Publications

Recent Publications

Linking a nuclear lncRNA to cytoplasmic lysosome integrity and cell death
Haibin Liu, Zhi-Ming Zheng
Proceedings of the National Academy of Sciences Feb 2022, 119 (8) e2123082119; DOI: 10.1073/pnas.2123082119

Intranuclear Positions of HIV-1 Proviruses Are Dynamic and Do Not Correlate with Transcriptional Activity.
Burdick RC, Deleage C, Duchon A, Estes JD, Hu WS, Pathak VK.
mBio. Jan 11;13(1): 2022 e0325621.

Genome-wide regulation of KSHV RNA splicing by viral RNA-binding protein ORF57
Vladimir Majerciak, Alexei Lobanov, Maggie Cam, Zhi-Ming Zheng
bioRxiv 2022.01.28.478141; doi: https://doi.org/10.1101/2022.01.28.478141

Human Papillomavirus Type 16 Circular RNA Is Barely Detectable for the Claimed Biological Activity.
Yu L, Zheng ZM.
mBio. 2022 Jan 18;13(1):e0359421. doi: 10.1128/mbio.03594-21. Epub ahead of print. PMID: 35038914; PMCID: PMC8764516.

Why the HIV reservoir never runs dry: Clonal expansion and the characterisitcs of HIV-infected cells challenge strategies to cure and control HIV infection
Lau CY, Adan MA, Maldarelli F
Viruses 13: 2512, 2021.

INSTIs and NNRTIs potently inhibit HIV-1 polypurine tract mutants in a single round infection assay

Smith SJ, Ferris A, Zhao X, Pauly G, Schneider JP, Burke TR, Jr, Hughes SH

Viruses 13: 2501, 2021.

New approaches to multi-parametric HIV-1 genetics using multiple displacement amplification: Determining the what, how, and where of the HIV-1 reservoir

Patro SC, Niyongabo A, Maldarelli F, Kearney MF

Viruses 13: 2475, 2021.

Therapeutic implications of ongoing alveolar viral replication in COVID-19

McGonagle D, Kearney MF, O'Regan A, O'Donnell JS, Quartuccio L, Watad A, Bridgewood C

Lancet Rheumatol Dec 1: doi 10.1016/S2665-9913(21)00322-2, 2021.

Selective packaging of HIV-1 RNA genome is guided by the stability of 5' untranslated region polyA stem

Nikolaitchik OA, Liu S, Kitzrow JP, Liu Y, Rawson JMO, Shakya S, Cheng Z, Pathak VK, Hu W-S, Musier-Forsyth K

Proc Natl Acad Sci USA 118: e2114494118, 2021.

Plasma membrane anchoring and Gag:Gag multimerization on viral RNA are critical properties of HIV-1 Gag required to mediate efficient genome packaging

Duchon A, Santos S, Chen J, Brown M, Nikolaitchik OA, Tai S, Chao JA, Freed EO, Pathak VK, Hu W-S

mBio Dec 7: doi 10.1128/mbio.03254-21, 2021.

RNA granules in antiviral innate immunity, a KSHV journey

Sharma N, Zheng Z-M

Front Microbiol Dec 2: doi 10.3389/fmicb.2021.794431, 2021.

Human immunodeficiency viruses: Replication

Ott M, Freed EO

In: Fields Virology, 7th edition, Vol 3: RNA Viruses (Knipe DM, Howley PM, eds), Lippincott, Williams, and Wilkins, in press November 2021.

Protein-RNA interactome analysis reveals wide association of KSHV ORF57 with host non-coding RNAs and polysomes

Alvarado-Hernandez B, Ma Y, Sharma NR, Majerciak V, Lobanov A, Cam M, Zhu J, Zheng Z-M

J Virol Nov 17: doi 10.1128/JVI.01782-21, 2021.

Anti-HIV antibody development up to one year after antiretroviral therapy initiation in acute HIV infection

Mitchell JL, Pollara J, Dietze K, Edwards RW, Nohara J, N'guessan KF, Zemil M, Buranapraditkun S, Takata H, Li Y, Muir R, Kroon E, Pinyakorn S, Jha S, Manasnayakorn S, Chottanapund S, Thantiworasit P, Prueksakaew P, Ratnaratorn N, Nuntapinit B, Fox L, Tovanabutra S, Paquin-Proulx D, Wieczorek L, Polonis VR, Maldarelli F, Haddad EK, Phanuphak P, Sacdalan CP, Rolland M, Phanuphak N, Ananworanich J, Vasan S, Ferrari G, Trautmann L

J Clin Invest Nov 11: doi 10.1172/JCI150937, 2021.

A combination of amino acid mutations leads to resistance to multiple nucleoside analogs in reverse transcriptases from HIV-1 subtypes B and C

Boyer PL, Rehm CA, Sneller MC, Mican J, Caplan MR, Dewar R, Ferris AL, Clark P, Johnson A, Maldarelli F, Hughes SH

Antimicrob Agents Chemother Nov 1: doi 10.1128/AAC.01500-21, 2021.

Reply to Briggs et al.: Genomic integration and expression of SARS-CoV-2 sequences can explain prolonged or recurrent viral RNA detection

Zhang L, Richards A, Barrasa MI, Hughes SH, Young RA, Jaenisch R

Proc Natl Acad Sci USA 118: e2114995118, 2021.

Rafting through the palms: S-acylation of SARS-CoV-2 spike protein induces lipid reorganization

Vilmen G, Banerjee A, Freed EO

Dev Cell 56: 2787-2789, 2021.

Environmental pollutants, mucosal barriers, and pathogen susceptibility; The case for aflatoxin B₁ as a risk factor for HIV transmission and pathogenesis

Madeen EP, Maldarelli F, Groopman JD

Pathogens 10: 1229, 2021.

Ecdysoneless protein regulates viral and cellular mRNA splicing to promote cervical oncogenesis

Mirza S, Kalluchi A, Raza M, Saleem I, Mohapatra B, Pal D, Ouellette MM, Qiu F, Yu L, Lobanov A, Zheng ZM, Zhang Y, Alsaleem MA, Rakha EA, Band H, Rowley MJ, Band V

Mol Cancer Res Oct 20: doi 10.1158/1541-7786.MCR-21-0567, 2021.

Clonal expansion of infected CD4+ T cells in people living with HIV

Coffin JM, Hughes SH
Viruses 13: 2078, 2021.

Lessons in self-defence: Inhibition of virus entry by intrinsic immunity

Majdoul S, Compton AA

Nat Rev Immunol Oct 13: doi 10.1038/s41577-021-00626-8, 2021.

Insertional activation of STAT3 and LCK by HIV-1 proviruses in T cell lymphomas

Mellors JW, Guo S, Naqvi A, Brandt LD, Su L, Sun Z, Joseph KW, Demirov D, Halvas EK, Butcher D, Scott B, Hamilton A, Heil M, Karim B, Wu X, Hughes SH

Sci Adv 7: eabi8795, 2021.

NanoHIV: A bioinformatics pipeline for producing accurate, near full-length HIV proviral genomes sequenced using the Oxford Nanopore Technology

Wright, I, Delaney KE, Katusiime MGK, Botha JC, Engelbrecht S, Kearney MF, van Zyl GU

Cells 10: 2577, 2021.

Show your cap or be packaged into HIV-1

Levin JG, Rein A

Proc Natl Acad Sci USA 118: e2115344118, 2021.

RNA helicase DDX6 in P-bodies is essential for the assembly of stress granules

Majerciak V, Zhou T, Zheng Z-M

bioRxiv Sep 25: doi 10.1101/2021.09.24.461736, 2021.

Human papillomavirus type 16 circular RNA is barely detectable for the claimed transformation activity

Yu, L, Zheng Z-M

bioRxiv Sep 22: doi 10.1101/2021.09.22.449294v1, 2021.

SERINC proteins potentiate antiviral type I IFN production and proinflammatory signaling pathways

Zeng C, Waheed AA, Li T, Yu J, Zheng Y-M, Yount J, Wen H, Freed EO, Liu S-L

Sci Signal 14: eabc7611, 2021.

Prevalence of HIV infection and resistance mutations in patients hospitalized for febrile illness in Singapore

Merati TP, Karyana M, Tjitra E, Kosasih H, Aman AT, Alisjahbana B, Lokida D, Arlinda D, Maldarelli F, Neal A, Arif M, Gasem MH, Lukman N, Sudarmono P, Lau CY, Hadi U, Lisdawati V, Wulan WN, Lane HC, Siddiqui S

Am J Trop Med Hyg 105: 960-5zhi-ming, 2021.

S-acylation of SARS-CoV-2 Spike protein: Mechanistic dissection, in vitro reconstitution and role in viral infectivity

Puthenveetil R, Lun CM, Murphy RE, Healy LB, Vilmen G, Christenson ET, Freed EO, Banerjee A

J Biol Chem 297: 101112, 2021.

Prevalence and risk of residual viremia after ART in low- and middle-income countries: A cross-sectional study

Gatechompol S, Zheng L, Bao Y, Avihingsanon A, Kerr SJ, Kumarasamy N, Hakim JG, Maldarelli F, Gorelick RJ, Welker JL, Lifson JD, Hosseinipour MC, Eron JJ, Ruxrungtham K

Medicine (Baltimore) 100: e26817, 2021.

SARS-CoV-2 viremia is associated with COVID-19 severity and predicts clinical outcomes

Jacobs JL, Bain W, Naqvi A, Staines B, Castanha PMS, Yang H, Boltz VF, Barratt-Boyes S, Marques ETA, Mitchell SL, Methé B, Olonisakin TF, Haidar G, Burke TW, Petzold E, Denny T, Woods CW, McVerry BJ, Lee JS, Watkins SC, St Croix CM, Morris A, Kearney MF, Ladinsky MS, Bjorkman PJ, Kitsios G, Mellors JW

Clin Infect Dis Aug 10: ciab686, 2021.

Structural basis for the inhibition of HTLV-1 integration inferred from cryo-EM deltaretroviral intasome structures

Barski MS, Vanzo T, Zhao XZ, Smith SJ, Ballandras-Colas A, Cronin NB, Pye VE, Hughes SH, Burke TR Jr, Cherepanov P, Maertens GN

Nat Commun 12: 4996, 2021.

Response to Parry et al.: Strong evidence for genomic integration of SARS-CoV-2 sequences and expression in patient tissues

Zhang L, Richards A, Barrasa MI, Hughes SH, Young RA, Jaenisch R

Proc Natl Acad Sci USA 118: e2109497118, 2021.

Maturation of HIV-1
Hikichi Y, Freed EO

Science 373: 621-622, 2021.

Mouse papillomavirus type 1 (MmuPV1) DNA is frequently integrated in benign tumors by microhomology-mediated end-joining

Yu L, Majerciak V, Xue XY, Uberoi A, Lobanov A, Chen X, Cam M, Hughes SH, Lambert PF, Zheng Z-M

PLoS Pathog 17: e1009812.

The indirect antiviral potential of long non-coding RNAs encoded by IFITM pseudogenes

Rahman K, Compton AA

J Virol 95: e0068021, 2021.

Immune reconstitution following allogenic stem cell transplantation in HIV infected individuals: Years of living danger-ously

Lange C, Maldarelli F

Clin Infect Dis Jun 22: doi 10.1093/cid/ciab565, 2021.

Current status of human papillomavirus-related head and neck cancer: From viral genome to patient care

Dong H, Shu X, Xu Q, Zhu C, Kaufmann AM, Zheng Z-M, Albers AE, Qian X

Virol Sin Jun 21: doi 10.1007/s12250-021-00413-8, 2021.

Crystal structure of a retroviral polyprotein: Prototype foamy virus protease-reverse transcriptase (PR-RT)
Harrison JJEK, Tuske S, Das K, Ruiz FX, Bauman JD, Boyer P, DeStefano JJ, Hughes SH, Eddy A
Viruses 13: 1495, 2021.

SARS-CoV-2: From its discovery to genome structure, transcription, and replication

Brant AC, Tian W, Majerciak V, Yang W, Zheng Z-M

Cell Biosci 11: 136, 2021.

HIVIntact: A python-based tool for HIV-1 genome intactness inference

Wright IA, Bale MJ, Shao W, Hu W-S, Coffin JM, van Zyl GU, Kearney MF

Retrovirology 18: 16, 2021.

Tracking HIV-1-infected cell clones using integration site-specific qPCR

Brandt LD, Guo S, Joseph KW, Jacobs JL, Naqvi A, Coffin JM, Kearney MF, Halvas EK, Wu X, Hughes SH, Mellors JW

Viruses 13: 1235, 2021.

HIV-1 persistence in children during suppressive ART

Katusiime MG, Van Zyl GU, Cotton MF, Kearney MF

Viruses 13: 1134, 2021.

Reverse-transcribed SARS-CoV-2 RNA can integrate into the genome of cultured human cells and can be expressed in patient-derived tissues

Zhang L, Richards A, Barrasa MI, Hughes SH, Young RA, Jaenisch R.

Proc Natl Acad Sci USA 118: e2105968118, 2021.

2020 SARS-CoV-2 diversification in the United States: Establishing a pre-vaccination baseline

Capoferri AA, Shao W, Spindler J, Coffin JM, Rausch JW, Kearney MF

medRxiv Jun 4: doi 10.1101/2021.06.01.21258185, 2021.

Rapalogs downmodulate intrinsic immunity and promote cell entry of SARS-CoV-2

Shi G, Chiramel AI, Majdoul S, Lai KK, Das S, Beare PA, Andresson T, Best SM, Compton AA

bioRxiv Apr 16: doi 10.1101/2021.04.15.440067, 2021.

CpG methylation profiles of HIV-1 proviral DNA in individuals on ART

Boltz VF, Ceriani C, Rausch JW, Shao W, Bale MJ, Keele BF, Hoh R, Milush JM, Deeks SG, Maldarelli F, Kearney MF, Coffin JM

Viruses 13: 799, 2021.

CryoET structures of immature HIV Gag reveal six-helix bundle

Mendonça L, Sun D, Ning J, Liu J, Kotecha A, Olek M, Frosio T, Fu X, Himes BA, Kleinpeter AB, Freed EO, Zhou J, Aiken C, Zhang P

Commun Biol 4: 481, 2021.

Integration in oncogenes plays only a minor role in determining the in vivo distribution of HIV integration sites before or during suppressive antiretroviral therapy

Coffin JM, Bale MJ, Wells D, Guo S, Luke B, Zerbato JM, Sobolewski MD, Sia T, Shao W, Wu X, Maldarelli F, Kearney MF, Mellors JW, Hughes SH

PLoS Pathog 17: e1009141, 2021.

Early emergence and long-term persistence of HIV-infected T-cell clones in children

Bale MJ, Katusiime MG, Wells D, Wu X, Spindler J, Halvas EK, Cyktor JC, Wiegand A, Shao W, Cotton MF, Hughes SH, Mellors JW, Coffin JM, van Zyl GU, Kearney MF

mBio 12: e00568-21, 2021.

Across the hall from pioneers (Perspective article in the Special Issue "In Memory of Stephen Oroszlan")

Rein A

Viruses 13: 491, 2021.

Targeting natural splicing plasticity of APOBEC3B restricts its expression and mutagenic activity

Banday AR, Onabajo OO, Lin SH, Obajemu A, Vargas JM, Delviks-Frankenberry KA, Lamy P, Bayanjargal A, Zettelmeyer C, Florez-Vargas O, Pathak VK, Dyrskjøt L, Prokunina-Olsson L

Commun Biol 4: 386, 2021.

Mechanism of viral glycoprotein targeting by membrane-associated RING-CH proteins

Lun CM, Waheed AA, Majadly A, Powell N, Freed EO

mBio 12: e00219-21, 2021.

HIV-1 integrase inhibitors with modifications that affect their potencies against drug resistant integrase mutants

Smith SJ, Zhao XZ, Passos DO, Pye VE, Cherepanov P, Lyumkis D, Burke TR Jr, Hughes SH

ACS Infect Dis 7: 1469-1482, 2021.

A stable immature lattice packages IP6 for HIV capsid maturation

Mallery DL, Kleinpeter AB, Renner N, Rifat Faysal KM, Novikova M, Kiss L, Wilson MSC, Ahsan B, Ke Z, Briggs JAG, Saiardi A, Böcking T, Freed EO*, James LC* (*Joint corresponding author)

Sci Adv 7: eabe4716, 2021.

HIV-1 cores retain their integrity until minutes before uncoating in the nucleus

Li C, Burdick RC, Nagashima K, Hu W-S, Pathak VK

Proc Natl Acad Sci USA 118: e2019467118, 2021.

CD225 proteins: A family portrait of fusion regulators

Coomer CA, Rahman K, Compton AA

Trends Genet 37: 406-410, 2021.

Integrase strand transfer inhibitors are effective anti-HIV drugs

Smith SJ, Zhao XZ, Passos DO, Lyumkis D, Burke TR Jr, Hughes SH

Viruses 13: 205, 2021.

Development of a cell-based luciferase complementation assay for identification of SARS-CoV-2 3CLpro inhibitors

Rawson JMO, Duchon A, Nikolaitchik OA, Pathak VK, Hu W-S

Viruses 13: 173, 2021.

Efficient HIV-1 in vitro reverse transcription: optimal capsid stability is required

Burdick RC, Pathak VK

Signal Transduct Target Ther 6: 13, 2021.

Mechanistic analysis of the broad antiretroviral resistance conferred by HIV-1 envelope glycoprotein mutations

Hikichi Y, Van Duyne R, Pham P, Groebner JL, Wiegand A, Mellors JW, Kearney MF, Freed EO

mBio 12: e03134-20, 2021.

Oncogenic HPV promotes the expression of the long noncoding RNA lnc-FANCI-2 through E7 and YY1

Liu H, Xu J, Yang Y, Wang X, Wu E, Majerciak V, Zhang T, Steenbergen RDM, Wang H-K, Banerjee NS, Li Y, Lu W, Meyers C, Zhu J, Xie X, Chow LT, Zheng Z-M

Proc Natl Acad Sci USA 118: e2014195118, 2021.

Opposing activities of IFITM proteins in SARS-CoV-2 infection.

Shi G, Kenney AD, Kudryashova E, Zani A, Zhang L, Lai KK, Hall-Stoodley L, Robinson RT, Kudryashov DS, Compton AA, Yount JS

EMBO J 40: e106501, 2021.

Structure-based non-nucleoside inhibitor design: Developing inhibitors that are effective against resistant mutants

Smith SJ, Pauly GT, Hewlett K, Schneider JP, Hughes SH

Chem Biol Drug Des 97: 4-17, 2021.

Specific guanosines in the HIV-2 leader RNA are essential for efficient viral genome packaging

Umunnakwe CN, Duchon A, Nikolaitchik OA, Abdul Rahman S, Liu Y, Chen J, Tai S, Pathak VK, Hu W-S

J Mol Biol 433: 166718, 2021.

Expression of HPV oncogenes from a single integration site in cervical cancer cell lines

Yu L, Lobanov A, Majerciak V, Mirza S, Band V, Liu H, Cam M, Zheng Z-M

bioRxiv Jun 27: doi 10.1101/2020.06.25.171959v1, 2020.

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Recent Publications