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 2018

Return to Progress index

1. Human cerebral organoids reveal deficits in neurogenesis and neuronal migration in MeCP2-deficient neural progenitors. 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 Psychiatry. pubmed:29565043;  doi:10.1038/mp.2018.5

2. 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 Chem. pubmed:29487130;  doi:10.1074/jbc.RA117.000731

3. 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 Psychiatry. pubmed:28439102;  doi:10.1038/mp.2017.86

4. Nephronectin is Correlated with Poor Prognosis in Breast Cancer and Promotes Metastasis via its Integrin-Binding Motifs. Steigedal TS, Toraskar J, Redvers RP, Valla M, Magnussen SN, Bofin AM, Opdahl S, Lundgren S, Eckhardt BL, Lamar JM, Doherty J, Hynes RO, Anderson RL, Svineng G. Neoplasia. pubmed:29539586;  doi:10.1016/j.neo.2018.02.008

5. The systemic response to surgery triggers the outgrowth of distant immune-controlled tumors in mouse models of dormancy. Krall JA, Reinhardt F, Mercury OA, Pattabiraman DR, Brooks MW, Dougan M, Lambert AW, Bierie B, Ploegh HL, Dougan SK, Weinberg RA. Sci Transl Med. pubmed:29643230;  doi:10.1126/scitranslmed.aan3464

6. Cost-effective high-throughput single-haplotype iterative mapping and sequencing for complex genomic structures. Bellott DW, Cho TJ, Hughes JF, Skaletsky H, Page DC. Nat Protoc. pubmed:29565902;  doi:10.1038/nprot.2018.019

7. Genetic editing of colonic organoids provides a molecularly distinct and orthotopic preclinical model of serrated carcinogenesis. Lannagan TRM, Lee YK, Wang T, Roper J, Bettington ML, Fennell L, Vrbanac L, Jonavicius L, Somashekar R, Gieniec K, Yang M, Ng JQ, Suzuki N, Ichinose M, Wright JA, Kobayashi H, Putoczki TL, Hayakawa Y, Leedham SJ, Abud HE, Yilmaz OH, Marker J, Klebe S, Wirapati P, Mukherjee S, Tejpar S, Leggett BA, Whitehall VLJ, Worthley DL, Woods SL. Gut. pubmed:29666172;  doi:10.1136/gutjnl-2017-315920

8. Comprehensive Identification and Spatial Mapping of Habenular Neuronal Types Using Single-Cell RNA-Seq. Pandey S, Shekhar K, Regev A, Schier AF. Curr Biol. pubmed:29576475;  doi:10.1016/j.cub.2018.02.040

9. Differences in Nanoparticle Uptake in Transplanted and Autochthonous Models of Pancreatic Cancer. Tao Z, Muzumdar MD, Detappe A, Huang X, Xu E, Yu Y, Mouhieddine TH, Song H, Jacks T, Ghoroghchian PP. Nano Lett. pubmed:29533667;  doi:10.1021/acs.nanolett.7b04043

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

11. Architecture of the human GATOR1 and GATOR1-Rag GTPases complexes. Shen K, Huang RK, Brignole EJ, Condon KJ, Valenstein ML, Chantranupong L, Bomaliyamu A, Choe A, Hong C, Yu Z, Sabatini DM. Nature. pubmed:29590090;  doi:10.1038/nature26158

12. Establishment of human pluripotent stem cell-derived pancreatic beta-like cells in the mouse pancreas. Ma H, Wert KJ, Shvartsman D, Melton DA, Jaenisch R. Proc Natl Acad Sci U S A. pubmed:29599125;  doi:10.1073/pnas.1702059115

13. MitoCPR-A surveillance pathway that protects mitochondria in response to protein import stress. Weidberg H, Amon A. Science. pubmed:29650645;  doi:10.1126/science.aan4146

14. Robustness encoded across essential and accessory replicons of the ecologically versatile bacterium Sinorhizobium meliloti. diCenzo GC, Benedict AB, Fondi M, Walker GC, Finan TM, Mengoni A, Griffitts JS. PLoS Genet. pubmed:29672509;  doi:10.1371/journal.pgen.1007357

15. Developmental and oncogenic programs in H3K27M gliomas dissected by single-cell RNA-seq. Filbin MG, Tirosh I, Hovestadt V, Shaw ML, Escalante LE, Mathewson ND, Neftel C, Frank N, Pelton K, Hebert CM, Haberler C, Yizhak K, Gojo J, Egervari K, Mount C, van Galen P, Bonal DM, Nguyen QD, Beck A, Sinai C, Czech T, Dorfer C, Goumnerova L, Lavarino C, Carcaboso AM, Mora J, Mylvaganam R, Luo CC, Peyrl A, Popovic M, Azizi A, Batchelor TT, Frosch MP, Martinez-Lage M, Kieran MW, Bandopadhayay P, Beroukhim R, Fritsch G, Getz G, Rozenblatt-Rosen O, Wucherpfennig KW, Louis DN, Monje M, Slavc I, Ligon KL, Golub TR, Regev A, Bernstein BE, Suva ML. Science. pubmed:29674595;  doi:10.1126/science.aao4750

16. A C elegans protein with a PRDM9-like SET domain localizes to chromatin-associated foci and promotes spermatocyte gene expression, sperm production and fertility. Engert CG, Droste R, van Oudenaarden A, Horvitz HR. PLoS Genet. pubmed:29702639;  doi:10.1371/journal.pgen.1007295

17. Transcriptional Dysregulation of MYC Reveals Common Enhancer-Docking Mechanism. Schuijers J, Manteiga JC, Weintraub AS, Day DS, Zamudio AV, Hnisz D, Lee TI, Young RA. Cell Rep. pubmed:29641996;  doi:10.1016/j.celrep.2018.03.056

18. Amide-forming chemical ligation via O-acyl hydroxamic acids. Dunkelmann DL, Hirata Y, Totaro KA, Cohen DT, Zhang C, Gates ZP, Pentelute BL. Proc Natl Acad Sci U S A. pubmed:29581295;  doi:10.1073/pnas.1718356115

19. Perfluoroaryl Bicyclic Cell-Penetrating Peptides for Delivery of Antisense Oligonucleotides. Wolfe JM, Fadzen CM, Holden RL, Yao M, Hanson GJ, Pentelute BL. Angew Chem Int Ed Engl. pubmed:29479836;  doi:10.1002/anie.201801167

20. Machine Learning To Predict Cell-Penetrating Peptides for Antisense Delivery. Wolfe JM, Fadzen CM, Choo ZN, Holden RL, Yao M, Hanson GJ, Pentelute BL. ACS Cent Sci. pubmed:29721534;  doi:10.1021/acscentsci.8b00098

21. Designing Well-Structured Cyclic Pentapeptides Based on Sequence-Structure Relationships. Slough DP, McHugh SM, Cummings AE, Dai P, Pentelute BL, Kritzer JA, Lin YS. J Phys Chem B. pubmed:29589926;  doi:10.1021/acs.jpcb.8b01747

22. Scalable Synthesis of Multivalent Macromonomers for ROMP. Nguyen HV, Gallagher NM, Vohidov F, Jiang Y, Kawamoto K, Zhang H, Park JV, Huang Z, Ottaviani MF, Rajca A, Johnson JA. ACS Macro Lett. pubmed:30271675;  doi:10.1021/acsmacrolett.8b00201

23. In silico optimization of a guava antimicrobial peptide enables combinatorial exploration for peptide design. Porto WF, Irazazabal L, Alves ESF, Ribeiro SM, Matos CO, Pires AS, Fensterseifer ICM, Miranda VJ, Haney EF, Humblot V, Torres MDT, Hancock REW, Liao LM, Ladram A, Lu TK, de la Fuente-Nunez C, Franco OL. Nat Commun. pubmed:29662055;  doi:10.1038/s41467-018-03746-3

24. 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 Biol. pubmed:29483642;  doi:10.1038/s41589-018-0004-9

25. Exploiting glycan topography for computational design of Env glycoprotein antigenicity. Yu WH, Zhao P, Draghi M, Arevalo C, Karsten CB, Suscovich TJ, Gunn B, Streeck H, Brass AL, Tiemeyer M, Seaman M, Mascola JR, Wells L, Lauffenburger DA, Alter G. PLoS Comput Biol. pubmed:29677181;  doi:10.1371/journal.pcbi.1006093

26. 3D matrix embedding inhibits cycloheximide-mediated sensitization to TNF-alpha-induced apoptosis of human endothelial cells. Saemisch M, Nickmann M, Riesinger L, Edelman ER, Methe H. J Tissue Eng Regen Med. pubmed:29131527;  doi:10.1002/term.2609

27. 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 Chem. pubmed:29465986;  doi:10.1021/acs.bioconjchem.7b00777

28. Directed evolution of broadly crossreactive chemokine-blocking antibodies efficacious in arthritis. Angelini A, Miyabe Y, Newsted D, Kwan BH, Miyabe C, Kelly RL, Jamy MN, Luster AD, Wittrup KD. Nat Commun. pubmed:29654232;  doi:10.1038/s41467-018-03687-x

29. Increased expression and modulated regulatory activity of co-inhibitory receptors PD-1, TIGIT and TIM-3 in lymphocytes of systemic sclerosis patients. Fleury M, Belkina AC, Proctor EA, Zammitti C, Simms RW, Lauffenburger DA, Snyder-Cappione JE, Lafyatis R, Dooms H. Arthritis Rheumatol. pubmed:29245183;  doi:10.1002/art.40399

30. Personalized RNA Medicine for Pancreatic Cancer. Gilles ME, Hao L, Huang L, Rupaimoole R, Lopez-Casas PP, Pulver E, Jeong JC, Muthuswamy SK, Hidalgo M, Bhatia SN, Slack FJ. Clin Cancer Res. pubmed:29330203;  doi:10.1158/1078-0432.CCR-17-2733

31. Optimizing Glutaraldehyde-Fixed Tissue Heart Valves with Chondroitin Sulfate Hydrogel for Endothelialization and Shielding against Deterioration. Lopez-Moya M, Melgar-Lesmes P, Kolandaivelu K, de la Torre Hernandez JM, Edelman ER, Balcells M. Biomacromolecules. pubmed:29539266;  doi:10.1021/acs.biomac.8b00077

32. 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 Biomech. pubmed:29452756;  doi:10.1016/j.jbiomech.2018.01.044

33. A model of dormant-emergent metastatic breast cancer progression enabling exploration of biomarker signatures. Clark AM, Kumar M, Wheeler S, Young C, Venkataramanan R, Stolz D, Griffith L, Lauffenburger DA, Wells A. Mol Cell Proteomics. pubmed:29353230;  doi:10.1074/mcp.RA117.000370

34. Convergence for Translation: Drug-Delivery Research in Multidisciplinary Teams. Traverso G, Kirtane AR, Schoellhammer CM, Langer R. Angew Chem Int Ed Engl. pubmed:29520902;  doi:10.1002/anie.201712512

35. Whole-exome sequencing of cell-free DNA and circulating tumor cells in multiple myeloma. Manier S, Park J, Capelletti M, Bustoros M, Freeman SS, Ha G, Rhoades J, Liu CJ, Huynh D, Reed SC, Gydush G, Salem KZ, Rotem D, Freymond C, Yosef A, Perilla-Glen A, Garderet L, Van Allen EM, Kumar S, Love JC, Getz G, Adalsteinsson VA, Ghobrial IM. Nat Commun. pubmed:29703982;  doi:10.1038/s41467-018-04001-5

36. Targeting minimal residual disease: a path to cure?. Luskin MR, Murakami MA, Manalis SR, Weinstock DM. Nat Rev Cancer. pubmed:29376520;  doi:10.1038/nrc.2017.125