Caroline Johnson, PhD
Research & Publications
Biography
News
Locations
Extensive Research Description
Microbial metabolites and colon cancer
Colon cancers that present on the right versus the left side of the colon have significantly worse prognosis for the patient. A recent discovery revealed that right-sided colon cancers (RCCs) harbor mucosal bacterial biofilms, whereas left-sided colon cancers (LCC) are predominantly devoid of biofilms. These biofilms are associated with increased cellular proliferation and inflammation even in normal colon tissues. Using mass spectrometry-based metabolomics, we investigated the metabolism of colon cancers with and without biofilms, and observed a correlation between increased diacetylspermine production and biofilm presence on RCCs. Using antibiotic treatment, IHC, and stable isotope-assisted metabolomics we showed that diacetylspermine is an end product of polyamine metabolism produced by bacterial biofilms. We thus hypothesized that microbiota use host-derived polyamines to form biofilms. It is still not known why biofilms only form only on RCC, but it could be due to other factors such as diet and genetic predisposition.
Therefore, we aim are to examine the influence of these factors in LCC and RCC pathogenicity by investigating the roles of dietary metabolites, microbial communities and genetic predisposition.
Identifying the biological effects of exposures
In the Johnson Lab, we use metabolomics to simultaneously analyze both exogenous chemicals, their metabolites, and changes to the endogenous metabolome to allow assessment of exposures and their biological impact. We also adjust for confounding using epidemiologic techniques, as shared factors could influence the metabolome and exposure measured. We are using this framework within various projects outlined below:
Peri-conception exposures and effects on the urinary metabolome
Conception is a critical window for female reproductive function, and environmental exposures may influence fertility. Using a metabolome-wide association study (MWAS) framework, we are investigating how parabens modulate the urinary metabolome of women attempting to conceive, to provide insight into mechanisms that may underlie the biological effects of these exposures.
We also discovered that changes to kidney function across the menstrual cycle can impact urine metabolite concentration, therefore we assessed different post-acquisition normalization approaches to identify the optimal method for urinary metabolomics. Our published data shows that either specific gravity or probabilistic quotient normalization are reliable methods to adjust for urinary concentration.
Dried blood spots are a window to early-life exposures that contribute to later-life cancers
Early-life exposures can have biological effects that lead to later-life adverse outcomes such as cancer. Dried blood spots (DBS) have been collected in large populations for decades, to screen infants for congenital metabolic disorders, however they represent an untapped resource for studies in epidemiology and population sciences. Metabolomics analysis of DBS from newborns provides the opportunity to measure both environmental exposures and metabolic perturbations simultaneously, offering both biomarkers of exposure and biological effect to gain insight into mechanisms of later life diseases.
No consensus exists for the optimal method for metabolite normalization in DBS untargeted LC-MS-based metabolomics. To address this issue and setup a robust experimental protocol for DBS metabolomics, we assessed the performance of various normalization methods. We identified that normalization using hemoglobin (Hb) is the best method. We also introduced a novel role of specific gravity as a predictor of Hb in DBS.
Coauthors
Research Interests
Environmental Exposure; Mass Spectrometry; Metabolomics; Biostatistics
Public Health Interests
Biomarkers; Cancer; Environmental Health; Genetics, Genomics, Epigenetics; Maternal & Child Health; Women's Health; Microbiome; Metabolomics; Perinatal/Prenatal Health
Research Image
Diacetylspermine and its role in biofilm-associated colon cancer
Selected Publications
- Discovery of decreased ferroptosis in male colorectal cancer patients with KRAS mutationsYan H, Talty R, Jain A, Cai Y, Zheng J, Shen X, Muca E, Paty P, Bosenberg M, Khan S, Johnson C. Discovery of decreased ferroptosis in male colorectal cancer patients with KRAS mutations. Redox Biology 2023, 62: 102699. PMID: 37086630, PMCID: PMC10172914, DOI: 10.1016/j.redox.2023.102699.
- Early-Onset Colorectal Cancer Somatic Gene Mutations by Population Subgroups.Shen X, DeWan A, Johnson C. Early-Onset Colorectal Cancer Somatic Gene Mutations by Population Subgroups. Cancer Discovery 2023, 13: 530-531. PMID: 36855917, DOI: 10.1158/2159-8290.cd-22-1464.
- In silico designed mRNA vaccines targeting CA-125 neoantigen in breast and ovarian cancerLu L, Ma W, Johnson C, Khan S, Irwin M, Pusztai L. In silico designed mRNA vaccines targeting CA-125 neoantigen in breast and ovarian cancer. Vaccine 2023, 41: 2073-2083. PMID: 36813666, PMCID: PMC10064809, DOI: 10.1016/j.vaccine.2023.02.048.
- Prenatal Choline Supplement in a Maternal Obesity Model Modulates Offspring Hepatic LipidomesKorsmo H, Kadam I, Reaz A, Bretter R, Saxena A, Johnson C, Caviglia J, Jiang X. Prenatal Choline Supplement in a Maternal Obesity Model Modulates Offspring Hepatic Lipidomes. Nutrients 2023, 15: 965. PMID: 36839327, PMCID: PMC9963284, DOI: 10.3390/nu15040965.
- Ferroptosis in colorectal cancer: a future target?Yan H, Talty R, Aladelokun O, Bosenberg M, Johnson C. Ferroptosis in colorectal cancer: a future target? British Journal Of Cancer 2023, 128: 1439-1451. PMID: 36703079, PMCID: PMC10070248, DOI: 10.1038/s41416-023-02149-6.
- Targeting ferroptosis to treat colorectal cancerYan H, Talty R, Johnson C. Targeting ferroptosis to treat colorectal cancer. Trends In Cell Biology 2022, 33: 185-188. PMID: 36473802, DOI: 10.1016/j.tcb.2022.11.003.
- Urinary phenol concentrations and fecundability and early pregnancy loss.Rosen Vollmar A, Weinberg C, Baird D, Wilcox A, Calafat A, Deziel N, Johnson C, Jukic A. Urinary phenol concentrations and fecundability and early pregnancy loss. Human Reproduction 2022, 38: 139-155. PMID: 36346334, PMCID: PMC10089295, DOI: 10.1093/humrep/deac230.
- Bile acid distributions, sex-specificity, and prognosis in colorectal cancerCai Y, Shen X, Lu L, Yan H, Huang H, Gaule P, Muca E, Theriot CM, Rattray Z, Rattray NJW, Lu J, Ahuja N, Zhang Y, Paty PB, Khan SA, Johnson CH. Bile acid distributions, sex-specificity, and prognosis in colorectal cancer. Biology Of Sex Differences 2022, 13: 61. PMID: 36274154, PMCID: PMC9590160, DOI: 10.1186/s13293-022-00473-9.
- Hemoglobin normalization outperforms other methods for standardizing dried blood spot metabolomics: A comparative studyJain A, Morris M, Lin EZ, Khan SA, Ma X, Deziel NC, Godri Pollitt KJ, Johnson CH. Hemoglobin normalization outperforms other methods for standardizing dried blood spot metabolomics: A comparative study. The Science Of The Total Environment 2022, 854: 158716. PMID: 36113793, DOI: 10.1016/j.scitotenv.2022.158716.
- Asparagine, colorectal cancer, and the role of sex, genes, microbes, and diet: A narrative reviewShen X, Jain A, Aladelokun O, Yan H, Gilbride A, Ferrucci LM, Lu L, Khan SA, Johnson CH. Asparagine, colorectal cancer, and the role of sex, genes, microbes, and diet: A narrative review. Frontiers In Molecular Biosciences 2022, 9: 958666. PMID: 36090030, PMCID: PMC9453556, DOI: 10.3389/fmolb.2022.958666.
- Evaluation of the role of KPNA2 mutations in breast cancer prognosis using bioinformatics datasetsAlnoumas L, van den Driest L, Apczynski Z, Lannigan A, Johnson CH, Rattray NJW, Rattray Z. Evaluation of the role of KPNA2 mutations in breast cancer prognosis using bioinformatics datasets. BMC Cancer 2022, 22: 874. PMID: 35948941, PMCID: PMC9364282, DOI: 10.1186/s12885-022-09969-4.
- TidyMass an object-oriented reproducible analysis framework for LC–MS dataShen X, Yan H, Wang C, Gao P, Johnson CH, Snyder MP. TidyMass an object-oriented reproducible analysis framework for LC–MS data. Nature Communications 2022, 13: 4365. PMID: 35902589, PMCID: PMC9334349, DOI: 10.1038/s41467-022-32155-w.
- Development of an Accessible Gene Expression Bioinformatics Pipeline to Study Driver Mutations of Colorectal Cancervan den Driest L, Johnson CH, Rattray NJW, Rattray Z. Development of an Accessible Gene Expression Bioinformatics Pipeline to Study Driver Mutations of Colorectal Cancer. Alternatives To Laboratory Animals 2022, 50: 282-292. PMID: 35765262, DOI: 10.1177/02611929221107546.
- Abstract 3052: Fusobacterial-dominant colorectal cancer biofilms are associated with high levels of the polyamine N1,N12-diacetylspermineDrewes J, Queen J, Domingue J, Wensel C, Cai Y, Wanyiri J, Roslani A, Vadivelu J, Johnson C, Sears C. Abstract 3052: Fusobacterial-dominant colorectal cancer biofilms are associated with high levels of the polyamine N1,N12-diacetylspermine. Cancer Research 2022, 82: 3052-3052. DOI: 10.1158/1538-7445.am2022-3052.
- Evaluation of Racial Disparities in Quality of Care for Patients With Gastrointestinal Tract Cancer Treated With SurgeryBakkila BF, Kerekes D, Nunez-Smith M, Billingsley KG, Ahuja N, Wang K, Oladele C, Johnson CH, Khan SA. Evaluation of Racial Disparities in Quality of Care for Patients With Gastrointestinal Tract Cancer Treated With Surgery. JAMA Network Open 2022, 5: e225664. PMID: 35377425, PMCID: PMC8980937, DOI: 10.1001/jamanetworkopen.2022.5664.
- HSR22-125: Quality of Gastrointestinal Surgical Oncology Care According to Insurance StatusBakkila B, Kerekes D, Johnson C, Khan S. HSR22-125: Quality of Gastrointestinal Surgical Oncology Care According to Insurance Status. Journal Of The National Comprehensive Cancer Network 2022, 20: hsr22-125. DOI: 10.6004/jnccn.2021.7261.
- Non-targeted metabolomics and associations with per- and polyfluoroalkyl substances (PFAS) exposure in humans: A scoping reviewGuo P, Furnary T, Vasiliou V, Yan Q, Nyhan K, Jones DP, Johnson CH, Liew Z. Non-targeted metabolomics and associations with per- and polyfluoroalkyl substances (PFAS) exposure in humans: A scoping review. Environment International 2022, 162: 107159. PMID: 35231839, PMCID: PMC8969205, DOI: 10.1016/j.envint.2022.107159.
- Asparagine Metabolism in Tumors Is Linked to Poor Survival in Females with Colorectal Cancer: A Cohort StudyShen X, Cai Y, Lu L, Huang H, Yan H, Paty PB, Muca E, Ahuja N, Zhang Y, Johnson CH, Khan SA. Asparagine Metabolism in Tumors Is Linked to Poor Survival in Females with Colorectal Cancer: A Cohort Study. Metabolites 2022, 12: 164. PMID: 35208238, PMCID: PMC8875032, DOI: 10.3390/metabo12020164.
- Molecular Mechanisms of Alcohol-Induced Colorectal CarcinogenesisJohnson CH, Golla JP, Dioletis E, Singh S, Ishii M, Charkoftaki G, Thompson DC, Vasiliou V. Molecular Mechanisms of Alcohol-Induced Colorectal Carcinogenesis. Cancers 2021, 13: 4404. PMID: 34503214, PMCID: PMC8431530, DOI: 10.3390/cancers13174404.
- Non-targeted metabolomics in evaluating alterations associated with per-fluoroalkyl and polyfluoroalkyl substances (PFAS) exposure in human studies: a scoping reviewGuo P, Furnary T, Vasiliou V, Yan Q, Jones D, Johnson C, Liew Z. Non-targeted metabolomics in evaluating alterations associated with per-fluoroalkyl and polyfluoroalkyl substances (PFAS) exposure in human studies: a scoping review. ISEE Conference Abstracts 2021, 2021 DOI: 10.1289/isee.2021.p-608.
- ENT2 facilitates brain endothelial cell penetration and blood-brain barrier transport by a tumor-targeting anti-DNA autoantibodyRattray Z, Deng G, Zhang S, Shirali A, May CK, Chen X, Cuffari BJ, Liu J, Zou P, Rattray N, Johnson CH, Dubljevic V, Campbell JA, Huttner A, Baehring JM, Zhou J, Hansen JE. ENT2 facilitates brain endothelial cell penetration and blood-brain barrier transport by a tumor-targeting anti-DNA autoantibody. JCI Insight 2021, 6: e145875. PMID: 34128837, PMCID: PMC8410084, DOI: 10.1172/jci.insight.145875.
- Kynurenic acid may underlie sex-specific immune responses to COVID-19Cai Y, Kim DJ, Takahashi T, Broadhurst DI, Yan H, Ma S, Rattray NJW, Casanovas-Massana A, Israelow B, Klein J, Lucas C, Mao T, Moore AJ, Muenker MC, Oh JE, Silva J, Wong P, team Y, Ko AI, Khan SA, Iwasaki A, Johnson CH. Kynurenic acid may underlie sex-specific immune responses to COVID-19. Science Signaling 2021, 14: eabf8483. PMID: 34230210, PMCID: PMC8432948, DOI: 10.1126/scisignal.abf8483.
- YIV-906 potentiated anti-PD1 action against hepatocellular carcinoma by enhancing adaptive and innate immunity in the tumor microenvironmentYang X, Lam W, Jiang Z, Guan F, Han X, Hu R, Cai W, Cheng W, Liu SH, Cheng P, Cai Y, Rattray NJW, Johnson CH, Chen L, Cheng YC. YIV-906 potentiated anti-PD1 action against hepatocellular carcinoma by enhancing adaptive and innate immunity in the tumor microenvironment. Scientific Reports 2021, 11: 13482. PMID: 34188068, PMCID: PMC8242098, DOI: 10.1038/s41598-021-91623-3.
- Intratumour microbiome associated with the infiltration of cytotoxic CD8+ T cells and patient survival in cutaneous melanomaZhu G, Su H, Johnson CH, Khan SA, Kluger H, Lu L. Intratumour microbiome associated with the infiltration of cytotoxic CD8+ T cells and patient survival in cutaneous melanoma. European Journal Of Cancer 2021, 151: 25-34. PMID: 33962358, PMCID: PMC8184628, DOI: 10.1016/j.ejca.2021.03.053.
- Identification of Dose-Dependent DNA Damage and Repair Responses From Subchronic Exposure to 1,4-Dioxane in Mice Using a Systems Analysis Approach.Charkoftaki G, Golla JP, Santos-Neto A, Orlicky DJ, Garcia-Milian R, Chen Y, Rattray NJW, Cai Y, Wang Y, Shearn CT, Mironova V, Wang Y, Johnson CH, Thompson DC, Vasiliou V. Identification of Dose-Dependent DNA Damage and Repair Responses From Subchronic Exposure to 1,4-Dioxane in Mice Using a Systems Analysis Approach. Toxicological Sciences 2021, 183: 338-351. PMID: 33693819, PMCID: PMC8921626, DOI: 10.1093/toxsci/kfab030.
- Use of Untargeted Metabolomics to Explore the Air Pollution-Related Disease ContinuumJin L, Godri Pollitt KJ, Liew Z, Rosen Vollmar AK, Vasiliou V, Johnson CH, Zhang Y. Use of Untargeted Metabolomics to Explore the Air Pollution-Related Disease Continuum. Current Environmental Health Reports 2021, 8: 7-22. PMID: 33420964, DOI: 10.1007/s40572-020-00298-x.
- Immune landscape and prognostic immune-related genes in KRAS-mutant colorectal cancer patientsLiu J, Huang X, Liu H, Wei C, Ru H, Qin H, Lai H, Meng Y, Wu G, Xie W, Mo X, Johnson CH, Zhang Y, Tang W. Immune landscape and prognostic immune-related genes in KRAS-mutant colorectal cancer patients. Journal Of Translational Medicine 2021, 19: 27. PMID: 33413474, PMCID: PMC7789428, DOI: 10.1186/s12967-020-02638-9.
- Gene Alterations of N6-Methyladenosine (m6A) Regulators in Colorectal Cancer: A TCGA Database StudyZhang Q, Cai Y, Kurbatov V, Khan SA, Lu L, Zhang Y, Johnson CH. Gene Alterations of N6-Methyladenosine (m6A) Regulators in Colorectal Cancer: A TCGA Database Study. BioMed Research International 2020, 2020: 8826456. PMID: 33415160, PMCID: PMC7769650, DOI: 10.1155/2020/8826456.
- Kynurenic acid underlies sex-specific immune responses to COVID-19.Cai Y, Kim DJ, Takahashi T, Broadhurst DI, Ma S, Rattray NJW, Casanovas-Massana A, Israelow B, Klein J, Lucas C, Mao T, Moore AJ, Muenker MC, Oh J, Silva J, Wong P, Ko AJ, Khan SA, Iwasaki A, Johnson CH. Kynurenic acid underlies sex-specific immune responses to COVID-19. MedRxiv : The Preprint Server For Health Sciences 2020 PMID: 32935119, PMCID: PMC7491534, DOI: 10.1101/2020.09.06.20189159.
- Tumor Tissue-Specific Biomarkers of Colorectal Cancer by Anatomic Location and StageCai Y, Rattray NJW, Zhang Q, Mironova V, Santos-Neto A, Muca E, Vollmar AKR, Hsu KS, Rattray Z, Cross JR, Zhang Y, Paty PB, Khan SA, Johnson CH. Tumor Tissue-Specific Biomarkers of Colorectal Cancer by Anatomic Location and Stage. Metabolites 2020, 10: 257. PMID: 32575361, PMCID: PMC7345993, DOI: 10.3390/metabo10060257.
- Accounting for urinary dilution in peri-implantation samples: implications for creatinine adjustment and specimen poolingRosen Vollmar AK, Johnson CH, Weinberg CR, Deziel NC, Baird DD, Wilcox AJ, Jukic AMZ. Accounting for urinary dilution in peri-implantation samples: implications for creatinine adjustment and specimen pooling. Journal Of Exposure Science & Environmental Epidemiology 2020, 31: 356-365. PMID: 32424331, PMCID: PMC7671945, DOI: 10.1038/s41370-020-0227-1.
- Sex Differences in Colon Cancer Metabolism Reveal A Novel SubphenotypeCai Y, Rattray NJW, Zhang Q, Mironova V, Santos-Neto A, Hsu KS, Rattray Z, Cross JR, Zhang Y, Paty PB, Khan SA, Johnson CH. Sex Differences in Colon Cancer Metabolism Reveal A Novel Subphenotype. Scientific Reports 2020, 10: 4905. PMID: 32184446, PMCID: PMC7078199, DOI: 10.1038/s41598-020-61851-0.
- Analyzing Metabolomics Data for Environmental Health and Exposome ResearchCai Y, Rosen Vollmar AK, Johnson CH. Analyzing Metabolomics Data for Environmental Health and Exposome Research. 2020, 2104: 447-467. PMID: 31953830, DOI: 10.1007/978-1-0716-0239-3_22.
- Molecular Pathway Analysis Indicates a Distinct Metabolic Phenotype in Women With Right-Sided Colon CancerSun Y, Mironova V, Chen Y, Lundh EPF, Zhang Q, Cai Y, Vasiliou V, Zhang Y, Garcia-Milian R, Khan SA, Johnson CH. Molecular Pathway Analysis Indicates a Distinct Metabolic Phenotype in Women With Right-Sided Colon Cancer. Translational Oncology 2019, 13: 42-56. PMID: 31760268, PMCID: PMC6883319, DOI: 10.1016/j.tranon.2019.09.004.
- Metabolic dysregulation in vitamin E and carnitine shuttle energy mechanisms associate with human frailtyRattray NJW, Trivedi DK, Xu Y, Chandola T, Johnson CH, Marshall AD, Mekli K, Rattray Z, Tampubolon G, Vanhoutte B, White IR, Wu FCW, Pendleton N, Nazroo J, Goodacre R. Metabolic dysregulation in vitamin E and carnitine shuttle energy mechanisms associate with human frailty. Nature Communications 2019, 10: 5027. PMID: 31690722, PMCID: PMC6831565, DOI: 10.1038/s41467-019-12716-2.
- Normalizing Untargeted Periconceptional Urinary Metabolomics Data: A Comparison of ApproachesVollmar A, Rattray NJW, Cai Y, Santos-Neto ÁJ, Deziel NC, Jukic AMZ, Johnson CH. Normalizing Untargeted Periconceptional Urinary Metabolomics Data: A Comparison of Approaches. Metabolites 2019, 9: 198. PMID: 31546636, PMCID: PMC6835889, DOI: 10.3390/metabo9100198.
- Joint effect of pre-operative anemia and perioperative blood transfusion on outcomes of colon-cancer patients undergoing colectomyLiu Z, Luo JJ, Pei KY, Khan SA, Wang XX, Zhao ZX, Yang M, Johnson CH, Wang XS, Zhang Y. Joint effect of pre-operative anemia and perioperative blood transfusion on outcomes of colon-cancer patients undergoing colectomy. Gastroenterology Report 2019, 8: 151-157. PMID: 32280475, PMCID: PMC7136710, DOI: 10.1093/gastro/goz033.
- 1,4-Dioxane as an emerging water contaminant: State of the science and evaluation of research needsGodri Pollitt K, Kim JH, Peccia J, Elimelech M, Zhang Y, Charkoftaki G, Hodges B, Zucker I, Huang H, Deziel N, Murphy K, Ishii M, Johnson CH, Boissevain A, O'Keefe E, Anastas P, Orlicky D, Thompson DC, Vasiliou V. 1,4-Dioxane as an emerging water contaminant: State of the science and evaluation of research needs. The Science Of The Total Environment 2019, 690: 853-866. PMID: 31302550, DOI: 10.1016/j.scitotenv.2019.06.443.
- Palbociclib and Fulvestrant Act in Synergy to Modulate Central Carbon Metabolism in Breast Cancer CellsWarth B, Palermo A, Rattray NJW, Lee NV, Zhu Z, Hoang LT, Cai Y, Mazurek A, Dann S, VanArsdale T, Fantin VR, Shields D, Siuzdak G, Johnson CH. Palbociclib and Fulvestrant Act in Synergy to Modulate Central Carbon Metabolism in Breast Cancer Cells. Metabolites 2019, 9: 7. PMID: 30609717, PMCID: PMC6359333, DOI: 10.3390/metabo9010007.
- Defining Early-Onset Colon and Rectal CancersJacobs D, Zhu R, Luo J, Grisotti G, Heller DR, Kurbatov V, Johnson CH, Zhang Y, Khan SA. Defining Early-Onset Colon and Rectal Cancers. Frontiers In Oncology 2018, 8: 504. PMID: 30460196, PMCID: PMC6232522, DOI: 10.3389/fonc.2018.00504.
- Evaluation of potential carcinogenicity of organic chemicals in synthetic turf crumb rubberPerkins AN, Inayat-Hussain SH, Deziel NC, Johnson CH, Ferguson SS, Garcia-Milian R, Thompson DC, Vasiliou V. Evaluation of potential carcinogenicity of organic chemicals in synthetic turf crumb rubber. Environmental Research 2018, 169: 163-172. PMID: 30458352, PMCID: PMC6396308, DOI: 10.1016/j.envres.2018.10.018.
- Distinctive features of gastrointestinal stromal tumors arising from the colon and rectumZhu R, Liu F, Grisotti G, Pérez-Irizarry J, Cha CH, Johnson CH, Boffa DJ, Han D, Johung KL, Zhang Y, Khan SA. Distinctive features of gastrointestinal stromal tumors arising from the colon and rectum. Journal Of Gastrointestinal Oncology 2018, 9: 231-240. PMID: 29755761, PMCID: PMC5934147, DOI: 10.21037/jgo.2017.11.12.
- Beyond genomics: understanding exposotypes through metabolomicsRattray NJW, Deziel NC, Wallach JD, Khan SA, Vasiliou V, Ioannidis JPA, Johnson CH. Beyond genomics: understanding exposotypes through metabolomics. Human Genomics 2018, 12: 4. PMID: 29373992, PMCID: PMC5787293, DOI: 10.1186/s40246-018-0134-x.
- Metabolomics Reveals that Dietary Xenoestrogens Alter Cellular Metabolism Induced by Palbociclib/Letrozole Combination Cancer TherapyWarth B, Raffeiner P, Granados A, Huan T, Fang M, Forsberg EM, Benton HP, Goetz L, Johnson CH, Siuzdak G. Metabolomics Reveals that Dietary Xenoestrogens Alter Cellular Metabolism Induced by Palbociclib/Letrozole Combination Cancer Therapy. Cell Chemical Biology 2018, 25: 291-300.e3. PMID: 29337187, PMCID: PMC5856613, DOI: 10.1016/j.chembiol.2017.12.010.
- Yale school of public health symposium on lifetime exposures and human health: the exposome; summary and future reflectionsJohnson CH, Athersuch TJ, Collman GW, Dhungana S, Grant DF, Jones DP, Patel CJ, Vasiliou V. Yale school of public health symposium on lifetime exposures and human health: the exposome; summary and future reflections. Human Genomics 2017, 11: 32. PMID: 29221465, PMCID: PMC5723043, DOI: 10.1186/s40246-017-0128-0.
- Metabolomics guided pathway analysis reveals link between cancer metastasis, cholesterol sulfate, and phospholipidsJohnson CH, Santidrian AF, LeBoeuf SE, Kurczy ME, Rattray NJW, Rattray Z, Warth B, Ritland M, Hoang LT, Loriot C, Higa J, Hansen JE, Felding BH, Siuzdak G. Metabolomics guided pathway analysis reveals link between cancer metastasis, cholesterol sulfate, and phospholipids. Cancer & Metabolism 2017, 5: 9. PMID: 29093815, PMCID: PMC5663111, DOI: 10.1186/s40170-017-0171-2.
- Exposome-Scale Investigations Guided by Global Metabolomics, Pathway Analysis, and Cognitive ComputingWarth B, Spangler S, Fang M, Johnson CH, Forsberg EM, Granados A, Martin RL, Domingo-Almenara X, Huan T, Rinehart D, Montenegro-Burke JR, Hilmers B, Aisporna A, Hoang LT, Uritboonthai W, Benton HP, Richardson SD, Williams AJ, Siuzdak G. Exposome-Scale Investigations Guided by Global Metabolomics, Pathway Analysis, and Cognitive Computing. Analytical Chemistry 2017, 89: 11505-11513. PMID: 28945073, DOI: 10.1021/acs.analchem.7b02759.
- Systems biology guided by XCMS Online metabolomicsHuan T, Forsberg EM, Rinehart D, Johnson CH, Ivanisevic J, Benton HP, Fang M, Aisporna A, Hilmers B, Poole FL, Thorgersen MP, Adams MWW, Krantz G, Fields MW, Robbins PD, Niedernhofer LJ, Ideker T, Majumder EL, Wall JD, Rattray NJW, Goodacre R, Lairson LL, Siuzdak G. Systems biology guided by XCMS Online metabolomics. Nature Methods 2017, 14: 461-462. PMID: 28448069, PMCID: PMC5933448, DOI: 10.1038/nmeth.4260.
- Environmental Influences in the Etiology of Colorectal Cancer: the Premise of MetabolomicsRattray NJW, Charkoftaki G, Rattray Z, Hansen JE, Vasiliou V, Johnson CH. Environmental Influences in the Etiology of Colorectal Cancer: the Premise of Metabolomics. Current Pharmacology Reports 2017, 3: 114-125. PMID: 28642837, PMCID: PMC5475285, DOI: 10.1007/s40495-017-0088-z.
- Metabolite and Microbiome Interplay in Cancer ImmunotherapyJohnson CH, Spilker ME, Goetz L, Peterson SN, Siuzdak G. Metabolite and Microbiome Interplay in Cancer Immunotherapy. Cancer Research 2016, 76: 6146-6152. PMID: 27729325, PMCID: PMC5093024, DOI: 10.1158/0008-5472.can-16-0309.
- Metabolomics: beyond biomarkers and towards mechanismsJohnson CH, Ivanisevic J, Siuzdak G. Metabolomics: beyond biomarkers and towards mechanisms. Nature Reviews Molecular Cell Biology 2016, 17: 451-459. PMID: 26979502, PMCID: PMC5729912, DOI: 10.1038/nrm.2016.25.
- Metabolism Links Bacterial Biofilms and Colon CarcinogenesisJohnson CH, Dejea CM, Edler D, Hoang LT, Santidrian AF, Felding BH, Ivanisevic J, Cho K, Wick EC, Hechenbleikner EM, Uritboonthai W, Goetz L, Casero RA, Pardoll DM, White JR, Patti GJ, Sears CL, Siuzdak G. Metabolism Links Bacterial Biofilms and Colon Carcinogenesis. Cell Metabolism 2015, 21: 891-897. PMID: 25959674, PMCID: PMC4456201, DOI: 10.1016/j.cmet.2015.04.011.
- Comprehensive bioimaging with fluorinated nanoparticles using breathable liquidsKurczy ME, Zhu ZJ, Ivanisevic J, Schuyler AM, Lalwani K, Santidrian AF, David JM, Giddabasappa A, Roberts AJ, Olivos HJ, O’Brien P, Franco L, Fields MW, Paris LP, Friedlander M, Johnson CH, Epstein AA, Gendelman HE, Wood MR, Felding BH, Patti GJ, Spilker ME, Siuzdak G. Comprehensive bioimaging with fluorinated nanoparticles using breathable liquids. Nature Communications 2015, 6: 5998. PMID: 25601659, PMCID: PMC4454288, DOI: 10.1038/ncomms6998.
- Autonomous Metabolomics for Rapid Metabolite Identification in Global ProfilingBenton HP, Ivanisevic J, Mahieu NG, Kurczy ME, Johnson CH, Franco L, Rinehart D, Valentine E, Gowda H, Ubhi BK, Tautenhahn R, Gieschen A, Fields MW, Patti GJ, Siuzdak G. Autonomous Metabolomics for Rapid Metabolite Identification in Global Profiling. Analytical Chemistry 2014, 87: 884-891. PMID: 25496351, PMCID: PMC4303330, DOI: 10.1021/ac5025649.
- Bioinformatics: The Next Frontier of MetabolomicsJohnson CH, Ivanisevic J, Benton HP, Siuzdak G. Bioinformatics: The Next Frontier of Metabolomics. Analytical Chemistry 2014, 87: 147-156. PMID: 25389922, PMCID: PMC4287838, DOI: 10.1021/ac5040693.
- Metabolomic data streaming for biology-dependent data acquisitionRinehart D, Johnson CH, Nguyen T, Ivanisevic J, Benton HP, Lloyd J, Arkin AP, Deutschbauer AM, Patti GJ, Siuzdak G. Metabolomic data streaming for biology-dependent data acquisition. Nature Biotechnology 2014, 32: 524-527. PMID: 24911492, PMCID: PMC4112958, DOI: 10.1038/nbt.2927.
- Liquid chromatography quadrupole time-of-flight mass spectrometry characterization of metabolites guided by the METLIN databaseZhu ZJ, Schultz AW, Wang J, Johnson CH, Yannone SM, Patti GJ, Siuzdak G. Liquid chromatography quadrupole time-of-flight mass spectrometry characterization of metabolites guided by the METLIN database. Nature Protocols 2013, 8: 451-460. PMID: 23391889, PMCID: PMC3666335, DOI: 10.1038/nprot.2013.004.
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