Professional Education

  • Bachelor of Science, Ball State University (2005)
  • Doctor of Philosophy, University of Iowa (2011)

Stanford Advisors

All Publications

  • Single-cell analysis delineates a trajectory toward the human early otic lineage PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Ealy, M., Ellwanger, D. C., Kosaric, N., Stapper, A. P., Heller, S. 2016; 113 (30): 8508-8513


    Efficient pluripotent stem cell guidance protocols for the production of human posterior cranial placodes such as the otic placode that gives rise to the inner ear do not exist. Here we use a systematic approach including defined monolayer culture, signaling modulation, and single-cell gene expression analysis to delineate a developmental trajectory for human otic lineage specification in vitro. We found that modulation of bone morphogenetic protein (BMP) and WNT signaling combined with FGF and retinoic acid treatments over the course of 18 days generates cell populations that develop chronological expression of marker genes of non-neural ectoderm, preplacodal ectoderm, and early otic lineage. Gene expression along this differentiation path is distinct from other lineages such as endoderm, mesendoderm, and neural ectoderm. Single-cell analysis exposed the heterogeneity of differentiating cells and allowed discrimination of non-neural ectoderm and otic lineage cells from off-target populations. Pseudotemporal ordering of human embryonic stem cell and induced pluripotent stem cell-derived single-cell gene expression profiles revealed an initially synchronous guidance toward non-neural ectoderm, followed by comparatively asynchronous occurrences of preplacodal and otic marker genes. Positive correlation of marker gene expression between both cell lines and resemblance to mouse embryonic day 10.5 otocyst cells implied reasonable robustness of the guidance protocol. Single-cell trajectory analysis further revealed that otic progenitor cell types are induced in monolayer cultures, but further development appears impeded, likely because of lack of a lineage-stabilizing microenvironment. Our results provide a framework for future exploration of stabilizing microenvironments for efficient differentiation of stem cell-generated human otic cell types.

    View details for DOI 10.1073/pnas.1605537113

    View details for Web of Science ID 000380346200056

    View details for PubMedID 27402757

    View details for PubMedCentralID PMC4968758

  • Mutations in apoptosis-inducing factor cause X-linked recessive auditory neuropathy spectrum disorder JOURNAL OF MEDICAL GENETICS Zong, L., Guan, J., Ealy, M., Zhang, Q., Wang, D., Wang, H., Zhao, Y., Shen, Z., Campbell, C. A., Wang, F., Yang, J., Sun, W., Lan, L., Ding, D., Xie, L., Qi, Y., Lou, X., Huang, X., Shi, Q., Chang, S., Xiong, W., Yin, Z., Yu, N., Zhao, H., Wang, J., Wang, J., Salvi, R. J., Petit, C., Smith, R. J., Wang, Q. 2015; 52 (8): 523-531


    Auditory neuropathy spectrum disorder (ANSD) is a form of hearing loss in which auditory signal transmission from the inner ear to the auditory nerve and brain stem is distorted, giving rise to speech perception difficulties beyond that expected for the observed degree of hearing loss. For many cases of ANSD, the underlying molecular pathology and the site of lesion remain unclear. The X-linked form of the condition, AUNX1, has been mapped to Xq23-q27.3, although the causative gene has yet to be identified.We performed whole-exome sequencing on DNA samples from the AUNX1 family and another small phenotypically similar but unrelated ANSD family.We identified two missense mutations in AIFM1 in these families: c.1352G>A (p.R451Q) in the AUNX1 family and c.1030C>T (p.L344F) in the second ANSD family. Mutation screening in a large cohort of 3 additional unrelated families and 93 sporadic cases with ANSD identified 9 more missense mutations in AIFM1. Bioinformatics analysis and expression studies support this gene as being causative of ANSD.Variants in AIFM1 gene are a common cause of familial and sporadic ANSD and provide insight into the expanded spectrum of AIFM1-associated diseases. The finding of cochlear nerve hypoplasia in some patients was AIFM1-related ANSD implies that MRI may be of value in localising the site of lesion and suggests that cochlea implantation in these patients may have limited success.

    View details for DOI 10.1136/jmedgenet-2014-102961

    View details for Web of Science ID 000358443800003

    View details for PubMedCentralID PMC4518735

  • Inner ear hair cell-like cells from human embryonic stem cells. Stem cells and development Ronaghi, M., Nasr, M., Ealy, M., Durruthy-Durruthy, R., Waldhaus, J., Diaz, G. H., Joubert, L., Oshima, K., Heller, S. 2014; 23 (11): 1275-1284


    In mammals, the permanence of many forms of hearing loss is the result of the inner ear's inability to replace lost sensory hair cells. Here, we apply a differentiation strategy to guide human embryonic stem cells (hESCs) into cells of the otic lineage using chemically defined attached-substrate conditions. The generation of human otic progenitor cells was dependent on fibroblast growth factor (FGF) signaling, and protracted culture led to the upregulation of markers indicative of differentiated inner ear sensory epithelia. Using a transgenic ESC reporter line based on a murine Atoh1 enhancer, we show that differentiated hair cell-like cells express multiple hair cell markers simultaneously. Hair cell-like cells displayed protrusions reminiscent of stereociliary bundles, but failed to fully mature into cells with typical hair cell cytoarchitecture. We conclude that optimized defined conditions can be used in vitro to attain otic progenitor specification and sensory cell differentiation.

    View details for DOI 10.1089/scd.2014.0033

    View details for PubMedID 24512547

    View details for PubMedCentralID PMC4028088

  • Rare Variants in BMP2 and BMP4 Found in Otosclerosis Patients Reduce Smad Signaling OTOLOGY & NEUROTOLOGY Ealy, M., Meyer, N. C., Corchado, J. C., Schrauwen, I., Bress, A., Pfister, M., Van Camp, G., Smith, R. J. 2014; 35 (3): 395-400


    Genetic variation in BMP2 and BMP4 found in otosclerosis patients result in altered Smad signaling.Otosclerosis is a common form of adult-onset conductive hearing loss resulting from abnormal bone remodeling of the bony labyrinth that surrounds the inner ear. Both genetic and environmental factors are implicated in the disease, yet very little is known about its pathogenesis. The evidence for a genetic component has been established through family-based linkage and population-based association studies. Previously, members of the TGF-β superfamily of genes have been associated with otosclerosis.Sequencing of BMP2 and BMP4 coding regions was performed to identify common and rare variation in German otosclerosis patients compared with controls. Functional analyses of rare variation in the patient cohort were conducted by exposing an osteosarcoma cell line to conditioned media containing either wild type or variant forms of BMP2 or BMP4 and analyzing Smad1/5/8 phosphorylation.Although no significant association with common variation in these 2 genes was detected, there were 8 singleton variants identified in the German population. Of the 4 coding variants found solely in otosclerosis patients, two--BMP4(N150K) and BMP2(K357-R396del)--were found to decrease Smad1/5/8 signaling.Rare variants in BMP2 and BMP4 are not a major genetic component in the otosclerosis population. However, those with functional affect showed decreased Smad signaling. Further analysis of Smad signaling molecules should be performed to determine if these pathways in combination are a major contributor to otosclerosis, which could lead to additional treatment options for otosclerosis patients.

    View details for DOI 10.1097/MAO.0000000000000244

    View details for Web of Science ID 000331732300007

    View details for PubMedID 24492129

  • COL1A1 association and otosclerosis: A meta-analysis AMERICAN JOURNAL OF MEDICAL GENETICS PART A Schrauwen, I., Khalfallah, A., Ealy, M., Fransen, E., Claes, C., Huber, A., Murillo, L. R., Masmoudi, S., Smith, R. J., van Camp, G. 2012; 158A (5): 1066-1070


    Otosclerosis is a disease of abnormal bone remodeling in the human otic capsule that can lead to progressive hearing loss. Little of the underlying disease etiology has been elucidated thus far, although several studies have suggested that COL1A1 may play a role based on its importance in bone metabolism and other diseases like osteoporosis and osteogenesis imperfecta. Genetic association studies between COL1A1 and otosclerosis, however, have been contradictory. To resolve this issue, we studied a large Belgian-Dutch and a Swiss population for a genetic association between COL1A1 and otosclerosis and additionally performed a meta-analysis to investigate the overall genetic effect of COL1A1 on all otosclerosis populations studied to date. We found a significant association both in the Belgian-Dutch population and in the meta-analysis. In aggregate, our analysis supports evidence for an association between COL1A1 and otosclerosis although effect sizes of the variants reported in the initial studies are likely to be an overestimate of true effect sizes.

    View details for DOI 10.1002/ajmg.a.35276

    View details for Web of Science ID 000303000200014

    View details for PubMedID 22489040

  • The Prevalence of Mitochondrial Mutations Associated with Aminoglycoside-Induced Sensorineural Hearing Loss in an NICU Population LARYNGOSCOPE Ealy, M., Lynch, K. A., Meyer, N. C., Smith, R. J. 2011; 121 (6): 1184-1186


    Several mitochondrial DNA variants increase risk for developing sensorineural hearing loss following exposure to aminoglycoside antibiotics, a particular concern in the premature infant population, as many of these babies spend time in neonatal intensive care units and are treated with aminoglycosides. To determine the relative prevalence of five mitochondrial DNA variants in the 12S rRNA gene, MT-RNR1, we genotyped 703 neonatal intensive care unit patients and 1473 individuals from the general Iowa population. We found that the aggregate frequency of these variants (∼1.8%) was comparable between populations. Although no hearing loss was detected by newborn hearing screens in the at-risk patients, these neonatal intensive care unit graduates have an increased life-time risk for developing aminoglycoside-induced deafness.

    View details for DOI 10.1002/lary.21778

    View details for Web of Science ID 000291259900010

    View details for PubMedID 21495045

  • Genetic variants in RELN are associated with otosclerosis in a non-European population from Tunisia ANNALS OF HUMAN GENETICS Khalfallah, A., Schrauwen, I., Mnaja, M., Fransen, E., Lahmar, I., Ealy, M., Dhouib, L., Ayadi, H., Charfedine, I., Driss, N., Ghorbel, A., Smith, R. J., Masmoudi, S., Van Camp, G. 2010; 74: 399-405


    Otosclerosis is a common form of conductive hearing loss, caused by an abnormal bone remodelling in the otic capsule. Both environmental and genetic factors have been implicated in the etiology of this disease. A recent genome wide association study identified two regions associated with otosclerosis, one on chr7q22.1, located in the RELN gene, and one on chr11q13.1. A second study in four European populations has replicated the association of the RELN gene with otosclerosis. To investigate the association of these loci with otosclerosis in a non-European population, we tested 11 SNPs from the two regions in 149 unrelated Tunisian patients and 152 controls. Four SNPs were significantly associated with otosclerosis. Three SNPs are located in the RELN region and the last one is located in the region on chromosome 11. We also observed a significant interaction with gender for rs3914132. This suggests an influence of sex on the association of RELN with otosclerosis. A meta-analysis showed that the disease-associated alleles in the Tunisian sample are the same as in all previously reported associations. Our study provides additional evidence implicating RELN in the development of otosclerosis. Additional functional studies should determine the role of RELN in the physiopathology of this disease.

    View details for DOI 10.1111/j.1469-1809.2010.00595.x

    View details for Web of Science ID 000280985700003

    View details for PubMedID 20642811

  • The Genetics of otosclerosis HEARING RESEARCH Ealy, M., Smith, R. J. 2010; 266 (1-2): 70-74


    Otosclerosis is a common form of conductive hearing loss with a prevalence of 0.3-0.4% in white adults. It is characterized by labyrinthine endochondral sclerosis which may invade the stapedio-vestibular joint and interfere with free motion of the stapes. Both environmental factors and genetic causes have been implicated in the disease process; however, the pathogenesis of otosclerosis still remains poorly understood. To date, several loci have been mapped in families segregating autosomal dominant otosclerosis although no disease-causing mutations have been identified. In contrast, several association studies have implicated specific genes but their effects on risk-of-disease are small. The goal of this paper is to review the genetics of otosclerosis and to provide insight into studies that could be performed to elucidate disease pathogenesis.

    View details for DOI 10.1016/j.heares.2009.07.002

    View details for Web of Science ID 000279973800007

    View details for PubMedID 19607896

  • Genetic variants in the RELN gene are associated with otosclerosis in multiple European populations HUMAN GENETICS Schrauwen, I., Ealy, M., Fransen, E., Vanderstraeten, K., Thys, M., Meyer, N. C., Cosgarea, M., Huber, A., Mazzoli, M., Pfister, M., Smith, R. J., Van Camp, G. 2010; 127 (2): 155-162


    Otosclerosis is a common form of hearing loss characterized by abnormal bone remodeling in the otic capsule. It is considered a complex disease caused by both genetic and environmental factors. In a previous study, we identified a region on chr7q22.1 located in the RELN gene that is associated with otosclerosis in Belgian-Dutch and French populations. Evidence for allelic heterogeneity was found in this chromosomal region in the form of two independent signals. To confirm this finding, we have completed a replication study that includes four additional populations from Europe (1,141 total samples). Several SNPs in this region replicated in these populations separately. While the power to detect significant association in each population is small, when all four populations are combined, six of seven SNPs replicate and show an effect in the same direction as in the previous populations. We also confirmed the presence of allelic heterogeneity in this region. These data further implicate RELN in the pathogenesis of otosclerosis. Functional research is warranted to determine the pathways through which RELN acts in the pathogenesis of otosclerosis.

    View details for DOI 10.1007/s00439-009-0754-2

    View details for Web of Science ID 000273625800003

    View details for PubMedID 19847460

  • No Evidence for Association Between the Renin-Angiotensin-Aldosterone System and Otosclerosis in a Large Belgian-Dutch Population OTOLOGY & NEUROTOLOGY Schrauwen, I., Thys, M., Vanderstraeten, K., Fransen, E., Ealy, M., Cremers, C. W., Dhooge, I., Van De Heyning, P., Offeciers, E., Smith, R. J., van Camp, G. 2009; 30 (8): 1079-1083


    Otosclerosis is a frequent cause of hearing impairment in the Caucasian population and is characterized by abnormal bone remodeling of the otic capsule. Associations with several genes have been reported, and recently, an association between the renin-angiotensin-aldosterone system and otosclerosis has been suggested. Polymorphisms in 3 genes were investigated: angiotensinogen (AGT), angiotensin I-converting enzyme (ACE), and angiotensin II receptor, type 1. The polymorphisms in AGT and ACE were associated with disease, and both were reported to interact with each other. In the current study, a replication study was done in a large Belgian-Dutch population to investigate whether this association could be replicated.The same 3 polymorphisms in AGT, ACE, and angiotensin II receptor, type 1 as analyzed in the original study were investigated in 692 otosclerosis patients and 692 controls of Belgian-Dutch origin.None of the polymorphisms were significantly associated with disease. Interaction between AGT and ACE polymorphisms was not significant either.We could not confirm the association between AGT and ACE, nor could we find evidence for interaction between both genes in otosclerosis. Because the current patient set is much larger than the one from the original study, this study holds sufficient power to detect the previously reported associations. Nonreplication in this case probably indicates that the initial results were false positive, although a role for these genes in otosclerosis cannot be definitively ruled out.

    View details for DOI 10.1097/MAO.0b013e3181ab3058

    View details for Web of Science ID 000276927300010

    View details for PubMedID 19503013

  • A Genome-wide Analysis Identifies Genetic Variants in the RELN Gene Associated with Otosclerosis AMERICAN JOURNAL OF HUMAN GENETICS Schrauwen, I., Ealy, M., Huentelman, M. J., Thys, M., Homer, N., Vanderstraeten, K., Fransen, E., Corneveaux, J. J., Craig, D. W., Claustres, M., Cremers, C. W., Dhooge, I., de Heyning, P. V., Vincent, R., Offeciers, E., Smith, R. J., Van Camp, G. 2009; 84 (3): 328-338


    Otosclerosis is a common form of progressive hearing loss, characterized by abnormal bone remodeling in the otic capsule. The etiology of the disease is largely unknown, and both environmental and genetic factors have been implicated. To identify genetic factors involved in otosclerosis, we used a case-control discovery group to complete a genome-wide association (GWA) study with 555,000 single-nucleotide polymorphisms (SNPs), utilizing pooled DNA samples. By individual genotyping of the top 250 SNPs in a stepwise strategy, we were able to identify two highly associated SNPs that replicated in two additional independent populations. We then genotyped 79 tagSNPs to fine map the two genomic regions defined by the associated SNPs. The region with the strongest association signal, p(combined) = 6.23 x 10(-10), is on chromosome 7q22.1 and spans intron 1 to intron 4 of reelin (RELN), a gene known for its role in neuronal migration. Evidence for allelic heterogeneity was found in this region. Consistent with the GWA data, expression of RELN was confirmed in the inner ear and in stapes footplate specimens. In conclusion, we provide evidence that implicates RELN in the pathogenesis of otosclerosis.

    View details for DOI 10.1016/j.ajhg.2009.01.023

    View details for Web of Science ID 000264304200004

    View details for PubMedID 19230858

  • Detection of Rare Nonsynonymous Variants in TGFB1 in Otosclerosis Patients ANNALS OF HUMAN GENETICS Thys, M., Schrauwen, I., Vanderstraeten, K., Dieltjens, N., Fransen, E., Ealy, M., Cremers, C. W., Van De Heyning, P., Vincent, R., Offeciers, E., SMITH, R. H., Van Camp, G. 2009; 73: 171-175


    Otosclerosis is one of the most common forms of hearing loss in the European population. We have identified a SNP in the TGFB1 (transforming growth factor beta 1) gene that is associated with susceptibility to otosclerosis. The protective allele of this variant, with isoleucine at position 263 of the protein, is more biologically active than the risk allele, which has a threonine in this position. Because recent studies have shown that not only common, but also rare variants can be involved in complex diseases, we performed DNA sequence analysis of the exons and intron-exon boundaries of TGFB1 in 755 otosclerosis patients and 877 control samples. We found 3 different nonsynonymous variants (E29, A29 and I241) in four otosclerosis patients, but no such changes were found in controls. In silico analysis shows that these variations could influence TGF-beta1 function and activity. Taking into account that most rare missense alleles are thought to have a biological effect, the data suggest that multiple rare amino acid changing variants in TGF-beta1 may contribute to susceptibility to otosclerosis.

    View details for DOI 10.1111/j.1469-1809.2009.00505.x

    View details for Web of Science ID 000263448700006

    View details for PubMedID 19207109

  • Gene expression analysis of human otosclerotic stapedial footplates HEARING RESEARCH Ealy, M., Chen, W., Ryu, G., Yoon, J., Welling, D. B., Hansen, M., Madan, A., Smith, R. J. 2008; 240 (1-2): 80-86


    Otosclerosis is a complex disease that results in a common form of conductive hearing loss due to impaired mobility of the stapes. Stapedial motion becomes compromised secondary to invasion of otosclerotic foci into the stapedio-vestibular joint. Although environmental factors and genetic causes have been implicated in this process, the pathogenesis of otosclerosis remains poorly understood. To identify molecular contributors to otosclerosis we completed a microarray study of otosclerotic stapedial footplates. Stapes footplate samples from otosclerosis and control patients were used in the analysis. One-hundred-and-ten genes were found to be differentially expressed in otosclerosis samples. Ontological analysis of differentially expressed genes in otosclerosis provides evidence for the involvement of a number of pathways in the disease process that include interleukin signaling, inflammation and signal transduction, suggesting that aberrant regulation of these pathways leads to abnormal bone remodeling. Functional analyses of genes from this study will enhance our understanding of the pathogenesis of this disease.

    View details for DOI 10.1016/j.heares.2008.03.001

    View details for Web of Science ID 000257531500008

    View details for PubMedID 18430532

  • Association of bone morphogenetic proteins with otosclerosis JOURNAL OF BONE AND MINERAL RESEARCH Schrauwen, I., Thys, M., Vanderstraeten, K., Fransen, E., Dieltjens, N., Huyghe, J. R., Ealy, M., Claustres, M., Cremers, C. R., Dhooge, I., Declau, F., de Heyning, P. V., Vincent, R., Somers, T., Offeciers, E., Smith, R. J., van Camp, G. 2008; 23 (4): 507-516


    We studied the role of polymorphisms in 13 candidate genes on the risk of otosclerosis in two large independent case-control sets. We found significant association in both populations with BMP2 and BMP4, implicating these two genes in the pathogenesis of this disease.Otosclerosis is a progressive disorder of the human temporal bone that leads to conductive hearing loss and in some cases sensorineural or mixed hearing loss. In a few families, it segregates as a monogenic disease with reduced penetrance, but in most patients, otosclerosis is more appropriately considered a complex disorder influenced by genetic and environmental factors.To identify major genetic factors in otosclerosis, we used a candidate gene approach to study two large independent case-control sets of Belgian-Dutch and French origin. Tag single nucleotide polymorphisms (SNPs) in 13 candidate susceptibility genes were studied in a stepwise strategy.Two SNPs were identified that showed the same significant effect in both populations. The first SNP, rs3178250, is located in the 3' untranslated region of BMP2. Individuals homozygote for the C allele are protected against otosclerosis (combined populations: p = 2.2 x 10(-4); OR = 2.027; 95% CI = 1.380-2.979). The second SNP, rs17563, is an amino acid changing (p.Ala152Val) SNP located in BMP4. The G allele, coding for the amino acid alanine, confers susceptibility in both populations (combined populations: p = 0.002; OR = 1.209; 95% CI: 1.070-1.370).These results indicate that polymorphisms in the BMP2 and BMP4 genes, both members of the TGF-beta superfamily, contribute to the susceptibility to otosclerosis and further strengthen the results from the recently reported association of TGFB1 with this disease.

    View details for DOI 10.1359/JBMR.071112

    View details for Web of Science ID 000254590000007

    View details for PubMedID 18021008

  • The coding polymorphism T263I in TGF-beta 1 is associated with otosclerosis in two independent populations HUMAN MOLECULAR GENETICS Thys, M., Schrauwen, I., Vanderstraeten, K., Janssens, K., Dieltjens, N., Van den Bogaert, K., Fransen, E., Chen, W., Ealy, M., Claustres, M., Cremers, C. R., Dhooge, I., Declau, F., Claes, J., Van De Heyning, P., Vincent, R., Somers, T., Offeciers, E., Smith, R. J., van Camp, G. 2007; 16 (17): 2021-2030


    Otosclerosis is a progressive hearing loss characterized by an abnormal bone homeostasis of the otic capsule that leads to stapes fixation. Although its etiology remains unknown, otosclerosis can be considered a complex disease. Transforming growth factor-beta 1 (TGF-beta1) was chosen for a case-control association study, because of several non-genetic indications of involvement in otosclerosis. Single nucleotide polymorphism (SNP) analysis in a large Belgian-Dutch sample set gave significant results (P = 0.0044) for an amino acid changing SNP, T263I. Analysis of an independent French population replicated this association with SNP T263I (P = 0.00019). The results remained significant after multiple testing correction in both populations. Haplotype analysis and the results of an independent effect test using the weighted haplotype (WHAP) computer program in both populations were both compatible with SNP T263I being the only causal variant. The variant I263 is under-represented in otosclerosis patients and hence protective against the disease. Combining the data of both case-control groups for SNP T263I with a Mantel-Haenszel estimate of common odds ratios gave a very significant result (P = 9.2 x 10(-6)). Functional analysis of SNP T263I with a luciferase reporter assay showed that the protective variant I263 of TGF-beta1 is more active than the WT variant T263 (P = 1.6 x 10(-6)). On the basis of very low P-values, replication in an independent population and a functional effect of the protective variant, we conclude that TGF-beta1 influences the susceptibility for otosclerosis, and that the I263 variant is protective against the disease.

    View details for DOI 10.1093/hmg/ddm150

    View details for Web of Science ID 000250086400001

    View details for PubMedID 17588962