Introduction

Approximately 1-2% of the global population is affected by intellectual disability (ID), representing a serious medical, social and economic problem. The clinical symptoms and aetiology of ID are highly heterogeneous, making diagnosis and treatment of the disease difficult. X-linked ID caused by UPF3B mutations is well-suited for more detailed investigation due to its clearly defined genetic cause. In this project, we will study the function of UPF3B to better understand the development of ID.
Normal brain development depends on the precise operation of molecular programs that lead to proliferation, migration, and maturation of neuronal and glial cells. Alterations in these programs and processes can impair the development of the brain and lead to intellectual disability. A varying proportion of intellectual disability cases (15% to 50%) is caused by genetic factors, such as mutations in certain genes.
Several mutations in the gene encoding UPF3B have been identified as the cause of syndromic and non-syndromic forms of X-linked intellectual disability in more than 10 families. The identified mutations include missense, frameshift and nonsense mutations presumably leading to a loss of UPF3B function. Some UPF3B patients show additional disease states, including schizophrenia, autism and attention deficit hyperactivity disorder. Thus, the UPF3B protein is crucial for normal brain development and functions by a yet unknown mechanism.
Here, we propose to dissect the mechanism of X-linked intellectual disability caused by UPF3B mutations. To gain insights into the molecular function of UPF3B, we will mutate UPF3B in cultured cells by CRISPR/Cas9 and analyse the molecular effects using different high-throughput analyses.

Our Aims

  1. to generate UPF3B-deficient human neuronal cells 
  2. to identify cellular mRNAs regulated by UPF3B
  3. to determine the impact of UPF3B on human brain development

Outcome of current funding period

In the current funding period we wanted to gain insights into the molecular functions of UPF3B and why mutations in the encoding gene result in neurological phenotypes. We first set out to characterize the functional impact on human cells when UPF3B is downregulated or missing. This task was challenging due to the fact that mammalian cells express a paralog of UPF3B, named UPF3A, which shows significant sequence similarity to UPF3B. In patients with mutated UPF3B, it was shown that the protein levels of UPF3A correlate negatively with the severity of the patient’s phenotype. This indicated a certain “back-up ability” of UPF3A, suggesting at least partial functional redundancy between both paralogs.
However, UPF3A was also reported to be an antagonist of UPF3B in the nonsense-mediated mRNA decay (NMD) pathway. Therefore, it remained to be determined to which extent UPF3A and UPF3B act redundantly or inhibit each other in human cells. To address these contradicting theories, we used different approaches (e.g. CRISPR-Cas9) to manipulate UPF3A and UPF3B expression levels and analyzed the interplay between both paralogs. In contrast to the reported NMD-inhibiting role, we found that UPF3A can actually functionally compensate the absence of its paralog UPF3B. Neither the single knockout of UPF3A nor UPF3B substantially altered the expression of NMD substrates, only co-depletion of the two paralogs resulted in a marked NMD inhibition.
These results support redundant functions of UPF3A and UPF3B.
Further experiments regarding the different domains of UPF3B revealed that UPF3 is not only fault-tolerant due to the redundant paralogs, but also because mutation of a single domain does not inactivate the protein (Figure 1). We published the results earlier this year in the EMBO Journal (Wallmeroth et al., 2022)

Figure 1

Fig. 1: Schematic representation of the UPF3 paralogs in the NMD machinery. UPF3A and UPF3B were characterized as redundant NMD activators. The fault-tolerance is ensured by their general functional redundancy and the tolerance of inactivation of single functional domains.

In addition to the function of UPF3 in NMD, we aimed to investigate the role of UPF3B in neuronal cells. We proposed to use SH-SY5Y cells, but they turned out to be non-optimal for the planned experimental approaches. Therefore, we concentrated our efforts directly on the work with human induced pluripotent stem cells (hiPSCs). Despite supply shortage and other obstacles, we set up a stem-cell suitable cell culture and were able to successfully differentiate the hiPSCs into cerebral organoids (Figure 2). First experiments with a new pharmacological NMD inhibitor showed encouraging results, indicating that this system has great potential for future research.

Figure 2

Fig. 2: Representative images of the formation, expansion and maturation of brain organoids generated in the Gehring lab.

Outlook

In the following weeks and months, we will analyze these wild-type cerebral organoids for general properties and start the generation of UPF3B-KO hiPSCs using the CRISPaint system. The deeper analyses like single cell RNA-seq to e.g. identify cell types that are most severely affected have to be carried out in a later project. Furthermore, we decided to broaden the investigation to global NMD in human cerebral organoid formation. We will modulate NMD activity in either direction (inhibition or hyperactivity) at different timepoints during organoid maturation (Figure 3). The results will provide important information about the relevance of NMD in brain development.

Figure 3

Fig. 3: Schematic overview of the proposed project. To enlighten the connection between NMD and brain disorders, we aim to manipulate NMD levels in hiPSCs, differentiate them into neuronal cells and cerebral organoids and analyze them in detail. This will provide insights into the aforementioned connection.
  • Gehring NH, Neu-Yilik G, Schell T, Hentze MW, Kulozik AE (2003) Y14 and hUpf3b form an NMD-activating complex. Mol Cell 11: 939-49
  • Kunz JB, Neu-Yilik G, Hentze MW, Kulozik AE, Gehring NH (2006) Functions of hUpf3a and hUpf3b in nonsense-mediated mRNA decay and translation. RNA 12: 1015-22
  • Boehm V, Haberman N, Ottens F, Ule J, Gehring NH (2014) 3' UTR length and messenger ribonucleoprotein composition determine endocleavage efficiencies at termination codons. Cell Rep 9: 555-68
  • Linder B, Fischer U, Gehring NH (2015) mRNA metabolism and neuronal disease. FEBS Lett 589: 1598-606
  • Gerbracht JV, Gehring NH (2018) The exon junction complex: structural insights into a faithful companion of mammalian mRNPs. Biochem Soc Trans 46: 153-161
  • Wallmeroth D, Lackmann JW, Kueckelmann S, Altmüller J, Dieterich C, Boehm V, Gehring NH (2022). Human UPF3A and UPF3B enable fault-tolerant activation of nonsense-mediated mRNA decay. EMBO J., e109191. doi: 10.15252/embj.2021109191. Online ahead of print. PMID: 35451084.
  • Schlautmann LP, Lackmann JW, Altmuller J, Dieterich C, Boehm V, and Gehring NH (2022). Exon junction complex-associated multi-adapter RNPS1 nucleates splicing regulatory complexes to maintain transcriptome surveillance. Nucleic Acids Res50, 5899-5918. doi:10.1093/nar/gkac428.
  • Boehm V, Kueckelmann S, Gerbracht JV, Kallabis S, Britto-Borges T, Altmuller J, Kruger M, Dieterich C, and Gehring NH (2021). SMG5-SMG7 authorize nonsense-mediated mRNA decay by enabling SMG6 endonucleolytic activity. Nat Commun12, 3965. doi:10.1038/s41467-021-24046-3.
                                                      • Erkelenz S, Stankovic D, Mundorf J, Bresser T, Claudius AK, Boehm V, Gehring NH, and Uhlirova M (2021). Ecd promotes U5 snRNP maturation and Prp8 stability. Nucleic Acids Res49, 1688-1707. doi:10.1093/nar/gkaa1274.
                                                      • Gehring NH, and Roignant JY (2021). Anything but Ordinary - Emerging Splicing Mechanisms in Eukaryotic Gene Regulation. Trends Genet37, 355-372. doi:10.1016/j.tig.2020.10.008.
                                                      • Wang Q, Boenigk S, Boehm V, Gehring NH, Altmueller J, Dieterich C. (2021) Single cell transcriptome sequencing on the Nanopore platform with ScNapBar. RNA. 2021 Apr 27;27(7):763-70. doi: 10.1261/rna.078154.120.
                                                      • Gerbracht JV, Boehm V, Britto-Borges T, Kallabis S, Wiederstein JL, Ciriello S, Aschemeier DU, Kruger M, Frese CK, Altmuller J, Dieterich C, and Gehring NH (2020). CASC3 promotes transcriptome-wide activation of nonsense-mediated decay by the exon junction complex. Nucleic acids research 48, 8626-44.
                                                      Prof. Dr. Niels Gehring
                                                      Prof. Dr. Niels Gehring

                                                      Institute for Genetics, Department of Biology

                                                      CMMC - PI - C 05

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