Publications

2024

Drug target prediction through deep learning functional representation of gene signatures.

Chen H, King FJ, Zhou B, Wang Y, Canedy CJ, Hayashi J, Zhong Y, Chang MW, Pache L, Wong JL, Jia Y, Joslin J, Jiang T, Benner C, Chanda SK, Zhou Y.

Nat Commun. 2024 Feb 29;15(1):1853. doi: 10.1038/s41467-024-46089-y.

PMID: 38424040

Molecular Determinants of PQBP1 Binding to the HIV-1 Capsid Lattice.

Piacentini J, Allen DS, Ganser-Pornillos BK, Chanda SK, Yoh SM, Pornillos O.

J Mol Biol. 2024 Feb 15;436(4):168409. doi: 10.1016/j.jmb.2023.168409. Epub 2023 Dec 20.

PMID: 38128824

2023

Breaking the Silence: Regulation of HIV Transcription and Latency on the Road to a Cure.

Duggan NN, Dragic T, Chanda SK, Pache L.

Viruses. 2023 Dec 15;15(12):2435. doi: 10.3390/v15122435.

PMID: 38140676 Review.

Proteomic and genetic analyses of influenza A viruses identify pan-viral host targets.

Haas KM, McGregor MJ, Bouhaddou M, Polacco BJ, Kim EY, Nguyen TT, Newton BW, Urbanowski M, Kim H, Williams MAP, Rezelj VV, Hardy A, Fossati A, Stevenson EJ, Sukerman E, Kim T, Penugonda S, Moreno E, Braberg H, Zhou Y, Metreveli G, Harjai B, Tummino TA, Melnyk JE, Soucheray M, Batra J, Pache L, Martin-Sancho L, Carlson-Stevermer J, Jureka AS, Basler CF, Shokat KM, Shoichet BK, Shriver LP, Johnson JR, Shaw ML, Chanda SK, Roden DM, Carter TC, Kottyan LC, Chisholm RL, Pacheco JA, Smith ME, Schrodi SJ, Albrecht RA, Vignuzzi M, Zuliani-Alvarez L, Swaney DL, Eckhardt M, Wolinsky SM, White KM, Hultquist JF, Kaake RM, García-Sastre A, Krogan NJ.Nat Commun. 2023 Sep 27;14(1):6030. doi: 10.1038/s41467-023-41442-z.

PMID: 37758692

Assessment of selection criteria using multi-year study for effective breeding program of Zingiber officinale L.

Begum T, Gogoi R, Gogoi A, Gupta T, Chanda SK, Lekhak H, Lal M.PeerJ. 2023 Sep 1;11:e15966. doi: 10.7717/peerj.15966. eCollection 2023.

PMID: 37671361

Estimation of genetic variation in yield, its contributing characters and capsaicin content of Capsicum chinense Jacq. (ghost pepper) germplasm from Northeast India.

Baruah J, Munda S, Sarma N, Begum T, Pandey SK, Chanda SK, Sastry GN, Lal M.PeerJ. 2023 Jun 22;11:e15521. doi: 10.7717/peerj.15521. eCollection 2023.

PMID: 37366425

Stability estimation through multivariate approach among solasodine-rich lines of Solanum khasianum (C.B. Clarke): an important industrial plant.

Begum T, Munda S, Gupta T, Gogoi R, Choubey VK, Chanda SK, Lekhak H, Sastry GN, Lal M.Front Plant Sci. 2023 May 11;14:1143778. doi: 10.3389/fpls.2023.1143778. eCollection 2023.

PMID: 37251772

Optical and physical properties of annealed amorphous niobium oxide thin films.

Aljumaily GA, Carver GE, Barton JB, Locknar SA, Chanda SK, Johnson RL.Appl Opt. 2023 Mar 1;62(7):B55-B62. doi: 10.1364/AO.471982.

PMID: 37132886

Activation of the Interferon Pathway in Trophoblast Cells Productively Infected with SARS-CoV-2.

Kallol S, Martin-Sancho L, Morey R, Aisagbonhi O, Pizzo D, Meads M, Chanda SK, Soncin F.

Stem Cells Dev. 2023 Mar 22. doi: 10.1089/scd.2022.0255. Online ahead of print.

PMID: 36803114

Identification of global inhibitors of cellular glycosylation.

Sørensen DM, Büll C, Madsen TD, Lira-Navarrete E, Clausen TM, Clark AE, Garretson AF, Karlsson R, Pijnenborg JFA, Yin X, Miller RL, Chanda SK, Boltje TJ, Schjoldager KT, Vakhrushev SY, Halim A, Esko JD, Carlin AF, Hurtado-Guerrero R, Weigert R, Clausen H, Narimatsu Y.

Nat Commun. 2023 Feb 20;14(1):948. doi: 10.1038/s41467-023-36598-7.

PMID: 36804936 Free PMC article.

2022

SARS-CoV-2 infects human brain organoids causing cell death and loss of synapses that can be rescued by treatment with Sofosbuvir.

Mesci P, de Souza JS, Martin-Sancho L, Macia A, Saleh A, Yin X, Snethlage C, Adams JW, Avansini SH, Herai RH, Almenar-Queralt A, Pu Y, Szeto RA, Goldberg G, Bruck PT, Papes F, Chanda SK, Muotri AR.

PLoS Biol. 2022 Nov 3;20(11):e3001845. doi: 10.1371/journal.pbio.3001845. eCollection 2022 Nov.

PMID: 36327326 Free PMC article.

Common and species-specific molecular signatures, networks, and regulators of influenza virus infection in mice, ferrets, and humans.

Forst CV, Martin-Sancho L, Tripathi S, Wang G, Dos Anjos Borges LG, Wang M, Geber A, Lashua L, Ding T, Zhou X, Carter CE, Metreveli G, Rodriguez-Frandsen A, Urbanowski MD, White KM, Stein DA, Moulton H, Chanda SK, Pache L, Shaw ML, Ross TM, Ghedin E, García-Sastre A, Zhang B.

Sci Adv. 2022 Oct 7;8(40):eabm5859. doi: 10.1126/sciadv.abm5859. Epub 2022 Oct 5.

PMID: 36197970 Free PMC article.

Recognition of HIV-1 capsid by PQBP1 licenses an innate immune sensing of nascent HIV-1 DNA.

Fuchs NV, Cianci GC, Riva L, Curry H, Yin X, Gambut S, Simons LM, Hultquist JF, König R, Xiong Y, García-Sastre A, Böcking T, Hope TJ, Chanda SK.

Mol Cell. 2022 Aug 4;82(15):2871-2884.e6. doi: 10.1016/j.molcel.2022.06.010. Epub 2022 Jul 8.

PMID: 35809572

Sec61 Inhibitor Apratoxin S4 Potently Inhibits SARS-CoV-2 and Exhibits Broad-Spectrum Antiviral Activity.

Pohl MO, Martin-Sancho L, Ratnayake R, White KM, Riva L, Chen QY, Lieber G, Busnadiego I, Yin X, Lin S, Pu Y, Pache L, Rosales R, Déjosez M, Qin Y, De Jesus PD, Beall A, Yoh S, Hale BG, Zwaka TP, Matsunaga N, García-Sastre A, Stertz S, Chanda SK, Luesch H.

ACS Infect Dis. 2022 Jul 8;8(7):1265-1279. doi: 10.1021/acsinfecdis.2c00008. Epub 2022 Jun 29.

PMID: 35766385 Free PMC article.

Synthetic lethality-based prediction of anti-SARS-CoV-2 targets.

Pal LR, Cheng K, Nair NU, Martin-Sancho L, Sinha S, Pu Y, Riva L, Yin X, Schischlik F, Lee JS, Chanda SK, Ruppin E.

iScience. 2022 May 20;25(5):104311. doi: 10.1016/j.isci.2022.104311. Epub 2022 Apr 27.

PMID: 35502318 Free PMC article.

NFAM1 Promotes Pro-Inflammatory Cytokine Production in Mouse and Human Monocytes.

Juchem KW, Gounder AP, Gao JP, Seccareccia E, Yeddula N, Huffmaster NJ, Côté-Martin A, Fogal SE, Souza D, Wang SS, Glynn ERA, Yung I, Ritchie J, Li L, Zheng J, Mbow ML, Li J, Chanda SK.

Front Immunol. 2022 Jan 13;12:773445. doi: 10.3389/fimmu.2021.773445. eCollection 2021.

PMID: 35095847 Free PMC article.

2021

Development of an In Vivo Probe to Track SARS-CoV-2 Infection in Rhesus Macaques.

Madden PJ, Arif MS, Becker ME, McRaven MD, Carias AM, Lorenzo-Redondo R, Xiao S, Midkiff CC, Blair RV, Potter EL, Martin-Sancho L, Dodson A, Martinelli E, Todd JM, Villinger FJ, Chanda SK, Aye PP, Roy CJ, Roederer M, Lewis MG, Veazey RS, Hope TJ.

Front Immunol. 2021 Dec 24;12:810047. doi: 10.3389/fimmu.2021.810047. eCollection 2021.

PMID: 35003140 Free PMC article.

A combined EM and proteomic analysis places HIV-1 Vpu at the crossroads of retromer and ESCRT complexes: PTPN23 is a Vpu-cofactor.

Stoneham CA, Langer S, De Jesus PD, Wozniak JM, Lapek J, Deerinck T, Thor A, Pache L, Chanda SK, Gonzalez DJ, Ellisman M, Guatelli J.

PLoS Pathog. 2021 Nov 29;17(11):e1009409. doi: 10.1371/journal.ppat.1009409. eCollection 2021 Nov.

PMID: 34843601 Free PMC article.

Genome-scale metabolic modeling reveals SARS-CoV-2-induced metabolic changes and antiviral targets.

Cheng K, Martin-Sancho L, Pal LR, Pu Y, Riva L, Yin X, Sinha S, Nair NU, Chanda SK, Ruppin E.

Mol Syst Biol. 2021 Nov;17(11):e10260. doi: 10.15252/msb.202110260.

PMID: 34709707 Free PMC article.

The Compound SBI-0090799 Inhibits Zika Virus Infection by Blocking De Novo Formation of the Membranous Replication Compartment.

Riva L, Goellner S, Biering SB, Huang CT, Rubanov AN, Haselmann U, Warnes CM, De Jesus PD, Martin-Sancho L, Terskikh AV, Harris E, Pinkerton AB, Bartenschlager R, Chanda SK.

J Virol. 2021 Oct 27;95(22):e0099621. doi: 10.1128/JVI.00996-21. Epub 2021 Sep 1.

PMID: 34468177 Free PMC article.

Restriction factor compendium for influenza A virus reveals a mechanism for evasion of autophagy.

Martin-Sancho L, Tripathi S, Rodriguez-Frandsen A, Pache L, Sanchez-Aparicio M, McGregor MJ, Haas KM, Swaney DL, Nguyen TT, Mamede JI, Churas C, Pratt D, Rosenthal SB, Riva L, Nguyen C, Beltran-Raygoza N, Soonthornvacharin S, Wang G, Jimenez-Morales D, De Jesus PD, Moulton HM, Stein DA, Chang MW, Benner C, Ideker T, Albrecht RA, Hultquist JF, Krogan NJ, García-Sastre A, Chanda SK.

Nat Microbiol. 2021 Oct;6(10):1319-1333. doi: 10.1038/s41564-021-00964-2. Epub 2021 Sep 23.

PMID: 34556855 Free PMC article.

Synthetic lethality-based prediction of anti-SARS-CoV-2 targets.

Pal LR, Cheng K, Nair NU, Martin-Sancho L, Sinha S, Pu Y, Riva L, Yin X, Schischlik F, Lee JS, Chanda SK, Ruppin E.

bioRxiv. 2021 Sep 15:2021.09.14.460408. doi: 10.1101/2021.09.14.460408. Preprint.

PMID: 34545363 Free PMC article. Updated.

Genome-scale metabolic modeling reveals SARS-CoV-2-induced metabolic changes and antiviral targets.

Cheng K, Martin-Sancho L, Pal LR, Pu Y, Riva L, Yin X, Sinha S, Nair NU, Chanda SK, Ruppin E.

bioRxiv. 2021 Aug 25:2021.01.27.428543. doi: 10.1101/2021.01.27.428543. Preprint.

PMID: 33532779 Free PMC article. Updated.

Functional landscape of SARS-CoV-2 cellular restriction.

Martin-Sancho L, Lewinski MK, Pache L, Stoneham CA, Yin X, Becker ME, Pratt D, Churas C, Rosenthal SB, Liu S, Weston S, De Jesus PD, O'Neill AM, Gounder AP, Nguyen C, Pu Y, Curry HM, Oom AL, Miorin L, Rodriguez-Frandsen A, Zheng F, Wu C, Xiong Y, Urbanowski M, Shaw ML, Chang MW, Benner C, Hope TJ, Frieman MB, García-Sastre A, Ideker T, Hultquist JF, Guatelli J, Chanda SK.

Mol Cell. 2021 Jun 17;81(12):2656-2668.e8. doi: 10.1016/j.molcel.2021.04.008. Epub 2021 Apr 13.

PMID: 33930332 Free PMC article.

TOP1 inhibition therapy protects against SARS-CoV-2-induced lethal inflammation.

Ho JSY, Mok BW, Campisi L, Jordan T, Yildiz S, Parameswaran S, Wayman JA, Gaudreault NN, Meekins DA, Indran SV, Morozov I, Trujillo JD, Fstkchyan YS, Rathnasinghe R, Zhu Z, Zheng S, Zhao N, White K, Ray-Jones H, Malysheva V, Thiecke MJ, Lau SY, Liu H, Zhang AJ, Lee AC, Liu WC, Jangra S, Escalera A, Aydillo T, Melo BS, Guccione E, Sebra R, Shum E, Bakker J, Kaufman DA, Moreira AL, Carossino M, Balasuriya UBR, Byun M, Albrecht RA, Schotsaert M, Garcia-Sastre A, Chanda SK, Miraldi ER, Jeyasekharan AD, TenOever BR, Spivakov M, Weirauch MT, Heinz S, Chen H, Benner C, Richt JA, Marazzi I.

Cell. 2021 May 13;184(10):2618-2632.e17. doi: 10.1016/j.cell.2021.03.051. Epub 2021 Mar 30.

PMID: 33836156 Free PMC article.

Clofazimine broadly inhibits coronaviruses including SARS-CoV-2.

Yuan S, Yin X, Meng X, Chan JF, Ye ZW, Riva L, Pache L, Chan CC, Lai PM, Chan CC, Poon VK, Lee AC, Matsunaga N, Pu Y, Yuen CK, Cao J, Liang R, Tang K, Sheng L, Du Y, Xu W, Lau CY, Sit KY, Au WK, Wang R, Zhang YY, Tang YD, Clausen TM, Pihl J, Oh J, Sze KH, Zhang AJ, Chu H, Kok KH, Wang D, Cai XH, Esko JD, Hung IF, Li RA, Chen H, Sun H, Jin DY, Sun R, Chanda SK, Yuen KY.

Nature. 2021 May;593(7859):418-423. doi: 10.1038/s41586-021-03431-4. Epub 2021 Mar 16.

PMID: 33727703

The Prolyl-tRNA Synthetase Inhibitor Halofuginone Inhibits SARS-CoV-2 Infection.

Sandoval DR, Clausen TM, Nora C, Cribbs AP, Denardo A, Clark AE, Garretson AF, Coker JKC, Narayanan A, Majowicz SA, Philpott M, Johansson C, Dunford JE, Spliid CB, Golden GJ, Payne NC, Tye MA, Nowell CJ, Griffis ER, Piermatteo A, Grunddal KV, Alle T, Magida JA, Hauser BM, Feldman J, Caradonna TM, Pu Y, Yin X, McVicar RN, Kwong EM, Weiss RJ, Downes M, Tsimikas S, Smidt AG, Ballatore C, Zengler K, Evans RM, Chanda SK, Croker BA, Leibel SL, Jose J, Mazitschek R, Oppermann U, Esko JD, Carlin AF, Gordts PLSM.

bioRxiv. 2021 Mar 26:2021.03.22.436522. doi: 10.1101/2021.03.22.436522. Preprint.

PMID: 33791697 Free PMC article.

MDA5 Governs the Innate Immune Response to SARS-CoV-2 in Lung Epithelial Cells.

Yin X, Riva L, Pu Y, Martin-Sancho L, Kanamune J, Yamamoto Y, Sakai K, Gotoh S, Miorin L, De Jesus PD, Yang CC, Herbert KM, Yoh S, Hultquist JF, García-Sastre A, Chanda SK.

Cell Rep. 2021 Jan 12;34(2):108628. doi: 10.1016/j.celrep.2020.108628.

PMID: 33440148 Free PMC article.

2020

Topoisomerase 1 inhibition therapy protects against SARS-CoV-2-induced inflammation and death in animal models.

Yuin Ho JS, Wing-Yee Mok B, Campisi L, Jordan T, Yildiz S, Parameswaran S, Wayman JA, Gaudreault NN, Meekins DA, Indran SV, Morozov I, Trujillo JD, Fstkchyan YS, Rathnasinghe R, Zhu Z, Zheng S, Zhao N, White K, Ray-Jones H, Malysheva V, Thiecke MJ, Lau SY, Liu H, Junxia Zhang A, Chak-Yiu Lee A, Liu WC, Aydillo T, Salom Melo B, Guccione E, Sebra R, Shum E, Bakker J, Kaufman DA, Moreira AL, Carossino M, Balasuriya UBR, Byun M, Miraldi ER, Albrecht RA, Schotsaert M, Garcia-Sastre A, Chanda SK, Jeyasekharan AD, TenOever BR, Spivakov M, Weirauch MT, Heinz S, Chen H, Benner C, Richt JA, Marazzi I.

bioRxiv. 2020 Dec 1:2020.12.01.404483. doi: 10.1101/2020.12.01.404483. Preprint.

PMID: 33299999 Free PMC article. Updated.

SARS-CoV-2 Infection Depends on Cellular Heparan Sulfate and ACE2.

Clausen TM, Sandoval DR, Spliid CB, Pihl J, Perrett HR, Painter CD, Narayanan A, Majowicz SA, Kwong EM, McVicar RN, Thacker BE, Glass CA, Yang Z, Torres JL, Golden GJ, Bartels PL, Porell RN, Garretson AF, Laubach L, Feldman J, Yin X, Pu Y, Hauser BM, Caradonna TM, Kellman BP, Martino C, Gordts PLSM, Chanda SK, Schmidt AG, Godula K, Leibel SL, Jose J, Corbett KD, Ward AB, Carlin AF, Esko JD.

Cell. 2020 Nov 12;183(4):1043-1057.e15. doi: 10.1016/j.cell.2020.09.033. Epub 2020 Sep 14.

PMID: 32970989 Free PMC article.

SARS-CoV-2 Orf6 hijacks Nup98 to block STAT nuclear import and antagonize interferon signaling.

Miorin L, Kehrer T, Sanchez-Aparicio MT, Zhang K, Cohen P, Patel RS, Cupic A, Makio T, Mei M, Moreno E, Danziger O, White KM, Rathnasinghe R, Uccellini M, Gao S, Aydillo T, Mena I, Yin X, Martin-Sancho L, Krogan NJ, Chanda SK, Schotsaert M, Wozniak RW, Ren Y, Rosenberg BR, Fontoura BMA, García-Sastre A.

Proc Natl Acad Sci U S A. 2020 Nov 10;117(45):28344-28354. doi: 10.1073/pnas.2016650117. Epub 2020 Oct 23.

PMID: 33097660 Free PMC article.

Discovery of SARS-CoV-2 antiviral drugs through large-scale compound repurposing.

Riva L, Yuan S, Yin X, Martin-Sancho L, Matsunaga N, Pache L, Burgstaller-Muehlbacher S, De Jesus PD, Teriete P, Hull MV, Chang MW, Chan JF, Cao J, Poon VK, Herbert KM, Cheng K, Nguyen TH, Rubanov A, Pu Y, Nguyen C, Choi A, Rathnasinghe R, Schotsaert M, Miorin L, Dejosez M, Zwaka TP, Sit KY, Martinez-Sobrido L, Liu WC, White KM, Chapman ME, Lendy EK, Glynne RJ, Albrecht R, Ruppin E, Mesecar AD, Johnson JR, Benner C, Sun R, Schultz PG, Su AI, García-Sastre A, Chatterjee AK, Yuen KY, Chanda SK.

Nature. 2020 Oct;586(7827):113-119. doi: 10.1038/s41586-020-2577-1. Epub 2020 Jul 24.

PMID: 32707573 Free PMC article.

Functional Landscape of SARS-CoV-2 Cellular Restriction.

Martin-Sancho L, Lewinski MK, Pache L, Stoneham CA, Yin X, Pratt D, Churas C, Rosenthal SB, Liu S, De Jesus PD, O'Neill AM, Gounder AP, Nguyen C, Pu Y, Oom AL, Miorin L, Rodriguez-Frandsen A, Urbanowski M, Shaw ML, Chang MW, Benner C, Frieman MB, García-Sastre A, Ideker T, Hultquist JF, Guatelli J, Chanda SK.

bioRxiv. 2020 Sep 30:2020.09.29.319566. doi: 10.1101/2020.09.29.319566. Preprint.

PMID: 33024967 Free PMC article. Updated.

The E3 Ubiquitin-Protein Ligase Cullin 3 Regulates HIV-1 Transcription

Langer S, Yin X, Diaz A, Portillo AJ, Gordon DE, Rogers UH, Marlett JM, Krogan NJ, Young JAT, Pache L, Chanda SK.

Cells. 2020 Sep 1;9(9):2010. doi: 10.3390/cells9092010.

PMID: 32882949 Free PMC article.

SARS-CoV-2 Infection Depends on Cellular Heparan Sulfate and ACE2.

Clausen TM, Sandoval DR, Spliid CB, Pihl J, Painter CD, Thacker BE, Glass CA, Narayanan A, Majowicz SA, Zhang Y, Torres JL, Golden GJ, Porell R, Garretson AF, Laubach L, Feldman J, Yin X, Pu Y, Hauser B, Caradonna TM, Kellman BP, Martino C, Gordts PLSM, Leibel SL, Chanda SK, Schmidt AG, Godula K, Jose J, Corbett KD, Ward AB, Carlin AF, Esko JD.

bioRxiv. 2020 Jul 14:2020.07.14.201616. doi: 10.1101/2020.07.14.201616. Preprint.

PMID: 32699853 Free PMC article. Updated.

Pharmacological Activation of Non-canonical NF-κB Signaling Activates Latent HIV-1 Reservoirs In Vivo.

Pache L, Marsden MD, Teriete P, Portillo AJ, Heimann D, Kim JT, Soliman MSA, Dimapasoc M, Carmona C, Celeridad M, Spivak AM, Planelles V, Cosford NDP, Zack JA, Chanda SK.

Cell Rep Med. 2020 Jun 23;1(3):100037. doi: 10.1016/j.xcrm.2020.100037. eCollection 2020 Jun 23.

PMID: 33205060 Free PMC article.

A Large-scale Drug Repositioning Survey for SARS-CoV-2 Antivirals.

Riva L, Yuan S, Yin X, Martin-Sancho L, Matsunaga N, Burgstaller-Muehlbacher S, Pache L, De Jesus PP, Hull MV, Chang M, Chan JF, Cao J, Poon VK, Herbert K, Nguyen TT, Pu Y, Nguyen C, Rubanov A, Martinez-Sobrido L, Liu WC, Miorin L, White KM, Johnson JR, Benner C, Sun R, Schultz PG, Su A, Garcia-Sastre A, Chatterjee AK, Yuen KY, Chanda SK.

bioRxiv. 2020 Apr 17:2020.04.16.044016. doi: 10.1101/2020.04.16.044016. Preprint.

PMID: 32511357 Free PMC article.

Viral Determinants in H5N1 Influenza A Virus Enable Productive Infection of HeLa Cells.

Rodriguez-Frandsen A, Martin-Sancho L, Gounder AP, Chang MW, Liu WC, De Jesus PD, von Recum-Knepper J, Dutra MS, Huffmaster NJ, Chavarria M, Mena I, Riva L, Nguyen CB, Dobariya S, Herbert KM, Benner C, Albrecht RA, García-Sastre A, Chanda SK.

J Virol. 2020 Jan 31;94(4):e01410-19. doi: 10.1128/JVI.01410-19. Print 2020 Jan 31.

PMID: 31776276 Free PMC article.

Sensor Sensibility-HIV-1 and the Innate Immune Response.

Yin X, Langer S, Zhang Z, Herbert KM, Yoh S, König R, Chanda SK.

Cells. 2020 Jan 20;9(1):254. doi: 10.3390/cells9010254.

PMID: 31968566 Free PMC article. Review.