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

Using Single Agent to Treat Cancer

Cancer Immunology Would tumor grow in another individual?

Effector Lympocytes Lymphocytes express highly specific antigen receptors on their surface, recognize specific structural (AA) motif Usually CD8+ cells which kill target cells by recognizing foreign peptide-MHC molecules on the target cell membrane. Cancer cells express neoantigen from mutations that are recognizable and accessible to the immune system -- tumor-specific “ antigenicity ” The immune system is able to mount a response against cells bearing such antigens

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

CAR Chimeric antigen receptors: proteins that allow the T cells to recognize specific antigen (e.g. CD19 on lymphoma) on tumors Side effects: rapid and massive release of cytokines into the bloodstream

Using Antibodies to Boost Immune Systems Checkpoint blockade antibodies can activate T- cell and boost immune to kill tumor

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

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 of Immunotherapy How much of different immune cells are around each tumor Which peptide will be presented on the cell surface Which mutations are immunogenic How does tumor evade immune system How do the patient T-cells respond to the tumor (TCR) Biomarkers of immunotherapy response

Deconvolve Tumor Immune Infiltrates 13 DNA-based estimation of tumor purity Merge TCGA tumor expression with reference immune dataset Select genes overexpressed in the microenvironment Filter in purity-selected genes for immune signature Linearly deconvolve six immune cells: B cell, CD4 T cell, CD8 T cell, neutrophil, macrophage and dendritic cell

TIL Association With Survival Adjusted for age, gender, tumor stage and viral infection status CD8 T cell with better survival and macrophage with worse outcome Single cell analysis? 14 TIL CYT: Rooney et al, Cell 2015

MHC Presentation MHC presents peptides (~9 aa) in the cell to the surface for immune examination (self vs non-self), important for transplanation MHC presents tumor neoantigen for immune elimination Different HLA have different affinity to different peptides Immune evasion: HLA mutation, antigen mutation

NetMHC: Predict HLA / peptide affinity Predict which peptide in the cell will be presented on the cell surface by which HLA There are 2500 different HLA alleles ~70 HLA alleles are characterized by binding data Reliable MHC class I binding predictions for ~50 HLA A and B molecules HLA-A*3001HLA-A*3002

Polysolver HLA Somatic Mutations Shukla et al, NBT 2015

T-Cell Repertoire and VDJ Recombination Assembled α- (light) and β- (heavy) chains form the αβ- TCR expressed on T cells Traditional TCR repertoire: PCR amply and sequence the rearranged VDJ region in the T cells 18

Infer T-Cell Repertoire and CDR3 Sequence from Tumor RNA-seq 19

Response BioMarkers High CD8 T-cell infiltrates High immune checkpoint gene expression High tumor mutation load

Epigenetic Drugs HDAC inhibitor to delay drug resistance Minimum 5-aza (DNA demethylation) 21

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

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

Summary Immunotherapy: a living drug! Different immunotherapy options Bioinformatics challenges of immunotherapy –Immune infiltrate –MHC presentation and HLA typing –T-cell receptor repertoire Epigenetic therapy: 5-aza immune response Targeted epigenetic therapy: DOT1L, EZH2, BRD4