accelerate treatment of CNS lymphoma
Central nervous system tumors often present with acute neurologic deficits. Unfortunately, even with the availability of relatively rapid imaging techniques, neurosurgeons must perform invasive brain biopsies to obtain a definitive diagnosis before treatment can begin. The authors recently described the clinical rationale for prospectively integrated targeted rapid genotyping of cerebrospinal fluid (CSF) and its use in evaluating 70 patients with central nervous system (CNS) lesions of unknown cause. They developed and validated a targeted rapid-sequencing (TetRS) assay to detect single-nucleotide variants in genes associated with CNS neoplasms. The targeted genes were MYD88 (p.L265P) for primary CNS lymphoma; H3F3A (p.K27M) for diffuse midline glioma; IDH2 (p.R140Q, p.R172K), IDH1 (p.R132H/C/G/S), and TERT (promotor C228T and C250T) for gliomas/glioblastomas; and BRAF (p.V600E/K) for melanoma and other cancers. For the current study, the authors prospectively implemented rapid genotyping of CSF-derived DNA in suspected CNS neoplasms and assessed the impact of this approach on diagnosis and treatment. They first detailed the diverse diagnoses and historical variability in diagnostic trajectories among patients with newly suspected neoplasms at their institution. They found that empiric treatment regimens were started in 40 of 62 (64.5 percent) patients despite ongoing workup and that the median time to diagnosis was nine days. The authors then reviewed genotyping findings alongside clinical trajectories to determine whether detection of variants in the TetRS panel from CSF could have facilitated earlier diagnosis or treatment. After taking into account variant frequency and lumbar puncture eligibility, they found that CSF genotyping was potentially beneficial for facilitating diagnosis or treatment in 38 of 72 (52.8 percent) patients, including 25 of 51 (49.0 percent) with primary CNS lymphoma and 13 of 21 (61.9 percent) with other nonlymphoma neoplasms. Next, the authors used the TetRS assay to prospectively evaluate hospitalized patients with new CNS lesions of unknown cause for which neoplasm was suspected. In a cohort of 70 patients, TetRS shortened turnaround time for obtaining diagnostic information to a median of 0.5 days versus 25 (11 to 34) days for conventional assays. TetRS identified a mutation in 14 of 33 (42.4 percent) patients who were ultimately diagnosed with a neoplasm. In six of the 33 (18 percent) patients, diagnoses were secured by TetRS results alone. TetRS influenced adjuvant treatment initiation in nine of 14 (64.3 percent) cases in which a mutation was prospectively detected in the rapid genotyping cohort. TetRS results eliminated the need for biopsy in seven of the 14 (50 percent) cases following tumor board discussion and shared decision-making. The authors acknowledged that information from the TetRS assay could not be used to subtype lymphomas or gliomas but could be used to rapidly and cost-effectively narrow and focus the differential diagnosis and guide surgical decision-making about obtaining biopsies versus resections. While larger studies are needed to determine the clinical impact and wider applicability of this type of evaluation, the authors have shown that a rapid targeted panel such as TetRS demonstrates clinical utility in the diagnostic workup of CNS neoplasms.
Gupta M, Bradley JD, Massaad E, et al. Rapid tumor DNA analysis of cerebrospinal fluid accelerates treatment of central nervous system lymphoma. Blood. 2024;144(10):1093–1100.
Correspondence: Dr. Ganesh M. Shankar at gshankar@mgh.harvard.edu