Children'S Hosp Of Philadelphia

NIH Research Projects · FY 2024 · 2020-06

Abstract This proposal tackles an urgent need for sensitive clinical outcome measures of autism spectrum disorder (ASD) by developing an objective, digital, multi-modal social communication metric using computational linguistics (e.g., acoustic features, turn-taking rates, word frequency metrics). Our automatic speech recognition and natural language analytics approach is designed to fix known weaknesses in traditional measurements by providing granular information in less time, with built-in scalability for characterizing very large samples. Since ASD is defined by observables, it is ripe for an automated approach to digitizing behavior (e.g., words, sounds, facial expressions, motor behaviors). This proposal piggybacks on a recently funded R01 that uses computer vision and machine learning to characterize nonverbal motor synchrony in teens with either ASD or another disorder in a brief social conversation (MH118327, PI: Schultz). Vocal components of the conversation are not studied in MH118327; thus, the richness of the verbal domain is left untapped. We hypothesize that automatically derived spoken language markers will significantly predict group and individual differences in social communication skill, and – when fused with nonverbal features – will lead to better prediction than either modality alone. Together, these two projects represent a rare chance to study all observable social signals emitted during social interaction in the same diverse sample of participants. If funded, this project will be the first to use short conversations and multi-modal data fusion to predict social communication skill and diagnostic group in a large, clinically diverse sample of individuals with ASD and other disorders. Our pilot studies showed that a relatively small set of vocal features from a six-minute interaction predicts diagnosis (ASD vs. typical development [TD]) with 84% accuracy. These machine learning analyses also predicted social communication skill dimensionally, providing a granular metric of individual differences. Combining this approach with nonverbal metrics (R01MH118327) using decision level data fusion resulted in significantly better ASD vs. TD prediction – 91% accuracy. These pilot results are promising, but several gaps remain. In Aim 1 of this proposal, we assess the specificity of our vocal social communication approach by including a non-ASD psychiatric control group in our machine learning classification models, in addition to ASD and TD groups (N=250/group). In Aim 2, we clinically validate our transdiagnostic dimensional metric in a large, diverse sample of participants. In Aim 3, we test whether novel, sophisticated multi-modal fusion methods that combine vocal and nonverbal social communication features result in improved individual and group prediction. This proposal lays critical groundwork for an automated, precision medicine approach to studying, diagnosing, and caring for individuals with ASD and other mental health conditions. Suc- cessful completion of this project will transform how we quantify human behavior for a broad array of applications that demand efficient, scalable, and reliable measurement (e.g., genetic association studies, clinical trials and standard clinical care), thus meeting multiple strategic priorities set by NIMH and NIDCD.

NIH Research Projects · FY 2024 · 2020-06

Project Summary Given the prevalence of crosstalk among oncogenic pathways and disease heterogeneity, it has become increasingly apparent that combination therapies are required to achieve long-term cure and to minimize development of resistance mutations and escape pathways. The majority of existing combination therapies are developed in an ad hoc fashion, namely one agent at a time, without systematic consideration of potential complex interactions among the gene targets by leveraging disease-specific omics data. Moreover, the existing combination therapies are based on targets of existing drugs, which only represent a small portion of the human proteome. To this end, we hypothesize that systematic identification of synergistic key regulators represents a promising approach for nominating targets of combination therapy. Towards this goal, we will forward engineer a platform for identifying synergistic regulatory nodes in a cancer gene regulatory network as the targets for combination therapy. We will generate disease-specific multi-omics data to construct an integrative gene regulatory network, a pre-requisite for understanding the deregulated gene network in the cancer cells and for developing effective and lasting therapy. We will focus our study on Philadelphia-like acute lymphoblastic leukemia as a proof-of-principle. Our team proposes a novel approach to this problem by leveraging the unique strengths of the investigators in systems biology, genomics, proteomics, and translational research, as well as the large cohort of patient samples available at our institutions. If successful, the proposed framework would be a tremendous advance and paradigm shift to understand genetic interactions among oncogenic pathways for eventual therapeutic intervention.

NIH Research Projects · FY 2026 · 2020-05

ABSTRACT This is an application by Mortimer Poncz, MD, for an NHLBI-supported R35 Outstanding Investigator Award (OIA). Dr. Poncz has made pioneering contributions to the field of platelet (Plt) biology. He isolated and charac- terized the first cDNAs and genes for the Plt proteins (integrin chains, aIIb and b3, and the chemokines, platelet factor 4 (PF4) and b-thromboglobulin). He characterized the first molecular defects in an inherited Plt disorder, Glanzmann thrombasthenia (GT). For over 30 years, Dr. Poncz has made insightful contributions to move the Plt field forward. He helped advance our understanding of megakaryopoiesis, defining many of the transcriptional factors (TFs) fundamental to that process and their role in inherited Plt disorders. He pioneered the use of induced pluripotent stem cells (iPSCs) to study megakaryocyte (Meg) biology and demonstrated the first strategy for genetically correcting the defect in GT and in Paris-Trousseau syndrome. Dr. Poncz proposes to pursue new insights into the molecular basis of the thrombocytopenia observed in RUNX1 haploinsufficiency, and how this intervention might decrease the risk of leukemic transformation in affected patients. This interest in megakaryopoiesis also lead to Dr. Poncz’s contribution to understanding where Plts are released, showing that infused Megs release Plts in the lungs. The resulting Plts are much more physiologic than any ex vivo-generated Plts released from in vitro-grown Megs to date. These studies supported a potential pulmonary site for a portion of thrombopoiesis with subsequent studies by others providing in situ-support for this model. Dr. Poncz now shows that the lung microcapillary bed is unique in being able to release Plts. Proposed studies will further our understanding of what makes the pulmonary bed unique for thrombopoiesis, and such insights may have clinical application in Plt transfusions. Dr. Poncz also proposed that Plts could store ectopic proteins in a granules, releasing them in a targeted, potent fashion at sites of vascular injury. He proposes advancing the use of Plt-targeted therapeutics by a novel new mechanism for loading such proteins into Plts to treat hemophilia A patients with inhibitors with Factor VIII variants and for use as a thromboprophylaxis agent with urokinase variants. Dr. Poncz has also advanced our understanding of the molecular basis of prothrombotic heparin-induced thrombocytopenia (HIT). His HIT-like antibody KKO and murine model for HIT are widely used in the field and both were used in his recent advances in understanding the role of neutrophil extracellular traps (NETs) in HIT. He now proposes that polyanions like NETs underlie the prothrombotic nature of HIT, and will test this in this R35. Moreover, he believes that these new insights have implications in the care of other thromboinflammatory diseases where NETs have an important role, and proposes use of PF4 and Fc-modified KKO in the treatment of sepsis and sickle cell disease. Support from this R35 OIA mechanism will also provide Dr. Poncz with the time to pursue his other passion of advancing the career of mentees in areas related to benign hematology.

NIH Research Projects · FY 2025 · 2020-03

SUMMARY/ABSTRACT Impaired sleep has been linked with lower bone density and increased risk of fracture in adults. However, it is not known if sleep patterns effect gains in bone density and strength during childhood. This knowledge gap needs to be addressed because bone accretion in childhood determines peak bone mass and risk of osteoporosis in later life. The long-term goal is to determine if sleep patterns predict bone density and strength during the bone accretion years of the lifespan. The overall objective of this application is to determine if sleep patterns predict changes in bone density and strength from early-to-mid adolescence. Adolescents aged 12-13y (7th grade) will be enrolled and prospectively followed-up annually for 2-years. This age range is being investigated because this is a critical period when a large proportion of peak bone mass and strength are gained, and when sleep duration tends to decline. At each time point, bone density will be measured using dual energy X-ray absorptiometry and bone strength will be measured by high resolution peripheral quantitative computed tomography. Sleep patterns will be measured by actigraphy and self-report. DNA will be collected and genotyped because bone density and strength are complex traits and genetic susceptibility to bone fragility may modify the association between sleep patterns and bone outcomes. The central hypothesis is that impaired sleep duration, timing and quality will be associated with lesser gains in bone density and strength in adolescence, with the associations stronger for those genetically predisposed to bone fragility. This hypothesis will be tested by pursuing three specific aims: 1) Determine if sleep patterns predict changes in bone density in adolescence; 2) Elucidate if bone strength changes during adolescence are influenced by sleep patterns; and 3) Investigate the combined effect of bone fragility genetic scores and sleep patterns on bone changes during adolescence. The applicants’ preliminary data among adolescents show an inverted U-shaped association between sleep duration and areal bone mineral density, and they observed that later timing of sleep onset predicted lower areal bone mineral density and lower bone strength. The investigators also demonstrated that bone fragility genetic scores associated with lower areal bone mineral density in children and adolescents, but a lifestyle factor (in this case physical activity) could help overcome the negative genetic effects. The rationale for the proposed research is the need to establish a rigorous base of epidemiological evidence supporting associations between sleep and bone outcomes, which will provide a foundation to perform intervention studies that target sleep patterns and evaluate bone accretion. The approach is innovative because sleep patterns have not yet been considered as predictors of bone mass and strength in adolescence, and advanced imaging methods will be combined with advanced growth, sleep and genetic epidemiological methods. With respect to outcomes, the investigators anticipate that they will establish sleep patterns as key predictors of bone density and strength in adolescence.

NIH Research Projects · FY 2025 · 2020-03

PROJECT SUMMARY. Primary mitochondrial diseases (PMD) are highly morbid energy deficiency disorders with remarkably heterogeneous etiologies and phenotypes across all ages and systems, caused by pathogenic variants in > 400 different genes across both nuclear and mitochondrial genomes. No cure, FDA-approved, nor clinical trial-validated therapies exist for the indication of PMD. As one-size-fits-all, single therapy is unlikely to benefit all patients, therapeutic modeling is essential to develop precision medicines that significantly improve health in distinct molecular, biochemical, and/or clinical PMD subtypes. Specifically, pre- clinical translational RC disease investigations in human patient cells and simple animal models may efficiently identify potent therapeutic leads, and specific mechanistic targets, to meaningfully improve overall cellular and organismal health. We will exploit for this purpose our unique and growing collection of ‘matched’ nuclear gene-based PMD model sets for complex I (NDUFS2, NUBPL), complex IV (SURF1), multiple respiratory chain complexes (FBXL4, C12ORF65, MT-ARS2), and interacting pathways (DLD, OPA1) in 3 evolutionarily distinct species using C. elegans (worm, invertebrate), D. rerio (zebrafish, vertebrate), and humans (derived cell lines), as well as our newer array of heteroplasmic mtDNA mutant zebrafish and cybrid cell models. Having validated many novel, in vivo approaches to quantify PMD effects on survival and diverse cellular and animal- level functions, we are strongly situated to harness this patented, multi-species preclinical modeling approach to gain further mechanistic insights and identify promising new therapeutic leads for diverse PMD subtypes and secondary mitochondrial disorders. NIGMS R35 MIRA support will enable this basic and translational research program, built over the past 18 years by an established physician-scientist research investigator who has been highly productive and provided many teaching opportunities, to continue to advance the scientific evidence base for precision mitochondrial medicine. Specifically, this translational research program will focus on harnessing PMD cells and simple animal models to investigate key questions across 2 overarching themes. Theme 1 is ‘Pathophysiology Investigations in PMD cell and animal models’, involving 2 project areas: (i) Understanding the mechanistic basis by which distinct organ pathophysiology and metabolic dysfunction predominates in different forms of PMD; and (ii) Determining which central nutrient-sensing signaling network node(s) and downstream biochemical pathways that regulate cellular proteotoxic stress underlie candidate therapies response in specific PMD subsets. Theme 2 is ‘Preclinical therapeutic discovery in PMD cell and animal models’, involving 2 project areas: (iii) Therapeutic target and compound discovery and validation in distinct PMD animal and cell translational disease variant models; and (iv) Identify whether treatments that improve health in genetic-based PMD will improve health in complex disorders with secondary forms of mitochondrial dysfunction that are chronic (eg, Down or Cockayne syndrome) or acute (toxin-induced).

NIH Research Projects · FY 2025 · 2019-10

ABSTRACT Neonatal Opioid Withdrawal Syndrome (NOWS) is a major public health problem in the USA. Since 2000- 2012, the incidence of NOWS has increased five-fold to almost 6 per 1,000 hospital births and the associated health care expenditures have increased from $200 million to $1.5 billion. Limited data are available on the effects of antenatal opioid exposure on the brain and neurodevelopment because of small sample sizes and difficulty controlling for important environmental variables. The OBOE (Outcomes of Babies with Opioid Exposure) study, an ongoing NICHD-funded longitudinal study enrolling infants with and without antenatal opioid exposure at birth and following them to two years of age, attempts to address these limitations by collecting comprehensive exposure data from parental report and from infant umbilical cord analysis; advanced neuroimaging data to evaluate brain development; standardized information on the home environment, maternal mental health, and parenting; and neuro- developmental outcomes to 2 years of age. The OBOE consortium, comprised of 4 highly performing clinical centers, a data coordinating center, and a neuroimaging core, has completed our goal enrollment of 200 opioid-exposed infants and 100 unexposed infants. In response to RFA-HD-24-014, we now propose to complete follow-up to age two years in our OBOE cohort to fulfill our main study objectives. The CHOP/PENN site has enrolled 46 infants (34 exposed and 12 controls), completing 53 MRIs across 2 timepoints thus far, contributing to the publication of multiple abstracts and three manuscripts using OBOE data, and developing the CONSENTER intervention to improve recruitment of exposed and control patients. For this renewal grant, we will continue progress toward our aims to: 1) determine the impact of antenatal opioid exposure on brain structure and connectivity over the first two years of life; 2) define medical, developmental, and behavioral trajectories over the first two years of life in exposed infants; and 3) determine how the home environment, maternal mental health, and parenting modify trajectories of brain connectivity and neurodevelopment over the first two years of life. Our progress so far, with enrollment completed and success in following this difficult population, shows that we can successfully complete the objectives of the OBOE study.

NIH Research Projects · FY 2025 · 2019-09

The Career Enhancement core is dedicated to the recruitment, support, and retention of qualified investigators and clinicians who will continue innovation in rare diseases such as the leukodystrophies. We propose formal mentorship and training opportunities in rare disease research to facilitate long-term commitment and retention. Aim 1 is to prepare pre-graduate students for a career in leukodystrophy and rare disease research. We will leverage programs supporting pre-doctoral mentorship and education: Translational Research Immersion Program (TRIP) and the leukodystrophy specific Predoctoral Preparatory Program (P3). The expected outcome of this Aim is an increased pipeline for future rare disease researchers needed to address clinical care needs in care disease. Aim 2 will be to support translational research scientist development in leukodystrophy research. Two leukodystrophy fellowships are offered, the Mass General-Brigham (MGB) Neurogenetics and Gene Therapy Fellowship and The Children’s Hospital of Philadelphia (CHOP) Leukodystrophy Fellowship, in addition to offering career development awards to early-stage investigators and those who are new to leukodystrophy research. The expected outcome is an increased retention of early-stage investigators in rare disease clinical research. Aim 3 is to support faculty development with focus on communities with high unmet need. We will develop a leukodystrophy-specific communication training program using the VitalTalk® platform and support the Leukodystrophy Education and Access Program (GLIA-LEAP). The expected outcome is an increased engagement with communities without access to leukodystrophy clinical care and translational research, including those at a geographic distance from tertiary care centers. Overall, the GLIA-CDC hopes to create a leukodystrophy training pipeline, engaging clinical scientists from undergraduate to postgraduate, in order to meet the emerging needs in diagnosis and therapy of this community.

NIH Research Projects · FY 2024 · 2019-07

Project Summary/Abstract Postpartum depressive (PPD) symptoms are common among women following the birth of a child and can adversely impact a mother's ability to care for her child. As a result, infants of mothers with PPD symptoms may experience less responsive parenting, placing them at greater risk for delays in development. Evidence- based parenting programs have been developed to guide mothers with caring for their infants but may not address the impact of depression on parenting, are intensive and expensive to administer with limited ability for scale up, or are not available in a format that facilitates participation by women with depressive symptoms. Therefore, these women may not be able to take advantage of the benefits of parenting programs. Our long- term goal is to develop effective parenting strategies to facilitate optimal child development for mothers suffering with PPD symptoms. Our overall objective for this application is to study whether this program combined with online depression treatment leads to more responsive parenting (target) and signals improved child language, socioemotional and cognitive development (outcomes) compared to depression treatment alone. The specific aims are 1) to determine whether a social media-based parenting program can improve responsive parenting (target) among mothers with PPD symptoms, 2) to determine whether a social media- based parenting program can improve responsive parenting (target) and signal greater child development (outcome) among mothers with PPD symptoms, and 3) to explore mediators and moderators of the effects of the parenting program on responsive parenting. The proposed study will occur at 3-4 primary care practices affiliated with a large urban children's hospital and consist of 2 phases: an initial pilot RCT testing engagement of the parenting program on responsive parenting (R61) and a subsequent RCT further testing engagement of the program and exploring child development and mediators and moderators of treatment effect (R33). In the first phase, 75 ethnically and racially diverse women who screen positive for PPD symptoms and have infants <6 months of age will be randomized to receive the parenting program plus online depression treatment or online depression treatment alone to assess target engagement. In the second phase, an additional 75 eligible women will be randomized to receive the parenting program plus online depression treatment or depression treatment alone. In this latter phase, we will further determine whether the parenting program effectively engages the proposed target, responsive parenting, and signals greater child developmental status than the online depression treatment program. In addition, we will explore mediators and moderators of treatment effects on responsive parenting. The results of this application would be expected to contribute important new knowledge and inform a future trial on parenting strategies to better assist mothers with PPD symptoms and improve child developmental outcomes.

NIH Research Projects · FY 2026 · 2019-04

PROJECT SUMMARY Dravet syndrome (DS) is a severe neurodevelopmental disorder affecting 1 in 15,000 children and defined by treatment-resistant epilepsy, intellectual disability, features of autism spectrum disorder (ASD), and high rate of sudden unexplained death (SUDEP). DS is caused by variants in the gene SCN1A encoding the voltage-gated sodium (Na+) channel subunit Nav1.1. Current treatments are palliative, and there is no cure. How variants in SCN1A lead to the circuit-level dysfunction underlying DS remains unclear. This gap in knowledge limits progress toward novel treatments or a cure, which would have enormous lifelong benefits for patients and families. Prior work in DS (Scn1a+/-) mice suggests that loss of Nav1.1 leads to dysfunction of GABAergic inhibitory interneurons (INs) in the cerebral cortex, with the most prominent identified abnormality being impaired action potential generation in a critical subtype known as the parvalbumin-positive fast-spiking GABAergic interneuron (PV-IN). However, we showed during the prior funding period that PV-IN dysfunction is transient, and restricted to a brief time window in early development, with striking recovery of high frequency firing; instead, we identified long-lasting impairment of action potential propagation at PV-IN axons. We discovered that another subset of IN – labeled by vasoactive intestinal peptide (VIP-INs) – express Nav1.1 and are dysfunctional in Scn1a+/- mice in vitro and in vivo; deletion of Scn1a specifically in VIP-INs leads to ASD-linked behavioral abnormalities but without seizure or epilepsy, dissociating these components of the disorder. Such findings refine our mechanistic understanding of DS and have important implications for treatment approaches currently under development such as cell transplantation, RNA therapeutics, and gene therapy. This renewal uses innovative neuroscience approaches including transcriptomic profiling, detailed electrophysiology and anatomy, closed-loop optogenetic manipulation of behavior, and two-photon calcium imaging in vivo to establish the role of impaired action potential propagation along interneuron axons as a key mechanism of DS pathology. Proposed experiments will establish the molecular identity and physiological properties of Na+ channels in PV-IN axons in Scn1a+/- mice vs. controls (Aim 1); assess the fidelity of spike propagation in VIP-IN axons (Aim 2.1) and role of VIP-IN subtypes in features of ASD (Aim 2.2); and move beyond individual cell types to provide an open-source large-scale transcriptomic atlas of the Scn1a+/- mouse brain across development (Aim 3). The outcome of the proposed experiments will set forth a unifying hypothesis as to the pathophysiology of DS, translational knowledge that is critical to furthering the design of targeted therapies. The long-term objective of this line of research is to drive the development of mechanistically informed treatments or an effective cure for human patients with Dravet Syndrome.

NIH Research Projects · FY 2025 · 2018-09

Project Summary/Abstract For almost 100 years, a large number of electrophysiology studies have reported on resting-state (RS) neural activity in humans. This research often focuses on RS alpha-band activity (8-12 Hz in adults), as RS alpha activity it is commonly interpreted as reflecting the brain's readiness to process information, predicting task performance and processing speed, and being integral to coordinating local- and long- range functional connectivity. Infant RS studies seek to understand infant RS neural processes and the maturation of these processes, with the first two years of life a peak period of neural reorganization, and with variation in the maturation of RS activity contributing to normal variation in development as well as clinical disorders. In infants and toddlers, this line of research is constrained by difficulty obtaining prototypical high SNR eyes-closed RS electrophysiology measures, with almost all infant studies obtaining RS measures while infants view visual stimuli, and with an eyes-open condition not generating a robust infant `alpha' response. During the current cycle of this R01 (locally referred to as Babies' Brains Change (BBC)), we developed methods that overcome barriers that have to date limited progress. Our intention is that findings from this continuation R01 will provide direct tests of theories of infant maturation of brain function, structure, and chemistry and their relationship to each other and behavior, change the way infant RS electrophysiology studies are conducted, and show the way forward for further discoveries about those relationships. Progress will be made via (1) the use of an eyes-open dark-room (DR) task advanced by the PI and which provides RS measures with a high-SNR dominant oscillation response in awake infants, (2) using recently developed algorithms to parameterize the RS power spectrum to obtain estimates of RS periodic activity (e.g., the canonical RS dominant oscillation) and RS aperiodic activity (i.e., the `background' neural activity), (3) assessing RS activity in brain space so that regional differences in RS neural activity can be identified, and so that hypothesized associations between RS neural activity and brain structure (gray and white matter), brain chemistry (glutamate (Glu) and gamma-aminobutyric acid (GABA)), and behavior can be optimally evaluated, and (4) obtaining temporally dense brain measures as understanding brain development requires assessing maturational processes. At Time 1, evaluable data (MEG measures of infant RS activity, MRI measures of gray and white matter, MRS measures of Glu and GABA, and developmental milestone measures) will be obtained from 70 infants, with a 4-month interval between visits, and with a total of 4 visits. It is predicted that the project findings will identify regional differences in the maturation of RS neural activity, show that brain structure and chemistry predict the structure of the RS activity, and that RS measures will predict the time to developmental milestones (e.g., age when first walking).

NIH Research Projects · FY 2025 · 2018-09

Overall Program-Abstract Blood coagulation derives from a series of specific proteolytic activation reactions that are catalyzed with narrow and defined specificity by trypsin-like serine proteinases. In several instances, these proteinases function in membrane assembled enzyme complexes. Distinctive protein substrate specificities and the modulation of function by interactions with membranes, cofactors and ligands are hallmarks of the proteolytic reactions of blood coagulation. There are major gaps in the current understanding of the molecular bases for these unique features that underlie the function of the hemostatic reactions. This program proposes an integrated approach focused on the modulation of enzymic function and specificity that uniquely arises from macromolecular interactions that underlie the action of the hemostatic enzymes. Project 1 (Krishnaswamy) uses the constituents of the prothrombinase complex as a paradigm to investigate functional and structural mechanisms underlying regulation of zymogen, proteinase and cofactor function. Project 2 (Camire) will investigate molecular mechanisms at play in the conversion of factor V to the cofactor, factor Va and the surprising new biological insights that these mechanisms reveal. Project 3 (Sullenger) employs RNA aptamers in a unique inhibitor strategy that combines specific aptamers targeting exosites linked to active site ligands to form potent and readily reversible bivalent EXosite-ACTive site (EXACT) inhibitors to modulate coagulation reactions for therapeutic gain. Project 4 (Samelson-Jones) is an ESI-led project that investigates mechanisms underlying the structural correlates of IXa and VIIIa function to develop novel approaches for the treatment of hemophilia B or to improve approaches for hemophilia A treatment by gene therapy. The objectives of the five projects will be supported by an administrative core (Core A) and a core that provides support for molecular biology, protein expression and structural biology (Core B). Overall, this project applies the expertise of the individual investigators towards addressing major unanswered questions in hemostasis and thrombosis extending from biochemical and structural insights, to biological function and the translation of of these insights to the treatment of disease. The proposed approaches will provide new insights into the chemistry and biology of the blood coagulation reactions with implications for an understanding of normal hemostasis and thrombosis and the treatment of clotting or bleeding disorders.

NIH Research Projects · FY 2024 · 2018-08

Project Summary: Numerous human diseases result from recurrent DNA rearrangements involving unstable genomic regions. They are facilitated by the presence of region-specific low-copy repeats (LCRs) and are the result of nonallelic homologous recombination (NAHR) between such paralogous genomic segments. The 22q11.2 region undergoes a significant number of germline rearrangements and has been classified as one of the most unstable regions of the human genome. Thus, the 22q11.2 deletion syndrome (22q11.2DS) is the most common microdeletion disorder. It is associated with phenotypic and neuropsychiatric pathology, both of which are widely variable. In most affected individuals, the deletion is de novo and is the result of NAHR mediated by four chromosome22-specific low copy repeats (LCRA, -B, -C and -D) in 22q11.2. Their size and the presence of numerous segments with near-identical sequence render these chromosome specific LCRs as substrates for NAHR. LCR22s are extremely difficult to reliably map and sequence because of their structural characteristics. Currently, an accurate reference sequence for the region does not exist. Also, they are recalcitrant to short and long read sequencing such that the level of their polymorphism and variability in the general population is unknown. However, optical mapping of the region with Bionano Genomics’ Saphyr technology has overcome this difficulty. Our optical mapping data suggests a complex organization of duplicated 160kb modules within LCRA and LCRD, including copy number and orientation differences. Further, a common inversion polymorphism within LCRD has been identified. Our preliminary data suggests that this and other polymorphisms are less prevalent in African Americans (AAs), which may finally explain the relative deficit of AAs in our CHOP-based 22q11.2DS cohort. Our funded R01 proposed to employ innovative Bionano optical mapping technology to determine the frequency of 22q11 LCR polymorphisms in the general population and explore the role they play in facilitating rearrangements. The prevalence of the LCRD inversion in several different populations (CEU, African, and African American subjects from the 1000 Genomes Project; local white and AA 22q11DS trios) is being determined. The LCR22-containing regions associated with 22q11.2DS is being examined in these populations to determine their structure and variation. Hence, by leveraging the increased sensitivity afforded by long single molecule optical mapping on nanochannel arrays, this proposal is elucidating the previously unmapped structure and variation of LCR22s and surrounding regions in detail. The data and maps generated herein will provide us with a roadmap to gain access to many other difficult to map and sequence genomic regions and other genomic disorders. However, our Generation 1 Saphyr System is being phased out of production by Bionano Genomics, Thus, to continue this work, we need to trade in our Generation 1 Saphyr system for a Generation 2 Saphyr replacement.

NIH Research Projects · FY 2026 · 2018-07

Pancreas agenesis (PA) is a developmental disorder characterized by either a reduction or complete lack of pancreatic mass. Notably, heterozygous loss of GATA6 accounts for >60% of all human pancreas agenesis cases; however, the pancreatic phenotype within each individual can be incompletely penetrant, ranging from severe neonatal diabetes to mild adult onset diabetes due to beta cell dysfunction. These findings suggest that additional genetic modifiers may contribute to the pathogenesis caused by the reduction in GATA6 expression. During the previous funding period, the collaboration between the Gadue and Sussel labs leveraged the strengths of human induced pluripotent stem cell (hiPSC)-based pancreas differentiation and in vivo murine models of development to discover robust synergy between GATA6 and retinoic acid (RA) signaling in regulating several stages of pancreas development. Our findings suggest two novel concepts: (1) an unappreciated role for RA signaling during endocrine progenitor specification and (2) synergy between RA and specifically GATA6 (but not GATA4) is required to specify beta cells in both mice and humans. The primary goals of this renewal application are to use these complementary genetic model systems to better define this synergy and elucidate the mechanisms by which the intersection of RA signaling and GATA6 regulate pancreas development. Furthermore, we will explore how human mutations in GATA6 disrupt this interaction to influence disease severity. Our published studies combined with new preliminary data in both the mice and human models has led us to hypothesize that this conserved synergy between RA signaling and GATA6 gene regulation is essential for pancreas development and the combined disruption of these pathways contributes to pancreas and islet cell development. We will test this hypothesis with the following specific aims: 1) Establish the synergistic roles of RA/GATA6 during pancreatic endocrine and β cell development and identify the specific stages of the hiPSC-derived pancreas differentiation protocol that require a combination of RA signaling and GATA6 function for optimal beta cell development; 2) Determine the precise molecular mechanism(s) underlying the intersection of RARa and GATA6 in the regulation gene expression pathways that promote pancreatic islet differentiation; and 3) Define how patient specific GATA6 disease mutations affect RA/GATA6 synergy and downstream pathways during pancreas development. The experiments proposed in this application will provide substantial novel insight into the conserved regulatory pathways that are required for appropriate pancreas development and islet cell differentiation and will further inform how mutations in GATA6 cause a wide range of pancreatic phenotypes in humans.

NIH Research Projects · FY 2025 · 2017-09

PROJECT SUMMARY After stunning improvements in patient outcomes for most childhood cancers in the latter half of the last century, cure rates have since plateaued, and treatment related morbidity continues to mount. Children with metastatic solid malignancies continue to have a less than 50% chance of survival despite being treated with highly intensive cytotoxic therapies. Neuroblastoma, a diverse malignancy typically affecting very young children that arises from the developing sympathetic nervous system, is responsible for a disproportionate amount of morbidity and mortality attributable to childhood cancer and is the main focus of this R35. Our primary motivation in this competitive renewal application is to improve patient outcomes, and we also deem neuroblastoma an outstanding model of cancer in general, such that discoveries of basic mechanisms of tumorigenesis are broadly applicable to other human malignancies. Over the next seven years, we will continue to seek to substantively improve cure rates for patients through a multidisciplinary and collaborative research program. Our broad goal is to discover the fundamental mechanisms that subvert normal neuronal development and orchestrate neuroblastoma tumorigenesis, and then to translate this knowledge into patient-specific therapies that will be more effective and less toxic. We thus propose to expand on our comprehensive approach to discover and develop novel therapeutic strategies for patients with high-risk neuroblastoma and other childhood cancers. We will build on progress in the current R35 and address genomic vulnerabilities with precision therapies with a focus on novel immunotherapies. Having developed methods to identify exquisitely tumor specific immunotherapeutic targets, we will create synthetic immunotherapies including antibodies, antibody drug conjugates, bi-specific T cell engagers, and chimeric antigen receptor (CAR) T cells. With several of the therapies created in the current R35 having entered clinical trials recently and throughout the next seven years, we have a unique opportunity to have robust correlative biology to guide our evolving armamentarium of therapeutics. We will enhance the efficacy and persistence of CAR T cells with through both T cell intrinsic (enhancing metabolic fitness) and extrinsic (vaccination to provide an antigenic stimulus) methods. While the current R35 focused almost exclusively on neuroblastoma, we have recently extended our immunotherapy target discovery efforts to other childhood cancers with a high unmet need, and this will be expanded moving forward through both new discovery efforts and the rigorous definition of biomarkers for immunotherapeutic selection across childhood cancers. We think that our research program proposes a variety of innovative experimental strategies to uncover basic mechanisms of oncogenesis, epigenetic adaptation, and immune evasion. This R35 is and will remain steadfastly translational. The significance of the proposed program is the discovery of fundamental mechanisms of tumorigenesis that will lead to new therapies with markedly improved probability of cure coupled with reduced morbidity for children, adolescents, and young adults with neuroblastoma and other childhood cancers.

NIH Research Projects · FY 2025 · 2017-09

CENTER OVERVIEW PROJECT SUMMARY With this renewal, the Pediatric Center of Excellence in Nephrology at the Children’s Hospital of Philadelphia (CHOP PCEN) will continue to facilitate extensive collaborative research around the causes, diagnoses, and treatment of childhood kidney diseases. Increasing efficiency and effectiveness, the CHOP PCEN will continue its focus to break down barriers to clinical trials implementation in our patients. In its initial four years of funding, the CHOP PCEN has partnered with PEDSnet through the Learning Health System (LHS) Core to establish a national interconnected, multi-institutional infrastructure focused on childhood kidney disease. The LHS Core has extended the data science work of PEDSnet to establish an embedded Pediatric Nephrology Data Resource that emphasizes data elements and data quality optimization central to studies of kidney disease. In the next funding cycle, the LHS Core will provide expanded services for comparative effectiveness and pragmatic trials in pediatric nephrology. Through the addition of the Molecular Precision Nephrology (MPN) Core, we will facilitate identification of novel targets to expand therapeutic options for children and youngadults with kidney disease. The MPN Core is uniquely poised to address critical barriers to the clinical and research implementation of molecular precision tools in pediatric nephrology. The Administrative Core facilitates consultation with experts in study design and analysis to achieve appropriate inferences from observational data, and in this proposal, to design comparative effectiveness studies and pragmatic clinical trials. The Administrative Core will support the Opportunity Pool Pilot and Feasibility Program, the Enrichment Program, and two Research Projects that apply innovative approaches to the data resources of the LHS Core and NIDDK consortia (CKiD and CureGN) to address clinically important evidence gaps. One project will examine comparative effectiveness of balanced fluids versus normal saline to reduce the risk of acute and chronic kidney diseasein children with sepsis. The second project will develop, test, and apply a novel class of marginal structural models to estimate time-varying treatment effects on different types of recurrent time-to-event outcomes, including proteinuria remission, infection-related acute care, and skeletal fracture. The PCEN will build upon the strong foundation of pediatric nephrology research at CHOP and Johns Hopkins University as well as successful collaborations with other pediatric nephrology centers and adult nephrology colleagues at the University of Pennsylvania. We will amplify these interactions across institutions to accelerate translation of discoveries into therapies for children and young adults with kidney disease.

NIH Research Projects · FY 2026 · 2017-09

OVERALL SUMMARY/ABSTRACT This is a revised competitive renewal application for a Program focused on high-risk neuroblastoma (NB), a diverse and enigmatic malignancy arising from the developing sympathetic nervous system that remains lethal in 50% of patients despite intensive multi-modal therapy. The primary goal of this multi-institutional and multi- disciplinary Program is to achieve improved outcomes for patients with high-risk NB by 1) discovering basic mechanisms of de novo and acquired resistance to modern therapies; 2) uncovering targetable vulnerabilities driving resistance; and 3) translating these insights into evidence-based clinical trials. The Program has been productive, with important basic, translational, and clinical research achievements over the past 5.5 years. The basic structure of the Program remains the same, with four Projects focusing on interrelated fundamental problems in the broad fields of epigenomics, tumor microenvironment, and immuno-oncology. The central hypothesis is that high-risk NBs evolve to evade therapeutic interventions but that these resistance mechanisms can be targeted therapeutically. The motivation for the proposed research is the urgent need to improve survival of patients with high-risk NB, and to decrease treatment-related morbidities. The four proposed Projects will each address the three Specific Aims of the overall Program: 1) discover mechanisms of NB therapy resistance; 2) discover tumor-intrinsic and -extrinsic therapeutic vulnerabilities imparted by therapy resistance; and 3) develop readily translatable therapeutic strategies to exploit de novo and acquired resistance mechanisms and molecular vulnerabilities. The Projects will each be supported by two Cores: A) Administrative core; B) Translational, statistical, and clinical trials core. Unique to the Program is the New Approaches to NB Therapy (NANT) consortium integrated into Core B now in its 22nd year. A major goal of the NANT is to prioritize new therapies from our Projects for Phase 1 and 2 clinical trials in the high-risk NB relapse population, with the goal of moving these to Phase 3 testing in newly diagnosed patients. The Program is responsible for the two targeted investigational agents currently being tested in an ongoing Children’s Oncology Group Phase 3 trial. The NANT also provides a unique resource of therapy resistant tumors and other biospecimens for Project investigators. Importantly, all Projects have clear milestones to deliver one or more clinical trial to the NANT, with Project specific studies designed to provide the portfolio of nonclinical data required for efficient translation to the refractory NB patient population. This highly integrated Program proposes a variety of innovative experimental strategies to uncover basic mechanisms of oncogenesis and therapy resistance, but is steadfastly translational, as the investigative team is constituted of physicians who care for children with this disease. The significance of the proposed Program is the continued discovery of fundamental mechanisms of cancer therapy resistance leading to substantively improved probability of cure coupled with reduced therapy-related morbidity for children, adolescents and adults afflicted with high-risk NB.

NIH Research Projects · FY 2025 · 2017-09

PROJECT SUMMARY We propose to develop and apply innovative structural biology, NMR, and complementary biophysical techniques to investigate molecular mechanisms of small molecule recognition by intracellular receptors. The MHC-I-related protein 1 (MR1) binds, traffics, and displays endogenous metabolites derived from aberrant metabolism to provide biomarkers of different intracellular states on the cell surface. It has been recently established that several human viruses, including CMV, HSV and SARS-CoV-2, can directly interfere with known components of the MR1 processing and ligand loading machinery. Thus, unravelling MR1's function will not only help us understand fundamental principles of host/pathogen interactions, but also holds great promise for the future development of universal therapies, since MR1 is highly conserved in the human population. Despite a body of functional and structural studies, key barriers remain pertaining to (i) the molecular determinants of specificity, given that MR1 can display a wide repertoire of chemically distinct ligands; (ii) how binding of small molecules on a limited pocket of the MR1 groove induces global structural adaptations on MR1 surfaces, leading to the formation of unique features that can be leveraged for interactions with chaperones and other components of the MR1 processing pathway, and (iii) How molecular chaperones, such as TAPBPR, can catalyze exchange between free and bound ligands. Because of the dynamic nature of ligand and chaperone interactions with MR1, and small size of the system by the standards of cryoEM, there are significant challenges to conventional structural approaches. To address these bottlenecks, I have developed an integrative structural approach, combining nuclear magnetic resonance (NMR) spectroscopy, complementary biophysical techniques and computational modeling to characterize MR1/metabolite complexes and their interactions with chaperones. Our preliminary data show that metabolite binding to MR1 creates unique conformational states, that can be leveraged by chaperones to promote exchange. In this renewal proposal, will further extend our integrative approach to elucidate molecular determinants of small molecule/MR1 assembly and stability, including the contribution of protein dynamics to the selection of ligands with distinct chemical features. Using a combination of methyl-based NMR constraints with structural modeling and in vitro assays, we will delve deeper into MR1/chaperone interactions, and elucidate the mechanism of ligand exchange. Our studies will provide a mechanistic paradigm of a highly malleable protein binding site that can accommodate a wide range of chemically distinct ligands, and further our understanding of how presentation of small molecules by MR1 can provide robust biomarkers for signaling different metabolic states.

NIH Research Projects · FY 2025 · 2016-09

Summary The human body is constructed during through tightly orchestrated patterns of gene expression during embryonic and postnatal development. Perturbations in gene regulation during development are thought to be a major substrate for natural selection and have likely contributed to the evolution of the human form. The molecular processes that contributed to sculpting human specific features of our limbs and brains, can have deleterious consequences when a critical gene or regulatory sequence is affected. Defective gene regulation during embryonic development can result in a variety of structural and functional defects such as congenital heart defects, orofacial clefting, or neurological dysfunction. In cases where a birth defect is not readily observed the individual may be instead be predisposed to various diseases later in life including diabetes or cancer. While our understanding of the genetic code for protein coding genes allows us to make predictions about disease risk our limited understanding of the information encoded in the rest of our genome prevents such predictions and causative assignments. Over the past several years functional annotations of the genome in tissue and developmental stage specific contexts have revealed over half a million potential regulatory elements. We and others have shown that variants linked to diseases and phenotypes of particular tissues are enriched in regulatory sequences that are active in those tissues or during their development. This has been particularly fruitful for defects related to craniofacial and heart development. The work proposed aims to build on these annotations to identify the genes that are controlled by these tissue-specific regulatory sequences and the consequences of variation in those sequences. Using culture and organoid models of early human cardiac development we aim to dissect the regulatory architecture that build the heart and malfunctions in congenital heart defects.

NIH Research Projects · FY 2024 · 2016-09

PROJECT SUMMARY Urinary Stone Disease (USD) is an increasingly prevalent and highly recurrent condition associated with major morbidity at a rising cost to society. Thus, improved management can significantly reduce its health burden. Increasing fluid intake is recommended to all USD patients. However, knowledge gaps persist regarding the impact of fluid therapy in preventing USD recurrence including effectiveness of strategies to achieve and maintain a high urine volume, and whether such strategies reduce USD recurrence. The Prevention of Urinary Stones with Hydration (PUSH) study is a randomized clinical trial investigating the impact of increased fluid intake and increased urine output on the recurrence rate of USD in adults and children. In this study 1,642 participants will be randomized to a control or intervention arm. Participants in both arms receive a “smart water bottle”. The intervention arm involves an additional program of behavioral interventions, including financial incentives, structured problem solving, and low touch interventions designed to improve adherence to a prescribed fluid intake regimen. The primary endpoint is occurrence of a stone event during a two-year observation period. The PUSH study is in its third year, and due to multiple challenges to recruitment of study participants, follow-up of participants and data collection have not yet been completed. Additional time is needed to ensure study completion and to accomplish all study goals. Although ureteral stenting is routinely performed after urological procedures for USD to mitigate peri-operative complications, stents cause significant patient discomfort. The causal mechanisms are only partly understood. The STudy to Enhance uNderstanding of sTent- associated Symptoms (STENTS) is a prospective observational cohort study enrolling adolescents and adults undergoing ureteroscopic intervention for ureteral and/or renal stones. Participants undergo detailed symptom assessment using validated questionnaires, a psychosocial assessment, quantitative sensory testing for evaluation of pain sensitization, and detailed collection of clinical and operative data. Biospecimens (blood and urine) are being collected for future research. Recruitment to the STENTS study and follow-up of the participants are expected to be completed on time. However, additional time and resources are needed for analysis of collected study data. In Aim 1 of this application, the investigators will continue and complete participant enrollment for the PUSH study, continue biospecimen collection for the NIDDK Repository, analyze the data, and prepare and submit several planned manuscripts related to the study hypotheses. In Aim 2 of this applications, the investigators will analyze the data from the STENTS studies, interpret findings, and disseminate findings through peer reviewed publications.

NIH Research Projects · FY 2025 · 2016-04

SUMMARY Mitral regurgitation (MR) is a highly prevalent heart valve disease that affects millions, and for which there is no effective medication to prevent or mitigate progression. As a result, severe MR can only be treated with valve repair or replacement. Clinical and biological evidence, from us and other groups, has demonstrated a direct role of serotonin (5-HT) receptor (HTR) signaling in heart valve disease. The 5-HT transporter (SERT) deactivates 5-HT, thereby limiting HTR signaling. Prior studies by our group over the past 22 years led to our recent discovery that SERT expression and activity are reduced in MR leaflets compared to normal human mitral valve (MV) leaflets (nMV). These investigations have shown: 1) SERT downregulation in human mitral valve interstitial cells (MVIC) due to the activation of the mechano-sensing Ca++ channel, PIEZO1; 2) MVIC exposed to mechano- transduction events in vitro, simulating MR, demonstrate dysregulation of both PIEZO1 and SERT; and 3) Clinical use of antidepressants, that are SERT inhibitors, by MR patients has a significant hazard ratio for surgery at a younger age; 4) Pharmacologic inhibition of SERT, using Fluoxetine administration to mice, results in a mitral valvulopathy, that can be mitigated with a 5-HT-2B receptor (HTR2B) inhibitor. Our recent results with human MVIC, have shown that PIEZO1 activation leads to a 5-HT-dependent increase in collagen production, together with both down regulation of SERT, and reduced SERT activity; inhibition of either HTR2B or tryptophan hydroxylase-1, the enzyme responsible for 5-HT biosynthesis, mitigates MVIC increased collagen production, resulting from PIEZO1 activation. This novel set of experimental results, in our opinion, represents a major discovery concerning the connection between PIEZO1-activation and MR, as well fibrotic diseases with 5-HT dependence. In this proposal, we test the hypothesis that reduced SERT expression and activity in MR contributes to progression due to enhanced HTR signaling, that results from either: PIEZO1 activation leading to SERT down regulation in MVIC; mechanotransduction events that dysregulate both PIEZO1 and SERT, or pharmacological inhibition of SERT. To test this hypothesis we developed three independent, but connected aims. We will first dissect, at the cellular level, the pathway between PIEZO1 activation, reduced SERT activity, and downstream effects on HTR2B signaling. We will study the biomechanical mechanisms responsible for SERT down regulation in MR; and we will investigate the impact of pharmacologic inhibition or absence of SERT on MV pathophysiology.

NIH Research Projects · FY 2025 · 2016-03

Project Summary/Abstract Although differences in auditory encoding and resting-state (RS) neural activity are often reported in children with typical development (TD) versus autism spectrum disorder (ASD), the pattern of findings across studies is inconsistent. The PI has sought to understand the above via studying the maturation of these processes, this work supported by his current R01 (locally referred to as the ‘Brains Change’ study). A consistent finding has been a pattern of brain development that indicates overly rapid followed by too slow brain maturation in ASD. The continuation R01 will demonstrate that this pattern of brain maturation in ASD continues through at least early adolescence as a basis for developing disease-stage-specific assessment and treatment methods. In addition to continuing to map the maturation of RS neural activity, two auditory cortex neural processes that emerge during late childhood are targeted. First is the auditory M100 response, with findings from the current R01 already suggesting that M100, reflecting higher-order auditory encoding, emerges too early in ASD. Second, a new 40 Hz auditory steady-state response exam will assess the emergence and development of cortical inhibitory interneuron and pyramidal cell excitation and inhibition processes. Maturation findings, expected to demonstrate early accelerated then later flat development in ASD, will show a process that repeats itself across childhood and thus leads to a patterned derailment of emerging neural processes in ASD that extends far beyond infancy and early childhood. Tied to the above are two additional goals. First, given group differences in brain maturation rates, studies that average findings across a large age range will miss effects, and cross-sectional comparisons will be complicated. The PI’s research identifies age-specific brain markers in order to provide a basis for developing disease-stage-specific assessment and treatment targets. Second, and building upon the PIs adult studies, analysis of simultaneously collected MEG and EEG is expected to demonstrate the advantage of obtaining regionally specific measures when assessing group differences as well as enable identification of EEG-only assessment methods that are routinely feasible in the clinic. Our intention is that Brains Change findings will change the way ASD research is conducted via demonstrations that the pattern of group differences changes across time (even across a 3-year period), and via identifying very specific brain abnormalities in ASD with respect to age, brain location, and brain process. The current project assesses brain function, structure, and clinical measures in children 6 to 8 years old, and then 18 and 36 months later. For the renewal R01, each child will be followed another 3 years (3 brain imaging exams with 18 months between exams). Allowing attrition of the current sample across time, the Time 3 sample (N = 35/group) will be increased by 65+/group to start the continuation with 100 ASD and 100 TD.

NIH Research Projects · FY 2025 · 2016-01

NK cell deficiency (NKD) is a subset of primary immunodeficiency diseases/inborn errors of immunity (IEI) in which the NK cell abnormality represents the main clinical immunodeficiency. Patients with abnormal NK cells are susceptible to lethal virus infections and certain cancers, offering us a unique window into how these critical immune cells work. For over 15 years we have cared for and investigated these complex patients, applying genomic techniques to discover causative genes and illuminate NK cell biology. With this application, we aspire to renew our coordinated NKD discovery program, with the ultimate goals of understanding how to care for these patients as well as how to best use NK cells therapeutically. Over the past 5 years of our program, we have defined 2 new genetic causes of NKD and 8 new causes of IEI that affect NK cells. We established and grew an international referral network for NKD patients, honed methods to clinically and immunologically define these rare patients, matured our genomic evaluation/discovery pathways, and optimized patient-focused functional genomics and NK cell biological techniques, all to advance progress in understanding NKD. At present, we have 156 patients enrolled in our NK cell evaluation and research (NEAR) program at Columbia: of these, 70 have undergone exome sequencing (ES) at Baylor College of Medicine, 13 have found genetic solutions for their disease, 11 have a promising gene identified, and 36 remain unsolved. During this renewal period, we will build on our successful momentum, adding new NKD patients to our pipeline, clinically and immunologically defining their disease through the use of databases, advanced biostatistical techniques and research level phenotypic and functional assessments (Aim 1), adding new genomic discovery and analytic techniques like whole genome sequencing and RNA sequencing to bring clarity to the patients whose NKD genes remain “unsolved” (Aim 2), and applying cutting-edge functional genomics and NK cell biological techniques to demonstrate the impact and relevance of the gene mutations we discover (Aim 3). We capitalize on strong, long-standing collaborations both within and beyond the field of Immunodeficiency in order to best define how the gene mutations we identify impact how NK cells function in human health. In so doing, we aim to not only better diagnose and care for these complex patients, but to better understand how NK cells protect humans from viruses and cancer.

NIH Research Projects · FY 2026 · 2015-05

Project Summary/Abstract The treatment for children and young adults with T-cell lymphoblastic leukemia (T-ALL) and T-cell lymphoblastic lymphoma (T-LL) has harmonized over time as T-LL patients were shown to have superior outcomes with T-ALL therapy. The recently completed Children’s Oncology Group (COG) phase 3 clinical trial AALL1231, however, found that T-LL but not T-ALL patients had improved event-free survival (EFS) and overall survival (OS) when randomized to the proteasome inhibitor bortezomib plus cytotoxic chemotherapy vs chemotherapy alone. In addition, corticosteroids were intensified on AALL1231 to eliminate prophylactic cranial radiation in most children. T-ALL patients benefited from the corticosteroid intensification and T-LL patients did not. This trial changed the treatment paradigm for T-ALL and T-LL and it is critical we identify the mechanisms underlying the differential response to therapy. For T-ALL patients, we performed comprehensive -omic analyses under R01CA193776 and an associated Gabriella Miller Kids First X01 award (X01HD100702). These studies included proteomic profiling on over 250 children with T-ALL and whole genome, whole exome, and RNA sequencing (WGS, WES, RNAseq) on over 1250 children with T-ALL. We also performed single cell genomic profiling (scRNASeq) on bone marrow from 30 T-ALL cases to understand clonal architecture and microenvironment. We now have access to tissues from over 250 children with T-LL which we will use to test our central hypothesis that specific proteomic, transcriptomic, and genomic profiles can: (1) identify patients with T-ALL and T-LL that have a higher risk of relapsing, (2) define patients that have a higher likelihood to benefit from novel therapies, and (3) delineate intrinsic (tumor) and extrinsic (microenvironment) biologic differences that lead to the differential response to therapy. We will leverage and expand our existing T-ALL data and generate new data in T-LL to test our hypothesis with the following specific aims. We will perform bulk genomic, transcriptomic, and proteomic profiling on T-LL tissues, as well as single cell profiling on T-LL bone marrow and T-ALL and T-LL CSF and compare the tumor and microenvironment in T-ALL and T-LL to identify biologic differences between the two (Aim 1). We will perform transcriptome and proteome profiling to define mechanisms of sensitivity and resistance to corticosteroids (Aim 2) and proteasome inhibitors (Aim 3) in T-ALL and T-LL and target dysregulated proteins driving resistance with small molecule inhibitors and CRISPR-Cas9 to overcome drug resistance. Impact: We are uniquely positioned to perform highly innovative studies in samples collected from children and young adults with T-ALL and T-LL treated on multi-center phase 3 trials. We will improve understanding of T- ALL and T-LL biology and define intrinsic (cancer cell) and extrinsic (microenvironment) biologic factors that distinguish the two. We will identify which T-ALL and T-LL patients should receive proteasome inhibitors and intensified corticosteroids as standard therapy and identify novel targets for the next generation of clinical trials.

NIH Research Projects · FY 2025 · 2014-09

Project Abstract ADHD is one of the most common childhood disorders and often persists into adolescence—a period in which many individuals get licensed to drive. The ability to drive is important to an individual's participation in modern society, as it enhances independence and social and economic opportunity. However, motor vehicle crashes are the leading cause of death among teens. Skills that are critical in driving, including executive functioning, are frequently impaired in individuals with ADHD. Thus, research is critically needed to establish the scientific foun- dation for driving risks among teens with ADHD so that evidence-based countermeasures to reduce crash risk can be developed. Our initial R01 project established that the risk of crash involvement for newly licensed teen drivers with ADHD is 30%-40% higher than same-aged drivers without ADHD (Curry 2017 and 2019). This R01 renewal directly addresses the next logical critical gap: understanding why crash risk is elevated for teen drivers with ADHD. Our overall objective is to identify specific factors that heighten driving risks for teen drivers with ADHD. We will accomplish this with three specific aims. In Aim 1 we will identify distal factors (outside vehicle environment) that heighten risk of adverse driving outcomes for teens with ADHD. In Aim 2 we will identify prox- imal factors (within vehicle environment) that heighten risk. Finally, in Aim 3 we will examine (among drivers with ADHD) the association between ADHD-related factors—including medication use, current ADHD impairment, and the presence of co-occurringdisruptivebehavioral disorder—andadversedriving outcomes. To achieveAim 1, we will conduct a prospective cohort study of 1,000 teen-parent dyads (500 with ADHD, 500 without ADHD). Participants will complete a baseline and four wave surveys that span from the learner phase through the first 15 months of independent driving. Survey data will be linked to objective driving outcomes captured via a smartphone data logger and existing state-level administrative data on moving violations and crashes. To achieve Aims 2 and 3, we will conduct a naturalistic driving study that will include 90 teens from Study 1 as they obtain an intermediate license (10 without ADHD, 40 with ADHD and prescribed ADHD medication, 40 with ADHD and not prescribed ADHD medication). Innovative in-vehicle technology in teens' vehicles will continu- ously monitor driving patterns, behaviors, and performance for the first 12 months of licensure. We will also collect daily medication use for the first 3 months of licensure utilizing innovative ecological momentary assess- ment methods via text prompts. This will enable us to conduct the first examination of how ADHD medication use influences real-world naturalistic driving performance. We expect that the rich foundational information gen- erated from this project will provide critical knowledge about driving risks for teens with ADHD. The project will make a positive impact in that it will enable us to begin addressing the pressing need for targeted interventions for teens with ADHD and their families during the learning-to-drive period—ultimately optimizing their safety as independent drivers.

NIH Research Projects · FY 2025 · 2014-07

PROJECT SUMMARY/ABSTRACT Training in the genetic basis of pediatric gastrointestinal disorders: The revolutions in genetics and genomics have led to discoveries in a range of GI diseases, many of which affect the health of children. Pediatric gastroenterologists who are trained in genetic research will be essential in the effort to identify novel genetic causes of GI disease, reveal their molecular mechanisms, and translate them into therapy. The outstanding laboratory, translational, and clinical research at CHOP and the Perelman School of Medicine (PSOM) present an ideal environment for research career development in the genetics of pediatric GI disease. The overarching goals of this training program are to: • Train a cadre of committed researchers to investigate the genetic basis of pediatric GI disease and to use this knowledge to improve the health of children and adults. • Provide these individuals with the skill sets and foundation for career advancement. • Encourage innovation and leadership in academic pediatric GI. The Specific Aims of this training program are to: • Identify, recruit and foster the career development of post-doctoral research trainees from the pool of CHOP GI fellows, PSOM GI fellows, and other scientists committed to training and career development in the genetics of pediatric gastrointestinal disease. • Match trainee strengths and interests with mentoring teams. • Provide intensive mentored research experience and training with dedicated faculty. • Provide career mentoring, including training on successful grant and manuscript preparation. • Bring together faculty and fellows through seminar series and other academic activities to create a collaborative community of physician-scientists. • Provide guidance for structured learning opportunities on the principles of genetic research, including research ethics and the protection of animal and human subjects. To achieve these goals, we have designed a program offering mentored independent research with a team approach and scholarship oversight. The program provides career mentorship, including individualized independent development plans (IDP) and workshops focusing on professional development and career advancement skills. Seminars are focused on cutting edge research and progress in the field. To date, we have trained 15 outstanding fellows, 12 of whom have graduated and are pursuing successful academic careers. Our goal over the next 5 years is to build upon this foundation to continuously improve our training program with innovative opportunities and continue our mission of training the next generation of physician scientists to investigate the complex genetics of GI disorders.