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, associate clinical laboratory director, Omniseq/Labcorp, Buffalo, NY; and Richard Wong, MD, PhD, assistant professor of pathology, University of California San Diego.
MARK2 variants as a cause of autism spectrum disorder via downregulation of a signaling pathway
January 2025—Autism spectrum disorder is a neurodevelopmental disorder that has behavioral and social effects. Average patient age at diagnosis is approximately five years old. However, symptoms can appear within the first 12 months of life. The symptoms and severity of autism spectrum disorder (ASD) vary widely. They can include difficulty with verbal and nonverbal societal interaction, limited or repetitive behaviors, varying intellectual abilities, and emotional dysregulation. Some people with ASD have distinct facial features, such as a prominent forehead, wider set eyes, and a broad nasal root. The disorder is highly heritable, and as many as 30 percent of cases have been attributed to a Mendelian disorder. Spontaneous or de novo mutations have also been described in a smaller percentage of cases. More than 300 genes have been associated with ASD. One such gene is microtubule affinity-regulating kinase 2 (MARK2), a member of the serine/threonine kinase family that plays a role in several cellular functions in the central nervous system. Although MARK2 alterations have been described in some people with ASD, the mechanism of this pathogenesis has been largely unknown. In this investigation, the authors analyzed the potential role of MARK2 in ASD by conducting in vitro and in vivo studies. A review of a multi-institutional global cohort via the GeneMatcher data-sharing platform revealed 31 people with clinically relevant MARK2 variants. The majority of the variants were identified in the evolutionarily conserved KA1 domain and resulted in loss of function of the protein product. To explore the effect of MARK2 loss, the investigators engineered mutant human induced pluripotent stem cells (iPSCs) and heterozygous-mutated mouse models. The MARK2-mutated iPSCs demonstrated abnormal neurodevelopment in the form of cellular disorganization and decreased proliferation. The heterozygous mouse models demonstrated a reduction in social interaction and an increase in stereotyped behaviors, as well as abnormalities in spacial working memory, in comparison to their wild-type counterparts. To investigate the molecular pathway of MARK2 mutations in early pathogenesis, the authors looked for potential dysregulated genes in iPSC-derived neural progenitor cells. WNT3A, a member of the WNT signaling pathway, was found to be the most common downregulated gene, and the abnormal phenotype was reversed with exogenous administration of the protein. Activation of the WNT/β-catenin signaling pathway with a known activator, such as lithium, also reversed the abnormal phenotype. Genes within the WNT signaling pathway have been associated with ASD in previous studies. The findings of this study support the association and suggest that activation of this pathway may have therapeutic implications.
Gong M, Li J, Qin Z, et al. MARK2 variants cause autism spectrum disorder via the downregulation of WNT/β-catenin signaling pathway. Am J Hum Genet. 2024. doi.org/10.1016/j.ajhg.2024.09.006
Correspondence: Dr. Chang-Mei Liu at liuchm@ioz.ac.cn or Dr. Xiaoli Chen at xiaolichen@pumc.edu.cn
Predicting development of brain metastasis with DNA methylation signatures
Lung cancer is the leading cause of cancer-related death worldwide, with metastasis to the brain linked to poor survival outcomes. Approximately 80 to 85 percent of lung cancers are classified as nonsmall cell lung cancer (NSCLC), with lung adenocarcinoma (LUAD) being the most common form of NSCLC. More than 30 percent of LUAD progress to brain metastasis, but the medical field cannot yet reliably predict which patients have an increased risk of developing such metastases. The authors conducted a study in which they investigated DNA methylation signatures as a prospective predictor of brain metastases. Methylation is an epigenetic modification in which a methyl group is added to cytosine residues in DNA (often found at CpG islands), generally silencing gene expression. Hypermethylation and hypomethylation of CpG islands can lead to altered protein expression. Distinct methylation signatures have been explored in classifying tumors and determining tumor origin. These methylation profiles may also be promising for making early diagnoses and determining progression and treatment. For this study, the authors compiled a data set of tissue and plasma samples, including paired tissue samples between the primary site and brain metastasis, for 346 patients. Clinical information, including stage and outcome, was available for 166 primary LUAD tumors. The methylation profiles, focusing on 5,553 methylated CpG sites, compared LUAD in patients with progression to brain metastasis to LUAD in those without such progression. The differences in the methylation landscape were used to establish a methylome-based predictor of developing brain metastases within five years of primary diagnosis. When applied to a validation cohort, the accuracy of this predictor was found to exceed that of an equivalent stage-based predictor. Plasma methylation signatures were also evaluated in confirmed cases of brain metastasis. The methylation signatures between paired plasma and tissue samples correlated well, suggesting a noninvasive way to differentiate brain metastases from other brain lesions. Further exploration into the distinctive methylated sites in brain metastasis samples revealed that these sites tended to be at the promoter region of genes involved in immunity and cellular interaction. The investigators also noted that many immune cell types were differentially abundant between brain metastases and LUAD primary, which could be explored in future studies of potential treatment targets. Differences in copy number alterations were also considered to be possible predictors of brain metastases independent of the methylation profile. Samples that showed development of brain metastases exhibited deletions at chromosomes 7q, 8p, 9, 10, 12–16, and 22q, as well as focal deletions of GLI2 and FGFR1. These samples also tended to have amplification of NF1 and KDM2A. ALK deletion and STK11 amplification were observed less often than in primary site LUAD. None of the copy number alterations were found to be independently prognostic. As understanding of the genetic complexity of tumor pathogenesis improves, the chemical modification of DNA may be a useful prognostic indicator and enable early intervention to improve overall patient outcomes.
Zuccato JA, Mamatjan Y, Nassiri F, et al. Prediction of brain metastasis development with DNA methylation signatures. Nat Med. 2024. doi.org/10.1038/s41591-024-03286-y
Correspondence: Dr. Vikas Patil at vikas.patil@uhn.ca or Dr. Gelareh Zadeh at gelareh.zadeh@uhn.ca