Faculty Bibliography

Germline variants that disrupt components of the epigenetic machinery cause syndromic neurodevelopmental disorders. Using exome and genome sequencing, we identified de novo variants in KDM2A, a lysine demethylase crucial for embryonic development, in 18 individuals with developmental delays and/or intellectual disabilities. The severity ranged from learning disabilities to severe intellectual disability. Other core symptoms included feeding difficulties; growth issues, such as intrauterine growth restriction, short stature, and microcephaly; and recurrent facial features, such as epicanthic folds, upslanted palpebral fissures, thin vermillion of the lips, and low-set ears. Expression of human disease-causing KDM2A variants in a Drosophila melanogaster model led to neural degeneration, motor defects, and reduced lifespan. Interestingly, pathogenic variants in KDM2A affected physiological attributes, including subcellular distribution, expression, and stability in human cells. Genetic epistasis experiments indicated that KDM2A variants act via a dual mechanism-loss of nuclear function for some variants tested and additional cytoplasmic gain-of-function toxicity for c.704C>T (p.Pro235Leu), as eliminating endogenous Drosophila Kdm2 did not produce noticeable neurodevelopmental phenotypes. Data from enzymatic-methylation sequencing support the suggested gene-disease association by showing aberrant methylome profiles in affected individuals' peripheral blood. Combining our genetic, phenotypic, and functional findings, we establish de novo variants in KDM2A as causative for a syndromic neurodevelopmental disorder.

Neurodevelopmental proteasomopathies are a group of disorders caused by variants in proteasome subunit genes, that disrupt protein homeostasis and brain development through poorly characterized mechanisms. Here, we report 26 distinct variants in PSMC5, encoding the AAA⁺ ATPase subunit PSMC5/RPT6, in individuals with syndromic neurodevelopmental conditions. Combining genetic, multi-omics and biochemical approaches across cellular models and Drosophila, we unveil the essential role of proteasomes in sustaining key cellular processes. Loss of PSMC5/RPT6 function impairs proteasome activity, leading to protein aggregation, disruption of mitochondrial homeostasis, and dysregulation of lipid metabolism and immune signaling. It also compromises synaptic balance, neuritogenesis, and neural progenitor cell stemness, causing deficits in higher-order functions, including learning and locomotion. Pharmacological targeting of integrated stress response kinases reveals a mechanistic link between proteotoxic stress and spontaneous type I interferon activation. These findings expand our understanding of proteasome-dependent quality control in neurodevelopment and suggest potential therapeutic strategies for neurodevelopmental proteasomopathies.

IMPORTANCE/UNASSIGNED:Incomplete electronic health record (EHR) documentation may limit the effectiveness of clinical decision support (CDS) algorithms designed to identify patients eligible for hereditary cancer genetic evaluation. OBJECTIVES/UNASSIGNED:To determine whether a CDS algorithm can identify patients who meet criteria for hereditary cancer genetic evaluation when family history data are incompletely documented in the EHR, and to examine whether data missingness is associated with identification patterns across patient subgroups. DESIGN, SETTING, AND PARTICIPANTS/UNASSIGNED:This cross-sectional study analyzed EHR data extracted in December 2020 from 2 large US health care systems: University of Utah Health (UHealth) and NYU Langone Health (NYULH). Eligible patients were adults aged 25 to 60 years who visited a primary care clinic within the previous 3 years and had some EHR documentation of cancer family history. Data analysis was conducted in August 2024. EXPOSURES/UNASSIGNED:Patient demographic factors (age, sex, race and ethnicity, and language preference) and cancer family history characteristics (number of cancer history records, number of affected first- and second-degree relatives, relatives with rising mortality cancers, presence of hereditary cancer-related terms in comments, and completeness of documentation). MAIN OUTCOMES AND MEASURES/UNASSIGNED:The primary outcome was meeting at least 1 CDS algorithm criterion for genetic evaluation of hereditary cancer risk based on National Comprehensive Cancer Network guidelines. Missing data patterns were assessed using the Little missing completely at random test, with analyses conducted using complete case analysis and multiple imputation. RESULTS/UNASSIGNED:This study included 157 207 patients: 55 918 from UHealth and 101 289 from NYULH. Their mean (SD) age was 43.5 (9.8) years, and most (65.7%) were female. A total of 5607 UHealth patients (10.0%) and 10 375 NYULH patients (10.2%) met CDS criteria for genetic evaluation. At UHealth, data appeared to be missing completely at random (χ239 = 39.09; P = .47), and complete case compared with multiple imputation analyses yielded similar results. At NYULH, data were not missing completely at random (χ255 = 914.89; P < .001). Compared with multiple imputation, complete case analysis produced different association magnitudes for older age and having relatives with rising mortality cancers, suggesting bias when excluding incomplete records. CONCLUSIONS AND RELEVANCE/UNASSIGNED:In this cross-sectional study, the magnitude of the association between incomplete family history documentation and identification of patients eligible for hereditary cancer genetic evaluation depended on whether data were missing randomly or systematically. These findings suggest that health care organizations implementing CDS algorithms should assess their specific missing data patterns and consider tailored approaches to handling incomplete family history information to ensure equitable identification of all patients who could benefit from genetic evaluation services.

BACKGROUND:Among the alternative solutions being tested to improve access to genetic services, chatbots (or conversational agents) are being increasingly used for service delivery. Despite the growing number of studies on the accessibility and feasibility of chatbot genetic service delivery, limited attention has been paid to user interactions with chatbots in a real-world health care context. OBJECTIVE:We examined users' interaction patterns with a pretest cancer genetics education chatbot as well as the associations between users' clinical and sociodemographic characteristics, chatbot interaction patterns, and genetic testing decisions. METHODS:We analyzed data from the experimental arm of Broadening the Reach, Impact, and Delivery of Genetic Services, a multisite genetic services pragmatic trial in which participants eligible for hereditary cancer genetic testing based on family history were randomized to receive a chatbot intervention or standard care. In the experimental chatbot arm, participants were offered access to core educational content delivered by the chatbot with the option to select up to 9 supplementary informational prompts and ask open-ended questions. We computed descriptive statistics for the following interaction patterns: prompt selections, open-ended questions, completion status, dropout points, and postchat decisions regarding genetic testing. Logistic regression models were used to examine the relationships between clinical and sociodemographic factors and chatbot interaction variables, examining how these factors affected genetic testing decisions. RESULTS:Of the 468 participants who initiated a chat, 391 (83.5%) completed it, with 315 (80.6%) of the completers expressing a willingness to pursue genetic testing. Of the 391 completers, 336 (85.9%) selected at least one informational prompt, 41 (10.5%) asked open-ended questions, and 3 (0.8%) opted for extra examples of risk information. Of the 77 noncompleters, 57 (74%) dropped out before accessing any informational content. Interaction patterns were not associated with clinical and sociodemographic factors except for prompt selection (varied by study site) and completion status (varied by family cancer history type). Participants who selected ≥3 prompts (odds ratio 0.33, 95% CI 0.12-0.91; P=.03) or asked open-ended questions (odds ratio 0.46, 95% CI 0.22-0.96; P=.04) were less likely to opt for genetic testing. CONCLUSIONS:Findings highlight the chatbot's effectiveness in engaging users and its high acceptability, with most participants completing the chat, opting for additional information, and showing a high willingness to pursue genetic testing. Sociodemographic factors were not associated with interaction patterns, potentially indicating the chatbot's scalability across diverse populations provided they have internet access. Future efforts should address the concerns of users with high information needs and integrate them into chatbot design to better support informed genetic decision-making.

PURPOSE/OBJECTIVE:XPO1 functions in key cellular processes, including nucleo-cytoplasmic export and mitosis. The gene is deleted in a subset of patients with the 2p15p16.1 microdeletion syndrome, however no monogenic XPO1-related disorder has been described to date. MATERIALS AND METHODS/METHODS:We collected clinical data of individuals with de novo XPO1 variants through online matchmaking. We employed Drosophila to study XPO1 function in development and habituation learning. RESULTS:A total of 22 individuals met the criteria to be included in the main study cohort. Of these, half have putative loss-of-function variants and half have coding variants (10 missense and 1 in-frame deletion variant). We find an overlapping phenotype, consistent with a monogenic neurodevelopmental disorder (NDD). We demonstrate XPO1 functions in development by ubiquitous and neuron-specific knockdown in Drosophila. GABAergic neuron specific knockdown flies demonstrated impaired habituation. CONCLUSION/CONCLUSIONS:Our results establish XPO1 as a novel dominant monogenic NDD gene and demonstrate a central role for XPO1 in development.

OBJECTIVE:To examine whether patient sociodemographic and clinical characteristics and prior interactions with the healthcare system were associated with opening patient portal messages related to cancer genetic services and beginning services. STUDY SETTING AND DESIGN/METHODS:The trial was conducted in the University of Utah Health (UHealth) and NYU Langone Health (NYULH) systems. Between 2020 and 2023, 3073 eligible primary care patients aged 25-60 years meeting family history-based criteria for cancer genetic evaluation were randomized 1:1 to receive a patient portal message with a hyperlink to a pretest genetics education chatbot or information about scheduling a pretest standard of care (SOC) appointment. DATA SOURCES AND ANALYTIC SAMPLE/UNASSIGNED:Primary data were collected. Eligible patients had a primary care visit in the previous 3 years, a patient portal account, no prior cancer diagnosis except nonmelanoma skin cancer, no prior cancer genetic services, and English or Spanish as their preferred language. Multivariable models identified predictors of opening patient portal messages by site and beginning pretest genetic services by site and experimental condition. PRINCIPAL FINDINGS/RESULTS:Number of previous patient portal logins (UHealth average marginal effect [AME]: 0.32; 95% CI: 0.27, 0.38; NYULH AME: 0.33; 95% CI: 0.27, 0.39), having a recorded primary care provider (NYULH AME: 0.15; 95% CI: 0.08, 0.22), and more primary care visits in the previous 3 years (NYULH AME: 0.09; 95% CI: 0.02, 0.16) were associated with opening patient portal messages about genetic services. Number of previous patient portal logins (UHealth AME: 0.14; 95% CI: 0.08, 0.21; NYULH AME: 0.18; 95% CI: 0.12, 0.23), having a recorded primary care provider (NYULH AME: 0.08; 95% CI: 0.01, 0.14), and more primary care visits in the previous 3 years (NYULH AME: 0.07; 95% CI: 0.01, 0.13) were associated with beginning pretest genetic services. Patient sociodemographic and clinical characteristics were not significantly associated with either outcome. CONCLUSIONS:As system-level initiatives aim to reach patients eligible for cancer genetic services, patients already interacting with the healthcare system may be most likely to respond. Addressing barriers to accessing healthcare and technology may increase engagement with genetic services.

Fanconi anemia (FA) is a rare genetic disease characterized by loss-of-function variants in any of the 22 previously identified genes (FANCA-FANCW) that encode proteins participating in the repair of DNA interstrand crosslinks (ICLs). Patient phenotypes are variable, but may include developmental abnormalities, early onset pancytopenia, and predisposition to hematologic and solid tumors. Here, we describe two unrelated families with multiple pregnancy losses and offspring presenting with severe developmental and hematologic abnormalities leading to death in utero or in early life. Homozygous loss-of-function variants in FAAP100 were identified in affected children of both families. The FAAP100 protein associates with FANCB and FANCL, the E3 ubiquitin ligase responsible for the monoubiquitination of FANCD2 and FANCI, which is necessary for FA pathway function. Patient-derived cells exhibited phenotypes consistent with FA. Expression of the wild-type FAAP100 cDNA, but not the patient-derived variants, rescued the observed cellular phenotypes. This establishes FAAP100 deficiency as a cause of Fanconi anemia, with FAAP100 gaining an alias as FANCX. The extensive developmental malformations of individuals with FAAP100 loss-of-function variants are among the most severe across previously described FA phenotypes, indicating that the FA pathway is essential for human development.

Pathogenic variants resulting in protein phosphatase 2A (PP2A) dysfunction result in mild to severe neurodevelopmental delay. PP2A is a trimer of a catalytic (C) subunit, scaffolding (A) subunit, and substrate binding/regulatory (B) subunit, encoded by 19 different genes. De novo missense variants in PPP2R5D (B56δ) or PPP2R1A (Aα) and de novo missense and loss-of-function variants in PPP2CA (Cα) lead to syndromes with overlapping phenotypic features, known as Houge-Janssens syndrome (HJS) types 1, 2, and 3, respectively. Here, we describe an additional condition in the HJS spectrum in 26 individuals with variants in PPP2R5C, encoding the regulatory B56γ subunit. Most changes were de novo and of the missense type. The clinical features were well within the HJS spectrum with strongest resemblance to HJS type 1, caused by B56δ variants. Common features were neurodevelopmental delay and hypotonia, with a high risk of epilepsy, behavioral problems, and mildly dysmorphic facial features. Head circumferences were above average or macrocephalic. The degree of intellectual disability was, on average, milder than in other HJS types. All variants affected either substrate binding (2/19), C-subunit binding (2/19), or both (15/19). Five variants were recurrent. Catalytic activity of the phosphatase was variably affected by the variants. Of note, PPP2R5C total loss-of-function variants could be inherited from a non-symptomatic parent. This implies that a dominant-negative mechanism on substrate dephosphorylation or general PP2A function is the most likely pathogenic mechanism.

BCL11B is a Cys2-His2 zinc-finger (C2H2-ZnF) domain-containing, DNA-binding, transcription factor with established roles in the development of various organs and tissues, primarily the immune and nervous systems. BCL11B germline variants have been associated with a variety of developmental syndromes. However, genotype-phenotype correlations along with pathophysiologic mechanisms of selected variants mostly remain elusive. To dissect these, we performed genotype-phenotype correlations of 92 affected individuals harboring a pathogenic or likely pathogenic BCL11B variant, followed by immune phenotyping, analysis of chromatin immunoprecipitation DNA-sequencing data, dual-luciferase reporter assays, and molecular modeling. These integrative analyses enabled us to define three clinical subtypes of BCL11B-related disorders. It is likely that gene-disruptive BCL11B variants and missense variants affecting zinc-binding cysteine and histidine residues cause mild to moderate neurodevelopmental delay with increased propensity for behavioral and dental anomalies, allergies and asthma, and reduced type 2 innate lymphoid cells. Missense variants within C2H2-ZnF DNA-contacting α helices cause highly variable clinical presentations ranging from multisystem anomalies with demise in the first years of life to late-onset, hyperkinetic movement disorder with poor fine motor skills. Those not in direct DNA contact cause a milder phenotype through reduced, target-specific transcriptional activity. However, missense variants affecting C2H2-ZnFs, DNA binding, and "specificity residues" impair BCL11B transcriptional activity in a target-specific, dominant-negative manner along with aberrant regulation of alternative DNA targets, resulting in more severe and unpredictable clinical outcomes. Taken together, we suggest that the phenotypic severity and variability is largely dependent on the DNA-binding affinity and specificity of altered BCL11B proteins.

INTRODUCTION/BACKGROUND:Heterozygous pathogenic variants in NTRK2 (HGNC: 8032) have been associated with global developmental delay. However, only scattered cases have been described in small or general studies. The aim of our work was to consolidate our understanding of NTRK2-related disorders and to delineate the clinical presentation METHODS: We report extended cohort of 44 affected individuals, of whom 19 are from the literature and 25 were previously unreported. RESULTS:Our analysis led to splitting the cohort into two entities. DISCUSSION/CONCLUSIONS:One group had variants in the cholesterol binding motif of the transmembrane domain, with most of these being the recurrent variant c.1301A>G p.(Tyr434Cys). These variants probably lead to upregulation of TRKB activity and to a severe phenotype of developmental delay/intellectual disability, muscular hypotonia, therapy-refractory epilepsy, visual impairment and blindness, and feeding difficulties. The second group had truncating variants or variants that presumably disturb the 3D structure of the protein leading to loss of function. These individuals had a remarkably milder phenotype of developmental delay, obesity and hyperphagia.