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: October 2020

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1. Netrin G1 promotes pancreatic tumorigenesis through cancer associated fibroblast driven nutritional support and immunosuppression. Francescone R, Barbosa Vendramini-Costa D, Franco-Barraza J, Wagner J, Muir A, Lau AN, Gabitova L, Pazina T, Gupta S, Luong T, Rollins D, Malik R, Thapa RJ, Restifo D, Zhou Y, Cai KQ, Hensley HH, Tan Y, Kruger WD, Devarajan K, Balachandran S, Klein-Szanto AJ, Wang H, El-Deiry WS, Vander Heiden MG, Peri S, Campbell KS, Astsaturov I, Cukierman E. Cancer Discov. pubmed:33127842;  doi:N/A

2. Multiplexed Plasma Immune Mediator Signatures Can Differentiate Sepsis From NonInfective SIRS: American Surgical Association 2020 Annual Meeting Paper. Cahill LA, Joughin BA, Kwon WY, Itagaki K, Kirk CH, Shapiro NI, Otterbein LE, Yaffe MB, Lederer JA, Hauser CJ. Ann Surg. pubmed:32932316;  doi:N/A

3. CAR-T cells targeting a nucleophosmin neoepitope exhibit potent specific activity in mouse models of acute myeloid leukaemia. Xie G, Ivica NA, Jia B, Li Y, Dong H, Liang Y, Brown D, Rizwan R, Chen J. Nat Biomed Eng. pubmed:33046866;  doi:N/A

4. Reactions to the National Academies/Royal Society Report on Heritable Human Genome Editing. Angrist M, Barrangou R, Baylis F, Brokowski C, Burgio G, Caplan A, Chapman CR, Church GM, Cook-Deegan R, Cwik B, Doudna JA, Evans JH, Greely HT, Hercher L, Hurlbut JB, Hynes RO, Ishii T, Kiani S, Lee LH, Levrier G, Liu DR, Lunshof JE, Macintosh KL, Mathews DJH, Meslin EM, Mills PHR, Montoliu L, Musunuru K, Nicol D, O'Neill H, Qiu R, Ranisch R, Sherkow JS, Soni S, Terry S, Topol E, Williamson R, Zhang F, Davies K. CRISPR J. pubmed:33095048;  doi:N/A

5. MONOCYTE EXOCYTOSIS OF MITOCHONDRIAL DAMPS IN SEPSIS SUPPRESSES NEUTROPHIL CHEMOTAXIS. Konecna B, Park J, Kwon WY, Vlkova B, Zhang Q, Huang W, In Kim H, Yaffe MB, Otterbein LE, Itagaki K, Hauser CJ. J Trauma Acute Care Surg. pubmed:33021603;  doi:N/A

6. lncRNA DIGIT and BRD3 protein form phase-separated condensates to regulate endoderm differentiation. Daneshvar K, Ardehali MB, Klein IA, Hsieh FK, Kratkiewicz AJ, Mahpour A, Cancelliere SOL, Zhou C, Cook BM, Li W, Pondick JV, Gupta SK, Moran SP, Young RA, Kingston RE, Mullen AC. Nat Cell Biol. pubmed:32895492;  doi:N/A

7. Inherited causes of clonal haematopoiesis in 97,691 whole genomes. Bick AG, Weinstock JS, Nandakumar SK, Fulco CP, Bao EL, Zekavat SM, Szeto MD, Liao X, Leventhal MJ, Nasser J, Chang K, Laurie C, Burugula BB, Gibson CJ, Lin AE, Taub MA, Aguet F, Ardlie K, Mitchell BD, Barnes KC, Moscati A, Fornage M, Redline S, Psaty BM, Silverman EK, Weiss ST, Palmer ND, Vasan RS, Burchard EG, Kardia SLR, He J, Kaplan RC, Smith NL, Arnett DK, Schwartz DA, Correa A, de Andrade M, Guo X, Konkle BA, Custer B, Peralta JM, Gui H, Meyers DA, McGarvey ST, Chen IY, Shoemaker MB, Peyser PA, Broome JG, Gogarten SM, Wang FF, Wong Q, Montasser ME, Daya M, Kenny EE, North KE, Launer LJ, Cade BE, Bis JC, Cho MH, Lasky-Su J, Bowden DW, Cupples LA, Mak ACY, Becker LC, Smith JA, Kelly TN, Aslibekyan S, Heckbert SR, Tiwari HK, Yang IV, Heit JA, Lubitz SA, Johnsen JM, Curran JE, Wenzel SE, Weeks DE, Rao DC, Darbar D, Moon JY, Tracy RP, Buth EJ, Rafaels N, Loos RJF, Durda P, Liu Y, Hou L, Lee J, Kachroo P, Freedman BI, Levy D, Bielak LF, Hixson JE, Floyd JS, Whitsel EA, Ellinor PT, Irvin MR, Fingerlin TE, Raffield LM, Armasu SM, Wheeler MM, Sabino EC, Blangero J, Williams LK, Levy BD, Sheu WH, Roden DM, Boerwinkle E, Manson JE, Mathias RA, Desai P, Taylor KD, Johnson AD, Auer PL, Kooperberg C, Laurie CC, Blackwell TW, Smith AV, Zhao H, Lange E, Lange L, Rich SS, Rotter JI, Wilson JG, Scheet P, Kitzman JO, Lander ES, Engreitz JM, Ebert BL, Reiner AP, Jaiswal S, Abecasis G, Sankaran VG, Kathiresan S, Natarajan P. Nature. pubmed:33057201;  doi:N/A

8. Knockout of the gene encoding the extracellular matrix protein SNED1 results in early neonatal lethality and craniofacial malformations. Barque A, Jan K, De La Fuente E, Nicholas CL, Hynes RO, Naba A. Dev Dyn. pubmed:33012048;  doi:N/A

9. Are redox changes a critical switch for mitotic progression?. Lim DC, Joukov V, Yaffe MB. Mol Cell Oncol. pubmed:33235921;  doi:10.1080/23723556.2020.1832419

10. Inherited myeloproliferative neoplasm risk affects haematopoietic stem cells. Bao EL, Nandakumar SK, Liao X, Bick AG, Karjalainen J, Tabaka M, Gan OI, Havulinna AS, Kiiskinen TTJ, Lareau CA, de Lapuente Portilla AL, Li B, Emdin C, Codd V, Nelson CP, Walker CJ, Churchhouse C, de la Chapelle A, Klein DE, Nilsson B, Wilson PWF, Cho K, Pyarajan S, Gaziano JM, Samani NJ, Regev A, Palotie A, Neale BM, Dick JE, Natarajan P, O'Donnell CJ, Daly MJ, Milyavsky M, Kathiresan S, Sankaran VG. Nature. pubmed:33057200;  doi:10.1038/s41586-020-2786-7

11. Calmodulin inhibitors improve erythropoiesis in Diamond-Blackfan anemia. Taylor AM, Macari ER, Chan IT, Blair MC, Doulatov S, Vo LT, Raiser DM, Siva K, Basak A, Pirouz M, Shah AN, McGrath K, Humphries JM, Stillman E, Alter BP, Calo E, Gregory RI, Sankaran VG, Flygare J, Ebert BL, Zhou Y, Daley GQ, Zon LI. Sci Transl Med. pubmed:33087503;  doi:10.1126/scitranslmed.abb5831

12. MCART1/SLC25A51 is required for mitochondrial NAD transport. Kory N, Uit de Bos J, van der Rijt S, Jankovic N, Gura M, Arp N, Pena IA, Prakash G, Chan SH, Kunchok T, Lewis CA, Sabatini DM. Sci Adv. pubmed:33087354;  doi:10.1126/sciadv.abe5310

13. A cell-free antibody engineering platform rapidly generates SARS-CoV-2 neutralizing antibodies. Chen X, Gentili M, Hacohen N, Regev A. bioRxiv. pubmed:33140055;  doi:10.1101/2020.10.29.361287

14. Impact of anatomic site on antigen-presenting cells in cancer. Zagorulya M, Duong E, Spranger S. J Immunother Cancer. pubmed:33020244;  doi:10.1136/jitc-2020-001204

15. Monitoring and modeling of lymphocytic leukemia cell bioenergetics reveals decreased ATP synthesis during cell division. Kang JH, Katsikis G, Li Z, Sapp KM, Stockslager MA, Lim D, Vander Heiden MG, Yaffe MB, Manalis SR, Miettinen TP. Nat Commun. pubmed:33020492;  doi:10.1038/s41467-020-18769-y

16. Purifying Selection against Pathogenic Mitochondrial DNA in Human T Cells. Walker MA, Lareau CA, Ludwig LS, Karaa A, Sankaran VG, Regev A, Mootha VK. N Engl J Med. pubmed:32786181;  doi:10.1056/NEJMoa2001265

17. Transcriptional activation of macropinocytosis by the Hippo pathway following nutrient limitation. Sivanand S, Vander Heiden MG. Genes Dev. pubmed:33004484;  doi:10.1101/gad.343632.120

18. Second-Strand Synthesis-Based Massively Parallel scRNA-Seq Reveals Cellular States and Molecular Features of Human Inflammatory Skin Pathologies. Hughes TK, Wadsworth MH2nd, Gierahn TM, Do T, Weiss D, Andrade PR, Ma F, de Andrade Silva BJ, Shao S, Tsoi LC, Ordovas-Montanes J, Gudjonsson JE, Modlin RL, Love JC, Shalek AK. Immunity. pubmed:33053333;  doi:10.1016/j.immuni.2020.09.015

19. The Human Cell Atlas and equity: lessons learned. Majumder PP, Mhlanga MM, Shalek AK. Nat Med. pubmed:33029017;  doi:N/A

20. A Small-Molecule Inhibitor to the Cytokine Interleukin-4. Quinnell SP, Leifer BS, Nestor ST, Tan K, Sheehy DF, Ceo L, Doyle SK, Koehler AN, Vegas AJ. ACS Chem Biol. pubmed:32902255;  doi:N/A

21. Exploiting Rules to Enhance Machine Learning in Extracting Information From Multi-Institutional Prostate Pathology Reports. Santus E, Schuster T, Tahmasebi AM, Li C, Yala A, Lanahan CR, Prinsen P, Thompson SF, Coons S, Mynderse L, Barzilay R, Hughes K. JCO Clin Cancer Inform. pubmed:33006906;  doi:N/A

22. Integrated Neurophotonics: Toward Dense Volumetric Interrogation of Brain Circuit Activity-at Depth and in Real Time. Moreaux LC, Yatsenko D, Sacher WD, Choi J, Lee C, Kubat NJ, Cotton RJ, Boyden ES, Lin MZ, Tian L, Tolias AS, Poon JKS, Shepard KL, Roukes ML. Neuron. pubmed:33058767;  doi:N/A

23. Modulating Androgen Receptor-Driven Transcription in Prostate Cancer with Selective CDK9 Inhibitors. Richters A, Doyle SK, Freeman DB, Lee C, Leifer BS, Jagannathan S, Kabinger F, Koren JV, Struntz NB, Urgiles J, Stagg RA, Curtin BH, Chatterjee D, Mathea S, Mikochik PJ, Hopkins TD, Gao H, Branch JR, Xin H, Westover L, Bignan GC, Rupnow BA, Karlin KL, Olson CM, Westbrook TF, Vacca J, Wilfong CM, Trotter BW, Saffran DC, Bischofberger N, Knapp S, Russo JW, Hickson I, Bischoff JR, Gottardis MM, Balk SP, Lin CY, Pop MS, Koehler AN. Cell Chem Biol. pubmed:33086052;  doi:N/A

24. RNA timestamps identify the age of single molecules in RNA sequencing. Rodriques SG, Chen LM, Liu S, Zhong ED, Scherrer JR, Boyden ES, Chen F. Nat Biotechnol. pubmed:33077959;  doi:N/A

25. Rational design of multistage drug delivery vehicles for pulmonary RNA interference therapy. Silva AS, Shopsowitz KE, Correa S, Morton SW, Dreaden EC, Casimiro T, Aguiar-Ricardo A, Hammond PT. Int J Pharm. pubmed:33122113;  doi:N/A

26. Nickel-Titanium peripheral stents: Which is the best criterion for the multi-axial fatigue strength assessment?. Berti F, Wang PJ, Spagnoli A, Pennati G, Migliavacca F, Edelman ER, Petrini L. J Mech Behav Biomed Mater. pubmed:33125952;  doi:N/A

27. Multimodal Loading Environment Predicts Bioresorbable Vascular Scaffolds' Durability. Wang PJ, Berti F, Antonini L, Nezami FR, Petrini L, Migliavacca F, Edelman ER. Ann Biomed Eng. pubmed:33123828;  doi:N/A

28. Gibberellin JRA-003: A Selective Inhibitor of Nuclear Translocation of IKKalpha. Annand JR, Henderson AR, Cole KS, Maurais AJ, Becerra J, Liu Y, Weerapana E, Koehler AN, Mapp AK, Schindler CS. ACS Med Chem Lett. pubmed:33062173;  doi:10.1021/acsmedchemlett.9b00613

29. Mining for humoral correlates of HIV control and latent reservoir size. Das J, Devadhasan A, Linde C, Broge T, Sassic J, Mangano M, O'Keefe S, Suscovich T, Streeck H, Irrinki A, Pohlmeyer C, Min-Oo G, Lin S, Weiner JA, Cihlar T, Ackerman ME, Julg B, Deeks S, Lauffenburger DA, Alter G. PLoS Pathog. pubmed:33048992;  doi:10.1371/journal.ppat.1008868

30. Nanoemulsion-Loaded Capsules for Controlled Delivery of Lipophilic Active Ingredients. Chen LH, Cheng LC, Doyle PS. Adv Sci (Weinh). pubmed:33101868;  doi:10.1002/advs.202001677

31. Activatable zymography probes enable in situ localization of protease dysregulation in cancer. Soleimany AP, Kirkpatrick JD, Su S, Dudani JS, Zhong Q, Bekdemir A, Bhatia SN. Cancer Res. pubmed:33106334;  doi:N/A

32. Prediction of the binding interface between monoclonal antibody m102.4 and Nipah attachment glycoprotein using structure-guided alanine scanning and computational docking. Tit-Oon P, Tharakaraman K, Artpradit C, Godavarthi A, Sungkeeree P, Sasisekharan V, Kerdwong J, Miller NL, Mahajan B, Khongmanee A, Ruchirawat M, Sasisekharan R, Fuangthong M. Sci Rep. pubmed:33106487;  doi:10.1038/s41598-020-75056-y

33. Sequence-to-function deep learning frameworks for engineered riboregulators. Valeri JA, Collins KM, Ramesh P, Alcantar MA, Lepe BA, Lu TK, Camacho DM. Nat Commun. pubmed:33028819;  doi:10.1038/s41467-020-18676-2

34. Repurposing a peptide toxin from wasp venom into antiinfectives with dual antimicrobial and immunomodulatory properties. Silva ON, Torres MDT, Cao J, Alves ESF, Rodrigues LV, Resende JM, Liao LM, Porto WF, Fensterseifer ICM, Lu TK, Franco OL, de la Fuente-Nunez C. Proc Natl Acad Sci U S A. pubmed:33046640;  doi:10.1073/pnas.2012379117

35. Inverse Pneumatic Artificial Muscles for Application in Low-Cost Ventilators. Mirvakili SM, Sim D, Langer R. Adv Intell Syst. pubmed:33173858;  doi:10.1002/aisy.202000200

36. Advances in oligonucleotide drug delivery. Roberts TC, Langer R, Wood MJA. Nat Rev Drug Discov. pubmed:32782413;  doi:10.1038/s41573-020-0075-7

37. A materials-science perspective on tackling COVID-19. Tang Z, Kong N, Zhang X, Liu Y, Hu P, Mou S, Liljestrom P, Shi J, Tan W, Kim JS, Cao Y, Langer R, Leong KW, Farokhzad OC, Tao W. Nat Rev Mater. pubmed:33078077;  doi:10.1038/s41578-020-00247-y

38. Multiplex CRISPRi System Enables the Study of Stage-Specific Biofilm Genetic Requirements in Enterococcus faecalis. Afonina I, Ong J, Chua J, Lu T, Kline KA. mBio. pubmed:33082254;  doi:10.1128/mBio.01101-20

39. Passive Transfer of Vaccine-Elicited Antibodies Protects against SIV in Rhesus Macaques. Alter G, Yu WH, Chandrashekar A, Borducchi EN, Ghneim K, Sharma A, Nedellec R, McKenney KR, Linde C, Broge T, Suscovich TJ, Linnekin T, Abbink P, Mercado NB, Nkolola JP, McMahan K, Bondzie EA, Hamza V, Peter L, Kordana N, Mahrokhian S, Seaman MS, Li W, Lewis MG, Lauffenburger DA, Hangartner L, Sekaly RP, Barouch DH. Cell. pubmed:33007262;  doi:10.1016/j.cell.2020.08.033