All Publications

  • Cell Type- and Tissue-specific Enhancers in Craniofacial Development. bioRxiv : the preprint server for biology Rajderkar, S. S., Paraiso, K., Amaral, M. L., Kosicki, M., Cook, L. E., Darbellay, F., Spurrell, C. H., Osterwalder, M., Zhu, Y., Wu, H., Afzal, S. Y., Blow, M. J., Kelman, G., Barozzi, I., Fukuda-Yuzawa, Y., Akiyama, J. A., Afzal, V., Tran, S., Plajzer-Frick, I., Novak, C. S., Kato, M., Hunter, R. D., von Maydell, K., Wang, A., Lin, L., Preissl, S., Lisgo, S., Ren, B., Dickel, D. E., Pennacchio, L. A., Visel, A. 2023

    Abstract

    The genetic basis of craniofacial birth defects and general variation in human facial shape remains poorly understood. Distant-acting transcriptional enhancers are a major category of non-coding genome function and have been shown to control the fine-tuned spatiotemporal expression of genes during critical stages of craniofacial development1-3. However, a lack of accurate maps of the genomic location and cell type-specific in vivo activities of all craniofacial enhancers prevents their systematic exploration in human genetics studies. Here, we combined histone modification and chromatin accessibility profiling from different stages of human craniofacial development with single-cell analyses of the developing mouse face to create a comprehensive catalogue of the regulatory landscape of facial development at tissue- and single cell-resolution. In total, we identified approximately 14,000 enhancers across seven developmental stages from weeks 4 through 8 of human embryonic face development. We used transgenic mouse reporter assays to determine the in vivo activity patterns of human face enhancers predicted from these data. Across 16 in vivo validated human enhancers, we observed a rich diversity of craniofacial subregions in which these enhancers are active in vivo. To annotate the cell type specificities of human-mouse conserved enhancers, we performed single-cell RNA-seq and single-nucleus ATAC-seq of mouse craniofacial tissues from embryonic days e11.5 to e15.5. By integrating these data across species, we find that the majority (56%) of human craniofacial enhancers are functionally conserved in mice, providing cell type- and embryonic stage-resolved predictions of their in vivo activity profiles. Using retrospective analysis of known craniofacial enhancers in combination with single cell-resolved transgenic reporter assays, we demonstrate the utility of these data for predicting the in vivo cell type specificity of enhancers. Taken together, our data provide an expansive resource for genetic and developmental studies of human craniofacial development.

    View details for DOI 10.1101/2023.06.26.546603

    View details for PubMedID 37425964

    View details for PubMedCentralID PMC10327103

  • Multisystem Inflammatory Syndrome in Children PEDIATRIC ANNALS Acholonu, C., Cohen, E., Afzal, S. Y., Jani, P., Tesher, M. 2023; 52 (3): E114-E121

    Abstract

    Multisystem inflammatory disease in children (MIS-C) is a condition typically seen 3 to 6 weeks after acute infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Believed to be a postinfection hyperinflammatory response, the clinical manifestation of this viral sequelae can vary significantly in severity and symptomatic presentation. Clinical prodrome includes persistent fever and dysfunction of at least two organ systems. Often developing after asymptomatic or mildly symptomatic coronavirus disease 2019 (COVID-19) infection, MIS-C is a diagnosis of exclusion that requires evaluation for other infectious or noninfectious etiology for symptoms. Vital sign instability, including fever, tachycardia, and hypotension; laboratory studies demonstrating elevated inflammatory markers and elevated cardiac markers; and positive SARS-CoV-2 polymerase chain reaction, SARS-CoV-2 antibodies, or exposure to someone with confirmed COVID-19 infection 4 to 6 weeks before clinical presentation are used to diagnose this condition. Skin and mucosal involvement, gastrointestinal symptoms, and neurologic manifestations are also commonly seen. An echocardiogram is indicated to evaluate for cardiac dysfunction, including but not limited to coronary artery enlargement, left ventricular dysfunction, arrythmias, or atrioventricular block. [Pediatr Ann. 2023;52(3):e114-e121.].

    View details for DOI 10.3928/19382359-20230119-03

    View details for Web of Science ID 000993286700007

    View details for PubMedID 36881797

  • Infant in extremis: respiratory failure secondary to lower airway infantile hemangioma. BMC pediatrics MacDougall, M. S., Afzal, S. Y., Freedman, M. S., Han, P. 2022; 22 (1): 744

    Abstract

    Infantile hemangiomas (IHs) are vascular tumors that commonly affect infants and usually regress spontaneously or can be easily treated as an outpatient with topical beta-blockers. However, IHs that present in the airway may cause life-threatening symptoms due to airway obstruction or risk of bleeding. Here we present the first documented case of an infant with rapid deterioration and acute respiratory failure secondary to a lower airway hemangioma.This 3-month-old male initially presented in respiratory distress with symptoms consistent with a viral respiratory infection, however showed no clinical improvement with standard therapies. An urgent CT scan revealed a mass occluding the right mainstem bronchus. Upon transfer to a tertiary care facility, he developed acute respiratory failure requiring emergent intubation and single lung ventilation. The availability of multiple subspecialists allowed for stabilization of a critically ill child, expedited diagnosis, and ultimately initiation of life-saving treatment with beta blockers. After 17 total hospital days, he was extubated successfully and discharged home in good condition.While IH is a rare cause of infantile respiratory distress, we present multiple pearls for the general pediatrician for management of IHs of the airway.

    View details for DOI 10.1186/s12887-022-03821-1

    View details for PubMedID 36581920

  • Unique hepatic manifestations of COVID-19-induced immune dysregulation in children. Clinical case reports Kleinhenz, J., Wagner, E., Afzal, S. Y., Shaarbaf, H., De Avila, J. L., Azzam, R. 2022; 10 (11): e6510

    Abstract

    The two cases we present are the first to demonstrate novel manifestations of COVID-19 related interaction between the liver and the immune system in pediatric patients. Written informed consent was obtained from the parent/guardian to publish this report in accordance with the journal's patient consent policy.

    View details for DOI 10.1002/ccr3.6510

    View details for PubMedID 36415706

  • Genome-wide fetalization of enhancer architecture in heart disease Cell Reports Spurrell, C. H., Barozzi, I., Kosicki, M., Mannion, B. J., Blow, M. J., Fukada-Yuzawa, Y., Slaven, N., Afzal, S. Y., Akiyama, J. A., Afzal, V., Tran, S., Plajzer-Frick, I., Novak, C. S., Kato, M., Lee, E. A., Garvin, T. H., Pham, Q. T., Kronshage, A. K., Lisgo, S., Bristow, J., Cappola, T. P., Morley, M. P., Margulies, K. B., Pennacchio, L. A., Dickel, D. E. 2022; 40 (12)

    View details for DOI 10.1016/j.celrep.2022.111400

  • Acute Pancreatitis in Children PEDIATRIC ANNALS Afzal, S., Kleinhenz, J. 2021; 50 (8): E330-E335

    Abstract

    Acute pancreatitis has become a common general pediatric condition with an increasing incidence over the past 2 decades. It presents with nonspecific complaints of abdominal pain, vomiting, and nausea. Therefore, it is crucial to have it on the differential diagnosis, as it requires prompt treatment and has the potential to become life-threatening. Although pancreatic rest, antiemetics, analgesia, and hydration remain the mainstay of treatment, a new perspective on fluid management, early enteral nutrition, and opioid use has evolved. This review identifies gaps in management awareness and provides understanding on long-term implications of acute and recurrent pancreatitis. This article also reviews the epidemiology, diagnostic criteria, imaging and procedural modalities, common causes, management, and complications of acute pancreatitis and is geared toward the general pediatric hospitalist. [Pediatr Ann. 2021;50(8):e330-e335.].

    View details for DOI 10.3928/19382359-20210713-01

    View details for Web of Science ID 000686261600007

    View details for PubMedID 34398718

  • Professional tribute: Dr. Mary D. Jones. Journal of pediatric rehabilitation medicine Afzal, S. Y. 2021; 14 (1): 5-6

    View details for DOI 10.3233/PRM-219003

    View details for PubMedID 33780382

  • Genome-Wide Fetalization of Enhancer Architecture in Heart Disease bioRxiv Cailyn, S. H. 2019

    View details for DOI 10.1101/591362

  • Enhancer redundancy provides phenotypic robustness in mammalian development. Nature Osterwalder, M., Barozzi, I., Tissières, V., Fukuda-Yuzawa, Y., Mannion, B. J., Afzal, S. Y., Lee, E. A., Zhu, Y., Plajzer-Frick, I., Pickle, C. S., Kato, M., Garvin, T. H., Pham, Q. T., Harrington, A. N., Akiyama, J. A., Afzal, V., Lopez-Rios, J., Dickel, D. E., Visel, A., Pennacchio, L. A. 2018; 554 (7691): 239-243

    Abstract

    Distant-acting tissue-specific enhancers, which regulate gene expression, vastly outnumber protein-coding genes in mammalian genomes, but the functional importance of this regulatory complexity remains unclear. Here we show that the pervasive presence of multiple enhancers with similar activities near the same gene confers phenotypic robustness to loss-of-function mutations in individual enhancers. We used genome editing to create 23 mouse deletion lines and inter-crosses, including both single and combinatorial enhancer deletions at seven distinct loci required for limb development. Unexpectedly, none of the ten deletions of individual enhancers caused noticeable changes in limb morphology. By contrast, the removal of pairs of limb enhancers near the same gene resulted in discernible phenotypes, indicating that enhancers function redundantly in establishing normal morphology. In a genetic background sensitized by reduced baseline expression of the target gene, even single enhancer deletions caused limb abnormalities, suggesting that functional redundancy is conferred by additive effects of enhancers on gene expression levels. A genome-wide analysis integrating epigenomic and transcriptomic data from 29 developmental mouse tissues revealed that mammalian genes are very commonly associated with multiple enhancers that have similar spatiotemporal activity. Systematic exploration of three representative developmental structures (limb, brain and heart) uncovered more than one thousand cases in which five or more enhancers with redundant activity patterns were found near the same gene. Together, our data indicate that enhancer redundancy is a remarkably widespread feature of mammalian genomes that provides an effective regulatory buffer to prevent deleterious phenotypic consequences upon the loss of individual enhancers.

    View details for DOI 10.1038/nature25461

    View details for PubMedID 29420474

    View details for PubMedCentralID PMC5808607

  • The effect of low magnitude mechanical stimulation (LMMS) on bone density in patients with Rett syndrome: a pilot and feasibility study. Journal of pediatric rehabilitation medicine Afzal, S. Y., Wender, A. R., Jones, M. D., Fung, E. B., Pico, E. L. 2014; 7 (2): 167-78

    Abstract

    Low magnitude mechanical stimulation (LMMS) has been used successfully to promote bone formation in certain patient populations. This study evaluated the feasibility and effectiveness of LMMS on improving bone mineral density (BMD) in patients with Rett syndrome.A 12-month crossover pilot study design of 6 months of intervention with LMMS and 6 months without was studied in 14 subjects divided in two subgroups. BMD was assessed using Dual Energy X-ray Absorptiometry (DXA). The levels of 25-hydroxy vitamin D (25OHD), Parathyroid Hormone (PTH), Insulin-Like Growth Factor 1 (IGF-1), and circulating markers of bone resorption (NTx) were analyzed in blood samples. Health questionnaires and diet logs were obtained at 0, 6, and 12 months.Of the 11 subjects who completed the protocol, 9 had an adherence of > 65% and showed an increase in spine BMD Z-scores from the intervention (Z: -2.51) compared to non-intervention period (Z: -2.27) of 0.23 SD (p=0.048). Following intervention, favorable trends were also observed for IGF-1 (p=0.06) and right distal femur BMD Z-scores (p=0.07).These preliminary results are promising for a larger, placebo-controlled randomized study of subjects with Rett syndrome.

    View details for DOI 10.3233/PRM-140286

    View details for PubMedID 25096869

https://orcid.org/0000-0002-3682-5536