Identification of transcriptional programs using dense vector representations defined by mutual information with GeneVector

Autor: Nicholas Ceglia, Zachary Sethna, Samuel S. Freeman, Florian Uhlitz, Viktoria Bojilova, Nicole Rusk, Bharat Burman, Andrew Chow, Sohrab Salehi, Farhia Kabeer, Samuel Aparicio, Benjamin D. Greenbaum, Sohrab P. Shah, Andrew McPherson

Publikováno v: Nature Communications, Vol 14, Iss 1, Pp 1-13 (2023)

Abstract Deciphering individual cell phenotypes from cell-specific transcriptional processes requires high dimensional single cell RNA sequencing. However, current dimensionality reduction methods aggregate sparse gene information across cells, witho

Externí odkaz: https://doaj.org/article/65a4f5b8f80d4f96bdbe1ea6e37f565d

Fundamental immune–oncogenicity trade-offs define driver mutation fitness

Autor: David Hoyos, Roberta Zappasodi, Isabell Schulze, Zachary Sethna, Kelvin César de Andrade, Dean F. Bajorin, Chaitanya Bandlamudi, Margaret K. Callahan, Samuel A. Funt, Sine R. Hadrup, Jeppe S. Holm, Jonathan E. Rosenberg, Sohrab P. Shah, Ignacio Vázquez-García, Britta Weigelt, Michelle Wu, Dmitriy Zamarin, Laura F. Campitelli, Edward J. Osborne, Mark Klinger, Harlan S. Robins, Payal P. Khincha, Sharon A. Savage, Vinod P. Balachandran, Jedd D. Wolchok, Matthew D. Hellmann, Taha Merghoub, Arnold J. Levine, Marta Łuksza, Benjamin D. Greenbaum

Publikováno v: Hoyos, D, Zappasodi, R, Schulze, I, Sethna, Z, de Andrade, K C, Bajorin, D F, Bandlamudi, C, Callahan, M K, Funt, S A, Hadrup, S R, Holm, J S, Rosenberg, J E, Shah, S P, Vázquez-García, I, Weigelt, B, Wu, M, Zamarin, D, Campitelli, L F, Osborne, E J, Klinger, M, Robins, H S, Khincha, P P, Savage, S A, Balachandran, V P, Wolchok, J D, Hellmann, M D, Merghoub, T, Levine, A J, Łuksza, M & Greenbaum, B D 2022, ' Fundamental immune–oncogenicity trade-offs define driver mutation fitness ', Nature, vol. 606, pp. 172-179 . https://doi.org/10.1038/s41586-022-04696-z

Missense driver mutations in cancer are concentrated in a few hotspots1. Various mechanisms have been proposed to explain this skew, including biased mutational processes2, phenotypic differences3–6 and immunoediting of neoantigens7,8; however, to

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::788159a08120de98426bcab992e37aaa
https://doi.org/10.1038/s41586-022-04696-z

ILC2s amplify PD-1 blockade by activating tissue-specific cancer immunity

Autor: Vinod P. Balachandran, David A. Tuveson, Zachary Sethna, Mithat Gonen, Jennifer Ruan, Anita Ramnarain, Gokce Askan, John Alec Moral, Ronald P. DeMatteo, Jedd D. Wolchok, Joanne Leung, Young-Kyu Park, Billel Gasmi, Julia Zhao, Steven D. Leach, Ela Elyada, Murali Gururajan, Luis A. Rojas, Umesh Bhanot, Taha Merghoub, David Redmond

Publikováno v: Nature

Group 2 innate lymphoid cells (ILC2s) regulate inflammation and immunity in mammalian tissues1,2. Although ILC2s are found in cancers of these tissues3, their roles in cancer immunity and immunotherapy are unclear. Here we show that ILC2s infiltrate

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::34af775134223cbde8e0d243c45f5340
http://europepmc.org/articles/PMC7060130

Phase I trial of adjuvant autogene cevumeran, an individualized mRNA neoantigen vaccine, for pancreatic ductal adenocarcinoma

Autor: Vinod P. Balachandran, Luis A. Rojas, Zachary Sethna, Kevin Soares, Evelyna Derhovanessian, Felicitas Mueller, Mahesh Yadav, Olca Basturk, Mithat Gonen, Alice Chia-chi Wei, Michael Ian D'Angelica, T. Peter Kingham, Benjamin Greenbaum, Taha Merghoub, William R. Jarnagin, Jeffrey A. Drebin, Ugur Sahin, Oezlem Tuereci, Jedd D. Wolchok, Eileen Mary O'Reilly

Publikováno v: Journal of Clinical Oncology. 40:2516-2516

2516 Background: Pancreas ductal adenocarcinoma (PDAC) is a lethal cancer that claims ̃90% of patients in + T cells in 50% (n=8/16) of patients from undetectable levels to large fractions (median 2.9%, Table) of all blood T cells. At an early median

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::f0b8667c9a04a8e81bf5ba3d2de630e0
https://doi.org/10.1200/jco.2022.40.16_suppl.2516

Generative models of T-cell receptor sequences

Autor: Yuval Elhanati, Giulio Isacchini, Aleksandra M. Walczak, Zachary Sethna, Thierry Mora, Armita Nourmohammad

Publikováno v: Physical Review E
Physical Review E, American Physical Society (APS), 2020, 101 (6), ⟨10.1103/PhysRevE.101.062414⟩

International audience; T-cell receptors (TCR) are key proteins of the adaptive immune system, generated randomly in each individual, whose diversity underlies our ability to recognize infections and malignancies. Modeling the distribution of TCR seq

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::77744e4eae9bd7dba2232271fff2d350
https://doi.org/10.1103/physreve.101.062414