The David H. Koch Institute for Integrative Cancer Research at MITThe David H. Koch Institute for Integrative Cancer Research at MIT

Massachusetts Institute of Technology

National Cancer Institute Cancer Center

Science + Engineering... Conquering Cancer Together

Progress: June 2018

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1. The Role of HSP90 in the Regulation of de novo Purine Biosynthesis. Pedley AM, Karras GI, Zhang X, Lindquist SL, Benkovic SJ. Biochemistry. pubmed:29553718;  doi:10.1021/acs.biochem.8b00140

2. Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis. Farrell JA, Wang Y, Riesenfeld SJ, Shekhar K, Regev A, Schier AF. Science. pubmed:29700225;  doi:10.1126/science.aar3131

3. The nutrient environment affects therapy. Muir A, Vander Heiden MG. Science. pubmed:29853672;  doi:10.1126/science.aar5986

4. Sequence, Structure, and Context Preferences of Human RNA Binding Proteins. Dominguez D, Freese P, Alexis MS, Su A, Hochman M, Palden T, Bazile C, Lambert NJ, Van Nostrand EL, Pratt GA, Yeo GW, Graveley BR, Burge CB. Mol Cell. pubmed:29883606;  doi:10.1016/j.molcel.2018.05.001

5. Genetic mechanisms of immune evasion in colorectal cancer. Grasso CS, Giannakis M, Wells DK, Hamada T, Mu XJ, Quist M, Nowak JA, Nishihara R, Qian ZR, Inamura K, Morikawa T, Nosho K, Abril-Rodriguez G, Connolly C, Escuin-Ordinas H, Geybels MS, Grady WM, Hsu L, Hu-Lieskovan S, Huyghe JR, Kim YJ, Krystofinski PE, Leiserson MD, Montoya DJ, Nadel BB, Pellegrini M, Pritchard CC, Puig-Saus C, Quist EH, Raphael BJ, Salipante SJ, Shin DS, Shinbrot E, Shirts B, Shukla S, Stanford JL, Sun W, Tsoi J, Upfill-Brown A, Wheeler DA, Wu CJ, Yu M, Zaidi SH, Zaretsky JM, Gabriel SB, Lander ES, Garraway LA, Hudson TJ, Fuchs CS, Ribas A, Ogino S, Peters U. Cancer Discov. pubmed:29510987;  doi:10.1158/2159-8290.CD-17-1327

6. In vivo RNAi screening identifies Pafah1b3 as a target for combination therapy with TKIs in BCR-ABL1(+) BCP-ALL. Fiedler ERC, Bhutkar A, Lawler E, Besada R, Hemann MT. Blood Adv. pubmed:29853524;  doi:10.1182/bloodadvances.2017015610

7. Mice with endogenous TDP-43 mutations exhibit gain of splicing function and characteristics of amyotrophic lateral sclerosis. Fratta P, Sivakumar P, Humphrey J, Lo K, Ricketts T, Oliveira H, Brito-Armas JM, Kalmar B, Ule A, Yu Y, Birsa N, Bodo C, Collins T, Conicella AE, Mejia Maza A, Marrero-Gagliardi A, Stewart M, Mianne J, Corrochano S, Emmett W, Codner G, Groves M, Fukumura R, Gondo Y, Lythgoe M, Pauws E, Peskett E, Stanier P, Teboul L, Hallegger M, Calvo A, Chio A, Isaacs AM, Fawzi NL, Wang E, Housman DE, Baralle F, Greensmith L, Buratti E, Plagnol V, Fisher EM, Acevedo-Arozena A. EMBO J. pubmed:29764981;  doi:10.15252/embj.201798684

8. Altered exocrine function can drive adipose wasting in early pancreatic cancer. Danai LV, Babic A, Rosenthal MH, Dennstedt EA, Muir A, Lien EC, Mayers JR, Tai K, Lau AN, Jones-Sali P, Prado CM, Petersen GM, Takahashi N, Sugimoto M, Yeh JJ, Lopez N, Bardeesy N, Fernandez-Del Castillo C, Liss AS, Koong AC, Bui J, Yuan C, Welch MW, Brais LK, Kulke MH, Dennis C, Clish CB, Wolpin BM, Vander Heiden MG. Nature. pubmed:29925948;  doi:10.1038/s41586-018-0235-7

9. Enhanced phosphocholine metabolism is essential for terminal erythropoiesis. Huang NJ, Lin YC, Lin CY, Pishesha N, Lewis CA, Freinkman E, Farquharson C, Millan JL, Lodish H. Blood. pubmed:29712634;  doi:10.1182/blood-2018-03-838516

10. The endoribonuclease YbeY is linked to proper cellular morphology and virulence in Brucella abortus. Budnick JA, Sheehan LM, Colquhoun JM, Dunman PM, Walker GC, Roop RM2nd, Caswell CC. J Bacteriol. pubmed:29632093;  doi:10.1128/JB.00105-18

11. Induction and transcriptional regulation of the co-inhibitory gene module in T cells. Chihara N, Madi A, Kondo T, Zhang H, Acharya N, Singer M, Nyman J, Marjanovic ND, Kowalczyk MS, Wang C, Kurtulus S, Law T, Etminan Y, Nevin J, Buckley CD, Burkett PR, Buenrostro JD, Rozenblatt-Rosen O, Anderson AC, Regev A, Kuchroo VK. Nature. pubmed:29899446;  doi:10.1038/s41586-018-0206-z

12. A molecular network of the aging human brain provides insights into the pathology and cognitive decline of Alzheimer's disease. Mostafavi S, Gaiteri C, Sullivan SE, White CC, Tasaki S, Xu J, Taga M, Klein HU, Patrick E, Komashko V, McCabe C, Smith R, Bradshaw EM, Root DE, Regev A, Yu L, Chibnik LB, Schneider JA, Young-Pearse TL, Bennett DA, De Jager PL. Nat Neurosci. pubmed:29802388;  doi:10.1038/s41593-018-0154-9

13. Advancements in Nanomedicine for Multiple Myeloma. Detappe A, Bustoros M, Mouhieddine TH, Ghoroghchian PP. Trends Mol Med. pubmed:29773319;  doi:10.1016/j.molmed.2018.04.005

14. Xenoprotein engineering via synthetic libraries. Gates ZP, Vinogradov AA, Quartararo AJ, Bandyopadhyay A, Choo ZN, Evans ED, Halloran KH, Mijalis AJ, Mong SK, Simon MD, Standley EA, Styduhar ED, Tasker SZ, Touti F, Weber JM, Wilson JL, Jamison TF, Pentelute BL. Proc Natl Acad Sci U S A. pubmed:29784819;  doi:10.1073/pnas.1722633115

15. Harnessing single-cell genomics to improve the physiological fidelity of organoid-derived cell types. Mead BE, Ordovas-Montanes J, Braun AP, Levy LE, Bhargava P, Szucs MJ, Ammendolia DA, MacMullan MA, Yin X, Hughes TK, Wadsworth MH2nd, Ahmad R, Rakoff-Nahoum S, Carr SA, Langer R, Collins JJ, Shalek AK, Karp JM. BMC Biol. pubmed:29871632;  doi:10.1186/s12915-018-0527-2

16. Material aid for vaccines. Irvine D. Nat Mater. pubmed:29795221;  doi:10.1038/s41563-018-0089-2

17. Artificial Anti-Tumor Opsonizing Proteins with Fibronectin Scaffolds Engineered for Specificity to Each of the Murine FcgammaR Types. Chen TF, Li KK, Zhu EF, Opel CF, Kauke MJ, Kim H, Atolia E, Wittrup KD. J Mol Biol. pubmed:29704491;  doi:10.1016/j.jmb.2018.04.021

18. Acceleration of Diabetic Wound Healing with PHD2- and miR-210-targeting Oligonucleotides. Dallas A, Trotsyuk A, Ilves H, Bonham CA, Rodrigues M, Engel K, Barrera JA, Kosaric N, Stern-Buchbinder ZA, White A, Mandell KJ, Hammond P, Mansbridge JN, Jayasena S, Gurtner GC, Johnston BH. Tissue Eng Part A. pubmed:29644938;  doi:10.1089/ten.TEA.2017.0484

19. Endothelial siRNA delivery in nonhuman primates using ionizable low-molecular weight polymeric nanoparticles. Khan OF, Kowalski PS, Doloff JC, Tsosie JK, Bakthavatchalu V, Winn CB, Haupt J, Jamiel M, Langer R, Anderson DG. Sci Adv. pubmed:29963629;  doi:10.1126/sciadv.aar8409

20. A mixed antagonistic/synergistic miRNA repression model enables accurate predictions of multi-input miRNA sensor activity. Gam JJ, Babb J, Weiss R. Nat Commun. pubmed:29934631;  doi:10.1038/s41467-018-04575-0

21. Expansion Microscopy: Enabling Single Cell Analysis In Intact Biological Systems. Alon S, Huynh GH, Boyden ES. FEBS J. pubmed:29938896;  doi:10.1111/febs.14597

22. Publisher Correction: Temporally precise single-cell-resolution optogenetics. Shemesh OA, Tanese D, Zampini V, Linghu C, Piatkevich K, Ronzitti E, Papagiakoumou E, Boyden ES, Emiliani V. Nat Neurosci. pubmed:29549318;  doi:10.1038/s41593-018-0097-1

23. Expansion microscopy: development and neuroscience applications. Karagiannis ED, Boyden ES. Curr Opin Neurobiol. pubmed:29316506;  doi:10.1016/j.conb.2017.12.012

24. Machine Learning Methods to Extract Documentation of Breast Cancer Symptoms from Electronic Health Records. Forsyth AW, Barzilay R, Hughes KS, Lui D, Lorenz KA, Enzinger A, Tulsky JA, Lindvall C. J Pain Symptom Manage. pubmed:29496537;  doi:10.1016/j.jpainsymman.2018.02.016

25. Machine learning to parse breast pathology reports in Chinese. Tang R, Ouyang L, Li C, He Y, Griffin M, Taghian A, Smith B, Yala A, Barzilay R, Hughes K. Breast Cancer Res Treat. pubmed:29380208;  doi:10.1007/s10549-018-4668-3

26. Combinatorial drug discovery in nanoliter droplets. Kulesa A, Kehe J, Hurtado JE, Tawde P, Blainey PC. Proc Natl Acad Sci U S A. pubmed:29899149;  doi:10.1073/pnas.1802233115

27. Stabilized single-injection inactivated polio vaccine elicits a strong neutralizing immune response. Tzeng SY, McHugh KJ, Behrens AM, Rose S, Sugarman JL, Ferber S, Langer R, Jaklenec A. Proc Natl Acad Sci U S A. pubmed:29784798;  doi:10.1073/pnas.1720970115

28. Stochastic Turing patterns in a synthetic bacterial population. Karig D, Martini KM, Lu T, DeLateur NA, Goldenfeld N, Weiss R. Proc Natl Acad Sci U S A. pubmed:29891706;  doi:10.1073/pnas.1720770115