Encephalitis and poor neuronal death-mediated control of herpes simplex virus in human inherited RIPK3 deficiency

Inborn errors of TLR3-dependent type I IFN immunity in cortical neurons underlie forebrain herpes simplex virus-1 (HSV-1) encephalitis (HSE) due to uncontrolled viral growth and subsequent cell death. We report an otherwise healthy patient with HSE who was compound heterozygous for nonsense (R422*) and frameshift (P493fs9*) RIPK3 variants. Receptor-interacting protein kinase 3 (RIPK3) is a ubiquitous cytoplasmic kinase regulating cell death outcomes, including apoptosis and necroptosis. In vitro, the R422* and P493fs9* RIPK3 proteins impaired cellular apoptosis and necroptosis upon TLR3, TLR4, or TNFR1 stimulation and ZBP1/DAI-mediated necroptotic cell death after HSV-1 infection. The patient's fibroblasts displayed no detectable RIPK3 expression. After TNFR1 or TLR3 stimulation, the patient's cells did not undergo apoptosis or necroptosis. After HSV-1 infection, the cells supported excessive viral growth despite normal induction of antiviral IFN-β and IFN-stimulated genes (ISGs). This phenotype was, nevertheless, rescued by application of exogenous type I IFN. The patient's human pluripotent stem cell (hPSC)-derived cortical neurons displayed impaired cell death and enhanced viral growth after HSV-1 infection, as did isogenic RIPK3-knockout hPSC-derived cortical neurons. Inherited RIPK3 deficiency therefore confers a predisposition to HSE by impairing the cell death-dependent control of HSV-1 in cortical neurons but not their production of or response to type I IFNs.

Abstract 946: Utility of intestinal organoids to model serrated colon cancer in vitro

Serrated colorectal cancer (CRC) is an aggressive and treatment-resistant form of colorectal carcinogenesis that accounts for one-fourth of the patients with CRC1. At the molecular level, serrated CRC is characterized by epigenetic modifications termed the CpG Island Methylator Phenotype (CIMP) and the presence of somatic mutations that activate the mitogen-activated protein kinase (MAPK) pathway1,2,3. The BRAFV600E is an early genetic change in serrated polyps, but it is not sufficient to drive tumor formation. Combinations of mutations and epigenetic modifications in P16INK4A, MLH1, ZNFR3, RNF43, and TGFBR2 are often seen in most patients4. Therefore, a combinatorial approach to develop BrafV600E-driven serrated CRC organoids harboring a variety of the above mutants will enable in vitro studies of the tumorigenic potential of each combination as well as allow engraftment into animals. In turn, the latter will allow for applying preclinical in-vivo pharmacology modalities in vitro, thereby bypassing the time required to create a specific knock-in/out strain for each genetic modification desired. Here, we describe a pipeline to directly genetically manipulate specific organoid systems in vitro. We first established organoid cultures from the small and large intestine of unique Tet-inducible RNAi mice where efficient gene knock-down can contribute to microsatellite instability. Using CRISPR/Cas9, we then edited these to generate CRC organoid models containing the BrafV600E mutation in combination with knock outs or knock-ins of cell cycle regulators and negative regulators of the Wnt pathway. These deficiencies mimic the progressive mutational changes upon acquisition BrafV600E. Our data lay the groundwork for future use of RNAi technology in combination with sequential gene editing for in vitro pharmacology and modeling diseases with complex genetic architecture both in vitro and in vivo.

Citation Format: Prem K. Premsrirut, Huaien Wang, Eduardo J. Garcia Reino, Isabella Breen, Ana A. Vasileva. Utility of intestinal organoids to model serrated colon cancer in vitro [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 946.

Herpes simplex encephalitis in a patient with a distinctive form of inherited IFNAR1 deficiency

Inborn errors of TLR3-dependent IFN-α/β- and IFN-λ-mediated immunity in the CNS can underlie herpes simplex virus 1 (HSV-1) encephalitis (HSE). The respective contributions of IFN-α/β and IFN-λ are unknown. We report a child homozygous for a genomic deletion of the entire coding sequence and part of the 3'-UTR of the last exon of IFNAR1, who died of HSE at the age of 2 years. An older cousin died following vaccination against measles, mumps, and rubella at 12 months of age, and another 17-year-old cousin homozygous for the same variant has had other, less severe, viral illnesses. The encoded IFNAR1 protein is expressed on the cell surface but is truncated and cannot interact with the tyrosine kinase TYK2. The patient's fibroblasts and EBV-B cells did not respond to IFN-α2b or IFN-β, in terms of STAT1, STAT2, and STAT3 phosphorylation or the genome-wide induction of IFN-stimulated genes. The patient's fibroblasts were susceptible to viruses, including HSV-1, even in the presence of exogenous IFN-α2b or IFN-β. HSE is therefore a consequence of inherited complete IFNAR1 deficiency. This viral disease occurred in natural conditions, unlike those previously reported in other patients with IFNAR1 or IFNAR2 deficiency. This experiment of nature indicates that IFN-α/β are essential for anti-HSV-1 immunity in the CNS.

Inborn Errors of RNA Lariat Metabolism in Humans with Brainstem Viral Infection

Viruses that are typically benign sometimes invade the brainstem in otherwise healthy children. We report bi-allelic DBR1 mutations in unrelated patients from different ethnicities, each of whom had brainstem infection due to herpes simplex virus 1 (HSV1), influenza virus, or norovirus. DBR1 encodes the only known RNA lariat debranching enzyme. We show that DBR1 expression is ubiquitous, but strongest in the spinal cord and brainstem. We also show that all DBR1 mutant alleles are severely hypomorphic, in terms of expression and function. The fibroblasts of DBR1-mutated patients contain higher RNA lariat levels than control cells, this difference becoming even more marked during HSV1 infection. Finally, we show that the patients' fibroblasts are highly susceptible to HSV1. RNA lariat accumulation and viral susceptibility are rescued by wild-type DBR1. Autosomal recessive, partial DBR1 deficiency underlies viral infection of the brainstem in humans through the disruption of tissue-specific and cell-intrinsic immunity to viruses.