Browsing by Author "Clish, Clary B."

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    A Metabolomics Approach to Identify Metabolites Associated With Mortality in Patients Receiving Maintenance Hemodialysis
    (Elsevier, 2024-06-29) Al Awadhi, Solaf; Myint, Leslie; Guallar, Eliseo; Clish, Clary B.; Wulczyn, Kendra E.; Kalim, Sahir; Thadhani, Ravi; Segev, Dorry L.; McAdams DeMarco, Mara; Moe, Sharon M.; Moorthi, Ranjani N.; Hostetter, Thomas H.; Himmelfarb, Jonathan; Meyer, Timothy W.; Powe, Neil R.; Tonelli, Marcello; Rhee, Eugene P.; Shafi, Tariq; Medicine, School of Medicine
    Introduction: Uremic toxins contributing to increased risk of death remain largely unknown. We used untargeted metabolomics to identify plasma metabolites associated with mortality in patients receiving maintenance hemodialysis. Methods: We measured metabolites in serum samples from 522 Longitudinal US/Canada Incident Dialysis (LUCID) study participants. We assessed the association between metabolites and 1-year mortality, adjusting for age, sex, race, cardiovascular disease, diabetes, body mass index, serum albumin, Kt/Vurea, dialysis duration, and country. We modeled these associations using limma, a metabolite-wise linear model with empirical Bayesian inference, and 2 machine learning (ML) models: Least absolute shrinkage and selection operator (LASSO) and random forest (RF). We accounted for multiple testing using a false discovery rate (pFDR) adjustment. We defined significant mortality-metabolite associations as pFDR < 0.1 in the limma model and metabolites of at least medium importance in both ML models. Results: The mean age of the participants was 64 years, the mean dialysis duration was 35 days, and there were 44 deaths (8.4%) during a 1-year follow-up period. Two metabolites were significantly associated with 1-year mortality. Quinolinate levels (a kynurenine pathway metabolite) were 1.72-fold higher in patients who died within year 1 compared with those who did not (pFDR, 0.009), wheras mesaconate levels (an emerging immunometabolite) were 1.57-fold higher (pFDR, 0.002). An additional 42 metabolites had high importance as per LASSO, 46 per RF, and 9 per both ML models but were not significant per limma. Conclusion: Quinolinate and mesaconate were significantly associated with a 1-year risk of death in incident patients receiving maintenance hemodialysis. External validation of our findings is needed.
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    The cytoplasmic prolyl-tRNA synthetase of the malaria parasite is a dual-stage target of febrifugine and its analogs
    (American Association for the Advancement of Science, 2015-05) Herman, Jonathan D.; Pepper, Lauren R.; Cortese, Joseph F.; Estiu, Guillermina; Galinsky, Kevin; Zuzarte-Luis, Vanessa; Derbyshire, Emily R.; Ribacke, Ulf; Lukens, Amanda K.; Santos, Sofia A.; Patel, Vishal; Clish, Clary B.; Sullivan, William J., Jr.; Zhou, Huihao; Bopp, Selina E.; Schimmel, Paul; Lindquist, Susan; Clardy, Jon; Mota, Maria M.; Keller, Tracy L.; Whitman, Malcolm; Wiest, Olaf; Wirth, Dyann F.; Mazitschek, Ralph; Department of Pharmacology and Toxicology, IU School of Medicine
    The emergence of drug resistance is a major limitation of current antimalarials. The discovery of new druggable targets and pathways including those that are critical for multiple life cycle stages of the malaria parasite is a major goal for developing next-generation antimalarial drugs. Using an integrated chemogenomics approach that combined drug resistance selection, whole-genome sequencing, and an orthogonal yeast model, we demonstrate that the cytoplasmic prolyl-tRNA (transfer RNA) synthetase (PfcPRS) of the malaria parasite Plasmodium falciparum is a biochemical and functional target of febrifugine and its synthetic derivative halofuginone. Febrifugine is the active principle of a traditional Chinese herbal remedy for malaria. We show that treatment with febrifugine derivatives activated the amino acid starvation response in both P. falciparum and a transgenic yeast strain expressing PfcPRS. We further demonstrate in the Plasmodium berghei mouse model of malaria that halofuginol, a new halofuginone analog that we developed, is active against both liver and asexual blood stages of the malaria parasite. Halofuginol, unlike halofuginone and febrifugine, is well tolerated at efficacious doses and represents a promising lead for the development of dual-stage next-generation antimalarials.
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    Higher susceptibility to sunburn is associated with decreased plasma glutamine and increased plasma glutamate levels among US women: An analysis of the Nurses' Health Study I and II
    (Elsevier, 2021) Yang, Keming; Li, Xin; Zeleznik, Oana A.; Eliassen, A. Heather; Clish, Clary B.; Cho, Eunyoung; Somani, Ally-Khan B.; Qureshi, Abrar A.; Giovannucci, Edward L.; Nan, Hongmei; Epidemiology, School of Public Health
    To the Editor: The metabolism of glutamine and glutamate, 2 important amino acids synthesized in the human body, may have an etiologic role in melanoma, an aggressive skin malignancy. 1 , 2 Preclinical experiments and clinical trials have found that metabotropic glutamate receptor 1 blocker and glutamate release inhibitor (eg, Riluzole) can suppress melanoma cell migration, invasion, and proliferation. 2 Additionally, inhibiting glutaminase, the enzyme that converts glutamine to glutamate, further reduced glutamate bioavailability and suppressed tumor progression. 1 Susceptibility to sunburn, a pigmentary trait, is a well-known risk factor for melanoma. 3 However, it is unclear whether plasma glutamate and glutamine are affected by this host factor even before cancer onset.
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    Plasma metabolites and physical function in patients undergoing hemodialysis
    (Springer Nature, 2024-04-10) Moorthi, Ranjani N.; Moe, Sharon M.; O’Connell, Thomas; Dickinson, Stephanie; Kalim, Sahir; Thadhani, Ravi; Clish, Clary B.; Shafi, Tariq; Rhee, Eugene P.; Avin, Keith G.; Medicine, School of Medicine
    Impaired physical function contributes to falls, fractures, and mortality among patients undergoing dialysis. Using a metabolomic approach, we identified metabolite alterations and effect size-based composite scores for constructs of impaired gait speed and grip strength. 108 participants incident to dialysis had targeted plasma metabolomics via liquid chromatography-mass spectrometry and physical function assessed (i.e., 4 m walk, handgrip strength). Physical function measures were categorized as above/ below median, with grip utilizing sex-based medians. To develop composite scores, metabolites were identified via Wilcoxon uncorrected p < 0.05 and effect size > 0.40. Receiver operating characteristic analyses tested whether scores differentiated between above/below function groups. Participants were 54% male, 77% Black and 53 ± 14 y with dialysis vintage of 101 ± 50 days. Median (IQR) grip strength was 35.5 (11.1) kg (males) and 20 (8.4) kg (females); median gait speed was 0.82 (0.34) m/s. Of 246 measured metabolites, composite scores were composed of 22 and 12 metabolites for grip strength and gait speed, respectively. Area under the curve for metabolite composite was 0.88 (gait) and 0.911 (grip). Composite scores of physical function performed better than clinical parameters alone in patients on dialysis. These results provide potential pathways for interventions and needed validation in an independent cohort.
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    Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program
    (Springer Nature, 2021) Taliun, Daniel; Harris, Daniel N.; Kessler, Michael D.; Carlson, Jedidiah; Szpiech, Zachary A.; Torres, Raul; Gagliano Taliun, Sarah A.; Corvelo, André; Gogarten, Stephanie M.; Kang, Hyun Min; Pitsillides, Achilleas N.; LeFaive, Jonathon; Lee, Seung-Been; Tian, Xiaowen; Browning, Brian L.; Das, Sayantan; Emde, Anne-Katrin; Clarke, Wayne E.; Loesch, Douglas P.; Shetty, Amol C.; Blackwell, Thomas W.; Smith, Albert V.; Wong, Quenna; Liu, Xiaoming; Conomos, Matthew P.; Bobo, Dean M.; Aguet, François; Albert, Christine; Alonso, Alvaro; Ardlie, Kristin G.; Arking, Dan E.; Aslibekyan, Stella; Auer, Paul L.; Barnard, John; Barr, R. Graham; Barwick, Lucas; Becker, Lewis C.; Beer, Rebecca L.; Benjamin, Emelia J.; Bielak, Lawrence F.; Blangero, John; Boehnke, Michael; Bowden, Donald W.; Brody, Jennifer A.; Burchard, Esteban G.; Cade, Brian E.; Casella, James F.; Chalazan, Brandon; Chasman, Daniel I.; Chen, Yii-Der Ida; Cho, Michael H.; Choi, Seung Hoan; Chung, Mina K.; Clish, Clary B.; Correa, Adolfo; Curran, Joanne E.; Custer, Brian; Darbar, Dawood; Daya, Michelle; de Andrade, Mariza; DeMeo, Dawn L.; Dutcher, Susan K.; Ellinor, Patrick T.; Emery, Leslie S.; Eng, Celeste; Fatkin, Diane; Fingerlin, Tasha; Forer, Lukas; Fornage, Myriam; Franceschini, Nora; Fuchsberger, Christian; Fullerton, Stephanie M.; Germer, Soren; Gladwin, Mark T.; Gottlieb, Daniel J.; Guo, Xiuqing; Hall, Michael E.; He, Jiang; Heard-Costa, Nancy L.; Heckbert, Susan R.; Irvin, Marguerite R.; Johnsen, Jill M.; Johnson, Andrew D.; Kaplan, Robert; Kardia, Sharon L. R.; Kelly, Tanika; Kelly, Shannon; Kenny, Eimear E.; Kiel, Douglas P.; Klemmer, Robert; Konkle, Barbara A.; Kooperberg, Charles; Köttgen, Anna; Lange, Leslie A.; Lasky-Su, Jessica; Levy, Daniel; Lin, Xihong; Lin, Keng-Han; Liu, Chunyu; Loos, Ruth J. F.; Garman, Lori; Gerszten, Robert; Lubitz, Steven A.; Lunetta, Kathryn L.; Mak, Angel C. Y.; Manichaikul, Ani; Manning, Alisa K.; Mathias, Rasika A.; McManus, David D.; McGarvey, Stephen T.; Meigs, James B.; Meyers, Deborah A.; Mikulla, Julie L.; Minear, Mollie A.; Mitchell, Braxton D.; Mohanty, Sanghamitra; Montasser, May E.; Montgomery, Courtney; Morrison, Alanna C.; Murabito, Joanne M.; Natale, Andrea; Natarajan, Pradeep; Nelson, Sarah C.; North, Kari E.; O'Connell, Jeffrey R.; Palmer, Nicholette D.; Pankratz, Nathan; Peloso, Gina M.; Peyser, Patricia A.; Pleiness, Jacob; Post, Wendy S.; Psaty, Bruce M.; Rao, D. C.; Redline, Susan; Reiner, Alexander P.; Roden, Dan; Rotter, Jerome I.; Ruczinski, Ingo; Sarnowski, Chloé; Schoenherr, Sebastian; Schwartz, David A.; Seo, Jeong-Sun; Seshadri, Sudha; Sheehan, Vivien A.; Sheu, Wayne H.; Shoemaker, M. Benjamin; Smith, Nicholas L.; Smith, Jennifer A.; Sotoodehnia, Nona; Stilp, Adrienne M.; Tang, Weihong; Taylor, Kent D.; Telen, Marilyn; Thornton, Timothy A.; Tracy, Russell P.; Van Den Berg, David J.; Vasan, Ramachandran S.; Viaud-Martinez, Karine A.; Vrieze, Scott; Weeks, Daniel E.; Weir, Bruce S.; Weiss, Scott T.; Weng, Lu-Chen; Willer, Cristen J.; Zhang, Yingze; Zhao, Xutong; Arnett, Donna K.; Ashley-Koch, Allison E.; Barnes, Kathleen C.; Boerwinkle, Eric; Gabriel, Stacey; Gibbs, Richard; Rice, Kenneth M.; Rich, Stephen S.; Silverman, Edwin K.; Qasba, Pankaj; Gan, Weiniu; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium; Papanicolaou, George J.; Nickerson, Deborah A.; Browning, Sharon R.; Zody, Michael C.; Zöllner, Sebastian; Wilson, James G.; Cupples, L. Adrienne; Laurie, Cathy C.; Jaquish, Cashell E.; Hernandez, Ryan D.; O'Connor, Timothy D.; Abecasis, Gonçalo R.; Epidemiology, Richard M. Fairbanks School of Public Health
    The Trans-Omics for Precision Medicine (TOPMed) programme seeks to elucidate the genetic architecture and biology of heart, lung, blood and sleep disorders, with the ultimate goal of improving diagnosis, treatment and prevention of these diseases. The initial phases of the programme focused on whole-genome sequencing of individuals with rich phenotypic data and diverse backgrounds. Here we describe the TOPMed goals and design as well as the available resources and early insights obtained from the sequence data. The resources include a variant browser, a genotype imputation server, and genomic and phenotypic data that are available through dbGaP (Database of Genotypes and Phenotypes)1. In the first 53,831 TOPMed samples, we detected more than 400 million single-nucleotide and insertion or deletion variants after alignment with the reference genome. Additional previously undescribed variants were detected through assembly of unmapped reads and customized analysis in highly variable loci. Among the more than 400 million detected variants, 97% have frequencies of less than 1% and 46% are singletons that are present in only one individual (53% among unrelated individuals). These rare variants provide insights into mutational processes and recent human evolutionary history. The extensive catalogue of genetic variation in TOPMed studies provides unique opportunities for exploring the contributions of rare and noncoding sequence variants to phenotypic variation. Furthermore, combining TOPMed haplotypes with modern imputation methods improves the power and reach of genome-wide association studies to include variants down to a frequency of approximately 0.01%.