Pan-cancer proteogenomics characterization of tumor immunity

Petralia, Francesca; Ma, Weiping; Yaron, Tomer M.; Caruso, Francesca Pia; Tignor, Nicole; Wang, Joshua M.; Charytonowicz, Daniel; Johnson, Jared L.; Huntsman, Emily M.; Marino, Giacomo B.; Calinawan, Anna; Evangelista, John Erol; Selvan, Myvizhi Esai; Chowdhury, Shrabanti; Rykunov, Dmitry; Krek, Azra; Song, Xiaoyu; Turhan, Berk; Christianson, Karen E.; Lewis, David A.; Deng, Eden Z.; Clarke, Daniel J.B.; Whiteaker, Jeffrey R.; Kennedy, Jacob J.; Zhao, Lei; Segura, Rossana Lazcano; Batra, Harsh; Raso, Maria Gabriela; Parra, Edwin Roger; Soundararajan, Rama; Tang, Ximing; Li, Yize; Yi, Xinpei; Satpathy, Shankha; Wang, Ying; Wiznerowicz, Maciej; González-Robles, Tania J.; Iavarone, Antonio; Gosline, Sara J.C.; Reva, Boris; Robles, Ana I.; Nesvizhskii, Alexey I.; Mani, D.R.; Gillette, Michael A.; Klein, Robert J.; Cieslik, Marcin; Zhang, Bing; Paulovich, Amanda G.; Sebra, Robert; Gümüş, Zeynep H.; Hostetter, Galen; Fenyö, David; Omenn, Gilbert S.; Cantley, Lewis C.; Ma'ayan, Avi; Lazar, Alexander J.; Ceccarelli, Michele; Wang, Pei; Abelin, Jennifer; Aguet, François; Akiyama, Yo; An, Eunkyung; Anand, Shankara; Anurag, Meenakshi; Babur, Özgün; Bavarva, Jasmin; Birger, Chet; Birrer, Michael J.; Cao, Song; Carr, Steven A.; Chan, Daniel W.; Chinnaiyan, Arul M.; Cho, Hanbyul; Clauser, Karl; Colaprico, Antonio; Zhou, Daniel Cui; da Veiga Leprevost, Felipe; Day, Corbin; Dhanasekaran, Saravana M.; Ding, Li; Domagalski, Marcin J.; Dou, Yongchao; Druker, Brian J.; Edwards, Nathan; Ellis, Matthew J.; Foltz, Steven M.; Francis, Alicia; Geffen, Yifat; Getz, Gad; Heiman, David I.; Hong, Runyu; Hu, Yingwei; Huang, Chen; Jaehnig, Eric J.; Jewell, Scott D.; Ji, Jiayi; Jiang, Wen; Katsnelson, Lizabeth; Ketchum, Karen A.; Kolodziejczak, Iga; Krug, Karsten; Kumar-Sinha, Chandan; Lei, Jonathan T.; Liang, Wen-Wei; Liao, Yuxing; Lindgren, Caleb M.; Liu, Tao; Liu, Wenke; McDermott, Jason; McKerrow, Wilson; Mesri, Mehdi; Mumphrey, Michael Brodie; Newton, Chelsea J.; Oldroyd, Robert; Payne, Samuel H.; Pugliese, Pietro; Rodland, Karin D.; Rodrigues, Fernanda Martins; Ruggles, Kelly V.; Savage, Sara R.; Schadt, Eric E.; Schnaubelt, Michael; Schraink, Tobias; Schürer, Stephan; Shi, Zhiao; Smith, Richard D.; Song, Feng; Song, Yizhe; Stathias, Vasileios; Storrs, Erik P.; Tan, Jimin; Terekhanova, Nadezhda V.; Thangudu, Ratna R.; Thiagarajan, Mathangi; Wang, Liang-Bo; Wen, Bo; Wu, Yige; Wyczalkowski, Matthew A.; Yao, Lijun; Li, Qing Kay; Zhang, Hui; Zhang, Qing; Zhang, Xu; Zhang, Zhen

doi:10.1016/j.cell.2024.01.027

Cited by 12 publications

(2 citation statements)

References 124 publications

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“…The integration of multi-omics, such as ATAC-seq, ChIP-seq, is a valuable approach to not only discover biomarkers and understand diseases, but also achieve precision medicine in medical research [54] , [55] , [56] , [57] . For example, in cancer research, multi-omics analysis gave rise to the pan-cancer molecular classification that sets subtypes based on frequently mutated genes, regardless of their tissue of origin [58] , [59] . Using this approach, we may witness the value of multi-omics analysis into medical research; ranging from cancer to aging, to neurodegenerative diseases, and more [60] .…”

Section: Discussionmentioning

confidence: 99%

A review of Ribosome profiling and tools used in Ribo-seq data analysis

Limbu,

Xiong,

Wang

2024

Computational and Structural Biotechnology Journal

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Section: Discussionmentioning

confidence: 99%

A review of Ribosome profiling and tools used in Ribo-seq data analysis

Limbu,

Xiong,

Wang

2024

Computational and Structural Biotechnology Journal

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“…Enhancing the immunostimulatory effects of radiotherapy, improving delivery methods for STING agonists and developing specific autophagy modulators will allow further investigation of their clinical potential as monotherapy or combinatorial therapy. Moreover, approaches such as proteogenomics ( 343 – 346 ) that provide information about tumor subtypes and tumor microenvironment may reveal new biomarkers to guide personalized therapy options. Finally, further efforts in understanding cGAS-STING signaling and autophagy pathways individually as well as their interactions will be instrumental for their targeting in cancer.…”

Section: Discussionmentioning

confidence: 99%

The interplay between autophagy and cGAS-STING signaling and its implications for cancer

Schmid,

Fischer,

Engl

et al. 2024

Front. Immunol.

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Autophagy is an intracellular process that targets various cargos for degradation, including members of the cGAS-STING signaling cascade. cGAS-STING senses cytosolic double-stranded DNA and triggers an innate immune response through type I interferons. Emerging evidence suggests that autophagy plays a crucial role in regulating and fine-tuning cGAS-STING signaling. Reciprocally, cGAS-STING pathway members can actively induce canonical as well as various non-canonical forms of autophagy, establishing a regulatory network of feedback mechanisms that alter both the cGAS-STING and the autophagic pathway. The crosstalk between autophagy and the cGAS-STING pathway impacts a wide variety of cellular processes such as protection against pathogenic infections as well as signaling in neurodegenerative disease, autoinflammatory disease and cancer. Here we provide a comprehensive overview of the mechanisms involved in autophagy and cGAS-STING signaling, with a specific focus on the interactions between the two pathways and their importance for cancer.

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