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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 5926: Determining classical-basal transcriptional subtypes of pancreatic ductal adenocarcinoma using circulating tumor DNA epigenomic profiling

Free
Karl Semaan, Marc Eid, Damien Vasseur, Gunsagar S. Gulati, Ji-Heui Seo, Alexander Jordan, Andressa Dias Costa, John Canniff, Leigh Culnane, Elizabeth Andrews, Emma C. Coleman, Noa Phillips, Brad Fortunato, Hunter Savignano, Rashad Nawfal, Razane El Hajj Chehade, Talal El Zarif, Ze Zhang, Paulo Cordeiro, Antoine Hollebecque, Antoine Italiano, Brandon M. Huffman, James M. Cleary, Jonathan Nowak, Jacob E. Berchuck, Toni K. Choueiri, Kimberly Perez, Andrew J. Aguirre, Sylvan C. Baca, Brian M. Wolpin, Matthew L. Freedman, Harshabad Singh
Journal: Cancer Research
Cancer Res (2025) 85 (8_Supplement_1): 5926.
https://doi.org/10.1158/1538-7445.AM2025-5926
Published: 21 April 2025
View articletitled, Abstract 5926: Determining classical-basal transcriptional subtypes of pancreatic ductal adenocarcinoma using circulating tumor DNA epigenomic profiling
Journal Articles

Abstract PR-21: Temporal stability and chemotherapy responsiveness of classical and basal transcriptional subtypes of pancreatic cancer

Free
Harshabad Singh, Joanne Xiu, Kevin Kapner, Chen Yuan, Raja R Narayan, Matthew Oberley, Alex Farrell, Rishi Surana, Brandon M Huffmann, Kimberly J Perez, James M Cleary, Alexander C Jordan, Andressa Dias Costa, Hannah L Williams, Srivatsan Raghavan, Benjamin Weinberg, Michael J Pishvaian, Rachna T Shroff, Sanjay Goel, Stephanie K Dougan, Jonathan Nowak, David Spetzler, George Sledge, Brian M Wolpin, Andrew J Aguirre
Journal: Cancer Research
Cancer Res (2024) 84 (17_Supplement_2): PR-21.
https://doi.org/10.1158/1538-7445.PANCREATIC24-PR-21
Published: 15 September 2024
View articletitled, Abstract PR-21: Temporal stability and chemotherapy responsiveness of classical and basal transcriptional subtypes of pancreatic cancer
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 B065: Eosinophils alter metastatic spread in pancreatic cancer

Free
Megan T Hoffman, Patrick J Lenehan, Alice Bertocchi, Jen Wang, Lestat Ali, Li Qiang, Amiko Uchida, Sara Vayrynen, Andressa Dias Costa, Michael Dougan, Max Heckler, Jonathan Nowak, Brian W Wolpin, Stephanie K Dougan
Journal: Cancer Research
Cancer Res (2024) 84 (17_Supplement_2): B065.
https://doi.org/10.1158/1538-7445.PANCREATIC24-B065
Published: 15 September 2024
View articletitled, Abstract B065: Eosinophils alter metastatic spread in pancreatic cancer
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 B016: Eosinophils alter metastatic spread in pancreatic cancer

Free
Megan T. Hoffman, Patrick J. Lenehan, Jen Wang, Lestat Ali, Amiko Uchida, Sara Vayrynen, Andressa Dias Costa, Michael Dougan, Max Heckler, Jonathan Nowak, Brian W. Wolpin, Stephanie K. Dougan
Journal: Cancer Research
Cancer Res (2024) 84 (2_Supplement): B016.
https://doi.org/10.1158/1538-7445.PANCA2023-B016
Published: 16 January 2024
View articletitled, Abstract B016: Eosinophils alter metastatic spread in pancreatic cancer
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 3014: Association between HLA-KIR allele interaction combinations and density of T-cell subsets in colorectal cancer

Free
Claire Elizabeth Thomas, Jeroen Huyghe, Tomotaka Ugai, Hang Yin, Yasutoshi Takashima, Daniel D. Buchanan, Conghui Qu, Li Hsu, Andressa Dias Costa, Stephen Gallinger, Robert Grant, Sushma Thomas, Shuji Ogino, Amanda I. Phipps, Jonathan Nowak, Ulrike Peters
Journal: Cancer Research
Cancer Res (2023) 83 (7_Supplement): 3014.
https://doi.org/10.1158/1538-7445.AM2023-3014
Published: 04 April 2023
View articletitled, Abstract 3014: Association between HLA-KIR allele interaction combinations and density of T-cell subsets in colorectal cancer
Journal Articles

Abstract 5760: Molecular, immune, and microbial profiles of early-onset, intermediate-onset, and later-onset CRCs

Free
Tomotaka Ugai, Yasutoshi Takashima, Andressa Dias Costa, Daniel Buchanan, Jeroen Huyghe, Li Hsu, Conghui Qu, Claire Thomas, Steve Gallinger, Robert Grant, Ulrike Peters, Amanda I. Phipps, Jonathan Nowak, Shuji Ogino
Journal: Cancer Research
Cancer Res (2023) 83 (7_Supplement): 5760.
https://doi.org/10.1158/1538-7445.AM2023-5760
Published: 04 April 2023
View articletitled, Abstract 5760: Molecular, immune, and microbial profiles of early-onset, intermediate-onset, and later-onset CRCs
Journal Articles

Abstract 3019: Density of T cell subsets in colorectal cancer in relation to disease-specific survival

Free
Amanda I. Phipps, Jonathan Nowak, Yasutoshi Takashima, Daniel Buchanan, Andressa Dias Costa, Steven Gallinger, Jeroen Huyghe, Li Hsu, Conghui Qu, Claire Thomas, Sushma Thomas, Tomotaka Ugai, Ulrike Peters, Shuji Ogino
Journal: Cancer Research
Cancer Res (2023) 83 (7_Supplement): 3019.
https://doi.org/10.1158/1538-7445.AM2023-3019
Published: 04 April 2023
View articletitled, Abstract 3019: Density of T cell subsets in colorectal cancer in relation to disease-specific survival
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 B018: Eosinophils alter metastatic spread in pancreatic cancer

Free
Megan T. Hoffman, Patrick J. Lenehan, Jennifer Wang, Lestat Ali, Li Qiang, Amiko Uchida, Sara Vayrynen, Andressa Dias Costa, Michael Dougan, Max Heckler, Jonathan Nowak, Brian W. Wolpin, Stephanie K. Dougan
Journal: Cancer Research
Cancer Res (2022) 82 (22_Supplement): B018.
https://doi.org/10.1158/1538-7445.PANCA22-B018
Published: 15 November 2022
View articletitled, Abstract B018: Eosinophils alter metastatic spread in pancreatic cancer
Journal Articles

Abstract PR005: Primary results of PanCAN-SR1, a phase 1b study evaluating Gemcitabine, nab-Paclitaxel, Canakinumab, and Spartalizumab to target IL-1β and PD-1 in metastatic pancreatic cancer with correlative tissue and blood biomarker analysis

Free
Paul E. Oberstein, Osama Rahma, Nina Beri, Amy Stoll-D'Astice, Emily A. Kawaler, Igor Dolgalev, Gregor Werba, Victoire Cardo-Ruffino, Naïma Böllenrücher, Andressa Dias Costa, Saloney Nazeer, Matthew Squires, Jonathan Nowak, Dafna Bar-Sagi, Brian Wolpin, Diane M Simeone, Stephanie K Dougan
Journal: Cancer Research
Cancer Res (2022) 82 (22_Supplement): PR005.
https://doi.org/10.1158/1538-7445.PANCA22-PR005
Published: 15 November 2022
View articletitled, Abstract PR005: Primary results of PanCAN-SR1, a phase 1b study evaluating Gemcitabine, nab-Paclitaxel, Canakinumab, and Spartalizumab to target IL-1β and PD-1 in metastatic pancreatic cancer with correlative tissue and blood biomarker analysis
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 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
Journal Articles

Abstract PO-058: Transcriptional subtype-specific microenvironmental crosstalk and tumor cell plasticity in metastatic pancreatic cancer

Free
Srivatsan Raghavan, Peter S. Winter, Andrew W. Navia, Hannah L. Williams, Alan DenAdel, Radha L. Kalekar, Jennyfer Galvez-Reyes, Kristen E. Lowder, Nolawit Mulugeta, Manisha S. Raghavan, Ashir A. Borah, Sara A. Vayrynen, Andressa Dias Costa, Junning Wang, Emma Reilly, Dorisanne Y. Ragon, Lauren K. Brais, Alex M. Jaeger, James M. Cleary, Lorin Crawford, Jonathan A. Nowak, Brian M. Wolpin, William C. Hahn, Andrew J. Aguirre, Alex K. Shalek
Journal: Cancer Research
Cancer Res (2020) 80 (22_Supplement): PO-058.
https://doi.org/10.1158/1538-7445.PANCA20-PO-058
Published: 13 November 2020
View articletitled, Abstract PO-058: Transcriptional subtype-specific microenvironmental crosstalk and tumor cell plasticity in metastatic pancreatic cancer
Journal Articles

Abstract PR-006: Spatially resolved, single cell assessment of pancreatic ductal adenocarcinoma expression subtypes reveals mixed and hybrid basal-classical marker expression with prognostic significance and discrete spatial localization

Free
Hannah L. Williams, Jinming Zhang, Srivatsan Raghavan, Peter S. Winter, Kevin Kapner, Sara Vayrynen, Andressa Dias Costa, Chen Yuan, Mai Chan Lau, Vicente Morales-Oyarvide, Douglas Rubinson, Lauren Brais, Emma Reilly, Margaret Kozak, David Linehan, Richard Dunne, Daniel Chang, Albert Koong, Aram Hezel, William C. Hahn, Alek K. Shalek, Andrew J. Aguirre, Jonathan A. Nowak, Brian M Wolpin
Journal: Cancer Research
Cancer Res (2020) 80 (22_Supplement): PR-006.
https://doi.org/10.1158/1538-7445.PANCA20-PR-006
Published: 13 November 2020
View articletitled, Abstract PR-006: Spatially resolved, single cell assessment of pancreatic ductal adenocarcinoma expression subtypes reveals mixed and hybrid basal-classical marker expression with prognostic significance and discrete spatial localization