Research Cores Town Hall - PowerPoint Presentation

1. Research Cores Town HallFebruary 16, 2021

2. AgendaIntroductions – Drs. Steve Lanier and Tim StemmlerResearch Core Presentations – Core DirectorsBreakout Rooms – One breakout room for each core to ask questions and obtain more information

3. Platform to Increase Awareness of WSU CoresWSU Research Infrastructure Events• Feb 16 – WSU Basic and Translational Science Cores Town Hall• March 16 – WSU Clinical Research Cores and Resources Town Hall• April 20 - WSU Community Based Research Resources Town Hall• Starting in late March, OVPR Based Seminars Highlighting 2 Cores/EventOVPR Cores Web Page:https://research.wayne.edu/cores-facilities

4. zWSU Basic and Translational Sciences CoresOVPR Cores  GenomicsLipidomicsLumigenMagnetic ResonanceProteomicsDLAR – Division of Laboratory Animal ResearchKCI CoresAnimal Model & Therapeutics EvaluationBehavioral & Field ResearchBiobanking & Correlative SciencesEpidemiology ResearchMicroscopy, Imaging & CytometryPharmacology & Metabolomics• OVPR Cores have an annual revenue of $3.1 million with an overall expenses of ca.      $6 million.• KCI cores are supplemented by OVPR with a $1 million annual investment.• Costs are heavily supplemented to provide affordable support to University      Researchers.

5. Order of PresentationsAnimal Model & Therapeutic Evaluation Core – Lisa Poliin and Sijana DzinicBehavioral & Field Research Core – Felicity Harper & Tanina MooreGenomics Core – Katherine GurdzielLipidomics Core- Rao MaddipatiLumigen Instrument Center – Judy WestrickMagnetic Resonance Core – E. Mark HaackeMicroscopy, Imaging & Cytometry Resources Core – Kamir MoinPharmacology & Metabolomics Core – Jing LiProteomics Core – Paul Stemmer

6. Animal Model and Therapeutic Evaluation CoreLocation: 421 E. Canfield – 1st Floor EllimanContact Information: Lisa Anne Polin, Ph.D., Director – polinl@karmanos.org or ac8694@wayne.edu – Office #1222; Phone (313) 578-4270Sijana Dzinic, Ph.D., Assistant Director – dzinics@karmanos.org or aj6640@wayne.edu – Office #1107; Phone (313) 578-4440Website:https://www.karmanos.org/karmanos/animal-model-and-therapeutics-evaluation-core

7. Animal Model and Therapeutics Evaluation Core (AMTEC) MissionThe purpose of AMTEC is to enhance the peer reviewed funded research activities of Karmanos Cancer Institute members whose research needs primarily involve the use of cancer–based animal models and/or preclinical efficacy evaluations of novel or enhanced therapies. Our goal is to provide expert scientific consultation, technical expertise and access to a wide breadth of relevant tumor models and associated animal-related services.

8. AMTEC ServicesCollaborates with KCI/WSU investigators to design and conduct tumor biology studies including in vivo efficacy evaluations of novel therapeutics:Study Design and Implementation that include cell/tumor implant, trial set-up and endpoint determinations; dose-range optimization and pilot toxicity studies; administration of novel therapeutic agents; end point data analyses; sample generation, preservation and storage (fresh and snap frozen animal tissues; Advanced Primary and Secondary Evaluations: Combination Therapies, Proof of Principle Designs, etc. Provides investigators with “in house” derived or purchased mouse and human cell lines or in vivo established tumor models (syngeneic, xenograft, PDX). Performs mouse breeding colony management (transgenic, KO).Provides ad hoc technical assistance including implants, injections, small animal surgical procedures.Assists with preparation of grants, contracts and regulatory filings.

9. AMTEC New ServiceAMTEC provides processing of formalin fixed tissues using an Excelsior AS Tissue Processor, with tissue embedding using a HistoStar Instrument Embedding Center with subsequent tissue sectioning available. We can help you further expand your in vivo study findings: Animal study tissue harvest and fixation: Generation of formalin fixed paraffin embedded (FFPE) blocks and slides for follow-up histological examination and pathological analyses.AMTEC service can also provide ad hoc one time training session and SOP to learn principles of H&E staining.

10. Behavioral and Field Research CoreLocation:Mid Med Research Building (Same Building as WSU’s IRB)Contact Information: Felicity Harper, Ph.D., Scientific Director – harperf@karmanos.orgTanina Moore, Ph.D., Director – fostert@karmanos.org Website: https://www.karmanos.org/karmanos/behavioral-and-field-science-core

11. Behavioral and Field Research CoreMissionThe Behavioral and Field Research Core (BFRC) is a human-based core with a dedicated staff that facilitates the integration of communication and behavioral research. The BFRC’s staff offers a wide range of research services and expertise in behavioral research methodologies and comprehensive services spanning the continuum of the research process. The BFRC offers management of evidence-based social and behavioral interventions to support the development and implementation of population science and patient-centered clinical research.

12. Behavioral and Field Research CoreServicesRegulatory (PRMC, IRB, Oncore)Clinic recruitmentBehavioral study designSurvey development (measure selection, cognitive interviewing, pilot testing)Data collection (qualitative and qualitative methods and techniques, e.g. focus groups, in-person and internet-based data collection)Data management and analysis (e.g. survey maintenance, survey and data merge, syntax creation, scale reliabilities)

13. Genomics CoreLocation:C.S. Mott Center – Ground floorContact: Katherine Gurdziel, Ph.D., Interim Director – gurdziel@wayne.edu or genomicscore@wayne.edu Phone: (313) 577-1002Website: https://genomesciencescore.wayne.edu/

14. Genomics Core MissionThe Genomics Core offers a streamlined set of services that includes competitive pricing with built-in quality assurance standards. The core has operationalized the latest next-generation sequencing platform – Illumina’s Nova Seq 6000 and consolidated functional space at the C.S. Mott Center for Human Growth and Development.

15. Genomics CoreServices ProvidedNext-generation Sequencing (NGS) - NovaSeq 6000 and MiSeq sequencing platformsLibrary preparation – transcriptome profiling, WG-seq (PCR-free), WGBS-seq, exome, 16SSingle cell sequencing - 10x Genomics Chromium System employing Next GEM Reagents and ChipsIllumina microarray services (human and mouse methylation arrays)SNP genotype analysis - pre-designed and custom TaqMan™ SNP Genotyping Assays run on the QuantStudio 12K Flex platformTaqMan™ Gene Expression Assays - real-time Polymerase Chain Reaction (RT-PCR) gene expression analysis run on the QuantStudio 12K Flex platformBioinformatics support

16. Lipidomics CoreLocation:430 A. Paul Schaap Chemistry Building -5101 Cass Ave.Contact:Krishna Rao Maddipati, Ph.D., Director – maddipati@wayne.edu – Phone (313) 577-2088Yinlong Cai, Ph.D., Lab Manager – yinlcai@wayne.edu – Phone (313) 577-2088Website: http://lipidomics.wayne.edu

17. Lipidomics CoreMissionComprehensive analysis of cellular lipids that encompass fatty acyls, glycerolipids, glycerophospholipids, sphingolipids, sterol lipids, prenol lipids, saccharolipids, and polyketides is in essence the study of the lipid metabolome. Currently, the Lipidomics Core Facility analyzes 5 of the 8 classes of lipids, viz. fatty acyls, glycerolipids, glycerophospholipids, sphingolipids, and sterol lipids on a regular basis and can analyze other classes as well, if needed. In addition, the core facility has developed methods for TCA cycle metabolites and amino acids analyses and gearing up for broader metabolomic analysis.

18. Lipidomics Core FacilityServicesSample preparation: LC-MS analysis of biological samples for lipids requires extraction, either by organic solvents or by solid phase extraction cartridges.Qualitative LC-MS or Shotgun lipid profiling: Evaluation of changing lipid profiles in samples collected under different conditions requires the establishment of the profile. This may involve the establishment of known lipid metabolite profile or identification of novel lipid metabolites, or a combination of both. This service is central to all discovery work.LC-MS method development: Methods are already in place for the detection and quantification of most eicosanoids and docosanoids. However, sample-specific and/or any novel metabolite-specific methods require developmental work.Data analysis: Analysis and presentation of both qualitative and quantitative LC-MS data in the form easily understandable to the investigator as well as interpretation assistance, where necessary.

19. Lumigen Instrument CenterLocation:5101 Cass Ave., A. Paul Schaap Chemistry Building (Basement)Contact:Judy Westrick, Ph.D., Director, judy.westrick@wayne.edu – (313) 577-2579NMR and EPR Laboratory – Dennis Anderson, dennis.p.Anderson@wayne.edu  Mass Spectrometry Laboratory – Johnna Birbeck, Ph.D., jbirbeck@chem.wayne.edu   Nick Peraino, Ph.D., nperaino@chem.wayne.eduElectron Microscopy Laboratory – Zhi Mei (Mike), Ph.D., zmei@chem.wayne.edu X-Ray Diffraction Laboratory – Cassie Ward, Ph.D., Associate Director, ward@wayne.edu    Sameera Perera, Ph.D., Samarage.Sameera.Perera@wayne.edu  Optical Spectroscopy Laboratory and other – Cassie Ward, Ph.D. Associate Director, ward@wayne.edu Website: http://chem.wayne.edu/lumigen/ 

20. Lumigen Instrument CenterMissionThe center supports fundamental and applied research for chemical and material characterization and quantification:NMR and EPR LaboratoryValidation (level 1) of synthetic and natural product compoundsAssessment of nutrition (metabolomics)Kinetic and equilibrium studiesMass Spectrometry LaboratoryMass Spectrometry ImagingHigh Resolution Mass Spectrometry, MSn  (levels 2, 3, and 4)Trace elements and metals quantificationContaminant quantification in environmental and biological matrices

21. Lumigen Instrument Center MissionX-Ray Diffraction LaboratoryStructural analysis, chemical composition and purity, and physical properties of solid-state materialsElectron Microscopy LaboratoryHigh resolution images of materials, cells, and tissuesOptical Spectroscopy and other small instrumentsThermoanaytical analysis of proteins, polymers, and macromolecular assembliesQuantitation and molecular information

22. Lumigen Instrument CenterServicesUsage and fee-for-service coreUsage ServicesTraining 24/7 access Instrument fee rate (cost/hour)Fee-for-ServiceCost per sampleMethod developmentExperimental designProject consultationThe Lumigen Instrument Center provides services to the greater Detroit-area and other Michigan scientific communities.

23. Magnetic Resonance CoreLocation:MR Research Facility @ Harper University Hospital – 3990 John R. Rd.Contact:E. Mark Haacke, Ph.D., Director – nmrimaging@aol.com Jiani Hu, Ph.D., Co-Director – jianihu@yahoo.com Bruce Berkowitz, 7T Director – baberko@med.wayne.edu Zahid Latif – Chief MR Technologist – zahidlatif@wayne.edu Pavan Jella – 3T MR Operator – pavan.jella@wayne.edu Robin Roberts – 7T MR Operator – rroberts@med.wayne.edu(313) 745-1388Website:http://mrc.wayne.edu

24. Magnetic Resonance CoreMissionThe Magnetic Resonance Core is committed to the development of magnetic resonance (MR) methods and their application in preclinical and clinical subjects to better understand human physiology and disease. The MR Research Facility (MRRF) will promote the use of MR methods to the WSU scientific community and support the implementation of MR methods through education, assistance in experimental design, data collection and analysis.

25. Magnetic Resonance CoreServicesSequence developmentProtocol developmentData acquisitionImage processingSignal processingData analysisMagnet time:Pre-clinicalClinical ResearchDevelopmental**Supported by Office of the Vice President for Research

26. Microscopy, Imaging & Cytometry Resources(MICR) CoreLocation: MICR-Microscopy: 6339 Scott Hall – (313) 577-2511MICR-Cytometry: 615 HW-CRC – (313) 576-8341MICR-In Vivo Imaging: 0125 Elliman – (313) 576-8254Contact:Kamiar Moin, Ph.D., Director: kmoin@wayne.edu Jessica Back, Ph.D., Associate Director: backj@karmanos.org Website:http://micr.med.wayne.edu/

27. Microscopy, Imaging & Cytometry ResourcesMissionThe mission of the Microscopy, Imaging & Cytometry Resources (MICR) core is to enhance the peer reviewed funded research activities of investigators whose research requires microscopy, imaging resources, flow cytometry and related techniques. The facility’s objective is to provide the research community with expert scientific consultation, technical expertise and access to state-of-the-art instrumentation.

28. Microscopy, Imaging and Cytometry Resources CoreServicesConfocal microscopy, multiphoton microscopy, super-resolution microscopy, conventional light microscopy; FRET and FRAP, TIRF and Atomic Force Microscopy; in vivo small animal imaging (including SPECT, CT, PET, X-ray, and optical imaging); Flow Cytometry (including cell sorting, imaging flow cytometry)Ratiometric analyses (e.g., intracellular pH and ion measurement studies), as well as three- and four- dimensional image reconstruction and quantitative measurements; Application and study design consultation; training and workshops.

29. Pharmacology and Metabolomics CoreLocation:Karmanos Cancer Institute – 4100 John R, HWCRC Room 523Contact: Jing Li, Ph.D., Director: Lijing@wayne.edu Phone: 313-576-8258Website:https://karmanos.org/karmanos/pharmacology-core

30. Pharmacology and Metabolomics CoreMission    Provide state-of-the-art bioanalytic technology and a broad range of pharmacology and metabolomics expertise to support basic, translational, and clinical research. 

31. Pharmacology and Metabolomics CoreBioanalysis ServicesDevelopment, validation, and implementation of liquid chromatography coupled with tandem mass spectrometer (LC-MS/MS) based analytical methods for quantitatively determining drugs, drug metabolites, or endogenous chemicals (metabolites) in biological samples (e.g., plasma/serum, blood, tissue, cell pellets). AB Sciex QTRAP 6500 LC-MS/MS systemWaters TQ-XS LC-MS/MS system

32. LC-MS/MS methods for determination of small molecule drugs and drug metabolites to support clinical or preclinical pharmacokinetic studies#Drugs, Metabolites#Drugs, Metabolites#Drugs, Metabolites1acetaminophen22dextrophan44phenacetin2AG12723diclofenac, 4’-hydroxy-diclofenac45phenylethylamine3aminoflavone, AFP46424DIM (Diindolmethane)46quercetin4AZD177525erlotinib47quercetin5benzylnirvanol26estrone 3-sulfate48quinidine6betulinic acid27everolimus49ribociclib7BGB-29028FAU, FMAU50RO49290978BMN67329fexofenadine51rosiglitazone, 5-hydroxy rosiglitazone9bupropion, hydroxy bupropion30furafylline52rosuvastatin10carboplatin31gefitinib53saquinavir11CDF (diflourinated-curcumin) 32HBC (Hydrazinobenzoylcurcumin)54sertraline, Venlafaxine12ceritinib33hydroxyflavone (di, tri, and tetra-)55s-mephenytoin, S-4’-hydroxy mephenytoin13combretastatin A434irinotecan, SN-38, SN-38G56sorafenib14Compound #9 (Rad6 inhibitor)35isoflavones (Daidzein, Genistein)57sulfaphenazole15CP-136ketoconazone58temozolomide, AIC16Cu2737lapatinib59thiourea17CuDDSF238methotrexate, DAMPA60thymoquinone 18curcumin39midazolam, 1’-hydroxy midazolam61tunicamycin A19decetaxel40O6-benzylguanine62UTL-5g, DCA, ISOX20dexamethasone41olaparib63veliparib, M821dextromethorphan42paclitaxel64zolmitriptan43pazopanib

33. LC-MS/MS based targeted metabolomics for quantitatively profiling ~ 300 endogenous metabolites *Typical metabolites measured are listed above but the capacity is not limited to these.  Assays can be tailored to investigators’ needs.Classes or PathwaysNumber of Metabolites Glycolytic, TCA cycle, and pentose phosphate pathway25Nucleosides, nucleotides and NAD-related metabolites40Amino acid and related metabolites60Acyl CoAs10Acyl Carnitines20Bile acids and metabolites15Ceramides10Steroids10Short chain fatty acids8Phospholipids15Gut microbial related metabolites15Miscellaneous Metabolites65Total293

34. Pharmacology and Metabolomics Core A broad range of pharmacology supportPharmacokinetic study design to assist study design for pharmacokinetic evaluation in clinical and preclinical studiesPharmacokinetic data analysis and modeling using traditional compartmental or non-compartmental analysis, nonlinear mixed-effect (population) pharmacokinetic modeling, or physiologically based pharmacokinetic modeling approachesIn vitro drug metabolism assay to determine metabolic pathways and potential drug-drug interactionIn vitro or ex vivo protein binding assay using equilibrium dialysis to determine drug binding to plasma proteins or tissuesPermeability and transporter assays using cellular models to determine drug transcellular permeability and interaction with drug transporters

35. Proteomics CoreLocation: Scott Hall – Room 2105Contact:Paul Stemmer, Ph.D., Director, pmstemmer@wayne.edu – (313) 577-6536Website: http://research.wayne.edu/proteomics/

36. Proteomics CoreMissionProvide Mass Spectrometry (MS) Technologies for: Proteome Profiling including Differential Abundance Identify Proteins ID & Quantify Chemical Modifications Targeted Quantitation BioinformaticsMolecular Interaction Measurement by Biolayer Interferometry (BLI)Particle Analysis by Microfluidic Pulse Resistance (MFPR) 

37. Proteomics CoreServicesProteome Profiling by LC-MS/MS on Orbitrap InstrumentTargeted Quantitative Analysis on a Triple Quadrupole MS systemAll MS systems are equipped with nanoFlow UHPLCSample Prep by Alkaline Reversed Phase Spin columnsSample Prep by Affinity Selection by antibody for selected proteins or TiO2 for phosphopeptidesPeptide and protein identification and quantification using Proteome Discoverer, MaxQuant or PEAKS are performed as part of the MS analysis serviceInformatics Services including Ingenuity Pathway Analysis (IPA) Molecular interaction analysis by Biolayer Interferometry (BLI) on an Octet Red96 Particle analysis using a Spectradyne nCS1 particle analyzer  All services and instrument reservations through the Infinity

38. Breakout Rooms