Craig Hauser, Ph'D', Assoc' Director, Shared Resources

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Cancer Center Shared Resources

• Craig Hauser, Ph.D., Assoc. Director, Shared
  Resources
• Joined Burnham faculty, 1989
• Associate Professor up to 2004
• Research focus on gene expression control and
  cancer
• Held full-time administrative positions since
  2004
• CC Associate Director, Shared Resources since
  2004
• Vice President, Scientific Resources (Institute
  role since 2008)

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Cancer Center Shared ResourcesEnhancements since
previous renewal in 2003

• Space for CC Shared Resources increased from
  13,000 sq ft to 27,000 sq ft (includes 6K sq ft
  for CPCCG)
• Equipment purchased by the Institute for CC
  Shared Resources since 2003 totaled over 10 MM
• Personnel in the SRs increased from 30 to 46
  FTEs, including 9 more PhD level facility
  managers
• Addition of seven specialized facilities (in the
  existing eight SRs), and a developing SR for
  Functional Genomics
• Improvements in SR operational and fiscal
  oversight

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Sources of CC Shared Resource Funding FY05-FY08
Total Costs (including equipment/remodel)
Total Operating Costs

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Burnham Team Leadership of CC Cores

• Faculty Supervisor (Scientific Director) provides
  scientific guidance, advises core users, performs
  scientific quality assessment planning
• Assoc. Dir. for Shared Resources (AD-SR) with
  science background provides operational oversight
  for all cores
• Resource Managers/Directors are advised by
  Faculty Supervisor, but report to AD-SR. This
  enhances objectivity - cores work for entire CC
• Assoc. Dir. for Administration provides ongoing
  financial review and analysis, collaborating with
  AD-SR to optimize use of funds and to review
  budgets and plans with each core
• CC Director actively oversees entire SR
  operation, assuring cores serve current and
  developing Center research priorities

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External Input for Core Management

• External advisory groups
• SAB (annual)
• Shared Resource Task Force (meets monthly)
• CC Program Planning Group (meets monthly)
• Survey results
• Institute-wide annual Shared Resource user survey
• Annual core rate survey of other Institutions
• Informal input
• Maintain culture of responsiveness, fairness,
  clear priority of science
• Burnham is a compact campus lots of informal
  input.

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Broad Usage of CC Shared ResourcesAll 9 Shared
Resources were used by all 4 Programs

• The average Shared Resource was used by 30
  Cancer Center
• members more than half of the 56 full-time
  members
• Over 400 CC publications used one or more
  Shared Resources

Cancer Center Users in Past Year
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Added Value From the Shared Resources

• In addition to providing cost-effective
  scientific services
• Nearly all sophisticated instruments at the
  Burnham are located in the SRs, where they are
  efficiently shared and maintained
• PhD level and/or experienced Resource Directors
  add expertise in the theory and application of
  the technology, providing assistance in preparing
  proposals, designing experiments, and analyzing
  data
• SRs lead research by introducing new technologies
  readily available new technology encourages CC
  investigators to broaden their experimental
  approaches, enhancing productivity

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Animal Resources

• Animal informatics project user-friendly
  web-based tracking of cage occupancy, breeding
  efficiency, health, survival, etc.
• Animal Imaging and Analysis facility
• Upgraded VEVO 770 performs automated 3D tumor
  measurement and tumor blood flow analysis
• Expanded luciferase labeled tumor cell line
  collection for use with the Xenogen IVIS 200
• Coda 6 blood pressure monitor measures 6 mice at
  once
• Added Faxitron X-ray imager for bone imaging

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Cell Imaging and Histopathology
Cell Imaging Increasing capabilities for live
cell imaging (new cameras, optics,
environmental chambers)
FRET time-lapse
Spinning Disk Confocal

• Histopathology
• Increased volume of traditional histology
  (gt25,000 slides)
• Pathologist enhances digital analysis with
  advanced slide scanner/software

Angiogenic Retardation and Hypoxia in
Adiponectin null Mice

Aperio ScanScope (visible light)
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Structural Biology

• X-ray Crystallography - moving to high throughput

Added automation for testing crystallization
conditions - both for HT dispensing of small
drops, and for image analysis (detecting
crystals) during incubation
22 C
4 C
Phoenix nanovolume drop dispenser
Crystal incubators with robotic image analysis
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Structural Biology

• Protein Expression and Analysis
• Full service protein expression, from accession
  number to purified protein increasingly also
  used for chemical biology
• Analytical ultracentrifuge service implemented
  (velocity or equilibrium), supporting analysis of
  proteins and large protein complexes.
• New Microcal ITC200 instrument, an alternative to
  Biacore for Kd determination
• Analytical service requests have generally
  increased - approaches such as fluorescence
  spectrometry, stopped-flow, DSC, and ITC

ITC analysis of vinculin head and tail fragment
binding Kd 1.27 µM (A. Bobkov for Liddington
lab)
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Genomics and Informatics

• Genomics added Illumina microarray capabilities
  for global analysis of miRNAs and for mRNAs from
  formalin fixed samples. Also added HT (384 well)
  real-time PCR instrument
• Analytical Genomics at Burnham Lake Nona will
  initially provide deep sequencing and Affymetrix
  microarray analysis
• Informatics and Data Management (IDM) continues
  to enhance downstream analysis of microarray
  data, using tools such as Ingenuity Pathways,
  GeneGo MetaCore, and NextBio software, increasing
  scientific value of array results
• IDM has enhanced their statistics capabilities,
  and has found outside consultants for more
  complex projects
• IDM is also implementing software tools from
  caBIG to enhance data analysis and sharing of
  cancer-related data with other NCI Centers.

caBIG
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Proteomics

• The LTQ Orbitrap Mass Spec is now routinely
  providing 2D analysis from complex samples -
  whole proteome analysis
• 3D analysis methods for phosphoproteome
  profiling were developed and now implemented on
  the Orbitrap
• Core provides either Label-free (with their own
  enhanced software) or isotopic comparative
  proteomics
• Gel-based analysis includes 1D and 2D protein
  IDs, as well as difference analysis in complex
  samples (2D-DIGE)
• While services utilizing the 3 other mass specs
  in the facility (MALDI TOF/TOF, LTQ, Brucker
  HCTultra) remain popular, additional LTQ
  Orbitrap capacity and enhanced data analysis will
  soon be needed.

LTQ Orbitrap
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Expanded Chemical Library Screening Capabilities

• New Equipment
• HRE integrated robotic screening system
• Hamamatsu FDSS 7000 Dispenser/imager
• (FLIPR TETRA like instrument)
• PE Opera High Content Confocal Imager

HRE integrated system

• Expanded Burnham compound collection
• More compounds (125K, building to gt300K)
• Small collections of drug-like and/or
  clinically tested compounds
• Medicinal Chemistry again a part of CLS
  located in new lab
• Investigator assay development lab
• (Enhanced CPCCG resources for BIMR PIs with 24/7
  access)
• Manager dedicated to facilitating Cancer Center
  projects
• Investigator priority for specific equipment
  including
• Flexstation III with M5 plate reader, Liquid
  handler and bulk dispenser.

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Functional Genomics Developing New Shared
Resource

• New Scientific Director Dr. Tariq Rana
  recently recruited faculty, expert in RNA biology
  and the mechanism of RNAi
• Facility provides siRNA assay development, siRNA
  libraries, and HT screening and analysis service
• Current siRNA libraries include human and mouse
  druggable collections (9,000 target genes each,
  4 siRNAs/target), and focused libraries for human
  kinases, proteases, E3 ligases
• Performing small-scale (technology development)
  lentiviral vector shRNA and plasmid vector cDNA
  overexpression analysis
• Builds on expertise and equipment in the CPCCG
  (Screening Center)

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BIMR Shared Resources OverviewOther
complementary cores available to CC members

• Cancer Center Shared Resources
• Animal Facility
• Animal Care In Vivo Imaging
• Cell Imaging and Histopathology
• Structural Biology
• NMR Crystallography Protein Production
• Genomics
• DNA Analysis Microarray/QPCR
• Proteomics
• Chemical Library Screening
• Assay Development. Chem Lib. and HTS HCS, Med
  Chem
• Flow Cytometry
• Informatics Data Management
• Bioinformatics Cheminformatics
• Functional Genomics (Developing SR)

• Other BIMR La Jolla Cores
• Model Organisms
• Stem Cells
• Viral Vectors
• Electrophysiology
• Other Developing cores at BIMR Lake Nona (FL)
• Analytical Genomics
• Deep sequencing and Affy microarrays
• Functional Genomics
• cDNAs and lentiviral shRNAs
• Ultra-HT Chem Library Screening
• Metabolomics
• Additional BIMR Cores for local use at Lake Nona,
  e.g., Vivarium, Imaging

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Organization Chart for All BIMR Cores
Vivarium

Kristiina Vuori, MD, PhD Cancer Center Director
EVP, Scientific Affairs
FL-Specific BIMR Cores
Animal Phenotyping
Dan Kelly, MD Scientific Director Lake Nona
Metabolomics
Eveline Hernandez, MBA CC Assoc. Dir.
Res. Finance Administrator
Craig Hauser, PhD Cancer Center Assoc. Dir. VP,
Scientific Resources
Maria Arango, MBA Assoc. Dir. Research Support,
Lake Nona
Analytical Genomics
Functional Genomics

Pharmacology
Medicinal Chemistry
Viral Vectors
Model Organisms
Stem Cells
Electrophysiology
Functional Genomics
Informatics Data Mgmt
Flow Cytometry
Chem Library Screening
Cell Imag Histopath
Structural Biology
Genomics
Proteomics
Animal Resources
Ultra-HTS
Florida Cores w/ BIMR-wide use
Cancer Center Shared Resources
Other BIMR La Jolla Cores
Each Cancer Center Shared Resource has a Faculty
Advisor and each facility has a full-time
Manager. Of the 18 facilities comprising 9 CC
Shared Resources, 15/18 Managers are PhD level
scientists.
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Plans for the Coming Year

• Animals Initiate tumor analysis facility to
  supporting xenograft and tumor transplant
  studies. Significantly expand Vivarium space
• Histopathology Add Aperio fluorescence slide
  scanner, enabling digital pathology with
  fluorescent samples
• Genomics Serve as a conduit for Next Generation
  sequencing (GAIIx), and Affymetrix microarrays in
  Lake Nona evaluate need for adding in La Jolla
• Proteomics Submit instrumentation grant for a
  second LTQ-Orbitrap, enhance MS data analysis
  infrastructure
• Chemical Library Screening Add compounds,
  instrumentation and personnel dedicated to
  supporting BIMR investigators, 400 MHz NMR.
• Flow Cytometry Add microfluidic sorter supporting
  cancer stem cell studies
• Informatics (IDM) Add expert in statistics to
  core staff, implement caBIG tools
• Functional Genomics Move to full SR status,
  acquire genome-wide siRNA and cDNA expression
  libraries as well as independent lab space