Biology 2.4-2.6
Personalized Medicine
"Preventive, diagnostic, and therapeutic interventions targeted to individuals based on their risk" - Risk defined through: •molecular testing •genomics •proteomics •metabolomics •epigenomics •family history & data mining - Goals: Greater effectiveness & efficiency of healthcare delivery improved health outcomes and quality of life
Next generation sequencing(ngs)
)1. library preparation (DNA sample is broken down and specialized adapters are glued to the two sides of the fragmented DNA, fragments are then led to polymerase chain reaction or PCR amplification they are then gel purified) 2. cluster generation (a DNA library is carefully placed into a flow cell DNA fragments attached to the top of the flow cell, flow cell contains ala ghosts that complement the incoming library adapters attached to the DNA fragments, every DNA fragment goes through a bridge amplification cycle) 3. sequencing (nucleotides are added and Illumina technology is able to identify single basis as they combine into each DNA strand) 4. data analysis (Once the scientists are able to visualize the various DNA sequences they are sequentially aligned using a reference DNA sequence also known as a reference genome a reference genome is a man-made DNA sequence that expresses a specific species set of genes this phase can only be done using an advanced bioinformatics program - helps distinguish any variances between the aligned reads and their reference DNA sequence)
Brca1 & brCA2 genes
- BRCA1 & BRCA2 genes are essential for repairing damaged DNA - BRCA1 and BRCA2 mutations are usually insertions or deletions of a small number of DNA base pairs in the gene - BRCA1 and BRCA2 are unrelated proteins, but both are normally expressed in the cells of breast and other tissue - DNA damage appears to be the primary underlying cause of cancer and deficiencies in DNA repair appears to underlie many forms of cancer
Epigenome Changes & Disease
- Central Result: it's not single modifications to the epigenome that matter in causing diseases - Combinations of modifications that cause changes in gene expression that are associated with the emergence of cancer & other diseases - Major difficulty relating disease to disruption of DNA function is that key epigenetic changes occur in poorly understood regions of the genome - Identifying locations of these enhancers & the genes they affect is necessary to understand the causal link between epigenetic changes and disease & to designing targeted treatments
Epigenome changes & Development
- Enhancers activated through interactions with transcription factors which bind to specific DNA sequences within the enhancer region - Enhancers active in epigenome areas determining cell type are enriched in DNA sequences to which cell type-determining transcription factors can bind - Changes in these epigenomic areas during developmental transitions affect cell differentiation and interactions with transcription factors - ENCODE uncovered hundreds of thousands of enhancer regions in the genome that regulate gene expression & development - Each cell type is regulated by a subset of 20,000 - 40,000 enhancers which determine its gene-expression profile
immune system therapies
- New therapies employ patients' own immune system to kill Chronic Lymphocytic Leukemia (CLL) cells - A disabled form of H.I.V. - the AIDS virus - re-engineered to carry cancer-fighting genes & mixed with patients' T-cells - Modified T-cells then injected back into patient & other engineered genes cause these cells to proliferate - Major turning point in the long struggle for effective gene therapies against cancer
CRISPR
- Prokaryotic Adaptive Immune System ¡Segments of prokaryotic DNA containing short repetitions of base sequences - Repetition is followed by short segments of "spacer DNA" from previous exposures to a bacterial virus or plasmid 1. identify sequence to be modified PAM 2. guide RNA or crRNA and trac RNA find sequence 3.cas9 protein attaches and assembles and causes a double strand break at the PAM sequence 4.non-homologous enjoining occurs for insertion/deletions for silencing a gene or homologous end joining occurs for gene editing
Development of Cancer
- Rarely occurs from a single mutation but rather from accumulation of mutations - Explains why most cancers associated with somatic cells which turnover frequently - due to random errors in division that lead to mutations - Typically do not see cancer arising from the germline (X/Y) chromosomes - 90% of all cancers are of epithelial cell origin: lung, breast, colon, skin
ROADMAP Epigenomics Project: 2015
- To find the switches & trace the circuits controlling genes researchers examined 100s of cell types taken from healthy people & patients suffering from diseases, as well as fetal cells & stem cells - Found millions of switches that control genes
XYY
- associated as a criminal gene - tall and with more acne
Research areas contributing to personalized medicine
- biomarker discovery - microbiome - pharmacogenomics - clinomics -epigenetics
Earth Biogenome Project:Sequencing all Eukaryotic life
- includes portable sequencers - autonomous vehicles - collect 1.5 samples - instrumented drones identify samples in the field - generate at least an exabyte of data
Zoonotic diseases or zoonosis
- infectious diseases that can be transmitted from other vertebrates to humans. May be direct or via a vector Of 1415 microbes infectious for humans, 868 (61%) zoonotic 70% of newly recognized pathogens are zoonoses - 5 stages pathogens evolve: only in animals, primary infection, limited outbreak, long outbreak, exclusive in humans
sex determination system
- presence of y makes a male - some organisms have females determine sex - sex can be determined by temperature in turtles and alligators etc
backing up in DNA
- putting files into DNA - 2013 - write code into synthetic DNA -sequence DNA to get information back out -ideal long term storage system with no shelf life and minimal effort
DNA computer
- regular silicon chips are replaced with DNA molecules and rather than the binary code used for traditional computers of zeros and ones this computer uses a genetic alphabet - DNA copies itself when it makes a command the computer grows - completely synthesized DNA
human genome project
- support from politics - originally used brute force by hand - importance of data sharing - brought in social scientists and ethics - apply to diseases like diabetes and cancer - Goal: Determine nucleotide sequence of all DNA in human genome Identify the location & sequence of every human gene - 2000 1st draft; 2003 complete version - Made possible by:(20 research centers in 6 countries, Increased computer power, Advances in gene sequencing, Competition between public & private teams)
ENCODE
- trying to translate those letters into a comprehensive instruction manual for building a person - characterize all functional elements within the human genome(genes, rna comes off of the genome, regulatory parts) - generates 100 terabytes of raw data - assigns biological function to 80% of human genome - tells a lot of where disease comes from in the genome - RNA is a major functional unit of the epigenome(76% of genome transcribed to RNA not to proteins) - Evolution can occur by selection for RNA sequences that alter gene regulation, not just selection for protein-coding sequences
angiogenesis inhibitors
-Angiogenesis is the formation of new blood vessels block the growth of new blood vessels to tumors(a process called tumor angiogenesis) -When growth factors bind to their receptors on endothelial cells, signals within these cells are initiated that promote the growth and survival of new blood vessels
mesenchymal stem cell
2 types: 1. Embryonic stem cells derived from embryos in vitro fertilized eggs 2. Adult stem cells - occur in every tissue - typically generate same type of differentiated cells. Originally thought NOT to be pluripotent (capable of differentiating into any type of cell). abilities: - reduce inflammation - fight apoptosis - differentiate into multiple tissues such as muscle, bone, fat, or cartilage - self replicate
Genomic Screening & Testing Newborns
3,500 genetic diseases cause problems in first month of life >20% of infant deaths due to a genetic disease 30% babies in intensive care unit have a genetic disease Can now sequence newborns with mystery conditions in 24 hrs >99.5 % specificity of genotypes Phenomizer & associated data bases: •Provides assistance in reaching correct diagnosis in patients with hereditary diseases •Phenomizer is an expert system for clinical diagnosis •Connects to the Phenomizer data base of 6000+ genetic variants with symptoms
COVID
CoV uses its Spike Glycoprotein (S), to bind its receptor, and mediate membrane fusion and virus entry. During virion assembly, N protein binds to viral RNA and leads to the formation of the helical nucleocapsid. Hemagglutinin esterase (HEs): a glycoprotein that certain enveloped viruses possess and use as invading mechanism. HEs help in the attachment and destruction of certain sialic acid receptors that are found on the host cell surface
Epigenomics
Examines which factors act on individual genes, and how certain changes in the epigenome affect our health
Nondisjunction
Failure of chromosomes or chromatids to separate during meiosis - Fertilization after nondisjunction yields zygotes with altered numbers of chromosomes -If nondisjunction occurs during meiosis I, all gametes will have an abnormal number of chromosome (Half will have two copies of the chromosome pair that failed to separate, Half will be missing copies of that chromosome) -If nondisjunction occurs during meiosis II •Half will have correct copies of the chromosome pair (n)(One quarter will have an extra chromosome, One quarter will be missing a chromosome (n-1))
Single Nucleotide Polymorphisms
Foundation for personalized medicine - patients know risks of developing diseases from personal SNP profile •Estimated 5 million SNPs in human genome •Haplotype: all SNPs found on a given chromosome •International effort to identify every SNP in human genome •Data used in genome wide association studies •Rapid scanning of many individual genomes to find SNPs associated with particular diseases •Crucial to identifying SNPs contributing to complex diseases: Schizophrenia, Alzheimer's, Bipolar disorder
x-linked disorders
Genes on X chromosome not on Y - These genes segregate based on X-chromosome segregation - Expression of trait dependent upon whether recessive or dominant - Hemophilia caused by an X-linked recessive gene - Color-blindness, muscular dystrophy and >300 other disorders associated with X-linked genes
Genome 10K Project
Goal: Sequence DNA of 10,000 vertebrates - Consortium of geneticists, paleontologists, ecologists, conservationists & other scientists around the world -10K database currently includes genomes of more than 16,000 vertebrate species - believe sequencing species prevents extinction, ensure to capture current genetic diversity -trying to reengineer species on the brink of extinction - found that 90% of DNA alterations associated with disease lie in gene switching areas that code for the epigenome, not in protein coding genes
dna viruses
Hepatitis, chicken pox, herpes
Galactosemia
Inability to fully break down galactose causing damage to liver, brain, kidneys, and eyes - 50% probability of being heterozygous - not expressed - 25% probability of homozygous recessive - expressed - Both parents aa, each child will inherit disease: 100% probability
MRSA - Methicillin-resistant Staphylococcus aureus
Penicillin resistant strains emerged in 1950s Methicillin resistance in 1960s Now resistant to almost all antibiotics Last resort treatment is Vancomycin - extremely toxic Harmless unless enters body through cut or wound Deadly to those with weakened immune systems Hospitals, assisted living facilities 2M people/year infected in hospitals ~100,000 deaths
Microbiome exploration
Profile an individual's microbiome to detect, prevent and diagnose infections and other diseases
Clinomics
The challenge is in the accurate interpretation of the vast amount of data and effectively using it to guide decisions about your health care
The Cancer Genome Atlas
To employ large scale genome sequencing of cancer cells to catalog genetic changes and identify new genes - specialized on what treatments work - Profound Impact: •Realization that there is not one cancer & one type of tumor •Drugs must target specific profile for a given individual - match to 33 cancer types
Pharmacogenomics
Using a patient's genetic profile to predict a drug's efficacy, guide dosage and improve patient safety - example - how fast the person will metabolize the medicine
Klinefelter syndrome
a condition in which human males have an extra X chromosome. Effects include low testosterone and low fertility.
biomarker
a measurable substance in an organism whose presence is indicative of some phenomenon such as disease, infection, or environmental exposure.
Autosomal Dominant Disorders:examples in Humans
achondroplasia - dwarfism Alzheimer's, Huntington's disease(affects muscle coordination leads to paralysis and dementia), hypercholesterolemia
recessive disorders
albinism, cystic fibrosis, galactosemia, phenylketonuria, sickle-cell disease, tay-sachs disease
Turner syndrome
an egg lacking a copy of the X or Y chromosome can be fertilized by a sperm carrying a copy of the X chromosome
Down Syndrome
an egg with two copies of chromosome 21 can be fertilized by a sperm carrying one copy of chromosome 21
pandemic
an epidemic that has spread to more than one area
signal transduction inhibitors
block the activities of molecules that participate in signal transduction, the process by which a cell responds to signals from its environment - Blocking these signals can affect many functions of the cell including cell division and cell death, and may kill cancer cells
Tyrosine Kinase Inhibitors
blocks EGFR
Oncogenes
cancer causing genes
gene insertion with CRISPR
cas9 enzyme cuts genomic DNA, new DNA is delivered with CRISPR plasmid, homology directed repair occurs creating new functional DNA
gene silencing CRISPR
cas9 enzyme cuts genomic DNA, non-homologous end joining occurs to cause an insertion/deletion mutation and create an inactivated gene
epigenetics
define epigenetic elements
monoclonal antibodies
deliver toxic molecules can cause the death of cancer cells specifically - bind monospecifically to certain cells or proteins - The objective is that this treatment will stimulate the patient's immune system to attack those specific cancer cells -binds pd1 or pdl1 molecule to reactivate ctls (1 examples)
genomics
determine genome sequence
interactomics
determine interacting molecules
epidemic
diseases that affect a large number of people in one area simultaneously
yamanaka inducible pluripotent stem cells
hypothesized that genes important to embryonic stem cell (ESC) function might be able to induce an embryonic state in adult cells
proteomics
identify all gene products
Synthetic biology
is a new interdisciplinary area that involves the application of engineering principles to biology. It aims at the (re)design and fabrication of biological components and systems that do not already exist in the natural world
Tumor Suppressor Genes
make proteins that stop cell division and kill cells - Mutations in these genes can cause cancer by disrupting the amount of the transcription factors
define the function
metabolomics
Association for Molecular Pathology v. Myriad Genetics
patents at issue directed to 'isolated DNA' containing sequences found in nature are unsustainable as a matter of law and are deemed unpatentable
shotgun sequencing
sequences small pieces of genomes (shotgun or cut many times at random) which are assembled by a computer with sanger sequencing - drawback comes when dealing with repeat sequences (don't know how long repeat sequence is or where overlap happens) -celera uses public data to fill in the gaps
hormone therapies
slow or stop the growth of hormone sensitive tumors, which require certain hormones to grow -Add, block, or remove hormones from the body to slow or stop the growth of cancer cells.
immunotherapy
trigger immune system to destroy cancer cells - uses substances made by the body or in a laboratory to improve how your immune system works to find and destroy cancer cells
Breast Cancer
•Accounts for one of every three cancer diagnoses •Breast cancer most common cancer in women (excluding cancers of the skin) •Highest incidence (80% of cases) in women over 50 •Four distinct genetic types of the disease were found •Tissue does not define the underlying genetic profile - for example, one type most similar to ovarian cancer
Promises of personalized medicine
•Advanced screening & early detection of disease •Informed prevention, proactive treatments & lifestyle changes •Select safer, more effective medications & dosages that reduce side effects •Develop better vaccines that activate an individual's immune system w/o causing infection •Greatly lower healthcare costs •BUT the epigenome is a major player & it's influence on different diseases needs much more research
Cancer
•All cancers derive from single cells •DNA in these cells acquired mutations that conferred the ability to continually divide •100 types of cancer each with different genetic causes, symptoms & treatments •Cancer cells behave abnormally because of changes in DNA of key cancer genes •Tumor Suppressor Genes & Oncogenes •These changes involve unknown degree of influence from epigenome Thus all cancers are genetic diseases
infectious diseases growing
•Contributing Factors: •Demographic changes (population growth, inhabiting new areas) •Increasing contact with wild & domestic animals •2/3 of EIDs originate from animals •Behavior (sexual, drug use, hygiene) •Poverty & social inequality •Climate & changing ecosystems Travel, commerce & transportation
Tumor Genotyping
•Genotype every lung cancer •Check for array of mutations •Drug therapy based on specific genes mutated - 15-20% of individual tumors can be matched to a specific drug
Cancer Genomics
•Most cancers caused by 2-8 sequential alterations over 20-30 yrs •~140 genes are known whose mutations drive cancer •Cancer genes function through dozens of signaling pathways •Every individual tumor is distinct with regard to genetic alterations, but pathways affected in different tumors are similar •Personalized treatment being informed by assessment of patient's germline genome & genome of his/her tumor
Epidermal Growth Factor Receptor
•Protein present on the cell surface •Bind to epidermal growth factor causing the cells to divide •Abnormally high levels on surface of many cancer cells, causing them to divide excessively in presence of epidermal growth factor
Sanger sequencing method
•Takes advantage of special nucleotides that are missing the hydroxyl (OH) on the 3' Carbon of the sugar base •This blocks DNA polymerase from adding the next base and elongating the DNA chain •Nucleotides are called ddNTP (dideoxynucleotide triphosphates) 1. denature DNA using heat 2. make multiple copies of a segment 3. attach a primer 4. add to 4 polymerase solutions 5. grow complementary chains until termination dye 6. denature the grown chains 7. electrophorese the 4 solutions
RNA Viruses
•unusually high rates of mutation lack the proofreading mechanisms seen in DNA replication •Common cold, measles, mumps, polio •HIV or AIDs virus West Nile & other emerging viruses causing encephalitis •SARS - severe acute respiratory syndrome (2002-2003) •Dengue & Zika •Ebola - hemorrhagic fever
Human Genome Project results
•~21,000 genes in 3.2 billion nucleotide pairs •As many pseudogenes [Inactivated, nonfunctional copies of genes] as functional genes •Only 1.5% of DNA codes for proteins •Remaining 98.5% of DNA contains control regions, noncoding DNA & repetitive DNA - 44% repetitive DNA, 24.5% regulatory sequences and introns, 15% noncoding DNA, 15% repetitive DNA unrelated to transposing elements), 1.5% exons