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: May 2020

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1. Cell atlas of aqueous humor outflow pathways in eyes of humans and four model species provides insight into glaucoma pathogenesis. van Zyl T, Yan W, McAdams A, Peng YR, Shekhar K, Regev A, Juric D, Sanes JR. Proc Natl Acad Sci U S A. pubmed:32341164;  doi:10.1073/pnas.2001250117

2. Efficient prevalence estimation and infected sample identification with group testing for SARS-CoV-2. Cleary B, Hay JA, Blumenstiel B, Gabriel S, Regev A, Mina MJ. medRxiv. pubmed:32511487;  doi:10.1101/2020.05.01.20086801

3. A Nutrient-Sensing Transition at Birth Triggers Glucose-Responsive Insulin Secretion. Helman A, Cangelosi AL, Davis JC, Pham Q, Rothman A, Faust AL, Straubhaar JR, Sabatini DM, Melton DA. Cell Metab. pubmed:32375022;  doi:10.1016/j.cmet.2020.04.004

4. Fibrinolytic therapy for refractory COVID-19 acute respiratory distress syndrome: Scientific rationale and review. Barrett CD, Moore HB, Moore EE, McIntyre RC, Moore PK, Burke J, Hua F, Apgar J, Talmor DS, Sauaia A, Liptzin DR, Veress LA, Yaffe MB. Res Pract Thromb Haemost. pubmed:32542213;  doi:10.1002/rth2.12357

5. Quantitative analysis of Y-Chromosome gene expression across 36 human tissues. Godfrey AK, Naqvi S, Chmatal L, Chick JM, Mitchell RN, Gygi SP, Skaletsky H, Page DC. Genome Res. pubmed:32461223;  doi:10.1101/gr.261248.120

6. ATRAID regulates the action of nitrogen-containing bisphosphonates on bone. Surface LE, Burrow DT, Li J, Park J, Kumar S, Lyu C, Song N, Yu Z, Rajagopal A, Bae Y, Lee BH, Mumm S, Gu CC, Baker JC, Mohseni M, Sum M, Huskey M, Duan S, Bijanki VN, Civitelli R, Gardner MJ, McAndrew CM, Ricci WM, Gurnett CA, Diemer K, Wan F, Costantino CL, Shannon KM, Raje N, Dodson TB, Haber DA, Carette JE, Varadarajan M, Brummelkamp TR, Birsoy K, Sabatini DM, Haller G, Peterson TR. Sci Transl Med. pubmed:32434850;  doi:10.1126/scitranslmed.aav9166

7. Rescue Therapy for Severe COVID-19 Associated Acute Respiratory Distress Syndrome (ARDS) with Tissue Plasminogen Activator (tPA): A Case Series. Barrett CD, Oren-Grinberg A, Chao E, Moraco AH, Martin MJ, Reddy SH, Ilg AM, Jhunjhunwala R, Uribe M, Moore HB, Moore EE, Baedorf-Kassis EN, Krajewski ML, Talmor DS, Shaefi S, Yaffe MB. J Trauma Acute Care Surg. pubmed:32427773;  doi:10.1097/TA.0000000000002786

8. A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors. Slyper M, Porter CBM, Ashenberg O, Waldman J, Drokhlyansky E, Wakiro I, Smillie C, Smith-Rosario G, Wu J, Dionne D, Vigneau S, Jane-Valbuena J, Tickle TL, Napolitano S, Su MJ, Patel AG, Karlstrom A, Gritsch S, Nomura M, Waghray A, Gohil SH, Tsankov AM, Jerby-Arnon L, Cohen O, Klughammer J, Rosen Y, Gould J, Nguyen L, Hofree M, Tramontozzi PJ, Li B, Wu CJ, Izar B, Haq R, Hodi FS, Yoon CH, Hata AN, Baker SJ, Suva ML, Bueno R, Stover EH, Clay MR, Dyer MA, Collins NB, Matulonis UA, Wagle N, Johnson BE, Rotem A, Rozenblatt-Rosen O, Regev A. Nat Med. pubmed:32405060;  doi:10.1038/s41591-020-0844-1

9. A PEROXO-Tag Enables Rapid Isolation of Peroxisomes from Human Cells. Ray GJ, Boydston EA, Shortt E, Wyant GA, Lourido S, Chen WW, Sabatini DM. iScience. pubmed:32417403;  doi:10.1016/j.isci.2020.101109

10. Coagulopathy signature precedes and predicts severity of end-organ heat stroke pathology in a mouse model. Proctor EA, Dineen SM, Van Nostrand SC, Kuhn MK, Barrett CD, Brubaker DK, Yaffe MB, Lauffenburger DA, Leon LR. J Thromb Haemost. pubmed:32367690;  doi:10.1111/jth.14875

11. Regenerative potential of prostate luminal cells revealed by single-cell analysis. Karthaus WR, Hofree M, Choi D, Linton EL, Turkekul M, Bejnood A, Carver B, Gopalan A, Abida W, Laudone V, Biton M, Chaudhary O, Xu T, Masilionis I, Manova K, Mazutis L, Pe'er D, Regev A, Sawyers CL. Science. pubmed:32355025;  doi:10.1126/science.aay0267

12. Endocrine-Exocrine Signaling Drives Obesity-Associated Pancreatic Ductal Adenocarcinoma. Chung KM, Singh J, Lawres L, Dorans KJ, Garcia C, Burkhardt DB, Robbins R, Bhutkar A, Cardone R, Zhao X, Babic A, Vayrynen SA, Dias Costa A, Nowak JA, Chang DT, Dunne RF, Hezel AF, Koong AC, Wilhelm JJ, Bellin MD, Nylander V, Gloyn AL, McCarthy MI, Kibbey RG, Krishnaswamy S, Wolpin BM, Jacks T, Fuchs CS, Muzumdar MD. Cell. pubmed:32304665;  doi:10.1016/j.cell.2020.03.062

13. A structural variation reference for medical and population genetics. Collins RL, Brand H, Karczewski KJ, Zhao X, Alfoldi J, Francioli LC, Khera AV, Lowther C, Gauthier LD, Wang H, Watts NA, Solomonson M, O'Donnell-Luria A, Baumann A, Munshi R, Walker M, Whelan CW, Huang Y, Brookings T, Sharpe T, Stone MR, Valkanas E, Fu J, Tiao G, Laricchia KM, Ruano-Rubio V, Stevens C, Gupta N, Cusick C, Margolin L, Taylor KD, Lin HJ, Rich SS, Post WS, Chen YI, Rotter JI, Nusbaum C, Philippakis A, Lander E, Gabriel S, Neale BM, Kathiresan S, Daly MJ, Banks E, MacArthur DG, Talkowski ME. Nature. pubmed:32461652;  doi:10.1038/s41586-020-2287-8

14. SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues. Ziegler CGK, Allon SJ, Nyquist SK, Mbano IM, Miao VN, Tzouanas CN, Cao Y, Yousif AS, Bals J, Hauser BM, Feldman J, Muus C, Wadsworth MH2nd, Kazer SW, Hughes TK, Doran B, Gatter GJ, Vukovic M, Taliaferro F, Mead BE, Guo Z, Wang JP, Gras D, Plaisant M, Ansari M, Angelidis I, Adler H, Sucre JMS, Taylor CJ, Lin B, Waghray A, Mitsialis V, Dwyer DF, Buchheit KM, Boyce JA, Barrett NA, Laidlaw TM, Carroll SL, Colonna L, Tkachev V, Peterson CW, Yu A, Zheng HB, Gideon HP, Winchell CG, Lin PL, Bingle CD, Snapper SB, Kropski JA, Theis FJ, Schiller HB, Zaragosi LE, Barbry P, Leslie A, Kiem HP, Flynn JL, Fortune SM, Berger B, Finberg RW, Kean LS, Garber M, Schmidt AG, Lingwood D, Shalek AK, Ordovas-Montanes J. Cell. pubmed:32413319;  doi:10.1016/j.cell.2020.04.035

15. Anthrax Protective Antigen Retargeted with Single-Chain Variable Fragments Delivers Enzymes to Pancreatic Cancer Cells. Loftis AR, Santos MS, Truex NL, Biancucci M, Satchell KJF, Pentelute BL. Chembiochem. pubmed:32369652;  doi:10.1002/cbic.202000201

16. Protein-Protein Cross-Coupling via Palladium-Protein Oxidative Addition Complexes from Cysteine Residues. Dhanjee HH, Saebi A, Buslov I, Loftis AR, Buchwald SL, Pentelute BL. J Am Chem Soc. pubmed:32364380;  doi:10.1021/jacs.0c03143

17. Single-Cell Analyses of Colon and Blood Reveal Distinct Immune Cell Signatures of Ulcerative Colitis and Crohn's Disease. Mitsialis V, Wall S, Liu P, Ordovas-Montanes J, Parmet T, Vukovic M, Spencer D, Field M, McCourt C, Toothaker J, Bousvaros A, Shalek AK, Kean L, Horwitz B, Goldsmith J, Tseng G, Snapper SB, Konnikova L. Gastroenterology. pubmed:32428507;  doi:10.1053/j.gastro.2020.04.074

18. Synergistic lipid compositions for albumin receptor mediated delivery of mRNA to the liver. Miao L, Lin J, Huang Y, Li L, Delcassian D, Ge Y, Shi Y, Anderson DG. Nat Commun. pubmed:32415122;  doi:10.1038/s41467-020-16248-y

19. Activity-Based Diagnostics: An Emerging Paradigm for Disease Detection and Monitoring. Soleimany AP, Bhatia SN. Trends Mol Med. pubmed:32359477;  doi:10.1016/j.molmed.2020.01.013

20. Transcription Factor Inhibition: Lessons Learned and Emerging Targets. Chen A, Koehler AN. Trends Mol Med. pubmed:32359481;  doi:10.1016/j.molmed.2020.01.004

21. Robotically handled whole-tissue culture system for the screening of oral drug formulations. von Erlach T, Saxton S, Shi Y, Minahan D, Reker D, Javid F, Lee YL, Schoellhammer C, Esfandiary T, Cleveland C, Booth L, Lin J, Levy H, Blackburn S, Hayward A, Langer R, Traverso G. Nat Biomed Eng. pubmed:32341538;  doi:10.1038/s41551-020-0545-6

22. Rho/SMAD/mTOR triple inhibition enables long-term expansion of human neonatal tracheal aspirate-derived airway basal cell-like cells. Lu J, Zhu X, Shui JE, Xiong L, Gierahn T, Zhang C, Wood M, Hally S, Love JC, Li H, Crawford BC, Mou H, Lerou PH. Pediatr Res. pubmed:32365352;  doi:10.1038/s41390-020-0925-3

23. Expansion microscopy of C elegans. Yu CJ, Barry NC, Wassie AT, Sinha A, Bhattacharya A, Asano S, Zhang C, Chen F, Hobert O, Goodman MB, Haspel G, Boyden ES. Elife. pubmed:32356725;  doi:10.7554/eLife.46249

24. Efficient blockade of locally reciprocated tumor-macrophage signaling using a TAM-avid nanotherapy. Wang SJ, Li R, Ng TSC, Luthria G, Oudin MJ, Prytyskach M, Kohler RH, Weissleder R, Lauffenburger DA, Miller MA. Sci Adv. pubmed:32494745;  doi:10.1126/sciadv.aaz8521