Photo of Jonathan A. Nowak, MD, PhD

Jonathan A. Nowak, MD, PhD

Brigham And Women's Hospital

Brigham And Women's Hospital
Phone: (617) 732-7510


janowak@bwh.harvard.edu

Photo of Jonathan A. Nowak, MD, PhD

Brigham And Women's Hospital
Phone: (617) 732-7510


janowak@bwh.harvard.edu

Visualize Collaborations

Jonathan A. Nowak, MD, PhD

Brigham And Women's Hospital

EDUCATIONAL TITLES

  • Assistant Professor, Pathology, Harvard Medical School
  • Associate Pathologist, Pathology, Brigham And Women's Hospital

HCC PROGRAM AFFILIATION

Research Abstract

My major research interests are gastrointestinal cancers, specifically colorectal and pancreatic cancer. My laboratory group uses multispectral immunofluorescence, spatial transcriptional profiling, digital imaging, machine learning and genomic profiling to deeply characterize the tumor microenvironment of human tissue specimens in a quantitative manner at single-cell or microscopic resolution. We conduct landscape surveys across cohorts of hundreds or thousands of patients and also perform correlative science analyses using specimens from clinical trial patients. I also develop algorithms and analysis pipelines to support clinical molecular diagnostics of solid tumors and hereditary cancer predisposition.

Publications from Harvard Catalyst Profiles

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  • Aney KJ, Jeong WJ, Koak P, Ohman AW, Nguyen CH, Wolpin BM, Nowak JA, Nissim S. Novel Acinar Metaplastic States Uncovered in Exocrine Pancreas Disease. Cell Mol Gastroenterol Hepatol 2025. PubMed
  • Gurjao C, Cazaubiel J, Tan C, Reardon B, Hofree M, Ugai T, Meyerhardt JA, Nowak JA, Giovannucci E, Townsend JP, Ogino S, Giannakis M. Germline predisposition to oncogenic alkylating damage in colorectal cancer. Cancer Epidemiol Biomarkers Prev 2025. PubMed
  • Harrison TA, Zaidi SH, Yin H, Steinfelder RS, Qu C, Aglago EK, Berndt SI, Boardman LA, Brenner H, Buchanan DD, Campbell PT, Cao Y, Chan AT, Chanock SJ, Doheny KF, Drew DA, Figueiredo JC, French AJ, Gallinger S, Georgeson P, Giannakis M, Goode EL, Gruber SB, Gsur A, Gunter MJ, Harlid S, Hoffmeister M, Huang WY, Hullar MA, Huyghe JR, Jenkins MA, Lin Y, Moreno V, Murphy N, Newcomb PA, Newton CC, Nowak JA, Obón-Santacana M, Ogino S, Shelford T, Song M, Thomas CE, Toland AE, Ugai T, Um CY, Van Guelpen B, Trinh QM, Sun W, Hudson TJ, Hsu L, Peters U, Phipps AI. Genomic characterization of colorectal tumors: insights into significantly mutated genes, pathways, and survival outcomes. BMC Cancer 2025. PubMed
  • Zhang GQ, Meyerhardt JA, Shi Q, Twombly T, Pederson L, Ma C, Väyrynen JP, Zhao M, Takashima Y, Shergill A, Kumar P, Couture F, Kuebler P, Krishnamurthi S, Tan B, O'Reilly EM, Giannakis M, Ogino S, Jurdi A, Sharma S, Aleshin A, Shields AF, Nowak JA. Predictive Role of Circulating Tumor DNA in Stage III Colon Cancer Treated With Celecoxib: A Post Hoc Analysis of the CALGB (Alliance)/SWOG 80702 Phase 3 Randomized Clinical Trial. JAMA Oncol 2025. PubMed
  • Takashima Y, Dias Costa A, Akimoto N, Ugai T, Bell P, Väyrynen JP, Hornick JL, Mino-Kenudson M, Zhong Y, Ugai S, Haruki K, Yao Q, Matsuda K, Higashioka M, Buchanan DD, Phipps AI, Peters U, Giannakis M, Song M, Chan AT, Fuchs CS, Nowak JA, Ogino S. T-cell Subset Features and Distributions Evolve Across the Colorectal Precancer-Cancer Spectrum. Cancer Immunol Res 2025. PubMed
  • Carstens EJ, Takahashi K, Sakamoto N, De Vizio M, Morgado M, Nikkhoi SK, Mangipudi A, Nguyen CH, Weltzin T, Nakayama I, Lv Q, Zeng J, Nie C, Deng C, Wang X, Liu L, Klempner SJ, Ramasubramanian A, Nowak JA, Aguirre AJ, Shitara K, Smith EL. Modeling and addressing on-target/off-tumor toxicity of claudin 18.2 targeted immunotherapies. Nat Commun 2025; 16:9651. PubMed
  • Odintsov I, Siegmund SE, Mahadevan NR, Church AJ, Sholl LM, Nowak JA. A Novel Mutational Signature in Cancers Following Solid Organ or Allogeneic Stem Cell Transplantation. Mod Pathol 2025. PubMed
  • Lindsay JR, Altreuter J, Alessi JV, Weirather JL, Giobbie-Hurder A, Dryg I, Hoebel K, Sharma B, Felt K, Hodi FS, Lindeman N, Sholl LM, Cerami E, Nowak JA, Awad MM, Rodig SJ, Lotter W. Pan-cancer spatial characterization of key immune biomarkers in the tumor microenvironment. Cell Rep Med 2025. PubMed
  • Chalitsios CV, Markozannes G, Aglago EK, Berndt SI, Buchanan DD, Campbell PT, Cao Y, Chan AT, Dimou N, Drew DA, French AJ, Georgeson P, Giannakis M, Gruber SB, Gunter MJ, Harrison TA, Hoffmeister M, Hsu L, Huang WY, Hullar MA, Huyghe JR, Lynch BM, Moreno V, Murphy N, Newton CC, Nowak JA, Obón-Santacana M, Ogino S, Qu C, Schmit SL, Steinfelder RS, Sun W, Thomas CE, Toland AE, Trinh QM, Ugai T, Um CY, Van Guelpen B, Zaidi SH, Schoen RE, Woods MO, Brenner H, Andreson L, Pellatt AJ, Peters U, Phipps AI, Tsilidis KK. Physical activity and molecular subtypes of colorectal cancer: a pooled observational analysis and mendelian randomisation study. JNCI Cancer Spectr 2025. PubMed
  • Bauer AH, Nowak JA, Redston M, Papke DJ. A paired sequencing study of goblet cell adenocarcinomas with coincident sessile serrated lesions and low-grade appendiceal mucinous neoplasms. Virchows Arch 2025. PubMed
  • Alessi JV, Lindsay JR, Giobbie-Hurder A, Sharma B, Felt K, Kumari P, Mazor T, Cerami E, Lotter W, Altreuter J, Weirather J, Dryg I, Hoebel K, Manos M, Adib E, Curtis JD, Ricciuti B, Di Federico A, Ghandour F, Saad E, Wang XA, Pecci F, Holovatska M, Gandhi MM, Hughes ME, O'Meara TA, Chan SJ, Pfaff K, Konstantinopoulos PA, Hodi FS, Shipp MA, Signoretti S, Choueiri T, Wei XX, Santagata S, Hanna GJ, Lin NU, Tolaney SM, Liu J, Sorger PK, Lindeman N, Sholl LM, Nowak JA, Barbie D, Awad MM, Johnson BE, Rodig SJ. Immunoprofiling at an Institutional Scale Reveals That High Numbers of Intratumoral CD8 and PD-1 Cells Predict Superior Patient Survival Across Major Cancer Types Independent of Major Risk Factors. JCO Precis Oncol 2025; 9:e2500240. PubMed
  • Manning DK, Ananda G, Eifert C, Rojas-Rudilla V, Swanton W, Keefe S, Garcia EP, D'Eletto M, Holdmore E, Mishra S, Borziak K, Lukasse P, Davineni P, Manam MD, Shivdasani P, Ghazani AA, Wang AL, Bastepe M, Beltran H, Janeway KA, Church A, Pollaci A, Chittenden AB, Koeller DR, Schwartz Levine A, Garber JE, Johnson BE, Lindeman NI, Nowak JA, Sholl LM, MacConaill LE. Clinical Implementation of Matched Tumor/Germline Sequencing Improves Accuracy of Tumor Genomic Profiling and Therapeutic Recommendations. J Mol Diagn 2025. PubMed
  • Zhang ML, Meredith DM, Bellizzi AM, Nowak JA, Papke DJ. Composite gangliocytoma/neuroma and neuroendocrine tumor: a clinicopathologic, immunohistochemical, and molecular genetic study of 11 cases. Virchows Arch 2025. PubMed
  • Wesselink E, Thomas CE, Takashima Y, Mizuno H, Buchanan DD, Qu C, Hsu L, Dias Costa A, Ugai S, Zhong Y, Huyghe JR, Thomas S, Gallinger S, Grant RC, Le Marchand L, Masugi Y, van Duijnhoven FJ, Ugai T, Ogino S, Nowak JA, Peters U, Phipps AI. Associations between calcium intake and T cell infiltration in colorectal tumours. Cancer Prev Res (Phila Pa) 2025. PubMed
  • Thomas CE, Takashima Y, Buchanan DD, Wesselink E, Qu C, Hsu L, Dias Costa A, Gallinger S, Grant RC, Huyghe JR, Thomas S, Ugai S, Zhong Y, Matsuda K, Ugai T, Peters U, Ogino S, Nowak JA, Phipps AI. Density of T cell subsets in colorectal cancer in relation to disease-specific survival. Cancer Epidemiol Biomarkers Prev 2025. PubMed
  • Maoz A, Bleday R, Goldsmith J, Matalon SA, Redston MS, Nestor M, Nowak JA, Yurgelun MB. Intratumoral Heterogeneity of Mismatch Repair Status and Outcome of Treatment With Dostarlimab in a Patient With Locally Advanced Rectal Adenocarcinoma. JCO Precis Oncol 2025; 9:e2500041. PubMed
  • Chalitsios CV, Markozannes G, Papagiannopoulos C, Aglago EK, Berndt SI, Buchanan DD, Campbell PT, Cao Y, Chan AT, Dimou N, Drew DA, French AJ, Georgeson P, Giannakis M, Gruber SB, Gunter MJ, Harrison TA, Hoffmeister M, Hsu L, Huang WY, Hullar MA, Huyghe JR, Lynch BM, Moreno V, Newton CC, Nowak JA, Obón-Santacana M, Ogino S, Qu C, Schmit SL, Steinfelder RS, Sun W, Thomas CE, Toland AE, Trinh QM, Ugai T, Um CY, Van Guelpen B, Zaidi SH, Murphy N, Peters U, Phipps AI, Tsilidis KK. Waist circumference, a body shape index, and molecular subtypes of colorectal cancer: A pooled analysis of four cohort studies. Cancer Epidemiol Biomarkers Prev 2025. PubMed
  • Lau MC, Borowsky J, Väyrynen JP, Haruki K, Zhao M, Dias Costa A, Gu S, da Silva A, Ugai T, Arima K, Nguyen MN, Takashima Y, Yeong J, Tai D, Hamada T, Lennerz JK, Fuchs CS, Wu CJ, Meyerhardt JA, Ogino S, Nowak JA. Tumor-immune partitioning and clustering algorithm for identifying tumor-immune cell spatial interaction signatures within the tumor microenvironment. PLoS Comput. Biol. 2025; 21:e1012707. PubMed
  • Hamada T, Ugai T, Gurjao C, Ugai S, Zhang X, Haruki K, Takashima Y, Akimoto N, Lau MC, Matsuda K, Nakazawa N, Higashioka M, Miyahara S, Kosumi K, Masugi Y, Liu L, Cao Y, Nevo D, Wang M, Nishihara R, Shukla SA, Wu CJ, Garraway LA, Meyerhardt JA, Giovannucci EL, Nowak JA, Fuchs CS, Chan AT, Song M, Giannakis M, Ogino S. Smoking habit and long-term colorectal cancer incidence by exome-wide mutational and neoantigen loads: evidence based on the prospective cohort incident-tumour biobank method. BMJ Oncol 2025; 4:e000787. PubMed
  • Singh H, Xiu J, Kapner KS, Yuan C, Narayan RR, Oberley M, Farrell A, Surana R, Huffman BM, Perez K, Cleary JM, Jordan AC, Dias Costa A, Williams HL, Raghavan S, Weinberg B, Pishvaian MJ, Shroff R, Goel S, Dougan SK, Nowak JA, Spetzler D, Sledge G, Wolpin BM, Aguirre AJ. Clinical and genomic features of classical and basal transcriptional subtypes in pancreatic cancer. Clin Cancer Res 2024. PubMed
  • Ugai S, Yao Q, Takashima Y, Zhong Y, Matsuda K, Kawamura H, Imamura Y, Okadome K, Mima K, Arima K, Kosumi K, Song M, Meyerhardt JA, Giannakis M, Nowak JA, Ugai T, Ogino S. Clinicopathological, molecular, and prognostic features of colorectal carcinomas with KRAS c.34G>T (p.G12C) mutation. Cancer Sci 2024. PubMed
  • Aglago EK, Qu C, Harlid S, Phipps AI, Steinfelder RS, Ogino S, Thomas CE, Hsu L, Toland AE, Brenner H, Berndt SI, Buchanan DD, Campbell PT, Cao Y, Chan AT, Drew DA, Figueiredo JC, French AJ, Gallinger S, Georgeson P, Giannakis M, Goode EL, Gruber SB, Gunter MJ, Harrison TA, Hoffmeister M, Huang WY, Hullar MA, Huyghe JR, Jenkins MA, Lynch BM, Moreno V, Murphy N, Newton CC, Nowak JA, Obón-Santacana M, Sun W, Ugai T, Um CY, Zaidi SH, Tsilidis KK, van Guelpen B, Peters U. Folate intake and colorectal cancer risk according to genetic subtypes defined by targeted tumor sequencing. Am J Clin Nutr 2024. PubMed
  • Oberstein PE, Dias Costa A, Kawaler EA, Cardot-Ruffino V, Rahma OE, Beri N, Singh H, Abrams TA, Biller LH, Cleary J, Enzinger P, Huffman BM, McCleary NJ, Perez KJ, Rubinson DA, Schlechter BL, Surana R, Yurgelun MB, Wang SJ, Remland J, Brais LK, Bollenrucher N, Chang E, Ali LR, Lenehan PJ, Dolgalev I, Werba G, Lima C, Keheler CE, Sullivan KM, Dougan M, Hajdu C, Dajee M, Pelletier MR, Nazeer S, Squires M, Bar-Sagi D, Wolpin BM, Nowak JA, Simeone DM, Dougan SK. Blockade of IL-1β and PD-1 with combination chemotherapy reduces systemic myeloid suppression in metastatic pancreatic cancer with heterogeneous effects in the tumor. Cancer Immunol Res 2024. PubMed
  • Dilly J, Hoffman MT, Abbassi L, Li Z, Paradiso F, Parent BD, Hennessey CJ, Jordan AC, Morgado M, Dasgupta S, Uribe GA, Yang A, Kapner KS, Hambitzer FP, Qiang L, Feng H, Geisberg J, Wang J, Evans KE, Lyu H, Schalck A, Feng N, Lopez AM, Bristow CA, Kim MP, Rajapakshe KI, Bahrambeigi V, Roth JA, Garg K, Guerrero PA, Stanger BZ, Cristea S, Lowe SW, Baslan T, Van Allen EM, Mancias JD, Chan E, Anderson A, Katlinskaya YV, Shalek AK, Hong DS, Pant S, Hallin J, Anderes K, Olson P, Heffernan TP, Chugh S, Christensen JG, Maitra A, Wolpin BM, Raghavan S, Nowak JA, Winter PS, Dougan SK, Aguirre AJ. Mechanisms of resistance to oncogenic KRAS inhibition in pancreatic cancer. 2024. PubMed
  • Nowak JA, Twombly T, Ma C, Shi Q, Haruki K, Fujiyoshi K, Väyrynen J, Zhao M, Knight J, Mane S, Shergill A, Kumar P, Couture F, Kuebler P, Krishnamurthi S, Tan B, Philip P, O'Reilly EM, Shields AF, Ogino S, Fuchs CS, Meyerhardt JA. Improved Survival With Adjuvant Cyclooxygenase 2 Inhibition in -Activated Stage III Colon Cancer: CALGB/SWOG 80702 (Alliance). J Clin Oncol 2024. PubMed
  • Furtado LV, Bifulco C, Dolderer D, Hsiao SJ, Kipp BR, Lindeman NI, Ritterhouse LL, Temple-Smolkin RL, Zehir A, Nowak JA. Recommendations for Tumor Mutational Burden Assay Validation and Reporting: A Joint Consensus Recommendation of the Association for Molecular Pathology, College of American Pathologists, and Society for Immunotherapy of Cancer. J Mol Diagn 2024. PubMed
  • Kawamura H, Ugai T, Takashima Y, Okadome K, Shimizu T, Mima K, Akimoto N, Haruki K, Arima K, Zhao M, Väyrynen JP, Wu K, Zhang X, Ng K, Nowak JA, Meyerhardt JA, Giovannucci EL, Giannakis M, Chan AT, Huttenhower C, Garrett WS, Song M, Ogino S. Appendectomy and Long-term Colorectal Cancer Incidence, Overall and by Tumor Fusobacterium nucleatum Status. Ann Surg 2024. PubMed
  • Schmit SL, Tsai YY, Bonner JD, Sanz-Pamplona R, Joshi AD, Ugai T, Lindsey SS, Melas M, McDonnell KJ, Idos GE, Walker CP, Qu C, Kast WM, Da Silva DM, Glickman JN, Chan AT, Giannakis M, Nowak JA, Rennert HS, Robins HS, Ogino S, Greenson JK, Moreno V, Rennert G, Gruber SB. Germline genetic regulation of the colorectal tumor immune microenvironment. BMC Genomics 2024; 25:409. PubMed
  • Blise KE, Sivagnanam S, Betts CB, Betre K, Kirchberger N, Tate BJ, Furth EE, Dias Costa A, Nowak JA, Wolpin BM, Vonderheide RH, Goecks J, Coussens LM, Byrne KT. Machine learning links T-cell function and spatial localization to neoadjuvant immunotherapy and clinical outcome in pancreatic cancer. Cancer Immunol Res 2024. PubMed
  • Elomaa H, Härkönen J, Väyrynen SA, Ahtiainen M, Ogino S, Nowak JA, Lau MC, Helminen O, Wirta EV, Seppälä TT, Böhm J, Mecklin JP, Kuopio T, Väyrynen JP. Quantitative Multiplexed Analysis of Indoleamine 2,3-Dioxygenase (IDO) and Arginase-1 (ARG1) Expression and Myeloid Cell Infiltration in Colorectal Cancer. Mod Pathol 2024; 37:100450. PubMed
  • Wang QL, Babic A, Rosenthal MH, Lee AA, Zhang Y, Zhang X, Song M, Rezende LFM, Lee DH, Biller L, Ng K, Giannakis M, Chan AT, Meyerhardt JA, Fuchs CS, Eliassen AH, Birmann BM, Stampfer MJ, Giovannucci EL, Kraft P, Nowak JA, Yuan C, Wolpin BM. Cancer Diagnoses After Recent Weight Loss. JAMA 2024; 331:318-328. PubMed
  • Thomas CE, Georgeson P, Qu C, Steinfelder RS, Buchanan DD, Song M, Harrison TA, Um CY, Hullar MA, Jenkins MA, Van Guelpen B, Lynch BM, Melaku YA, Huyghe JR, Aglago EK, Berndt SI, Boardman LA, Campbell PT, Cao Y, Chan AT, Drew DA, Figueiredo JC, French AJ, Giannakis M, Goode EL, Gruber SB, Gsur A, Gunter MJ, Hoffmeister M, Hsu L, Huang WY, Moreno V, Murphy N, Newcomb PA, Newton CC, Nowak JA, Obón-Santacana M, Ogino S, Sun W, Toland AE, Trinh QM, Ugai T, Zaidi SH, Peters U, Phipps AI. Epidemiologic factors in relation to colorectal cancer risk and survival by genotoxic colibactin mutational signature. Cancer Epidemiol Biomarkers Prev 2024. PubMed
  • Takashima Y, Kawamura H, Okadome K, Ugai S, Haruki K, Arima K, Mima K, Akimoto N, Nowak JA, Giannakis M, Garrett WS, Sears CL, Song M, Ugai T, Ogino S. Enrichment of Bacteroides fragilis and enterotoxigenic Bacteroides fragilis in CpG island methylator phenotype-high colorectal carcinoma. Clin. Microbiol. Infect. 2024. PubMed
  • Thomas CE, Takashima Y, Wesselink E, Ugai T, Steinfelder RS, Buchanan DD, Qu C, Hsu L, Dias Costa A, Gallinger S, Grant RC, Huyghe JR, Thomas SS, Ogino S, Phipps AI, Nowak JA, Peters U. Association between somatic microsatellite instability, hypermutation status, and specific T cell subsets in colorectal cancer tumors. 2024; 15:1505896. PubMed
  • Katz MHG, Petroni GR, Bauer T, Reilley MJ, Wolpin BM, Stucky CC, Bekaii-Saab TS, Elias R, Merchant N, Dias Costa A, Lenehan P, Cardot-Ruffino V, Rodig S, Pfaff K, Dougan SK, Nowak JA, Varadhachary GR, Slingluff CL, Rahma O. Multicenter randomized controlled trial of neoadjuvant chemoradiotherapy alone or in combination with pembrolizumab in patients with resectable or borderline resectable pancreatic adenocarcinoma. J Immunother Cancer 2023. PubMed
  • Baranov E, Nowak JA. Pathologic Evaluation of Therapeutic Biomarkers in Colorectal Adenocarcinoma. 2023; 16:635-650. PubMed
  • Shi S, Wang K, Ugai T, Giannakis M, Cazaubiel J, Chan AT, Giovannucci EL, Nowak JA, Meyerhardt JA, Ogino S, Song M. Vitamin C intake and colorectal cancer survival according to KRAS and BRAF mutation: a prospective study in two US cohorts. Br J Cancer 2023; 129:1793-1800. PubMed
  • Ali LR, Lenehan PJ, Cardot-Ruffino V, Dias Costa A, Katz MHG, Bauer TW, Nowak JA, Wolpin BM, Abrams TA, Patel A, Clancy TE, Wang J, Mancias JD, Reilley MJ, Stucky CH, Bekaii-Saab TS, Elias R, Merchant N, Slingluff CL, Rahma OE, Dougan SK. PD-1 blockade induces reactivation of non-productive T cell responses characterized by NF-kB signaling in patients with pancreatic cancer. Clin Cancer Res 2023. PubMed
  • Yang MH, Tran TH, Hunt B, Agnor R, Johnson CW, Shui B, Waybright TJ, Nowak JA, Stephen AG, Simanshu DK, Haigis KM. Allosteric regulation of switch-II domain controls KRAS oncogenicity. Cancer Res 2023. PubMed
  • Singh H, Keller RB, Kapner KS, Dilly J, Raghavan S, Yuan C, Cohen EF, Tolstorukov M, Andrews E, Brais LK, da Silva A, Perez K, Rubinson DA, Surana R, Giannakis M, Ng K, Clancy TE, Yurgelun MB, Schlechter BL, Clark JW, Shapiro GI, Rosenthal MH, Hornick JL, Nardi V, Li YY, Gupta H, Cherniack AD, Meyerson M, Cleary JM, Nowak JA, Wolpin BM, Aguirre AJ. Oncogenic drivers and therapeutic vulnerabilities in KRAS wild-type pancreatic cancer. Clin Cancer Res 2023. PubMed
  • Babic A, Rosenthal MH, Sundaresan TK, Khalaf N, Lee V, Brais LK, Loftus M, Caplan L, Denning S, Gurung A, Harrod J, Schawkat K, Yuan C, Wang QL, Lee AA, Biller LH, Yurgelun MB, Ng K, Nowak JA, Aguirre AJ, Bhatia SN, Vander Heiden MG, Van Den Eeden SK, Caan BJ, Wolpin BM. Adipose tissue and skeletal muscle wasting precede clinical diagnosis of pancreatic cancer. Nat Commun 2023; 14:4317. PubMed
  • Zhao M, Lau MC, Haruki K, Väyrynen JP, Gurjao C, Väyrynen SA, Dias Costa A, Borowsky J, Fujiyoshi K, Arima K, Hamada T, Lennerz JK, Fuchs CS, Nishihara R, Chan AT, Ng K, Zhang X, Meyerhardt JA, Song M, Wang M, Giannakis M, Nowak JA, Yu KH, Ugai T, Ogino S. Bayesian risk prediction model for colorectal cancer mortality through integration of clinicopathologic and genomic data. NPJ Precis Oncol 2023; 7:57. PubMed
  • Elomaa H, Ahtiainen M, Väyrynen SA, Ogino S, Nowak JA, Lau MC, Helminen O, Wirta EV, Seppälä TT, Böhm J, Mecklin JP, Kuopio T, Väyrynen JP. Spatially resolved multimarker evaluation of CD274 (PD-L1)/PDCD1 (PD-1) immune checkpoint expression and macrophage polarisation in colorectal cancer. Br J Cancer 2023; 128:2104-2115. PubMed
  • Zhang Y, Wang QL, Yuan C, Lee AA, Babic A, Ng K, Perez K, Nowak JA, Lagergren J, Stampfer MJ, Giovannucci EL, Sander C, Rosenthal MH, Kraft P, Wolpin BM. Pancreatic cancer is associated with medication changes prior to clinical diagnosis. Nat Commun 2023; 14:2437. PubMed
  • Marinoff AE, Spurr LF, Fong C, Li YY, Forrest SJ, Ward A, Doan D, Corson L, Mauguen A, Pinto N, Maese L, Colace S, Macy ME, Kim A, Sabnis AJ, Applebaum MA, Laetsch TW, Glade-Bender J, Weiser DA, Anderson M, Crompton BD, Meyers P, Zehir A, MacConaill L, Lindeman N, Nowak JA, Ladanyi M, Church AJ, Cherniack AD, Shukla N, Janeway KA. Clinical Targeted Next-Generation Panel Sequencing Reveals Amplification Is a Poor Prognostic Factor in Osteosarcoma. JCO Precis Oncol 2023; 7:e2200334. PubMed
  • Ugai T, Haruki K, Harrison TA, Cao Y, Qu C, Chan AT, Campbell PT, Akimoto N, Berndt S, Brenner H, Buchanan DD, Chang-Claude J, Fujiyoshi K, Gallinger SJ, Gunter MJ, Hidaka A, Hoffmeister M, Hsu L, Jenkins MA, Milne RL, Moreno V, Newcomb PA, Nishihara R, Pai RK, Sakoda LC, Slattery ML, Sun W, Amitay EL, Alwers E, Thibodeau SN, Toland AE, Van Guelpen B, Woods MO, Zaidi SH, Potter JD, Giannakis M, Song M, Nowak JA, Phipps AI, Peters U, Ogino S. Molecular Characteristics of Early-Onset Colorectal Cancer According to Detailed Anatomical Locations: Comparison With Later-Onset Cases. Am J Gastroenterol 2023. PubMed
  • Ugai T, Akimoto N, Haruki K, Harrison TA, Cao Y, Qu C, Chan AT, Campbell PT, Berndt SI, Buchanan DD, Cross AJ, Diergaarde B, Gallinger SJ, Gunter MJ, Harlid S, Hidaka A, Hoffmeister M, Brenner H, Chang-Claude J, Hsu L, Jenkins MA, Lin Y, Milne RL, Moreno V, Newcomb PA, Nishihara R, Obon-Santacana M, Pai RK, Sakoda LC, Schoen RE, Slattery ML, Sun W, Amitay EL, Alwers E, Thibodeau SN, Toland AE, Van Guelpen B, Zaidi SH, Potter JD, Meyerhardt JA, Giannakis M, Song M, Nowak JA, Peters U, Phipps AI, Ogino S. Prognostic role of detailed colorectal location and tumor molecular features: analyses of 13,101 colorectal cancer patients including 2994 early-onset cases. J Gastroenterol 2023. PubMed
  • Ugai T, Shimizu T, Kawamura H, Ugai S, Takashima Y, Usui G, Väyrynen JP, Okadome K, Haruki K, Akimoto N, Masugi Y, da Silva A, Mima K, Zhang X, Chan AT, Wang M, Garrett WS, Freeman GJ, Meyerhardt JA, Nowak JA, Song M, Giannakis M, Ogino S. Inverse relationship between amount and tumor CD274 (PD-L1) expression in colorectal carcinoma. Clin Transl Immunology 2023; 12:e1453. PubMed
  • Williams HL, Dias Costa A, Zhang J, Raghavan S, Winter PS, Kapner KS, Ginebaugh SP, Väyrynen SA, Väyrynen JP, Yuan C, Navia AW, Wang J, Yang A, Bosse TL, Kalekar RL, Lowder KE, Lau MC, Elganainy D, Morales-Oyarvide V, Rubinson DA, Singh H, Perez K, Cleary JM, Clancy TE, Wang J, Mancias JD, Brais LK, Hill ER, Kozak MM, Linehan DC, Dunne RF, Chang DT, Koong AC, Hezel AF, Hahn WC, Shalek AK, Aguirre AJ, Nowak JA, Wolpin BM. Spatially-resolved single-cell assessment of pancreatic cancer expression subtypes reveals co-expressor phenotypes and extensive intra-tumoral heterogeneity. Cancer Res 2022. PubMed
  • Ugai T, Liu L, Tabung FK, Hamada T, Langworthy BW, Akimoto N, Haruki K, Takashima Y, Okadome K, Kawamura H, Zhao M, Kahaki SMM, Glickman JN, Lennerz JK, Zhang X, Chan AT, Fuchs CS, Song M, Wang M, Yu KH, Giannakis M, Nowak JA, Meyerhardt JA, Wu K, Ogino S, Giovannucci EL. Prognostic role of inflammatory diets in colorectal cancer overall and in strata of tumor-infiltrating lymphocyte levels. Clin Transl Med 2022; 12:e1114. PubMed
  • Dias Costa A, Väyrynen SA, Chawla A, Zhang J, Väyrynen JP, Lau MC, Williams HL, Yuan C, Morales-Oyarvide V, Elganainy D, Singh H, Cleary JM, Perez K, Ng K, Freed-Pastor W, Mancias JD, Dougan SK, Wang J, Rubinson DA, Dunne RF, Kozak MM, Brais L, Reilly E, Clancy T, Linehan DC, Chang DT, Hezel AF, Koong AC, Aguirre A, Wolpin BM, Nowak JA. Neoadjuvant chemotherapy is associated with altered immune cell infiltration and an anti-tumorigenic microenvironment in resected pancreatic cancer. Clin Cancer Res 2022. PubMed
  • Wang F, Ugai T, Haruki K, Wan Y, Akimoto N, Arima K, Zhong R, Twombly TS, Wu K, Yin K, Chan AT, Giannakis M, Nowak JA, Meyerhardt JA, Liang L, Song M, Smith-Warner SA, Zhang X, Giovannucci EL, Willett WC, Ogino S. Healthy and unhealthy plant-based diets in relation to the incidence of colorectal cancer overall and by molecular subtypes. Clin Transl Med 2022; 12:e893. PubMed
  • Berchuck JE, Boiarsky D, Silver R, Sunkara R, McClure HM, Tsai HK, Siegmund S, Tewari AK, Nowak JA, Lindeman NI, Rana HQ, Choudhury AD, Pomerantz MM, Freedman ML, Van Allen EM, Taplin ME. Addition of Germline Testing to Tumor-Only Sequencing Improves Detection of Pathogenic Germline Variants in Men With Advanced Prostate Cancer. JCO Precis Oncol 2022; 6:e2200329. PubMed
  • Väyrynen JP, Haruki K, Lau MC, Väyrynen SA, Ugai T, Akimoto N, Zhong R, Zhao M, Dias Costa A, Borowsky J, Bell P, Takashima Y, Fujiyoshi K, Arima K, Kishikawa J, Shi SS, Twombly TS, Song M, Wu K, Chan AT, Zhang X, Fuchs CS, Meyerhardt JA, Giannakis M, Ogino S, Nowak JA. Spatial Organization and Prognostic Significance of NK and NKT-like Cells via Multimarker Analysis of the Colorectal Cancer Microenvironment. Cancer Immunol Res 2022; 10:215-227. PubMed
  • Ugai T, Väyrynen JP, Lau MC, Borowsky J, Akimoto N, Väyrynen SA, Zhao M, Zhong R, Haruki K, Dias Costa A, Fujiyoshi K, Arima K, Wu K, Chan AT, Cao Y, Song M, Fuchs CS, Wang M, Lennerz JK, Ng K, Meyerhardt JA, Giannakis M, Nowak JA, Ogino S. Immune cell profiles in the tumor microenvironment of early-onset, intermediate-onset, and later-onset colorectal cancer. Cancer Immunol Immunother 2021. PubMed
  • Väyrynen JP, Haruki K, Väyrynen SA, Lau MC, Dias Costa A, Borowsky J, Zhao M, Ugai T, Kishikawa J, Akimoto N, Zhong R, Shi S, Chang TW, Fujiyoshi K, Arima K, Twombly TS, Da Silva A, Song M, Wu K, Zhang X, Chan AT, Nishihara R, Fuchs CS, Meyerhardt JA, Giannakis M, Ogino S, Nowak JA. Prognostic significance of myeloid immune cells and their spatial distribution in the colorectal cancer microenvironment. J Immunother Cancer 2021. PubMed
  • Väyrynen JP, Haruki K, Lau MC, Väyrynen SA, Zhong R, Dias Costa A, Borowsky J, Zhao M, Fujiyoshi K, Arima K, Twombly TS, Kishikawa J, Gu S, Aminmozaffari S, Shi S, Baba Y, Akimoto N, Ugai T, da Silva A, Guerriero JL, Song M, Wu K, Chan AT, Nishihara R, Fuchs CS, Meyerhardt JA, Giannakis M, Ogino S, Nowak JA. The prognostic role of macrophage polarization in the colorectal cancer microenvironment. Cancer Immunol Res 2020. PubMed
  • Du C, da Silva A, Morales-Oyarvide V, Dias Costa A, Kozak MM, Dunne RF, Rubinson DA, Perez K, Masugi Y, Hamada T, Brais LK, Yuan C, Babic A, Ducar MD, Thorner AR, Aguirre A, Kulke MH, Ng K, Clancy TE, Findeis-Hosey JJ, Chang DT, Hornick JL, Fuchs CS, Ogino S, Koong AC, Hezel AF, Wolpin BM, Nowak JA. Insulin-Like Growth Factor-1 Receptor Expression and Disease Recurrence and Survival in Patients with Resected Pancreatic Ductal Adenocarcinoma. Cancer Epidemiol Biomarkers Prev 2020. PubMed
  • Väyrynen JP, Lau MC, Haruki K, Väyrynen SA, Dias Costa A, Borowsky J, Zhao M, Fujiyoshi K, Arima K, Twombly TS, Kishikawa J, Gu S, Aminmozaffari S, Shi S, Baba Y, Akimoto N, Ugai T, da Silva A, Song M, Wu K, Chan AT, Nishihara R, Fuchs CS, Meyerhardt JA, Giannakis M, Ogino S, Nowak JA. Prognostic significance of immune cell populations identified by machine learning in colorectal cancer using routine hematoxylin & eosin stained sections. Clin Cancer Res 2020. PubMed
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