Geremy Clair
Geremy Clair
Professional Title:
Scientist
Phone Number:
(509) 371-7240
Email:
geremy.clair@pnnl.gov
Biography:
Dr. Clair’s educational background, research, teaching interests and experience are strongly interdisciplinary. His graduate work and teaching experience were in multi-omics analysis, Lung biology, microbiology, and biochemistry. After his graduation in France, He completed performed two post-doctorates using a combination of omics technologies, bioinformatics, and biochemistry.
Dr. Clair is involved in a wide variety of projects including projects dealing with Lung pediatric biology, the development of tools to achieve omics measurements from extremely small samples including single mammalian cells proteomics, and the study of bacterial pathogens:
- He is multi-PI of a Research Center of the LungMAP consortium Omics, a large project funded by NHLBI (National Heart, Lung, and Blood Institute, NIH). The overarching goal of this initiative is to create a molecular atlas of the developing lung to serve as a research resource and public education tool. The LungMAP project allows researchers to explore the spatio-temporal molecular atlas of the normal and diseased developing lung (e.g., Cystic Fibrosis, Bronchio Pulmonary Dysplasia, etc.). In this context, he has been leading, co-leading author, and key contributor of several publications. Specifically, he has participated in: (i) the development of technologies enabling to quantify the proteins contained in small tissue samples at scales unattainable before, including microdissected tissue section of less than 4000 cells and single-cell samples ; (ii) the description of the dynamics of thousands of protein and lipids in during the process of lung development; and (iii) the elucidation of essential processes in the production of lung surfactant an essential fluid that allows respiration; and in the development of tools facilitating lipid analysis.
- Dr. Clair has developed new innovative technologies and strategies to analyze proteins in minute samples including small microdissected functional units such as lung alveolar tissue or single kidney glomeruli.
- Dr. Clair has bioinformatic R packages and shiny apps to perform functional enrichment analysis of lipids (e.g., Lipid Mini-On) and to analyze reproducibly omics dataset (e.g., RomicsProcessor)
- Dr. Clair has described how the pathogens of the group Bacillus cereus were regulating the expression of their virulence factors in response to redox variations found in their host environment, demonstrated how the foodborne pathogen Campylobacter jejuni was modulating its virulence program in response, elucidated the mode of action of Campylobacter secreted effector, participated to the first description of the mechanism by which the multi-resistant Staphylococcus aureus (MRSA) goes in a dormancy state called persister responsible for reoccurring infections.
Publications:
2021
- C.Campbell, C. Fingleton, M.S. Zeden, E. Bueno, L.A. Gallagher, D. Shinde, J. Ahn, H.M. Olson, T.L. Fillmore, J.N. Adkins, F. Razvi, K.W. Bayles, P.D. Fey, V.C. Thomas, F. Cava, G.C. Clair, and J.P. O’Gara. “Accumulation of Succinyl Coenzyme A Perturbs the Methicillin-Resistant Staphylococcus aureus (MRSA) Succinylome and Is Associated with Increased Susceptibility to Beta-Lactam Antibiotics”. mBio DOI:10.1128/mBio.00530-21
- J.E. Kyle, L. Aimo, A.J. Bridge , G. Clair, M. Fedorova, J.B. Helms, M.R. Molenaar, Z. Ni, M. Orešič, D. Slenter, E. Willighagen, BJ. M. Webb-Robertson. "Interpreting the lipidome: bioinformatic approaches to embrace the complexity". Metabolomics. DOI: 10.1007/s11306-021-01802-6
- J. Wang, S.Y. Kim, E. House, C.J. Johnston, D. Chalupa, E. Hernady, T.J. Mariani, G. Clair, C. Ansong, W.J. Quian, J.N. Finkelstein, M.D. McGraw. "Repetitive diacetyl vapor exposure promotes ubiquitin proteasome stress and precedes bronchiolitis obliterans pathology". Archives of Toxicology. DOI:10.1007/s00204-021-03076-2
- V.A. Petyuk, L. Yu, H.M. Olson, F. Yu, G. Clair, W.J. Qian, J.M. Shulman, D.A. Bennett. "Proteomic Profiling of the Substantia Nigra to Identify Determinants of Lewy Body Pathology and Dopaminergic Neuronal Loss". Journal of Proteome Research. DOI:10.1021/acs.jproteome.0c00747
- J. Woo, S.M. Williams, V. Aguilera-Vazquez, R.L. Sontag, R.J. Moore, L.M. Markillie, H.S. Mehta, J. Cantlon, J.N. Adkins, R.D. Smith, G.C. Clair, L. Pasa-Tolic, Y. Zhu. “High-throughput and high-efficiency sample preparation for single-cell proteomics using a nested nanowell chip”. BioRXiv (preprint). DOI:10.1101/2021.02.17.431689
- J. Woo, G.C. Clair, S.M. Williams, S. Feng, R.J. Moore, W.B. Chrisler, R.D. Smith, R.T. Kelly, L. Pasa-Tolic, C. Ansong, Y. Zhu. “Robust, sensitive, and quantitative single-cell proteomics based on ion mobility filtering”. BioRXiv (preprint). DOI:10.1101/2021.01.30.428333
- D. Zamith-Miranda, H.M. Heyman, M.C. Burnet, S.P. Couvillion, X. Zheng, N. Munoz, J.E. Kyle, E.M. Zink, K.K. Weitz, K.J. Bloodsworth, G.C. Clair, J.D. Zucker, J.R. Teuton, S.H. Payne, YM. Kim, M. Reyes Gil, E.S. Baker, E.L. Bredeweg, J.D. Nosanchuk, E.S. Nakayasu. “A Histoplasma capsulatum lipid metabolic map identifies antifungal targets and virulence factors”. BioRXiv (preprint). DOI:10.1101/2020.03.02.973412
2020
- K.L. Nunn, G. Clair, J.N. Adkins, K. Engbrecht, T. Fillmore, L.J. Forney. “Amylases in the Human Vagina”. mSphere. DOI: 10.1128/mSphere.00943-20
- N.M. Negretti, Y. Ye, L.M. Malavasi, S.M. Pokharel, S. Huynh, S. Noh, C.L. Klima, C.R. Gourley, C.A. Ragle, S. Bose, T. Looft, C.T. Parker, G. Clair, J.N. Adkins, M.E. Konkel. “A porcine ligated loop model reveals new insight into the host immune response against Campylobacter jejuni”. Gut microbes. DOI:10.1080/19490976.2020.1814121
- G. Clair, J. Esbelin, S. Mallea, I. Bornard, F. Carlin. “The spore coat is essential for Bacillus subtilis spore resistance to pulsed light, and pulsed light treatment eliminates some spore coat proteins”. International journal of food microbiology. DOI:10.1016/j.ijfoodmicro.2020.108592
2019
- E.A. Zalis, A.S. Nuxoll, S. Manuse, G. Clair, L.C. Radlinski, B.P. Conlon, J. Adkins, K. Lewis. “Stochastic Variation in Expression of the Tricarboxylic Acid Cycle Produces Persister Cells”. mbio. DOI: 10.1128/mBio.01930-19
- M. Dou, G. Clair, C.F. Tsai, K. Xu, W.B. Chrisler, R.L. Sontag, R. Zhao, R.J. Moore, T. Liu, L. Paša-Tolić, R.D. Smith, T. Shi, J.N. Adkins, W.J. Qian, R.T. Kelly, C. Ansong, Y. Zhu. “High-Throughput Single Cell Proteomics Enabled by Multiplex Isobaric Labelling in a Nanodroplet Sample Preparation Platform”. Analytical Chemistry. doi:10.1021/acs.analchem.9b03349
- G.C. Clair. “A multi-omics zoom on the molecular networks of Lung development”. AJPLung. 10.1152/ajplung.00364.2019
- Y. Du, G.C. Clair, D. Al Alam, S. Danopoulos, D. Schnell, J.A. Kitzmiller, R.S. Misra, S. Bhattacharya, D. Warburton, T.J. Mariani, G.S. Pryhuber, J.A. Whitsett, C. Ansong, and Y. Xu. “Integration of transcriptomic and proteomic data identifies biological functions in cell populations from human infant lung”. AJP-Lung. DOI: 10.1152/ajplung.00475.2018
- D. Zamith-Miranda, H.M. Heyman, L.G. Cleare, S.P. Couvillion, G.C. Clair, E.L. Bredeweg, A. Gacser, L. Nimrichter, E.S. Nakayasu, J.D. Nosanchuk. “Multi-omics Signature of Candida auris, an Emerging and Multidrug-Resistant Pathogen”. mSystems. DOI: 10.1128/mSystems.00257-19
- G. Clair, S. Reehl, K.G. Stratton, M.E. Monroe, M.M. Tfaily, C. Ansong, J.E. Kyle 2019. “Lipid Mini-On: Mining and ontology tool for enrichment analysis of lipidomic data.” Bioinformatics, btz250. doi:10.1093/bioinformatics/btz250
- N.M. Negretti, G. Clair, P.K. Talukdar, C.R. Gourley, S. Huynh, J.N. Adkins, C.T. Parker, C.M.Corneau, M.E. Konkel 2019. “Campylobacter jejuni demonstrates conserved proteomic and transcriptomic responses when co-cultured with human INT 407 and Caco-2 epithelial cells.” Frontiers in Microbiology 10, 755. doi:10.3389/fmicb.2019.00755
2018
- I.K. Kushner, G. Clair , S.O. Purvine , J.Y. Lee , J.N. Adkins, S.H. Payne 2018. “Individual Variability of Protein Expression in Human Tissues.” J. Proteome Res., 2018, 17 (11), pp 3914–3922. doi:10.1021/acs.jproteome.8b00580
- Y. Zhu, G. Clair, W.B. Chrisler, Y. Shen, R. Zhao, A.K. Shukla, and R.J. Moore, et al. 2018. "Proteomic Analysis of Single Mammalian Cells Enabled by Microfluidic Nanodroplet Sample Preparation and Ultrasensitive NanoLC-MS." Angewandte Chemie International Edition 57, no. 38:12370-12374. PNNL-SA-132946. doi:10.1002/anie.201802843
- J.E. Kyle, G. Clair, G. Bandyopadhyay, R. Misra, E.M. Zink, K.J. Bloodsworth, and A.K. Shukla, et al. 2018. "Cell type-resolved human lung lipidome reveals cellular cooperation in lung function." Scientific Reports 8, no. 1:Article No. 13455. PNNL-SA-132404. doi:10.1038/s41598-018-31640-x
- A. Moghieb, G. Clair, H.D. Mitchell, J. Kitzmiller, E.M. Zink, Y.M. Kim, V. Petyuk, A. Shukla, R.J. Moore, T.O. Metz, J. Carson, J.E. McDermott, R.A. Corley, J.A. Whitsett, C. Ansong 2018. “Time-resolved proteome profiling of normal lung development.” Am. J Physiol Lung Cell Mol Physiol. 2018 Jul 1;315(1):L11-L24. doi: 10.1152/ajplung.00316.2017
2017
- T.N. Rindler, C.A. Stockman, A.L. Filuta, K.M. Brown, J.M. Snowball, W. Zhou, R. Veldhuizen, E.M. Zink, S.E. Dautel, G. Clair, C. Ansong, Y. Xu, J.P. Bridges, J.A. Whitsett 2017. “Alveolar injury and regeneration following deletion of ABCA3.” JCI Insight. 2017 Dec 21; 2(24): e97381. doi:10.1172/jci.insight.97381
- X. Tang, J.M. Snowball, Y. Xu, C. Na, T.E. Weaver, G. Clair, and J.E. Kyle, et al. 2017. "EMC3 coordinates surfactant protein and lipid homeostasis required for respiration." Journal of Clinical Investigation 127, no. 12:4314-4325. PNNL-SA-127808. doi:10.1172/JCI94152
- M.E. Ardini-Poleske , R.F. Clark, C.K. Ansong, J.P. Carson, R.A. Corley, G. Deutsch, and J.S. Hagood, et al. 2017. "LungMAP: The Molecular Atlas of Lung Development Program." American Journal of Physiology-Lung Cellular and Molecular Physiology 313, no. 5:L733-L740. PNNL-SA-136379. doi:10.1152/ajplung.00139.2017
- S.E. Dautel, J.E. Kyle, G. Clair, R.L. Sontag, K.K. Weitz, A.K. Shukla, and S.N. Nguyen, et al. 2017. "Lipidomics reveals dramatic lipid compositional changes in the maturing postnatal lung." Scientific Reports 7. PNNL-SA-21148. doi:10.1038/srep40555
- N.M. Negretti, C.R. Gourley, G. Clair, J.N. Adkins, and M. Konkel 2017. "The food-borne pathogen Campylobacter jejuni responds to the bile salt deoxycholate with countermeasures to reactive oxygen species." Scientific Reports 7. PNNL-SA-122926. doi:10.1038/s41598-017-15379-5
- P.D. Piehowski, R. Zhao, R.J. Moore, G. Clair, C. Ansong 2017. “Quantitative Proteomic Analysis of Mass Limited Tissue Samples for Spatially Resolved Tissue Profiling.” (Book Chapter) Methods Mol Biol. 2018;1788:269-277. doi:10.1007/7651_2017_78
- E.M. Waters, J.K. Rudkin, S. Coughlan, G. Clair, J.N. Adkins, S. Gore, and G. Xia, et al. 2017. "Redeploying ß-Lactam Antibiotics as a Novel Antivirulence Strategy for the Treatment of Methicillin-Resistant Staphylococcus aureus Infections." The Journal of Infectious Disease215, no. 1:80-87. PNNL-SA-120576. doi:10.1093/infdis/jiw461
2016
- G. Clair, P.D. Piehowski, T. Nicola, J. Kitzmiller, E.L. Huang, E.M. Zink, and R.L. Sontag, et al. 2016. "Spatially-Resolved Proteomics: Rapid Quantitative Analysis of Laser Capture Microdissected Alveolar Tissue Samples." Scientific Reports 6. PNNL-SA-119185. doi:10.1038/srep39223
- Conlon B.P., S.E. Rowe, A.V. Brown-Gandt, A.S. Nuxoll, N.P. Donegan, E.A. Zalis, and G. Clair, et al. 2016. "Persister formation in Staphylococcus aureus is associated with ATP depletion." Nature Microbiology 1. doi:10.1038/nmicrobiol.2016.51
- J. Esbelin, S. Mallea, G. Clair, F. Carlin 2016. “Inactivation by Pulsed Light of Bacillus subtilis Spores with Impaired Protection Factors.” Photochemistry and photobiology 92 (2), 301-307. doi:10.1111/php.1256