Pathophys Exam 1

L1

pathology

the causes of disease and the changes in cells, tissues, and organs that are associated with development of disease; same pathology does not mean same etiology/pathogenesis

etiology

the origin of a disease, including the underlying causes and modifying factors; can be multiple

ex: hypoxia, ischemia, toxins, infections, abnormal immune reactions, genetic abnormalities, nutritional imbalances, physical agents

pathogenesis

steps in disease development

ex: biochemical changes, structural changes

homeostasis

steady state of steady internal physical and chemical conditions

adaptation

a new steady state that preserved viability and function

reversible injury

changes in function and morphology that cells can recover from if damaging stimulus is removed

irreversible injury

1. inability to restore mitochondrial function even after removal of stimulus

2. altered structure and loss of function of plasma and intracellular membranes

3. loss of structural integrity of DNA and chromatin

leads to cell death

types of cellular stress

• oxidative stress

• ER stress and UPR

• disruption of calcium homeostasis

oxidative stress

cellular damage induced by the accumulation of reactive oxygen species (ROS; form of free radicals)

• unstable and “attack” cellular components

  • peroxidation of membrane lipids

  • crosslinking and modification of proteins

  • DNA damage

• types of injury that cause oxidative stress —> by inc rate of production or dec clearance

  • chemical and radiation injury

  • hypoxia

  • cellular aging

  • tissue injury by inflammatory cells

  • ischemia-reperfusion injury

• **normal cell functions can produce ROS so it needs to be maintained in a balance

  • cleared enzymatically or by antioxidants → block formation of free radicals or by scavenging

  • enzymes: glutathione peroxidase, catalase

chaperones

proteins in ER that ensure proper folding of newly synthesized proteins

Unfolded protein response (UPR)

• adaptive response

• inc chaperone expression → fix misfolded proteins & sense cellular stress

• reduces protein synthesis

• inc protein degradation

• misfolded proteins in ER activate UPR via sensors (ex: IRE1)

ER stress

• causes of intracellular accumulation of misfolded proteins

  • abnormalities that inc production of misfolded proteins

  • reduced ability to eliminate misfolded proteins

  • mutations in protein that is misfolding or UPR pathway

  • aging → dec adaptive capability w age

  • viral infections

  • intracellular pH and redox state

  • hypoxia

  • ischemia

• high levels of misfolded proteins can trigger apoptosis via mitochondrial intrinsic pathway

• injury leads to problems w protein folding

• misfolded proteins can cause disease by

  • creating a deficiency of an essential protein - loss of function

  • inducing apoptosis

  • gaining a toxic function

proteasome

endopeptidase protein complex; cell’s trash can

Ubiquitin-proteasome system

• proteins tagged by ubiquitin ligases

• UPS proteolyzes ubiquitinated proteins

• disruption of UPS plays role in disease

  • polyglutamine repeat disease

  • parkin in Parkinson’s disease

disruption of calcium homeostasis

• intracellular Ca2+ → LOW

• extracellular Ca2+ → HIGH

• having high intracellular Ca2+ disrupts signaling pathways and activates enzymes (proteases, phospholipases) that damage cellular components (plasma membrane, cytoskeleton)

• ischemia and certain toxins inc cytosolic Ca2+ due to release from intracellular stores in mitochondria and ER and later from across a damaged plasma membrane

cellular adaptations

• hypertrophy

• hyperplasia

• atrophy

• metaplasia

cellular adaptations to stress

reversible changes in the number, size, phenotype, metabolic activity, or functions of cells in response to changes in their environment; physiologic and pathologic

physiologic adaptation

the responses of cells to normal stimulation by hormones or endogenous chemical mediators, or to the demands of mechanical stress

pathologic adaptations

the responses to stress that allow cells to modulate their structure and function and thus escape injury, but at the expense of normal function

hypertrophy

• inc cell size and organ size; NO inc in cell number

• often in response to inc workload

• induced by growth factors produced in response to mechanical stress or other stimuli

• occurs in tissues with a limited capacity to divide

• can progress to cell injury if the stress is not relieved or if it exceeds the adaptive capacity of the tissue

• ex:

  • physiologic enlargement of uterus during pregnancy → caused by estrogen stimulus (hypertrophy + hyperplasia)

  • pathologic hypertrophy of the heart in response to inc workload (hypertrophy)

hyperplasia

• inc cell number; inc proliferation in response to hormones and other growth factors

• occurs in tissues whose cells can divide or contain abundant tissue stem cells

• often occurs concurrently w hypertrophy in response to the same stimulus

• stops when initial stimulus is removed

• ex:

  • physiologic

    • hormonal → proliferation of the glandular epithelium of the female breast at puberty and during pregnancy

    • compensatory → residual tissue grows after removal or loss of part of an organ

  • pathologic

    • endometrial hyperplasia → inc uterine epithelial proliferation due to inc estrogenic stimulation

    • benign prostatic hyperplasia → disruption of androgens and estrogens leads to hyperplasia in the prostate

  • bone marrow cells

  • epidermal cells

  • epithelial cells

atrophy

• dec cell and organ size

• associated w dec synthesis of cellular building blocks and inc breakdown of cellular organelles

• combo of dec protein synthesis + inc protein degradation (UPS)

• accompanied by inc autophagy

• may undergo apoptosis as atrophy worsens

• both pathologic and physiologic causes

  • dec workload

  • loss of innervation

  • diminished blood supply

  • inadequate nutrition

  • loss of endocrine stimulation

  • aging

metaplasia

• change in which one adult cell type is replaced by another adult cell type

• often due to reprogramming of stem cells in response to chronic irritation

  • epithelial metaplasia → replacement of normal columnar epithelial cells of trachea w tough, stratified squamous epithelial cells - in chronic smokers

  • chronic gastric reflux → normal stratified squamous epithelium of the lower esophagus undergo metaplastic transformation to gastric or intestinal-type columnar epithelium

• makes cells better able to withstand the stress

• may result in reduced functions or inc propensity for malignant transformation

• always pathological

• high risk of malignant transformation and development of cancer

causes of cell injury

ex: hypoxia, ischemia, toxins, infections, abnormal immune reactions, genetic abnormalities, nutritional imbalances, physical agents

mechanisms of cell injury/death

• cell response to injuries depends on type of injury and duration and severity

• depends on type of cell and its metabolic state, adaptability, and genetic makeup

  • survival without oxygen of

    • skeletal muscle (2-3 hrs)

    • cardiac muscle (20-30 mins)

    • neurons (1-2 mins)

  • genetic diff in cytochrome p450 pathways

• injury results from functional and biochemical abnormalities in one or more essential cellular components

morphological changes in reversible cell injury

• cellular swelling

  • inc cell size

  • swollen organelles

  • accumulation of degenerated organelles and lipids within injured cells

  • morphology → pallor (bc of compression of capillaries), turgor, inc organ weight

  • microscopic changes → hydroponic change, vacuolar degeneration

  • common during hypoxia

• fatty changes

  • lipid vacuoles in cytoplasm

  • common in organs inv w lipid metabolism (liver)

mitochondrial dysfunction and damage

• due to hypoxia, ischemia, mitochondrial toxicants, radiation, high intracellular calcium

• dec atp generation which leads to

  • reduced activity of plasma membrane atp-dependent sodium pumps → cellular swelling → dilation of ER

  • compensatory inc in anaerobic glycolysis → inc lactic acid accumulation → dec intracellular pH → dec activity of cellular enzymes

• prolonged atp depletion leads to structural disruption of protein synthetic apparatus

  • detachment of ribosomes from rough ER

  • dissociation of polysomes

  • reduction in protein synthesis

• formation of mitochondrial permeability transition pore (mPTP)

• mitochondrial fragmentation

• production of ROS → oxidative stress

• prolonged damage leads to apoptosis

membrane damage

• inc permeability → necrosis

• damage due to inc ROS production, loss of ATP, and inc intracellular calcium

• mitochondrial membrane

  • formation of mitochondrial permeability transition pore (mPTP) → reduction of atp production due to loss of membrane potential and pH changes

• plasma membrane

  • loss of osmotic balance

  • influx of fluids and ions

  • loss of cellular contents

• lysosomal membranes

  • leakage of enzymes into cytosol and break down necessary cellular components

  • these enzymes only function at low pH

DNA damage

• exposure of cells to radiation or chemotherapeutic agents, intracellular generation of ROS, and acquisition of mutations may all induce DNA damage which may trigger apoptotic death

• basic mechanism of cancer

  • sentinel proteins detect DNA damage and transmit signals that lead to p53 accumulation

  • p53 causes cell cycle arrest for DNA to repair itself before replication

  • if DNA damage is excessive → p53 triggers apoptosis via mitochondrial intrinsic pathway

  • TP53 (gene for p53) is mutated in more than 50% of tumors

intracellular depositions

abnormal accumulations caused by dec removal and degradation or inc production of endogenous substance or deposition of abnormal exogenous material

• fatty change (steatosis)

  • abnormal accumulation of triglycerides within parenchymel cells; common in liver

    • cholesterol and cholesteryl esters → occur due to inc intake or dec catabolism of lipids; as seen in artherosclerosis

• proteins

  • caused by inc uptake or synthesis, misfolding, dec degradation

• glycogen

  • abnormalities in metabolism of glucose or glycogen

• pigments

  • colored substances that may be exogenous (carbon) or endogenous (melanin)

extracellular deposits

• pathologic calcification

  • dystrophic calcification

  • metastatic calcification

pathologic calcification

seen in a wide variety of disease states; result of abnormal deposition of calcium salts (fine white granules or clumps and gritty deposits)

dystrophic calcification

deposition of crystalline calcium phosphate in membrane bound vesicles

• found in areas of necrosis

• seen in plaques in atherosclerosis and necrotic cells in tuberculosis

• can cause dysfunction

• often incidental finding of past cell injury

metastatic calcification

associated w hypercalcemia; affects interstitial tissues of vasculature, kidneys, lungs, and gastric mucosa; does not cause clinical dysfunction

• inc secretion of parathyroid hormone

• destruction of bone

• high vit D levels

• renal failure

aging

progressive decline of physiologic, cellular, and molecular homeostatic mechanisms after the reproductive years

mechanisms of cellular aging

• DNA damage → mutations in mitochondrial and nuclear DNA accumulate w age and cause

  • telomere dysfunction and cellular senescence (proliferative arrest)

  • mitochondrial dysfunction

• specific signaling pathways → certain environmental stresses, such as calorie restriction, alter signaling pathways that influence aging, IGF-1, and mTOR signaling

• persistent inflammation → due to accumulation of damaged cell components

telomeres

short repeated sequences of DNA at ends of chromosomes

• ensure complete replication of chromosome ends

• protect chromosome ends from fusion and degradation

• progressively shortened w each division of somatic cells

• when completely eroded → cell cycle arrest

telomerase

maintains telomere length in germ cells and stem cells; but not somatic cells

• reactivated in many cancer cells

telomeropathies

inherited deficiencies in telomerase activity include aplastic anemia, pulmonary liver fibrosis, premature graying of hair, and characteristic changes in skin pigmentation and nails

mechanisms of cellular aging

• environmental and metabolic insults → (ROS) accumulation of mutations in DNA → (defective DNA repair) dec cell functions, cell loss

• telomere shortening → dec cellular respiration → cell loss

• abnormal protein homeostasis → dec proteins, damaged proteins → dec cell functions

• signaling pathways → (dec TOR, dec IGF signaling) altered transcription → dec cell functions

• persistent low-level inflammation → chronic diseases (atherosclerosis, type 2 diabetes)

slowing aging

• exercise and physical activity

• caloric restriction (30% dec in food intake without malnutrition or deprivation of essential nutrients)

• stress can accelerate aging

necrosis characteristics

• cell size

  • enlarged

• nucleus

  • variable fragmentation and condensation

  • nuclear membrane rupture

• plasma membrane

  • disrupted

• cellular contents

  • enzymatic digestion

  • may leak out of cell

• adjacent inflammation

  • frequent

• physiologic/pathologic role

  • invariably pathologic

• always pathologic

apoptosis characteristics

• cell size

  • reduced

• nucleus

  • chromatin condensation and DNA fragmentation into nucleosome-sized fragments

  • nuclear fragmentation into membrane-bound apoptotic bodies

• plasma membrane

  • intact

  • altered structure, especially orientation of lipids

• cellular contents

  • intact

  • may be released in apoptotic bodies

• adjacent inflammation

  • absent

• physiologic/pathologic role

  • often physiologic

  • means of eliminating unnecessary cells

  • may be pathologic

necrosis cellular morphology

• cytoplasmic changes

  • glassy, homogenous appearance

  • vacuolated cytoplasm

  • breakdown of plasma and organelle membranes → everything spills out

  • swelling (dilation) of mitochondria w large amorphous deposits

  • disruption of lysosomes; enzymes spill out and break things down in cell

  • intracytoplasmic myelin (shape around them) figure; deposition of phospholipids

• nuclear changes

  • breakdown of DNA and chromatin

  • pyknosis

  • karyorrhexis

  • karyolysis

pyknosis

DNA condensation and nuclear shrinkage

karyorrhexis

fragmentation

karyolysis

digestion of DNA

apoptosis cellular morphology

• allows regulation without post-death response

• programmed pathway

• cells degrade their own DNA and proteins causing cellular and nuclear fragmentation and chromatin condensation

• membrane blebs

• intact plasma membrane

• no inflammatory reaction (bc fragments are cleaned up)

membrane blebs

fragments of apoptotic cells break off and form apoptotic bodies; membrane-bound fragments

apoptosis conditions and mechanisms

• physiologic

  • during normal development of organism

  • highly proliferative and hormone-responsive tissues undergo cycles

  • determined by levels of growth factors of survival signals

  • immune system - apoptosis removes excess leukocytes, B lymphocytes in germinal centers, and lymphocytes that recognize self antigens

• pathologic

  • eliminates cells w certain types of irreparable damage

  • ex: severe DNA damage after exposure to radiation and cytotoxic drugs

  • infectious agents, specifically some viruses

mitochondrial (intrinsic) pathway

• most physiologic and pathologic situations

• permeability is controlled by Bcl-2 proteins (some are pro-apoptotic and some are anti-)

• release of pro-apoptotic proteins from mitochondria

• cytosolic cytochrome-c leads to activation of caspase cascade

1. environmental conditions releases BH3-only proteins

2. causes release of BCL-2 family effectors

3. BAX/BAK dimerize to form channel

4. cytochrome c (inside intermembranous space of mitochondria) and other proapoptotic proteins released from channel into cytosol

5. activate caspase-9

Extrinsic (death receptor) pathway

• controlled by death receptors (TNF receptor family and Fas)

• when ligand binds, receptors cross-link via death domain and bind adapter proteins

• leads to activation of caspase cascade

1. external signal causes cross-link between Fas and FasL

2. Fas binds to adaptor protein

3. activates caspase-8

caspase cascade

• procaspase —> caspase (cut up to activate and activates other enzymes)

• degradation of cellular proteins and nuclear fragmentation

• apoptotic cells recruit phagocytes that clearance of apoptotic bdoies

• no inflammatory response

1. caspase activates enzymes (incl endonuclease)

2. causes nuclear fragmentation

3. causes breakdown of proteins and cytoskeelton

4. causes secretion of soluble factors by apoptotic cells

5. membrane alteration and formation of “eat me” signals for phagocytes

pyroptosis

mediated by the inflammasome

necroptosis

induced by TNF w necrotic and apoptotic features

ferroptosis

dependent of cellular iron levels

autophagy

• self-eating

• lysosomal digestion of a cell’s own components

• recycling mechanism during nutrient deprivation; allows a starved cell to survive

• autophagosome fuses w lysosome where enzymes digest cellular components

• can trigger apoptosis if too severe

autophagosome formation

1. nutrient depletion causes cytoplasmic sensors to initiate creation of Atg proteins

2. elongates and matures into autophagosome

3. fuses w enzymes from lysosome and enzymes digest cellular components

hypoxia/ischemia —>

necrosis

• radiation, other injurious agents —> [mitochondria] dec E and inc ROS —> dec E-dependent functions and inc damage to lipids, proteins, nucleic acids —> cell injury —> necrosis

ROS —>

necrosis

• ROS, other injurious agents → [cell membranes] damage to lysosomal membranes and plasma membranes —> leakage of enzymes and impaired transport functions, leakage of cell contents —> necrosis

DNA damage —>

apoptosis

• radiation mutations —> [nucleus] DNA damage —> cell cycle arrest OR activation of BH3-only sensors —> apoptosis

ER stress —>

apoptosis

• mutations, cell stress, infections —> [ER] accumulation of misfolded proteins —> unfolded protein response OR —> apoptosis

• injury and death are a continuum

• changes in function are only apparent wayy after cell function starts degrading

• need to find markers where dysfunction exists but isn’t fully shown to make it reversible

hypoxia

• low oxygen levels

• blood flow is maintained

• anaerobic metabolism ONLY

ischemia

• reduced or blocked blood flow

• NO anaerobic metabolism

• causes more rapid and severe cell and tissue injury

hypoxia and ischemia

• cells activate compensatory mechanisms to help it survive —> reversible adaptations

• ex: inc growth factors, stimulate uptake of glucose

• persistent conditions lead to depletion of ATP

  • failure of plasma membrane Na/K pump

  • dec of intracellular pH → changes activity of enzymes

  • inc ROS production

  • reduction in protein synthesis

  • ER swelling, membrane damage, mitochondrial damage

  • inflammation is triggered

• severe conditions leads to necrosis

ischemia-reperfusion injury

• restoration of blood flow to ischemic but viable tissues results in inc cell injury and necrosis

• contributes to tissue damage esp after stroke

• inc ROS production during reoxygenation → too much too soon as they adapted to low O2 conditions

• influx of calcium disrupts calcium homeostasis

• inflammation-induced by ischemic injury may inc w reperfusion due to influx and activation of leukocytes

direct-acting cell injury

caused by toxins and toxicants; combine directly to cellular proteins or organelles

• ex:

  • mercury poisoning from seafood

    • mercury binds to cell membrane proteins, inhibiting ATP-dependent transport and inc membrane permeability

  • chemotherapy drugs

    • directly damage DNA to induce cell death

latent cell injury

caused by toxins and toxicants; chemical must be converted to a reactive metabolite that acts on target cells to exert toxic effect, usually by cytochrome p450 in the liver

• ex:

  • acetaminophen poisoning

    • high doses saturate metabolic pathways leading to the production of a highly hepatotoxic metabolite

L2

human genome

• 3.3 billion DNA base pairs

• 22 pairs of autosomes, 1 pair of sex chromosomes

• 85% of genome is transcribed into RNA (not all goes to protein)

• 80% of genome is devoted to regulation of gene expression

non-protein coding sequences

• promoters and enhancers

• non-coding regulatory RNAs

• transposons

• telomeres and centromeres

promoters and enhancers

• bind transcription factors

• binding sites for DNA-binding proteins that organize and maintain chromatin structure

non-coding regulatory RNAs

genes that are transcribed but not translated

• includes microRNAs, long non-coding RNAs

transposons

mobile genetic elements; “jumping genes”

telomeres and centromeres

structural regions of DNA

epigenetic mechanisms

stably but reversibly control gene expression without changing the sequence; mimic a mutation

• covalent modifications of DNA

  • 5-methylcytosine (cancer)

  • 5-hydroxymethylcytosine

• post-translational modifications of histones

• 3D chromatin structure

• important in cancer

single nucleotide polymorphisms (SNPs)

variants at single nucleotide positions in coding and non-coding regions

• non-coding SNPs → may alter regulation of gene expression

• coding SNPs → may change the sequence of a protein

• neutral SNPs → have no effect on gene function or phenotype; can be used as biomarkers

• wide variation of frequency amongst diff populations

• weak disease susceptibility due to individual SNPs

copy number variations (CNVs)

variation in number of large continuous stretches of DNA

• abt 50% of CNVs involve coding sequences

• ex: duplications, triplications, deletions, inversions

mutations in protein-coding genes

permanent changes in DNA sequence

• point mutations

• frameshift mutations

• trinucleotide repeat mutations

• structural variations

point mutations

substitution of a single nucleotide base by a diff base

missense point mutation

changes an amino acid

nonsense point mutation

creates a stop coding

frameshift mutation

insertion or deletion of 1-2 base pairs alters the reading frame of DNA strand

trinucleotide repeat mutation

amplification of repeated sequence of 3 bases

• causes lower protein expression

structural variations

genomic rearrangement leads to amplifications, deletions, or translocations of chromosomal segments

• single genes to entire chromosomes

• intra- or inter-chromosomal

• cause CNVs → linked to higher risk of disorder

gene editing (CRISPR)

• clustered regularly interspaced short palindromic repeats

• form of bacterial immunity

• uses artificial guide RNAs that target a DNA sequence of interest to introduce mutations

• first CRISPR/Cas9 based therapy approved in 12/2023 for sickle cell disease

epigenetic and genetic mechanisms in cancer

• inactivation of tumor suppressor genes (promoter hypermethylation)

• activation of oncogenes (promoter demethylation)

genetic disorders

• disease-causing mutations

  • mendelian disorders

  • cytogenetic diseases

  • non-mendelian genetic diseases

• disease-associated mutations

  • complex disorders

mendelian disorders

result from mutation in single genes

• hereditary

• high penetrance

• show phenotypic effects

cytogenetic diseases

arise from changes in chromosomal number or structure

ex: CML, down syndrome

non-mendelian genetic diseases

arise from single gene mutations w atypical pattern of expression

ex: trinucleotide repeat, mitochondrial DNA disorder

complex disorders

involve multiple genes as well as environmental influences

• affect risk of disease

• very common

• do not cause disease on their own

• ex: hypertension

autosomal dominant

one copy is sufficient to cause disease, disease manifests in heterozygous state

• does not skip a generation

• affected offspring have affected parents

• male and female offspring are equally likely to be affected

autosomal recessive

two copies are needed to cause disease, disease manifests in homozygous state

• typically skips a generation

• affected offspring may have unaffected parents

• male and female offspring are equally likely to be affected

sex-linked

most are X-linked

• heterozygous females can transmit only to sons

• daughters may be carriers

• affected males cannot transmit the disorder to sons

pleiotropy

a single gene mutation has many phenotypic effects

genetic heterogeneity

multiple genes cause the same trait

penetrance

the proportion of individuals w the mutation that exhibit clinical symptoms among all individuals w such mutation

• incomplete penetrance → BRCA1 mutations