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Jonathan A. Nowak
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Journal Articles

Abstract 6535: Association of Bacteroides fragilis and enterotoxigenic Bacteroides fragilis with specific T-cell subsets in the colorectal carcinoma microenvironment

Free
Satoko Ugai, Yuxue Zhong, Yasutoshi Takashima, Kosuke Matsuda, Claire E. Thomas, Daniel D. Buchanan, Conghui Qu, Li Hsu, Steven Gallinger, Robert C. Grant, Marios Giannakis, Meredith Hullar, Jeroen R. Huyghe, Sushma S. Thomas, Ulrike Peters, Amanda I. Phipps, Jonathan A. Nowak, Tomotaka Ugai, Shuji Ogino
Journal: Cancer Research
Cancer Res (2025) 85 (8_Supplement_1): 6535.
https://doi.org/10.1158/1538-7445.AM2025-6535
Published: 21 April 2025
View articletitled, Abstract 6535: Association of Bacteroides fragilis and enterotoxigenic Bacteroides fragilis with specific T-cell subsets in the colorectal carcinoma microenvironment
Journal Articles

Abstract 5858: Prognostic and predictive role of T cell infiltration in stage III colon cancer (CC) treated with celecoxib: CALGB/SWOG 80702

Free
Yasutoshi Takashima, Chao Ma, Qian Shi, Andressa Dias Costa, Tyler Twombly, Juha P. Väyrynen, Melissa Zhao, Ardaman Shergill, Pankaj Kumar, Felix Couture, Philip Kuebler, Smitha Krishnamurthi, Benjamin Tan, Eileen M. O'Reilly, Anthony F. Shields, Shuji Ogino, Charles S. Fuchs, Jeffrey A. Meyerhardt, Jonathan A. Nowak
Journal: Cancer Research
Cancer Res (2025) 85 (8_Supplement_1): 5858.
https://doi.org/10.1158/1538-7445.AM2025-5858
Published: 21 April 2025
View articletitled, Abstract 5858: Prognostic and predictive role of T cell infiltration in stage III colon cancer (CC) treated with celecoxib: CALGB/SWOG 80702
Journal Articles

Abstract 6316: Predictive performance comparison of foundational and CNN models for single-cell immune profiling

Free
Colwyn Jia Kang Lai, Wei Kit Tan, Marcia Zhang, Timothy Wang, Felicia Wee, Ai Lin Wang, Solomonraj Wilson, Tomotaka Ugai, Joe Sheng Yeong Poh, Jonathan A. Nowak, Shuji Ogino, Juha P. Väyrynen, Mai Chan Lau
Journal: Cancer Research
Cancer Res (2025) 85 (8_Supplement_1): 6316.
https://doi.org/10.1158/1538-7445.AM2025-6316
Published: 21 April 2025
View articletitled, Abstract 6316: Predictive performance comparison of foundational and CNN models for single-cell immune profiling
Journal Articles

Abstract A029: Evaluating and interpreting scGPT: A foundation model for single-cell biology in real-world cancer clinical trial data

Free
Runzi Tan, Haotian Cui, Bo Wang, Kimberly Perez, Andressa Dias Costa, Alexander Jordan, Thomas Karacic, Dalia Elganainy, Dan Y Gui, Suryun Kim, Chen Yuan, Morgan Truitt, Michael Downes, Ronald Evans, Tae Gyu Oh, Peter O’Dwyer, Andrew Aguirre, Jonathan A Nowak, Brian Wolpin, Simona Cristea
Journal: Cancer Research
Cancer Res (2024) 84 (17_Supplement_2): A029.
https://doi.org/10.1158/1538-7445.PANCREATIC24-A029
Published: 15 September 2024
View articletitled, Abstract A029: Evaluating and interpreting scGPT: A foundation model for single-cell biology in real-world cancer clinical trial data
Journal Articles

Abstract NG07: Association between somatic microsatellite instability, hypermutation status, and specific T cell subsets in colorectal cancer tumors

Free
Claire Elizabeth Thomas, Yasutoshi Takashima, Tomotaka Ugai, Daniel D. Buchanan, Conghui Qu, Li Hsu, Andressa Dias Costa, Stephen Gallinger, Robert C. Grant, Jeroen R. Huyghe, Sushma S. Thomas, Robert S. Steinfelder, Shuji Ogino, Amanda I. Phipps, Jonathan A. Nowak, Ulrike Peters
Journal: Cancer Research
Cancer Res (2024) 84 (7_Supplement): NG07.
https://doi.org/10.1158/1538-7445.AM2024-NG07
Published: 05 April 2024
View articletitled, Abstract NG07: Association between somatic microsatellite instability, hypermutation status, and specific T cell subsets in colorectal cancer tumors
Journal Articles

Abstract 1933: Dissecting acquired resistance to KRASG12D inhibition in a mouse model of pancreatic ductal adenocarcinoma

Free
Julien Dilly, Laleh Abbassi, Connor J. Hennessey, Giselle A. Uribe, Brendan Parent, Annan Yang, Kevin S. Kapner, Ziyue Li, Kyle E. Evans, Shatavisha Dasgupta, Megan T. Hoffman, Li Qiang, Felix P. Hambitzer, Seema Chugh, Alex K. Shalek, Stephanie K. Dougan, Brian M. Wolpin, Jonathan A. Nowak, Srivatsan Raghavan, Peter S. Winter, Andrew J. Aguirre
Journal: Cancer Research
Cancer Res (2024) 84 (6_Supplement): 1933.
https://doi.org/10.1158/1538-7445.AM2024-1933
Published: 22 March 2024
View articletitled, Abstract 1933: Dissecting acquired resistance to KRASG12D inhibition in a mouse model of pancreatic ductal adenocarcinoma
Journal Articles

Abstract A035: Stromal composition, fibroblast heterogeneity and spatial organization in pancreatic adenocarcinoma

Free
Dalia Elganainy, Andressa Dias Costa, Alexander Jordan, Suryun Kim, Sara A. Väyrynen, Hannah L. Williams, Chen Yuan, Douglas A. Rubinson, Kimberly Perez, Harshabad Singh, Richard F. Dunne, Thomas E. Clancy, David C. Linehan, Daniel T. Chang, Aram F. Hezel, Albert C. Koong, Andrew Aguirre, Brian M. Wolpin, Jonathan A. Nowak
Journal: Cancer Research
Cancer Res (2024) 84 (2_Supplement): A035.
https://doi.org/10.1158/1538-7445.PANCA2023-A035
Published: 16 January 2024
View articletitled, Abstract A035: Stromal composition, fibroblast heterogeneity and spatial organization in pancreatic adenocarcinoma
Journal Articles

Abstract A093: Deciphering acquired resistance to KRASG12D inhibition in a mouse model of pancreatic ductal adenocarcinoma

Free
Julien Dilly, Laleh Abbassi, Connor J. Hennessey, Giselle A. Uribe, Brendan Parent, Annan Yang, Kevin S. Kapner, Ziyue Li, Shatavisha Dasgupta, Alexander Jordan, Megan T. Hoffman, Li Qiang, Felix P. Hambitzer, Seema Chugh, Alex K. Shalek, Stephanie K. Dougan, Brian M. Wolpin, Jonathan A. Nowak, Srivatsan Raghavan, Peter S. Winter, Andrew J. Aguirre
Journal: Cancer Research
Cancer Res (2024) 84 (2_Supplement): A093.
https://doi.org/10.1158/1538-7445.PANCA2023-A093
Published: 16 January 2024
View articletitled, Abstract A093: Deciphering acquired resistance to KRASG12D inhibition in a mouse model of pancreatic ductal adenocarcinoma
Journal Articles

Allosteric Regulation of Switch-II Domain Controls KRAS Oncogenicity

Available to Purchase
Moon Hee Yang, Timothy H. Tran, Bethany Hunt, Rebecca Agnor, Christian W. Johnson, Bing Shui, Timothy J. Waybright, Jonathan A. Nowak, Andrew G. Stephen, Dhirendra K. Simanshu, Kevin M. Haigis
Journal: Cancer Research
Cancer Res (2023) 83 (19): 3176–3183.
https://doi.org/10.1158/0008-5472.CAN-22-3210
Published: 02 October 2023
View articletitled, Allosteric Regulation of Switch-II Domain Controls KRAS Oncogenicity
Open the PDF for Allosteric Regulation of Switch-II Domain Controls KRAS Oncogenicity in another window
Includes: Supplementary data
Journal Articles

Abstract 5706: ImmunoPROFILE: A prospective implementation of clinically validated, quantitative immune cell profiling test identifies tumor-infiltrating CD8+ and PD-1+ cell densities as prognostic biomarkers across a 2,023 patient pan-cancer cohort treated with different therapies

Free
James Lindsay, Bijaya Sharma, Kristen D. Felt, Anita Giobbie-Hurder, Ian Dryg, Jason L. Weirather, Jennifer Altreuter, Tali Mazor, Priti Kumari, Joao V. Alessi, Ajit J. Nirmal, Michael P. Manos, Ananth R. Kumar, William Lotter, Ethan Cerami, Burce E. Johnson, Neil I. Lindeman, Lynette M. Sholl, Jonathan A. Nowak, Scott J. Rodig
Journal: Cancer Research
Cancer Res (2023) 83 (7_Supplement): 5706.
https://doi.org/10.1158/1538-7445.AM2023-5706
Published: 04 April 2023
View articletitled, Abstract 5706: ImmunoPROFILE: A prospective implementation of clinically validated, quantitative immune cell profiling test identifies tumor-infiltrating CD8+ and PD-1+ cell densities as prognostic biomarkers across a 2,023 patient pan-cancer cohort treated with different therapies
Journal Articles

Spatially Resolved Single-Cell Assessment of Pancreatic Cancer Expression Subtypes Reveals Co-expressor Phenotypes and Extensive Intratumoral Heterogeneity

Available to Purchase
Hannah L. Williams, Andressa Dias Costa, Jinming Zhang, Srivatsan Raghavan, Peter S. Winter, Kevin S. Kapner, Scott P. Ginebaugh, Sara A. Väyrynen, Juha P. Väyrynen, Chen Yuan, Andrew W. Navia, Junning Wang, Annan Yang, Timothy L. Bosse, Radha L. Kalekar, Kristen E. Lowder, Mai Chan Lau, Dalia Elganainy, Vicente Morales-Oyarvide, Douglas A. Rubinson, Harshabad Singh, Kimberly Perez, James M. Cleary, Thomas E. Clancy, Jiping Wang, Joseph D. Mancias, Lauren K. Brais, Emma R. Hill, Margaret M. Kozak, David C. Linehan, Richard F. Dunne, Daniel T. Chang, Albert C. Koong, Aram F. Hezel, William C. Hahn, Alex K. Shalek, Andrew J. Aguirre, Jonathan A. Nowak, Brian M. Wolpin
Journal: Cancer Research
Cancer Res (2023) 83 (3): 441–455.
https://doi.org/10.1158/0008-5472.CAN-22-3050
Published: 03 February 2023
View articletitled, Spatially Resolved Single-Cell Assessment of Pancreatic Cancer Expression Subtypes Reveals Co-expressor Phenotypes and Extensive Intratumoral Heterogeneity
Open the PDF for Spatially Resolved Single-Cell Assessment of Pancreatic Cancer Expression Subtypes Reveals Co-expressor Phenotypes and Extensive Intratumoral Heterogeneity in another window
Includes: Supplementary data
Journal Articles

Abstract B001: Inverse relationship between tissue fusobacterium nucleatum amount and CD274 (PD-L1) expression of colorectal carcinoma

Free
Tomotaka Ugai, Takashi Shimizu, Hidetaka Kawamura, Yasutoshi Takashima, Juha P. Väyrynen, Seyed Mostafa Mousavi Kahaki, Kazuo Okadome, Yohei Masugi, Annacarolina da Silva, Xuehong Zhang, Andrew T. Chan, Molin Wang, Jeffrey A. Meyerhardt, Jonathan A. Nowak, Mingyang Song, Marios Giannakis, Shuji Ogino
Journal: Cancer Research
Cancer Res (2022) 82 (23_Supplement_1): B001.
https://doi.org/10.1158/1538-7445.CRC22-B001
Published: 01 December 2022
View articletitled, Abstract B001: Inverse relationship between tissue fusobacterium nucleatum amount and CD274 (PD-L1) expression of colorectal carcinoma
Journal Articles

Abstract B002: History of appendectomy and colorectal cancer oncidence, overall and by intratumoral fusobacterium nucleatum status

Free
Tomotaka Ugai, Hidetaka Kawamura, Yasutoshi Takashima, Kazuo Okadome, Takashi Shimizu, Kosuke Mima, Seyed Mostafa Mousavi Kahaki, Melissa Zhao, Juha P. Väyrynen, Xuehong Zhang, Kimmie Ng, Jonathan A. Nowak, Jeffrey A. Meyerhardt, Edward L. Giovannucci, Marios Giannakis, Andrew T. Chan, Curtis Huttenhower, Wendy S. Garrett, Mingyang Song, Shuji Ogino
Journal: Cancer Research
Cancer Res (2022) 82 (23_Supplement_1): B002.
https://doi.org/10.1158/1538-7445.CRC22-B002
Published: 01 December 2022
View articletitled, Abstract B002: History of appendectomy and colorectal cancer oncidence, overall and by intratumoral fusobacterium nucleatum status
Journal Articles

Abstract A001: Clinical-genomic analysis of KRAS wild-type pancreatic cancer confirms alternative targetable drivers and provides insight for age and risk related clinical stratification

Free
Harshabad Singh, Rachel B. Keller, Kevin S. Kapner, Julien Dilly, Srivatsan Raghavan, Chen Yuan, Eizabeth Cohen, Michael Tolstorukov, Emma Hill, Elizabeth Andrews, Lauren K. Brais, Annacarolina Da Silva, Kimberly Perez, Douglas A. Rubinson, Benjamin L. Schlechter, Michael H. Rosenthal, Jason L. Hornick, Valentina Nardi, Yvonne Li, Hersh Gupta, Andrew Cherniack, Mathew L. Meyerson, James M. Cleary, Jonathan A. Nowak, Brian M. Wolpin, Andrew A. Aguirre
Journal: Cancer Research
Cancer Res (2022) 82 (22_Supplement): A001.
https://doi.org/10.1158/1538-7445.PANCA22-A001
Published: 15 November 2022
View articletitled, Abstract A001: Clinical-genomic analysis of KRAS wild-type pancreatic cancer confirms alternative targetable drivers and provides insight for age and risk related clinical stratification
Journal Articles

Abstract A075: NCOA4-mediated ferritinophagy is a pancreatic cancer dependency via maintenance of iron bioavailability for iron-sulfur cluster proteins

Free
Naiara Santana-Codina, Huan Zhang, Maria Quiles del Rey, Kevin S. Kapner, Ajami Gikandi, Callum Malcolm, Clara Poupault, Miljan Kuljanin, Kristen John, Douglas E. Biancur, Brandon Chen, Nupur Das, Kristen Lowder, Connor J. Hennessey, Wesley Huang, Annan Yang, Yatrik M. Shah, Jonathan A. Nowak, Andrew J. Aguirre, Joseph D. Mancias
Journal: Cancer Research
Cancer Res (2022) 82 (22_Supplement): A075.
https://doi.org/10.1158/1538-7445.PANCA22-A075
Published: 15 November 2022
View articletitled, Abstract A075: NCOA4-mediated ferritinophagy is a pancreatic cancer dependency via maintenance of iron bioavailability for iron-sulfur cluster proteins
Journal Articles

Abstract 684: Body mass index throughout adulthood and incidence of colorectal cancer subclassified by T cell, macrophage, and myeloid cell infiltrates in cancer tissue

Free
Tomotaka Ugai, Juha P. Väyrynen, Yasutoshi Takashima, Seyed Mostafa Mousavi Kahaki, Benjamin Langworthy, Koichiro Haruki, Naohiko Akimoto, Mai Chan Lau, Rong Zhong, Sara A. Väyrynen, Melissa Zhao, Andressa Dias Costa, Jennifer Borowsky, Jennifer L. Guerriero, Xuehong Zhang, Andrew T. Chan, Molin Wang, Marios Giannakis, Jeffrey A. Meyerhardt, Edward L. Giovannucci, Jonathan A. Nowak, Shuji Ogino
Journal: Cancer Research
Cancer Res (2022) 82 (12_Supplement): 684.
https://doi.org/10.1158/1538-7445.AM2022-684
Published: 15 June 2022
View articletitled, Abstract 684: Body mass index throughout adulthood and incidence of colorectal cancer subclassified by T cell, macrophage, and myeloid cell infiltrates in cancer tissue
Journal Articles

Abstract CT005: T cell inflammation in the tumor microenvironment after agonist CD40 antibody: Clinical and translational results of a neoadjuvant clinical trial

Free
Katelyn T. Byrne, Courtney B. Betts, Rosemarie Mick, Shamilene Sivagnanam, David L. Bajor, Daniel A. Laheru, E. Gabriela Chiorean, Mark H. O'Hara, Shannon M. Liudahl, Craig Newcomb, Cécile Alanio, Ana P. Ferreira, Byung S. Park, Takuya Ohtani, Austin P. Huffman, Sara A. Väyrynen, Andressa Dias Costa, Judith C. Kaiser, Andreanne M. Lacroix, Colleen Redlinger, Martin Stern, Jonathan A. Nowak, E. John Wherry, Martin A. Cheever, Brian M. Wolpin, Emma E. Furth, Elizabeth M. Jaffee, Lisa M. Coussens, Robert H. Vonderheide
Journal: Cancer Research
Cancer Res (2021) 81 (13_Supplement): CT005.
https://doi.org/10.1158/1538-7445.AM2021-CT005
Published: 01 July 2021
View articletitled, Abstract CT005: T cell inflammation in the tumor microenvironment after agonist CD40 antibody: Clinical and translational results of a neoadjuvant clinical trial
Journal Articles

Abstract 2733: Smoking and colorectal cancer Iincidence by tumor microenvironment in cancer tissue

Free
Tomotaka Ugai, Juha P. Väyrynen, Koichiro Haruki, Naohiko Akimoto, Mai Chan Lau, Rong Zhong, Sara A. Väyrynen, Melissa Zhao, Andressa Dias Costa, Jennifer Borowsky, Jennifer L. Guerriero, Charles S. Fuchs, Xuehong Zhang, Molin Wang, Marios Giannakis, Jeffrey A. Meyerhardt, Jonathan A. Nowak, Shuji Ogino
Journal: Cancer Research
Cancer Res (2021) 81 (13_Supplement): 2733.
https://doi.org/10.1158/1538-7445.AM2021-2733
Published: 01 July 2021
View articletitled, Abstract 2733: Smoking and colorectal cancer Iincidence by tumor microenvironment in cancer tissue
Journal Articles

Abstract PR-001: Neoadjuvant therapy is associated with altered composition of immune cell infiltration and an anti-tumorigenic microenvironment in resected pancreatic cancer

Free
Andressa Dias Costa, Sara Väyrynen, Akhil Chawla, Jinming Zhang, Juha P. Väyrynen, Mai Chan Lau, Hannah L. Williams, Chen Yuan, Vicente Morales-Oyarvide, Douglas A. Rubinson, Thomas E. Clancy, Lauren K. Brais, Emma Reilly, Margaret M. Kozak, David C. Linehan, Richard F. Dunne, Daniel T. Chang, Aram F. Hezel, Albert C. Koong, Andrew J. Aguirre, Brian M. Wolpin, Jonathan A. Nowak
Journal: Cancer Research
Cancer Res (2020) 80 (22_Supplement): PR-001.
https://doi.org/10.1158/1538-7445.PANCA20-PR-001
Published: 13 November 2020
View articletitled, Abstract PR-001: Neoadjuvant therapy is associated with altered composition of immune cell infiltration and an anti-tumorigenic microenvironment in resected pancreatic cancer
Journal Articles

Abstract PO-013: MTAP protein expression is lost in nearly one-third of primary pancreatic cancers and is associated with sensitivity to MAT2A inhibition in patient-derived organoid models

Free
Sara A. Väyrynen, Annan Yang, Junning Wang, Jinming Zhang, Kristen Lowder, Kevin S. Kapner, Tim Bosse, Sri Raghavan, Andressa Dias Costa, Hannah Williams, Chen Yuan, Ashley Pelton, Vicente Morales-Oyarvide, Douglas A. Rubinson, Lauren Brais, Emma Reilly, Margaret M. Kozak, David C. Linehan, Richard F. Dunne, Daniel T. Chang, Albert C. Koong, Aram F. Hezel, Brian M. Wolpin, Jonathan A Nowak, Andrew J Aguirre
Journal: Cancer Research
Cancer Res (2020) 80 (22_Supplement): PO-013.
https://doi.org/10.1158/1538-7445.PANCA20-PO-013
Published: 13 November 2020
View articletitled, Abstract PO-013: MTAP protein expression is lost in nearly one-third of primary pancreatic cancers and is associated with sensitivity to MAT2A inhibition in patient-derived organoid models