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: September 2020

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1. Engineered tissues and strategies to overcome challenges in drug development. Khalil AS, Jaenisch R, Mooney DJ. Adv Drug Deliv Rev. pubmed:32987094;  doi:10.1016/j.addr.2020.09.012

2. CHD7 and Runx1 interaction provides a braking mechanism for hematopoietic differentiation. Hsu J, Huang HT, Lee CT, Choudhuri A, Wilson NK, Abraham BJ, Moignard V, Kucinski I, Yu S, Hyde RK, Tober J, Cai X, Li Y, Guo Y, Yang S, Superdock M, Trompouki E, Calero-Nieto FJ, Ghamari A, Jiang J, Gao P, Gao L, Nguyen V, Robertson AL, Durand EM, Kathrein KL, Aifantis I, Gerber SA, Tong W, Tan K, Cantor AB, Zhou Y, Liu PP, Young RA, Gottgens B, Speck NA, Zon LI. Proc Natl Acad Sci U S A. pubmed:32883883;  doi:10.1073/pnas.2003228117

3. Human T Cells Expressing a CD19 CAR-T Receptor Provide Insights into Mechanisms of Human CD19-Positive beta Cell Destruction. Ma H, Jeppesen JF, Jaenisch R. Cell Rep Med. pubmed:33205073;  doi:10.1016/j.xcrm.2020.100097

4. LILRB3 (ILT5) is a myeloid cell checkpoint that elicits profound immunomodulation. Yeboah M, Papagregoriou C, Jones DC, Chan HTC, Hu G, McPartlan JS, Schiott T, Mattson U, Mockridge CI, Tornberg UC, Hambe B, Ljungars A, Mattsson M, Tews I, Glennie MJ, Thirdborough SM, Trowsdale J, Frendeus B, Chen J, Cragg MS, Roghanian A. JCI Insight. pubmed:32870822;  doi:10.1172/jci.insight.141593

5. Loss of Sbds in zebrafish leads to neutropenia and pancreas and liver atrophy. Oyarbide U, Shah AN, Amaya-Mejia W, Snyderman M, Kell MJ, Allende DS, Calo E, Topczewski J, Corey SJ. JCI Insight. pubmed:32759502;  doi:10.1172/jci.insight.134309

6. CAR-NK cells: A promising cellular immunotherapy for cancer. Xie G, Dong H, Liang Y, Ham JD, Rizwan R, Chen J. EBioMedicine. pubmed:32853984;  doi:10.1016/j.ebiom.2020.102975

7. Endogenous Glucocorticoid Signaling Regulates CD8(+) T Cell Differentiation and Development of Dysfunction in the Tumor Microenvironment. Acharya N, Madi A, Zhang H, Klapholz M, Escobar G, Dulberg S, Christian E, Ferreira M, Dixon KO, Fell G, Tooley K, Mangani D, Xia J, Singer M, Bosenberg M, Neuberg D, Rozenblatt-Rosen O, Regev A, Kuchroo VK, Anderson AC. Immunity. pubmed:32937153;  doi:10.1016/j.immuni.2020.08.005

8. MFSD7C switches mitochondrial ATP synthesis to thermogenesis in response to heme. Li Y, Ivica NA, Dong T, Papageorgiou DP, He Y, Brown DR, Kleyman M, Hu G, Chen WW, Sullivan LB, Del Rosario A, Hammond PT, Vander Heiden MG, Chen J. Nat Commun. pubmed:32973183;  doi:10.1038/s41467-020-18607-1

9. Integrated regulatory models for inference of subtype-specific susceptibilities in glioblastoma. Liu Y, Shi N, Regev A, He S, Hemann MT. Mol Syst Biol. pubmed:32974985;  doi:10.15252/msb.20209506

10. COVID-19: All the wrong moves in all the wrong places. Barrett CD, Yaffe MB. Sci Signal. pubmed:32934074;  doi:N/A

11. Microfluidic label-free bioprocessing of human reticulocytes from erythroid culture. Zeming KK, Sato Y, Yin L, Huang NJ, Wong LH, Loo HL, Lim YB, Lim CT, Chen J, Preiser PR, Han J. Lab Chip. pubmed:32793940;  doi:N/A

12. Over 60 Years of Experimental Hematology (without a License). Lodish HF. Exp Hematol. pubmed:32798645;  doi:N/A

13. Plasticity of ether lipids promotes ferroptosis susceptibility and evasion. Zou Y, Henry WS, Ricq EL, Graham ET, Phadnis VV, Maretich P, Paradkar S, Boehnke N, Deik AA, Reinhardt F, Eaton JK, Ferguson B, Wang W, Fairman J, Keys HR, Dancik V, Clish CB, Clemons PA, Hammond PT, Boyer LA, Weinberg RA, Schreiber SL. Nature. pubmed:32939090;  doi:N/A

14. Induction of a Timed Metabolic Collapse to Overcome Cancer Chemoresistance. van Gastel N, Spinelli JB, Sharda A, Schajnovitz A, Baryawno N, Rhee C, Oki T, Grace E, Soled HJ, Milosevic J, Sykes DB, Hsu PP, Vander Heiden MG, Vidoudez C, Trauger SA, Haigis MC, Scadden DT. Cell Metab. pubmed:32763164;  doi:N/A

15. The Human and Mouse Enteric Nervous System at Single-Cell Resolution. Drokhlyansky E, Smillie CS, Van Wittenberghe N, Ericsson M, Griffin GK, Eraslan G, Dionne D, Cuoco MS, Goder-Reiser MN, Sharova T, Kuksenko O, Aguirre AJ, Boland GM, Graham D, Rozenblatt-Rosen O, Xavier RJ, Regev A. Cell. pubmed:32888429;  doi:N/A

16. Innate Lymphoid Cell Activation and Sustained Depletion in Blood and Tissue of Children Infected with HIV from Birth Despite Antiretroviral Therapy. Singh A, Kazer SW, Roider J, Krista KC, Millar J, Asowata OE, Ngoepe A, Ramsuran D, Fardoos R, Ardain A, Muenchhoff M, Kuhn W, Karim F, Ndung'u T, Shalek AK, Goulder P, Leslie A, Kloverpris HN. Cell Rep. pubmed:32937142;  doi:10.1016/j.celrep.2020.108153

17. Improved haplotype inference by exploiting long-range linking and allelic imbalance in RNA-seq datasets. Berger E, Yorukoglu D, Zhang L, Nyquist SK, Shalek AK, Kellis M, Numanagic I, Berger B. Nat Commun. pubmed:32938926;  doi:10.1038/s41467-020-18320-z

18. Pulmonary-arterial-hypertension (PAH)-on-a-chip: fabrication, validation and application. Al-Hilal TA, Keshavarz A, Kadry H, Lahooti B, Al-Obaida A, Ding Z, Li W, Kamm R, McMurtry IF, Lahm T, Nozik-Grayck E, Stenmark KR, Ahsan F. Lab Chip. pubmed:32749432;  doi:10.1039/d0lc00605j

19. Multifaceted Effects of Antigen Valency on B Cell Response Composition and Differentiation In Vivo. Kato Y, Abbott RK, Freeman BL, Haupt S, Groschel B, Silva M, Menis S, Irvine DJ, Schief WR, Crotty S. Immunity. pubmed:32857950;  doi:10.1016/j.immuni.2020.08.001

20. Light microscopy based approach for mapping connectivity with molecular specificity. Shen FY, Harrington MM, Walker LA, Cheng HPJ, Boyden ES, Cai D. Nat Commun. pubmed:32934230;  doi:10.1038/s41467-020-18422-8

21. Translation elongation factor 2 depletion by siRNA in mouse liver leads to mTOR-independent translational upregulation of ribosomal protein genes. Gerashchenko MV, Nesterchuk MV, Smekalova EM, Paulo JA, Kowalski PS, Akulich KA, Bogorad R, Dmitriev SE, Gygi S, Zatsepin T, Anderson DG, Gladyshev VN, Koteliansky VE. Sci Rep. pubmed:32968084;  doi:10.1038/s41598-020-72399-4

22. Repertoire-scale determination of class II MHC peptide binding via yeast display improves antigen prediction. Rappazzo CG, Huisman BD, Birnbaum ME. Nat Commun. pubmed:32887877;  doi:10.1038/s41467-020-18204-2

23. Light-regulated allosteric switch enables temporal and subcellular control of enzyme activity. Shaaya M, Fauser J, Zhurikhina A, Conage-Pough JE, Huyot V, Brennan M, Flower CT, Matsche J, Khan S, Natarajan V, Rehman J, Kota P, White FM, Tsygankov D, Karginov AV. Elife. pubmed:32965214;  doi:10.7554/eLife.60647

24. Distinct Early Serological Signatures Track with SARS-CoV-2 Survival. Atyeo C, Fischinger S, Zohar T, Slein MD, Burke J, Loos C, McCulloch DJ, Newman KL, Wolf C, Yu J, Shuey K, Feldman J, Hauser BM, Caradonna T, Schmidt AG, Suscovich TJ, Linde C, Cai Y, Barouch D, Ryan ET, Charles RC, Lauffenburger D, Chu H, Alter G. Immunity. pubmed:32783920;  doi:10.1016/j.immuni.2020.07.020

25. Evolution of Early SARS-CoV-2 and Cross-Coronavirus Immunity. Loos C, Atyeo C, Fischinger S, Burke J, Slein MD, Streeck H, Lauffenburger D, Ryan ET, Charles RC, Alter G. mSphere. pubmed:32878931;  doi:10.1128/mSphere.00622-20

26. Platform for micro-invasive membrane-free biochemical sampling of brain interstitial fluid. Raman R, Rousseau EB, Wade M, Tong A, Cotler MJ, Kuang J, Lugo AA, Zhang E, Graybiel AM, White FM, Langer R, Cima MJ. Sci Adv. pubmed:32978160;  doi:10.1126/sciadv.abb0657

27. Identifying Improved Sites for Heterologous Gene Integration Using ATAC-seq. Brady JR, Tan MC, Whittaker CA, Colant NA, Dalvie NC, Love KR, Love JC. ACS Synth Biol. pubmed:32786350;  doi:10.1021/acssynbio.0c00299

28. Induction of a regulatory myeloid program in bacterial sepsis and severe COVID-19. Reyes M, Filbin MR, Bhattacharyya RP, Sonny A, Mehta A, Billman K, Kays KR, Pinilla-Vera M, Benson ME, Cosimi LA, Hung DT, Levy BD, Villani AC, Sade-Feldman M, Baron RM, Goldberg MB, Blainey PC, Hacohen N. bioRxiv. pubmed:32908980;  doi:10.1101/2020.09.02.280180

29. Peptide Spiders: Peptide-Polymer Conjugates to Traffic Nucleic Acids. Kwon EJ, Ko H, Bhatia SN. Mol Pharm. pubmed:32786959;  doi:N/A

30. Fully synthetic matrices for in vitro culture of primary human intestinal enteroids and endometrial organoids. Hernandez-Gordillo V, Kassis T, Lampejo A, Choi G, Gamboa ME, Gnecco JS, Brown A, Breault DT, Carrier R, Griffith LG. Biomaterials. pubmed:32502894;  doi:N/A

31. Case 30-2020: A 54-Year-Old Man with Sudden Cardiac Arrest. Edelman ER, Butala NM, Avery LL, Lundquist AL, Dighe AS. N Engl J Med. pubmed:32966726;  doi:N/A

32. Deep learning to estimate RECIST in patients with NSCLC treated with PD-1 blockade. Arbour KC, Luu AT, Luo J, Rizvi H, Plodkowski AJ, Sakhi M, Huang KB, Digumarthy SR, Ginsberg MS, Girshman J, Kris MG, Riely GJ, Yala A, Gainor JF, Barzilay R, Hellmann MD. Cancer Discov. pubmed:32958579;  doi:N/A

33. Angiogenic responses in a 3D micro-engineered environment of primary endothelial cells and pericytes. Bai J, Khajavi M, Sui L, Fu H, Tarakkad Krishnaji S, Birsner AE, Bazinet L, Kamm RD, D'Amato RJ. Angiogenesis. pubmed:32955682;  doi:N/A

34. Comparison of cytokines in the peritoneal fluid and conditioned medium of adolescents and adults with and without endometriosis. Bailey AP, Hill AS, Beste MT, Cook CD, Sarda V, Laufer MR, Isaacson KB, Griffith LG, Missmer SA. Am J Reprod Immunol. pubmed:32946598;  doi:N/A

35. Illuminating Host-Mycobacterial Interactions with Genome-wide CRISPR Knockout and CRISPRi Screens. Lai Y, Babunovic GH, Cui L, Dedon PC, Doench JG, Fortune SM, Lu TK. Cell Syst. pubmed:32970993;  doi:N/A

36. Electrostatic Conjugation of Nanoparticle Surfaces with Functional Peptide Motifs. Boehnke N, Dolph KJ, Juarez VM, Lanoha JM, Hammond PT. Bioconjug Chem. pubmed:32786506;  doi:N/A