Genomes Diseases and Diversity

what causes cancer

mutations that alter the function or regulation of genes involved in affecting mitotic/apoptotic rates

what are cell numbers the product of

rates of cell division-mitosis- and cell death-apoptosis

is cancer a single disease

NO it is a diverse group of conditions sharing in an increase of cell numbers within a particular tissue

malignant versus benign

malignant=invasive and spreads to other tissues

benign=non life threatening and does not spread to other tissues

where is cancer most common

in epithelial tissues known as carcinomas and is about 80% of cancer

epithelial tissues

sheets of cells forming the upper layers of skin and lining the walls of cavities and tubes within organs

sarcoma

arising from connective tissue (bone or cartiledge)

why are epithelial cells the most commonly subject to cancer

1. highest exposure to carcinogens

2. prone to damage due to environmental exposure so they have a high division rate

why do cancers arise more frequently in tissues with high division

with higher mitotic rates comes fewer barriers to cell division and more frequent cell division increasing the likelihood of mutation

do all cells divide at the same rate

no→muscle and brain tissue divide slowly

p53

tumour suppressor gene and is considered a critical domain that forms a tetramer

loss of function mutation

reduction of function of protein encoded by a gene

hypomorhpic is partial loss

null is total loss

tumour suppressor

gain of function mutation

activity of resulting protein is increased

Ras

dominant interfering

protein opposes wild type protein function typically by binding to it or its target blocking the function

P53 mutation

explain why p53 mutations are so bad

if even a single subunit of tertramer is mutated then there is a complete function loss and mutant p53 that still binds to the tetramer is a dominant interfering mutation

what do carcinogens cause

cancer/ are mutagenic agents

two options for cells with dna damage

1. apoptosis

2. senescence(placed in a non replicative state)

how do viruses invoke cancer

insertion into the genome of their hosts

1. viral gene may carry a gene that enables the host cell to evade normal controls

2. viruses may integrate their genomes close to a host gene that regulates cell division leading to aberrant gene expression

how often do human cells divide

a rate of 10^7 per second

how do cancer cells typically arise

from a single cell eventually forming a tumor population

was debated due to many tumours appearing to be polyclonal upon diagnsois however most tumours are monoclonal meaning they comes from a single precurors cell

how did they determine monoclonality of tumours

2 ways

B-call tumors create single antibodies for specific antigens and therefore they would produce many different antibodies if they arose from multiple, individually transformed cellls

they producde a single antigen

and from chromosomal lesion analysis which had all cells of the same tumour presenting with the same legions

Philadelphia(Ph) chromosomes found in chronic myeloid leukamia and results in the translocation of BCR gene and its promoter upstream of the Abl gene to create new fusion gene (Bcr-Abl) with the protein product creating an increase in kinase acitivty

how many independent mutations generally required for cancer

6-8→cancer isnt caused by a single mutation

multicellular organisms cannot be successfull if cells dont work together to ensure success as a whole

chromothripsis

large scale chromosomal breakage producing multiple mutations similtanesouly

oncogene

👉 Proto-oncogene = normal "go" signal
👉 Oncogene = stuck accelerator leading to cancer

An oncogene is a gene that, when mutated or overexpressed, can turn a normal cell into a cancerous one by promoting uncontrolled growth and division.

usually a gain of function mutation

tumour suppressor gene

normally opposes cancer and generally results in a loss of function of dominant interfering mutation

what are the four barriers to transformation

1. requirement for growth factors: they enable division and are provided by other cells via paracrine signalling→cancers msut find a way to increase the supply and do this by either making it themselves are mutating the signalling molecule downstream to appear that they are always switched on

2. Tumour suppression genes act as a break on proliferation: P53 trasncription factor collaborates with other proteins(ATM, ATR, CHk1 and 2) involved in DNA damage detection and repair; when activated it blocks entry in mitosis to allow dna repair to be carried out

   extensive DNA damage results in apoptosis via Noxa, Bax, Puma since it is safer to destroy then repair

3. requirement for O2 and nutrients→ this is regulated by blood vessel proximity so they require new blood vessels via neovascularisation to grow beyond 1cm³

   new blood vessels are produced via angiogenesis and this is linked to production of vascular endothelial growth factor by the tumour

4. the immune system so evasion of cytotoxic T cells and natural killer cells

how common is mutant p53 gene

half of all cancers

what are the six characteristics of transformed cells

1. ability to grow in lab cultures(in vitro) for long periods of time; in exposure to serum growth factor non transformed cells only can go through about 25 cell division(Hay Flicks limit) due to telomere shortening→cells that are transformed express telomerase which repairs telomeres and is usually only found in stem and embryonic cells but many cancers experience reactivation of the gene

2. reduced requirement for growth factors via ability to make their own GF via autocrine growth or by increasing growth factor receptors or mutating gene functioning in GF receptor pathways such that the signaling cascade is permanently switched on as with Ras and Braf

3. anchorage independence: most cells minus red blood cells wont grow unless attached to solid support and normal cell in vitro will stop dividing once a monolayer of cells is formed whereas transformed cells will continue dividing on top of one another

4. altered morphology: normal cells adopt a fully flattened confirmation in culture whereas transformed cells become more rounded or adopt a spindle morphology which relates to cytoskeleton changes of disorganization and flexibility

5. loss of contact inhibition: normal cells cease to divide when in contact with other cells on all sides

6. ability to form tumours in immunocompromised mice which are those that lack T Cells by blocking thymus development which is where T cells develop

How do transformed cells often portray their presence in conjugation with healthy cells

by forming foci where cells pile up into 3-D aggregates

transformed versus healthy cells in culture

normal cells adopt a fully flattened conformation whereas transformed cells become more rounded or adopt a spindle morphology relating to cytoskeleton changes in disregulation

describe the process of transfection

it introduces individual genes into cells

involves formation of a complex between DNA and calcium salt which precipiates the DDNA which when added to cells is taken up via pinocytosis and escapes into the cell cytosol where it can enter the nucleas and become expressed

individual mutations may produce features of transformed cells without full transformation

oncogenes

greek for bulk or mass and generally are genes promoting cell division and in mutant forms act at an advanced rate

driver versus passenger mutations

passenger: most mutations in a tumour are irrelevant

driver= drive cancer development such as Ras and B Raf

without a driver passengers are not going anywhere however without passengers the drive can still get to the destination

how was it determined that cancer was a disease of the genes

Francis Peyton Rous viruses can cause cancer.

Rous investigated a chicken with a malignant tumor. He extracted material from the tumor, filtered it to remove cells, and injected it into healthy chickens. Remarkably, the recipient chickens developed similar tumors, demonstrating that a virus—later named the Rous sarcoma virus (RSV)—was responsible for transmitting cancer

Bishop isolated the RSV gene and termed is Src for sarcomes and quickly realized that the gene was present in genomes of all cells

V-Src is a hijacked hene that become part of the viral genome through selective advantage upon host entry

what was the first oncogene discovered

Src

how do growth factors promote cell divison

by turning on signaling cascades switching new genes required for replication

describe epidermal growth factor recpetor(erB) in cancer

it is upregulated in stomach, brain and breast cancer and makes cells hyper responsive to ambient levels of GF that wouldnt normally stimulate cell division

roles of ras and braf

🧬 RAS

• RAS (like KRAS, HRAS, NRAS) is a small GTPase.

• It acts like an on/off switch for signaling pathways that control cell growth, differentiation, and survival.

• When a growth factor binds to a receptor (like EGFR), RAS gets activated (binds GTP) and sends signals downstream.

• If RAS is mutated (gain-of-function), it stays "ON" all the time → leading to constant cell division and cancer.

🧬 BRAF

• BRAF is a serine/threonine kinase that is part of the MAPK/ERK pathway — it acts downstream of RAS.

• When RAS is activated, it activates BRAF, which then activates MEK → ERK → genes that cause cell growth and survival.

• BRAF mutations (like the famous V600E mutation) make BRAF constantly active, even without RAS signals, promoting uncontrolled cell growth.

how does ras GTP drive raf activation

it recruits it to the plasma membrane where it can then be phosphorylated by membrane-associated kinase

Ras cannot bind to Raf unless Ras is GTP bound and in binding a GTP molecules it needs help from a protein called GDP/GTP exchange factor that assists Raf in letting go of GDP in exchange for GTP

Sos

function of Sos(son of sevenless)

helps Ras bind GTP; acts as a GDP/GTP exchange factor'

Sos also doesnt live at the plasma membrane so gets there via the growth factor receptor binding protein 2 which has a domain SH3 that Sos bind to

what does ligand induced activation of growth factor receptor cause

it creates binding sites for GRB2 and Sos and induced Ras activation through Sos-mediated stimulation of GTP exchange on Ras where it can then recruit Raf to the membrane where it becomes phosphorylated and further amplifies the signal by activating downstream kinase MEK and ERK

what do Ras mutations cause and what percent of cancers have Ras mutations and where are they found

, 30%, an increase in GTP affinity. they occur at positins 12 and 13 of Ras proteins around the edges of the GTP binding loop(P-loop)

gain of function mutations

what enables mutant Ras to transform cells more efficiently

if p53 is also mutated

what is the most difficult to treat cancer form and how does it arise

malignant melanoma due to chemotherapeutic drug resistance

it arises due to pigment-producing cells(melanocytes) becoming transformed due to chromosomal lesions frequently involving B-Raf kinase

most arise in the exposed areas of the skin due to sunlight

one of the few cancers that incidence does not correlate with age

what is the drug used to treat malignant melanomas

dacarbazine which elicits a response in 15-25% of melanoma patients but complete response are only at 5%

How was Raf discovered

in 1983 as a viral oncogene designated V-Raf(rapidly accelerated fibrosarcoma) that was isolated from 3611-MSV a retrovirus that induces fibrosarcoma in mice

what are Raf family members

serine/threonine kinases that are regulated via extracellular cues and mutations in B-raf kinase are found in about 70% of melanomas

what do Braf mutations predominantly alter

a single AA residue with 80% of mutations found at position 600 of Braf kinase where a valine is altered to a glutamic acid (V600E) producing a 500 times more active kinase than wild type and increases MEK and ERK levels

why are additional mutations on top of Braf required

Braf mutations V600E are found in benign moles and mutations in CDKN2a encoding for ARF and P16 proteins cooperate with Raf to transform cells

name two Raf inhibitors

they represent cancer chemotherapies

sorafenib= C-Raf inhibitor for renal cancer

Zelboraf=inhibits V600E B-Raf

how does p53 stop the cell cycle

via p21 or apoptosis through Noxa, Puma, Bax

how was p53 discovered

normal p53 functions to suppress transformation and contributes to apoptosis and usually as a tetramer and mutant P53 joins the tetramer distrupting its functions

single p53 mutant molecules could disrupt the functions of the tetramer such that only 1/16 of p53 in cell carrying dominant negative p53 allele would be functional

half life of p53

short at about 20 minutes and its stability is controlled through Mdm2 which binds to p53 and targets the protein for degradation via ubiquitin proteasome protein destruction pathway

Mdm2 expression is controlled by p53 which is interesting since it controls the synthesis of its own inhibitor

what is p53

a transcription factor

how is mdm2 degraded

in response to cell damage

in healthy cells Mdm2 has the upper hand to P53 and the half life of p53 is enhanced by DNA damage which results in its degradation being inhibited, allowing for p53 stabilization and activation in stress response.

what happens when p53 is stabilized

p21 is rapidly expressed halting the cell cycle by inhibiting certain kinases crucial for cell division like cyclin dependent kinases

different between high versus low levels of DNA damage

high=apoptosis

low=limiting divison

where are P53 mutations most commonly found

in the DNA binding domain and they are dominant interfering by neutralizing protein function of wild type p53 in the same tetramer

what is a hallmark of cancer

elevated P53

Li Fraumeni Syndrome

inheriting p53 mutation and 60% get cancer by 22

what are actionable cancer genes

KRAS, EGFR, BRCA 1 and 2

what is the result of most mutagenic events

little or no functional consequence but certain mutations can dedispose acquistion of further mutation

what is a candidate oncogene

mutation shared among different tumours

how is cancer mainly diagnosed

through histology

what mutations are more common in people who have already recieved cancer treatment previously

ligan binding domain mutations in the gene encoding the oestrogen receptor(ESR1) in metastatic breast cancer

metastatic

cancer spreading from original location to other locations in the body

microbiome

entire microbial ecosystem within a host including the microorganisms, their genomes, and surrounding environmental conditions

can be acquired vertically, horizontally, and environmentally

germ theory of communicable diseases and its ramifcations

a specific microbial pathogen causes a discrete communicable human disease

1885 Louis Pasteur speculated that life of an animal host is not possible without its resident microbes but commitment to germ theory led to backlash at the idea of positive microbes

how many virus particles per individuals

10^13

what is included in the virome

viruses that can infect human cells, other microorganisms, and bacteriophages

what influences microbiome

diet, breast milk versus formula, medications such as antidepressants, host genetics, geography, and age

significance of gut mycobiome

fungi, small but important

Candida and Aspergillus influence the gut bacterial microbiome

what is the term for the gut microbiota

a microbial organ within a host organ since the metabolic activities resemble those of an organ and it has roles in metabolism and immunity

what microorganism in the gut are responsible for methane production

archae

is fungal abundance on the skin high or low

it is low even on the feet where its diversity is high

what dominates the vaginal microbiota

lactobacillus

offers more protection compared to a diverse microbiota

where is the primary source for the lung microbiome

upper respiratory and it is dominated by staphylococcus

what is the underworlds project

human health cencus by sampling urban gut at multiple locations by sewage sampling

how does the soil contribute to human health and what is the one health concept

both directly and indirectly through the plants and animals we consume

humans are inseparably linked health of other ecosystem compenents

holobiont

a complex and interconnected system of organisms living in close association with each other often involves assemblages of smaller organisms known as the symbiome in a larger host

what does the early life microbiome development do and what is the difference between c section verus vaginal delivery

trains the immune system

C section birth is dominated with staphylococcus and Vaginal delivery is lactobacillus

is there an increase or decrease in microbiome diversity in urban environments

a decrease

how do microbiome studies characterize presence of bacteria in a sample

by sequencing a fragment of 16S ribosomal RNA encoding gene however the resolution is limited

shotgun metagenomics versus shotgun metatranscriptonomics

metagenomics: DNA sequencing cannot distinguish between live or dead bacteria

transcirptongenomics= real time functional programming

problem with donating feacal samples

difficult to safe gaurd privacy of donor due to things such as gender being able to be deduced through gene sequencing

microbiota versus microbiome

living organisms in a defined or specific environment

microbiome encompasses the genomesof those organisms

where are obligate anaerobic bacteria found

they dominate the gut microbiome

bacteriodetes and Clostridia

what role do gut microbiota play

they produce short chain fatty acids by playing a crucial fermentation role with the by products of butyrate and acetate

SCFAs

short chain fatty acids: microbial derived metabolite which has a pyruvate precursor

profile depends on the fibre fermentation of different bacteria and the bacterial metablism of amino acids derived from protein

used as an energy source by colonocytes which supports the maintenance and growth of intestinal epithelial cells

can improve integrity, glucose and lipid metabolism, and the immune response

what is promoted by a high fibre diet

lower gut Ph

virome

all bacteriophage, other viruses and endogenous viral elements that have integarted into the host genome

is characterizing the human virome easy or hard

difficult due to absence of conserved gene region such as bacterial 16S and an incomplete viral genome library

Dysbiosis

imbalance of microbial community composition generally between beneficial such as lactobacillus and harmful Ecoli

‘Factors influencing dysbiosis include loss of symbionts, outgrowth of pathobionts and opportunistic bacteria

overall disruption of ecological links

does dysbiosis cause disease

a tricky discussion topic because it is hard to determine whether or not it is the result or cause of disease and purely observational data is not helpful if action is implied

what is loss of gut microbial diversity linked to

obesity and autoimmine conidtions generally due to antibiotic use, sterile water, processed foods, C section

BLOSSUM versus VANISH

blossum taxa are those that are selected for in urbanized societies and VANISH are volatile in industrialized societies taxa

what do traditional populations have more of versus ubranized

carbohydrate active enzymes

Cazymes

IBD

including Crohns and ulcerative colitis is a chronic inflammation of the intestine

decrease in SCFA producing organisms such as Clostridium spp

describe the colonic epithelium

hypotoxic, but intestinal inflammatin or antibiotic use can increase epithelial oxygenation and distrupt anaerobisis leading the dysbiotic expression of proteobacteria

gut microbiota transplantation in mice

implies a causal relationship between gut microbiome and obesity development since gut derived SCFA interventions combat obesity and metabolic disorders