Review
Oncology
Arun Kumar, Asgar Ali, Raj Kishore Kapardar, Ghulam Mehdi Dar, Abhay Kumar Sharma, Renu Verma, Real Sumayya Abdul Sattar, Ejaj Ahmad, Bhawna Mahajan, Sundeep Singh Saluja
Summary: Colorectal cancer (CRC) is the third most common cancer, and the association between gut microbiota and CRC is crucial. Diet plays a significant role in the composition of gut microbiota and may increase the risk of CRC. Patients with CRC exhibit dysbiosis of the gut microbiota, which can be identified by a decline in beneficial bacterial species and an increase in harmful bacterial populations. Using probiotics or altering the gut microbiota could be effective in CRC treatment.
JOURNAL OF CANCER RESEARCH AND CLINICAL ONCOLOGY
(2023)
Article
Microbiology
Zhi Liu, Xuemei Zhang, Haoding Zhang, Hong Zhang, Zhongyuan Yi, Qingqing Zhang, Qisha Liu, Xingyin Liu
Summary: Using multi-omics data, this study explores the role of intratumor microbes in influencing immune-cell infiltration patterns, prognosis, and therapy response in colorectal cancer (CRC). The study identifies the components and structure of the intratumor microbiome as primary contributors to the difference in survival between immune-cell infiltration subtypes. It suggests that intratumor microbes may influence response to immune checkpoint blockade therapy by mediating tumor-infiltrating immune cells.
MICROBIOLOGY SPECTRUM
(2023)
Review
Cell Biology
Sanaz Keshavarz Shahbaz, Khadijeh Koushki, Seyed Hassan Ayati, Abigail R. Bland, Evgeny E. Bersonov, Amirhossein Sahebkar
Summary: Inflammasomes play contradictory roles in inflammation-induced cancer development, as they can both promote carcinogenesis and exhibit anticancer effects through triggering pyroptosis and immunoregulatory functions.
Article
Microbiology
Yu Chen, Hongjian Sun, Mengzhe Sun, Changguo Shi, Hongmei Sun, Xiaoli Shi, Binbin Ji, Jinpeng Cui
Summary: Microbes play a crucial role in the formation and development of diseases. A novel computational model, NLLMDA, was developed to identify potential associations between microbes and diseases, particularly in colon cancer and colorectal carcinoma. Through various algorithms and information integration methods, NLLMDA successfully predicted the potential associations between microbes and diseases with high accuracy and effectiveness, showcasing its superiority compared to other classical MDA methods.
FRONTIERS IN MICROBIOLOGY
(2021)
Review
Pharmacology & Pharmacy
Cong Xia, Yantao Cai, Shuangyi Ren, Chenglai Xia
Summary: The human gut microbiota plays a significant role in the development and progression of colorectal cancer, and manipulating the gut microbiota could be a novel approach for prevention and treatment. Specific bacteria have been found to have anti-tumor activity and can improve the tumor microenvironment by activating immune cells and upregulating the secretion of pro-tumor immune cytokines. This paper summarizes the potential benefits of certain bacteria in colorectal cancer, highlights their roles in the tumor microenvironment, discusses the application of gut microbes in combination with immunosuppressive agents, and provides suggestions for further experimental studies and clinical practice applications.
FRONTIERS IN PHARMACOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Paulina Czajka-Francuz, Sylwia Cison-Jurek, Aleksander Czajka, Maciej Kozaczka, Jerzy Wojnar, Jerzy Chudek, Tomasz Francuz
Summary: Tumor microenvironment (TME) consists of tumor, stromal, and immune cells interacting with each other. Early and advanced colorectal tumors have different structures and altered levels of serum cytokines. The crosstalk among TME infiltrating cells can influence patients' prognosis by shifting the balance towards immune suppression or pro-inflammatory, antitumor responses. Understanding TME processes could aid in therapeutic planning and accurate patient prognosis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biology
Shanwen Chen, Yunfan Jin, Siqi Wang, Shaozhen Xing, Yingchao Wu, Yuhuan Tao, Yongchen Ma, Shuai Zuo, Xiaofan Liu, Yichen Hu, Hongyan Chen, Yuandeng Luo, Feng Xia, Chuanming Xie, Jianhua Yin, Xin Wang, Zhihua Liu, Ning Zhang, Zhenjiang Zech Xu, Zhi John Lu, Pengyuan Wang
Summary: The utility of cell-free nucleic acids in monitoring cancer has been recognized. By profiling cfRNAs in plasma samples, human and microbe-derived plasma cfRNAs were found to have diagnostic value for cancer detection. Adding microbial features improved the accuracy of tumor classification.
Review
Gastroenterology & Hepatology
Michael W. Dougherty, Christian Jobin
Summary: The development of colorectal cancer is influenced by the presence of bacterial communities in the gastrointestinal tract. These microorganisms obtain essential nutrients from indigestible compounds and play a role in molecular signaling pathways that are necessary for normal tissue and immune function. Several bacterial species, such as Fusobacterium nucleatum, Enterotoxigenic Bacteroides fragilis, and pks(+) E. coli, have been identified to potentially increase the risk of colorectal cancer. Recent research has expanded on this topic to include host mutational status, microbial heterogeneity within tumors, transient infections, and the cumulative effects of multiple carcinogenic bacteria. This review provides an updated overview of how host-bacteria interactions influence colorectal cancer development, potential applications in diagnosis or prevention, and the impact of the gut microbiome on colorectal cancer treatment efficacy.
Article
Oncology
Suguru Maruyama, Akihiko Okamura, Yasukazu Kanie, Kei Sakamoto, Daisuke Fujiwara, Jun Kanamori, Yu Imamura, Koichi Takeda, Masayuki Watanabe
Summary: This study found that preoperative fecal microbiota is associated with the host's inflammatory and nutritional status, and may influence the outcomes after oncologic esophagectomy.
ANNALS OF SURGICAL ONCOLOGY
(2022)
Review
Oncology
Yan Chen, Ying-Xuan Chen
Summary: In the past decade, research on the interaction between intestinal microbiota and colorectal cancer has been active, with microbial metabolites playing a significant role in the development of colorectal cancer, especially through immune responses. There are close links between human gut microbiota and colorectal cancer, with specific bacteria and microbiota-derived metabolites influencing complex immune responses that affect carcinogenesis. Diet greatly impacts the microbiota structure and its metabolism, with some metabolites like short-chain fatty acids and indole derivatives acting as protectors against cancer by regulating immune responses, while others may promote cancer.
Review
Oncology
Viktoriia Cherkasova, Olga Kovalchuk, Igor Kovalchuk
Summary: Recent preclinical studies have shown that the changes in endocannabinoid system signaling can have various effects on intestinal inflammation and colorectal cancer. Due to the heterogeneity of colorectal cancer, the choice of cannabinoids for prevention and treatment depends on the type of the disease, its etiology, driver mutations, and the expression levels of cannabinoid receptors.
Review
Biochemistry & Molecular Biology
Annamaria Bardelcikova, Jindrich Soltys, Jan Mojzis
Summary: Colorectal cancer (CRC) is the second leading cause of cancer-related deaths globally. Inflammation and oxidative stress (OS) are involved in the development of CRC. Chronic OS can lead to biomolecule oxidation or inflammatory signaling activation, resulting in tumor initiation or cancer cell survival. There is also a link between OS and inflammatory bowel disease (IBD), which is associated with an increased risk of cancer.
Article
Medicine, Research & Experimental
Debrup Chakraborty, Wei Jin, Jing Wang
Summary: Adiponectin is closely associated with metabolism and cancer, with low levels reported in obesity, inflammatory diseases, and various cancers including colorectal cancer. However, the exact function and mechanisms of adiponectin in colorectal cancer remain unclear, with contradictory reports on its role in cancer. Further research is needed to better understand adiponectin's function in tumor development.
Review
Immunology
Xinxin Hou, Zongmei Zheng, Jiao Wei, Ling Zhao
Summary: There is a relationship between gut microbial dysbiosis and colorectal cancer (CRC) initiation and progression, as well as with the host immune system. Understanding this interaction can lead to the development of microbiota-based immunotherapy strategies for CRC.
FRONTIERS IN IMMUNOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Antonios N. Gargalionis, Kostas A. Papavassiliou, Athanasios G. Papavassiliou
Summary: STAT3 plays a critical role in the development of colorectal cancer by enhancing tumor cell proliferation and growth through inflammatory mechanisms. However, the mechanisms underlying the role of STAT3 in tumor immunity are not fully understood, and STAT3 inhibitors have not yet been widely used in clinical practice.
Article
Biochemical Research Methods
Liam F. Spurr, Mehdi Touat, Alison M. Taylor, Adrian M. Dubuc, Juliann Shih, David M. Meredith, William Pisano, Matthew L. Meyerson, Keith L. Ligon, Andrew D. Cherniack, Yvonne Y. Li, Rameen Beroukhim
Summary: The expansion of targeted panel sequencing efforts has created opportunities for large-scale genomic analysis, but tools for copy-number quantification on panel data are lacking. We introduce ASCETS, a method for the efficient quantitation of arm and chromosome-level copy-number changes from targeted sequencing data.
Article
Oncology
Jian Carrot-Zhang, Giovanny Soca-Chafre, Nick Patterson, Aaron R. Thorner, Anwesha Nag, Jacqueline Watson, Giulio Genovese, July Rodriguez, Maya K. Gelbard, Luis Corrales-Rodriguez, Yoichiro Mitsuishi, Gavin Ha, Joshua D. Campbell, Geoffrey R. Oxnard, Oscar Arrieta, Andres F. Cardona, Alexander Gusev, Matthew Meyerson
Summary: This study found significant associations between Native American ancestry and somatic genomic landscape in lung cancer patients, suggesting that germline genetics may play a key role in tumor mutation burden and specific driver mutations. Further studies are needed to identify the genetic alleles underlying the variation in EGFR and KRAS mutation frequencies.
Article
Immunology
Mark N. Lee, Matthew Meyerson
Summary: This study introduces a high-throughput epitope identification system that combines T cell-secreted cytokines capture, cell sorting, and next-generation sequencing to identify new class I- and class II-restricted epitopes. The technology successfully validated known viral, neoepitope, and autoimmune epitope-specific TCR targets, as well as discovered new epitopes encoded by the human cytomegalovirus genome. This cytokine capture-based assay enables pooled screening of thousands of encoded peptides for epitope discovery and may lead to identification of HLA-epitope-TCR complexes relevant to disease control, etiology, or treatment.
SCIENCE IMMUNOLOGY
(2021)
Correction
Cell Biology
Jian Carrot-Zhang, Xiaotong Yao, Siddhartha Devarakonda, Aditya Deshpande, Jeffrey S. Damrauer, Tiago Chedraoui Silva, Christopher K. Wong, Hyo Young Choi, Ina Felau, A. Gordon Robertson, Mauro A. A. Castro, Lisui Bao, Esther Rheinbay, Eric Minwei Liu, Tuan Trieu, David Haan, Christina Yau, Toshinori Hinoue, Yuexin Liu, Ofer Shapira, Kiran Kumar, Karen L. Mungall, Hailei Zhang, Jake June-Koo Lee, Ashton Berger, Galen F. Gao, Binyamin Zhitomirsky, Wen-Wei Liang, Meng Zhou, Sitapriya Moorthi, Alice H. Berger, Eric A. Collisson, Michael C. Zody, Li Ding, Andrew D. Cherniack, Gad Getz, Olivier Elemento, Christopher C. Benz, Josh Stuart, J. C. Zenklusen, Rameen Beroukhim, Jason C. Chang, Joshua D. Campbell, D. Neil Hayes, Lixing Yang, Peter W. Laird, John N. Weinstein, David J. Kwiatkowski, Ming S. Tsao, William D. Travis, Ekta Khurana, Benjamin P. Berman, Katherine A. Hoadley, Nicolas Robine, Matthew Meyerson, Ramaswamy Govindan, Marcin Imielinski
Article
Multidisciplinary Sciences
Marsha C. Wibowo, Zhen Yang, Maxime Borry, Alexander Huebner, Kun D. Huang, Braden T. Tierney, Samuel Zimmerman, Francisco Barajas-Olmos, Cecilia Contreras-Cubas, Humberto Garcia-Ortiz, Angelica Martinez-Hernandez, Jacob M. Luber, Philipp Kirstahler, Tre Blohm, Francis E. Smiley, Richard Arnold, Sonia A. Ballal, Sunje Johanna Pamp, Julia Russ, Frank Maixner, Omar Rota-Stabelli, Nicola Segata, Karl Reinhard, Lorena Orozco, Christina Warinner, Meradeth Snow, Steven LeBlanc, Aleksandar D. Kostic
Summary: This study used ancient fecal samples to study microbial genomes, revealing that these samples are more similar to non-industrialized human gut microbiomes and contain previously unknown microbial species. The fecal samples showed lower abundance of antibiotic resistance and mucin-degrading genes, as well as enrichment of mobile genetic elements relative to industrial gut microbiomes.
Article
Biochemistry & Molecular Biology
Jeremy E. Wilkinson, Eric A. Franzosa, Christine Everett, Chengchen Li, Frank B. Hu, Dyann F. Wirth, Mingyang Song, Andrew T. Chan, Eric Rimm, Wendy S. Garrett, Curtis Huttenhower
Summary: Microbiome science has rapidly advanced and is increasingly integrated into public health, providing opportunities for researchers, practitioners, and policymakers. There are opportunities for incorporating microbiome-based technologies into public health practice in the near future, along with a growing need for policymaking and regulation in related areas.
Article
Multidisciplinary Sciences
Braden T. Tierney, Yingxuan Tan, Aleksandar D. Kostic, Chirag J. Patel
Summary: The study explores strain-specific and cross-disease associations in the microbiome across seven human diseases, finding gene-level signatures shared by coronary artery disease, inflammatory bowel diseases, and liver cirrhosis, as well as a distinct metagenomic signature for type 2 diabetes. Discrepancies are observed in the reported connection between Solobacterium moorei and colorectal cancer across models, but strain-specific gene associations are identified.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Salina Moon, John J. Tsay, Heather Lampert, Zaipul I. Md Dom, Aleksandar D. Kostic, Adam Smiles, Monika A. Niewczas
Summary: The study suggests that Medium Chain Fatty Acids (MCFAs) and Short Chain Fatty Acids (SCFAs) may contribute to protecting against the development of albuminuria in patients with Type 1 Diabetes (T1D), independent of mechanisms associated with changes in renal function.
SCIENTIFIC REPORTS
(2021)
Article
Oncology
Zhouwei Zhang, Lior Golomb, Matthew Meyerson
Summary: This study provides functional genomic insight into the sensitivity of cancer cells to CDK4 or CDK6 inhibition, and identifies unique cancer cell populations that might be sensitive to CDK4-selective or CDK6-selective inhibitors.
Article
Microbiology
Jason Nomburg, Wei Zou, Thomas C. Frost, Chandreyee Datta, Shobha Vasudevan, Gabriel J. Starrett, Michael J. Imperiale, Matthew Meyerson, James A. DeCaprio
Summary: The study compares the transcriptome of different polyomaviruses and identifies complex transcription patterns and novel transcripts that increase the coding capacity of the viruses. This research provides insights into the transcriptome architecture of polyomaviruses and their role in human diseases.
Article
Genetics & Heredity
Netta Makinen, Meng Zhou, Zhouwei Zhang, Yosuke Kasai, Elizabeth Perez, Grace E. Kim, Chrissie Thirlwell, Eric Nakakura, Matthew Meyerson
Summary: This study reveals the major genomic diversity among multifocal ileal NETs, showing that synchronous primary tumors within each patient develop independently with different somatic variations. Additionally, tumors from the same patient can gain or lose different parental alleles, emphasizing the need to identify and remove all primary tumors to prevent metastasis and to optimize targeted treatments.
Editorial Material
Oncology
Blake E. Sanders, Guanxi Qiao, Jodi Hirschman, Matthew Meyerson
Summary: The role of the microbiome in human cancer is a subject of intense research and debate. The physical association of Fusobacterium with colorectal cancer has been extensively studied, offering potential for diagnosis and treatment, but controversies remain regarding the impact of Fusobacterium species on colorectal cancer proliferation and the immune microenvironment.
Article
Biochemistry & Molecular Biology
Sooncheol Lee, Stephanie Hoyt, Xiaoyun Wu, Colin Garvie, Joseph McGaunn, Mrinal Shekhar, Marcus Totzl, Matthew G. Rees, Andrew D. Cherniack, Matthew Meyerson, Heidi Greulich
Summary: The study reveals that Velcrin compounds kill cancer cells by inducing complex formation between phosphodiesterase 3A (PDE3A) and Schlafen family member 12 (SLFN12). SLFN12 specifically digests tRNA(Leu)(TAA), and Velcrin treatment promotes the cleavage of tRNA(Leu)(TAA) by inducing PDE3A-SLFN12 complex formation. This leads to downregulation of tRNA(Leu)(TAA), ribosome pausing at Leu-TTA codons, and global inhibition of protein synthesis, defining a new mechanism of apoptosis initiation.
NATURE CHEMICAL BIOLOGY
(2023)
Review
Oncology
Geniver El Tekle, Wendy S. Garrett
Summary: Cancer cells originate from acquired genetic mutations that drive uncontrolled proliferation and immune evasion. Environmental factors, including the human microbiota, can influence tumor behavior and shape the tumor microenvironment. Dysbiosis of the gut microbiome is recognized as a hallmark of cancer. This review explores the role of microbiota in cancer initiation, promotion, and progression, focusing on gastrointestinal tract malignancies, as well as lung, breast, and prostate cancers. It also discusses the potential of targeting bacteria for personalized cancer prevention, diagnostics, and treatment.
NATURE REVIEWS CANCER
(2023)
Review
Medicine, Research & Experimental
Slater L. Clay, Diogo Fonseca-Pereira, Wendy S. Garrett
Summary: The microbiota plays an important role in the development of colorectal cancer (CRC). Identifying specific microbial features that impact CRC initiation and progression is crucial. Bacterial factors, such as toxins, contribute to colorectal carcinogenesis. However, further research is needed to understand the host determinants of a toxin's cancer-promoting effects. For bacteria associated with CRC but lacking toxins, defining cancer-relevant virulence factors is challenging. Additionally, gut microbes can have beneficial effects on CRC antitumor immunity through the production of certain metabolites.
JOURNAL OF CLINICAL INVESTIGATION
(2022)
