2022

Monian B, Tu AA, Ruiter B, Morgan DM, Petrossian PM, Smith NP, Gierahn TM, Ginder JH, Shreffler WG, Love JC. 2022. Peanut oral immunotherapy differentially suppresses clonally distinct subsets of T helper cells. J Clin Invest 132:e150634. doi:10.1172/JCI150634

2021

Beyaz S, Chung C, Mou H, Bauer-Rowe KE, Xifaras ME, Ergin I, Dohnalova L, Biton M, Shekhar K, Eskiocak O, Papciak K, Ozler K, Almeqdadi M, Yueh B, Fein M, Annamalai D, Valle-Encinas E, Erdemir A, Dogum K, Shah V, Alici-Garipcan A, Meyer HV, Özata DM, Elinav E, Kucukural A, Kumar P, McAleer JP, Fox JG, Thaiss CA, Regev A, Roper J, Orkin SH, Yilmaz ÖH. 2021. Dietary suppression of MHC class II expression in intestinal epithelial cells enhances intestinal tumorigenesis. Cell Stem Cell. doi:10.1016/j.stem.2021.08.007

Burger ML, Cruz AM, Crossland GE, Gaglia G, Ritch CC, Blatt SE, Bhutkar A, Canner D, Kienka T, Tavana SZ, Barandiaran AL, Garmilla A, Schenkel JM, Hillman M, de Los Rios Kobara I, Li A, Jaeger AM, Hwang WL, Westcott PMK, Manos MP, Holovatska MM, Hodi FS, Regev A, Santagata S, Jacks T. 2021. Antigen dominance hierarchies shape TCF1+ progenitor CD8 T cell phenotypes in tumors. Cell 184:4996-5014.e26. doi:10.1016/j.cell.2021.08.020

Chou JJ, Berger AG, Jalili-Firoozinezhad S, Hammond PT. 2021. A design approach for layer-by-layer surface-mediated siRNA delivery. Acta Biomater S1742-7061(21)00575–4. doi:10.1016/j.actbio.2021.08.042

Concepcion CP, Ma S, LaFave LM, Bhutkar A, Liu M, DeAngelo LP, Kim JY, Priore ID, Schoenfeld AJ, Miller M, Kartha VK, Westcott PMK, Sanchez-Rivera FJ, Meli K, Gupta M, Bronson RT, Riely GJ, Rekhtman N, Rudin CM, Kim CF, Regev A, Buenrostro JD, Jacks T. 2021. SMARCA4 inactivation promotes lineage-specific transformation and early metastatic features in the lung. Cancer Discov. doi:10.1158/2159-8290.CD-21-0248

Einstein DJ, Choudhury AD, Saylor PJ, Werner L, Erlander MG, Ridinger M, Bubley G. 2021. A phase II study of onvansertib in combination with abiraterone and prednisone in patients with metastatic castration-resistant prostate cancer (mCRPC). JCO 38:TPS266–TPS266. doi:10.1200/JCO.2020.38.6_suppl.TPS266

Ferraro GB, Ali A, Luengo A, Kodack DP, Deik A, Abbott KL, Bezwada D, Blanc L, Prideaux B, Jin X, Possada JM, Chen J, Chin CR, Amoozgar Z, Ferreira R, Chen IX, Naxerova K, Ng C, Westermark AM, Duquette M, Roberge S, Lindeman NI, Lyssiotis CA, Nielsen J, Housman DE, Duda DG, Brachtel E, Golub TR, Cantley LC, Asara JM, Davidson SM, Fukumura D, Dartois VA, Clish CB, Jain RK, Vander Heiden MG. 2021. Fatty acid synthesis is required for breast cancer brain metastasis. Nature Cancer 1–15. doi:10.1038/s43018-021-00183-y

Frangieh CJ, Melms JC, Thakore PI, Geiger-Schuller KR, Ho P, Luoma AM, Cleary B, Jerby-Arnon L, Malu S, Cuoco MS, Zhao M, Ager CR, Rogava M, Hovey L, Rotem A, Bernatchez C, Wucherpfennig KW, Johnson BE, Rozenblatt-Rosen O, Schadendorf D, Regev A, Izar B. 2021. Multimodal pooled Perturb-CITE-seq screens in patient models define mechanisms of cancer immune evasion. Nature Genetics 1–10. doi:10.1038/s41588-021-00779-1

Hu Z, Leet DE, Allesøe RL, Oliveira G, Li S, Luoma AM, Liu J, Forman J, Huang T, Iorgulescu JB, Holden R, Sarkizova S, Gohil SH, Redd RA, Sun J, Elagina L, Giobbie-Hurder A, Zhang W, Peter L, Ciantra Z, Rodig S, Olive O, Shetty K, Pyrdol J, Uduman M, Lee PC, Bachireddy P, Buchbinder EI, Yoon CH, Neuberg D, Pentelute BL, Hacohen N, Livak KJ, Shukla SA, Olsen LR, Barouch DH, Wucherpfennig KW, Fritsch EF, Keskin DB, Wu CJ, Ott PA. 2021. Personal neoantigen vaccines induce persistent memory T cell responses and epitope spreading in patients with melanoma. Nat Med 1–11. doi:10.1038/s41591-020-01206-4

Iyer S, Zhang S, Yucel S, Horn H, Smith SG, Reinhardt F, Hoefsmit E, Assatova B, Casado J, Meinsohn M-C, Barrasa MI, Bell GW, Pérez-Villatoro F, Huhtinen K, Hynninen J, Oikkonen J, Galhenage PM, Pathania S, Hammond PT, Neel BG, Farkkila A, Pépin D, Weinberg RA. 2021. Genetically Defined Syngeneic Mouse Models of Ovarian Cancer as Tools for the Discovery of Combination Immunotherapy. Cancer Discov 11:384–407. doi:10.1158/2159-8290.CD-20-0818

Kehe J, Ortiz A, Kulesa A, Gore J, Blainey PC, Friedman J. 2021. Positive interactions are common among culturable bacteria. Sci Adv 7:eabi7159. doi:10.1126/sciadv.abi7159

Lu Z, Truex NL, Melo MB, Cheng Y, Li N, Irvine DJ, Pentelute BL. 2021. IgG-Engineered Protective Antigen for Cytosolic Delivery of Proteins into Cancer Cells. ACS Cent Sci 7:365–378. doi:10.1021/acscentsci.0c01670

Mana MD, Hussey AM, Tzouanas CN, Imada S, Barrera Millan Y, Bahceci D, Saiz DR, Webb AT, Lewis CA, Carmeliet P, Mihaylova MM, Shalek AK, Yilmaz ÖH. 2021. High-fat diet-activated fatty acid oxidation mediates intestinal stemness and tumorigenicity. Cell Rep 35:109212. doi:10.1016/j.celrep.2021.109212

Mathewson ND, Ashenberg O, Tirosh I, Gritsch S, Perez EM, Marx S, Jerby-Arnon L, Chanoch-Myers R, Hara T, Richman AR, Ito Y, Pyrdol J, Friedrich M, Schumann K, Poitras MJ, Gokhale PC, Castro LNG, Shore ME, Hebert CM, Shaw B, Cahill HL, Drummond M, Zhang W, Olawoyin O, Wakimoto H, Rozenblatt-Rosen O, Brastianos PK, Liu XS, Jones PS, Cahill DP, Frosch MP, Louis DN, Freeman GJ, Ligon KL, Marson A, Chiocca EA, Reardon DA, Regev A, Suvà ML, Wucherpfennig KW. 2021. Inhibitory CD161 receptor identified in glioma-infiltrating T cells by single-cell analysis. Cell 0. doi:10.1016/j.cell.2021.01.022

Morgan DM, Ruiter B, Smith NP, Tu AA, Monian B, Stone BE, Virk-Hundal N, Yuan Q, Shreffler WG, Love JC. 2021. Clonally expanded, GPR15-expressing pathogenic effector TH2 cells are associated with eosinophilic esophagitis. Sci Immunol 6. doi:10.1126/sciimmunol.abi5586

Ouspenskaia T, Law T, Clauser KR, Klaeger S, Sarkizova S, Aguet F, Li B, Christian E, Knisbacher BA, Le PM, Hartigan CR, Keshishian H, Apffel A, Oliveira G, Zhang W, Chen S, Chow YT, Ji Z, Jungreis I, Shukla SA, Justesen S, Bachireddy P, Kellis M, Getz G, Hacohen N, Keskin DB, Carr SA, Wu CJ, Regev A. 2021. Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer. Nat Biotechnol 1–9. doi:10.1038/s41587-021-01021-3

Prakadan SM, Alvarez-Breckenridge CA, Markson SC, Kim AE, Klein RH, Nayyar N, Navia AW, Kuter BM, Kolb KE, Bihun I, Mora JL, Bertalan MS, Shaw B, White M, Kaplan A, Stocking JH, Wadsworth MH, Lee EQ, Chukwueke U, Wang N, Subramanian M, Rotem D, Cahill DP, Adalsteinsson VA, Miller JW, Sullivan RJ, Carter SL, Brastianos PK, Shalek AK. 2021. Genomic and transcriptomic correlates of immunotherapy response within the tumor microenvironment of leptomeningeal metastases. Nat Commun 12:5955. doi:10.1038/s41467-021-25860-5

Rakhra K, Abraham W, Wang C, Moynihan KD, Li N, Donahue N, Baldeon AD, Irvine DJ. 2021. Exploiting albumin as a mucosal vaccine chaperone for robust generation of lung-resident memory T cells. Science Immunology 6.

Roux B, Vaganay C, Vargas JD, Alexe G, Benaksas C, Pardieu B, Fenouille N, Ellegast JM, Malolepsza E, Ling F, Sodaro G, Ross L, Pikman Y, Conway AS, Tang Y, Wu T, Anderson DJ, Moigne RL, Zhou H-J, Luciano F, Hartigan CR, Galinsky I, DeAngelo DJ, Stone RM, Auberger P, Schenone M, Carr SA, Guirouilh-Barbat J, Lopez B, Khaled M, Lage K, Hermine O, Hemann MT, Puissant A, Stegmaier K, Benajiba L. 2021. Targeting acute myeloid leukemia dependency on VCP-mediated DNA repair through a selective second-generation small-molecule inhibitor. Sci Transl Med 13. 

2020

Ackerman CM, Myhrvold C, Thakku SG, Freije CA, Metsky HC, Yang DK, Ye SH, Boehm CK, Kosoko-Thoroddsen T-SF, Kehe J, et al. 2020. Massively multiplexed nucleic acid detection using Cas13. Nature 582: 277-282. http://www.nature.com/articles/s41586-020-2279-8

Arvanitis CD, Ferraro GB, Jain RK. 2020. The blood–brain barrier and blood–tumour barrier in brain tumours and metastases. Nat Rev Cancer 20(1): 26-41.

Barberio AE, Smith SG, Correa S, Nguyen C, Nhan B, Melo M, Tokatlian T, Suh H, Irvine DJ, Hammond PT. 2020. Cancer Cell Coating Nanoparticles for Optimal Tumor-Specific Cytokine Delivery. ACS Nano. doi:10.1021/acsnano.0c03109

Boehnke N, Dolph KJ, Juarez VM, Lanoha JM, Hammond PT. 2020. Electrostatic Conjugation of Nanoparticle Surfaces with Functional Peptide Motifs. Bioconjugate Chem 31:2211–2219. doi:10.1021/acs.bioconjchem.0c00384

Brastianos PK, Lee EQ, Cohen JV, Tolaney SM, Lin NU, Wang N, Chukwueke U, White MD, Nayyar N, Kim A, Alvarez-Breckenridge C, Krop I, Mahar MK, Bertalan MS, Shaw B, Mora JL, Goss N, Subramanian M, Nayak L, Dietrich J, Forst DA, Nahed BV, Batchelor TT, Shih HA, Gerstner ER, Moy B, Lawrence D, Giobbie-Hurder A, Carter SL, Oh K, Cahill DP, Sullivan RJ. 2020. Single-arm, open-label phase 2 trial of pembrolizumab in patients with leptomeningeal carcinomatosis. Nat Med 26:1280–1284. doi:10.1038/s41591-020-0918-0

Calibasi-Kocal G, Mashinchian O, Basbinar Y, Ellidokuz E, Cheng C-W, Yilmaz ÖH. 2020. Nutritional Control of Intestinal Stem Cells in Homeostasis and Tumorigenesis. Trends Endocrinol Metab 0. doi:10.1016/j.tem.2020.11.003

Cheng C-W, Yilmaz OH, Mihaylova MM. 2020. Strategies for Measuring Induction of Fatty Acid Oxidation in Intestinal Stem and Progenitor Cells In: Ordóñez-Morán P, editor. Intestinal Stem Cells: Methods and Protocols, Methods in Molecular Biology. New York, NY: Springer US. pp. 53–64. doi:10.1007/978-1-0716-0747-3_4

Dagogo-Jack, Schrock, Kem, Jessop, Lee, Ali, Ross, Lennerz, Shaw, Mino-Kenudson. 2020. Clinicopathologic Characteristics of BRG1-Deficient Non-Small Cell Lung Cancer. J Thorac Oncol 15(5):766-776

Gupta M, Concepcion CP, Fahey CG, Keshishian H, Bhutkar A, Brainson CF, Sanchez-Rivera FJ, Pessina P, Kim JY, Simoneau A, Paschini M, Beytagh MC, Stanclift CR, Schenone M, Mani DR, Li C, Oh A, Li F, Hu H, Karatza A, Bronson RT, Shaw AT, Hata AN, Wong K-K, Zou L, Carr SA, Jacks T, Kim CF. 2020. BRG1 loss predisposes lung cancers to replicative stress and ATR dependency. Cancer Res. doi:10.1158/0008-5472.CAN-20-1744

Hughes TK, Wadsworth MH, Gierahn TM, Do T, Weiss D, Andrade PR, Ma F, de Andrade Silva BJ, Shao S, Tsoi LC, Ordovas-Montanes J, Gudjonsson JE, Modlin RL, Love JC, Shalek AK. 2020. Second-Strand Synthesis-Based Massively Parallel scRNA-Seq Reveals Cellular States and Molecular Features of Human Inflammatory Skin Pathologies. Immunity 53:878-894.e7. doi:10.1016/j.immuni.2020.09.015

Jin X, Demere Z, Nair K, Ali A, Ferraro GB, Natoli T, Deik A, Petronio L, Tang AA, Zhu C, Wang L, Rosenberg D, Mangena V, Roth J, Chung K, Jain RK, Clish CB, Vander Heiden MG, Golub TR. 2020. A metastasis map of human cancer cell lines. Nature 588:331–336. doi:10.1038/s41586-020-2969-2

Lam FC, Kong YW, Huang Q, Vu Han T-L, Maffa AD, Kasper EM, Yaffe MB. 2020. BRD4 prevents the accumulation of R-loops and protects against transcription–replication collision events and DNA damage. Nat Commun 11:4083. doi:10.1038/s41467-020-17503-y

Lam FC, Kong YW, Yaffe MB. 2020. Inducing DNA damage through R-loops to kill cancer cells. Mol Cell Oncol.

Lu Z, Paolella BR, Truex NL, Loftis AR, Liao X, Rabideau AE, Brown MS, Busanovich J, Beroukhim R, Pentelute BL. 2020. Targeting Cancer Gene Dependencies with Anthrax-Mediated Delivery of Peptide Nucleic Acids. ACS Chem Biol 15:1358–1369. doi:10.1021/acschembio.9b01027

McKenny AS, Lau AN, Somasundara AVH, Spitzer B, Intlekofer AM, Ahn J, Shank K, Rapaport FT, Patel MA, Papalexi E, Shih AH, Chiu A, Feinkman E, Akbay EA, Steadman M, Nagaraja R, Yen K, Teruya-Feldstein J, Wong K-K, Rampal R, Vander Heiden MG, Thompson CB, Levine RL. 2020. JAK2/IDH-mutant–driven myeloproliferative neoplasm is sensitive to combined targeted inhibition.  J Clin Invest 128:789-804.

Ngo B, Kim E, Osorio-Vasquez V, Doll S, Bustraan S, Liang RJ, Luengo A, Davidson SM, Ali A, Ferraro GB, Fischer GM, Eskandari R, Kang DS, Ni J, Plasger A, Rajasekhar VK, Kastenhuber ER, Bacha S, Sriram RK, Stein BD, Bakhoum SF, Snuderl M, Cotzia P, Healey JH, Mainolfi N, Suri V, Friedman A, Manfredi M, Sabatini DM, Jones DR, Yu M, Zhao JJ, Jain RK, Keshari KR, Davies MA, Heiden MGV, Hernando E, Mann M, Cantley LC, Pacold ME. 2020. Limited Environmental Serine and Glycine Confer Brain Metastasis Sensitivity to PHGDH Inhibition. Cancer Discov 10:1352–1373. doi:10.1158/2159-8290.CD-19-1228

Parsons HA, Rhoades J, Reed SC, Gydush G, Ram P, Exman P, Xiong K, Lo CC, Li T, Fleharty M, Kirkner G, Rotem D, Cohen O, Yu F, Fitarelli-Kiehl M, Leong KW, Hughes M, Rosenberg SM, Collins LC, Miller KD, Blumenstiel B, Trippa L, Cibulskis C, Neuberg D, DeFelice M, Freeman SS, Lennon NJ, Wagle N, Ha G, Stover DG, Choudhury AD, Getz G, Winer EP, Meyerson M, Lin NU, Krop IE, Love JC, Makrigiorgos GM, Partridge A, Mayer E, Golub TR, Adalsteinsson VA. 2020. Sensitive detection of minimal residual disease in patients treated for early-stage breast cancer. Clin Cancer Res 26(11): 2556-2564.

Richters A, Doyle SK, Freeman DB, Lee C, Leifer BS, Jagannathan S, Kabinger F, Koren JV, Struntz NB, Urgiles J, Stagg RA, Curtin BH, Chatterjee D, Mathea S, Mikochik PJ, Hopkins TD, Gao H, Branch J, Xin H, Westover L, Bignan GC, Rupnow BA, Karlin KL, Olson CM, Westbrook TF, Vacca J, Wilfong CM, Trotter BW, Saffran DC, Bischofberger N, Knapp S, Russo JW, Hickson I, Bischoff JR, Gottardis MM, Balk SP, Lin CY, Pop MS, Koehler AN. 2020. Modulating Androgen Receptor-Driven Transcription in Prostate Cancer with Selective CDK9 Inhibitors. Cell Chem Biol 0. doi:10.1016/j.chembiol.2020.10.001

Sarkizova S, Klaeger S, Le PM, Li LW, Oliveira G, Keshishian H, Hartigan CR, Zhang W, Braun DA, Ligon KL, Bachireddy P, Zervantonakis IK, Rosenbluth JM, Ouspenskaia T, Law T, Justesen S, Stevens J, Lane WJ, Eisenhaure T, Lan Zhang G, Clauser KR, Hacohen N, Carr SA, Wu CJ, Keskin DB. 2020. A large peptidome dataset improves HLA class I epitope prediction across most of the human population. Nat Biotechnol 38: 199–209.

Stopsack KH, Gerke T, Zareba P, Pettersson A, Chowdhury D, Ebot EM, Flavin R, Finn S, Kantoff PW, Stampfer MJ, Loda M, Fiorentino M, Mucci LA. 2020. Tumor protein expression of the DNA repair gene BRCA1 and lethal prostate cancer. Carcinogenesis 41:904–908. doi:10.1093/carcin/bgaa061

Tay RE, Olawoyin O, Cejas P, Xie Y, Meyer CA, Weng QY, Fisher DE, Long HW, Brown M, Kim H-J, Wucherpfennig KW. Hdac3 is an epigenetic inhibitor of the cytotoxicity program in CD8 T cells. 2020. J Exper Med. 217:e20191453.

Touat M, Li YY, Boynton AN, Spurr LF, Iorgulescu JB, Bohrson CL, Cortes-Ciriano I, Birzu C, Geduldig JE, Pelton K, Lim-Fat MJ, Sangita Pal S,  Ruben Ferrer-Luna R, Ramkissoon SH, Dubois F, Bellamy C, Currimjee N, Bonardi J, Qian K, Ho P, Malinowski S, Taquet L, Jones RE, Shetty A, Chow K-H, Sharaf R, Pavlick D, Albacker LA, Younan N, Baldini C, Verreault M, Giry M, Guillerm E, Ammari S, Beuvon F, Mokhtari K , Alentorn A, Dehais C, Houillier C, Laigle-Donadey F, Psimaras D, Lee EQ, Nayak L, McFaline-Figueroa JR, Carpentier A, Cornu P, Capelle L, Mathon B, Barnholtz-Sloan JS, Chakravarti A, Bi WL, Chiocca EA, Pricola Fehnel K, Alexandrescu S, Chi SN, Haas-Kogan D, Batchelor TT, Frampton GM, Alexander BM, Huang RY, H. Ligon AH, Coulet C, Delattre J-Y, Hoang-Xuan K. Meredith DM, Santagata S, Duval A, Sanson M, Cherniack AD, Wen PY, Reardon DA, Marabelle A, Park PJ, Idbaih A, Beroukhim R, Bandopadhayay P, Bielle F, Ligon KL. 2020. Mechanisms and therapeutic implications of hypermutation in gliomas. Nature 580: 517-523.  doi:10.1038/s41586-020-2209-9

Truex NL, Holden RL, Wang B-Y, Chen P-G, Hanna S, Hu Z, Shetty K, Olive O, Neuberg D, Hacohen N, Keskin DB, Ott PA, Wu CJ, Pentelute BL. 2020. Automated Flow Synthesis of Tumor Neoantigen Peptides for Personalized Immunotherapy. Sci Rep 10: 1–11.

van Gastel N, Spinelli JB, Sharda A, Schajnovitz A, Baryawno N, Rhee C, Oki T, Grace E, Soled HJ, Milosevic J, Sykes DB, Hsu PP, Vander Heiden MG, Vidoudez C, Trauger SA, Haigis MC, Scadden DT. 2020. Induction of a Timed Metabolic Collapse to Overcome Cancer Chemoresistance. Cell Metab 32:391-403.e6. doi:10.1016/j.cmet.2020.07.009

Wang C, Wang Y, Hughes KS, Parmigiani G, Braun D. 2020. Penetrance of Colorectal Cancer Among Mismatch Repair Gene Mutation Carriers: A Meta-Analysis. JNCI Cancer Spectr 4:pkaa027. doi:10.1093/jncics/pkaa027

Zhang H, Christensen CL, Dries R, Oser MG, Deng J, Diskin B, Li F, Pan Y, Zhang X, Yin Y, Papadopoulos E, Pyon V, Thakurdin C, Kwiatkowski N, Jani K, Rabin AR, Castro DM, Chen T, Silver H, Huang Q, Bulatovic M, Dowling CM, Sundberg B, Leggett A, Ranieri M, Han H, Li S, Yang A, Labbe KE, Almonte C, Sviderskiy VO, Quinn M, Donaghue J, Wang ES, Zhang T, He Z, Velcheti V, Hammerman PS, Freeman GJ, Bonneau R, Kaelin WG, Sutherland KD, Kersbergen A, Aguirre AJ, Yuan G-C, Rothenberg E, Miller G, Gray NS, Wong K-K. 2020. CDK7 Inhibition Potentiates Genome Instability Triggering Anti-tumor Immunity in Small Cell Lung Cancer. Cancer Cell 37:37-54.e9. doi:10.1016/j.ccell.2019.11.003

2019

Askoxylakis V, Ferraro GB, Badeaux M, Kodack DP, Kirst I, Shankaraiah RC, Wong CSF, Duda DG, Fukumura D, Jain RK. 2019. Dual endothelin receptor inhibition enhances T-DM1 efficacy in brain metastases from HER2-positive breast cancer. NPJ Breast Cancer 5:4. doi:10.1038/s41523-018-0100-8

Bandopadhayay P, Piccioni F, O’Rourke R, Ho P, Gonzalez EM, Buchan G, Qian K, Gionet G, Girard E, Coxon M, Rees MG, Brenan L, Dubois F, Shapira O, Greenwald NF, Pages M, Balboni Iniguez A, Paolella BR, Meng A, Sinai C, Roti G, Dharia NV, Creech A, Tanenbaum B, Khadka P, Tracy A, Tiv HL, Hong AL, Coy S, Rashid R, Lin J-R, Cowley GS, Lam FC, Goodale A, Lee Y, Schoolcraft K, Vazquez F, Hahn WC, Tsherniak A, Bradner JE, Yaffe MB, Milde T, Pfister SM, Qi J, Schenone M, Carr SA, Ligon KL, Kieran MW, Santagata S, Olson JM, Gokhale PC, Jaffe JD, Root DE, Stegmaier K, Johannessen CM, Beroukhim R. 2019. Neuronal differentiation and cell-cycle programs mediate response to BET-bromodomain inhibition in MYC-driven medulloblastoma. Nat Commun 10. doi:10.1038/s41467-019-10307-9

Bao Y, Deng Z, Wang Y, Kim H, Armengol VD, Acevedo F, Ouardaoui N, Wang C, Parmigiani G, Barzilay R, Braun D, Hughes KS. 2019. Using Machine Learning and Natural Language Processing to Review and Classify the Medical Literature on Cancer Susceptibility Genes. JCO Clin Cancer Inform 3:1–9. doi:10.1200/CCI.19.00042

Ben-David U, Beroukhim R, Golub TR. 2019. Genomic evolution of cancer models: perils and opportunities. Nat Rev Cancer 19:97–109. doi:10.1038/s41568-018-0095-3

Ceppi L, Bardhan NM, Na Y, Siegel A, Rajan N, Fruscio R, Del Carmen MG, Belcher AM, Birrer MJ. 2019. Real-Time Single-Walled Carbon Nanotube-Based Fluorescence Imaging Improves Survival after Debulking Surgery in an Ovarian Cancer Model. ACS Nano 13:5356–5365. doi:10.1021/acsnano.8b09829

Chauhan VP, Chen IX, Tong R, Ng MR, Martin JD, Naxerova K, Wu MW, Huang P, Boucher Y, Kohane DS, Langer R, Jain RK. 2019. Reprogramming the microenvironment with tumor-selective angiotensin blockers enhances cancer immunotherapy. Proc Natl Acad Sci USA 116:10674–10680. doi:10.1073/pnas.1819889116

Chen IX, Chauhan VP, Posada J, Ng MR, Wu MW, Adstamongkonkul P, Huang P, Lindeman N, Langer R, Jain RK. 2019. Blocking CXCR4 alleviates desmoplasia, increases T-lymphocyte infiltration, and improves immunotherapy in metastatic breast cancer. Proc Natl Acad Sci USA 116:4558–4566. doi:10.1073/pnas.1815515116

Cheng C-W, Biton M, Haber AL, Gunduz N, Eng G, Gaynor LT, Tripathi S, Calibasi-Kocal G, Rickelt S, Butty VL, Moreno-Serrano M, Iqbal AM, Bauer-Rowe KE, Imada S, Ulutas MS, Mylonas C, Whary MT, Levine SS, Basbinar Y, Hynes RO, Mino-Kenudson M, Deshpande V, Boyer LA, Fox JG, Terranova C, Rai K, Piwnica-Worms H, Mihaylova MM, Regev A, Yilmaz ÖH. 2019. Ketone Body Signaling Mediates Intestinal Stem Cell Homeostasis and Adaptation to Diet. Cell 178:1115-1131.e15. doi:10.1016/j.cell.2019.07.048

Dang X, Bardhan NM, Qi J, Gu L, Eze NA, Lin C-W, Kataria S, Hammond PT, Belcher AM. 2019. Deep-tissue optical imaging of near cellular-sized features. Sci Rep 9:3873. doi:10.1038/s41598-019-39502-w

Deng Z, Yin K, Bao Y, Armengol VD, Wang C, Tiwari A, Barzilay R, Parmigiani G, Braun D, Hughes KS. 2019. Validation of a Semiautomated Natural Language Processing-Based Procedure for Meta-Analysis of Cancer Susceptibility Gene Penetrance. JCO Clin Cancer Inform 3:1–9. doi:10.1200/CCI.19.00043

Kehe J, Kulesa A, Ortiz A, Ackerman CM, Thakku SG, Sellers D, Kuehn S, Gore J, Friedman J, Blainey PC. 2019. Massively parallel screening of synthetic microbial communities. Proc Natl Acad Sci USA 116:12804–12809. doi:10.1073/pnas.1900102116

Leong KW, Yu F, Adalsteinsson VA, Reed S, Gydush G, Ladas I, Li J, Tantisira KG, Makrigiorgos GM. 2019. A nuclease-polymerase chain reaction enables amplification of probes used for capture-based DNA target enrichment. Nucleic Acids Res 47:e147. doi:10.1093/nar/gkz870

Lossos C, Liu Y, Kolb KE, Christie AL, Scoyk A van, Prakadan SM, Shigemori K, Stevenson KE, Morrow S, Plana OD, Fraser C, Jones KL, Liu H, Pallasch CP, Modiste R, Nguyen Q-D, Craig JW, Morgan EA, Vega F, Aster JC, Sarosiek KA, Shalek AK, Hemann MT, Weinstock DM. 2019. Mechanisms of lymphoma clearance induced by high-dose alkylating agents. Cancer Discov. doi:10.1158/2159-8290.CD-18-1393

Olson CM, Liang Y, Leggett A, Park WD, Li L, Mills CE, Elsarrag SZ, Ficarro SB, Zhang T, Düster R, Geyer M, Sim T, Marto JA, Sorger PK, Westover KD, Lin CY, Kwiatkowski N, Gray NS. 2019. Development of a Selective CDK7 Covalent Inhibitor Reveals Predominant Cell-Cycle Phenotype. Cell Chem Biol 26:792-803.e10. doi:10.1016/j.chembiol.2019.02.012

Patterson JC, Joughin BA, Prota AE, Mühlethaler T, Jonas OH, Whitman MA, Varmeh S, Chen S, Balk SP, Steinmetz MO, Lauffenburger DA, Yaffe MB. 2019a. VISAGE Reveals a Targetable Mitotic Spindle Vulnerability in Cancer Cells. Cell Syst 9:74-92.e8. doi:10.1016/j.cels.2019.05.009

Patterson JC, Joughin BA, van de Kooij B, Lim DC, Lauffenburger DA, Yaffe MB. 2019. ROS and oxidative stress are elevated in mitosisduring asynchronous cell cycle progression and are exacerbated by mitotic arrest. Cell Syst 8(2): 163–167.

Stopsack KH, Whittaker CA, Gerke TA, Loda M, Kantoff PW, et al. 2019. Aneuploidy drives lethal progression in prostate cancer. PNAS 116(23): 11390-11395.

Tu AA, Gierahn TM, Monian B, Morgan DM, Mehta NK, Ruiter B, Shreffler WG, Shalek AK, Love JC. TCR Sequencing Paired With Massively Parallel 3' RNA-seq Reveals Clonotypic T Cell Signatures. Nat Immunol. 2019 Dec;20(12):1692-1699. doi: 10.1038/s41590-019-0544-5. Epub 2019 Nov 19.

Wu M-R, Jusiak B, Lu TK. 2019. Engineering advanced cancer therapies with synthetic biology. Nat Rev Cancer 19:187–195. doi:10.1038/s41568-019-0121-0

Wu M-R, Nissim L, Stupp D, Pery E, Binder-Nissim A, Weisinger K, Enghuus C, Palacios SR, Humphrey M, Zhang Z, Maria Novoa E, Kellis M, Weiss R, Rabkin SD, Tabach Y, Lu TK. 2019. A high-throughput screening and computation platform for identifying synthetic promoters with enhanced cell-state specificity (SPECS). Nat Commun 10:2880. doi:10.1038/s41467-019-10912-8

 

2018

Andronesi OC, Arrillaga-Romany IC, Ly KI, Bogner W, Ratai EM, et al. 2018. Pharmacodynamics of mutant IDH1 inhibitors in glioma patients probed by in vivo 3D MRS imaging of 2-hydroxyglutarate. Nat Commun 9: 1474.

Arai S, Jonas O, Whitman MA, Corey E, Balk SP, Chen S. 2018. Tyrosine kinase inhibitors increase MCL1 degradation and in combination with BCLXL/BCL2 inhibitors drive prostate cancer apoptosis. Clin Cancer Res 24: 5458-5470.

Ben-David U, Siranosian B, Ha G, Tang H, Oren Y, et al. 2018. Genetic and transcriptional evolution alters cancer cell line drug response. Nature 560: 325-330.

Calistri NL, Kimmerling RJ, Malinowski SW, Touat M, Stevens MM, Olcum S, Ligon KL, Manalis SR. 2018. Microfluidic active loading of single cells enables analysis of complex clinical specimens. Nat Commun 9. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6235965/

Dougan M, Ingram JR, Jeong H-J, Mosaheb MM, Bruck PT, Ali L, Pishesha N, Blomberg O, Tyler PM, Servos MM, Rashidian M, Nguyen Q-D, von Andrian UH, Ploegh HL, Dougan SK. 2018. Targeting Cytokine Therapy to the Pancreatic Tumor Microenvironment Using PD-L1-Specific VHHs. Cancer Immunol Res 6:389–401. doi:10.1158/2326-6066.CIR-17-0495

Drapkin BJ, George J, Christensen CL, Mino-Kenudson M, Dries R,  et al. 2018. Genomic and functional fidelity of small cell lung cancer patient-derived xenografts. Cancer Discov 8: 1-16.

Ferrari de Andrade L, Tay RE, Pan D, Luoma AM, Ito Y, Badrinath S, Tsoucas D, Franz B, May KF, Harvey CJ, Kobold S, Pyrdol JW, Yoon C, Yuan G-C, Hodi FS, Dranoff G, Wucherpfennig KW. 2018. Antibody-mediated inhibition of MICA and MICB shedding promotes NK cell-driven tumor immunity. Science 359:1537–1542. doi:10.1126/science.aao0505

Guimaraes PPG, Gaglione S, Sewastianik T, Carrasco RD, Langer R, Mitchell MJ. 2018. Nanoparticles for immune cytokine TRAIL-based cancer therapy. ACS Nano 12: 912-931.

Hill SJ, Decker B, Roberts EA, Horowitz NS, Muto MG, Worley MJ, Feltmate CM, Nucci MR, Swisher EM, Nguyen H, Yang C, Morizane R, Kochupurakkal BS, Do KT, Konstantinopoulos PA, Liu JF, Bonventre JV, Matulonis UA, Shapiro GI, Berkowitz RS, Crum CP, D’Andrea AD. 2018. Prediction of DNA Repair Inhibitor Response in Short Term Patient-Derived Ovarian Cancer Organoids. Cancer Discov 8:1404–1421. doi:10.1158/2159-8290.CD-18-0474

Iniguez AB, Stolte B, Wang EJ, Conway AS, Alexe G, et al. 2018. EWS/FLI confers tumor cell synthetic lethality to CDK12 inhibition in Ewing sarcoma. Cancer Cell 33: 202-216. 

Khan OF, Kowalski PS, Doloff JC, Tsosie JK, Bakthavatchalu V, Winn CB, Haupt J, Jamiel M, Langer R, Anderson DG. 2018. Endothelial siRNA delivery in nonhuman primates using ionizable low–molecular weight polymeric nanoparticles. Sci Adv 4. doi:10.1126/sciadv.aar8409

Kulesa A, Kehe J, Hurtado J, Tawde P, Blainey C. 2018. Combinatorial drug discovery in nanoliter droplets. PNAS 115: 6685-6690.

Lam FC, Morton SW, Wyckoff J, Han TLV, Hwang MK, et al. 2018. Enhanced efficacy of combined temozolomide and bromodomain inhibitor therapy for gliomas using targeted nanoparticles. Nat Commun 9: 1991.

Luskin MR, Murakami MA, Manalis SR, Weinstock DM. 2018. Targeting minimal residual disease: a path to cure? Nat Revs Cancer 18: 255-263.

McBrayer SK, Mayers JR, DiNatale GJ, Shi DD, Khanal J, Chakraborty AA, Sarosiek KA, Briggs KJ, Robbins AK, Sewastianik T, Shareef SJ, Olenchock BA, Parker SJ, Tateishi K, Spinelli JB, Islam M, Haigis MC, Looper RE, Ligon KL, Bernstein BE, Carrasco RD, Cahill DP, Asara JM, Metallo CM, Yennawar NH, Vander Heiden MG, Kaelin WG. 2018. Transaminase Inhibition by 2-Hydroxyglutarate Impairs Glutamate Biosynthesis and Redox Homeostasis in Glioma. Cell 175:101-116.e25. doi:10.1016/j.cell.2018.08.038

Moynihan KD, Holden RL, Mehta NK, Wang C, Karver MR, et al. 2018. Enhancement of peptide vaccine immunogenicity by increasing lymphatic drainage and boosting serum stability. Cancer Immunol Res 6: 1025-1038.

Nagarajan MB, Tentori AM, Zhang WC, Slack FJ, Doyle PS.  2018. Nonfouling, encoded hydrogel microparticles for multiplex microRNA profiling directly from formalin-fixed, paraffin-embedded tissue. Anal Chem 90(17): 10279-10285.

Olson CM, Jiang B, Erb MA, Liang Y, Doctor ZM, et al. 2018. Pharmacological perturbation of CDK9 using selective CDK9 inhibition or degradation. Nat Chem Biol 14: 163-170.

Pan D, Kobayashi A, Jiang P, Ferrari de Andrade L, Tay RE, Luoma AM, Tsoucas D, Qiu X, Lim K, Rao P, Long HW, Yuan G-C, Doench J, Brown M, Liu XS, Wucherpfennig KW. 2018. A major chromatin regulator determines resistance of tumor cells to T cell-mediated killing. Science 359:770–775. doi:10.1126/science.aao1710

Rezaei Araghi R, Bird GH, Ryan JA, Jenson JM, Godes M, Pritz JR, Grant RA, Letai A, Walensky LD, Keating AE. 2018. Iterative optimization yields Mcl-1-targeting stapled peptides with selective cytotoxicity to Mcl-1-dependent cancer cells. Proc Natl Acad Sci USA 115:E886–E895. doi:10.1073/pnas.1712952115

Tentori AM, Nagarajan MB, Kim JJ, Zhang WC, Slack FJ, Doyle PS. 2018. Quantitative and multiplex microRNA assays from unprocessed cells in isolated nanoliter well arrays. Lab Chip 18(16): 2410-2424.

Wang Y, Li BB, Li J, Roberts TM, Zhao JJ. 2018. A conditional dependency on MELK for the proliferation of triple-negative breast cancer cells. iScience. 9: 149-160. 

 

2017

Awad MM, Mastini C, Blasco RB, Mologni L, Voena C, et al. 2017. Epitope mapping of spontaneous autoantibodies to anaplastic lymphoma kinase (ALK) in non-small cell lung cancer. Oncotarget 8: 92265-92274.

Cetin AE, Stevens MM, Calistri NL, Fulciniti M, Olcum S, Kimmerling RJ, Munshi NC, Manalis SR. 2017. Determining therapeutic susceptibility in multiple myeloma by single-cell mass accumulation. Nat Commun 8: 1613.

Chahal JS, Fang T, Woodham AW, Khan OF, Ling J, Anderson DG, Ploegh HL. 2017. An RNA nanoparticle vaccine against Zika virus elicits antibody and CD8+ T cell responses in a mouse model. Sci Rep 7: 252.

Dougan SK. 2017. The pancreatic cancer microenvironment. Cancer J 23(6): 321-325.

Fenouille N, Bassil CF, Ben-Sahra I, Benajiba L, Alexe G,  et al. 2017. The creatine kinase pathway is a metabolic vulnerability in EVI1-positive acute myeloid leukemia. Nat Med 23: 301-313.

Gierahn TM, Wadsworth MH, Hughes TK, Bryson BD, Butler A, et al. 2017. Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput. Nat Methods 14: 395-398.

Huang HT, Seo HS, Zhang T, Wang Y, Jiang B, et al. 2017. MELK is not necessary for the proliferation of basal-like breast cancer cells. Elife. 19: 6.

Jenson JM, Ryan JA, Grant RA, Letai A, Keating AE. 2017. Epistatic mutations in PUMA BH3 drive an alternate binding mode to potently and selectively inhibit anti-apoptotic Bfl-1. Elife 6. doi:10.7554/eLife.25541

Kodack DP, Askoxylakis V, Ferraro GB, Sheng Q, Badeaux M, et al. 2017. The brain microenvironment mediates resistance in luminal breast cancer to PI3K inhibition through HER3 activation. Sci Transl Med 9: eaal4682.

Ladas I, Fitarelli-Kiehl M, Song C, Adalsteinsson VA, Parsons HA, et al. 2017. Multiplexed elimination of wild-type DNA and high-resolution melting prior to targeted resequencing of liquid biopsies. Clinical Chemistry 63: 1605-1613.

Moynihan KD & Irvine DJ. Roles for Innate Immunity in Combination Immunotherapies. Cancer Res, 77, 5215–5221 (2017).

Nissim L, Wu M-R, Pery E, Binder-Nissim A, Suzuki HI, Stupp D, Wehrspaun C, Tabach Y, Sharp PA, Lu TK. 2017. Synthetic RNA-Based Immunomodulatory Gene Circuits for Cancer Immunotherapy. Cell 171:1138-1150.e15. doi:10.1016/j.cell.2017.09.049

Soto-Feliciano YM, Bartlebaugh JME, Liu Y, Sánchez-Rivera FJ, Bhutkar A, Weintraub AS, Buenrostro JD, Cheng CS, Regev A, Jacks TE, Young RA, Hemann MT. 2017. PHF6 regulates phenotypic plasticity through chromatin organization within lineage-specific genes. Genes Dev 31:973–989. doi:10.1101/gad.295857.117

Tanenbaum LM, Mantzavinou A, Subramanyam KS, del Carmen MG, Cima MJ. 2017. Ovarian cancer spheroid shrinkage following continuous exposure to cisplatin is a function of spheroid diameter. Gynecologic Oncology 146: 161-169.

Tao Z, Dang X, Huang X, Muzumdar MD, Xu ES, et al. 2017. Early tumor detection afforded by in vivo imaging of near-infrared II fluorescence. Biomaterials 134: 202-215.

Tsang TY, Wei W, Itamochi H, Tambouret R, Birrer MJ. 2017. Integrated genomic analysis of clear cell ovarian cancers identified PRKCI as a potential therapeutic target. Oncotarget 8: 96482-96495. 

 

2016

Andronesi OC, Loebel F, Bogner W, Marjańska M, Vander Heiden MG, et al. 2016. Treatment response assessment in IDH-mutant glioma patients by noninvasive 3D functional spectroscopic mapping of 2-hydroxyglutarate. Clin Cancer Res 22: 1632-1641.

Cermak N, Olcum S, Delgado FF, Wasserman SC, Payer KR, et al. 2016. High-throughput measurement of single-cell growth rates using serial microfluidic mass sensor arrays. Nat Biotechnol 34: 1052–1059.

Indolfi L, Ligorio M, Ting DT, Xega K, Tzafriri AR, et al. 2016. A tunable delivery platform to provide local chemotherapy for pancreatic ductal adenocarcinoma. Biomaterials 93: 71-82.

Moynihan KD, Opel CF, Szeto GL, Tzeng A, Zhu EF, et al. 2016. Eradication of large established tumors in mice by combination immunotherapy that engages innate and adaptive immune responses. Nat Med 22: 1402-1410.

Rezaei Araghi R, Keating AE. 2016. Designing helical peptide inhibitors of protein-protein interactions. Curr Opin Struct Biol 39: 27-38.

Rezaei Araghi R, Ryan JA, Letai A, Keating AE. 2016. Rapid optimization of Mcl-1 inhibitors using stapled peptide libraries including non-natural side chains. ACS Chem Biol 11: 1238-1244.

Stevens MM, Maire CL, Chou N, Murakami MA, Knoff DS, et al. 2016. Drug sensitivity of single cancer cells is predicted by changes in mass accumulation rate. Nat Biotechnol 34: 1161-1167.

Wang H, Osseiran S, Igras V, Nichols AJ, Roider EM, et al. 2016. In vivo coherent Raman imaging of the melanomagenesis-associated pigment pheomelanin. Sci Rep 6: 37986.

Wang Y, Begley M, Li Q, Huang H-T, Lako A, Eck MJ, Gray NS, Mitchison TJ, Cantley LC, Zhao JJ. 2016. Mitotic MELK-eIF4B signaling controls protein synthesis and tumor cell survival. Proc Natl Acad Sci USA 113:9810–9815. doi:10.1073/pnas.1606862113

Wucherpfennig KW, Cartwright AN. 2016. Genetic screens to study the immune system in cancer. Curr Opin Immunol 41: 55–61.

 

2015

Faber AC, Farago AF, Costa C, Dastur A, Gomez-Caraballo M, et al. 2015. Assessment of ABT-263 activity across a cancer cell line collection leads to a potent combination therapy for small-cell lung cancer. Proc Natl Acad Sci USA 112: E1288-1296.

Voena C, Menotti M, Mastini C, Di Giacomo F, Longo DL, et al. 2015. Efficacy of a cancer vaccine against ALK-Rearrangedlung tumors. Cancer Immunol Res 3: 1333–1343.

Ye H, Tanenbaum LM, Na YJ, Mantzavinou A, Fulci G, et al. 2015. Sustained, low-dose intraperitoneal cisplatin improves treatment outcome in ovarian cancer mouse models. J Control Release 220: 358–367.

Zhang C-Z, Adalsteinsson VA, Francis J, Cornils H, Jung J, et al. 2015. Calibrating genomic and allelic coverage bias in single-cell sequencing. Nat Commun 6: 6822.

 

2014

Blasco RB, Karaca E, Ambrogio C, Cheong T-C, Karayol E, et al. 2014. Simple and rapid in vivo generation of chromosomal rearrangements using CRISPR/Cas9 technology. Cell Rep 9: 1219-1227.

Christensen CL, Kwiatkowski N, Abraham BJ, Carretero J, Al-Shahrour F, et al. 2014. Targeting transcriptional addictions in small cell lung cancer with a covalent CDK7 inhibitor. Cancer Cell 26: 909-922.

Francis JM, Zhang C-Z, Maire CL, Jung J, Manzo VE, et al. 2014. EGFR variant heterogeneity in glioblastoma resolved through single-nucleus sequencing. Cancer Discov 4: 956-971.

Ghosh D, Bagley AF, Na YJ, Birrer MJ, Bhatia SN, Belcher AM. Deep, noninvasive imaging and surgical guidance of submillimeter tumors using targeted M13-stabilized single-walled carbon nanotubes. PNAS 111: 13948-13953. 

Grassian AR, Parker SJ, Davidson SM, Divakaruni AS, Green CR, Zhang X, Slocum KL, Pu M, Lin F, Vickers C, Joud-Caldwell C, Chung F, Yin H, Handly ED, Straub C, Growney JD, Vander Heiden MG, Murphy AN, Pagliarini R, Metallo CM. 2014. IDH1 mutations alter citric acid cycle metabolism and increase dependence on oxidative mitochondrial metabolism. Cancer Res  74:3317-3331.

Lewis CA, Parker SJ, Fiske BP, McCloskey D, Gui DY, Green CR, Vokes NI, Feist AM, Vander Heiden MG, Metallo CM. 2014. Tracing compartmentalized NADPH metabolism in the cytosol and mitochondria of mammalian cells. Mol Cell 55:253-263.

Wakimoto H, Tanaka S, Curry WT, Loebel F, Zhao D, et al. 2014. Targetable signaling pathway mutations are associated with malignant phenotype in IDH-mutant gliomas. Clin Cancer Res 20: 2898–2909.

Zhou P, Shaffer DR, Alvarez Arias DA, Nakazaki Y, Pos W, et al. 2014. In vivo discovery of immunotherapy targets in the tumour microenvironment. Nature 506: 52–57.

 

2013

Chauhan VP, Martin JD, Liu H, Lacorre DA, Jain SR, et al. 2013. Angiotensin inhibition enhances drug delivery and potentiates chemotherapy by decompressing tumour blood vessels. Nat Commun 4: 2516.