Publications

2024

Absence of SMARCB1 in rhabdoid tumor cells increases sensitivity to translation inhibition and alters translation efficiency of specific mRNAs.

Nguyen LT, Hains AE, Aziz-Zanjani MO, Dalsass M, Farooqee SBUD, Lu Y, Jackson PK, Van Rechem C. J Biol Chem. 2024 Nov 13;300(12):107988. doi: 10.1016/j.jbc.2024.107988. Epub ahead of print. PMID: 39542244.

A multi-modal single-cell and spatial expression map of metastatic breast cancer biopsies across clinicopathological features.

Klughammer J, Abravanel DL, Segerstolpe Å, Blosser TR, Goltsev Y, Cui Y, Goodwin DR, Sinha A, Ashenberg O, Slyper M, Vigneau S, Jané-Valbuena J, Alon S, Caraccio C, Chen J, Cohen O, Cullen N, DelloStritto LK, Dionne D, Files J, Frangieh A, Helvie K, Hughes ME, Inga S, Kanodia A, Lako A, MacKichan C, Mages S, Moriel N, Murray E, Napolitano S, Nguyen K, Nitzan M, Ortiz R, Patel M, Pfaff KL, Porter CBM, Rotem A, Strauss S, Strasser R, Thorner AR, Turner M, Wakiro I, Waldman J, Wu J, Gómez Tejeda Zañudo J, Zhang D, Lin NU, Tolaney SM, Winer EP, Boyden ES, Chen F, Nolan GP, Rodig SJ, Zhuang X, Rozenblatt-Rosen O, Johnson BE, Regev A, Wagle N. Nat Med. 2024 Nov;30(11):3236-3249. doi: 10.1038/s41591-024-03215-z. Epub 2024 Oct 30. PMID: 39478111; PMCID: PMC11564109.

Sex-biased human thymic architecture guides T cell development through spatially defined niches.

Stankiewicz LN, Salim K, Flaschner EA, Wang YX, Edgar JM, Durland LJ, Lin BZB, Bingham GC, Major MC, Jones RD, Blau HM, Rideout EJ, Levings MK, Zandstra PW, Rossi FMV. Dev Cell. 2024 Oct 3:S1534-5807(24)00539-2. doi: 10.1016/j.devcel.2024.09.011. Epub ahead of print. PMID: 39383865.

Neuromuscular impairment at different stages of human sarcopenia.

Sarto F, Franchi MV, McPhee JS, Stashuk DW, Paganini M, Monti E, Rossi M, Sirago G, Zampieri S, Motanova ES, Valli G, Moro T, Paoli A, Bottinelli R, Pellegrino MA, De Vito G, Blau HM, Narici MV. J Cachexia Sarcopenia Muscle. 2024 Oct;15(5):1797-1810. doi: 10.1002/jcsm.13531. Epub 2024 Sep 5. PMID: 39236304; PMCID: PMC11446718.

Hydrogel biomaterials that stiffen and soften on demand reveal that skeletal muscle stem cells harbor a mechanical memory.

Madl CM, Wang YX, Holbrook CA, Su S, Shi X, Byfield FJ, Wicki G, Flaig IA, Blau HM. Proc Natl Acad Sci U S A. 2024 Aug 27;121(35):e2406787121. doi: 10.1073/pnas.2406787121. Epub 2024 Aug 20. PMID: 39163337; PMCID: PMC11363279.

Tracking single hiPSC-derived cardiomyocyte contractile function using CONTRAX an efficient pipeline for traction force measurement.

Pardon G, Vander Roest AS, Chirikian O, Birnbaum F, Lewis H, Castillo EA, Wilson R, Denisin AK, Blair CA, Holbrook C, Koleckar K, Chang ACY, Blau HM, Pruitt BL. Nat Commun. 2024 Jun 26;15(1):5427. doi: 10.1038/s41467-024-49755-3. PMID: 38926342; PMCID: PMC11208611.

Automated spatial omics landscape analysis approach reveals novel tissue architectures in ulcerative colitis.

Holman DR, Rubin SJS, Ferenc M, Holman EA, Koron AN, Daniel R, Boland BS, Nolan GP, Chang JT, Rogalla S. Sci Rep. 2024 Aug 15;14(1):18934. doi: 10.1038/s41598-024-68397-5. PMID: 39147769; PMCID: PMC11327370.

Graph Fourier transform for spatial omics representation and analyses of complex organs.

Chang Y, Liu J, Jiang Y, Ma A, Yeo YY, Guo Q, McNutt M, Krull JE, Rodig SJ, Barouch DH, Nolan GP, Xu D, Jiang S, Li Z, Liu B, Ma Q. Nat Commun. 2024 Aug 29;15(1):7467. doi: 10.1038/s41467-024-51590-5. PMID: 39209833; PMCID: PMC11362340.

Subcortical-cortical white matter connectivity in adults with autism spectrum disorder and schizophrenia patients.

Weerasekera A, Ion-Mărgineanu A, Nolan GP, Mody M. Psychiatry Res Neuroimaging. 2024 Jun;340:111806. doi: 10.1016/j.pscychresns.2024.111806. Epub 2024 Mar 7. PMID: 38508025.

A Spatial Multi-Modal Dissection of Host-Microbiome Interactions within the Colitis Tissue Microenvironment.

Zhu B, Bai Y, Yeo YY, Lu X, Rovira-Clavé X, Chen H, Yeung J, Gerber GK, Angelo M, Shalek AK, Nolan GP, Jiang S. bioRxiv [Preprint]. 2024 Mar 6:2024.03.04.583400. doi: 10.1101/2024.03.04.583400. PMID: 38496402; PMCID: PMC10942342.

Neuromuscular impairment at different stages of human sarcopenia.

Sarto F, Franchi MV, McPhee JS, Stashuk DW, Paganini M, Monti E, Rossi M, Sirago G, Zampieri S, Motanova ES, Valli G, Moro T, Paoli A, Bottinelli R, Pellegrino MA, De Vito G, Blau HM, Narici MV. J Cachexia Sarcopenia Muscle. 2024 Sep 5. doi: 10.1002/jcsm.13531. Epub ahead of print. PMID: 39236304.

The tidyomics ecosystem: enhancing omic data analyses.

Hutchison WJ, Keyes TJ; tidyomics Consortium; Crowell HL, Serizay J, Soneson C, Davis ES, Sato N, Moses L, Tarlinton B, Nahid AA, Kosmac M, Clayssen Q, Yuan V, Mu W, Park JE, Mamede I, Ryu MH, Axisa PP, Paiz P, Poon CL, Tang M, Gottardo R, Morgan M, Lee S, Lawrence M, Hicks SC, Nolan GP, Davis KL, Papenfuss AT, Love MI, Mangiola S. Nat Methods. 2024 Jul;21(7):1166-1170. doi: 10.1038/s41592-024-02299-2. Epub 2024 Jun 14. PMID: 38877315.

A fast-acting lipid checkpoint in G1 prevents mitotic defects.

Köberlin MS, Fan Y, Liu C, Chung M, Pinto AFM, Jackson PK, Saghatelian A, Meyer T. Nat Commun. 2024 Mar 18;15(1):2441. doi: 10.1038/s41467-024-46696-9. PMID: 38499565; PMCID: PMC10948896.

A spatial cell atlas of neuroblastoma reveals developmental, epigenetic and spatial axis of tumor heterogeneity.

Patel AG, Ashenberg O, Collins NB, Segerstolpe Å, Jiang S, Slyper M, Huang X, Caraccio C, Jin H, Sheppard H, Xu K, Chang TC, Orr BA, Shirinifard A, Chapple RH, Shen A, Clay MR, Tatevossian RG, Reilly C, Patel J, Lupo M, Cline C, Dionne D, Porter CBM, Waldman J, Bai Y, Zhu B, Barrera I, Murray E, Vigneau S, Napolitano S, Wakiro I, Wu J, Grimaldi G, Dellostritto L, Helvie K, Rotem A, Lako A, Cullen N, Pfaff KL, Karlström Å, Jané-Valbuena J, Todres E, Thorner A, Geeleher P, Rodig SJ, Zhou X, Stewart E, Johnson BE, Wu G, Chen F, Yu J, Goltsev Y, Nolan GP, Rozenblatt-Rosen O, Regev A, Dyer MA. bioRxiv [Preprint]. 2024 Jan 16:2024.01.07.574538. doi: 10.1101/2024.01.07.574538. PMID: 38260392; PMCID: PMC10802404.

Multimodal and spatially resolved profiling identifies distinct patterns of T cell infiltration in nodal B cell lymphoma entities.

Roider T, Baertsch MA, Fitzgerald D, Vöhringer H, Brinkmann BJ, Czernilofsky F, Knoll M, Llaó-Cid L, Mathioudaki A, Faßbender B, Herbon M, Lautwein T, Bruch PM, Liebers N, Schürch CM, Passerini V, Seifert M, Brobeil A, Mechtersheimer G, Müller-Tidow C, Weigert O, Seiffert M, Nolan GP, Huber W, Dietrich S. Nat Cell Biol. 2024 Mar;26(3):478-489. doi: 10.1038/s41556-024-01358-2. Epub 2024 Feb 20. PMID: 38379051; PMCID: PMC10940160.

BCG vaccination stimulates integrated organ immunity by feedback of the adaptive immune response to imprint prolonged innate antiviral resistance.

Lee A, Floyd K, Wu S, Fang Z, Tan TK, Froggatt HM, Powers JM, Leist SR, Gully KL, Hubbard ML, Li C, Hui H, Scoville D, Ruggiero AD, Liang Y, Pavenko A, Lujan V, Baric RS, Nolan GP, Arunachalam PS, Suthar MS, Pulendran B. Nat Immunol. 2024 Jan;25(1):41-53. doi: 10.1038/s41590-023-01700-0. Epub 2023 Nov 30. PMID: 38036767; PMCID: PMC10932731.

Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer.

Matusiak M, Hickey JW, van IJzendoorn DGP, Lu G, Kidziński L, Zhu S, Colburg DRC, Luca B, Phillips DJ, Brubaker SW, Charville GW, Shen J, Loh KM, Okwan-Duodu DK, Nolan GP, Newman AM, West RB, van de Rijn M. Cancer Discov. 2024 Aug 2;14(8):1418-1439. doi: 10.1158/2159-8290.CD-23-1300. PMID: 38552005; PMCID: PMC11294822.

MAPS: Pathologist-level cell type annotation from tissue images through machine learning.

Shaban M, Bai Y, Qiu H, Mao S, Yeung J, Yeo YY, Shanmugam V, Chen H, Zhu B, Nolan GP, Shipp MA, Rodig SJ, Jiang S, Mahmood F. Nat Commun. 2024 Jan 2;15(1):28. doi: 10.1038/s41467-023-44188-w. PMID: 37425872; PMCID: PMC10327211.

Integration of spatial and single-cell data across modalities with weakly linked features.

Chen S, Zhu B, Huang S, Hickey JW, Lin KZ, Snyder M, Greenleaf WJ, Nolan GP, Zhang NR, Ma Z. Nat Biotechnol. 2024 Jul;42(7):1096-1106. doi: 10.1038/s41587-023-01935-0. Epub 2023 Sep 7. PMID: 37679544.

2023

Regeneration of neuromuscular synapses after acute and chronic denervation by inhibiting the gerozyme 15-prostaglandin dehydrogenase.

Bakooshli MA, Wang YX, Monti E, Su S, Kraft P, Nalbandian M, Alexandrova L, Wheeler JR, Vogel H, Blau HM. Sci Transl Med. 2023 Oct 11;15(717):eadg1485. doi: 10.1126/scitranslmed.adg1485. Epub 2023 Oct 11. PMID: 37820010; PMCID: PMC10763629.

Dasatinib overcomes glucocorticoid resistance in B-cell acute lymphoblastic leukemia.

Sarno J, Domizi P, Liu Y, Merchant M, Pedersen CB, Jedoui D, Jager A, Nolan GP, Gaipa G, Bendall SC, Bava FA, Davis KL. Nat Commun. 2023 May 22;14(1):2935. doi: 10.1038/s41467-023-38456-y. PMID: 37217509; PMCID: PMC10203345.

UHRF1 is a mediator of KRAS driven oncogenesis in lung adenocarcinoma.

Kostyrko K, Román M, Lee AG, Simpson DR, Dinh PT, Leung SG, Marini KD, Kelly MR, Broyde J, Califano A, Jackson PK, Sweet-Cordero EA. Nat Commun. 2023 Jul 5;14(1):3966. doi: 10.1038/s41467-023-39591-2. PMID: 37407562; PMCID: PMC10322837.

Hardwiring tissue-specific AAV transduction in mice through engineered receptor expression.

Zengel J, Wang YX, Seo JW, Ning K, Hamilton JN, Wu B, Raie M, Holbrook C, Su S, Clements DR, Pillay S, Puschnik AS, Winslow MM, Idoyaga J, Nagamine CM, Sun Y, Mahajan VB, Ferrara KW, Blau HM, Carette JE. Nat Methods. 2023 Jul;20(7):1070-1081. doi: 10.1038/s41592-023-01896-x. Epub 2023 Jun 8. PMID: 37291262; PMCID: PMC10333121.

SARS-CoV-2 replication in airway epithelia requires motile cilia and microvillar reprogramming.

Wu CT, Lidsky PV, Xiao Y, Cheng R, Lee IT, Nakayama T, Jiang S, He W, Demeter J, Knight MG, Turn RE, Rojas-Hernandez LS, Ye C, Chiem K, Shon J, Martinez-Sobrido L, Bertozzi CR, Nolan GP, Nayak JV, Milla C, Andino R, Jackson PK. Cell. 2023 Jan 5;186(1):112-130.e20. doi: 10.1016/j.cell.2022.11.030. Epub 2022 Dec 2. PMID: 36580912; PMCID: PMC9715480.

Organization of the human intestine at single-cell resolution.

Hickey JW, Becker WR, Nevins SA, Horning A, Perez AE, Zhu C, Zhu B, Wei B, Chiu R, Chen DC, Cotter DL, Esplin ED, Weimer AK, Caraccio C, Venkataraaman V, Schürch CM, Black S, Brbić M, Cao K, Chen S, Zhang W, Monte E, Zhang NR, Ma Z, Leskovec J, Zhang Z, Lin S, Longacre T, Plevritis SK, Lin Y, Nolan GP, Greenleaf WJ, Snyder M. Nature. 2023 Jul;619(7970):572-584. doi: 10.1038/s41586-023-05915-x. Epub 2023 Jul 19. PMID: 37468586; PMCID: PMC10356619.

The IFT81-IFT74 complex acts as an unconventional RabL2 GTPase-activating protein during intraflagellar transport.

Boegholm N, Petriman NA, Loureiro-López M, Wang J, Vela MIS, Liu B, Kanie T, Ng R, Jackson PK, Andersen JS, Lorentzen E. EMBO J. 2023 Sep 18;42(18):e111807. doi: 10.15252/embj.2022111807. Epub 2023 Aug 22. PMID: 37606072; PMCID: PMC10505919.

Expanded vacuum-stable gels for multiplexed high-resolution spatial histopathology.

Bai Y, Zhu B, Oliveria JP, Cannon BJ, Feyaerts D, Bosse M, Vijayaragavan K, Greenwald NF, Phillips D, Schürch CM, Naik SM, Ganio EA, Gaudilliere B, Rodig SJ, Miller MB, Angelo M, Bendall SC, Rovira-Clavé X, Nolan GP, Jiang S. Nat Commun. 2023 Jul 7;14(1):4013. doi: 10.1038/s41467-023-39616-w. PMID: 37419873; PMCID: PMC10329015.

Organ Mapping Antibody Panels: a community resource for standardized multiplexed tissue imaging.

Quardokus EM, Saunders DC, McDonough E, Hickey JW, Werlein C, Surrette C, Rajbhandari P, Casals AM, Tian H, Lowery L, Neumann EK, Björklund F, Neelakantan TV, Croteau J, Wiblin AE, Fisher J, Livengood AJ, Dowell KG, Silverstein JC, Spraggins JM, Pryhuber GS, Deutsch G, Ginty F, Nolan GP, Melov S, Jonigk D, Caldwell MA, Vlachos IS, Muller W, Gehlenborg N, Stockwell BR, Lundberg E, Snyder MP, Germain RN, Camarillo JM, Kelleher NL, Börner K, Radtke AJ. Nat Methods. 2023 Aug;20(8):1174-1178. doi: 10.1038/s41592-023-01846-7. Epub 2023 Jul 19. PMID: 37468619; PMCID: PMC10406602.

Single-molecule imaging in the primary cilium.

Weiss LE, Love JF, Yoon J, Comerci CJ, Milenkovic L, Kanie T, Jackson PK, Stearns T, Gustavsson AK. Methods Cell Biol. 2023;176:59-83. doi: 10.1016/bs.mcb.2023.01.003. Epub 2023 Feb 24. PMID: 37164543; PMCID: PMC10509820.

Physioxia improves the selectivity of hematopoietic stem cell expansion cultures.

Igarashi KJ, Kucinski I, Chan YY, Tan TK, Khoo HM, Kealy D, Bhadury J, Hsu I, Ho PY, Niizuma K, Hickey JW, Nolan GP, Bridge KS, Czechowicz A, Gottgens B, Nakauchi H, Wilkinson AC. Blood Adv. 2023 Jul 25;7(14):3366-3377. doi: 10.1182/bloodadvances.2023009668. PMID: 36809781; PMCID: PMC10345863.

T cell-mediated curation and restructuring of tumor tissue coordinates an effective immune response.

Hickey JW, Haist M, Horowitz N, Caraccio C, Tan Y, Rech AJ, Baertsch MA, Rovira-Clavé X, Zhu B, Vazquez G, Barlow G, Agmon E, Goltsev Y, Sunwoo JB, Covert M, Nolan GP. Cell Rep. 2023 Dec 26;42(12):113494. doi: 10.1016/j.celrep.2023.113494. Epub 2023 Dec 11. PMID: 38085642; PMCID: PMC10765317.

A spatial map of human macrophage niches reveals context-dependent macrophage functions in colon and breast cancer.

Matusiak M, Hickey JW, Luca B, Lu G, Kidziński L, Zhu S, Colburg DRC, Phillips DJ, Brubaker SW, Charville GW, Shen J, Nolan GP, Newman AM, West RB, van de Rijn M. Res Sq [Preprint]. 2023 Jan 10:rs.3.rs-2393443. doi: 10.21203/rs.3.rs-2393443/v1. PMID: 36711732; PMCID: PMC9882614.

Transcription factor stoichiometry, motif affinity and syntax regulate single-cell chromatin dynamics during fibroblast reprogramming to pluripotency.

Nair S, Ameen M, Sundaram L, Pampari A, Schreiber J, Balsubramani A, Wang YX, Burns D, Blau HM, Karakikes I, Wang KC, Kundaje A. bioRxiv [Preprint]. 2023 Oct 21:2023.10.04.560808. doi: 10.1101/2023.10.04.560808. PMID: 37873116; PMCID: PMC10592962.

Sex biased human thymic architecture guides T cell development through spatially defined niches.

Stankiewicz LN, Salim K, Flaschner EA, Wang YX, Edgar JM, Lin BZ, Bingham GC, Major MC, Jones RD, Blau HM, Rideout EJ, Levings MK, Zandstra PW, Rossi FM. bioRxiv [Preprint]. 2023 Apr 16:2023.04.13.536804. doi: 10.1101/2023.04.13.536804. PMID: 37090676; PMCID: PMC10120731.

Tidytof: a user-friendly framework for scalable and reproducible high-dimensional cytometry data analysis.

Keyes TJ, Koladiya A, Lo YC, Nolan GP, Davis KL. Bioinform Adv. 2023 Jun 9;3(1):vbad071. doi: 10.1093/bioadv/vbad071. PMID: 37351311; PMCID: PMC10281957.

Integrating multiplexed imaging and multiscale modeling identifies tumor phenotype conversion as a critical component of therapeutic T cell efficacy.

Hickey JW, Agmon E, Horowitz N, Lamore M, Sunwoo J, Covert M, Nolan GP. Cell Syst. 2024 Apr 17;15(4):322-338.e5. doi: 10.1016/j.cels.2024.03.004. PMID: 38106218

TRF2 rescues telomere attrition and prolongs cell survival in Duchenne muscular dystrophy cardiomyocytes derived from human iPSCs.

Eguchi A, Gonzalez AFGS, Torres-Bigio SI, Koleckar K, Birnbaum F, Zhang JZ, Wang VY, Wu JC, Artandi SE, Blau HM.Proc Natl Acad Sci U S A. 2023 Feb 7;120(6):e2209967120. doi: 10.1073/pnas.2209967120. Epub 2023 Jan 31.PMID: 36719921

Machine learning-based classification of dual fluorescence signals reveals muscle stem cell fate transitions in response to regenerative niche factors.

Togninalli M, Ho ATV, Madl CM, Holbrook CA, Wang YX, Magnusson KEG, Kirillova A, Chang A, Blau HM.NPJ Regen Med. 2023 Jan 14;8(1):4. doi: 10.1038/s41536-023-00277-4.PMID: 36639373

A tissue atlas of ulcerative colitis revealing evidence of sex-dependent differences in disease-driving inflammatory cell types and resistance to TNF inhibitor therapy.

Mayer AT, Holman DR, Sood A, Tandon U, Bhate SS, Bodapati S, Barlow GL, Chang J, Black S, Crenshaw EC, Koron AN, Streett SE, Gambhir SS, Sandborn WJ, Boland BS, Hastie T, Tibshirani R, Chang JT, Nolan GP, Schürch CM, Rogalla S.Sci Adv. 2023 Jan 20;9(3):eadd1166. doi: 10.1126/sciadv.add1166. Epub 2023 Jan 20.PMID: 36662860

Multiplexed screens identify RAS paralogues HRAS and NRAS as suppressors of KRAS-driven lung cancer growth.

Tang R, Shuldiner EG, Kelly M, Murray CW, Hebert JD, Andrejka L, Tsai MK, Hughes NW, Parker MI, Cai H, Li YC, Wahl GM, Dunbrack RL, Jackson PK, Petrov DA, Winslow MM.Nat Cell Biol. 2023 Jan;25(1):159-169. doi: 10.1038/s41556-022-01049-w. Epub 2023 Jan 12.PMID: 36635501

A hierarchical pathway for assembly of the distal appendages that organize primary cilia.

Kanie T, Love JF, Fisher SD, Gustavsson AK, Jackson PK.bioRxiv. 2023 Jan 10:2023.01.06.522944. doi: 10.1101/2023.01.06.522944. Preprint.PMID: 36711481

Single-cell profiling of alveolar rhabdomyosarcoma reveals RAS pathway inhibitors as cell-fate hijackers with therapeutic relevance.

Danielli SG, Porpiglia E, De Micheli AJ, Navarro N, Zellinger MJ, Bechtold I, Kisele S, Volken L, Marques JG, Kasper S, Bode PK, Henssen AG, Gürgen D, Delattre O, Surdez D, Roma J, Bühlmann P, Blau HM, Wachtel M, Schäfer BW.Sci Adv. 2023 Feb 10;9(6):eade9238. doi: 10.1126/sciadv.ade9238. Epub 2023 Feb 8.PMID: 36753540

Myristoylated Neuronal Calcium Sensor-1 captures the ciliary vesicle at distal appendages.

Kanie T, Ng R, Abbott KL, Pongs O, Jackson PK.bioRxiv. 2023 Jan 10:2023.01.06.523037. doi: 10.1101/2023.01.06.523037. Preprint.PMID: 36712037

Predictive models demonstrate age-dependent association of subcortical volumes and cognitive measures.

Weerasekera A, Ion-Mărgineanu A, Green C, Mody M, Nolan GP.Hum Brain Mapp. 2023 Feb 1;44(2):801-812. doi: 10.1002/hbm.26100. Epub 2022 Oct 12.PMID: 36222055

Robust single-cell matching and multimodal analysis using shared and distinct features.

Zhu B, Chen S, Bai Y, Chen H, Liao G, Mukherjee N, Vazquez G, McIlwain DR, Tzankov A, Lee IT, Matter MS, Goltsev Y, Ma Z, Nolan GP, Jiang S.Nat Methods. 2023 Feb;20(2):304-315. doi: 10.1038/s41592-022-01709-7. Epub 2023 Jan 9.PMID: 36624212

Fluorogenic reporter enables identification of compounds that inhibit SARS-CoV-2.

Yang J, Xiao Y, Lidsky PV, Wu CT, Bonser LR, Peng S, Garcia-Knight MA, Tassetto M, Chung CI, Li X, Nakayama T, Lee IT, Nayak JV, Ghias K, Hargett KL, Shoichet BK, Erle DJ, Jackson PK, Andino R, Shu X.Nat Microbiol. 2023 Jan;8(1):121-134. doi: 10.1038/s41564-022-01288-5. Epub 2023 Jan 5.PMID: 36604514

Spatial compartmentalization of signaling imparts source-specific functions on secreted factors.

Groppa E, Martini P, Derakhshan N, Theret M, Ritso M, Tung LW, Wang YX, Soliman H, Hamer MS, Stankiewicz L, Eisner C, Erwan LN, Chang C, Yi L, Yuan JH, Kong S, Weng C, Adams J, Chang L, Peng A, Blau HM, Romualdi C, Rossi FMV.Cell Rep. 2023 Jan 31;42(2):112051. doi: 10.1016/j.celrep.2023.112051. Online ahead of print.PMID: 36729831

Glucose dissociates DDX21 dimers to regulate mRNA splicing and tissue differentiation.

Miao W, Porter DF, Lopez-Pajares V, Siprashvili Z, Meyers RM, Bai Y, Nguyen DT, Ko LA, Zarnegar BJ, Ferguson ID, Mills MM, Jilly-Rehak CE, Wu CG, Yang YY, Meyers JM, Hong AW, Reynolds DL, Ramanathan M, Tao S, Jiang S, Flynn RA, Wang Y, Nolan GP, Khavari PA.Cell. 2023 Jan 5;186(1):80-97.e26. doi: 10.1016/j.cell.2022.12.004.PMID: 36608661

SARS-CoV-2 replication in airway epithelia requires motile cilia and microvillar reprogramming.

Wu CT, Lidsky PV, Xiao Y, Cheng R, Lee IT, Nakayama T, Jiang S, He W, Demeter J, Knight MG, Turn RE, Rojas-Hernandez LS, Ye C, Chiem K, Shon J, Martinez-Sobrido L, Bertozzi CR, Nolan GP, Nayak JV, Milla C, Andino R, Jackson PK.Cell. 2023 Jan 5;186(1):112-130.e20. doi: 10.1016/j.cell.2022.11.030. Epub 2022 Dec 2.PMID: 36580912

2022

Integrated plasma proteomic and single-cell immune signaling network signatures demarcate mild, moderate, and severe COVID-19.

Feyaerts D, Hédou J, Gillard J, Chen H, Tsai ES, Peterson LS, Ando K, Manohar M, Do E, Dhondalay GKR, Fitzpatrick J, Artandi M, Chang I, Snow TT, Chinthrajah RS, Warren CM, Wittman R, Meyerowitz JG, Ganio EA, Stelzer IA, Han X, Verdonk F, Gaudillière DK, Mukherjee N, Tsai AS, Rumer KK, Jacobsen DR, Bjornson-Hooper ZB, Jiang S, Saavedra SF, Valdés Ferrer SI, Kelly JD, Furman D, Aghaeepour N, Angst MS, Boyd SD, Pinsky BA, Nolan GP, Nadeau KC, Gaudillière B, McIlwain DR. Cell Rep Med. 2022 Jul 19;3(7):100680. doi: 10.1016/j.xcrm.2022.100680. Epub 2022 Jun 28. PMID: 35839768; PMCID: PMC9238057.

Tip60-mediated H2A.Z acetylation promotes neuronal fate specification and bivalent gene activation.

Janas JA, Zhang L, Luu JH, Demeter J, Meng L, Marro SG, Mall M, Mooney NA, Schaukowitch K, Ng YH, Yang N, Huang Y, Neumayer G, Gozani O, Elias JE, Jackson PK, Wernig M. Mol Cell. 2022 Dec 15;82(24):4627-4646.e14. doi: 10.1016/j.molcel.2022.11.002. Epub 2022 Nov 22. PMID: 36417913; PMCID: PMC9779922.

GIMAP6 regulates autophagy, immune competence, and inflammation in mice and humans.

Yao Y, Du Jiang P, Chao BN, Cagdas D, Kubo S, Balasubramaniyam A, Zhang Y, Shadur B, NaserEddin A, Folio LR, Schwarz B, Bohrnsen E, Zheng L, Lynberg M, Gottlieb S, Leney-Greene MA, Park AY, Tezcan I, Akdogan A, Gocmen R, Onder S, Rosenberg A, Soilleux EJ, Johnson E, Jackson PK, Demeter J, Chauvin SD, Paul F, Selbach M, Bulut H, Clatworthy MR, Tuong ZK, Zhang H, Stewart BJ, Bosio CM, Stepensky P, Clare S, Ganesan S, Pascall JC, Daumke O, Butcher GW, McMichael AJ, Simon AK, Lenardo MJ. J Exp Med. 2022 Jun 6;219(6):e20201405. doi: 10.1084/jem.20201405. Epub 2022 May 13. PMID: 35551368; PMCID: PMC9111091.

Spatial epitope barcoding reveals clonal tumor patch behaviors.

Rovira-Clavé X, Drainas AP, Jiang S, Bai Y, Baron M, Zhu B, Dallas AE, Lee MC, Chu TP, Holzem A, Ayyagari R, Bhattacharya D, McCaffrey EF, Greenwald NF, Markovic M, Coles GL, Angelo M, Bassik MC, Sage J, Nolan GP. Cancer Cell. 2022 Nov 14;40(11):1423-1439.e11. doi: 10.1016/j.ccell.2022.09.014. Epub 2022 Oct 13. PMID: 36240778; PMCID: PMC9673683.

Elevated CD47 is a hallmark of dysfunctional aged muscle stem cells that can be targeted to augment regeneration.

Porpiglia E, Mai T, Kraft P, Holbrook CA, de Morree A, Gonzalez VD, Hilgendorf KI, Frésard L, Trejo A, Bhimaraju S, Jackson PK, Fantl WJ, Blau HM. Cell Stem Cell. 2022 Dec 1;29(12):1653-1668.e8. doi: 10.1016/j.stem.2022.10.009. Epub 2022 Nov 15. PMID: 36384141; PMCID: PMC9746883.

Identification of cell types in multiplexed in situ images by combining protein expression and spatial information using CELESTA.

Zhang W, Li I, Reticker-Flynn NE, Good Z, Chang S, Samusik N, Saumyaa S, Li Y, Zhou X, Liang R, Kong CS, Le QT, Gentles AJ, Sunwoo JB, Nolan GP, Engleman EG, Plevritis SK.Nat Methods. 2022 Jun;19(6):759-769. doi: 10.1038/s41592-022-01498-z. Epub 2022 Jun 2. PMID: 35654951; PMCID: PMC9728133.

Spatial mapping of protein composition and tissue organization: a primer for multiplexed antibody-based imaging.

Hickey JW, Neumann EK, Radtke AJ, Camarillo JM, Beuschel RT, Albanese A, McDonough E, Hatler J, Wiblin AE, Fisher J, Croteau J, Small EC, Sood A, Caprioli RM, Angelo RM, Nolan GP, Chung K, Hewitt SM, Germain RN, Spraggins JM, Lundberg E, Snyder MP, Kelleher NL, Saka SK. Nat Methods. 2022 Mar;19(3):284-295. doi: 10.1038/s41592-021-01316-y. Epub 2021 Nov 22. PMID: 34811556; PMCID: PMC9264278.

The Mettl3 epitranscriptomic writer amplifies p53 stress responses.

Raj N, Wang M, Seoane JA, Zhao RL, Kaiser AM, Moonie NA, Demeter J, Boutelle AM, Kerr CH, Mulligan AS, Moffatt C, Zeng SX, Lu H, Barna M, Curtis C, Chang HY, Jackson PK, Attardi LD. Mol Cell. 2022 Jul 7;82(13):2370-2384.e10. doi: 10.1016/j.molcel.2022.04.010. Epub 2022 May 4. PMID: 35512709; PMCID: PMC9807187.

SARS-CoV-2 replication in airway epithelia requires motile cilia and microvillar reprogramming.

Multi-omic analysis reveals divergent molecular events in scarring and regenerative wound healing.

Mascharak S, Talbott HE, Januszyk M, Griffin M, Chen K, Davitt MF, Demeter J, Henn D, Bonham CA, Foster DS, Mooney N, Cheng R, Jackson PK, Wan DC, Gurtner GC, Longaker MT. Cell Stem Cell. 2022 Feb 3;29(2):315-327.e6. doi: 10.1016/j.stem.2021.12.011. Epub 2022 Jan 24. PMID: 35077667; PMCID: PMC8988390.

New Views of Old Proteins: Clarifying the Enigmatic Proteome.

Burnum-Johnson KE, Conrads TP, Drake RR, Herr AE, Iyengar R, Kelly RT, Lundberg E, MacCoss MJ, Naba A, Nolan GP, Pevzner PA, Rodland KD, Sechi S, Slavov N, Spraggins JM, Van Eyk JE, Vidal M, Vogel C, Walt DR, Kelleher NL. Mol Cell Proteomics. 2022 Jul;21(7):100254. doi: 10.1016/j.mcpro.2022.100254. Epub 2022 May 30. PMID: 35654359; PMCID: PMC9256833.

Predictive models demonstrate age-dependent association of subcortical volumes and cognitive measures.

Weerasekera A, Ion-Mărgineanu A, Green C, Mody M, Nolan GP. Hum Brain Mapp. 2023 Feb 1;44(2):801-812. doi: 10.1002/hbm.26100. Epub 2022 Oct 12. PMID: 36222055; PMCID: PMC9842902.

A Comprehensive Atlas of Immunological Differences Between Humans, Mice, and Non-Human Primates.

Bjornson-Hooper ZB, Fragiadakis GK, Spitzer MH, Chen H, Madhireddy D, Hu K, Lundsten K, McIlwain DR, Nolan GP. Front Immunol. 2022 Mar 11;13:867015. doi: 10.3389/fimmu.2022.867015. PMID: 35359965; PMCID: PMC8962947.

A real-time GPU-accelerated parallelized image processor for large-scale multiplexed fluorescence microscopy data.

Lu G, Baertsch MA, Hickey JW, Goltsev Y, Rech AJ, Mani L, Forgó E, Kong C, Jiang S, Nolan GP, Rosenthal EL.Front Immunol. 2022 Sep 23;13:981825. doi: 10.3389/fimmu.2022.981825. PMID: 36211386; PMCID: PMC9539451.

Oxaliplatin disrupts nucleolar function through biophysical disintegration.

Schmidt HB, Jaafar ZA, Wulff BE, Rodencal JJ, Hong K, Aziz-Zanjani MO, Jackson PK, Leonetti MD, Dixon SJ, Rohatgi R, Brandman O. Cell Rep. 2022 Nov 8;41(6):111629. doi: 10.1016/j.celrep.2022.111629. PMID: 36351392; PMCID: PMC9749789.

Plasticity of muscle stem cells in homeostasis and aging.

Porpiglia E, Blau HM. Curr Opin Genet Dev. 2022 Dec;77:101999. doi: 10.1016/j.gde.2022.101999. Epub 2022 Oct 26. PMID: 36308777.

Annotation of spatially resolved single-cell data with STELLAR.

Brbić M, Cao K, Hickey JW, Tan Y, Snyder MP, Nolan GP, Leskovec J. Nat Methods. 2022 Nov;19(11):1411-1418. doi: 10.1038/s41592-022-01651-8. Epub 2022 Oct 24. PMID: 36280720.

Inflammatory molecular endotypes of nasal polyps derived from White and Japanese populations.

Nakayama T, Lee IT, Le W, Tsunemi Y, Borchard NA, Zarabanda D, Dholakia SS, Gall PA, Yang A, Kim D, Akutsu M, Kashiwagi T, Patel ZM, Hwang PH, Frank DN, Haruna SI, Ramakrishnan VR, Nolan GP, Jiang S, Nayak JV. J Allergy Clin Immunol. 2022 Apr;149(4):1296-1308.e6. doi: 10.1016/j.jaci.2021.11.017. Epub 2021 Dec 1. PMID: 34863854.

Combined protein and nucleic acid imaging reveals virus-dependent B cell and macrophage immunosuppression of tissue microenvironments.

Jiang S, Chan CN, Rovira-Clavé X, Chen H, Bai Y, Zhu B, McCaffrey E, Greenwald NF, Liu C, Barlow GL, Weirather JL, Oliveria JP, Nakayama T, Lee IT, Matter MS, Carlisle AE, Philips D, Vazquez G, Mukherjee N, Busman-Sahay K, Nekorchuk M, Terry M, Younger S, Bosse M, Demeter J, Rodig SJ, Tzankov A, Goltsev Y, McIlwain DR, Angelo M, Estes JD, Nolan GP. Immunity. 2022 Jun 14;55(6):1118-1134.e8. doi: 10.1016/j.immuni.2022.03.020. Epub 2022 Apr 20. PMID: 35447093; PMCID: PMC9220319.

Multicellular modules as clinical diagnostic and therapeutic targets.

Baertsch MA, Nolan GP, Hickey JW. Trends Cancer. 2022 Mar;8(3):164-173. doi: 10.1016/j.trecan.2021.11.004. Epub 2021 Dec 3. PMID: 34872889; PMCID: PMC8854341.

Primary cilia on muscle stem cells are critical to maintain regenerative capacity and are lost during aging.

Palla AR, Hilgendorf KI, Yang AV, Kerr JP, Hinken AC, Demeter J, Kraft P, Mooney NA, Yucel N, Burns DM, Wang YX, Jackson PK, Blau HM. Nat Commun. 2022 Mar 17;13(1):1439. doi: 10.1038/s41467-022-29150-6. PMID: 35301320; PMCID: PMC8931095.

SARS-CoV-2 infection drives an inflammatory response in human adipose tissue through infection of adipocytes and macrophages.

Martínez-Colón GJ, Ratnasiri K, Chen H, Jiang S, Zanley E, Rustagi A, Verma R, Chen H, Andrews JR, Mertz KD, Tzankov A, Azagury D, Boyd J, Nolan GP, Schürch CM, Matter MS, Blish CA, McLaughlin TL. Sci Transl Med. 2022 Dec 7;14(674):eabm9151. doi: 10.1126/scitranslmed.abm9151. Epub 2022 Dec 7. PMID: 36137009; PMCID: PMC9529056.

CellSeg: a robust, pre-trained nucleus segmentation and pixel quantification software for highly multiplexed fluorescence images.

Lee MY, Bedia JS, Bhate SS, Barlow GL, Phillips D, Fantl WJ, Nolan GP, Schürch CM. BMC Bioinformatics. 2022 Jan 18;23(1):46. doi: 10.1186/s12859-022-04570-9. PMID: 35042474; PMCID: PMC8767664.

Immunotherapy of glioblastoma explants induces interferon-γ responses and spatial immune cell rearrangements in tumor center, but not periphery.

Shekarian T, Zinner CP, Bartoszek EM, Duchemin W, Wachnowicz AT, Hogan S, Etter MM, Flammer J, Paganetti C, Martins TA, Schmassmann P, Zanganeh S, Le Goff F, Muraro MG, Ritz MF, Phillips D, Bhate SS, Barlow GL, Nolan GP, Schürch CM, Hutter G. Sci Adv. 2022 Jul;8(26):eabn9440. doi: 10.1126/sciadv.abn9440. Epub 2022 Jul 1. PMID: 35776791; PMCID: PMC10883360.

Tamoxifen treatment ameliorates contractile dysfunction of Duchenne muscular dystrophy stem cell-derived cardiomyocytes on bioengineered substrates.

Birnbaum F, Eguchi A, Pardon G, Chang ACY, Blau HM. NPJ Regen Med. 2022 Mar 18;7(1):19. doi: 10.1038/s41536-022-00214-x. PMID: 35304486; PMCID: PMC8933505.

Multiparameter analysis of timelapse imaging reveals kinetics of megakaryocytic erythroid progenitor clonal expansion and differentiation.

Scanlon VM, Thompson EN, Lawton BR, Kochugaeva M, Ta K, Mayday MY, Xavier-Ferrucio J, Kang E, Eskow NM, Lu YC, Kwon N, Laumas A, Cenci M, Lawrence K, Barden K, Larsuel ST, Reed FE, Peña-Carmona G, Ubbelohde A, Lee JP, Boobalan S, Oppong Y, Anderson R, Maynard C, Sahirul K, Lajeune C, Ivathraya V, Addy T, Sanchez P, Holbrook C, Van Ho AT, Duncan JS, Blau HM, Levchenko A, Krause DS. Sci Rep. 2022 Sep 28;12(1):16218. doi: 10.1038/s41598-022-19013-x. PMID: 36171423; PMCID: PMC9519589.

LKB1 drives stasis and C/EBP-mediated reprogramming to an alveolar type II fate in lung cancer.

Murray CW, Brady JJ, Han M, Cai H, Tsai MK, Pierce SE, Cheng R, Demeter J, Feldser DM, Jackson PK, Shackelford DB, Winslow MM. Nat Commun. 2022 Feb 28;13(1):1090. doi: 10.1038/s41467-022-28619-8. PMID: 35228570; PMCID: PMC8885825.

Variation of Immune Cell Responses in Humans Reveals Sex-Specific Coordinated Signaling Across Cell Types.

Fragiadakis GK, Bjornson-Hooper ZB, Madhireddy D, Sachs K, Chen H, McIlwain DR, Spitzer MH, Bendall SC, Nolan GP. Front Immunol. 2022 Mar 28;13:867016. doi: 10.3389/fimmu.2022.867016. PMID: 35419006; PMCID: PMC8995898.

Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors.

Bhate SS, Barlow GL, Schürch CM, Nolan GP. Cell Syst. 2022 Feb 16;13(2):109-130.e6. doi: 10.1016/j.cels.2021.09.012. Epub 2021 Oct 14. PMID: 34653369.

Postmitotic G1 phase survivin drives mitogen-independent cell division of B lymphocytes.

Singh A, Spitzer MH, Joy JP, Kaileh M, Qiu X, Nolan GP, Sen R. Proc Natl Acad Sci U S A. 2022 May 3;119(18):e2115567119. doi: 10.1073/pnas.2115567119. Epub 2022 Apr 27. PMID: 35476510; PMCID: PMC9170024.

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