Publications

2022

Porter, LD The Importance of Patient Engagement to Improve Healthcare Research and Safety. Global Journal on Quality and Safety in Healthcare 1 May 2022; 5 (2): 27–30. doi: https://doi.org/10.36401/JQSH-22-X1

Arima K, Zhong R, Ugai T, Zhao M, Haruki K, Akimoto N, Lau MC, Okadome K, Mehta RS, Väyrynen JP, Kishikawa J, Twombly TS, Shi S, Fujiyoshi K, Kosumi K, Ogata Y, Baba H, Wang F, Wu K, Song M, Zhang X, Fuchs CS, Sears CL, Willett WC, Giovannucci EL, Meyerhardt JA, Garrett WS, Huttenhower C, Chan AT, Nowak JA, Giannakis M, Ogino S. Western-style Diet, pks Island-Carrying Escherichia coli, and Colorectal Cancer: Analyses from Two Large Prospective Cohort Studies. Gastroenterology. 2022 Jun 23:S0016-5085(22)00672-2. doi: 10.1053/j.gastro.2022.06.054. Epub ahead of print. PMID: 35760086.

Drewes JL, Chen J, Markham NO, Knippel RJ, Domingue JC, Tam AJ, Chan JL, Kim L, McMann M, Stevens C, Dejea CM, Tomkovich S, Michel J, White JR, Mohammad F, Campodonico VL, Heiser CN, Wu X, Wu S, Ding H, Simner P, Carroll K, Shrubsole MJ, Anders RA, Walk ST, Jobin C, Wan F, Coffey RJ, Housseau F,

Lau KS, Sears CL. Human colon cancer-derived Clostridioides difficile strains drive colonic tumorigenesis in mice. Cancer Discov. 2022 Jun 9:candisc.1273.2021-10-4 15:58:09.930. doi: 10.1158/2159-8290.CD-21-1273. Epub ahead of print. PMID: 35678528.

Fang L, Ford-Roshon D, Russo M, O’Brien C, Xiong X, Gurjao C, Grandclaudon M, Raghavan S, Corsello SM, Carr SA, Udeshi ND, Berstler J, Sicinska E, Ng K, Giannakis M. RNF43 G659fs is an oncogenic colorectal cancer mutation and sensitizes tumor cells to PI3K/mTOR inhibition. Nat Commun. 2022 Jun 8;13(1):3181. doi: 10.1038/s41467-022-30794-7. PMID: 35676246; PMCID: PMC9177965.

Li R, Ugai T, Xu L, Zucker D, Ogino S, Wang M. Utility of Continuous Disease Subtyping Systems for Improved Evaluation of Etiologic Heterogeneity. Cancers (Basel). 2022 Apr 2;14(7):1811. doi: 10.3390/cancers14071811. PMID: 35406583; PMCID: PMC8997600.

2021

Sakamoto Y, Mima K, Ishimoto T, Ogata Y, Imai K, Miyamoto Y, Akiyama T, Daitoku N, Hiyoshi Y, Iwatsuki M, Baba Y, Iwagami S, Yamashita YI, Yoshida N, Komohara Y, Ogino S, Baba H. Relationship between Fusobacterium nucleatum and antitumor immunity in colorectal cancer liver metastasis. Cancer Sci. 2021 Nov;112(11):4470-4477. doi: 10.1111/cas.15126. Epub 2021 Sep 23. PMID: 34464993; PMCID: PMC8586672.

Thornton AM, Fang L, Lo A, McSharry M, Haan D, O’Brien C, Berger AH, Giannakis M, Brooks AN. eVIP2: Expression-based variant impact phenotyping to predict the function of gene variants. PLoS Comput Biol. 2021 Jul 2;17(7):e1009132. doi: 10.1371/journal.pcbi.1009132. PMID: 34214079; PMCID: PMC8281988.

Borowsky J, Haruki K, Lau MC, Dias Costa A, Väyrynen JP, Ugai T, Arima K, da Silva A, Felt KD, Zhao M, Gurjao C, Twombly TS, Fujiyoshi K, Väyrynen SA, Hamada T, Mima K, Bullman S, Harrison TA, Phipps AI, Peters U, Ng K, Meyerhardt JA, Song M, Giovannucci EL, Wu K, Zhang X, Freeman GJ, Huttenhower C, Garrett WS, Chan AT, Leggett BA, Whitehall VLJ, Walker N, Brown I, Bettington M, Nishihara R, Fuchs CS, Lennerz JK, Giannakis M, Nowak JA, Ogino S. Association of Fusobacterium nucleatum with Specific T-cell Subsets in the Colorectal Carcinoma Microenvironment. Clin Cancer Res. 2021 May 15;27(10):2816-2826. doi: 10.1158/1078-0432.CCR-20-4009. Epub 2021 Feb 25. PMID: 33632927; PMCID: PMC8127352.

Despins CA, Brown SD, Robinson AV, Mungall AJ, Allen-Vercoe E, Holt RA. Modulation of the Host Cell Transcriptome and Epigenome by Fusobacterium nucleatum. mBio. 2021 Oct 26;12(5):e020622.

Brennan, CA, Clay, SL, Lavoie, SL, Bae, S, Lang, JK, Fonseca-Pereira, D, Rosinski, KG, Ou, N, Glickman, JN, Garrett, WS. Fusobacterium nucleatum drives a pro-inflammatory intestinal microenvironment through metabolite receptor-dependent modulation of IL-17 expression, Gut Microbes 13:1, 2021

Wang Y, Nguyen LH, Mehta RS, Song M, Huttenhower C, Chan AT. Association Between the Sulfur Microbial Diet and Risk of Colorectal Cancer. JAMA Network Open. 2021;4(11).

Borozan, I, Zaidi, SH, Harrison, TA, Phipps, AI, Zheng, J, Lee, S, Trinh, QM, Steinfelder, RS, Adams, J, Banbury, BL, Berndt, SI, Brezina, S, Buchanan, DD, Bullman, S, Cao, Y, Farris, AB, Figueiredo, JC, Giannakis, M, Heisler, LE, Hopper, JL, Lin, Y, Luo, X, Nishihara, R, Mardis, ER, Papadopoulos, N, Qu, C, Reid, EG, Thibodeau, SN, Harlid, S, Um, CY, Hsu, L, Gsur, A, Campbell, PT, Gallinger, S, Newcomb, PA, Ogino, S, Sun, W, Hudson, TJ, Ferretti, V and Peters, U. Molecular and pathology features of colorectal tumors and patient outcomes are associated with Fusobacterium nucleatum and its subspecies animalis. Cancer Epidemiology Biomarkers & Prevention November 4, 2021.

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 Immunology, Immunotherapy September 16, 2021.

Gurjao C, Zhong R, Haruki K, Li YY, Spurr L F, Lee-Six H, Reardon B, Ugai T, Zhang X, Cherniack AD, Song M, Van Allen EM, Meyerhardt JA, Nowak JA, Giovannucci EL, Fuchs CS, Wu K, Ogino S, Giannakis M. Discovery and Features of an Alkylating Signature in Colorectal Cancer. Cancer Discovery August 16 2021

Puschhof J, Pleguezuelos-Manzano C, Martinez-Silgado A, Akkerman N, Saftien A, Boot C, de Waal A, Beumer J, Dutta D, Heo I, Clevers H. Intestinal organoid cocultures with microbes. Nature Protocols. 2021 Aug 11. Epub ahead of print. PMID: 34381208.

Sikavi DR, Nguyen LH, Haruki K, Ugai T, Ma W, Wang DD, Thompson KN, Yan Y, Branck T, Wilkinson JE, Akimoto N, Zhong R, Lau MC, Mima K, Kosumi K, Morikawa T, Rimm EB, Garrett WS, Izard J, Cao Y, Song M, Huttenhower C, Ogino S, Chan AT. The Sulfur Microbial Diet and Risk of Colorectal Cancer by Molecular Subtypes and Intratumoral Microbial Species in Adult Men. Clinical and Translational Gastroenterology. 2021 Aug 1;12(8)

DeStefano Shields CE, White JR, Chung L, Wenzel A, Hicks JL, Tam AJ, Chan JL, Dejea CM, Fan H, Michel J, Maiuri AR, Sriramkumar S, Podicheti R, Rusch DB, Wang H, De Marzo AM, Besharati S, Anders RA, Baylin SB, O’Hagan HM, Housseau F, Sears CL. Bacterial-driven inflammation and mutant BRAF expression combine to promote murine colon tumorigenesis that is sensitive to immune checkpoint therapy. Cancer Discovery. 2021 July.

Renwick S, Ganobis CM, Elder RA, Gianetto-Hill C, Higgins G, Robinson AV, Vancuren SJ, Wilde J, Allen-Vercoe E. Culturing Human Gut Microbiomes in the Laboratory. Annual Review Microbiology. 2021 May 26. doi: 10.1146/annurev-micro-031021-084116.

Beghini F, McIver LJ, Blanco-Míguez A, Dubois L, Asnicar F, Maharjan S, Mailyan A, Manghi P, Scholz M, Thomas AM, Valles-Colomer M, Weingart G, Zhang Y, Zolfo M, Huttenhower C, Franzosa EA, Segata N. Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3. Elife. 2021 May 4;10:e65088.

Brennan CA, Nakatsu G, Gallini Comeau CA, Drew DA, Glickman JN, Schoen RE, Chan AT, Garrett WS. Aspirin Modulation of the Colorectal Cancer-Associated Microbe Fusobacterium nucleatum. mBio. 2021 Apr 6;12(2):e00547-21.

Rosendahl Huber A, Pleguezuelos-Manzano C, Puschhof J. A bacterial mutational footprint in colorectal cancer genomes. British Journal of Cancer. 2021 May;124(11):1751-1753. doi: 10.1038/s41416-021-01273-5. Epub 2021 Mar 19.

Young C, Wood HM, Fuentes Balaguer A, Bottomley D, Gallop N, Wilkinson L, Benton SC, Brealey M, John C, Burtonwood C, Thompson KN, Yan Y, Barrett JH, Morris EJA, Huttenhower C, Quirke P. Microbiome Analysis of More Than 2,000 NHS Bowel Cancer Screening Programme Samples Shows the Potential to Improve Screening Accuracy. Clinical Cancer Research. 2021 Mar 3.

Young C, Wood HM, Seshadri RA, Van Nang P, Vaccaro C, Melendez LC, Bose M, Van Doi M, Piñero TA, Valladares CT, Arguero J, Balaguer AF, Thompson KN, Yan Y, Huttenhower C, Quirke P. The colorectal cancer-associated faecal microbiome of developing countries resembles that of developed countries. Genome Medicine. 2021 Feb 16;13(1):27.

Nevo D, Ogino S, Wang M. Reflection on modern methods: causal inference considerations for heterogeneous disease etiology. International Journal of Epidemiol. 2021 Jan 23.

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. 2021 Jan;9(1):8-19.

2020

Babic A, Zhang X, Morales-Oyarvide V, Yuan C, Khalaf N, Khalili H, Lochhead P, Chan AT, Ogino S, Wolpin BM, Wu K, Fuchs CS, Giovannucci EL, Stampfer MJ, Ng K. Acid-suppressive medications and risk of colorectal cancer: results from three large prospective cohort studies. Br J Cancer. 2020 Sep;123(5):844-851.

Pleguezuelos-Manzano C, Puschhof J, van den Brink S, Geurts V, Beumer J, Clevers H. Establishment and Culture of Human Intestinal Organoids Derived from Adult Stem Cells. Curr Protoc Immunol. 2020 Sep;130(1):e106.

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 and Eosin-Stained Sections. Clin Cancer Res. 2020 Aug 15;26(16):4326-4338.

Yan Y, Nguyen LH, Franzosa EA, Huttenhower C. Strain-level epidemiology of microbial communities and the human microbiome. Genome Med. 2020 Aug 13;12(1):71. doi: 10.1186/s13073-020-00765-y. PMID: 32791981; PMCID: PMC7427293.

Serna G, Ruiz-Pace F, Hernando J, Alonso L, Fasani R, Landolfi S, Comas R, Jimenez J, Elez E, Bullman S, Tabernero J, Capdevila J, Dienstmann R, Nuciforo P. Fusobacterium nucleatum persistence and risk of recurrence after preoperative treatment in locally advanced rectal cancer. Ann Oncol. 2020 Jun 20:S0923-7534(20)39890-2.

Beumer J, Puschhof J, Bauzá-Martinez J, Martínez-Silgado A, Elmentaite R, James KR, Ross A, Hendriks D, Artegiani B, Busslinger GA, Ponsioen B, Andersson-Rolf A, Saftien A, Boot C, Kretzschmar K, Geurts MH, Bar-Ephraim YE, Pleguezuelos-Manzano C, Post Y, Begthel H, van der Linden F, Lopez-Iglesias C, van de Wetering WJ, van der Linden R, Peters PJ, Heck AJR, Goedhart J, Snippert H, Zilbauer M, Teichmann SA, Wu W, Clevers H. High-Resolution mRNA and Secretome Atlas of Human Enteroendocrine Cells. Cell. 2020 Jun 11;181(6):1291-1306.e19

McCuaig S, Barras D, Mann EH, Friedrich M, Bullers SJ, Janney A, Garner LC, Domingo E, Koelzer VH, Delorenzi M, Tejpar S, Maughan TS, West NR, Powrie F. The Interleukin 22 Pathway Interacts with Mutant KRAS to Promote Poor Prognosis in Colon Cancer. Clinical Cancer Research. 19 May 2020;26:4313–25.

Fujiyoshi K, Chen Y, Haruki K, Ugai T, Kishikawa J, Hamada T, Liu L, Arima K, Borowsky J, Väyrynen JP, Zhao M, Lau MC, Gu S, Shi S, Akimoto N, Twombly TS, Drew DA, Song M, Chan AT, Giovannucci EL, Meyerhardt JA, Fuchs CS, Nishihara R, Lennerz JK, Giannakis M, Nowak JA, Zhang X, Wu K, Ogino S. Smoking Status at Diagnosis and Colorectal Cancer Prognosis According to Tumor Lymphocytic Reaction. JNCI Cancer Spectr. 2020 May 14;4(5):pkaa040. doi: 10.1093/jncics/pkaa040. PMID: 32923934; PMCID: PMC7477375.

Haruki K, Kosumi K, Hamada T, Twombly TS, Väyrynen JP, Kim SA, Masugi Y, Qian ZR, Mima K, Baba Y, da Silva A, Borowsky J, Arima K, Fujiyoshi K, Lau MC, Li P, Guo C, Chen Y, Song M, Nowak JA, Nishihara R, Yanaga K, Zhang X, Wu K, Bullman S, Garrett WS, Huttenhower C, Meyerhardt JA, Giannakis M, Chan AT, Fuchs CS, Ogino S. Association of autophagy status with amount of Fusobacterium nucleatum in colorectal cancer. J Pathol. 2020 Apr;250(4):397-408.

Haruki K, Kosumi K, Li P, Arima K, Väyrynen JP, Lau MC, Twombly TS, Hamada T, Glickman JN, Fujiyoshi K, Chen Y, Du C, Guo C, Väyrynen SA, Dias Costa A, Song M, Chan AT, Meyerhardt JA, Nishihara R, Fuchs CS, Liu L, Zhang X, Wu K, Giannakis M, Nowak JA, Ogino S. An integrated analysis of lymphocytic reaction, tumour molecular characteristics, and patient survival in colorectal cancer. Br J Cancer. 2020 Apr;122(9):1367-1377.

Nguyen LH, Ma W, Wang DD, Cao Y, Mallick H, Gerbaba TK, Lloyd-Price J, Abu-Ali G, Hall AB, Sikavi D, Drew DA, Mehta RS, Arze C, Joshi AD, Yan Y, Branck T, DuLong C, Ivey KL, Ogino S, Rimm EB, Song M, Garrett WS, Izard J, Huttenhower C, Chan AT. Association Between Sulfur-Metabolizing Bacterial Communities in Stool and Risk of Distal Colorectal Cancer in Men. Gastroenterology. 2020 Apr;158(5):1313-1325.

Lavoie S, Chun E, Bae S, Brennan CA, Comeau CAG, Lang JK, Michaud M, Hoveyda HR, Fraser GL, Fuller MH, Layden BT, Glickman JN, Garrett WS. Expression of FFAR2 by Dendritic Cells Prevents Their Expression of IL27 and is Required For Maintenance of Mucosal Barrier and Immune Response Against Colorectal Tumors in Mice. Gastroenterology. 2020. Apr;158(5):1359-1372.e9.

Yan Y, Drew DA, Markowitz A, Lloyd-Price J, Abu-Ali G, Nguyen LH, Tran C, Chung DC, Gilpin KK, Meixell D, Parziale M, Schuck M, Patel Z, Richter JM, Kelsey PB, Garrett WS, Chan AT, Stadler ZK, Huttenhower C. Structure of the mucosal and stool microbiome in Lynch syndrome. Cell Host & Microbe. 2020. Apr 8;27(4):585-600.e4

Pleguezuelos-Manzano C*, Puschhof J*, Rosendahl Huber A*, van Hoeck A, Wood, H, Nomburg JL., Gurjao C, Manders F, Dalmasso G, Stege P, Paganelli F, Geurts MH, Beumer J, Mizutani T, van der Linden R, van Elst S, The Genomics England Consortium, Top J, Willems R, Giannakis M, Bonnet R, Quirke P, Meyerson M, Cuppen E, van Boxtel R, Clevers H. Mutational signature in colorectal cancer induced by genotoxic pks+ E. coli. Nature, 2020 Apr;580(7802):269-273

2019

Gurjao C, Liu D, Hofree M, AlDubayan SH, Wakiro I, Su MJ, Felt K, Gjini E, Brais LK, Rotem A, Rosenthal MH, Rozenblatt-Rosen O, Rodig S, Ng K, Van Allen EM, Corsello SM, Ogino S, Regev A, Nowak JA, Giannakis M. Intrinsic Resistance to Immune Checkpoint Blockade in a Mismatch Repair-Deficient Colorectal Cancer. Cancer Immunol Res. 2019;7:1230-1236.

2022

Inamura K, Hamada T, Bullman S, Ugai T, Yachida S, Ogino S. Cancer as microenvironmental, systemic and environmental diseases: opportunity for transdisciplinary microbiomics science. Gut. 2022 Jul 12:gutjnl-2022-327209. doi: 10.1136/gutjnl-2022-327209. Epub ahead of print. PMID: 35820782.

Clay SL, Fonseca-Pereira D, Garrett WS. Colorectal cancer: the facts in the case of the microbiota. J Clin Invest. 2022 Feb 15;132(4):e155101. doi: 10.1172/JCI155101. PMID: 35166235; PMCID: PMC8843708.

2021

Knippel RJ, Drewes, JL, Sears CL The Cancer Microbiome: Recent Highlights and Knowledge Gaps. Cancer Discovery August 16, 2021 DOI: 10.1158/2159-8290.CD-21-0324

Knippel RJ, Sears CL. The Microbiome Colorectal Cancer Puzzle: Initiator, Propagator, and Avenue for Treatment and Research. J Natl Compr Canc Netw. 2021 Aug 1;19(8):986-992. doi: 10.6004/jnccn.2021.7062. PMID: 34416704.

Zhang, Y, Thompson, KN, Branck, T, Yan, Y, Nguyen, LH, Franzosa, EA, Huttenhower, C. Metatranscriptomics for the Human Microbiome and Microbial Community Functional Profiling. Annual Review of Biomedical Data Science, Volume 4, 2021, pp 279-311.

Mima K, Kosumi K, Baba Y, Hamada T, Baba H, Ogino S. The microbiome, genetics, and gastrointestinal neoplasms: the evolving field of molecular pathological epidemiology to analyze the tumor-immune-microbiome interaction. Hum Genet. 2021 May;140(5):725-746. doi: 10.1007/s00439-020-02235-2. Epub 2020 Nov 12. PMID: 33180176; PMCID: PMC8052267.

Wilkinson JE, Franzosa EA, Everett C, Li C; HCMPH researchers and trainees; HCMPH investigators, Hu FB, Wirth DF, Song M, Chan AT, Rimm E, Garrett WS, Huttenhower C. A framework for microbiome science in public health. Nat Med. 2021 May;27(5):766-774. doi: 10.1038/s41591-021-01258-0. Epub 2021 Apr 5. PMID: 33820996.

Akimoto N, Ugai T, Zhong R, Hamada T, Fujiyoshi K, Giannakis M, Wu K, Cao Y, Ng K, Ogino S. Rising incidence of early-onset colorectal cancer – a call to action. Nat Rev Clin Oncol. 2021 Apr;18(4):230-243. doi: 10.1038/s41571-020-00445-1. Epub 2020 Nov 20. PMID: 33219329; PMCID: PMC7994182.

2020

Mann EH, Maughan TS. Fusobacterium nucleatum, rectal cancer and radiotherapy. Ann Oncol. 2020 Oct;31(10):1277-1278

Biller LH and Ng K. Pioneering a new care model for young-onset colorectal cancer: innovations in clinical care and scientific discovery. Colorectal Cancer 26 October 2020

Yan Y, Nguyen LH, Franzosa EA, Huttenhower C. Strain-level epidemiology of microbial communities and the human microbiome. Genome Med. 2020 Aug 13;12(1):71.

Meyerson M. Bacterial invaders drive CRC progression. Science Signaling 2020 Aug 11; 13(644):eabc4218

Domingue JC, Drewes JL, Housseau F, Sears CL. Host Responses to Mucosal Biofilms in the Lung and Gut. Mucosal Immunology. 2020 May;13(3):413-422.

Sears CL, Salzberg SL. Microbial Diagnostics for Cancer: A step forward but not prime time yet. Cancer Cell 37:625-627, 2020.

Shaikh F, Sears CL. Messengers from the microbiota. Science 369:1427-1428, 2020.

Janney, A., Powrie, F. & Mann, E.H. Host–microbiota maladaptation in colorectal cancer. Nature 585, 509–517 (2020).

2019

Elinav E, Garrett WS, Trinchieri G, Wargo J. The Cancer Microbiome. Nat Rev Cancer. 2019 Jul;19(7):371-376.

Garrett, WS. The Gut Microbiota and Colon Cancer. Science. 2019 Jun 21;364(6446):1133-1135.