Bio

Bio


Dr. Steven Baker is a clinical instructor in the Department of Pathology. He graduated from Cornell University with a B.S. in Biological Sciences before completing an M.D. and Ph.D., in Developmental Biology, at Baylor College of Medicine. Clinically he specializes in the laboratory analysis of hemostatic disorders.

Clinical Focus


  • Pathology
  • Blood Coagulation Disorders

Academic Appointments


  • Clinical Instructor, Pathology

Professional Education


  • Doctor of Philosophy, Baylor College Of Medicine (2012)
  • Doctor of Medicine, Baylor College Of Medicine (2014)
  • Bachelor of Science, Cornell University (2004)
  • Residency:Stanford University Department of PathologyCA

Stanford Advisors


Publications

All Publications


  • Implementation of Whole-Blood Impedance Aggregometry for Heparin-Induced Thrombocytopenia Functional Assay and Case Discussion. American journal of clinical pathology Jin, J., Baker, S. A., Hall, E. T., Gombar, S., Bao, A., Zehnder, J. L. 2019; 152 (1): 50–58

    Abstract

    The diagnosis of heparin-induced thrombocytopenia (HIT) ideally requires a functional assay to confirm. 14C-serotonin release assay (SRA) as "gold standard" is technically challenging and unsuitable for routine use. We conducted a study to assess the performance of whole-blood impedance aggregometry (WBIA) as a simple and rapid HIT functional assay.Platelet factor 4 (PF4)/immunoglobulin G (IgG) antibody, WBIA, and SRA were tested on 70 patients suspected of having HIT. Patients with a 4Ts score of 4 or more, positive PF4/IgG, and positive SRA were considered HIT positive; others were designated HIT negative.WBIA had 85.7% (6/7) sensitivity and 98.4% (61/62) specificity, which were not statistically different compared with SRA. Sixty-two of 70 patients had concordant results (five positive and 57 negative) by both WBIA and SRA. Eight discordant cases revealed the importance of recognizing donor effect, interferences, and the presence of heparin-independent or non-heparin-dependent antibodies in functional assays.Implementation of WBIA could facilitate timely diagnosis and management of HIT.

    View details for DOI 10.1093/ajcp/aqz013

    View details for PubMedID 31165165

  • CASE REPORT: MONOCLONAL IGM & LAMBDA; COAGULATION INHIBITOR WITH PHOSPHATIDYLSERINE SPECIFICITY INTERFERING WITH PLASMA, BUT NOT WHOLE-BLOOD BASED COAGULATION TESTING Jin, J., Baker, S. A., Shokry, M., Zehnder, J. L. WILEY. 2018: E30
  • Genome-wide distribution of linker histone H1.0 is independent of MeCP2. Nature neuroscience Ito-Ishida, A., Yamalanchili, H. K., Shao, Y., Baker, S. A., Heckman, L. D., Lavery, L. A., Kim, J. Y., Lombardi, L. M., Sun, Y., Liu, Z., Zoghbi, H. Y. 2018; 21 (6): 794–98

    Abstract

    Previous studies suggested that MeCP2 competes with linker histone H1, but this hypothesis has never been tested in vivo. Here, we performed chromatin immunoprecipitation followed by sequencing (ChIP-seq) of Flag-tagged-H1.0 in mouse forebrain excitatory neurons. Unexpectedly, Flag-H1.0 and MeCP2 occupied similar genomic regions and the Flag-H1.0 binding was not changed upon MeCP2 depletion. Furthermore, mild overexpression of H1.0 did not alter MeCP2 binding, suggesting that the functional binding of MeCP2 and H1.0 are largely independent.

    View details for DOI 10.1038/s41593-018-0155-8

    View details for PubMedID 29802390

    View details for PubMedCentralID PMC6099063

  • An RNA interference screen identifies druggable regulators of MeCP2 stability SCIENCE TRANSLATIONAL MEDICINE Lombardi, L. M., Zaghlula, M., Sztainberg, Y., Baker, S. A., Klisch, T. J., Tang, A. A., Huang, E. J., Zoghbi, H. Y. 2017; 9 (404)

    Abstract

    Alterations in gene dosage due to copy number variation are associated with autism spectrum disorder, intellectual disability (ID), and other psychiatric disorders. The nervous system is so acutely sensitive to the dose of methyl-CpG-binding protein 2 (MeCP2) that even a twofold change in MeCP2 protein-either increased or decreased-results in distinct disorders with overlapping features including ID, autistic behavior, and severe motor dysfunction. Rett syndrome is caused by loss-of-function mutations in MECP2, whereas duplications spanning the MECP2 locus result in MECP2 duplication syndrome (MDS), which accounts for ~1% of X-linked ID. Despite evidence from mouse models that restoring MeCP2 can reverse the course of disease, there are currently no U.S. Food and Drug Administration-approved therapies available to clinically modulate MeCP2 abundance. We used a forward genetic screen against all known human kinases and phosphatases to identify druggable regulators of MeCP2 stability. Two putative modulators of MeCP2, HIPK2 (homeodomain-interacting protein kinase 2) and PP2A (protein phosphatase 2A), were validated as stabilizers of MeCP2 in vivo. Further, pharmacological inhibition of PP2A in vivo reduced MeCP2 in the nervous system and rescued both overexpression and motor abnormalities in a mouse model of MDS. Our findings reveal potential therapeutic targets for treating disorders of altered MECP2 dosage.

    View details for PubMedID 28835516

    View details for PubMedCentralID PMC5736385

  • Real-Time Clinical Decision Support Decreases Inappropriate Plasma Transfusion AMERICAN JOURNAL OF CLINICAL PATHOLOGY Shah, N., Baker, S. A., Spain, D., Shieh, L., Shepard, J., Hadhazy, E., Maggio, P., Goodnough, L. T. 2017; 148 (2): 154–60

    Abstract

    To curtail inappropriate plasma transfusions, we instituted clinical decision support as an alert upon order entry if the patient's recent international normalized ratio (INR) was 1.7 or less.The alert was suppressed for massive transfusion and within operative or apheresis settings. The plasma order was automatically removed upon alert acceptance while clinical exception reasons allowed for continued transfusion. Alert impact was studied comparing a 7-month control period with a 4-month intervention period.Monthly plasma utilization decreased 17.4%, from a mean ± SD of 3.40 ± 0.48 to 2.82 ± 0.6 plasma units per hundred patient days (95% confidence interval [CI] of difference, -0.1 to 1.3). Plasma transfused below an INR of 1.7 or less decreased from 47.6% to 41.6% (P = .0002; odds ratio, 0.78; 95% CI, 0.69-0.89). The alert recommendation was accepted 33% of the time while clinical exceptions were chosen in the remaining cases (active bleeding, 31%; other clinical indication, 33%; and apheresis, 2%). Alert acceptance rate varied significantly among different provider specialties.Clinical decision support can help curtail inappropriate plasma use but needs to be part of a comprehensive strategy including audit and feedback for comprehensive, long-term changes.

    View details for PubMedID 28898990

  • A study of the mutational landscape of pediatric-type follicular lymphoma and pediatric nodal marginal zone lymphoma. Modern pathology Ozawa, M. G., Bhaduri, A., Chisholm, K. M., Baker, S. A., Ma, L., Zehnder, J. L., Luna-Fineman, S., Link, M. P., Merker, J. D., Arber, D. A., Ohgami, R. S. 2016; 29 (10): 1212-1220

    Abstract

    Pediatric-type follicular lymphoma and pediatric marginal zone lymphoma are two of the rarest B-cell lymphomas. These lymphomas occur predominantly in the pediatric population and show features distinct from their more common counterparts in adults: adult-type follicular lymphoma and adult-type nodal marginal zone lymphoma. Here we report a detailed whole-exome deep sequencing analysis of a cohort of pediatric-type follicular lymphomas and pediatric marginal zone lymphomas. This analysis revealed a recurrent somatic variant encoding p.Lys66Arg in the transcription factor interferon regulatory factor 8 (IRF8) in 3 of 6 cases (50%) of pediatric-type follicular lymphoma. This specific point mutation was not detected in pediatric marginal zone lymphoma or in adult-type follicular lymphoma. Additional somatic point mutations in pediatric-type follicular lymphoma were observed in genes involved in transcription, intracellular signaling, and cell proliferation. In pediatric marginal zone lymphoma, no recurrent mutation was identified; however, somatic point mutations were observed in genes involved in cellular adhesion, cytokine regulatory elements, and cellular proliferation. A somatic variant in AMOTL1, a recurrently mutated gene in splenic marginal zone lymphoma, was also identified in a case of pediatric marginal zone lymphoma. The overall non-synonymous mutational burden was low in both pediatric-type follicular lymphoma and pediatric marginal zone lymphoma (4.6 mutations per exome). Altogether, these findings support a distinctive genetic basis for pediatric-type follicular lymphoma and pediatric marginal zone lymphoma when compared with adult subtypes and to one another. Moreover, identification of a recurrent point mutation in IRF8 provides insight into a potential driver mutation in the pathogenesis of pediatric-type follicular lymphoma with implications for novel diagnostic or therapeutic strategies.Modern Pathology advance online publication, 24 June 2016; doi:10.1038/modpathol.2016.102.

    View details for DOI 10.1038/modpathol.2016.102

    View details for PubMedID 27338637

  • How I use clinical decision support to improve red blood cell utilization TRANSFUSION Goodnough, L. T., Baker, S. A., Shah, N. 2016; 56 (10): 2406-2411

    Abstract

    Despite 20 years of published medical society guidelines for blood transfusion and a pivotal clinical trial in 1999 providing Level 1 evidence that restrictive transfusion practices can be utilized safely, blood transfusions did not begin to decline in the United States until 2010. Widespread adoption of electronic medical records allowed implementation of computerized systems such as clinical decision support (CDS) with best practice alerts to improve blood utilization. We describe our own experience using well-designed and highly targeted CDS to promote restrictive transfusion practices and improve red blood cell utilization, with a 42% reduction in blood transfusions from 2009 through 2015, accompanied by improved clinical outcomes.

    View details for DOI 10.1111/trf.13767

    View details for Web of Science ID 000385834800004

  • Transportation Cooler Interventions Reduce Plasma and RBC Product Wastage. American journal of clinical pathology Metcalf, R. A., Baker, S. A., Goodnough, L. T., Shah, N. 2016; 146 (1): 18-24

    Abstract

    The rate of plasma product wastage for the United States in 2011 was approximately 1.8%. The plasma wastage rate at our institution was higher, mainly due to products returned out of temperature range from procedural areas. A process review and intervention to reduce plasma wastage was undertaken, which included modifications to our transport cooler.A new cooler system was designed, and this device was implemented alongside an updated protocol for delivering plasma while also enhancing the previous RBC cooler validation time. We audited plasma and RBC product wastage prior to these interventions, from January 2013 to February 2014, vs after the intervention from April 2014 to March 2015.After the intervention, the monthly plasma wastage rate declined 60% (12.6 units/100 units transfused preintervention vs 5.0 units/100 units transfused postintervention; P < .0001). The monthly RBC wastage rate also decreased 28% (3.2 units/100 units transfused preintervention vs 2.3 units/100 units transfused postintervention; P < .01).Our intervention resulted in significantly decreased plasma and RBC wastage and is broadly applicable, since out-of-temperature product wastage in procedural areas is likely a significant problem at many institutions.

    View details for DOI 10.1093/ajcp/aqw082

    View details for PubMedID 27357292

  • MeCP2 binds to non-CG methylated DNA as neurons mature, influencing transcription and the timing of onset for Rett syndrome. Proceedings of the National Academy of Sciences of the United States of America Chen, L., Chen, K., Lavery, L. A., Baker, S. A., Shaw, C. A., Li, W., Zoghbi, H. Y. 2015; 112 (17): 5509–14

    Abstract

    Epigenetic mechanisms, such as DNA methylation, regulate transcriptional programs to afford the genome flexibility in responding to developmental and environmental cues in health and disease. A prime example involving epigenetic dysfunction is the postnatal neurodevelopmental disorder Rett syndrome (RTT), which is caused by mutations in the gene encoding methyl-CpG binding protein 2 (MeCP2). Despite decades of research, it remains unclear how MeCP2 regulates transcription or why RTT features appear 6-18 months after birth. Here we report integrated analyses of genomic binding of MeCP2, gene-expression data, and patterns of DNA methylation. In addition to the expected high-affinity binding to methylated cytosine in the CG context (mCG), we find a distinct epigenetic pattern of substantial MeCP2 binding to methylated cytosine in the non-CG context (mCH, where H = A, C, or T) in the adult brain. Unexpectedly, we discovered that genes that acquire elevated mCH after birth become preferentially misregulated in mouse models of MeCP2 disorders, suggesting that MeCP2 binding at mCH loci is key for regulating neuronal gene expression in vivo. This pattern is unique to the maturing and adult nervous system, as it requires the increase in mCH after birth to guide differential MeCP2 binding among mCG, mCH, and nonmethylated DNA elements. Notably, MeCP2 binds mCH with higher affinity than nonmethylated identical DNA sequences to influence the level of Bdnf, a gene implicated in the pathophysiology of RTT. This study thus provides insight into the molecular mechanism governing MeCP2 targeting and sheds light on the delayed onset of RTT symptoms.

    View details for DOI 10.1073/pnas.1505909112

    View details for PubMedID 25870282

    View details for PubMedCentralID PMC4418849

  • Karyopherin α 3 and karyopherin α 4 proteins mediate the nuclear import of methyl-CpG binding protein 2. The Journal of biological chemistry Baker, S. A., Lombardi, L. M., Zoghbi, H. Y. 2015; 290 (37): 22485–93

    Abstract

    Methyl-CpG binding protein 2 (MeCP2) is a nuclear protein with important roles in regulating chromatin structure and gene expression, and mutations in MECP2 cause Rett syndrome (RTT). Within the MeCP2 protein sequence, the nuclear localization signal (NLS) is reported to reside between amino acids 255-271, and certain RTT-causing mutations overlap with the MeCP2 NLS, suggesting that they may alter nuclear localization. One such mutation, R270X, is predicted to interfere with the localization of MeCP2, but recent in vivo studies have demonstrated that this mutant remains entirely nuclear. To clarify the mechanism of MeCP2 nuclear import, we isolated proteins that interact with the NLS and identified karyopherin α 3 (KPNA3 or Kap-α3) and karyopherin α 4 (KPNA4 or Kap-α4) as key binding partners of MeCP2. MeCP2-R270X did not interact with KPNA4, consistent with a requirement for an intact NLS in this interaction. However, this mutant retains binding to KPNA3, accounting for the normal localization of MeCP2-R270X to the nucleus. These data provide a mechanism for MeCP2 nuclear import and have implications for the design of therapeutics aimed at modulating the function of MeCP2 in RTT patients.

    View details for DOI 10.1074/jbc.M115.658104

    View details for PubMedID 26245896

    View details for PubMedCentralID PMC4566224

  • MECP2 disorders: from the clinic to mice and back. The Journal of clinical investigation Lombardi, L. M., Baker, S. A., Zoghbi, H. Y. 2015; 125 (8): 2914–23

    Abstract

    Two severe, progressive neurological disorders characterized by intellectual disability, autism, and developmental regression, Rett syndrome and MECP2 duplication syndrome, result from loss and gain of function, respectively, of the same critical gene, methyl-CpG-binding protein 2 (MECP2). Neurons acutely require the appropriate dose of MECP2 to function properly but do not die in its absence or overexpression. Instead, neuronal dysfunction can be reversed in a Rett syndrome mouse model if MeCP2 function is restored. Thus, MECP2 disorders provide a unique window into the delicate balance of neuronal health, the power of mouse models, and the importance of chromatin regulation in mature neurons. In this Review, we will discuss the clinical profiles of MECP2 disorders, the knowledge acquired from mouse models of the syndromes, and how that knowledge is informing current and future clinical studies.

    View details for DOI 10.1172/JCI78167

    View details for PubMedID 26237041

    View details for PubMedCentralID PMC4563741

  • An AT-hook domain in MeCP2 determines the clinical course of Rett syndrome and related disorders. Cell Baker, S. A., Chen, L., Wilkins, A. D., Yu, P., Lichtarge, O., Zoghbi, H. Y. 2013; 152 (5): 984–96

    Abstract

    Mutations in the X-linked MECP2 cause Rett syndrome, a devastating neurological disorder typified by a period of apparently normal development followed by loss of cognitive and psychomotor skills. Data from rare male patients suggest symptom onset and severity can be influenced by the location of the mutation, with amino acids 270 and 273 marking the difference between neonatal encephalopathy and death, on the one hand, and survival with deficits on the other. We therefore generated two mouse models expressing either MeCP2-R270X or MeCP2-G273X. The mice developed phenotypes at strikingly different rates and showed differential ATRX nuclear localization within the nervous system, over time, coinciding with phenotypic progression. We discovered that MeCP2 contains three AT-hook-like domains over a stretch of 250 amino acids, like HMGA DNA-bending proteins; one conserved AT-hook is disrupted in MeCP2-R270X, lending further support to the notion that one of MeCP2's key functions is to alter chromatin structure.

    View details for DOI 10.1016/j.cell.2013.01.038

    View details for PubMedID 23452848

    View details for PubMedCentralID PMC3641682

  • Dendritic arborization and spine dynamics are abnormal in the mouse model of MECP2 duplication syndrome. The Journal of neuroscience : the official journal of the Society for Neuroscience Jiang, M., Ash, R. T., Baker, S. A., Suter, B., Ferguson, A., Park, J., Rudy, J., Torsky, S. P., Chao, H. T., Zoghbi, H. Y., Smirnakis, S. M. 2013; 33 (50): 19518–33

    Abstract

    MECP2 duplication syndrome is a childhood neurological disorder characterized by intellectual disability, autism, motor abnormalities, and epilepsy. The disorder is caused by duplications spanning the gene encoding methyl-CpG-binding protein-2 (MeCP2), a protein involved in the modulation of chromatin and gene expression. MeCP2 is thought to play a role in maintaining the structural integrity of neuronal circuits. Loss of MeCP2 function causes Rett syndrome and results in abnormal dendritic spine morphology and decreased pyramidal dendritic arbor complexity and spine density. The consequences of MeCP2 overexpression on dendritic pathophysiology remain unclear. We used in vivo two-photon microscopy to characterize layer 5 pyramidal neuron spine turnover and dendritic arborization as a function of age in transgenic mice expressing the human MECP2 gene at twice the normal levels of MeCP2 (Tg1; Collins et al., 2004). We found that spine density in terminal dendritic branches is initially higher in young Tg1 mice but falls below control levels after postnatal week 12, approximately correlating with the onset of behavioral symptoms. Spontaneous spine turnover rates remain high in older Tg1 animals compared with controls, reflecting the persistence of an immature state. Both spine gain and loss rates are higher, with a net bias in favor of spine elimination. Apical dendritic arbors in both simple- and complex-tufted layer 5 Tg1 pyramidal neurons have more branches of higher order, indicating that MeCP2 overexpression induces dendritic overgrowth. P70S6K was hyperphosphorylated in Tg1 somatosensory cortex, suggesting that elevated mTOR signaling may underlie the observed increase in spine turnover and dendritic growth.

    View details for DOI 10.1523/JNEUROSCI.1745-13.2013

    View details for PubMedID 24336718

    View details for PubMedCentralID PMC3858623