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 2020

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1. Intravital imaging of mouse embryos. Huang Q, Cohen MA, Alsina FC, Devlin G, Garrett A, McKey J, Havlik P, Rakhilin N, Wang E, Xiang K, Mathews P, Wang L, Bock C, Ruthig V, Wang Y, Negrete M, Wong CW, Murthy PKL, Zhang S, Daniel AR, Kirsch DG, Kang Y, Capel B, Asokan A, Silver DL, Jaenisch R, Shen X. Science. pubmed:32273467;  doi:10.1126/science.aba0210

2. Tissue Plasminogen Activator (tPA) Treatment for COVID-19 Associated Acute Respiratory Distress Syndrome (ARDS): A Case Series. Wang J, Hajizadeh N, Moore EE, McIntyre RC, Moore PK, Veress LA, Yaffe MB, Moore HB, Barrett CD. J Thromb Haemost. pubmed:32267998;  doi:10.1111/jth.14828

3. Urinary detection of lung cancer in mice via noninvasive pulmonary protease profiling. Kirkpatrick JD, Warren AD, Soleimany AP, Westcott PMK, Voog JC, Martin-Alonso C, Fleming HE, Tammela T, Jacks T, Bhatia SN. Sci Transl Med. pubmed:32238573;  doi:10.1126/scitranslmed.aaw0262

4. RNA helicase DDX21 mediates nucleotide stress responses in neural crest and melanoma cells. Santoriello C, Sporrij A, Yang S, Flynn RA, Henriques T, Dorjsuren B, Custo Greig E, McCall W, Stanhope ME, Fazio M, Superdock M, Lichtig A, Adatto I, Abraham BJ, Kalocsay M, Jurynec M, Zhou Y, Adelman K, Calo E, Zon LI. Nat Cell Biol. pubmed:32231306;  doi:10.1038/s41556-020-0493-0

5. Towards a treatment for genetic prion disease: trials and biomarkers. Vallabh SM, Minikel EV, Schreiber SL, Lander ES. Lancet Neurol. pubmed:32199098;  doi:10.1016/S1474-4422(19)30403-X

6. Targeting the cyclin-dependent kinase 5 in metastatic melanoma. Sharma S, Zhang T, Michowski W, Rebecca VW, Xiao M, Ferretti R, Suski JM, Bronson RT, Paulo JA, Frederick D, Fassl A, Boland GM, Geng Y, Lees JA, Medema RH, Herlyn M, Gygi SP, Sicinski P. Proc Natl Acad Sci U S A. pubmed:32193336;  doi:10.1073/pnas.1912617117

7. Imprinted Maternally Expressed microRNAs Antagonize Paternally Driven Gene Programs in Neurons. Whipple AJ, Breton-Provencher V, Jacobs HN, Chitta UK, Sur M, Sharp PA. Mol Cell. pubmed:32032531;  doi:10.1016/j.molcel.2020.01.020

8. Formation of Human Neuroblastoma in Mouse-Human Neural Crest Chimeras. Cohen MA, Zhang S, Sengupta S, Ma H, Bell GW, Horton B, Sharma B, George RE, Spranger S, Jaenisch R. Cell Stem Cell. pubmed:32142683;  doi:10.1016/j.stem.2020.02.001

9. Spindle pole bodies function as signal amplifiers in the Mitotic Exit Network. Campbell IW, Zhou X, Amon A. Mol Biol Cell. pubmed:32074005;  doi:10.1091/mbc.E19-10-0584

10. Cancer Cell-Derived Matrisome Proteins Promote Metastasis in Pancreatic Ductal Adenocarcinoma. Tian C, Ohlund D, Rickelt S, Lidstrom T, Huang Y, Hao L, Zhao RT, Franklin O, Bhatia SN, Tuveson DA, Hynes RO. Cancer Res. pubmed:32029550;  doi:10.1158/0008-5472.CAN-19-2578

11. Proteomic Profiling of the ECM of Xenograft Breast Cancer Metastases in Different Organs Reveals Distinct Metastatic Niches. Hebert JD, Myers SA, Naba A, Abbruzzese G, Lamar JM, Carr SA, Hynes RO. Cancer Res. pubmed:32019869;  doi:10.1158/0008-5472.CAN-19-2961

12. TGF-beta-induced epigenetic deregulation of SOCS3 facilitates STAT3 signaling to promote fibrosis. Dees C, Potter S, Zhang Y, Bergmann C, Zhou X, Luber M, Wohlfahrt T, Karouzakis E, Ramming A, Gelse K, Yoshimura A, Jaenisch R, Distler O, Schett G, Distler JH. J Clin Invest. pubmed:31990678;  doi:10.1172/JCI122462

13. Influence of tranexamic acid on the complement system in trauma. Barrett CD, Yaffe MB. ANZ J Surg. pubmed:32339419;  doi:10.1111/ans.15538

14. Emerging Mechanisms by which EMT Programs Control Stemness. Wilson MM, Weinberg RA, Lees JA, Guen VJ. Trends Cancer. pubmed:32312682;  doi:10.1016/j.trecan.2020.03.011

15. Salvage use of tissue plasminogen activator (tPA) in the setting of acute respiratory distress syndrome (ARDS) due to COVID-19 in the USA: a Markov decision analysis. Choudhury R, Barrett CD, Moore HB, Moore EE, McIntyre RC, Moore PK, Talmor DS, Nydam TL, Yaffe MB. World J Emerg Surg. pubmed:32312290;  doi:10.1186/s13017-020-00305-4

16. The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution. Rozenblatt-Rosen O, Regev A, Oberdoerffer P, Nawy T, Hupalowska A, Rood JE, Ashenberg O, Cerami E, Coffey RJ, Demir E, Ding L, Esplin ED, Ford JM, Goecks J, Ghosh S, Gray JW, Guinney J, Hanlon SE, Hughes SK, Hwang ES, Iacobuzio-Donahue CA, Jane-Valbuena J, Johnson BE, Lau KS, Lively T, Mazzilli SA, Pe'er D, Santagata S, Shalek AK, Schapiro D, Snyder MP, Sorger PK, Spira AE, Srivastava S, Tan K, West RB, Williams EH. Cell. pubmed:32302568;  doi:10.1016/j.cell.2020.03.053

17. Region-Specific Proteome Changes of the Intestinal Epithelium during Aging and Dietary Restriction. Gebert N, Cheng CW, Kirkpatrick JM, Di Fraia D, Yun J, Schadel P, Pace S, Garside GB, Werz O, Rudolph KL, Jasper H, Yilmaz OH, Ori A. Cell Rep. pubmed:32348758;  doi:10.1016/j.celrep.2020.107565

18. ISTH interim guidance on recognition and management of coagulopathy in COVID-19: A comment. Barrett CD, Moore HB, Yaffe MB, Moore EE. J Thromb Haemost. pubmed:32302462;  doi:10.1111/jth.14860

19. Insights from immuno-oncology: the Society for Immunotherapy of Cancer Statement on access to IL-6-targeting therapies for COVID-19. Ascierto PA, Fox BA, Urba WJ, Anderson AC, Atkins MB, Borden EC, Brahmer JR, Butterfield LH, Cesano A, Chen DC, de Gruijl TD, Dillman RO, Drake CG, Emens LA, Gajewski TF, Gulley JL, Stephen Hodi FJ, Hwu P, Kaufman D, Kaufman HL, Lotze MT, McNeel DG, Margolin KM, Marincola FM, Mastrangelo MJ, Maus MV, Parkinson DR, Romero PJ, Sondel PM, Spranger S, Sznol M, Weiner GJ, Wigginton JM, Weber JS. J Immunother Cancer. pubmed:32300051;  doi:10.1136/jitc-2020-000878

20. Integrated single-cell analysis of multicellular immune dynamics during hyperacute HIV-1 infection. Kazer SW, Aicher TP, Muema DM, Carroll SL, Ordovas-Montanes J, Miao VN, Tu AA, Ziegler CGK, Nyquist SK, Wong EB, Ismail N, Dong M, Moodley A, Berger B, Love JC, Dong KL, Leslie A, Ndhlovu ZM, Ndung'u T, Walker BD, Shalek AK. Nat Med. pubmed:32251406;  doi:10.1038/s41591-020-0799-2

21. Efficient flow synthesis of human antimicrobial peptides. Albin JS, Pentelute BL. Aust J Chem. pubmed:32431323;  doi:10.1071/CH20043

22. Design of a Multiplexed Analyte Biosensor using Digital Barcoded Particles and Impedance Spectroscopy. Prakash S, Ashley BK, Doyle PS, Hassan U. Sci Rep. pubmed:32273525;  doi:10.1038/s41598-020-62894-z

23. Dynamic Modulation of Device-Arterial Coupling to Determine Cardiac Output and Vascular Resistance. Keller SP, Chang BY, Tan Q, Zhang Z, El Katerji A, Edelman ER. Ann Biomed Eng. pubmed:32285344;  doi:10.1007/s10439-020-02510-3

24. Nanoscale imaging of clinical specimens using conventional and rapid-expansion pathology. Bucur O, Fu F, Calderon M, Mylvaganam GH, Ly NL, Day J, Watkin S, Walker BD, Boyden ES, Zhao Y. Nat Protoc. pubmed:32238952;  doi:10.1038/s41596-020-0300-1

25. Current and Future Roles of Artificial Intelligence in Medicinal Chemistry Synthesis. Struble TJ, Alvarez JC, Brown SP, Chytil M, Cisar J, DesJarlais RL, Engkvist O, Frank SA, Greve DR, Griffin DJ, Hou X, Johannes JW, Kreatsoulas C, Lahue B, Mathea M, Mogk G, Nicolaou CA, Palmer AD, Price DJ, Robinson RI, Salentin S, Xing L, Jaakkola T, Green WH, Barzilay R, Coley CW, Jensen KF. J Med Chem. pubmed:32243158;  doi:10.1021/acs.jmedchem.9b02120

26. Suspended Nanochannel Resonator Arrays with Piezoresistive Sensors for High-Throughput Weighing of Nanoparticles in Solution. Gagino M, Katsikis G, Olcum S, Virot L, Cochet M, Thuaire A, Manalis SR, Agache V. ACS Sens. pubmed:32233476;  doi:10.1021/acssensors.0c00394

27. Tuning Material Properties of Nanoemulsion Gels by Sequentially Screening Electrostatic Repulsions and Then Thermally Inducing Droplet Bridging. Cheng LC, Kuei Vehusheia SL, Doyle PS. Langmuir. pubmed:32216359;  doi:10.1021/acs.langmuir.0c00199

28. Hydrogel-Based Colorimetric Assay for Multiplexed MicroRNA Detection in a Microfluidic Device. Lee H, Lee J, Lee SG, Doyle PS. Anal Chem. pubmed:32207967;  doi:10.1021/acs.analchem.9b05043

29. The Vaginal Microbiome as a Tool to Predict rASRM Stage of Disease in Endometriosis: a Pilot Study. Perrotta AR, Borrelli GM, Martins CO, Kallas EG, Sanabani SS, Griffith LG, Alm EJ, Abrao MS. Reprod Sci. pubmed:32046455;  doi:10.1007/s43032-019-00113-5

30. Modeling Nanocarrier Transport across a 3D In Vitro Human Blood-Brain-Barrier Microvasculature. Lee SWL, Campisi M, Osaki T, Possenti L, Mattu C, Adriani G, Kamm RD, Chiono V. Adv Healthc Mater. pubmed:32125776;  doi:10.1002/adhm.201901486

31. In-depth structural characterization of pentosan polysulfate sodium complex drug using orthogonal analytical tools. Alekseeva A, Raman R, Eisele G, Clark T, Fisher A, Lee SL, Jiang X, Torri G, Sasisekharan R, Bertini S. Carbohydr Polym. pubmed:32070534;  doi:10.1016/j.carbpol.2020.115913

32. Downregulation of the Arg/N-degron Pathway Sensitizes Cancer Cells to Chemotherapy In Vivo. Leboeuf D, Abakumova T, Prikazchikova T, Rhym L, Anderson DG, Zatsepin TS, Piatkov KI. Mol Ther. pubmed:32087767;  doi:10.1016/j.ymthe.2020.01.021

33. Chemical modifications of adenine base editor mRNA and guide RNA expand its application scope. Jiang T, Henderson JM, Coote K, Cheng Y, Valley HC, Zhang XO, Wang Q, Rhym LH, Cao Y, Newby GA, Bihler H, Mense M, Weng Z, Anderson DG, McCaffrey AP, Liu DR, Xue W. Nat Commun. pubmed:32332735;  doi:10.1038/s41467-020-15892-8

34. Engineering Intracellular Protein Sensors in Mammalian Cells. Duhkinova M, Crina C, Weiss R, Siciliano V. J Vis Exp. pubmed:32420982;  doi:10.3791/60878

35. A Deep Learning Approach to Antibiotic Discovery. Stokes JM, Yang K, Swanson K, Jin W, Cubillos-Ruiz A, Donghia NM, MacNair CR, French S, Carfrae LA, Bloom-Ackermann Z, Tran VM, Chiappino-Pepe A, Badran AH, Andrews IW, Chory EJ, Church GM, Brown ED, Jaakkola TS, Barzilay R, Collins JJ. Cell. pubmed:32302574;  doi:10.1016/j.cell.2020.04.001