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: April 2017

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1. Virus-driven inflammation is associated with the development of bNAbs in spontaneous controllers of HIV. Dugast AS, Arnold K, Lofano G, Moore S, Hoffner M, Simek M, Poignard P, Seaman M, Suscovich T, Pereyra F, Walker BD, Lauffenburger D, Kwon D, Keele BF, Alter G. Clin Infect Dispubmed:28158448;  doi:10.1093/cid/cix057

2. Integrated assessment of diclofenac biotransformation, pharmacokinetics, and omics-based toxicity in a 3D human liver-immunocompetent co-culture system. Sarkar U, Ravindra KC, Large E, Young CL, Rivera-Burgos D, Yu J, Cirit M, Hughes DJ, Wishnok JS, Lauffenburger DA, Griffith LG, Tannenbaum SR. Drug Metab Dispospubmed:28450578;  doi:10.1124/dmd.116.074005

3. Swimming bacteria promote dispersal of non-motile staphylococcal species. Samad T, Billings N, Birjiniuk A, Crouzier T, Doyle PS, Ribbeck K. ISME Jpubmed:28398350;  doi:10.1038/ismej.2017.23

4. A novel role for transcription-coupled nucleotide excision repair for the in vivo repair of 3,N4-ethenocytosine. Chaim IA, Gardner A, Wu J, Iyama T, Wilson DM3rd, Samson LD. Nucleic Acids Respubmed:28115629;  doi:10.1093/nar/gkx015

5. Cell-Cycle-Targeting MicroRNAs as Therapeutic Tools against Refractory Cancers. Hydbring P, Wang Y, Fassl A, Li X, Matia V, Otto T, Choi YJ, Sweeney KE, Suski JM, Yin H, Bogorad RL, Goel S, Yuzugullu H, Kauffman KJ, Yang J, Jin C, Li Y, Floris D, Swanson R, Ng K, Sicinska E, Anders L, Zhao JJ, Polyak K, Anderson DG, Li C, Sicinski P. Cancer Cell.pubmed:28399412;  doi:10.1016/j.ccell.2017.03.004

6. Genome-wide CRISPR Screen Identifies Regulators of MAPK as Suppressors of Liver Tumors in Mice. Song CQ, Li Y, Mou H, Moore J, Park A, Pomyen Y, Hough S, Kennedy Z, Fischer A, Yin H, Anderson DG, Conte DJr, Zender L, Wang XW, Thorgeirsson S, Weng Z, Xue W. Gastroenterologypubmed:27956228;  doi:10.1053/j.gastro.2016.12.002

7. First-Generation Bioresorbable Vascular Scaffolds: Disappearing Stents or Disappearing Evidence?. Bangalore S, Edelman ER, Bhatt DL. J Am Coll Cardiolpubmed:28412390;  doi:10.1016/j.jacc.2017.04.012

8. Engagement of the medical-technology sector with society. Williams D, Edelman ER, Radisic M, Laurencin C, Untereker D. Sci Transl Medpubmed:28404862;  doi:10.1126/scitranslmed.aal4359

9. Stents: Biomechanics, Biomaterials, and Insights from Computational Modeling. Karanasiou GS, Papafaklis MI, Conway C, Michalis LK, Tzafriri R, Edelman ER, Fotiadis DI. Ann Biomed Eng.pubmed:28160103;  doi:10.1007/s10439-017-1806-8

10. Ultra-Hydrophilic Stent Platforms Promote Early Vascular Healing and Minimize Late Tissue Response - A Potential Alternative to Second-Generation Drug Eluting Stents. Kolandaivelu K, Bailey L, Buzzi S, Zucker A, Milleret V, Ziogas A, Ehrbar M, Khattab AA, Stanley JR, Wong GK, Zani B, Markham PM, Tzafriri AR, Bhatt DL, Edelman ER. EuroIntervention.pubmed:27993749;  doi:10.4244/EIJ-D-15-00497

11. Local remodeling of synthetic extracellular matrix microenvironments by co-cultured endometrial epithelial and stromal cells enables long-term dynamic physiological function. Cook CD, Hill AS, Guo M, Stockdale L, Papps JP, Isaacson KB, Lauffenburger DA, Griffith LG. Integr Biol (Camb)pubmed:28317948;  doi:10.1039/c6ib00245e

12. Multi-functional scaling methodology for translational pharmacokinetic and pharmacodynamic applications using integrated microphysiological systems (MPS). Maass C, Stokes CL, Griffith LG, Cirit M. Integr Biol (Camb)pubmed:28267162;  doi:10.1039/c6ib00243a

13. Wireless Power Transfer to Millimeter-Sized Gastrointestinal Electronics Validated in a Swine Model. Abid A, O'Brien JM, Bensel T, Cleveland C, Booth L, Smith BR, Langer R, Traverso G. Sci Reppubmed:28447624;  doi:10.1038/srep46745

14. Biodegradable scaffolds promote tissue remodeling and functional improvement in non-human primates with acute spinal cord injury. Slotkin JR, Pritchard CD, Luque B, Ye J, Layer RT, Lawrence MS, O'Shea TM, Roy RR, Zhong H, Vollenweider I, Edgerton VR, Courtine G, Woodard EJ, Langer R. Biomaterialspubmed:28167393;  doi:10.1016/j.biomaterials.2017.01.024

15. Ultrasound-Mediated Delivery of RNA to Colonic Mucosa of Live Mice. Schoellhammer CM, Lauwers GY, Goettel JA, Oberli MA, Cleveland C, Park JY, Minahan D, Chen Y, Anderson DG, Jaklenec A, Snapper SB, Langer R, Traverso G. Gastroenterologypubmed:28088460;  doi:10.1053/j.gastro.2017.01.002

16. Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput. Gierahn TM, Wadsworth MH2nd, Hughes TK, Bryson BD, Butler A, Satija R, Fortune S, Love JC, Shalek AK. Nat Methodspubmed:28192419;  doi:10.1038/nmeth.4179

17. An inter-residue network model to identify mutational-constrained regions on the Ebola coat glycoprotein. Quinlan DS, Raman R, Tharakaraman K, Subramanian V, Del Hierro G, Sasisekharan R. Sci Reppubmed:28397835;  doi:10.1038/srep45886

18. Antimicrobial Peptides: Role in Human Disease and Potential as Immunotherapies. de la Fuente-Nunez C, Silva ON, Lu TK, Franco OL. Pharmacol Ther.pubmed:28435091;  doi:10.1016/j.pharmthera.2017.04.002

19. Meioc maintains an extended meiotic prophase I in mice. Soh YQ, Mikedis MM, Kojima M, Godfrey AK, de Rooij DG, Page DC. PLoS Genet.pubmed:28380054;  doi:10.1371/journal.pgen.1006704

20. Epithelial-to-mesenchymal Transition contributes to Immunosuppression in Breast Carcinomas. Dongre A, Rashidian M, Reinhardt F, Bagnato A, Keckesova Z, Ploegh HL, Weinberg RA.Cancer Respubmed:28428275;  doi:10.1158/0008-5472.CAN-16-3292

21. MeCP2-regulated miRNAs control early human neurogenesis through differential effects on ERK and AKT signaling. Mellios N, Feldman DA, Sheridan SD, Ip JPK, Kwok S, Amoah SK, Rosen B, Rodriguez BA, Crawford B, Swaminathan R, Chou S, Li Y, Ziats M, Ernst C, Jaenisch R, Haggarty SJ, Sur M. Mol Psychiatrypubmed:28439102;  doi:10.1038/mp.2017.86

22. SMARCE1 is required for the invasive progression of in situ cancers. Sokol ES, Feng YX, Jin DX, Tizabi MD, Miller DH, Cohen MA, Sanduja S, Reinhardt F, Pandey J, Superville DA, Jaenisch R, Gupta PB. Proc Natl Acad Sci U S Apubmed:28377514;  doi:10.1073/pnas.1703931114

23. Vesicular stomatitis virus N protein-specific single-domain antibody fragments inhibit replication. Hanke L, Schmidt FI, Knockenhauer KE, Morin B, Whelan SP, Schwartz TU, Ploegh HL.EMBO Reppubmed:28396572;  doi:10.15252/embr.201643764

24. Human knockouts and phenotypic analysis in a cohort with a high rate of consanguinity. Saleheen D, Natarajan P, Armean IM, Zhao W, Rasheed A, Khetarpal SA, Won HH, Karczewski KJ, O'Donnell-Luria AH, Samocha KE, Weisburd B, Gupta N, Zaidi M, Samuel M, Imran A, Abbas S, Majeed F, Ishaq M, Akhtar S, Trindade K, Mucksavage M, Qamar N, Zaman KS, Yaqoob Z, Saghir T, Rizvi SN, Memon A, Hayyat Mallick N, Ishaq M, Rasheed SZ, Memon FU, Mahmood K, Ahmed N, Do R, Krauss RM, MacArthur DG, Gabriel S, Lander ES, Daly MJ, Frossard P, Danesh J, Rader DJ, Kathiresan S. Naturepubmed:28406212;  doi:10.1038/nature22034

25. Improved imputation accuracy of rare and low-frequency variants using population-specific high-coverage WGS-based imputation reference panel. Mitt M, Kals M, Parn K, Gabriel SB, Lander ES, Palotie A, Ripatti S, Morris AP, Metspalu A, Esko T, Magi R, Palta P. Eur J Hum Genetpubmed:28401899;  doi:10.1038/ejhg.2017.51

26. ANGPTL3 Deficiency and Protection Against Coronary Artery Disease. Stitziel NO, Khera AV, Wang X, Bierhals AJ, Vourakis AC, Sperry AE, Natarajan P, Klarin D, Emdin CA, Zekavat SM, Nomura A, Erdmann J, Schunkert H, Samani NJ, Kraus WE, Shah SH, Yu B, Boerwinkle E, Rader DJ, Gupta N, Frossard PM, Rasheed A, Danesh J, Lander ES, Gabriel S, Saleheen D, Musunuru K, Kathiresan S. J Am Coll Cardiolpubmed:28385496;  doi:10.1016/j.jacc.2017.02.030

27. De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Dudchenko O, Batra SS, Omer AD, Nyquist SK, Hoeger M, Durand NC, Shamim MS, Machol I, Lander ES, Aiden AP, Aiden EL. Sciencepubmed:28336562;  doi:10.1126/science.aal3327

28. rAMPing Up Stress Signaling: Protein AMPylation in Metazoans. Truttmann MC, Ploegh HL. Trends Cell Biolpubmed:28433487;  doi:10.1016/j.tcb.2017.03.004

29. A CD47-associated super-enhancer links pro-inflammatory signalling to CD47 upregulation in breast cancer. Betancur PA, Abraham BJ, Yiu YY, Willingham SB, Khameneh F, Zarnegar M, Kuo AH, McKenna K, Kojima Y, Leeper NJ, Ho P, Gip P, Swigut T, Sherwood RI, Clarke MF, Somlo G, Young RA, Weissman IL. Nat Communpubmed:28378740;  doi:10.1038/ncomms14802

30. Dicer loss and recovery induce an oncogenic switch driven by transcriptional activation of the oncofetal Imp1-3 family. JnBaptiste CK, Gurtan AM, Thai KK, Lu V, Bhutkar A, Su MJ, Rotem A, Jacks T, Sharp PA. Genes Devpubmed:28446596;  doi:10.1101/gad.296301.117

31. Unclogging sickle cell anaemia. Li H, Lodish H. Nat Rev Mol Cell Biolpubmed:28248321;  doi:10.1038/nrm.2017.17

32. Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors. Villani AC, Satija R, Reynolds G, Sarkizova S, Shekhar K, Fletcher J, Griesbeck M, Butler A, Zheng S, Lazo S, Jardine L, Dixon D, Stephenson E, Nilsson E, Grundberg I, McDonald D, Filby A, Li W, De Jager PL, Rozenblatt-Rosen O, Lane AA, Haniffa M, Regev A, Hacohen N. Science.pubmed:28428369;  doi:10.1126/science.aah4573

33. Nucleic acid detection with CRISPR-Cas13a/C2c2. Gootenberg JS, Abudayyeh OO, Lee JW, Essletzbichler P, Dy AJ, Joung J, Verdine V, Donghia N, Daringer NM, Freije CA, Myhrvold C, Bhattacharyya RP, Livny J, Regev A, Koonin EV, Hung DT, Sabeti PC, Collins JJ, Zhang F. Sciencepubmed:28408723;  doi:10.1126/science.aam9321

34. Critical role of IRF1 and BATF in forming chromatin landscape during type 1 regulatory cell differentiation. Karwacz K, Miraldi ER, Pokrovskii M, Madi A, Yosef N, Wortman I, Chen X, Watters A, Carriero N, Awasthi A, Regev A, Bonneau R, Littman D, Kuchroo VK. Nat Immunolpubmed:28166218;  doi:10.1038/ni.3683

35. Aneuploidy Causes Non-genetic Individuality. Beach RR, Ricci-Tam C, Brennan CM, Moomau CA, Hsu PH, Hua B, Silberman RE, Springer M, Amon A. Cell.pubmed:28388408;  doi:10.1016/j.cell.2017.03.021

36. Combining DNP NMR with segmental and specific labeling to study a yeast prion protein strain that is not parallel in-register. Frederick KK, Michaelis VK, Caporini MA, Andreas LB, Debelouchina GT, Griffin RG, Lindquist S. Proc Natl Acad Sci U S Apubmed:28330994;  doi:10.1073/pnas.1619051114

37. PIK3CA mutant tumors depend on oxoglutarate dehydrogenase. Ilic N, Birsoy K, Aguirre AJ, Kory N, Pacold ME, Singh S, Moody SE, DeAngelo JD, Spardy NA, Freinkman E, Weir BA, Tsherniak A, Cowley GS, Root DE, Asara JM, Vazquez F, Widlund HR, Sabatini DM, Hahn WC. Proc Natl Acad Sci U S Apubmed:28396387;  doi:10.1073/pnas.1617922114

38. Physiologic Medium Rewires Cellular Metabolism and Reveals Uric Acid as an Endogenous Inhibitor of UMP Synthase. Cantor JR, Abu-Remaileh M, Kanarek N, Freinkman E, Gao X, Louissaint AJr, Lewis CA, Sabatini DM. Cellpubmed:28388410;  doi:10.1016/j.cell.2017.03.023

39. Pyruvate kinase M2 activation may protect against the progression of diabetic glomerular pathology and mitochondrial dysfunction. Qi W, Keenan HA, Li Q, Ishikado A, Kannt A, Sadowski T, Yorek MA, Wu IH, Lockhart S, Coppey LJ, Pfenninger A, Liew CW, Qiang G, Burkart AM, Hastings S, Pober D, Cahill C, Niewczas MA, Israelsen WJ, Tinsley L, Stillman IE, Amenta PS, Feener EP, Vander Heiden MG, Stanton RC, King GL. Nat Medpubmed:28436957;  doi:10.1038/nm.4328

40. A subset of platinum-containing chemotherapeutic agents kills cells by inducing ribosome biogenesis stress. Bruno PM, Liu Y, Park GY, Murai J, Koch CE, Eisen TJ, Pritchard JR, Pommier Y, Lippard SJ, Hemann MT. Nat Medpubmed:28263311;  doi:10.1038/nm.4291

41. Highlight: A new way to block the development of asthma from dust mites. Yaffe M. Sci Signalpubmed:28420752;  doi:10.1126/scisignal.aan3693

42. EMT, CSCs, and drug resistance: the mechanistic link and clinical implications. Shibue T, Weinberg RA. Nat Rev Clin Oncolpubmed:28397828;  doi:10.1038/nrclinonc.2017.44