Immuno and Epigenetic Therapies Xiaole Shirley Liu STAT115, STAT215, BIO298, BIST520

Cancer Immunology Would tumor grow in another individual?

Effector Lympocytes Lymphocytes express highly specific ANTIGEN RECEPTORS on their surface Lymphocytes are highly specific for a given structural motif Usually CD8+ cells which kill target cells by recognizing foreign peptide-MHC molecules on the target cell membrane.

Tumors Cancer cells must express antigen (foreign particles) recognizable and accessible to the immune system -- antigenicity The immune system must in turn be able to mount a response against cells bearing such antigens Tumors possess a varying degree of immune “ Antigenicity ” that is unique to each tumor and thus be rejected by immunocompetent hosts.

Cytokines Low molecular weight protein mediators involved in cell growth, inflammation, immunity, differentiation and repair Production triggered by presence of foreign particles Interleukins (ex. IL-2) and interferons Acts as a potent immunomodulator and antitumor element, but might have extensive multiorgan toxicity

Active Immonotherapy High dose IL-2 (FDA approved for kidney cancer and melanoma) Boost overall immune cells inside the patient body

Using Antibodies to Boost Immune Systems Anti CTLA-4 and anti-PD1 antibodies can allow T-cell activation, boost immune to kill tumor

Adoptive Immunotherapy Isolate tumor-infiltrating lymphocytes (TILs) Expand their number artificially in cell culture Infuse TIL back into the bloodstream, recognize and destroy the tumor cells

CAR Chimeric antigen receptors: proteins that allow the T cells to recognize specific antigen on tumors Side effects: rapid and massive release of cytokines into the bloodstream

Find mutations from exome sequencing Use bioinformatics program to find mutations that might be immunogenic Create vectors expressing the small peptides containing the mutations Co-culture to activate TIL

Personalized ImmunoTherapy Great for melanoma, lung and colon cancer Immunotherapy specific to each patients’ tumor mutations

Bioinformatics? Which mutations are expressed? Which peptides are immunogenetic? Cancer vaccine?

Epigenetic Drugs HDAC inhibitor to delay drug resistance Minimum 5-aza (DNA demethylation) 13

Treat Cell Lines

Directly Treating Mice

Effect of 5-aza Minimum dosage and toxicity, well tolerated Activate suppressed immune genes Can use DNA methylation status at these immune genes to predict patient response Small % of patients directly cured. Others re-sensitized for chemotherapy Can be used with other drugs?

Targeted Epigenetic Drug DOT1L inhibitor for MLL Leukemia Meyer et al, Nat 2013

Targeted Epigenetic Drug JQ1 as a BET domain inhibitor, also works on MLL leukemia

Targeted Epigenetic Drug EZH2 inhibitors Diffuse large B-cell lymphoma Hormone independent prostate cancer Rhabdoid tumor with SNF5 mutation Martinez-Garcia & Licht, Nat Genetics 2010

Summary Immunotherapy: a living drug! Active vs adoptive immunotherapy Personalized immunotherapy: bioinformatics? Epigenetic therapy: 5-aza immune response Targeted epigenetic therapy: DOT1L, EZH2, BRD4

Final Review Programming: python and R Statistics: –Tukey bi-weight, median polish, qnorm –Hierarchical models, FDR, KS test –K-means and hierarchical clustering –PCA, SVM –HMM –EM, Gibbs –LASSO and logistic regression –Survival analysis

Final Review Binformatics: –Microarrays (RMA, LIMMA) –Ontology and pathway (DAVID, GSEA) –Batch removal (COMBAT, SVA) –NGS for DNA-seq (FastQC, Bowtie, BWA, STAR) –RNA-seq (Cufflinks, DESeq) –ChIP/DNase-seq (MACS, BETA) –GWAS (plink, GRAIL) –Genome-resequencing (GATK) –Web resources: GEO, UCSC, CBioPortal

Final Review Biological problems –Transcriptome and epigenetic profiling –Transcriptional regulation and TFs –Epigenetics and chromatin –Linkage disequilibrium and disease susceptibility –Tumor sequencing and personalized medicine –High throughput screening

Acknowledgement Chris Cunningham & Asad Usman Yang Li, Stephanie Chan Yushu Pang Taiwen Li, Yue Kang Shenglin Mei, Bo Li, Peng Jiang