Alterations in Patterns of Gene Expression and Perturbed Pathways in the Gut-Brain Axis Are Associated With Chemotherapy-Induced Nausea

Roila, 2016, 2016 MASCC and ESMO guideline update for the prevention of chemotherapy- and radiotherapy-induced nausea and vomiting and of nausea and vomiting in advanced cancer patients, Ann Oncol, 27, v119, 10.1093/annonc/mdw270 Singh, 2018, Risk factors associated with chemotherapy-induced nausea in the week before the next cycle and impact of nausea on quality of life outcomes, J Pain Symptom Manage, 56, 352, 10.1016/j.jpainsymman.2018.05.019 Dranitsaris, 2017, The development of a prediction tool to identify cancer patients at high risk for chemotherapy-induced nausea and vomiting, Ann Oncol, 28, 1260, 10.1093/annonc/mdx100 Singh, 2018, A review of the literature on the relationships between genetic polymorphisms and chemotherapy-induced nausea and vomiting, Crit Rev Oncol Hematol, 121, 51, 10.1016/j.critrevonc.2017.11.012 van Vliet, 2010, The role of intestinal microbiota in the development and severity of chemotherapy-induced mucositis, PLoS Pathog, 6, e1000879, 10.1371/journal.ppat.1000879 Bajic, 2018, From the bottom-up: chemotherapy and gut-brain axis dysregulation, Front Behav Neurosci, 12, 104, 10.3389/fnbeh.2018.00104 Sonis, 2004, The pathobiology of mucositis, Nat Rev Cancer, 4, 277, 10.1038/nrc1318 Touchefeu, 2014, Systematic review: the role of the gut microbiota in chemotherapy- or radiation-induced gastrointestinal mucositis—current evidence and potential clinical applications, Aliment Pharmacol Ther, 40, 409 Keefe, 2004, Gastrointestinal mucositis, Semin Oncol Nurs, 20, 38, 10.1053/j.soncn.2003.10.007 Donovan, 2016, Nausea as a sentinel symptom for cytotoxic chemotherapy effects on the gut-brain axis among women receiving treatment for recurrent ovarian cancer: an exploratory analysis, Support Care Cancer, 24, 2635, 10.1007/s00520-015-3071-4 Mark, 2017, Modifiable and non-modifiable characteristics associated with sleep disturbance in oncology outpatients during chemotherapy, Support Care Cancer, 25, 2485, 10.1007/s00520-017-3655-2 Karnofsky, 1977 Sangha, 2003, The Self-Administered Comorbidity Questionnaire: a new method to assess comorbidity for clinical and health services research, Arthritis Rheum, 49, 156, 10.1002/art.10993 Babor, 2001 Kozlowski, 1994, Predicting smoking cessation with self-reported measures of nicotine dependence: FTQ, FTND, and HSI, Drug Alcohol Depend, 34, 211, 10.1016/0376-8716(94)90158-9 Portenoy, 1994, The Memorial Symptom Assessment Scale—an instrument for the evaluation of symptom prevalence, characteristics and distress, Eur J Cancer, 30A, 1326, 10.1016/0959-8049(94)90182-1 Carrico, 2018, Recent stimulant use and leukocyte gene expression in methamphetamine users with treated HIV infection, Brain Behav Immun, 71, 108, 10.1016/j.bbi.2018.04.004 Kober, 2016, Gene expression profiling of evening fatigue in women undergoing chemotherapy for breast cancer, Biol Res Nurs, 18, 370, 10.1177/1099800416629209 Kober, 2018, Expression of mitochondrial dysfunction-related genes and pathways in paclitaxel-induced peripheral neuropathy in breast cancer survivors, Mol Pain, 14, 10.1177/1744806918816462 Flowers, 2018, Differential expression of genes and differentially perturbed pathways associated with very high evening fatigue in oncology patients receiving chemotherapy, Support Care Cancer, 26, 739, 10.1007/s00520-017-3883-5 Fisher, 1925 Fisher, 1948, Questions and answers #14, Am Stat, 2, 30 Hochberg, 1990, More powerful procedures for multiple significance testing, Stat Med, 9, 811, 10.1002/sim.4780090710 Draghici, 2007, A systems biology approach for pathway level analysis, Genome Res, 17, 1537, 10.1101/gr.6202607 Landau, 2013, Dispersion estimation and its effect on test performance in RNA-seq data analysis: a simulation-based comparison of methods, PLoS One, 8, e81415, 10.1371/journal.pone.0081415 Kauffmann, 2009, arrayQualityMetrics--a bioconductor package for quality assessment of microarray data, Bioinformatics, 3, 415, 10.1093/bioinformatics/btn647 Limma, 2005, Linear models for microarray data, 397 Logan, 2007, The role of pro-inflammatory cytokines in cancer treatment-induced alimentary tract mucositis: pathobiology, animal models and cytotoxic drugs, Cancer Treat Rev, 33, 448, 10.1016/j.ctrv.2007.03.001 Melo, 2008, Role of cytokines (TNF-alpha, IL-1beta and KC) in the pathogenesis of CPT-11-induced intestinal mucositis in mice: effect of pentoxifylline and thalidomide, Cancer Chemother Pharmacol, 61, 775, 10.1007/s00280-007-0534-4 Bowen, 2007, Irinotecan changes gene expression in the small intestine of the rat with breast cancer, Cancer Chemother Pharmacol, 59, 337, 10.1007/s00280-006-0275-9 Kim, 2018, Ursodeoxycholic acid attenuates 5-fluorouracil-induced mucositis in a rat model, Oncol Lett, 16, 2585 Logan, 2007, Nuclear factor-kappaB (NF-kappaB) and cyclooxygenase-2 (COX-2) expression in the oral mucosa following cancer chemotherapy, Oral Oncol, 43, 395, 10.1016/j.oraloncology.2006.04.011 Thomas, 2012, Targeting leukocyte migration and adhesion in Crohn's disease and ulcerative colitis, Inflammopharmacology, 20, 1, 10.1007/s10787-011-0104-6 Lu, 2015, The chemokine CXCL9 exacerbates chemotherapy-induced acute intestinal damage through inhibition of mucosal restitution, J Cancer Res Clin Oncol, 141, 983, 10.1007/s00432-014-1869-y Mathias, 2014, Role of secretory IgA in the mucosal sensing of commensal bacteria, Gut Microbes, 5, 688, 10.4161/19490976.2014.983763 Artis, 2008, Epithelial-cell recognition of commensal bacteria and maintenance of immune homeostasis in the gut, Nat Rev Immunol, 8, 411, 10.1038/nri2316 Viaud, 2013, The intestinal microbiota modulates the anticancer immune effects of cyclophosphamide, Science, 342, 971, 10.1126/science.1240537 Montassier, 2015, Chemotherapy-driven dysbiosis in the intestinal microbiome, Aliment Pharmacol Ther, 42, 515, 10.1111/apt.13302 Roy, 2017, Microbiota: a key orchestrator of cancer therapy, Nat Rev Cancer, 17, 271, 10.1038/nrc.2017.13 Roda, 2010, Intestinal epithelial cells in inflammatory bowel diseases, World J Gastroenterol, 16, 4264, 10.3748/wjg.v16.i34.4264 Macpherson, 2008, The immune geography of IgA induction and function, Mucosal Immunol, 1, 11, 10.1038/mi.2007.6 Qiao, 2002, Immune responses in rhesus rotavirus-challenged BALB/c mice treated with Bifidobacteria and prebiotic supplements, Pediatr Res, 51, 750, 10.1203/00006450-200206000-00015 Shu, 2001, A dietary probiotic (Bifidobacterium lactis HN019) reduces the severity of Escherichia coli O157:H7 infection in mice, Med Microbiol Immunol, 189, 147, 10.1007/s430-001-8021-9 Pels, 2017, Oral mucositis and saliva IgA, IgG and IgM concentration during anti-tumor treatment in children suffering from acute lymphoblastic leukemia, Adv Clin Exp Med, 26, 1351, 10.17219/acem/64940 Manoharan, 2016, Homeostatic PPAR alpha signaling limits inflammatory responses to commensal microbiota in the intestine, J Immunol, 196, 4739, 10.4049/jimmunol.1501489 Ivanov, 2009, Induction of intestinal Th17 cells by segmented filamentous bacteria, Cell, 139, 485, 10.1016/j.cell.2009.09.033 Resta-Lenert, 2006, Probiotics and commensals reverse TNF-alpha and IFN-gamma-induced dysfunction in human intestinal epithelial cells, Gastroenterology, 130, 731, 10.1053/j.gastro.2005.12.015 Li, 2009, Clinical trial: prophylactic intravenous alanyl-glutamine reduces the severity of gastrointestinal toxicity induced by chemotherapy—a randomized crossover study, Aliment Pharmacol Ther, 30, 452, 10.1111/j.1365-2036.2009.04068.x Sayles, 2016, Oral glutamine in preventing treatment-related mucositis in adult patients with cancer: a systematic review, Nutr Clin Pract, 31, 171, 10.1177/0884533615611857 Jolfaie, 2015, The effect of glutamine intake on complications of colorectal and colon cancer treatment: a systematic review, J Res Med Sci, 20, 910 Hensley, 2013, Glutamine and cancer: cell biology, physiology, and clinical opportunities, J Clin Invest, 123, 3678, 10.1172/JCI69600 Tsan, 2004, Heat shock protein and innate immunity, Cell Mol Immunol, 1, 274 Meng, 2018, Toward developing chemical modulators of Hsp60 as potential therapeutics, Front Mol Biosci, 5, 35, 10.3389/fmolb.2018.00035 O'Neil, 2013, Ribosomal RNA depletion for efficient use of RNA-seq capacity, Curr Protoc Mol Biol, Chapter 4, 10.1002/0471142727.mb0419s103 Mastrokolias, 2012, Increased sensitivity of next generation sequencing-based expression profiling after globin reduction in human blood RNA, BMC Genomics, 13, 28, 10.1186/1471-2164-13-28 Choi, 2014, Increasing gene discovery and coverage using RNA-seq of globin RNA reduced porcine blood samples, BMC Genomics, 15, 954, 10.1186/1471-2164-15-954 Sinha, 2017, Index switching causes “spreading-of-signal” among multiplexed samples in Illumina HiSeq 4000 DNA sequencing, bioRxiv Conesa, 2016, A survey of best practices for RNA-seq data analysis, Genome Biol, 17, 13, 10.1186/s13059-016-0881-8 Kukurba, 2015, RNA sequencing and analysis, Cold Spring Harb Protoc, 2015, 951, 10.1101/pdb.top084970 Carrico, 2018, Recent stimulant use and leukocyte gene expression in methamphetamine users with treated HIV infection, Brain Behav Immun, 71, 108, 10.1016/j.bbi.2018.04.004 Flentje, 2018, Minority stress and leukocyte gene expression in sexual minority men living with treated HIV infection, Brain Behav Immun, 70, 335, 10.1016/j.bbi.2018.03.016 Bolger, 2014, Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinformatics, 30, 2114, 10.1093/bioinformatics/btu170 Ewels, 2016, MultiQC: summarize analysis results for multiple tools and samples in a single report, Bioinformatics, 32, 3047, 10.1093/bioinformatics/btw354 Harrow, 2012, GENCODE: the reference human genome annotation for the ENCODE Project, Genome Res, 22, 1760, 10.1101/gr.135350.111 Dobin, 2013, STAR: ultrafast universal RNA-seq aligner, Bioinformatics, 29, 15, 10.1093/bioinformatics/bts635 DeLuca, 2012, RNA-SeQC: RNA-seq metrics for quality control and process optimization, Bioinformatics, 28, 1530, 10.1093/bioinformatics/bts196 Liao, 2014, featureCounts: an efficient general purpose program for assigning sequence reads to genomic features, Bioinformatics, 30, 923, 10.1093/bioinformatics/btt656 Robinson, 2010, edgeR: a Bioconductor package for differential expression analysis of digital gene expression data, Bioinformatics, 26, 139, 10.1093/bioinformatics/btp616 Zerbino, 2018, Ensembl 2018, Nucleic Acids Res, 46, D754, 10.1093/nar/gkx1098 Maglott, 2011, Entrez Gene: gene-centered information at NCBI, Nucleic Acids Res, 39, D52, 10.1093/nar/gkq1237 Robinson, 2010, A scaling normalization method for differential expression analysis of RNA-seq data, Genome Biol, 11, R25, 10.1186/gb-2010-11-3-r25 Flowers, 2018, Differential expression of genes and differentially perturbed pathways associated with very high evening fatigue in oncology patients receiving chemotherapy, Support Care Cancer, 26, 739, 10.1007/s00520-017-3883-5 Kober, 2016, Gene expression profiling of evening fatigue in women undergoing chemotherapy for breast cancer, Biol Res Nurs, 18, 370, 10.1177/1099800416629209 Dunning, 2007, beadarray: R classes and methods for Illumina bead-based data, Bioinformatics, 23, 2183, 10.1093/bioinformatics/btm311 Gentleman, 2004, Bioconductor: open software development for computational biology and bioinformatics, Genome Biol, 5, R80, 10.1186/gb-2004-5-10-r80 Reimers, 2010, Making informed choices about microarray data analysis, PLoS Comput Biol, 6, e1000786, 10.1371/journal.pcbi.1000786 Ritchie, 2011, BeadArray expression analysis using bioconductor, PLoS Comput Biol, 7, e1002276, 10.1371/journal.pcbi.1002276 Butte, 2002, The use and analysis of microarray data, Nat Rev Drug Discov, 1, 951, 10.1038/nrd961 Kauffmann, 2010, Microarray data quality control improves the detection of differentially expressed genes, Genomics, 95, 138, 10.1016/j.ygeno.2010.01.003 Kauffmann, 2009, arrayQualityMetrics—a bioconductor package for quality assessment of microarray data, Bioinformatics, 25, 415, 10.1093/bioinformatics/btn647 Shi, 2010, Optimizing the noise versus bias trade-off for Illumina whole genome expression BeadChips, Nucleic Acids Res, 38, e204, 10.1093/nar/gkq871 Ritchie, 2007, A comparison of background correction methods for two-colour microarrays, Bioinformatics, 23, 2700, 10.1093/bioinformatics/btm412 Leek, 2007, Capturing heterogeneity in gene expression studies by surrogate variable analysis, PLoS Genet, 3, 1724, 10.1371/journal.pgen.0030161 Leek, 2012, The sva package for removing batch effects and other unwanted variation in high-throughput experiments, Bioinformatics, 28, 882, 10.1093/bioinformatics/bts034 Landau, 2013, Dispersion estimation and its effect on test performance in RNA-seq data analysis: a simulation-based comparison of methods, PLoS One, 8, e81415, 10.1371/journal.pone.0081415 McCarthy, 2012, Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation, Nucleic Acids Res, 40, 4288, 10.1093/nar/gks042 Cox, 1987, Parameter orthogonality and approximate conditional inference, J Roy Stat Soc Ser B Method, 49, 1 Flowers, 2019, A pilot study using a multi-staged integrated analysis of gene expression and methylation to evaluate mechanisms for evening fatigue, Biol Res Nurs, 21, 142, 10.1177/1099800418823286 Smyth, 2005, Limma: linear models for microarray data, 397 McCarthy, 2009, Testing significance relative to a fold-change threshold is a TREAT, Bioinformatics, 25, 765, 10.1093/bioinformatics/btp053 Fisher, 1925 Fisher, 1948, Questions and answers #14, Am Stat, 2, 30 Hochberg, 1990, More powerful procedures for multiple significance testing, Stat Med, 9, 811, 10.1002/sim.4780090710 Mitrea, 2013, Methods and approaches in the topology-based analysis of biological pathways, Front Physiol, 4, 278, 10.3389/fphys.2013.00278 Draghici, 2007, A systems biology approach for pathway level analysis, Genome Res, 17, 1537, 10.1101/gr.6202607 Aoki-Kinoshita, 2007, Gene annotation and pathway mapping in KEGG, Methods Mol Biol, 396, 71, 10.1007/978-1-59745-515-2_6 Gray, 2013, Genenames.org: the HGNC resources in 2013, Nucleic Acids Res, 41, D545, 10.1093/nar/gks1066