Personalized Medicine

about how many patients in trials respond positively to a drug for it to be approved?

what percentage of drug candidates fail clinical trials?

only 20-40% of patients benefit to get approved

70-80% fail!

what are the external factors that affect the response of a drug?

environment and concomitant drug use

what are the internal factors that affect the response of a drug?

demographic (age, gender)

disease states

genetics (polymorphisms mpacting PK and PD)

goals of precision/personalized medicine

1. genotype specific dosing

2. selecting populations for clinical trials and therapies

3. safety + efficacy

the study of genetic basis for variation in drug response

pharmacogenetics

which early study was done that emphasized that the way pharmacokinetics of drugs (what the body does to the drug) has a large part to do with out genetics? (pharmacogenetics)

the set of fraternal twins that do not share identical genes responded differently to antipyrene (different half lifes) wheras identical twins with identical genes responded to the drug simmilary and had the same half life

sequence gene from upstream to downstream:

proximal promotor

5” untranslated region

Start codon

Stop Codon

3’ untranslated region

• region of gene directly upstream from start codon contains regulatory elements

• region of gene directly downstream from the termination/stop codon. contains regulatory elements

5” untranslated region

3’ untranslated region

• portions of a gene that code for amino acids. this seqence is retained in the ______ _______ _______

• portions of gene that DO NOT code for an amino acid. intervening sequences that is REMOVED turing _______ ______ process

exons- mature messenger mRNA

introns - mRNA splicing

stretches of DNA sequences located between genes (NOT junk DNA)

intergenic regions

polymorphisms are more likely to take place in which regions of the gene?

• 3’ and 5’ untranslated regions

• promoter and enhancer

• introns

• intergenic regions

NONCODING REGIONS

noncoding single nucleotide polymorphisms (SNPs) in promotors or enhancers may alter ____ or _______ acting elements that regulate

• gene _________

• transcript __________

cis and trans

transcription

stability

what are the two biomarker categories?

prognostic vs predictive

what is the difference between prognostic and predictive biomarkers?

Prognostic - show up if you are SUSCEPTIBLE to a disease

Predictive - if these biomarkers show up, you know you HAVE a disease, and you can check if treatment is working

Screening for specific strains of HPV to predict disease susceptibility or for BCRA gene variants (potential to be cancerous) would be done using which type of biomarker?

prognostic

which type of biomarker

• predicts the benefit of therapy

• avoids adverse drug reactions associated with therapy that isnt needed (this biomarker will show you if you have disease or not)

what are some examples?

predictive

clopidogrel and 2C19 resistance

Warfarin and CYPP450 2C9/vitamin K epoxidase reductase complex subunit1 (VKORC1) Dosing

are the following examples of predictive or prognostic biomarkers?

• Clopidogrel and 2C19 resistance

• Warfarin and CYP450 2C9/ vitamin K epoxidase reductase complex subunit 1 (VKIRC1) dosing

predictive

allows you to determine whether or not you have a disease and if treatment is working

you can learn whether or not you have specific generic variants that may not affect your health but may affect your CHILDS health using which type of biomarker?

prognostic

component of ____________ biomarkers:

identifying individuals who are more likely to respond yo a particular drug

efficacy

component of _________ biomarkers:

identifying individuals who are less likely to have an adverse effect of a particular drug

safety

__________ is an INHERITED allelic variant that should be screened for especially in Asian patients before prescribing CARPAMANAPINE

Patients with these varients are at increased risk for _______ and ______

HLA-B*1502

Steven Johnson’s Syndrome and Toxic Epidermal Necrolysis

products and assays used in conjunction with a therapeutic product

companion diagnostics

Companion Diagnostics inform

• _________ selection

• _______

• _____ customization

• avoidance

co-development with _______ drug

post-_________ experience

_____ Guidance

• treatment

• initiation

• dose

parent

market

FDA

ONCOLOGY Personalized Medicine:

• What are the traditional diagnostic tests in oncology?

• New _______ has broadened the use of diagnostics

• Evolving discovery of ______ leading world of oncology towards personalized medicine

• Personalized medicine to have a significant impact on developmental and _______ of oncology drugs

PET, MRI, CT

research

biomarkers

commercialization

Molecular models for biomarker testing in solid tumors:

protein-based assay for the detection of expression

immunohistochemistry (IHC)

Molecular models for biomarker testing in solid tumors:

hybridization using fluorescence labeled probes to detect gene COPY NUMBER changes or gene REARRANGGMENTS/FUSIONS

Florescence in situ hybridization (FISH)

Molecular models for biomarker testing in solid tumors:

detection of TARGETED gene mutations, fusions, copy number alterations, DNA METHYLATION

Polymerase Chain Reaction (PCR)

Molecular models for biomarker testing in solid tumors:

MASSIVELY PARALLEL sequencing of MULTIPLE GENES for detecting mutations, fusions, and copy-number alterations

Next-Generation Sequencing (NGS)

Molecular models for biomarker testing in solid tumors:

DIFFERENTIAL gene expression between tumor/normal or pre/post treated tumor

Gene Expression Profiling (GEP)

The following are advantages and limitations of which biomarker testing method?

Advantages:

• DIRECT VISUALIZATION of PROTEIN expression

• cheap, rapid, widely available

Limitations:

• uses antibodies that are NOT readily available

• subjective interpretation/ quantification

Immunohistochemistry (IHC)

The following are advantages and limitations of which biomarker testing method?

Advantages:

• simple assay design

• direct visualization of SINGALS WITHIN CELLS of interest

Limitations:

• probe available

• restricted to specific locus/gene tested

Florescence In Situ Hybridization FISH

The following are advantages and limitations of which biomarker testing method?

Advantages:

• high SENSITIVITY and specificity

• simple assay design

• low cost

Limitations:

• limited throughput

• restricted to TARGETED GENES and regions of interest interrogated

Polymerase Chain Reaction (PCR)

The following are advantages and limitations of which biomarker testing method?

Advantages:

• high throughput

Limitations:

• restricted to TARGET genes

• BIOINFORMATICS (Computational tools)

Next Generation Sequencing (NGIS)

what are the three categories of alterations in terms of cancer driven medication

1. _______ in Principle

   tier 1: ____-______ drugs

   tier 2: drugs in ______ _________

2. prognostic or predictive?

3. ______ of uncertain significant (VUS)

1. actionable

tier 1= FDA approved

tier 2= clinical trials

2. prognostic (deals with varients)

3. variants

what are the 7 types of alterations that can be detected through prognostic biomarkers?

of those alterations which are copy number?

1. indel (insertion/deletion)

2. point mutation

3. homozygous deletion

4. heterozygous deletion

5. gain

6. translocation breakpoint

7. pathogen

copy number = heterozygous deletion, homozygous deletion, gain

are the following factors of the previous or current approaches to cancer treatment?

• descriptive medicine

• empirical diagnosis

• grouped by organ site

• uniform treatment

• retrospectively diagnose disease

• acute care

previous treatment

are the following factors of the previous or current approaches to cancer treatment?

• understanding disease mechanisms

• mechanism based diagnosis/treatment

• sub-grouped by molecular/biological classification

• individualized treatment

• prospectively evaluate relative disease risk

• early detection and intervention

current approaches

Innovative/ Personalized medicine allows colon cancer patients to receive personalized therapy based on their ____________ which can be found through blood, urine, and genetics tests

biomarkerrs

Which signaling networks regulate the operations of the cancer cell, allowing them to be targets for cancer treatment?

1. _______ ______ receptors

2. non-________ signalling molecules (RAS, RAF, MAPKK)

3. _________ regulators (gene transcription factors)

4. ________ modulators

5. inhibitors of ________ proteins

6. immune ________ proteins

7. ANGIOGENESIS ____________

1. growth factor

2. receptor

3. epigenetic

4. metabolic

5. apoptosis

6. checkpoint

7. regulators

what are 4 examples of reliable biomarkers in clinical use (oncology)?

1. HER2 in breast cancer

2. EGFR mutations

3. PD-L1 (programmed cell death ligand 1)

4. MSI0H/dMMR (High Microsatellite Instability/ Deficient MisMatch Repair)

Which predictive biomarker is used in oncology for predicting the response to trastuzumab (Herceptin) with standardized IHC/FISH testing protocols

trastuzumab prevents dimerization of _____ in ER+ breast cancer

HER2 amplification

which biomarker is used for checkpoint inhibitors (ex.pembrolizumab)

its reliability varies by cancer type (better predictable biomarker for non small cell lung cancer)

PD-L1

Programmed Cell Death- Ligand1

which biomarker is highly predictive of immunotherapy response across multiple cancers (ex. pembrolizumab in colorectal cancer)

MSI-H/ dMMR

MicroSatellite Instability/

Deficicent MisMatch Repair System

which biomarkers are strong predictors of inhibitor efficacy in non-small cell lung cancer (ex. Osimertinib for T790M- positive tumors)?

EGFR mutations

Putting more science into clinical trials:

What goes into the creation of an investigational drugs n terms of MOLECULAR DIAGNOSTICS?

What else is considered?

molecular diagnostics =

1. unbiased approach

2. candidate approach

   pharmacodynamic measurements also considered in creation of investigational drug

using _________ __________ such as the unbiased approach and candidate approach we are able to make individualized treatments for patients with different forms of cancers

ex. a lung cancer patient and a prostate cancer patients may be dealing with the same type of mutation (ex. receptor binding, checkpoint mutations) they would take similar medication compared to two breast cancer patients who have different pathways involved in their disease

molecular diagnostics

cancer is a disease of the __________

if we precisely define the above we will understand and cure cancer

genome

lesions that lead to genomic/chromosomal instability and are often not fully transforming (ex. p53 and RB)

founder mutations-first genomic mutation

mutations that are required for expression of FULLY transformed phenotype

driver- mutations

is our goal to target and inhibit the function of driver or founder mutations?

driver mutations

since they fully transform the normal phenotype

These mutations are “collateral damage” resulting from genomic instability and are not required for maintaining the transformed genotype and therefore are “noise” in the system

passenger mutations

since most cancers are rapidly evolving biological entitiies it is a major task to sort out the ______ mutations from the ______ mutations and these may change over time

separate driver and passenger mutations

what are the three types of genomic mutations that were discussed in class?

1. founder mutations - first genomic mutation

   passenger mutations (collateral damage)

2. driver mutations (fully transformed phenotype — TARGET)

Which cancer treatment is used for Sustained proliferating signaling

EGFR inhibitor

which cancer therapy is used when cancer cells resist cell death?

proapoptotic BH3 mimetics

which cancer therapy is used when there is genome instability and mutation?

PARP inhibitors

which cancer therapy is used when there is deregulating cellular energetics?

aerobic glycolysis inhibitors

which cancer therapy is used when there is evasion of growth suppressors?

cyclin dependent kinase inhibitors

which cancer therapy is used when cancer cells avoid immune destruction?

immune activating anti-CTLA4 mAb

Which cancer therapy is used when cancer cells enable replicative immortality?

telomerase inhibitors

which cancer therapy is used when there is tumor promoting inflammation?

selective anti—inflammatory drugs

which cancer therapy is used when there is activating invasions and metastasis?

inhibitors of HGF/c- Met

which cancer therapy is used when there is cancer induced angiogenesis?

VEGF inhibitors

what are some complexities and challenges with precision medicine?

include an example

although they can help patients immensely by targeting the specific pathway that is disregulated, there is a remission and relapse after multiple weeks of the therapy

ex. Vemurafenib (B-raf inhibitor) alleviated symptoms after 15 weeks, but they were back after 21 weeks of therapy

what was the issue that occurred with the personalized medication Vemurafenib (B-raf inhibitor)

relapse and remission after 23 weeks of therapy despite relief of symptoms after 15 weeks

SEQ the patient journey through Precision Medication

1. ________ setting: tumor shrinkage/ response prediction — treatment before surgery

2. ________ setting: recurrence prevention—— treatment AFTER surgery

3. __________ early detection/reassessment

4. __________ long term disease control

neoadjuvant setting

adjuvant setting

relapse

metastasis

From neoadjuvant —> adjuvant —> relapse —> metastatic

• Which is most comprehensive, and which is focused/specific

• which is more tissue dx and which is mre liquid dx

metastatic is more focused, neoadjuvant aims to reduce tumor in general and is comprehensive

neoadjuvant medications target tumors mostly found in tissues

metastatic medications target tumors mostly found in bodily liquids (blood/plasma/extracellular)

Erbitux (cetuximab) is indicated for which type of cancer?

Cetuximab is used after both _______ and ______ have failed as treatment

Cetuximab can be taken in combination with _________ for patients who refractory to the medication alone

EGF- expressing metastatic colorectal cancer

irinotecan and oxaliplatin

irrinotecan

______ is a transmembrane growth-factor receptor belonging to a family of ____- related proteins

ligand binding to this receptor triggers _______ through ____ ______ activity

EGFR HER

phosphorylation through tyrosine kinase

SEQ signaling cascade of EGFR pathway

1. ligand binds to EGFR

2. dimerization of receptor

3. autophosphorylation of receptors

4. Ras (KRAS)

5. Raf (MAPKKK)

6. MEK (MAKK)

7. ERK (MAPK )

8. PI3K/ AKT

9. PROLIFERATION

Unregulated EGFR signal transduction ultimately leads to

• ________ of cancer cell _________
  

• blockade of _________

• activation and invasion of _________

• stimulation of ____________

induction proliferation

apoptosis

metastasis

neovascularization

Search for Predictive Biomarker:

Cetuuximab (Erbitux) was initially granted approval only for ____- expressing patients with ________

60-80% _______ tumors express _______ proteins (measured with IHC— using antibodies)

CRITICAL ANALYSISES: NO coorelation between extent of _____ expression and response to anti-____ mAbs

Findings prompted intense research for predictive biomarkers for ___________

EGFR expressing patients with Metastatic Colorectal Cancer (mCRC)

mCRC EGFR

EGFR expression and response to antiEGFR antibodies

antiEGFR

true/false: there was NO correlation between the extent of EGFR expression and response to anti-EGFR mAbs

what happened as result?

true

EGFR expression was found to be unchanged with antiEGFR mAbs

began studies to find predictable biomarkers for mAbs and which genetic populations would respond to antiEGFR mAb treatment

_____ mutations occurs in about 40% of Colorectal Cancer patients

specifically a single nucleotide point mutations mainly in codon ______ and _____ of exon ___

mutation is maintained throughout Colorectal Cancer development, progression, and metastasis

_______ mutation was tested by direct sequencing or PCR

KRAS

12 and 13th amino acid/ codon of exon 2

KRAS

early clinical data on KRAS

• 2006 study: first reported link between KRAS mutation and lack of response to ______

Multiple Phase __ Studies of KRAS mutation status:

• cumulative data from 9 studies of 536 patients

• KRAS mutation detected in 36% of patients

• Response rate (RR), time to tumor progression (TTP), progression free survival (PFS), overall survival (OS),significantly better in WT patients

antiEGFR

phase 2 studies

How does the following compare in cancer patients taking Cetuximab with wild-type vs mutatated KRA

• Overall Survival (OS)

• Progression Free Survival (PFS)

• ORR (Overall Response Rate)

overall survival, progression free survival, and overall response rate of cetuximab HIGHER IN WILDTYPE KRAS

KRAS mutations significantly decreased OS, PFS, and ORR

explain why mutations in KRAS would lead to decreased levels of

• Overall Survival

• Progression Free Survival

• Overall Response rate

  in colorectal cancer patients on Cetuximab

normally, when ligand binds to EGFR

KRAS is activated leading to RAF/MEK/ERK → PI3K/Akt

cetuximab blocks the EGFR to prevent proliferation of cancer cells

HOWEVER when KRAS is mutated it no longer needs a ligand to bind to EGFR to be activated and increases proliferation despite being on Cetuximab

mutated ______ causes increased signaling despite upstream EGFR inhibition by Cetuximab

if a tumor has mutated/activated ______ it will grow in the presence of ____ inhibitors

KRAS

KRAS GF

KRAS is an example of how ________ biomarkers can spare patients using drug without potential benefit and with unwanted toxicity of cost

how?

predictive

lets say you are thinking of starting your cancer patient on cetuximab treatment. If you do genetic testing and find a KRAS mutation then you can AVOID that medication from the start since it won’t be effective in THEIR case

_________ and __________ are personalized/precision medications used for the treatment of KRASG12C mutant lung cancers

SOTOrasib and ADAGrasib

the ability of obtain full ______ data on a tumor will allow us to make rational choices for therapy

________ _______ may provide help in choosing COMBINATION therapy

• although not easy due to enhanced toxicities

genomic

functional genome

Cancer as a _______ disease is not a bad thing as long as we recognize rapid development of ___________ and clonal __________

chronic

resistance

evolution

________ is a rate limiting step to effective anti-tumor immunity

immunosuppression

which components of tumors cause immunosuppression?

drugs are made to block these components and allow the immune system to fight against the tumor

1. CTLA4 (competes with CD28, preventing activation of T cells

2. PD-L1/PD-1 (signals T cells to inactive—> normal function is now excessive)

which drugs are anti-CTLA4?

how do these drugs block immunosuppression caused by tumor cells?

• Ipili mumab

• tremili mumab

the MUMBABS inhibit CTLA-4 from binding and inactivating T cells (4 is baby blocked by MUM)

mum goes uphill using treadmill

which drugs are anti-PD-L1 / PD-1?

how do these drugs block immunosuppression caused by tumor cells?

ni volumab

Pembroli zumab

Atezoli zumab

Dur valumab

new PAD blocking Programmed Cell Death Ligand (PD-L1) from EXCESIVELY binding to Programed Cell Death Receptor (PD-1)

low sound like brown names

• nivo

• pem

• atez

• druv

Explain how immunotherapy is being used with CART-cell therapy and customized vaccines

1. collect T- cells from patients blood

2. reprogram T-cells to find and attack cancer cells (grow in large numbers)

3. infuse T cells back into patient

what are the two immune checkpoints that are inhibited as cancer treatment.

How does their inhibition treat cancer?

1. CTLA-4

   prevents dendric cells from priming T cells to recognize tumors

2. PD-1

   Prevents T cells from attacking cancer cells

the inhibition of which checkpoint is BROAD but only subset 10-30% of patients benefit ?

PD-L1

PD-1

Combinations of Immunotherapeutic or Immunotherapeutic with SOC (standard of care) /targeted therapies:

• agents must be safe with ________

• Targeted/chemotherapy should not interfere with _______ response or _______________mechanism of action

anti-PD-L1

NO Interferance with immune response or immunotherapeutic MOA

Personalized medicine can be regarded as the 21st centuries answer to the _______ use of drugs

RIGHT _____ FOR RIGHT ________

rational

drug patient

what are the key drivers in personalized medicine?

1. molecular diagnostics

2. academic groups

3. patient advocacy groups

4. authorities

5. health insurance companies

implementing personalized medicine into clinical practices will be a challenge that need to address various issues such as

• _______ requirements

• __________

• __________

• ___________

regulatory

reimbursement

education

logistics