Environmental Biomarkers Core

About

Beyond making available state-of-the-art, user-friendly facility and services, the Biomarkers Core enables education, assay development, and sample analysis services for the environmental health researchers at the University of Illinois at Chicago and the University of Chicago, regarding biomarkers of exposure, disease and therapeutic response as well as the levels of the environmental toxins. In particular, CACHET investigators/members will have access to resources within this core at discounted, internal rates, regardless of their campus affiliation.
Technologies and types of measurements that will be provided including qualitative and quantitative analysis of a wide variety of biomarkers and environmental toxins using ultrahigh-pressure or high performance liquid chromatography-mass spectrometry (UHP)LC-MS and gas chromatography-mass spectrometry (GC-MS) measurements and measurement of metals in biological specimens and environmental samples using inductively-coupled plasma (ICP)-MS. All the equipment and instrument are consolidated at Mass spectrometry, metabolomics & proteomics facility (MMPF) at UIC campus. A majority of CACHET members from UIC and U of C campus will take the advantage of obtaining fast turn-around analytical measurement locally instead of sending samples out of state as is the current practice for many. The following workflow shows the interactions of CACHET members with the Biomarkers Core:

Approach

The EBC will provide a suite of measurements to CACHET investigators by combining unique resources available at UIC (ICP-MS, LC-MS/MS, MALDI-TOF etc.) and UofC (microbiome, metabolomics, GC-MS) with DNA and RNA sequencing and bioinformatics at each site. Making these resources equally available to CACHET members on both campuses will continue to increase collaborations and output. Importantly, providing stream-lined, prioritized and subsidized access to existing resources will enhance the productivity of CACHET researchers. EBC will provide services in five areas: 1) LC-MS and GC-MS of biomarkers and environmental toxins; 2) ICP-MS metal analysis; 3) microbiome and metabolomics; 4) DNA/RNA -omics; and 5) bioinformatics.

EBC Leadership

Richard D. Minshall, PhD, is Professor of Pharmacology and Anesthesiology in the College of Medicine at UIC, with a research focus on pulmonary disease and molecular mechanisms of lung injury. Dr. Minshall currently serves as Co-Leader of the CACHET Biomarkers Core, implementing services within the RRC Mass Spectrometry Core (RRC-MSC). At UIC, he previously served as Director of the RRC and as Associate Director of Shared Resources for the University of Illinois Cancer Center. He is the current Co-Director of Team Science for the UIC Center for Clinical and Translational Sciences. His efforts have been instrumental in reorganizing and rejuvenating core service facilities critical to basic, translational and clinical research activities at UIC. As the RRC Director, he was instrumental in upgrading the RRC-MSC as well as other core facilities for NMR, flow cytometry, imaging, genomics, gene editing, single cell proteomics, transcriptomic profiling, biobanking and bioinformatics, which are all important for CACHET investigators. In addition to serving the UIC research community, Dr. Minshall plays a central role in the Chicago Biomedical Consortium (CBC), a collaborative agreement between UIC, UofC and Northwestern University that provides access for all investigators to shared resources at each institution at internal rates. As a UIC leader and representative to the CBC open access executive advisory panel that directs acquisition of new shared instrumentation not otherwise available in Chicago, he has enabled development of quantitative assays for analysis of a wide variety of biomarkers such as isoprostanes, DNA oxidation products and sulfatides in clinical specimens, and environmental pollutants, e.g BPA, heavy metals. Dr. Minshall’s primary role as EBC Co-Leader is to provide direction, advice and “lead blocking” that enables CACHET members to access relevant key Facility Cores at UIC and UofC and to help coordinate access and P30-subsidized copay mechanisms that reduce costs to PIs for facility/service fees while providing high-quality prioritized access to critical instrumentation and expertise.

Eric G. Pamer, MD, is Director of the DFI and Microbiome Center and Professor of Medicine and Microbiology at UofC. He is a renowned physician–scientist who specializes in immune defense against infections associated with cancer treatment, with a research focus on the microbiome’s impact on infection resistance. Dr. Pamer was previously the Chief of Infectious Disease at Memorial Sloan Kettering in NYC, Director of the Lucille Castori Center for Microbes, Inflammation and Cancer and Professor at Weil Cornell Medical University. He is a member of the NIH-NIAID Board of Scientific Counselors and the Bill and Melinda Gates Foundation’s Global Health Scientific Advisory Committee. His multidisciplinary expertise encompasses microbial genomics, transcriptomics and metabolomics in relation to health and immunity. At DFI, Dr. Pamer’s research team promotes wellness through groundbreaking science on the immune system, genetics, the microbiome and their shared environments. UofC has provided significant research resources and infra-structure support (e.g. physical infrastructure, major instrumentation, multiple faculty recruitment slots), which benefit the newly streamlined EBC to support CACHET’s mission. Dr. Pamer’s role as Co-Leader of the EBC entails providing direction, oversight and operational guidance to core services pertaining to analyses of micro-biome, microbial metabolites and other -omics-related assays, enabling CACHET members at UofC and UIC to timely and seamless access while ensuring quality and prioritization to meet evolving CACHET needs.

Environmental Exposures (EE) Sub-Core

The EE Sub-Core is a P30-specific unit that partners with the UIC RRC-MSC to leverage its equipment and expertise, providing CACHET members with identification and quantitative measurements of analytes in biological and environmental samples. The RRC-MSC/EE Sub-Core, equipped with eight modern mass spectrometers available to CACHET members, recently re-located to renovated space in the Center for Structural Biology Building, adjacent to the UIC- School of Public Health (SPH). This unit of the EBC is located centrally within the Illinois Medical District and is easily accessible. The facility and labs have a secure card-reader entrance affording 24-hour availability and adjacent parking to all staff and users. Investigators who are frequent users from off-campus locations (e.g., UofC PIs) are given special identification cards for laboratory access. Experienced users may arrange to start experiments before the staff leaves and continue after hours. Data are archived in an informatics center maintained by the RRC and may be retrieved remotely for processing.

Leadership

 

Stephanie Cologna, PhD, will serve as Academic Leader for the EE Sub-Core. Dr. Cologna is an Associate Professor of Chemistry in the College of Liberal Arts and Sciences at UIC and Academic Director of the RRC-MSC. She is an expert in MS and is fully engaged in providing expert advisory support to Core Director Hui Chen in the design of new MS assays, trouble-shooting problematic assays, and interfacing with Dr. Minshall and other CACHET and campus members on MS, instrumentation, personnel needs and, importantly, rigor and reproducibility. Dr. Cologna received her PhD in analytical chemistry, specifically mass spectrometry from Texas A&M University, with postdoctoral training at the NIH working on proteomics of rare genetic disorders. Dr. Cologna will ensure that the P30-specific EE Sub-Core and affiliated institutional MS core facilities at UIC and UofC are an educational resource for CACHET investigators, postdoctoral fellows and staff. Dr. Cologna has a training record in MS techniques and established the annual Chicago Mass Spectrometry Day to provide MS education to regional scientists. For CACHET, Dr. Cologna works with Drs. Minshall and Prins to implement the specific aims for the EE Sub-Core, which include critical new instrumentation for analysis of heavy metals, metabolomics/small molecule identification and quantification that specifically addresses critical research needs highlighted in the 2019 CACHET membership survey.

 

Hui Chen, PhD, is Director of the RRC-MSC and the CACHET EE Sub-Core Co-Leader at UIC. He is a technical expert in MS for heavy metals, small molecules, lipids, metabolites and proteins. Dr. Chen currently oversees daily operations of this critical MS-based core resource. Dr. Chen received his PhD in analytical chemistry and has worked with MS for >20 years, including liquid and gas chromatography and various types of MS such as FT-ICR-MS, MALDI-TOF, Q-TOF, QQQ and ICP-MS. Dr. Chen will train CACHET faculty and senior postdoctoral fellows in LC-MS/MS and ICP-MS sample preparation and analysis. He will also coordinate proteomics analyses for BEES as needed by CACHET members.

 

 

Key Accomplishments

  • Purchased a Perkin Elmer NEXion-2000 ICP-MS, built a dedicated suite, and activated services for heavy metal analysis including high throughput sampling, microwave digestion and metal speciation capabilities;
  • Enrolled and participated (certified) in the Quebec Multi-element External Quality Assessment Scheme to ensure service quality in metal analysis across multiple matrices;
  • Established quantitative LC-MS/MS assays for pesticides, herbicides, bisphenols and PFAS;
  • Purchased a new Q-Exactive Orbitrap LC-MS/MS and developed tandem mass tag protocols for quantitative proteomics analysis for protein biomarker identification and quantification;
  • Established untargeted metabolomics and lipidomics assays for biomarker discovery;
  • Recruited Stephanie Cologna, PhD, as Academic Leader of CACHET EE Sub-Core;
  • Hired Assistant Manager for EE Sub-Core, Dr. Jayathilaka (0.5 FTE for CACHET), who will focus on metals analysis by ICP-MS and MS-based targeted assays mentioned above.
  • Implemented the iLab research management and billing system, which streamlines billing for subsidized and co-pay mechanisms and tracks Core usage by CACHET members regardless of institutional affiliation.
  • Established a service hub to facilitate CACHET member’s needs in multi-analyte analysis of completed in-house and outsourced services. Results are returned to users in a single report.
Biomarkers of Exposure Effects and Susceptibility (BEES) Sub-Core

The overall goal of BEES Sub-Core is to advance EHS research of CACHET members by providing ready access to state-of-the-art “-Omics” technologies and expertise across the two campuses, facilitating effective utilization of resources, enhancing training opportunities and providing subsidized rates for services to Center members. To accomplish this goal, the BEES Sub-Core leverages existing institutional resources at UofC and UIC in microbiome analysis, metabolomics, proteomics, genomics and bioinformatic services. To enable streamlined access to these varied services by CACHET members and provide advice on appropriate experimental design and resource utilization, each BEES Sub-Core has a Center-supported Facilitator who is the director of that institutional facility core and a subject-matter expert. In addition to providing guidance and priority access to CACHET members, they will provide training to CACHET investigators who wish to master these technologies, particularly young investigators and those new to the fields. The BEES Sub-Core uses the Office of Shared Research Facilities cores (OSRF) central web-based ordering system at UofC for services and subsidy/co-pay requests which enables efficient turnaround time for all CACHET members on both campuses. This system permits tracking of subsidized services and Core/Unit utilization in a centralized database for efficient metrics analysis of facility usage and outcomes.

Leadership

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Key Accomplishments

For CACHET members interested in services

Service

The Biomarkers Core provides CACHET investigators qualitative and quantitative analysis regarding biomarkers of exposure, disease and therapeutic response as well as the levels of environmental toxins.

Biomarkers and toxic agents will be analyzed in human subjects, model systems and environmental samples in the following areas based on the instrumentation:

Trace Elements/Metals analysis by ICP-MS
Equipped for quantitative and qualitative analysis of a full spectrum of heavy metals and metalloids in trace and larger concentrations in biological and environmental samples. Trace metal quality sample preparation is also available.
Trace Metals are typically analyzed including V, Cr, Mn, Fe, Co, Ni, Cu, Zn, As, Se, Mo, Cd, Sn, Sb, Hg, Pb. g. Materials are frequently analyzed including tissue, soil, water, nails, hair, urine, blood and milk.
View ICP-MS PowerPoint
Biomarkers/toxins analysis by LC/MS
Seven state-of-the-art LC/MS are available for services, providing identification and quantitative analysis for different sample matrices including tissue, water, blood and urine. The analytes include protein/peptide, nucleic acid, carbohydrate, lipid and other organic compounds. Sample preparation and bioinformatics services are also available.

Targeted/untargeted Metabolomics/proteomics by LC/MS
Taking advantage of technologies such as nanoLC, UHPLC and SFC (super-critical fluid chromatography), both targeted and untargeted metabolomics/proteomics services are available for complex samples in the Biomarkers Core, aiming to improve diagnosis, prevention and monitoring of many diseases through metabolic and proteomic profiling.

Pesticide analysis by LC/MS
Followed the standardized EPA protocol, LC/MS analysis on common pesticides has been established in the core, including DTT, glyphosate, atrazine and simazine from food, water and biological fluids.

Trace organic pollutant analysis by GC/MS
For the analysis of volatile molecules including many pesticides and halogenated persistent pollutants, GC-MS measurement is available. The samples can be prepared from soils, sediment, dust, sludge, air sampling cartridges, and human blood and tissues.
Scientists in our core can design and conduct experimental protocols, analyze data and provide pre-experimental consultation to CACHET investigators who seek to incorporate mass spectrometry based experimental strategies into their research programs. Researchers may submit samples to the Biomarkers Core for service directly. Alternatively, qualified users may schedule instrument time to analyze their own samples after taking training courses of instrument operation.

Mass Spectrometry Core_Assay List 

Please note on each page there is a clickable “Back to Category List”, which will bring you back to the first page.

Pricing available upon request.
For general information, please contact Dr. Hui Chen, Director of Mass Spectrometry, Metabolomics and Proteomics Facility at ch1208@uic.edu or (312) 996-7357.

Service Description Internal External
Trace elements in solution* Samples in solution or already digested $14 $21
Hot-Block digestion Acid digestion in hot-block for solid samples $20 $30
Bio-sample clean-up Nail or hair cleaning before digestion $5 $8
Mercury analysis by Direct Mercury Analyzer   $5 $8
Method development   On request On request

*Standard suite includes Al, V, Cr, Mn, Fe, Ni, Co, Cu, Zn, As, Se, Mo, Cd, Sb, Sn, Pb

ADDITIONAL RESOURCES:

Equipment

Equipped with the state-of-the-art modern mass spectrometers, Biomarkers Core provides many types of mass spectrometry-based measurements to facilitate the research of CACHET members. The following mass spectrometers located in UIC are available for use by CACHET members:

  • NexION 300/250S ICP-MS spectrometer with tri-mode detection
  • Thermo Orbitrap Velos PRO with Agilent NanoLC system.
  • Agilent 6410 triple quadrupole mass spectrometer equipped with electrospray and atmospheric pressure chemical ionization (APCI), and Agilent 1200 HPLC system.
  • Agilent 6410 triple quadrupole mass spectrometer equipped with Agilent 1200 HPLC and electrospray, APCI, and atmospheric pressure photoionization (APPI).
  • Agilent 6545 Jet-stream QToF high resolution MS/MS equipped with electrospray, APCI and Agilent 1290 UPLC/SFC systems.
  • Shimadzu IT-ToF high resolution ion trap time-of-flight hybrid mass spectrometer equipped with electrospray, APCI, and a Shimadzu UHPLC system.
  • Applied Biosystems API 5500 Q-trap tandem mass spectrometer equipped with Agilent 1260 UPLC.
  • Applied Biosystems API 6500 Q-trap tandem mass spectrometer with Agilent 1290 UHPLC system.
  • JEOL GCMate II​Magnetic Sector Gas chromatography mass spectrometer

 

Featured Equipment

 

 

NexION 300 ICP

QTRAP 6500

Agilent 6545

 

 

Information about services here:

External Core Services

UChicago BSD Core Facilities

Biostatistics

CRI Bioinformatics Core

Genomics Facility

Human Imaging Research Office (HIRO)

Human Tissue Resources Center (HTRC)

Metabolomics

Proteomics

Survey Lab

UChicago Practice-Based Research Network (PBRN)

 

Pricing available upon request.