Faculty Publications

Review of factors affecting virus inactivation in aerosols and droplets. Longest AK, Rockey NC, Lakdawala SS, Marr LC. J R Soc Interface. 2024 Jun;21(215):18. doi: 10.1098/rsif.2024.0018. Epub 2024 Jun 26. PMID: 38920060; PMCID: PMC11285516. 

Persistence of Influenza H5N1 and H1N1 Viruses in Unpasteurized Milk on Milking Unit Surfaces. Le Sage V, Campbell AJ, Reed DS, Duprex WP, Lakdawala SS. Emerg Infect Dis. 2024 Aug;30(8):1721-1723. doi: 10.3201/eid3008.240775. Epub 2024 Jun 24. PMID: 38914418; PMCID: PMC11286056.

Potential pandemic risk of circulating swine H1N2 influenza viruses. Le Sage V, Rockey NC, French AJ, McBride R, McCarthy KR, Rigatti LH, Shephard MJ, Jones JE, Walter SG, Doyle JD, Xu L, Barbeau DJ, Wang S, Frizzell SA, Myerburg MM, Paulson JC, McElroy AK, Anderson TK, Vincent Baker AL, Lakdawala SS.  Nat Commun. 2024 Jun 13;15(1):5025. doi: 10.1038/s41467-024-49117-z. PMID: 38871701; PMCID: PMC11176300.

Ventilation does not affect influenza virus transmission efficiency in a ferret playpen setup. Rockey NC, Le Sage V, Shephard M, Vargas-Maldonado N, French AJ, Walter S, Ferreri LM, Holmes KE, VanInsberghe D, Clack H, Prussin II AJ, Lowen AC, Marr LC, Lakdawala SS. Ventilation does not affect influenza virus transmission efficiency in a ferret playpen setup. PNAS Aug 2024.

Deciphering visceral adipose tissue regulatory T cells: Key contributors to metabolic health. Elkins C, Li C. Immunol Rev. 2024 Jul;324(1):52-67. doi: 10.1111/imr.13336. Epub 2024 Apr 26. PMID: 38666618; PMCID: PMC11262988.

CD4⁺ and CD8⁺ T cells are required to prevent SARS-CoV-2 persistence in the nasal compartment. Kar M, Johnson KEE, Vanderheiden A, Elrod EJ, Floyd K, Geerling E, Stone ET, Salinas E, Banakis S, Wang W, Sathish S, Shrihari S, Davis-Gardner ME, Kohlmeier J, Pinto A, Klein R, Grakoui A, Ghedin E, Suthar MS. Sci Adv. 2024 Aug 23;10(34):eadp2636. doi: 10.1126/sciadv.adp2636. Epub 2024 Aug 23. PMID: 39178263; PMCID: PMC11343035.

An aberrant immune-epithelial progenitor niche drives viral lung sequelae. Narasimhan H, Cheon IS, Qian W, Hu SS, Parimon T, Li C, Goplen N, Wu Y, Wei X, Son YM, Fink E, de Almeida Santos G, Tang J, Yao C, Muehling L, Canderan G, Kadl A, Cannon A, Young S, Hannan R, Bingham G, Arish M, Sen Chaudhari A, Im JS, Mattingly CLR, Pramoonjago P, Marchesvsky A, Sturek J, Kohlmeier JE, Shim YM, Woodfolk J, Zang C, Chen P, Sun J. Nature. 2024 Sep 4. doi: 10.1038/s41586-024-07926-8. Epub ahead of print. PMID: 39232171.

Epigenetic tuning of PD-1 expression improves exhausted T cell function and viral control. Weiss SA, Huang AY, Fung ME, Martinez D, Chen ACY, LaSalle TJ, Miller BC, Scharer CD, Hegde M, Nguyen TH, Rowe JH, Osborn JF, Patterson DG, Sifnugel N, Mei-An Nolan C, Davidson RA, Schwartz MA, Bally APR, Neeld DK, LaFleur MW, Boss JM, Doench JG, Nicholas Haining W, Sharpe AH, Sen DR. Nat Immunol. 2024 Sep 17. doi: 10.1038/s41590-024-01961-3. Epub ahead of print. PMID: 39289557.

Human Immune Organoids to Decode B Cell Response in Healthy Donors and Lymphoma PatientsZhe Zhong, Manuel Q. Perez, Zhonghao Dai, Valeria M. Juarez , Eshant Bhatia, Christopher Carlson, Shivem B. Shah, Anjali Patel, Zhou Fang, Thomas Hu, Mayar Allam, Sakeenah L. Hicks, Mansi Gupta, Sneh Lata Gupta,  Ethan Weeks, Stephanie D. Vagelos, Alejandro Molina, Adriana Mulero-Russe, Ana Mora Boza , Devyani J. Joshi, Rafick Sekaly, Todd Sulchek, Steven Goudy, Jens Wrammert, Krishnendu Roy, Jeremy M. Boss, Ahmet Coskun, Christopher D. Scharer, Andrés J. García, Jean Koff, Ankur Singh. 2024. Nature Materials, accepted. 

Factors associated with immune responses to SARS-CoV-2 vaccination in individuals with autoimmune diseases. Anderson E, Powell M, Yang E, Kar A, Leung TM, Sison C, Steinberg R, Mims R, Choudhury A, Espinosa C, Zelmanovich J, Okoye NC, Choi EJ, Marder G, Narain S, Gregersen PK, Mackay M, Diamond B, Levy T, Zanos TP, Khosroshahi A, Sanz I, Luning Prak ET, Bar-Or A, Merrill J, Arriens C, Pardo G, Guthridge J, James J, Payne A, Utz PJ, Boss JM, Aranow C, Davidson A. JCI Insight. 2024 Jun 4;9(13):e180750. doi: 10.1172/jci.insight.180750. PMID: 38833310; PMCID: PMC11383356.

Transcriptional responses of Neisseria gonorrhoeae to glucose and lactate: implications for resistance to oxidative damage and biofilm formation. Ayala JC, Balthazar JT, Shafer WM. mBio. 2024 Aug 14;15(8):e0176124. doi: 10.1128/mbio.01761-24. Epub 2024 Jul 16. PMID: 39012148; PMCID: PMC11323468.

Structural and functional diversity of Resistance-Nodulation-Division (RND) efflux pump transporters with implications for antimicrobial resistance.Kavanaugh LG, Dey D, Shafer WM, Conn GL. Microbiol Mol Biol Rev. 2024 Sep 5:e0008923. doi: 10.1128/mmbr.00089-23. Epub ahead of print. PMID: 39235227.

Ensuring a sustained workforce to combat antibiotic resistance in the 21st century: the critical need for training the next-gen of scientists at the pre-doctoral level.Shafer WM, Conn GL. Antimicrob Agents Chemother. 2024 Apr 19:e0024424. doi: 10.1128/aac.00244-24. Epub ahead of print. PMID: 38639492.

Active Tuberculosis Is Associated with Depletion of HIV-Specific CD4 and CD8 T Cells in People with HIV. Khayumbi J, Sasser LE, McLaughlin TA, Muchiri B, Ongalo J, Tonui J, Ouma SG, Campbell A, Odhiambo FH, Kiprotich C, Gandhi NR, Day CL. AIDS Res Hum Retroviruses. 2024 Mar 14. doi: 10.1089/AID.2023.0088. Epub ahead of print. PMID: 38366732.

A laboratory-based predictive pathway for the development of Neisseria gonorrhoeae high-level resistance to corallopyronin A, an inhibitor of bacterial RNA polymerase.  Balthazar JT, Golparian D, Unemo M, Read TD, Grosse M, Stadler M, Pfarr K, Schiefer A, Hoerauf A, Edwards JL, Vassylyev DG and Shafer WM. 2024. (In Press, Microbiology Spectrum)

Hormonal steroids induce multidrug resistance and stress response genes in Neisseria gonorrhoeae by binding to MtrR. Hooks GM, Ayala JC, Holley CL, Dhulipala V, Beggs GA, Perfect JR, Schumacher MA, Shafer WM, Brennan RG.  Nat Commun. 2024 Feb 7;15(1):1153. doi: 10.1038/s41467-024-45195-1. PMID: 38326294; PMCID: PMC10850145.

Genetic drift and purifying selection shape within-host influenza A virus populations during natural swine infections. VanInsberghe D, McBride DS, DaSilva J, Stark TJ, Lau MSY, Shepard SS, Barnes JR, Bowman AS, Lowen AC, Koelle K. bioRxiv [Preprint]. 2023 Oct 25:2023.10.23.563581. doi: 10.1101/2023.10.23.563581. PMID: 37961583; PMCID: PMC10634741.

Virology-the path forward. Rasmussen AL, Gronvall GK, Lowen AC, et al. J Virol. 2024 Jan 23;98(1):e0179123. doi: 10.1128/jvi.01791-23. Epub 2024 Jan 3. Erratum in: J Virol. 2024 Mar 19;98(3):e0007424. PMID: 38168672; PMCID: PMC10804978. (Dr. Anice Lowen co-led this commentary article and subsequent replies to letters submitted to the journal)

Seasonal influenza viruses decay more rapidly at intermediate humidity in droplets containing saliva compared to respiratory mucus. Rockey NC, Le Sage V, Marr LC, Lakdawala SS. Appl Environ Microbiol. 2024;90(2):e0201023. doi:10.1128/aem.02010-23

Prevention of respiratory virus transmission by resident memory CD8⁺ T cells. Uddbäck I, Michalets SE, Saha A, Mattingly C, Kost KN, Williams ME, Lawrence LA, Hicks SL, Lowen AC, Ahmed H, Thomsen AR, Russell CJ, Scharer CD, Boss JM, Koelle K, Antia R, Christensen JP, Kohlmeier JE. Nature. 2024;626(7998):392-400. doi:10.1038/s41586-023-06937-1

Both Humoral and Cellular Immunity Limit the Ability of Live Attenuated Influenza Vaccines to Promote T Cell Responses. Lobby JL, Danzy S, Holmes KE, Lowen AC, Kohlmeier JE. J Immunol. 2024;212(1):107-116. doi:10.4049/jimmunol.2300343

The menstrual cycle regulates migratory CD4 T-cell surveillance in the female reproductive tract via CCR5 signaling. Williams ME, Wein AN, Hardnett FP, Sheth AN, Li ZT, Basu JR, Zheng HQ, Dinh C, Haddad LB, Collins EMB, Lobby JL, Kost K, Hayward SL, Ofotokun I, Antia R, Scharer CD, Lowen AC, Garcia-Lerma JG, Kohlmeier JE, Swaims-Kohlmeier A. Mucosal Immunol. 2024;17(1):41-53. doi:10.1016/j.mucimm.2023.10.002

Evidence for Rho-dependent control of a virulence switch in Acinetobacter baumannii. Pérez-Varela M, Singh R, Colquhoun JM, Starich OG, Tierney ARP, Tipton KA, Rather PN. mBio. 2024;15(1):e0270823. doi:10.1128/mbio.02708-23

The RgaS-RgaR two-component system promotes Clostridioides difficile sporulation through a small RNA and the Agr1 system. Edwards AN, McBride SM. PLoS Genet. 2023;19(10):e1010841. Published 2023 Oct 16. doi:10.1371/journal.pgen.1010841

Genetic analysis reveals a robust and hierarchical recruitment of the LolA chaperone to the LolCDE lipoprotein transporter. Lehman KM, May KL, Marotta J, Grabowicz M. mBio. 2024;15(2):e0303923. doi:10.1128/mbio.03039-23

Transcriptional activation of ompA in Neisseria gonorrhoeae mediated by the XRE family member protein NceR. Holley CL, Dhulipala V, Maurakis SA, Greenawalt AN, Read TD, Cornelissen CN, Shafer WM. mBio. 2023;14(4):e0124423. doi:10.1128/mbio.01244-23

Obesity-induced dysregulation of skin-resident PPARγ⁺ Treg cells promotes IL-17A-mediated psoriatic inflammation. Sivasami P, Elkins C, Diaz-Saldana PP, Goss K, Peng A, Hamersky M 4th, Bae J, Xu M, Pollack BP, Horwitz EM, Scharer CD, Seldin L, Li C.  Immunity. 2023;56(8):1844-1861.e6. doi:10.1016/j.immuni.2023.06.021

Variability in Donor Lung Culture and Relative Humidity Impact the Stability of 2009 Pandemic H1N1 Influenza Virus on Nonporous Surfaces. Qian Z, Morris DH, Avery A, Kormuth KA, Le Sage V, Myerburg MM, Lloyd-Smith JO, Marr LC, Lakdawala SS. Appl Environ Microbiol. 2023;89(7):e0063323. doi:10.1128/aem.00633-23

Local changes in viral RNA sequence drive global changes in influenza nucleoprotein binding. Le Sage V, Kanarek JP, Lakdawala SS*, Lee N*. J Med Virol. 2023 Jul;95(7):e28896. doi: 10.1002/jmv.28896. PMID: 37386887. *co-corresponding

When does humoral memory enhance infection? Nikas A, Ahmed H, Moore MR, Zarnitsyna VI, Antia R.  PLoS Comput Biol. 2023;19(8):e1011377. Published 2023 Aug 21. doi:10.1371/journal.pcbi.1011377

Teasing apart the evolution of lipoprotein trafficking in gram-negative bacteria reveals a bifunctional LolA. Smith HC, May KL, Grabowicz M.  Proc Natl Acad Sci U S A. 2023;120(6):e2218473120. doi:10.1073/pnas.2218473120

Potent In Vitro and Ex Vivo Anti-Gonococcal Activity of the RpoB Inhibitor Corallopyronin A. Edwards JL, Balthazar JT, Esposito DLA, Ayala JC, Schiefer A, Pfarr K, Hoerauf A, Alt S, Hesterkamp T, Grosse M, Stadler M, Golparian D, Unemo M, Read TD, Shafer WM. mSphere. 2022 Oct 26;7(5):e0036222. doi: 10.1128/msphere.00362-22. Epub 2022 Sep 12. PMID: 36094073; PMCID: PMC9599356.

Identification of Functional Spo0A Residues Critical for Sporulation in Clostridioides difficile. DiCandia MA, Edwards AN, Jones JB, Swaim GL, Mills BD, McBride SM. J Mol Biol. 2022;434(13):167641. doi:10.1016/j.jmb.2022.167641

Three Orphan Histidine Kinases Inhibit Clostridioides difficile Sporulation. Edwards AN, Wetzel D, DiCandia MA, McBride SM.  J Bacteriol. 2022;204(5):e0010622. doi:10.1128/jb.00106-22

Transcriptional regulation of the mtrCDE efflux pump operon: importance for Neisseria gonorrhoeae antimicrobial resistance. Ayala JC, Balthazar JT, Shafer WM. Microbiology (Reading). 2022;168(8):001231. doi:10.1099/mic.0.001231

Sialylated and sulfated N-Glycans in MDCK and engineered MDCK cells for influenza virus studies. Byrd-Leotis L, Jia N, Matsumoto Y, Lu D, Kawaoka Y, Steinhauer DA, Cummings RD. Sci Rep. 2022;12(1):12757. Published 2022 Jul 26. doi:10.1038/s41598-022-16605-5

President’s Address to Annual AAI Meeting, IMMUNOLOGY 2020/2021, The Regulation of Immunity.  Boss, JM. 2022.  The Journal of Immunology 208(11):2450-2455. DOI: 10.4049/jimmunol.2290007.

Ayala JC, Schmerer MW, Kersh EN, Unemo M, Shafer WM. 2022.  mBio. 2022 Mar 8:e0027622. doi: 10.1128/mbio.00276-22. Online ahead of print.

Gonococcal Clinical Strains Bearing a Common gdhR Single Nucleotide Polymorphism That Results in Enhanced Expression of the Virulence Gene lctP Frequently Possess a mtrR Promoter Mutation That Decreases Antibiotic Susceptibility. Ayala JC, Schmerer MW, Kersh EN, Unemo M, Shafer WM.  mBio. 2022;13(2):e0027622. doi:10.1128/mbio.00276-22

A Single Amino Acid Substitution in Elongation Factor G Can Confer Low-Level Gentamicin Resistance in Neisseria gonorrhoeae. Holley CL, Dhulipala V, Balthazar JT, Le Van A, Begum AA, Chen SC, Read TD, Matoga M, Hoffman IF, Golparian D, Unemo M, Jerse AE, Shafer WM. Antimicrob Agents Chemother. 2022;66(5):e0025122. doi:10.1128/aac.00251-22

Group A Streptococcus induces GSDMA-dependent pyroptosis in keratinocytes. LaRock DL, Johnson AF, Wilde S, Sands JS, Monteiro MP, LaRock CN. Nature. 2022;605(7910):527-531. doi:10.1038/s41586-022-04717-x

Somatic Diversification of Rearranged Antibody Gene Segments by Intra- and Interchromosomal Templated Mutagenesis. Dale GA, Wilkins DJ, Rowley J, Scharer CD, Tipton CM, Hom J, Boss JM, Corces V, Sanz I, Jacob J. J Immunol. 2022;208(9):2141-2153. doi:10.4049/jimmunol.2100434

Defining Discriminatory Antibody Fingerprints in Active and Latent Tuberculosis [published correction appears in Front Immunol. Nziza N, Cizmeci D, Davies L, Irvine EB, Jung W, Fenderson BA, de Kock M, Hanekom WA, Franken KLMC, Day CL*, Ottenhoff THM*, Alter G*. 2023 Nov 21;14:1329784]. Front Immunol. 2022;13:856906. Published 2022 Apr 20. doi:10.3389/fimmu.2022.856906 *Corresponding authors

H3K27me3 Demethylase UTX Restrains Plasma Cell Formation. Kania AK, Price MJ, George-Alexander LE, Patterson DG, Hicks SL, Scharer CD, Boss JM.  J Immunol. 2022;208(8):1873-1885. doi:10.4049/jimmunol.2100948

Timing of exposure is critical in a highly sensitive model of SARS-CoV-2 transmission. Ganti K, Ferreri LM, Lee CY, Bair CR, Delima GK, Holmes KE, Suthar MS, Lowen AC. PLoS Pathog. 2022 Mar 25;18(3):e1010181. doi: 10.1371/journal.ppat.1010181.

Interferon-α-producing plasmacytoid dendritic cells drive the loss of adipose tissue regulatory T cells during obesity.   Li C*, Wang G, Sivasami P, Ramirez RN, Zhang Y, Benoist C, Mathis D.*  Cell Metab. 2021 Aug 3;33(8):1610-1623.e5. doi: 10.1016/j.cmet.2021.06.007. Epub 2021 Jul 12. *co-corresponding author

PPARγ marks splenic precursors of multiple nonlymphoid-tissue Treg compartments. Li C*, Muñoz-Rojas AR*, Wang G, Mann AO, Benoist C, Mathis D.  Proc Natl Acad Sci U S A. 2021 Mar 30;118(13):e2025197118. doi: 10.1073/pnas.2025197118. *co-first author

Rab11a mediates cell-cell spread and reassortment of influenza A virus genomes via tunneling nanotubes.  Ketaki Ganti, Julianna Han, Balaji Manicassamy, Anice C. Lowen. 2021  Plos Pathogens. 

PD-1 blockade and vaccination provide therapeutic benefit against SIV by inducing broad and functional CD8⁺ T cells in lymphoid tissue.  Rahman SA, Yagnik B, Bally AP, Morrow KN, Wang S, Vanderford TH, Freeman GJ, Ahmed R, Amara RR.  Sci Immunol. 2021 Sep 10;6(63):eabh3034. doi: 10.1126/sciimmunol.abh3034.

An IRF4-MYC-mTORC1 Integrated Pathway Controls Cell Growth and the Proliferative Capacity of Activated B Cells during B Cell Differentiation In Vivo.Patterson DG, Kania AK, Price MJ, Rose JR, Scharer CD, Boss JM. J Immunol. 2021 Oct 1;207(7):1798-1811. doi: 10.4049/jimmunol.2100440. Epub 2021 Sep 1.PMID: 34470852

Epigenetic gene regulation in plasma cells.Patterson DG, Kania AK, Zuo Z, Scharer CD, Boss JM. Immunol Rev. 2021 Sep;303(1):8-22. doi: 10.1111/imr.12975. Epub 2021 May 19.PMID: 34010461 Review.

CXCR6 regulates localization of tissue-resident memory CD8 T cells to the airways.
Wein AN, McMaster SR, Takamura S, Dunbar PR, Cartwright EK, Hayward SL, McManus DT, Shimaoka T, Ueha S, Tsukui T, Masumoto T, Kurachi M, Matsushima K, Kohlmeier JE.
J Exp Med. 2019 Dec 2;216(12):2748-2762. doi: 10.1084/jem.20181308. Epub 2019 Sep 26.

Epigenetic programming underpins B cell dysfunction in human SLE.
Scharer CD, Blalock EL, Mi T, Barwick BG, Jenks SA, Deguchi T, Cashman KS, Neary BE, Patterson DG, Hicks SL, Khosroshahi A, Eun-Hyung Lee F, Wei C, Sanz I, Boss JM. 
Nat Immunol. 2019 Aug;20(8):1071-1082. doi: 10.1038/s41590-019-0419-9. Epub 2019 Jul 1.

Incidence and clinical profile of tuberculosis after allogeneic stem cell transplantation.
Agrawal N, Aggarwal M, Kapoor J, Ahmed R, Shrestha A, Kaushik M, Bhurani D.
Transpl Infect Dis. 2017 Oct 24. doi: 10.1111/tid.12794. [Epub ahead of print] PMID: 29064140