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: February 2018

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1. Mechanical circulatory support device-heart hysteretic interaction can predict left ventricular end diastolic pressure. Chang BY, Keller SP, Bhavsar SS, Josephy N, Edelman ER. Sci Transl Medpubmed:29491185;  doi:10.1126/scitranslmed.aao2980

2. CD38 bispecific antibody pretargeted radioimmunotherapy for multiple myeloma and other B cell malignancies. Green DJ, O'Steen S, Lin Y, Comstock ML, Kenoyer AL, Hamlin DK, Wilbur DS, Fisher DR, Nartea M, Hylarides MD, Gopal AK, Gooley TA, Orozco JJ, Till BG, Orcutt KD, Wittrup KD, Press OW. Bloodpubmed:29158362;  doi:10.1182/blood-2017-09-807610

3. In vivo systems biology approaches to chronic immune/inflammatory pathophysiology. Starchenko A, Lauffenburger DA. Curr Opin Biotechnolpubmed:29494996;  doi:10.1016/j.copbio.2018.02.006

4. Towards a defined ECM and small molecule based monolayer culture system for the expansion of mouse and human intestinal stem cells. Tong Z, Martyn K, Yang A, Yin X, Mead BE, Joshi N, Sherman NE, Langer RS, Karp JM. Biomaterialspubmed:29120819;  doi:10.1016/j.biomaterials.2017.10.038

5. Optogenetic Tractography for anatomo-functional characterization of cortico-subcortical neural circuits in non-human primates. Senova S, Poupon C, Dauguet J, Stewart HJ, Dugue GP, Jan C, Hosomi K, Ralph GS, Barnes L, Drouot X, Pouzat C, Mangin JF, Pain F, Doignon I, Aron-Badin R, Brouillet E, Boyden ES, Mitrophanous KA, Hantraye P, Palfi S. Sci Reppubmed:29463867;  doi:10.1038/s41598-018-21486-8

6. Structure-property relationships of amphiphilic nanoparticles that penetrate or fuse lipid membranes. Atukorale P, Guven ZP, Bekdemir A, Carney R, Van Lehn RC, Yun DS, Jacob Silva PH, Demurtas D, Yang YS, Alexander-Katz A, Stellacci F, Irvine DJ. Bioconjug Chempubmed:29465986;  doi:10.1021/acs.bioconjchem.7b00777

7. Integrated in vivo multiomics analysis identifies p21-activated kinase signaling as a driver of colitis. Lyons J, Brubaker DK, Ghazi PC, Baldwin KR, Edwards A, Boukhali M, Strasser SD, Suarez-Lopez L, Lin YJ, Yajnik V, Kissil JL, Haas W, Lauffenburger DA, Haigis KM. Sci Signalpubmed:29487189;  doi:10.1126/scisignal.aan3580

8. Tyro3-mediated phosphorylation of ACTN4 at tyrosines is FAK-dependent and decreases susceptibility to cleavage by m-Calpain. Shao H, Wang A, Lauffenburger D, Wells A. Int J Biochem Cell Biolpubmed:29274473;  doi:10.1016/j.biocel.2017.12.014

9. Temporal variation in HIV-specific IgG subclass Abs during acute infection differentiates spontaneous controllers from chronic progressors. Sadanand S, Das J, Chung AW, Schoen MK, Lane S, Suscovich TJ, Streeck H, Smith D, Little S, Lauffenburger DA, Richman D, Alter G. AIDSpubmed:29239894;  doi:10.1097/QAD.0000000000001716

10. How many human proteoforms are there?. Aebersold R, Agar JN, Amster IJ, Baker MS, Bertozzi CR, Boja ES, Costello CE, Cravatt BF, Fenselau C, Garcia BA, Ge Y, Gunawardena J, Hendrickson RC, Hergenrother PJ, Huber CG, Ivanov AR, Jensen ON, Jewett MC, Kelleher NL, Kiessling LL, Krogan NJ, Larsen MR, Loo JA, Ogorzalek Loo RR, Lundberg E, MacCoss MJ, Mallick P, Mootha VK, Mrksich M, Muir TW, Patrie SM, Pesavento JJ, Pitteri SJ, Rodriguez H, Saghatelian A, Sandoval W, Schluter H, Sechi S, Slavoff SA, Smith LM, Snyder MP, Thomas PM, Uhlen M, Van Eyk JE, Vidal M, Walt DR, White FM, Williams ER, Wohlschlager T, Wysocki VH, Yates NA, Young NL, Zhang B. Nat Chem Biolpubmed:29443976;  doi:10.1038/nchembio.2576

11. Could antiretrovirals be treating EBV in MS A case report. Drosu NC, Edelman ER, Housman DE. Mult Scler Relat Disordpubmed:29510325;  doi:10.1016/j.msard.2018.02.029

12. Quantification of thrombus formation in malapposed coronary stents deployed in vitro through imaging analysis. Brown J, O'Brien CC, Lopes AC, Kolandaivelu K, Edelman ER. J Biomechpubmed:29452756;  doi:10.1016/j.jbiomech.2018.01.044

13. Rapamycin activates TGF receptor independently of its ligand: implications for endothelial dysfunction. Miyakawa AA, Girao-Silva T, Krieger JE, Edelman ER. Clin Sci (Lond)pubmed:29343616;  doi:10.1042/CS20171457

14. Structurally modulated codelivery of siRNA and Argonaute 2 for enhanced RNA interference. Li J, Wu C, Wang W, He Y, Elkayam E, Joshua-Tor L, Hammond PT. Proc Natl Acad Sci U S Apubmed:29432194;  doi:10.1073/pnas.1719565115

15. Biocompatible Semiconductor Quantum Dots as Cancer Imaging Agents. McHugh KJ, Jing L, Behrens AM, Jayawardena S, Tang W, Gao M, Langer R, Jaklenec A. Adv Materpubmed:29468747;  doi:10.1002/adma.201706356

16. Drug delivery across length scales. Delcassian D, Patel AK, Cortinas AB, Langer R. J Drug Targetpubmed:29415575;  doi:10.1080/1061186X.2018.1438440

17. Nanoparticles for Immune Cytokine TRAIL-Based Cancer Therapy. Guimaraes PPG, Gaglione S, Sewastianik T, Carrasco RD, Langer R, Mitchell MJ. ACS Nanopubmed:29378114;  doi:10.1021/acsnano.7b05876

18. Association of Cell-Free DNA Tumor Fraction and Somatic Copy Number Alterations With Survival in Metastatic Triple-Negative Breast Cancer. Stover DG, Parsons HA, Ha G, Freeman SS, Barry WT, Guo H, Choudhury AD, Gydush G, Reed SC, Rhoades J, Rotem D, Hughes ME, Dillon DA, Partridge AH, Wagle N, Krop IE, Getz G, Golub TR, Love JC, Winer EP, Tolaney SM, Lin NU, Adalsteinsson VA. J Clin Oncolpubmed:29298117;  doi:10.1200/JCO.2017.76.0033

19. Erythrocyte efferocytosis modulates macrophages towards recovery after intracerebral hemorrhage. Chang CF, Goods BA, Askenase MH, Hammond MD, Renfroe SC, Steinschneider AF, Landreneau MJ, Ai Y, Beatty HE, da Costa LHA, Mack M, Sheth KN, Greer DM, Huttner A, Coman D, Hyder F, Ghosh S, Rothlin CV, Love JC, Sansing LH. J Clin Investpubmed:29251628;  doi:10.1172/JCI95612

20. Programming gene and engineered-cell therapies with synthetic biology. Kitada T, DiAndreth B, Teague B, Weiss R. Sciencepubmed:29439214;  doi:10.1126/science.aad1067

21. Yeast-Based Synthetic Biology Platform for Antimicrobial Peptide Production. Cao J, de la Fuente-Nunez C, Ou RW, Torres MT, Pande SG, Sinskey AJ, Lu TK. ACS Synth Biolpubmed:29366323;  doi:10.1021/acssynbio.7b00396

22. Theoretical Insight into the Biodegradation of Solitary Oil Microdroplets Moving through a Water Column. Kapellos GE, Paraskeva CA, Kalogerakis N, Doyle PS. Bioengineering (Basel)pubmed:29439555;  doi:10.3390/bioengineering5010015

23. Knots modify the coil-stretch transition in linear DNA polymers. Soh BW, Narsimhan V, Klotz AR, Doyle PS. Soft Matterpubmed:29423476;  doi:10.1039/c7sm02195j

24. Neuromicrobiology: How Microbes Influence the Brain. de la Fuente-Nunez C, Meneguetti BT, Franco OL, Lu TK. ACS Chem Neuroscipubmed:29220570;  doi:10.1021/acschemneuro.7b00373

25. A robotic multidimensional directed evolution approach applied to fluorescent voltage reporters. Piatkevich KD, Jung EE, Straub C, Linghu C, Park D, Suk HJ, Hochbaum DR, Goodwin D, Pnevmatikakis E, Pak N, Kawashima T, Yang CT, Rhoades JL, Shemesh O, Asano S, Yoon YG, Freifeld L, Saulnier JL, Riegler C, Engert F, Hughes T, Drobizhev M, Szabo B, Ahrens MB, Flavell SW, Sabatini BL, Boyden ES. Nat Chem Biolpubmed:29483642;  doi:10.1038/s41589-018-0004-9

26. Evidence for long-timescale patterns of synaptic inputs in CA1 of awake behaving mice. Kolb I, Franzesi GT, Wang M, Kodandaramaiah SB, Forest CR, Boyden ES, Singer AC. J Neuroscipubmed:29279309;  doi:10.1523/JNEUROSCI.1519-17.2017

27. 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 Managepubmed:29496537;  doi:10.1016/j.jpainsymman.2018.02.016

28. Conserved microRNA targeting reveals preexisting gene dosage sensitivities that shaped amniote sex chromosome evolution. Naqvi S, Bellott DW, Lin KS, Page DC. Genome Respubmed:29449410;  doi:10.1101/gr.230433.117

29. Mapping a functional cancer genome atlas of tumor suppressors in mouse liver using AAV-CRISPR-mediated direct in vivo screening. Wang G, Chow RD, Ye L, Guzman CD, Dai X, Dong MB, Zhang F, Sharp PA, Platt RJ, Chen S. Sci Advpubmed:29503867;  doi:10.1126/sciadv.aao5508

30. Transcriptional Pause Sites Delineate Stable Nucleosome-Associated Premature Polyadenylation Suppressed by U1 snRNP. Chiu AC, Suzuki HI, Wu X, Mahat DB, Kriz AJ, Sharp PA. Mol Cellpubmed:29398447;  doi:10.1016/j.molcel.2018.01.006

31. Rescue of Fragile X Syndrome Neurons by DNA Methylation Editing of the FMR1 Gene. Liu XS, Wu H, Krzisch M, Wu X, Graef J, Muffat J, Hnisz D, Li CH, Yuan B, Xu C, Li Y, Vershkov D, Cacace A, Young RA, Jaenisch R. Cellpubmed:29456084;  doi:10.1016/j.cell.2018.01.012

32. BET bromodomain proteins regulate enhancer function during adipogenesis. Brown JD, Feldman ZB, Doherty SP, Reyes JM, Rahl PB, Lin CY, Sheng Q, Duan Q, Federation AJ, Kung AL, Haldar SM, Young RA, Plutzky J, Bradner JE. Proc Natl Acad Sci U S Apubmed:29444854;  doi:10.1073/pnas.1711155115

33. High MITF Expression is Associated with Super-enhancers and Suppressed by CDK7 Inhibition in Melanoma. Eliades P, Abraham BJ, Ji Z, Miller DM, Christensen CL, Kwiatkowski N, Kumar R, Njauw CN, Taylor M, Miao B, Zhang T, Wong KK, Gray NS, Young RA, Tsao H. J Invest Dermatolpubmed:29408204;  doi:10.1016/j.jid.2017.09.056

34. EWS/FLI Confers Tumor Cell Synthetic Lethality to CDK12 Inhibition in Ewing Sarcoma. Iniguez AB, Stolte B, Wang EJ, Conway AS, Alexe G, Dharia NV, Kwiatkowski N, Zhang T, Abraham BJ, Mora J, Kalev P, Leggett A, Chowdhury D, Benes CH, Young RA, Gray NS, Stegmaier K. Cancer Cellpubmed:29358035;  doi:10.1016/j.ccell.2017.12.009

35. Pharmacological perturbation of CDK9 using selective CDK9 inhibition or degradation. Olson CM, Jiang B, Erb MA, Liang Y, Doctor ZM, Zhang Z, Zhang T, Kwiatkowski N, Boukhali M, Green JL, Haas W, Nomanbhoy T, Fischer ES, Young RA, Bradner JE, Winter GE, Gray NS. Nat Chem Biolpubmed:29251720;  doi:10.1038/nchembio.2538

36. Tissue-selective effects of nucleolar stress and rDNA damage in developmental disorders. Calo E, Gu B, Bowen ME, Aryan F, Zalc A, Liang J, Flynn RA, Swigut T, Chang HY, Attardi LD, Wysocka J. Naturepubmed:29364875;  doi:10.1038/nature25449

37. Mass Spectrometric Evidence for Neuropeptide-Amidating Enzymes in C elegans. Van Bael S, Watteyne J, Boonen K, De Haes W, Menschaert G, Ringstad N, Horvitz HR, Schoofs L, Husson S, Temmerman L. J Biol Chempubmed:29487130;  doi:10.1074/jbc.RA117.000731

38. DEPTOR Suppresses Lipogenesis and Ameliorates Hepatic Steatosis and Acute-on-Chronic Liver Injury in Alcoholic Liver Disease. Chen H, Shen F, Sherban A, Nocon A, Li Y, Wang H, Xu MJ, Rui X, Han J, Jiang B, Lee D, Li N, Keyhani-Nejad F, Fan JG, Liu F, Kamat A, Musi N, Guarente L, Pacher P, Gao B, Zang M. Hepatologypubmed:29457836;  doi:10.1002/hep.29849

39. Multiple kinases inhibit origin licensing and helicase activation to ensure reductive cell division during meiosis. Phizicky DV, Berchowitz LE, Bell SP. Elifepubmed:29388912;  doi:10.7554/eLife.33309

40. Inhibiting mitochondrial phosphate transport as an unexploited antifungal strategy. McLellan CA, Vincent BM, Solis NV, Lancaster AK, Sullivan LB, Hartland CL, Youngsaye W, Filler SG, Whitesell L, Lindquist S. Nat Chem Biolpubmed:29227471;  doi:10.1038/nchembio.2534

41. Identification of PNG kinase substrates uncovers interactions with the translational repressor TRAL in the oocyte-to-embryo transition. Hara M, Lourido S, Petrova B, Lou HJ, Von Stetina JR, Kashevsky H, Turk BE, Orr-Weaver TL. Elifepubmed:29480805;  doi:10.7554/eLife.33150

42. Activating Embryonic Development in Drosophila. Aviles-Pagan EE, Orr-Weaver TL. Semin Cell Dev Biolpubmed:29448071;  doi:10.1016/j.semcdb.2018.02.019

43. Variant cell cycles regulated by Notch signaling control cell size and ensure a functional blood-brain barrier. Von Stetina JR, Frawley LE, Unhavaithaya Y, Orr-Weaver TL. Developmentpubmed:29440220;  doi:10.1242/dev.157115

44. Adaptive and reversible resistance to Kras inhibition in pancreatic cancer cells. Chen PY, Muzumdar MD, Dorans KJ, Robbins RA, Bhutkar A, Del Rosario AM, Mertins P, Qiao J, Schafer C, Gertler FB, Carr SA, Jacks T. Cancer Respubmed:29279356;  doi:10.1158/0008-5472.CAN-17-2129

45. Serine Catabolism by SHMT2 Is Required for Proper Mitochondrial Translation Initiation and Maintenance of Formylmethionyl-tRNAs. Minton DR, Nam M, McLaughlin DJ, Shin J, Bayraktar EC, Alvarez SW, Sviderskiy VO, Papagiannakopoulos T, Sabatini DM, Birsoy K, Possemato R. Mol Cellpubmed:29452640;  doi:10.1016/j.molcel.2018.01.024

46. Height, obesity, and the risk of TMPRSS2:ERG-defined prostate cancer. Graff RE, Ahearn TU, Pettersson A, Ebot EM, Gerke T, Penney KL, Wilson KM, Markt SC, Pernar CH, Gonzalez-Feliciano AG, Song M, Lis RT, Schmidt DR, Vander Heiden MG, Fiorentino M, Giovannucci EL, Loda M, Mucci LA. Cancer Epidemiol Biomarkers Prevpubmed:29167279;  doi:10.1158/1055-9965.EPI-17-0547

47. FAOund the Link: Phospholipid Remodeling and Intestinal Stem Cell Growth and Tumorigenesis. Cheng CW, Yilmaz OH. Cell Stem Cellpubmed:29395049;  doi:10.1016/j.stem.2018.01.009

48. Colonoscopy-based colorectal cancer modeling in mice with CRISPR-Cas9 genome editing and organoid transplantation. Roper J, Tammela T, Akkad A, Almeqdadi M, Santos SB, Jacks T, Yilmaz OH. Nat Protocpubmed:29300388;  doi:10.1038/nprot.2017.136

49. EMT in cancer. Brabletz T, Kalluri R, Nieto MA, Weinberg RA. Nat Rev Cancerpubmed:29326430;  doi:10.1038/nrc.2017.118

50. Palladium Oxidative Addition Complexes for Peptide and Protein Crosslinking. Kubota K, Dai P, Pentelute BL, Buchwald SL. J Am Chem Socpubmed:29406701;  doi:10.1021/jacs.8b00172

51. Stereochemical Sequence Dictates Unimolecular Diblock Copolymer Assembly. Golder MR, Jiang Y, Teichen PE, Nguyen HV, Wang W, Milos N, Freedman SA, Willard AP, Johnson JA. J Am Chem Socpubmed:29356516;  doi:10.1021/jacs.7b12696