Leaders in Pharmaceutical Business Intelligence (LPBI) Group

• The Immune System, Stress Signaling, Infectious Diseases and Therapeutic Implications: VOLUME 2: Infectious Diseases and Therapeutics and VOLUME 3: The Immune System and Therapeutics (Series D: BioMedicine & Immunology) Kindle Edition – on Amazon.com since September 4, 2017

https://www.amazon.com/dp/B075CXHY1B

SYMPOSIUM SCHEDULE

OCTOBER 16 – DAY 1

7:00 – 8:15 Registration

8:15 – 8:30Introductory Remarks
Darrell Irvine | MIT, Koch Institute; HHMI

• Stimulating the Immune system not only sustaining it for therapies

K. Dane Wittrup | MIT, Koch Institute

8:30 – 9:45Session I
Moderator: Douglas Lauffenburger | MIT, Biological Engineering and Koch Institute

Garry P. Nolan – Stanford University School of Medicine
Pathology from the Molecular Scale on Up

• Intracellular molecules,
• how molecules are organized to create tissue
• Meaning from data Heterogeneity is an illusion: Order in Data ?? Cancer is heterogeneous, Cells in suspension – number of molecules
• System-wide changes during Immune Response (IR)
• Untreated, Ineffective therapy, effective therapy
• Days 3-8 Tumor, Lymph node…
• Variation is a Feature – not a bug: Effective therapy vs Ineffective – intercellular modules – virtual neighborhoods
• ordered by connectivity: very high – CD4 T-cells, CD8 T-cels, moderate, not connected
• Landmark nodes, Increase in responders
• CODEX: Multiples epitome detection
• Adaptable to proteins & mRNA
• Rendering antibody staining via removal to neighborhood mapping
• Human tonsil – 42 parameters: CD7, CD45, CD86,
• Automated Annotations of tissues: F, P, V,
• Normal BALBs
• Marker expression defined by the niche: B220 vs CD79
• Marker expression defines the niche
• Learn neighborhoods and Trees
• Improving Tissue Classification and staining – Ce3D – Tissue and Immune Cells in 3D
• Molecular level cancer imaging
• Proteomic Profiles: multi slice combine
• Theory is formed to explain 3D nuclear images of cells – Composite Ion Image, DNA replication
• Replication loci visualization on DNA backbone – nascent transcriptome – bar code of isotopes – 3D  600 slices
• use CRISPR Cas9 for Epigenetics

Susan Napier Thomas – Georgia Institute of Technology
Transport Barriers in the Tumor Microenvironment: Drug Carrier Design for Therapeutic Delivery to Sentinel Lymph Nodes

• Lymph Nodes important therapeutics target tissue
• Lymphatic flow support passive and active antigen transport to lymph nodes
• clearance of biomolecules and drug formulations: Interstitial transport barriers influence clearance: Arteriole to Venule –
• Molecular tracers to analyze in vivo clearance mechanisms and vascular transport function
• quantifying molecular clearance and biodistribution
• Lymphatic transport increases tracer concentrations within dLN by orders of magnitude
• Melanoma growth results in remodeled tumor vasculature
• passive transport via lymphatic to dLN sustained in advanced tumors despite abrogated cell trafficking
• Engineered biomaterial drug carriers to enhance sentinel lymph node-drug delivery: facilitated by exploiting lymphatic transport
• TLR9 ligand therapeutic tumor in situ vaccination – Lymphatic-draining CpG-NP enhanced
• Sturcutral and Cellular barriers: transport of particles is restriced by
• Current drug delivery technology: lymph-node are undrugable
• Multistage delivery platform to overcome barriers to lymphatic uptake and LN targeting
• nano particles – OND – Oxanorbornade OND Time sensitive Linker synthesized large cargo – NP improve payload
• OND release rate from nanoparticles changes retention in lymph nodes – Axilliary-Brachial delivery
• Two-stage OND-NP delivery and release system dramatically – OND acumulate in lymphocyte
•  delivers payload to previously undraggable lymphe tissue
• improved drug bioactivity  – OND-NP eliminate LN LYMPHOMAS
• Engineered Biomaterials

Douglas Lauffenburger – MIT, Biological Engineering and Koch Institute
Integrative Multi-Omic Analysis of Tissue Microenvironment in Inflammatory Pathophysiology

• How to intervene, in predictive manner, in immunesystem-associated complex diseases
• Understand cell communication beteen immune cells and other cells, i.e., tumor cells
• Multi-Variate in Vivo – System Approach: Integrative Experiment & COmputational Analysis
• Cell COmmunication & Signaling in CHronic inflammation – T-cell transfer model for colitis
• COmparison of diffrential Regulation (Tcell transfer-elicited vs control) anong data types – relying solely on mRNA can be misleading
• Diparities in differential responses to T cell transfer across data types yield insights concerning broader multi-organ interactions
• T cell transfer can be ascertained and validated by successful experimental test
• Cell COmmunication in Tumor MIcro-Environment — integration of single-cell transcriptomic data and protein interaction
• Standard Cluster Elucidation – Classification of cell population on Full gene expression Profiles using Training sets: Decision Tree for Cell Classification
• Wuantification of Pairwise Cell-Cell Receptor/Ligand Interactions: Cell type Pairs vs Receptor/Ligand Interaction
• Pairwise Cell-Cell Receptor/Ligand Interactions
• Calculate strength of interaction and its statistical significance
• How the interaction is related to Phenotypic Behaviors – tumor growth rate, MDSC levels,
• Correlated the Interactions translated to Phynotypic behavior for Therapeutic interventions (AXL via macrophage and fibroblasts)
• Mouth model translation to Humans – New machine learning approach
• Pathways, false negative, tumor negative expression
• Molecular vs Phynotypical expression
• Categories of inter-species translation
• Semi-supervised Learning ALgorithms on Transcriptomic Data can ascertain Key Pathways/Processes in Human IBD from mapping mouse IBD

9:45 – 10:15 Break

10:15 – 11:30Session II
Moderator: Tyler Jacks | MIT, Koch Institute; HHMI

Tyler Jacks – MIT, Koch Institute; HHMI
Using Genetically Engineered Mouse Models to Probe Cancer-Immune Interactions

• Utility of genetically-engineered mouse models of Cancer:

1. Immune Response (IR),
2. Tumor0immune microenvironment

• Lung adenocarcinoma – KRAS mutation: Genetically-engineered model, applications: CRISPR, genetic interactions
• Minimal Immune response to KP lung tumors: H&E, T cells (CD3), Bcells (B220) for Lenti-x 8 weeks
• Exosome sequencing : Modeling loss-and gain-of-function mutations in Lung Cancer by CRISPR-Cas9 – germline – tolerance in mice, In vivo CRISPR-induced knockout of Msh2
• Signatures of MMR deficient
• Mutation burden and response to Immunotherapy (IT)
• Programmed neoantigen expression – robust infiltration of T cells (evidence of IR)
• Immunosuppression – T cell rendered ineffective
• Lymphoid infiltration: Acute Treg depletion results in T cell infiltration — this depletion causes autoimmune response
• Lung Treg from KP tumor-bearing mice have a distinct transcriptional heterogeneity through single cell mRNA sequencing
• KP, FOXP3+, CD4
• Treg from no existent to existance, Treg cells increase 20 fold =>>>  Treg activation and effectiveness
• Single cells cluster by tissue and cell type: Treg, CD4+, CD8+, Tetramer-CD4+
• ILrl1/II-33r unregulated in Treg at late time point
• Treg-specific deletion of IL-33r results in fewer effector Tregs in Tumor-bearing lungs
• CD8+ T cell infiltration
• Tetramer-positive T cells cluster according to time point: All Lung CD8+ T cells
• IR is not uniform functional differences – Clones show distinct transcriptional profiles
• Different phynotypes Exhaustive signature
• CRISPR-mediated modulation of CD8 T cell regulatory genes
• Genetic dissection of the tumor-immune microenvironment
• Single cell analysis, CRISPR – CRISPRa,i, – Drug development

Wendell Lim – University of California, San Francisco

Synthetic Immunology: Hacking Immune Cells

• Precision Cell therapies – engineered by synthetic biology
• Anti CD19 – drug approved
• CAR-T cells still face major problems

Darrell Irvine – MIT, Koch Institute; HHMI
Engineering Enhanced Cancer Vaccines to Drive Combination Immunotherapies

• Vaccine to drive IT
• Intervening in the cancer-immunity cycle – Peptide Vaccines
• poor physiology  of solute transport to tissue
• endogenous albumin affinity – Lymphe Node dying
• Designing Albumin-hitchhiking vaccines
• Amphiphile-vaccine enhance uptake in lymph nodes in small and large animal models
• soluble vaccine vs Amphiphile-vaccine
• DIRECTING Vaccines to the Lymph nodes
• amph-peptide antigen: Prime, booster, tetramer
• albimin-mediated LN-targeting of both antigen and adjuvant maximizes IR
• Immuno-supressed microenvironment will not be overcome by vaccines
• Replacing adoptive T cell transfer with potent vaccine
• exploiting albumin biology for mucosal vaccine delivery by amph-vaccines
• Amph-peptides and -adjuvants show enhanced uptake/retention in lung tissue
•  Enhancing adoptive T cell therapy: loss of T cell functionality, expand in vivo
• boost in vivo enhanced adoptive T cell therapy
• CAR-T cells: Enable T cells to target any cell surface protein
• “Adaptor”-targeting CAR-T cells to deal with tumor cell heterogeneity
• Lymph node-targeting Amph as CAR T booster vaccine: prining, production of cytokines
• Boosting CAR T with amph-caccines: anti FITC CAR-T by DSPE=PEG-FITC coated
• Targeting FITC to lymph node antigen presenting cells
• Modulatory Macrophages
• Amph-FITC expands FITC-CAR T cells in vivo – Adjuvant is needed
• Hijacking albumin’s natural trafficking pathway

11:30 – 1:00  Lunch Break

1:00 – 2:15Session III
Moderator: Darrell Irvine | MIT, Koch Institute; HHMI

Nicholas P. Restifo – National Cancer Institute
Extracellular Potassium Regulates Epigenetics and Efficacy of Anti-Tumor T Cells

Why T cell do not kill Cancer cells?

• co-inhibition
• hostile tumor microenvironment

CAR T – does not treat solid tumors

Somatic mutation

1. resistence of T cell based IT due to loss of function mutations
2. Can other genes be lost?

CRISPR Cas9 – used to identify agents – GeCKOv2 Human library

Two cell-type (2CT) CRISPR assay system for genome-wide mutagenesis

• work flow for genome-scale SRISPR mutagenesis profiling of genes essential for T cell mediate cytosis
• sgRNA enrichment at the individual gene level by multiple methods:

1. subunits of the MHC Class I complex
2. CRISPR mutagenesis cut germline

• Measutring the generalizability of resistance mechanism and mice in vivo validation
• Validation of top gene candidates using libraries: MART-1
• Checkpoint blockade: cells LOF causes tumor growth and immune escape
• Weird genesL Large Ribisomal Subunit Proteins are nor all essential for cell survival
• Bias in enrichment of 60S vs 40S
• Novel elements of MHC class I antigen processing and presentation
• Association of top CRISPR hits with response rates to IT – antiCTLA-4
• CRISPR help identify novel regulators of T cells
• Analyzed sgRNA – second rarest sgRNA for gene BIRC2 – encoded the Baculoviral Inhibitor
• Drugs that inhibit BIRC2
• How T cells can kill tumor cells more efficiently
• p38kiaseas target for adoptive immunotherapy
• FACS-based – Mapk14
• Potent targets p38 – Blockade PD-1 or p38 ??
• p38 signaling: Inhibition augments expansion and memory-marked human PBMC and TIL cells, N. P. Restifo
• Tumor killing capacity of human CD19-specific, gene engineered T cells

Jennifer Elisseeff – Johns Hopkins University
The Adaptive Immune Response to Biomaterials and Tissue Repair

• design scafolds, tissue-specific microenvironment
• clinical translation of biosynthetic implants for soft tissue reconstruction
• Local environment affects biomaterials: Epidermis, dermis
• CD4+ T cells
• Immune system – first reponders to materials: Natural or Synthetic
• Biological (ECM) scaffolds to repair muscle injury
• Which immune cells enter the WOUND?
• ECM alters Macrophages: CD86, CD206
• Adaptive system impact on Macrophages: CD86
• mTOR signaling pathway M2 depend on Th2 Cells in regeneration of cell healing of surgical wounds
• Systemic Immunological changes
• Is the response antigen specific? – IL-4 expression in ILN,
• Tissue reconstruction Clinical Trial: FDA ask to look at what cells infiltrate the scaffold
• Trauma/biomaterial response – Injury induction of Senescence, anti apoptosis
• Injury to skin or muscle
• Is pro-regenerative environment (Th2/M2) pro-tumorigenic?
• SYNTHETIC Materials for scafolds
• Biomaterials and Immunology

1. Immune response to bioscafolds
2. environment modulate the immune system

• Regenerative Immunetherapy

Marcela Maus – Massachusetts General Hospital

Engineering Better T Cells

2:15 – 2:45 Break

2:45 – 4:00 Session IV
Moderator: Arup K. Chakraborty | MIT, IMES

Laura Walker – Adimab, LLC
Molecular Dissection of the Human Antibody Response to Respiratory Syncytial Virus

• prophylactic antibody is available
• Barriers for development of Vaccine
• Prefusion and Postfusion RSV structures
• Six major antigenic sites on RSV F
• Blood samples Infants less 6 month of age and over 6 month: High abundance RSV F -specific memory B Cells are group  less 6 month

Arup K. Chakraborty – MIT, Institute for Medical Engineering & Science
How to Hit HIV Where it Hurts

• antibody  – Model IN SILICO
• Check affinity of each Ab for the Seaman panel of strain
• Breadth of coverage
• immmunize with cocktail of variant antigens
• Mutations on Affinity Maturation: Molecular dynamics
• bnAb eveolution: Hypothesis – mutations evolution make the antigen binding region more flexible,
• Tested hypothesisi: carrying out affinity maturation – LOW GERMLINE AFFINITY TO CONSERVE RESIDUES IN 10,000 trials, acquire the mutation (generation 300)

William Schief – The Scripps Research Institute
HIV Vaccine Design Targeting the Human Naive B Cell Repertoire

• HIV Envelope Trimer Glycan): the Target of neutralizing Antibodies (bnAbs)
• Proof of principle for germline-targeting: VRC)!-class bnAbs
• design of a nanoparticle
• can germline -targeting innumogens prime low frequency precursors?
• Day 14 day 42 vaccinate
• Precursor frequency and affinity are limiting for germline center (GC) entry at day 8
• Germline-targeting immunogens can elicit robust, high quality SHM under physiological conditions of precursor frequency and affinity at day 8, 16, 36
• Germline-targeting immunogens can lead to production of memory B cells