Chen, J; Xu, H; Jegga, A; Zhang, K; White, PS; Zhang, G. Novel phenotype-disease matching tool for rare genetic diseases. Genetics in Medicine. 2019; 88(2):341-348.
Our study was a proof of concept to utilize phenotypic information from clinical data, such as clinical notes or electronic health records (EHRs), as a step toward developing a full-fledged bioinformatics tool that can help clinicians diagnose genetic disease at high accuracy. Our results demonstrated that the phenotypic information was valuable to genetic disease diagnosis, and the computational methods we proposed could effectively utilize that information for genetic disease diagnosis.
Swertfeger, DK; Rebholz, S; Li, H; Shah, AS; Davidson, WS; Lu, LJ. Feasibility of a plasma bioassay to assess oxidative protection of low-density lipoproteins by high-density lipoproteins. Journal of Clinical Lipidology. 2018; 12(6):1539-1548.
HDL’s inverse association with decreased atherosclerosis risk likely results from its many functions, including anti-oxidation and immune modulation, as well as its regulation of complement, hemostasis, thrombosis, and protease inhibition. We have shown that HDL’s anti-oxidant function is a minor component of the total plasma anti-oxidant activity, and thus the development of a bioassay to measure HDL’s anti-oxidant capacity will require its separation from plasma, which contains many other potent anti-oxidant components.
Churko, JM; Garg, P; Treutlein, B; Venkatasubramanian, M; Wu, H; Lee, J; Wessells, QN; Chen, S; Chen, W; Chetal, K; Mantalas, G; Neff, N; Jabart, E; Sharma, A; Nolan, GP; Salomonis, N; Wu, JC. Defining human cardiac transcription factor hierarchies using integrated single-cell heterogeneity analysis. Nature Communications. 2018; 9(1).
To accelerate the development of new drugs for the treatment of major cardiac disorders, we desperately need improved ways to mimic the human heart in a dish. Here, we applied advanced single-cell profiling technologies with new bioinformatics methods to define new developmental hierarchies that inform heart development and enable improved methods for drug screening.
Nielsen, SCA; Roskin, KM; Jackson, KJ L; Joshi, SA; Nejad, P; Lee, J; Wagar, LE; Pham, TD; Hoh, RA; Nguyen, KD; Tsunemoto, HY; Patel, SB; Tibshirani, R; Ley, C; Davis, MM; Parsonnet, J; Boyd, SD. Shaping of infant B cell receptor repertoires by environmental factors and infectious disease. Science Translational Medicine. 2019; 11(481).
B cells and the antibodies they produce are central to immune defense. In this paper, we look at data from a birth cohort and analyze how the infant B cell repertoire "boots up" to better understand how the immune system is shaped by early antigen exposures and how that could lead to allergy and other immune diseases.
Turnier, JL; Brunner, HI; Bennett, M; Aleed, A; Gulati, G; Haffey, WD; Thornton, S; Wagner, M; Devarajan, P; Witte, D; Greis, KD; Aronow, B. Discovery of SERPINA3 as a candidate urinary biomarker of lupus nephritis activity. Rheumatology. 2019; 58(2):321-330.
This manuscript used advanced—but difficult and expensive-to-use—proteomics technology to study Lupus Nephritis patients who face uncertain outcomes that can greatly affect the severity of their disease. We identified SERPINA3, a known inhibitor of neutrophil cathepsin G and angiotensin II production, as a potential urine biomarker capable of predicting differential Lupus Nephritis (LN) disease activity patterns. Histopathological confirmation of its expression in diseased kidney biopsies confirmed the implications of the proteomic data analyses and supported the idea that urine SERPINA3 holds potential as a novel biomarker of LN activity. Monitoring its level in further studies may be useful for following the effectiveness of clinical treatment regimens.