LSP Bibliography

Yu WW, Barrett JNP, Tong J, Lin MJ, Marohn M, Devlin JC, Herrera A, Remark J, Levine J, Liu PK, Fang V, Zellmer AM, Oldridge DA, Wherry EJ, Lin JR, Chen JY, Sorger P, Santagata S, Krueger JG, Ruggles KV, Wang F, Su C, Koralov SB, Wang J, Chiu ES, Lu CP. Skin immune-mesenchymal interplay within tertiarylymphoid structures promotes autoimmunepathogenesis in hidradenitis suppurativa. Immunity. 2024 Dec 10;57(12):2827-2842.e5. PMID: 39662091

Launonen IM, Niemiec I, Hincapié-Otero M, Erkan EP, Junquera A, Afenteva D, Falco MM, Liang Z, Salko M, Chamchougia F, Szabo A, Perez-Villatoro F, Li Y, Micoli G, Nagaraj A, Haltia UM, Kahelin E, Oikkonen J, Hynninen J, Virtanen A, Nirmal AJ, Vallius T, Hautaniemi S, Sorger PK, Vähärautio A, Färkkilä A. Chemotherapy induces myeloid-driven spatially confined T cell exhaustion in ovarian cancer. Cancer Cell. 2024 Dec 9;42(12):2045-2063.e10. PMID: 39658541

Loi P, Schade AE, Rodriguez CL, Krishnan A, Perurena N, Nguyen VTM, Xu Y, Watanabe M, Davis RA, Gardner A, Pilla NF, Mattioli K, Popow O, Gunduz N, Lannagan TRM, Fitzgerald S, Sicinska ET, Lin JR, Tan W, Brais LK, Haigis KM, Giannakis M, Ng K, Santagata S, Helin K, Sansom OJ, Cichowski K. Epigenetic and Oncogenic Inhibitors Cooperatively Drive Differentiation and Kill KRAS-Mutant Colorectal Cancers. Cancer Discov. 2024 Dec 2;14(12):2430–2449. PMCID: PMC11609823

Tobochnik S, Regan MS, Dorotan MKC, Reich D, Lapinskas E, Hossain MA, Stopka S, Meredith DM, Santagata S, Murphy MM, Arnaout O, Bi WL, Chiocca EA, Golby AJ, Mooney MA, Smith TR, Ligon KL, Wen PY, Agar NYR, Lee JW. Pilot Trial of Perampanel on Peritumoral Hyperexcitability in Newly Diagnosed High-grade Glioma. Clin Cancer Res. 2024 Dec 2;30(23):5365–5373. PMCID: PMC11611619

Shimada K, Michaud DE, Cui YX, Zheng K, Goldberg J, Ju Z, Schnitt SJ, Pastorello R, Kania LD, Hoffer J, Muhlich JL, Hyun N, Krueger R, Gottlieb A, Nelson A, Wanderley CW, Antonellis G, McAllister SS, Tolaney SM, Waks AG, Jeselsohn R, Sorger PK, Agudo J, Mittendorf EA, Guerriero JL. An estrogen receptor signaling transcriptional program linked to immune evasion in human hormone receptor-positive breast cancer [Internet]. Cancer Biology; 2024 [cited 2024 Nov 26]. Available from: http://biorxiv.org/lookup/doi/10.1101/2024.11.23.619172

Rand EA, Owen SV, Quinones-Olvera N, Jean KDC, Hernandez-Perez C, Baym M. Phage DisCo: targeted discovery of bacteriophages by co-culture [Internet]. 2024 [cited 2024 Dec 5]. Available from: http://biorxiv.org/lookup/doi/10.1101/2024.11.22.624878

Vaelli P, Fujita A, Jo S, Zhang HXB, Osorno T, Ma X, Bean BP. State-Dependent Inhibition of Nav1.8 Sodium Channels by VX-150 and VX-548. Mol Pharmacol. 2024 Nov 18;106(6):298–308. PMID: 39322410

Souque C, González Ojeda I, Baym M. From Petri Dishes to Patients to Populations: Scales and Evolutionary Mechanisms Driving Antibiotic Resistance. Annu Rev Microbiol. 2024 Nov;78(1):361–382. PMID: 39141706

Baker GJ, Novikov E, Zhao Z, Vallius T, Davis JA, Lin JR, Muhlich JL, Mittendorf EA, Santagata S, Guerriero JL, Sorger PK. Quality control for single-cell analysis of high-plex tissue profiles using CyLinter. Nat Methods. 2024 Oct 30; PMID: 39478175

Mollaoglu G, Tepper A, Falcomatà C, Potak HT, Pia L, Amabile A, Mateus-Tique J, Rabinovich N, Park MD, LaMarche NM, Brody R, Browning L, Lin JR, Zamarin D, Sorger PK, Santagata S, Merad M, Baccarini A, Brown BD. Ovarian cancer-derived IL-4 promotes immunotherapy resistance. Cell. 2024 Oct 25;S0092-8674(24)01154–1. PMID: 39481380

Lu D, Faizi M, Drown B, Simerzin A, François J, Bradshaw G, Kelleher N, Jambhekar A, Gunawardena J, Lahav G. Temporal regulation of gene expression through integration of p53 dynamics and modifications. Sci Adv. 2024 Oct 25;10(43):eadp2229. PMCID: PMC11506164

Stojanovic L, Abbotts R, Tripathi K, Coon CM, Rajendran S, Farid EA, Hostetter G, Guarnieri JW, Wallace DC, Liu S, Wan J, Calendo G, Marker R, Gohari Z, Inayatullah MMA, Tiwari VK, Kader T, Santagata S, Drapkin R, Kommoss S, Pfisterer J, Konecny GE, Coopergard R, Issa JP, Winterhoff BJN, Topper MJ, Sandusky GE, Miller KD, Baylin SB, Nephew KP, Rassool FV. ZNFX1 is a Novel Master Regulator in Epigenetically-induced Pathogen Mimicry and Inflammasome Signaling in Cancer. bioRxiv. 2024 Oct 21;2024.10.18.618659. PMCID: PMC11526927

Schade AE, Perurena N, Yang Y, Rodriguez CL, Krishnan A, Gardner A, Loi P, Xu Y, Nguyen VTM, Mastellone GM, Pilla NF, Watanabe M, Ota K, Davis RA, Mattioli K, Xiang D, Zoeller JJ, Lin JR, Morganti S, Garrido-Castro AC, Tolaney SM, Li Z, Barbie DA, Sorger PK, Helin K, Santagata S, Knott SRV, Cichowski K. AKT and EZH2 inhibitors kill TNBCs by hijacking mechanisms of involution. Nature. 2024 Oct 9; PMID: 39385030

Ji W, Du G, Jiang J, Lu W, Mills CE, Yuan L, Jiang F, He Z, Bradshaw GA, Chung M, Jiang Z, Byun WS, Hinshaw SM, Zhang T, Gray NS. Discovery of bivalent small molecule degraders of cyclin-dependent kinase 7 (CDK7). Eur J Med Chem. 2024 Oct 5;276:116613. PMCID: PMC11316633

Kader T, Lin JR, Hug C, Coy S, Chen YA, de Bruijn I, Shih N, Jung E, Pelletier RJ, Leon ML, Mingo G, Omran DK, Lee JS, Yapp C, Satravada BA, Kundra R, Xu Y, Chan S, Tefft JB, Muhlich J, Kim S, Gysler SM, Agudo J, Heath JR, Schultz N, Drescher C, Sorger PK, Drapkin R, Santagata S. Multimodal Spatial Profiling Reveals Immune Suppression and Microenvironment Remodeling in Fallopian Tube Precursors to High-Grade Serous Ovarian Carcinoma. bioRxiv; 2024. PMCID: PMC11463462

Wala J, de Bruijn I, Coy S, Gagné A, Chan S, Chen YA, Hoffer J, Muhlich J, Schultz N, Santagata S, Sorger PK. Integrating spatial profiles and cancer genomics to identify immune-infiltrated mismatch repair proficient colorectal cancers. bioRxiv; 2024. PMCID: PMC11463659

Minichetti DG, Boyd A, Lemire E, Hacker J, Haber AL, Roditi RE, Albers MW, Lee S, Buchheit KM, Laidlaw TM, Bankova LG. Determinants of Persistence and Recovery of Chronic COVID19 Chemosensory Dysfunction. J Allergy Clin Immunol. 2024 Sep 11;S0091-6749(24)00913–8. PMID: 39270802

Ghosh HS, Patel RV, Woodward E, Greenwald NF, Bhave VM, Maury EA, Cello G, Hoffman SE, Li Y, Gupta H, Youssef G, Spurr LF, Vogelzang J, Touat M, Dubois F, Cherniack AD, Guo X, Tavakol S, Cioffi G, Lindeman NI, Ligon AH, Chiocca EA, Reardon DA, Wen PY, Meredith D, Santagata S, Barnholtz-Sloan JS, Ligon KL, Beroukhim R, Bi WL. Contemporary Prognostic Signatures and Refined Risk Stratification of Gliomas: An Analysis of 4,400 Tumors. Neuro Oncol. 2024 Aug 21;noae164. PMID: 39164213

Do BT, Hsu PP, Vermeulen SY, Wang Z, Hirz T, Abbott KL, Aziz N, Replogle JM, Bjelosevic S, Paolino J, Nelson SA, Block S, Darnell AM, Ferreira R, Zhang H, Milosevic J, Schmidt DR, Chidley C, Harris IS, Weissman JS, Pikman Y, Stegmaier K, Cheloufi S, Su XA, Sykes DB, Vander Heiden MG. Nucleotide depletion promotes cell fate transitions by inducing DNA replication stress. Dev Cell. 2024 Aug 19;59(16):2203-2221.e15. PMID: 38823395

Sarfraz I, Wang Y, Shastry A, Teh WK, Sokolov A, Herb BR, Creasy HH, Virshup I, Dries R, Degatano K, Mahurkar A, Schnell DJ, Madrigal P, Hilton J, Gehlenborg N, Tickle T, Campbell JD. MAMS: matrix and analysis metadata standards to facilitate harmonization and reproducibility of single-cell data. Genome Biol. 2024 Aug 1;25(1):205. PMCID: PMC11292877

Maliga Z, Kim DY, Bui ATN, Lin JR, Dewan AK, Jadeja S, Murphy GF, Nirmal AJ, Lian CG, Sorger PK, LeBoeuf NR. Immune Profiling of Dermatologic Adverse Events from Checkpoint Blockade Using Tissue Cyclic Immunofluorescence: A Pilot Study. J Invest Dermatol. 2024 Aug;144(8):1887-1890.e5. PMCID: PMC11447745

Ahdritz G, Bouatta N, Floristean C, Kadyan S, Xia Q, Gerecke W, O’Donnell TJ, Berenberg D, Fisk I, Zanichelli N, Zhang B, Nowaczynski A, Wang B, Stepniewska-Dziubinska MM, Zhang S, Ojewole A, Guney ME, Biderman S, Watkins AM, Ra S, Lorenzo PR, Nivon L, Weitzner B, Ban YEA, Chen S, Zhang M, Li C, Song SL, He Y, Sorger PK, Mostaque E, Zhang Z, Bonneau R, AlQuraishi M. OpenFold: retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization. Nat Methods. 2024 Aug;21(8):1514–1524. PMID: 38744917

Conger KO, Chidley C, Ozgurses ME, Zhao H, Kim Y, Semina SE, Burns P, Rawat V, Lietuvninkas L, Sheldon R, Ben-Sahra I, Frasor J, Sorger PK, DeNicola GM, Coloff JL. ASCT2 is a major contributor to serine uptake in cancer cells. Cell Rep. 2024 Jul 26;43(8):114552. PMID: 39068660

Fang R, Vallius T, Zhang A, Van Cura D, Alicandri F, Fischer G, Draper E, Xu S, Pelletier R, Katsyv I, Sorger PK, Murphy GF, Lian CG. PRAME expression in melanoma is negatively regulated by TET2-mediated DNA hydroxymethylation [Internet]. bioRxiv; 2024. Available from: http://biorxiv.org/lookup/doi/10.1101/2024.07.26.605293 PMCID: PMC11291125

De Bruijn I, Nikolov M, Lau C, Clayton A, Gibbs DL, Mitraka E, Pozhidayeva D, Lash A, Sumer SO, Altreuter J, Anton K, DeFelice M, Li X, Lisman A, R Longabaugh WJ, Muhlich J, Santagata S, Nandakumar S, Sorger PK, Suver C, Schultz N, Taylor AJ, Thorsson V, Cerami E, Eddy JA. Sharing Data from the Human Tumor Atlas Network through Standards, Infrastructure, and Community Engagement. bioRxiv; 2024.

Warchol S, Troidl J, Muhlich J, Krueger R, Hoffer J, Lin T, Beyer J, Glassman E, Sorger P, Pfister H. psudo: Exploring Multi‐Channel Biomedical Image Data with Spatially and Perceptually Optimized Pseudocoloring. Computer Graphics Forum. 2024 Jun 10;e15103.

Grinshpun A, Russo D, Ma W, Verma A, Hermida-Prado F, Sherman S, Gaglia G, Kabraji S, Kirkner G, Hughes ME, Lin NU, Sandusky Z, Nardone A, Guarducci C, Nguyen QD, Santagata S, Nagy Z, Jeselsohn R. Pure estrogen receptor antagonists potentiate capecitabine activity in ESR1-mutant breast cancer. NPJ Breast Cancer. 2024 Jun 8;10(1):42. PMCID: PMC11162492

Susa KJ, Bradshaw GA, Eisert RJ, Schilling CM, Kalocsay M, Blacklow SC, Kruse AC. A spatiotemporal map of co-receptor signaling networks underlying B cell activation. Cell Rep. 2024 Jun 7;43(6):114332. PMID: 38850533

König LE, Rodriguez S, Hug C, Daneshvari S, Chung A, Bradshaw GA, Sahin A, Zhou G, Eisert RJ, Piccioni F, Das S, Kalocsay M, Sokolov A, Sorger P, Root DE, Albers MW. TYK2 as a novel therapeutic target in Alzheimer’s Disease with TDP-43 inclusions. bioRxiv; 2024.

Deng X, Seguinot BO, Bradshaw G, Lee JS, Coy S, Kalocsay M, Santagata S, Mitchison T. STMND1 is a phylogenetically ancient stathmin which localizes to motile cilia and exhibits nuclear translocation that is inhibited when soluble tubulin concentration increases. Mol Biol Cell. 2024 Jun 1;35(6):ar82. PMCID: PMC11238091

Park JH, Mortaja M, Son HG, Zhao X, Sloat LM, Azin M, Wang J, Collier MR, Tummala KS, Mandinova A, Bardeesy N, Semenov YR, Mino-Kenudson M, Demehri S. Statin prevents cancer development in chronic inflammation by blocking interleukin 33 expression. Nat Commun. 2024 May 30;15(1):4099. PMCID: PMC11139893

Nirmal AJ, Sorger PK. SCIMAP: A Python Toolkit for Integrated Spatial Analysis of Multiplexed Imaging Data. J Open Source Softw. 2024 May 29;9(97):6604. PMCID: PMC11173324

Jain A, Gyori BM, Hakim S, Jain A, Sun L, Petrova V, Bhuiyan SA, Zhen S, Wang Q, Kawaguchi R, Bunga S, Taub DG, Ruiz-Cantero MC, Tong-Li C, Andrews N, Kotoda M, Renthal W, Sorger PK, Woolf CJ. Nociceptor-immune interactomes reveal insult-specific immune signatures of pain. Nat Immunol. 2024 May 28; PMID: 38806708

Zhou FY, Yapp C, Shang Z, Daetwyler S, Marin Z, Islam MT, Nanes BA, Jenkins E, Gihana GM, Chang BJ, Weems A, Dustin M, Morrison SJ, Fiolka RP, Dean KM, Jamieson A, Sorger PK, Danuser GK. A general algorithm for consensus 3D cell segmentation from 2D segmented stacks [Internet]. bioRxiv; 2024 [cited 2024 Oct 1]. Available from: http://biorxiv.org/lookup/doi/10.1101/2024.05.03.592249 PMCID: PMC11100681

Gallo PN, Mihelc E, Eisert R, Bradshaw GA, Dimek F, Leffler A, Kalocsay M, Moiseenkova-Bell V. The dynamic TRPV2 ion channel proximity proteome reveals functional links of calcium flux with cellular adhesion factors NCAM and L1CAM in neurite outgrowth. Cell Calcium. 2024 May 4;121:102894. PMID: 38728789

Olesinski EA, Bhatia KS, Wang C, Pioso MS, Lin XX, Mamdouh AM, Ng SX, Sandhu V, Jasdanwala SS, Yilma B, Bohl S, Ryan JA, Malani D, Luskin MR, Kallioniemi O, Porkka K, Adamia S, Chng WJ, Osato M, Weinstock DM, Garcia JS, Letai A, Bhatt S. Acquired Multidrug Resistance in AML Is Caused by Low Apoptotic Priming in Relapsed Myeloblasts. Blood Cancer Discov. 2024 May 1;5(3):180–201. PMCID: PMC11061585

Chidley C, Darnell AM, Gaudio BL, Lien EC, Barbeau AM, Vander Heiden MG, Sorger PK. A CRISPRi/a screening platform to study cellular nutrient transport in diverse microenvironments. Nat Cell Biol. 2024 May;26(5):825–838. PMCID: PMC11098743

Sutcliffe SG, Kraemer SA, Ellmen I, Knapp JJ, Overton AK, Nash D, Nissimov JI, Charles TC, Dreifuss D, Topolsky I, Baykal PI, Fuhrmann L, Jablonski KP, Beerenwinkel N, Levy JI, Olabode AS, Becker DG, Gugan G, Brintnell E, Poon AFY, Valieris R, Drummond RD, Defelicibus A, Dias-Neto E, Rosales RA, Tojal da Silva I, Orfanou A, Psomopoulos F, Pechlivanis N, Pipes L, Chen Z, Baaijens JA, Baym M, Shapiro BJ. Tracking SARS-CoV-2 variants of concern in wastewater: an assessment of nine computational tools using simulated genomic data. Microb Genom. 2024 May;10(5). PMID: 38785221

Ke S, Dang F, Wang L, Chen JY, Naik MT, Li W, Thavamani A, Kim N, Naik NM, Sui H, Tang W, Qiu C, Koikawa K, Batalini F, Stern Gatof E, Isaza DA, Patel JM, Wang X, Clohessy JG, Heng YJ, Lahav G, Liu Y, Gray NS, Zhou XZ, Wei W, Wulf GM, Lu KP. Reciprocal antagonism of PIN1-APC/CCDH1 governs mitotic protein stability and cell cycle entry. Nat Commun. 2024 Apr 15;15(1):3220. PMCID: PMC11018817

Quinones-Olvera N, Owen SV, McCully LM, Marin MG, Rand EA, Fan AC, Martins Dosumu OJ, Paul K, Sanchez Castaño CE, Petherbridge R, Paull JS, Baym M. Diverse and abundant phages exploit conjugative plasmids. Nat Commun. 2024 Apr 12;15(1):3197. PMCID: PMC11015023

Callahan TJ, Tripodi IJ, Stefanski AL, Cappelletti L, Taneja SB, Wyrwa JM, Casiraghi E, Matentzoglu NA, Reese J, Silverstein JC, Hoyt CT, Boyce RD, Malec SA, Unni DR, Joachimiak MP, Robinson PN, Mungall CJ, Cavalleri E, Fontana T, Valentini G, Mesiti M, Gillenwater LA, Santangelo B, Vasilevsky NA, Hoehndorf R, Bennett TD, Ryan PB, Hripcsak G, Kahn MG, Bada M, Baumgartner WA, Hunter LE. An open source knowledge graph ecosystem for the life sciences. Sci Data. 2024 Apr 11;11(1):363. PMCID: PMC11009265

Ricciuti B, Lamberti G, Puchala SR, Mahadevan NR, Lin JR, Alessi JV, Chowdhury A, Li YY, Wang X, Spurr L, Pecci F, Di Federico A, Venkatraman D, Barrichello AP, Gandhi M, Vaz VR, Pangilinan AJ, Haradon D, Lee E, Gupta H, Pfaff KL, Welsh EL, Nishino M, Cherniack AD, Johnson BE, Weirather JL, Dryg ID, Rodig SJ, Sholl LM, Sorger P, Santagata S, Umeton R, Awad MM. Genomic and Immunophenotypic Landscape of Acquired Resistance to PD-(L)1 Blockade in Non-Small-Cell Lung Cancer. J Clin Oncol. 2024 Apr 10;42(11):1311–1321. PMID: 38207230

Pan RA, Wang Y, Qiu S, Villalobos-Ortiz M, Ryan J, Morris E, Halilovic E, Letai A. BH3 profiling as pharmacodynamic biomarker for the activity of BH3 mimetics. Haematologica. 2024 Apr 1;109(4):1253–1258. PMCID: PMC10985422

Wan G, Maliga Z, Yan B, Vallius T, Shi Y, Khattab S, Chang C, Nirmal AJ, Yu KH, Liu D, Lian CG, DeSimone MS, Sorger PK, Semenov YR. SpatialCells: automated profiling of tumor microenvironments with spatially resolved multiplexed single-cell data. Brief Bioinform. 2024 Mar 27;25(3):bbae189. PMCID: PMC11066940

Eschbacher KL, Tran QT, Moskalev EA, Jenkins S, Fritchie K, Stoehr R, Caron A, Link MJ, Brown PD, Guajardo A, Brat DJ, Wu A, Santagata S, Louis DN, Brastianos PK, Kaplan AB, Alexander B, Rossi S, Ferrarese F, Raleigh DR, Nguyen MP, Gross J, Velazquez Vega J, Rodriguez F, Perry A, Martinez-Lage M, Orr BA, Haller F, Giannini C. NAB2::STAT6 fusions and genome-wide DNA methylation profiling: Predictors of patient outcomes in meningeal solitary fibrous tumors. Brain Pathol. 2024 Mar 24;e13256. PMID: 38523251

Marques C, Held A, Dorfman K, Sung J, Song C, Kavuturu AS, Aguilar C, Russo T, Oakley DH, Albers MW, Hyman BT, Petrucelli L, Lagier-Tourenne C, Wainger BJ. Neuronal STING activation in amyotrophic lateral sclerosis and frontotemporal dementia. Acta Neuropathol. 2024 Mar 13;147(1):56. PMCID: PMC10937762

De Los Angeles A, Hug CB, Gladyshev VN, Church GM, Velychko S. Sendai virus persistence questions the transient naive reprogramming method for iPSC generation [Internet]. bioRxiv; 2024. Available from: http://biorxiv.org/lookup/doi/10.1101/2024.03.07.583804 PMCID: PMC10979911

Coy S, Lee JS, Chan SJ, Woo T, Jones J, Alexandrescu S, Wen PY, Sorger PK, Ligon KL, Santagata S. Systematic characterization of antibody-drug conjugate targets in central nervous system tumors. Neuro Oncol. 2024 Mar 4;26(3):458–472. PMCID: PMC10912007

Gomez SM, Axtman AD, Willson TM, Major MB, Townsend RR, Sorger PK, Johnson GL. Illuminating function of the understudied druggable kinome. Drug Discov Today. 2024 Mar;29(3):103881. PMCID: PMC11262466

Zhou I, Plana D, Palmer AC. Tumor-Specific Activity of Precision Medicines in the NCI-MATCH Trial. Clin Cancer Res. 2024 Feb 16;30(4):786–792. PMID: 38109210