Translational Research Program

1
Translational Research Program

• An Overview 2000-2005

2
Mission

• The Translational Research Program was designed
  to provide the laboratory component for
  achieving the overall INCTR mission of improving
  clinical outcome of cancer patients from
  developing countries.
• Laboratory for generation of molecular correlates
  from clinical studies.
• Conduct molecular epidemiological and educational
  programs.

3
Objectives

• Major elements of the program driven by
• Clinical studies conducted by INCTR (ALL in
  India)
• Epidemiological studies of interest to INCTR
• Differences in distribution of molecular subtypes
  of ALLs
• Gene-environment interactions modulating
  oncogenic translocations
• Epigenetic changes in bladder ca. modulated by
  infection
• Enable capacity building
• Training in molecular biology platforms that can
  provide clinically relevant tools
• Pilot research studies for future fundable
  programs (ALL in India)

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Specific ObjectivesBidirectional Interactions

• Catalyze the translation of unique clinical
  observations from the patient setting in
  developing countries to a laboratory environment.
• Is outcome of childhood ALL a function of the
  subtype distribution?
• Rapidly move key and novel laboratory
  observations made in the West, to the patient
  setting in developing countries.
• Are novel tumor types identified by molecular
  profiling clinically relevant in low resource
  settings?

5
Resources

• Human
• Scientists technicians from KFNCCCR
• Trainees from developing countries
• Space
• KFNCCCR, Riyadh, Saudi Arabia
• Facilities
• PCR, real time PCR, sequencer, tissue arrayer,
  microarrays, more.
• Major Collaborators
• 3 Indian Institutions (TMH, AIIMS, WIA)
• NCI, Cairo, Egypt
• Univ of Istanbul, Turkey

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Strategy
7
ALL Program

• 5 Projects
• Molecular subclassification
• Gene expression profiling
• Epigenetics
• Pharmacogenetics
• Proteomics of Apoptosis - target for treatment

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ALL Program1- Molecular subclassification

• Real-time RT-PCR for most common chromosomal
  translocations
• Trained laboratory staff of INCTR centers in
  India
• SOP for sample collection, storage, usage and
  analyses
• Distribution of molecular subgroups
• TEL-AML1 are less frequent, BCR-ABLs are more
  frequent
• in India but not in Saudi Arabia
• Clin Cancer Res, 2002
• Leukemia, 2003
• Am J Hematol, 2004
• J Mol Diagnostics, 2005
• Clinical correlates - recent INCTR protocol

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ALL Program2- Gene Expression Profiling

• Real-time RT-PCR validation of data from the West
• VEGF and its receptors are expressed in ALL
• TEL/ETV6 expression can identify 12p del
• Hox11L2 expression in T-ALL
• Novel molecular subgroup identified in the West
  (Yeoh et al) is also found in India
• Leuk Res, 2004
• Int J Biol Markers, 2004
• Cancer Lett (in press)
• Affymetrix microarrays

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ALL Program3- Epigenetics

• MSP and COBRA assays for multiple genes and
  sequence analyses
• Concurrent methylation pattern of ALL
• E-cad is frequently methylated
• B gt T MLL gt E2A-PBX1
• Differences with adult ALL
• Less epigenetic lesions in cell cycle genes
• Comparison with AML
• Methylator phenotype DAP-Kinase, p15, ER, SOCS1
• Peak of methylation in young adults
• Leukemia 2003
• Cancer Epidemiol Biomarkers Prev 2003
• Am J Hematol 2004, 2005

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ALL Program4- Pharmacogenetics

• PCR-RFLP assays for multiple genes involved in
  metabolization of drugs and xenobiotics.
• Population-based SNPs influencing cancer risk
• Middle-Eastern Arab population
• The Pharmacogenomic J, 2004
• Patient-based SNPs determining risk of toxicity
  and efficacy of treatment
• Over 200 Indian patients
• 100 pts in MCP943
• Clinical correlates level of toxicity?

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ALL Program5- Proteomics of Apoptosis

• Standardized Western blot assay for proteins
  involved in the intrinsic and extrinsic pathways
  of apoptosis using cell lines.
• Validated its application in clinical samples.
• Proof of principle Apoptosis as a target for
  therapy.
• Haematologica 2003
• Leuk Lymphoma 2004
• Genes, Chromosomes Cancer 2004

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Additional ActivitiesManagement of ALL

• Real time PCR assay for detection and
  quantification of fungal infections can predict
  IFI? Preemptive therapy?
• J Med Microbiol 2005
• Proof of principle of a novel marker of MRD and
  CNS involvement in ALL and AML (real time
  quantitative PCR for TdT)
• Haematologica (2nd revision)
• Real time PCR assay for EBV load (BMT).

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Other Activities

• Epigenetics of Bilharzial bladder cancer
• SA gt NSA
• Modern Pathol 2004
• Geographic variation of oncogenic transl. in
  healthy individuals (Middle Eastern Arabs)
• JH-BCL2 - 37 (gt in older individuals)
• BCR-ABL 27
• TEL-AML1 4
• More than 1 translocation increased with age
• Modulation by SNPs in DNA repair and synthesis
  genes (37 SNPs in 11 genes).
• Manuscript in preparation

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Future Directions1-Improvements

• Provide the missing clinical links to prove the
  reliability and the usefulness of the assays and
  biomarkers developed.
• Recent INCTR Protocol for ALL (India)
• Uniform data collection and availability.
• Establish a quality control system.

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Future Directions2-Pathway

• Comprehensively pursue the ALL translational
  program in India.
• The pilot ALL project has already provided
• basic ground work to define feasibility.
• technological training and capacity.
• identified the team process required.
• Now the Indo Leukemia Study Group should engage
  in writing a proposal to attract funding.

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Future Directions 3-Suggested Steps

• 1) Form a strategy group to prioritize the
  clinical and translational questions.
  Coordination and quality control.
• 2) Use data from the pilot project to write a
  grant application.
• 3) Identify partners (investigators from USA/
  Europe) who can provide additional technological
  expertise and extend comparative studies.
• 4) Identify funding sources that will consider
  the proposal.