The Institute for Immunity, Transplantation and Infection

at Stanford

In order to fulfill the mission of the ITI, the followinggoals were set:

(1) To help recruit faculty whose interests are in ITI based diseases, and whose research is aimed toward moving discoveries from the bench to bedside or bedside to bench.

(2) To develop and fund young clinical faculty in the area of clinical trial development and technology transfer in order to both understand the pathophysiology as well as the treatment of ITI based diseases.

(3) To establish a Postdoctoral Fellowship Program for MD or MD PhD fellows who will do a project either in basic research aimed toward pre-clinical models or clinical trials.

Continued; Goals of the ITI

(4) To establish new interactions among the ITI faculty through seminars, retreats and educational initiatives

(5)* To support high school summer students who will spend at least eight weeks studying in a lab oriented toward ITI based disease pathophysiology or therapy. (established; Dr P.J. Utz, Director)

(6)* To develop an “Immune Monitoring Unit.”This unit will allow innovative techniques in monitoring the immune system developed at Stanford and elsewhere to be applied to patient care.

(7)* To Develop Innovative Curriculum, a new program has beendeveloped to teach clinical approaches to PhD students from multiple disciplines.

A “Clinical Immunology” Summer School for High School Students

P.J. Utz, M.D.

Summer Student Model

Background:

• Initiated in summer 2000 with 10 students• Funded by donors and the NCAF• Expanded to 25 students in 2001 - 2004• ~15, 42, 141, and 193 applications• 2003 statistics: Mean GPA 4.06, SAT 1363, s3 valedictorians, 10 #1 in class• Students from public and private schools• 80% women

Goals for High School and Undergraduate Program:

• Interest students in careers in biomedical research• Improve teaching skills of graduate students and postdoctoral fellows• Encourage interactions among faculty members• Community outreach

UniversityMedical SchoolIndustry

Existing MODEL

Program:

• Lab selection by student from faculty• 15 lectures on basic immunology• 300 page syllabus with assigned reading • Lectures by individual faculty• Lectures on poster assembly and presentation• Intensive research experience• Poster presentation• Longitudinal study of “program graduates” is ongoing

This model has been exported nationally to10 of 30 FOCIS Centers of Excellence:

• Centralized educational materialsSyllabusPowerPoint lectures

• All administrative materialsAdvertisementsApplication formsLetters of acceptance/rejection/waitlistOrganizational materialsLecture schedulesPublic relations materialsInformation for participating mentors/labs

Immune Monitoring Core at Stanford

Needed to support new therapies and innovative trials.– Current facilities are in multiple labs – A centralized facility will provide better patient care– Advantages of proposed immune monitoring core

• Provide a resource to the “community” • Designed to allow novel techniques in genomics and

proteomics to be integrated as information based medicine by new “bioinformatics” technology

– Substantial opportunity currently exists to build on existing expertise in research and to increase both clinical investigation and delivery of novel therapies.

Potentially Useful Multiplex Proteomics Assays:

• FACS/Phospho FACS• Autoantibody Profiling• Cytokine Profiling

Bead-BasedCleavable TagsPlanar Arrays

• Signaling Molecule AssaysFACS-Based TechniquesPlanar Capture ArraysCleavable TagsLysate Arrays

• Serum Proteome Analysis by Mass Spectroscopy

Activated vs Static Signaling Proteomics in

Autoimmunity.

Garry P. Nolan, Ph.D.

Stanford UniversityDept. of Microbiology &

Immunology Signaling Phenotypes in single

immune cells

Why use Flow Cytometry to Measure Signaling?

Revealing Lupus (SLE) Immune Deficiencies requires stimulation of cells

AutoimmuneNormal

T cells

Peter KrutzikMatt Hale

SLE prone animals wereSLE prone animals weregiven a “drug” iv andgiven a “drug” iv andisolated cells assayed before isolated cells assayed before and following activationand following activationex vivoex vivo

Proteomic Assays

P.J. Utz, M.D.and Bill Robinson, MD. Ph.D.

Stanford University

Produce arrays usinga robotic microarrayer

The 1152 Feature “CTD Chip”

Details of Current Arrays:

• Coated Glass Slides• 150 Slides Per Print Run• Approximately 4,000-5,000 Spots/Features Per Slide• Features are Duplicated• 200uM Feature, 200pg Antigen• Protein, Peptide, Nucleic Acid, RNP, Complex• Monoclonal Antibody or Complex Mixtures• 30ul Volume• Fluorescent Detection (Cy3, Cy5, BoDipy)• Secondary Antibody vs Competition• Sensitive and Specific

Potential Applications:

• Multiplex Diagnostic Test• Epitope Spreading• Follow Response to Therapy• Guide Selection of Therapy• Discovery Tool

Reverse Phase Protein Lysate MicroarraysP.J. Utz, M.D.

Protein Microarrays:Detection of Phosphorylated Proteins

In Vitro Studies Using Lysate Arrays:

Analysis of Rare Cell Populations

• FACS-Sorted Cells• Laser Capture Microdissection• Antigen-Specific Cells (e.g., Tetramers)

Correlation With Transcript Profiling (genomics) Experiments

A Cellular MicroArray

MHC-Cytokine Arrays

Secondary cytokineDetection antibodyConjugated to a flurophore

Cytokine secreted byT cell after recognition ofPeptide/MHC

Co-spotted CytokineCapture antibody

CD8 Co-Spots MART1/A2 Co-Spots

CD8 brightfield

MART1/A2 brightfield

Functional T Cell Responses to Peptide Vaccines

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# of BlocksDenotes gp100Specific Activity

Key

What is now possible

• Identifying disease subsets by proteomic signatures

• Correlating proteomic signatures with clinical or therapy induced outcome in disease

• DIRECT build-out of patient-specific proteomic maps and mechanistic inferences

• Observation of rare subsets that would be missed by all other signaling analyses (mass spec, chromatography, elisa, bead)

Introduction to Medicine for PhD students

Immunology 230

How to learn about a disease using a prototype (diabetes)

Betsy Mellins MD

Course Goals

• Understand how medical knowledge is organized

• Appreciate the concerns and tools of the various scientific fields and clinical disciplines within medicine

• Identify quality sources of medical information

• Gain some familiarity with medical language

• Learn specific information about human physiology and pathophysiology

• Identify opportunities to apply your primary discipline to unsolved medical problems

Focus on one disease

• This models the situation that may be confronted in the future• The idea is that a guided learning experience about one disease

will teach skills that can be applied to learning about other diseases

Focus on Diabetes• Multi-system disorder: Many branches of medicine needed to

understand it• Relatively common• Partially understood: many ?s that will draw on your expertise

Projects

Project goals– To work in inter-disciplinary teams on a medical

problem that draws on each student’s primary expertise

– To practice learning about medicine in the context of a focused effort to solve a problem

– To demonstrate your acquisition of medical knowledge in the project report

Project teams– 3-4 students from different disciplines with a

“coach” who is a graduate of last year’s course

Design of Human Microarray Experiment for Identifying Genes Associated with

Insulin Resistance

Presented by

Su-In Lee, Mechanical Engineering

& Kevin Pan, Biophysics

“Our Commitment to medical research and education and their role in serving the public go to the very core of what the University is about.” John Hennessy, President