Bacterial Pathogenesis
Rodriguez R, Campbell-Kruger N, Camba JG, Berude J, Fetterman R, Stanley SA. MarR-Dependent Transcriptional Regulation of mmpSL5 induces Ethionamide Resistance in Mycobacterium abscessus. BioRxiv 2022. Antimicrob Agents Chemother. 2023. PMID 36988462.
Van Dis E, Morrison HM, Fines DM, Babirye JP, McCann LH, Rawal S, Cox JS, Stanley SA. IFN-γ-independent control of M. tuberculosis requires CD4 T cell-derived GM-CSF and activation of HIF-1α. bioRxiv 2021. PLoS Pathog 2022 Jul 25;18(7):e1010721. PMID: 35877763.
Darwin KH, Stanley SA. The aldehyde hypothesis: metabolic intermediates as antimicrobial effectors. Open Biol. 2022 Apr;12(4):220010.PMID: 35414258.
*Jong RM, *Van Dis E, Berry SB, Nguyenla X, Baltodano A, Pastenkos G, Xu C, Fox D, Yosef N, McWhirter SM, Stanley SA. Mucosal Vaccination with Cyclic Dinucleotide Adjuvants Induces Effective T Cell Homing and IL-17-Dependent Protection against Mycobacterium tuberculosis Infection. J Immunol. 2022 Jan 15;208(2):407–419. PMCID: PMC8755605. *co-authors
*Lien KA, *Dinshaw K, Nichols RJ, Cassidy-Amstutz C, Knight M, Singh R, Eltis LD, Savage DF, Stanley SA. A nanocompartment system contributes to defense against oxidative stress in Mycobacterium tuberculosis. eLife. 2021 Nov 9;10. Available from: http://dx.doi.org/10.7554/eLife.74358 PMCID: PMC8635971. *co-authors
Ravesloot-Chávez MM, Van Dis E, Stanley SA. The Innate Immune Response to Mycobacterium tuberculosis Infection. Annu Rev Immunol. Annual Reviews; 2021 Apr 26;39(1):611–637. PMID: 33637017
Knight M, Stanley SA. HIF-1α as a central mediator of cellular resistance to intracellular pathogens. Curr Opin Immunol. 2019 Oct;60:111–116. PMCID: PMC8592400
Van Dis E, Sogi KM, Rae CS, Sivick KE, Surh NH, Leong ML, Kanne DB, Metchette K, Leong JJ, Bruml JR, Chen V, Heydari K, Cadieux N, Evans T, McWhirter SM, Dubensky TW, Portnoy DA, Stanley SA. STING-Activating Adjuvants Elicit a Th17 Immune Response and Protect against Mycobacterium tuberculosis Infection. Cell Rep. 2018 May;23(5):1435–1447. PMCID: PMC6003617
*Knight M, *Braverman J, Asfaha K, Gronert K, Stanley SA. Lipid droplet formation in Mycobacterium tuberculosis infected macrophages requires IFN-γ/HIF-1α signaling and supports host defense. PLoS Pathog. 2018 Jan 25;14(1):e1006874. PMCID: PMC5800697. *co-authors
Braverman J, Stanley SA. Nitric Oxide Modulates Macrophage Responses to Mycobacterium tuberculosis Infection through Activation of HIF-1α and Repression of NF-κB. Mian Yi Xue Za Zhi. 2017 Sep;199(5):1805–1816. PMCID: PMC5568107
Sogi KM, Lien KA, Johnson JR, Krogan NJ, Stanley SA. The Tyrosine Kinase Inhibitor Gefitinib Restricts Mycobacterium tuberculosis Growth through Increased Lysosomal Biogenesis and Modulation of Cytokine Signaling. ACS Infectious Diseases. 2017 Aug 11;3(8):564–574. PMCID: PMC5728371
Braverman J, Sogi KM, Benjamin D, Nomura DK, Stanley SA. HIF-1α Is an Essential Mediator of IFN-γ-Dependent Immunity to Mycobacterium tuberculosis. Mian Yi Xue Za Zhi. 2016 Aug 15;197(4):1287–1297. PMCID: PMC4976004
COVID-19
Biering SB, de Sousa FTG, Tjang LV, Pahmeier F, Zhu C, Ruan R, Blanc SF, Patel TS, Worthington CM, Glasner DR, Castillo-Rojas B, Servellita V, Lo NTN, Wong MP, Warnes CM, Sandoval DR, Clausen TM, Santos YA, Fox DA, Ortega V, Naar AM, Baric RS, Stanley SA, Aguilar HC, Esko JD, Chiu CY, Pak JE, Beatty PR, Harris E. SARS-CoV-2 Spike triggers barrier dysfunction and vascular leak via integrins and TGF-β signaling. bioRxiv 2021 Dec 13; Nature Communications, 2023. PMID: 34931188.
Nguyenla X, Wehri E, Van Dis E, Biering SB, Yamashiro LH, Stroumza J, Dugast-Darzacq C, Graham T, Stanley SA†, Schaletzky J†. Discovery of SARS-CoV-2 antiviral synergy between remdesivir and approved drugs in human lung cells. bioRxiv. 2020, Scientific Reports, 12, 18506 (2022). †co-corresponding.
Chandrasekaran SS, Agrawal S, Fanton A, Jangid AR, Charrez B, Escajeda AM, Son S, Mcintosh R, Tran H, Bhuiya A, de León Derby MD, Switz NA, Armstrong M, Harris AR, Prywes N, Lukarska M, Biering SB, Smock DCJ, Mok A, Knott GJ, Dang Q, Van Dis E, Dugan E, Kim S, Liu TY, IGI Testing Consortium, Moehle EA, Kogut K, Eskenazi B, Harris E, Stanley SA, Lareau LF, Tan MX, Fletcher DA, Doudna JA, Savage DF, Hsu PD. Rapid detection of SARS-CoV-2 RNA in saliva via Cas13. Nat Biomed Eng. 2022 Aug;6(8):944–956. PMID: 35953650
Biering SB, Sarnik SA, Wang E, Zengel JR, Leist SR, Schäfer A, Sathyan V, Hawkins P, Okuda K, Tau C, Jangid AR, Duffy CV, Wei J, Gilmore RC, Alfajaro MM, Strine MS, Nguyenla X, Van Dis E, Catamura C, Yamashiro LH, Belk JA, Begeman A, Stark JC, Shon DJ, Fox DM, Ezzatpour S, Huang E, Olegario N, Rustagi A, Volmer AS, Livraghi-Butrico A, Wehri E, Behringer RR, Cheon DJ, Schaletzky J, Aguilar HC, Puschnik AS, Button B, Pinsky BA, Blish CA, Baric RS, O’Neal WK, Bertozzi CR, Wilen CB, Boucher RC, Carette JE, Stanley SA, Harris E, Konermann S, Hsu PD. Genome-wide bidirectional CRISPR screens identify mucins as host factors modulating SARS-CoV-2 infection. Nat Genet. 2022 Aug;54(8):1078–1089. PMCID: PMC9355872
Zhu C, Lee JY, Woo JZ, Xu L, Nguyenla X, Yamashiro LH, Ji F, Biering SB, Van Dis E, Gonzalez, Fox D, Wehri, E, Rustagi A, Pinsky BA, Schaletzky J, Blish CA, Chiu C, Harris E, Sadreyev RI, Stanley SA, Kauppinen S, Rouskin S, Naar A. An intranasal ASO therapeutic targeting SARS-CoV-2. Nat Commun. 2022;13(1):1–13. PMID: 35922434
Zeng L, Liu Y, Nguyenla XH, Abbott TR, Han M, Zhu Y, Chemparathy A, Lin X, Chen X, Wang H, Rane DA, Spatz JM, Jain S, Rustagi A, Pinsky B, Zepeda AE, Kadina AP, Walker JA 3rd, Holden K, Temperton N, Cochran JR, Barron AE, Connolly MD, Blish CA, Lewis DB, Stanley SA†, La Russa MF†, Qi LS†. Broad-spectrum CRISPR-mediated inhibition of SARS-CoV-2 variants and endemic coronaviruses in vitro. Nat Commun. 2022 May 19;13(1):2766. PMCID: PMC9119983. †co-corresponding.
Carroll T, Fox D, van Doremalen N, Ball E, Morris MK, Sotomayor-Gonzalez A, Servellita V, Rustagi A, Yinda CK, Fritts L, Port JR, Ma ZM, Holbrook MG, Schulz J, Blish CA, Hanson C, Chiu CY, Munster V†, Stanley SA†, Miller CJ†. The B.1.427/1.429 (epsilon) SARS-CoV-2 variants are more virulent than ancestral B.1 (614G) in Syrian hamsters. PLoS Pathog. 2022 Feb;18(2):e1009914. PMCID: PMC8865701. †co-corresponding.
Golovkine GR, Roberts AW, Cooper C, Riano S, DiCiccio AM, Worthington DL, Clarkson JP, Krames M, Zhang J, Gao Y, Zhou L, Biering SB, Stanley SA. Practical considerations for Ultraviolet-C radiation mediated decontamination of N95 respirator against SARS-CoV-2 virus. PLoS One. 2021 Oct 12;16(10):e0258336. PMCID: PMC8509861.
Geldert A, Su A, Roberts AW, Golovkine G, Grist SM, Stanley SA, Herr AE. Mapping of UV-C dose and SARS-CoV-2 viral inactivation across N95 respirators during decontamination. Sci Rep. 2021 Oct 13;11(1):20341. PMCID: PMC8514565
Jack A, Ferro LS, Trnka MJ, Wehri E, Nadgir A, Nguyenla X, Fox D, Costa K, Stanley SA, Schaletzky J, Yildiz A. SARS-CoV-2 nucleocapsid protein forms condensates with viral genomic RNA. PLoS Biol. 2021 Oct;19(10):e3001425. PMCID: PMC8553124
Biering SB, Van Dis E, Wehri E, Yamashiro LH, Nguyenla X, Dugast-Darzacq C, Graham TGW, Stroumza JR, Golovkine GR, Roberts AW, Fines DM, Spradlin JN, Ward CC, Bajaj T, Dovala D, Schulze-Gamen U, Bajaj R, Fox DM, Ott M, Murthy N, Nomura DK, Schaletzky J†, Stanley SA†. Screening a Library of FDA-Approved and Bioactive Compounds for Antiviral Activity against SARS-CoV-2. ACS Infect Dis. 2021 Aug 13;7(8):2337–2351. PMCID: PMC8231672. †co-corresponding
Graham TGW, Dugast-Darzacq C, Dailey GM, Nguyenla XH, Van Dis E, Esbin MN, Abidi A, Stanley SA, Darzacq X, Tjian R. Inexpensive, versatile and open-source methods for SARS-CoV-2 detection. medRxiv; 2020. PLoS One. 2021; 16(2): e0246647. PMID:33534838.
BioRxiv Submissions
Jong RM, Ching KL, Garelis NE, Zilinskas A, Nguyenla X, Rawal S, Hill BC, Luckie BA, Shallow L, Cox JS, Barton GM, Stanley SA. Cas9+ conditionally immortalized neutrophil progenitors as a tool for genome wide CRISPR screening for neutrophil differentiation and function. bioRxiv. 2022.
Work Published as a trainee
Stanley SA, Barczak AK, Silvis MR, Luo SS, Sogi K, Vokes M, Bray MA, Carpenter AE, Moore CB, Siddiqi N, Rubin EJ, Hung DT. Identification of host-targeted small molecules that restrict intracellular Mycobacterium tuberculosis growth. PLoS Pathog. 2014 Feb 20;10(2):e1003946. PMCID: PMC3930586
Grant SS, Kawate T, Nag PP, Silvis MR, Gordon K, Stanley SA, Kazyanskaya E, Nietupski R, Golas A, Fitzgerald M, Cho S, Franzblau SG, Hung DT. Identification of novel inhibitors of nonreplicating Mycobacterium tuberculosis using a carbon starvation model. ACS Chem Biol. 2013 Oct 18;8(10):2224–2234. PMCID: PMC3864639
Stanley SA, Kawate T, Iwase N, Shimizu M, Clatworthy AE, Kazyanskaya E, Sacchettini JC, Ioerger TR, Siddiqi NA, Minami S, Aquadro JA, Grant SS, Rubin EJ, Hung DT. Diarylcoumarins inhibit mycolic acid biosynthesis and kill Mycobacterium tuberculosis by targeting FadD32. Proc Natl Acad Sci U S A. 2013 Jul 9;110(28):11565–11570. PMCID: PMC3710825
Stanley SA, Cox JS. Host-pathogen interactions during Mycobacterium tuberculosis infections. Curr Top Microbiol Immunol. 2013;374:211–241.
Stanley SA, Grant SS, Kawate T, Iwase N, Shimizu M, Wivagg C, Silvis M, Kazyanskaya E, Aquadro J, Golas A, Fitzgerald M, Dai H, Zhang L, Hung DT. Identification of novel inhibitors of M. tuberculosis growth using whole cell based high-throughput screening. ACS Chem Biol. 2012 Aug 17;7(8):1377–1384. PMCID: PMC3560293
Barczak AK, Gomez JE, Kaufmann BB, Hinson ER, Cosimi L, Borowsky ML, Onderdonk AB, Stanley SA, Kaur D, Bryant KF, Knipe DM, Sloutsky A, Hung DT. RNA signatures allow rapid identification of pathogens and antibiotic susceptibilities. Proc Natl Acad Sci U S A. 2012 Apr 17;109(16):6217–6222. PMCID: PMC3341018
Chindelevitch L, Stanley S, Hung D, Regev A, Berger B. MetaMerge: scaling up genome-scale metabolic reconstructions with application to Mycobacterium tuberculosis. Genome Biol. 2012 Jan 31;13(1):r6. PMCID: PMC3488975
Voehringer D, Stanley SA, Cox JS, Completo GC, Lowary TL, Locksley RM. Nippostrongylus brasiliensis: identification of intelectin-1 and -2 as Stat6-dependent genes expressed in lung and intestine during infection. Exp Parasitol. 2007 Aug;116(4):458–466. PMCID: PMC2699772
Stanley SA, Johndrow JE, Manzanillo P, Cox JS. The Type I IFN response to infection with Mycobacterium tuberculosis requires ESX-1-mediated secretion and contributes to pathogenesis. Mian Yi Xue Za Zhi. 2007 Mar;178(5):3143–3152.
Champion PAD, Stanley SA, Champion MM, Brown EJ, Cox JS. C-terminal signal sequence promotes virulence factor secretion in Mycobacterium tuberculosis. Science. 2006 Sep 15;313(5793):1632–1636.
MacGurn JA, Raghavan S, Stanley SA, Cox JS. A non-RD1 gene cluster is required for Snm secretion in Mycobacterium tuberculosis. Mol Microbiol. 2005 Sep;57(6):1653–1663.
Stanley SA, Raghavan S, Hwang WW, Cox JS. Acute infection and macrophage subversion by Mycobacterium tuberculosis require a specialized secretion system. Proc Natl Acad Sci U S A. 2003 Oct 28;100(22):13001–13006. PMCID: PMC240734