Organelle-Based Diseases: A Deep Dive PDF

Introduction to Cell Biology & Biochemistry Foundations of Cell Biology Organelle-based diseases Dr. Andrea Knight @Kightleys  Learning Objectives Discuss the genetic origins of a range of organelle-based diseases Revie...

Introduction to Cell Biology & Biochemistry Foundations of Cell Biology Organelle-based diseases Dr. Andrea Knight @Kightleys  Learning Objectives Discuss the genetic origins of a range of organelle-based diseases Review exemplar diseases of different organelles in the cell Relate changes in protein structure and function to the pathology of organelle-based diseases Discuss possible interventions as therapies for the discussed diseases  Organelle-Based Diseases Nuclear Envelope: Cytoplasm: Progeria Sickle cell anaemia Emery-Dreifuss muscular dystrophy Endoplasmic Reticulum: Lysosome: Phenylketonuria (PKU) Lysosomal storage diseases Endoplasmic storage disease Tay-Sachs Hurler Syndrome Niemann-Pick Pompe Disease Plasma Membrane: Cystic Fibrosis (CF) Cytoskeleton: Hereditary spherocytosis Epidermolysis bullosa Muscular dystrophy Golgi Apparatus: Congenital disorders of Mitochondria: glycosylation Leigh Syndrome Alzheimer’s disease MELAS Adapted from DOI: 10.1016/j.jddst.2020.102315  Genetic Disease Chromosomal: underpinned by changes in chromosome structure or number Monogenic: underpinned by mutation within a single gene Dominant Recessive X-linked Polygenic: underpinned by the combined impact of mutations within multiple genes wikicommons  Chromosomal Abnormalities Aneuploidy: deviation from normal number of chromosomes resulting in loss or gain of chromosomes. Usually occurs as a result of non-disjunction during meiosis Downs Syndrome: Trisomy 21 Turner Syndrome: Monosomy X Deletion: involves loss of a chromosome segment resulting in monosomy for a group of genes encoded by the lost segment Duplication: involves an additional copy of a chromosome segment resulting Deletion Duplication Inversion in trisomy for a group of genes encoded by the extra segment Inversion: is caused by a break at two different sites on one chromosome followed by the inverted recombination of the segment Translocation Ring Chromosome Insertion: section of one chromosome is inserted into another chromosome Translocation: exchange of material between chromosomes Kort BR Ch16 in Clinical & Translational Science 2nd Ed Ring chromosome: caused by breaks in the chromosome followed by recombination into a ring structure  Germline vs. Somatic Mutations www.genomicseducation.hee.nhs.uk SNPs vs. Point Mutations Point Mutation Germline or somatic substitution, insertion, or deletion of a single nucleotide at a specific location within the genome where the variant is rare within the population (1%) within the population Hereditary: able to be passed from parent to offspring Can occur in coding or non-coding regions / once in every 300 nucleotides there are ~ 10 million SNPs in the human genome https://www.ncbi.nlm.nih.gov/snp/ Linked SNPs: do not reside within genes do not affect protein function do correspond to a particular drug response or to the risk for getting a certain disease Causative SNPs: affect the protein functions correlating with a disease or influencing a person's response to medication missense= changing the aa nonsense= creates a stopcodon Extensively studied in: forensic analysis (DNA profiling) mapping disease genes Parkinson, Alzeimer, diabetes, schizophrenia inheritance of disease genes in the family as predictive markers of effectiveness to drugs  Sickle Cell Anaemia Caused by a SNP in HBB gene resulting in a missense mutation in β-globin Estimated that 7% of world's population (~420 million) are carriers β-globin Glu → Val (S allele) causes the haemoglobin subunits to clump in long inflexible chains WT β-globin (A allele) forms normal heterotetrametric protein Homozygous SS allele individuals the clustering of the mutant β-globin into long inflexible chains causes the red blood cells to have a sickle shape Cells are rigid and stick to walls of the blood vessels causing clots Sickle cells prone to lysis and causes anaemia due rate of lysis Pain, fatigue, higher risk of stroke, frequent infections Heterozygous AS allele individuals have ‘sickle cell trait’ that gives them partial protection (50 – 90%) against Plasmodium falciparum infection sicklecell.com  Mutations Affecting Protein Function Missense Mutation: DNA nucleotide change results in a codon that encodes for a different amino acid at that position Nonsense Mutation: DNA nucleotide change results in a codon that encodes for a stop codon at a position that would normally encode for an amino acid Frameshift Mutation: Insertion or deletion of a DNA nucleotide results in a shift of the reading frame, therefore all codons downstream of the frameshift mutation encode for different amino acids www.genome.gov/genetics-glossary  Mutations Affecting Gene Expression Silent or synonymous mutation: DNA nucleotide change results in a codon that encodes for the same amino acid at that position Altered codon usage Change in translation speed Altered protein folding Altered splice site (exon boundary) Mutations within non-coding regions: Altered structure of enhancer/promoter regions Altered binding of transcription factors Altered post-transcriptional processing Altered exon/intron splicing Altered mRNA stability 3’ and 5’ UTR miRNA binding sites (gene silencing) DOI: 10.1186/s12859-020-03695-z Typical Consequences of Genetic Disease Gene Defect Abnormal function of: Protein Defect Enzymes Altered expression Receptors Structural proteins Signalling molecules Transcription factors Regulatory proteins Altered Chemistry Splicing factors Clinical Symptoms  The Cytoskeleton The cytoskeleton is the network of filaments and tubules that enable the spatial and mechanical functions of a cell Cells need to: Organise and rearrange their intracellular compartments Actin filaments: pink Carry out coordinated movements Microtubules: green Nucleus: blue @cytoskeletown Adopt the correct shape Interact mechanically with the environment & other cells Be physically robust Cytoskeleton components share fundamental features but differ in their mechanical properties, dynamics and biological roles. McCance & Huether Pathophysiology: the biologic basis for disease in adults and children, 5th Ed.  Hereditary Spherocytosis Caused by one or more mutations in: Spectrin (⍺ and β) Ankyrin Band-3 Band-4.2 Prevents proper tethering of the cytoskeleton to the plasma membrane RBCs adopt a spherical shape and are more prone to mechanical and osmotic stress resulting in lysis Symptoms: Anaemia and fatigue Jaundice Splenomegaly Affects 1:2000 people of Northern European ancestry DOI: 10..1056/NEJMcps1701742  Epidermolysis Bullosa (EB) Can be caused in either an autosomal dominant or autosomal recessive manner depending on the gene involved: Collagen VII Desmoplakin Keratin 5/14 Plakoglobin Plectin Laminin332 Bullous pemphigoid antigen 1e Collagen X Kindlin-1 Collagen VII Plakophilin-1 EB simplex (keratin): blisters form due to a failure in keratinisation that affects the integrity of the skin and the ability to withstand mechanical stress Junctional EB (laminin & collagen): blister formation at basement membranes, particularly affects the hands and feet Treatments include: pain killers, antibiotics, wound dressings  Muscular Dystrophies There are over 30 different muscular dystrophies which result in progressive weakness and breakdown of the skeletal muscles Can be recessive X-linked autosomal recessive or autosomal dominant depending on the gene/s affected Duchenne muscular dystrophy (DMD) accounts for ~50% of all muscular dystrophies Caused by loss-of-function of dystrophin Dystrophin encoded by DMD gene located at Xp21 X-linked recessive disorder No cure and treatments aim to limit symptoms and maximise quality of life: Steroids for short-term improvement in muscle strength Respiratory support Pacemaker to treat cardiac symptoms Life expectancy average is 26, some survival to 30-40 years of age is possible The Nuclear Envelope Double membraned nuclear envelope Two lipid bilayers: inner and outer separated by the perinuclear space The outer membrane is continuous with the rough endoplasmic reticulum and both are covered with ribosomes The inner membrane is associated with heterochromatin and the nuclear lamina Nuclear pore complexes form channels through the nuclear envelope Nucleoplasm is the term given to the internal nucleus that is not the nucleolus  Emery-Dreifuss Muscular Dystrophy Majority of cases of Emery-Dreifuss MD are caused by loss-of-function of either lamin or emerin proteins Emerin is an integral protein of the inner nuclear membrane Lamin are intermediate filaments that form a large proportion of the nuclear lamina and anchor to emerin wikicommons Emerin is encoded by the X-chromosome EDMD affects the skeletal and cardiac muscles causing contractures, atrophy, and eventually weakness No cure, treatment involves managing symptoms: Orthopaedic surgery to manage contractures and scoliosis Pacemakers and beta-blockers to manage cardiac symptoms  Progeria Also known as Hutchinson-Gilford syndrome caused by loss-of-function mutations within LMNA gene that encodes for lamin Mutations involved in progeria are different to those of EDMD, thus affect the resultant protein in different ways Mutations involved in Progeria result in abnormal processing of prelamin A WT LMNA to lamin A Prelamin A accumulates on the nuclear envelope causing nuclear blebbing Progeria is associated with premature aging and people born with Progeria do not survive past the age of 20 wikicommons Mut LMNA  Endoplasmic Reticulum Extracellular Nucleus DOI: 10.1364/OPTICA.3.000667 Network of membranes that penetrate much of cytoplasm Rough (RER) continuous with the nuclear envelope Smooth (SER) - connected and continuous with RER Distinct in terms of structure and function Rough ER: studded with ribosomes and is a site of protein synthesis Smooth ER: lipid, steroid synthesis; metabolic role in detoxification  Phenylketonuria Phenylketonuria (PKU) is caused by reduced function (or lack) of the enzyme phenylalanine hydroxylase Phenylalanine hydroxylase encoded by PAH gene Located on chr. 12, encoded by 13 exons (>1282 variants identified) Missense mutations, nonsense, Frameshift (insertions and deletions) Tetrameric enzyme catalyses the metabolism of phenylalanine to tyrosine Excessive amounts of phenylalanine is neurotoxic Inheritance pattern: Autosomal recessive Symptoms (if left untreated): Intellectual disability Seizures Mental disorders Microcephaly Prevention/Treatment: Neonatal screening programmes Elimination of foods high in Phe from the diet Specialised nutritional supplementation  Lysosomes Acidic membrane-bound organelles that contain enzymes that degrade proteins, nucleic acids, polysaccharides, and lipids  Lysosomal Storage Diseases Arise through enzyme deficiencies that inhibit the ability of lysosomes to break down particular cellular components, resulting in the processive accumulation of substrates over time Tay-Sachs Disease caused by mutation in HEXA gene that encodes the enzyme beta-hexominidase A Accumulation of GM2 ganglioside in neurons of brain and spinal cord Symptoms include: seizures, vision loss, muscle weakness, tremors, loss of mental functions Pompe Disease caused by mutation in GAA gene that encodes the enzyme acid alpha glucosidase Accumulation of glycogen within muscles Symptoms include: muscle weakness leading to problems with movement, difficulty breathing, heart failure Mitochondria Double membraned organelle Inner membrane and outer membrane separated by intermembrane space Enables compartmentalisation → generation of proton gradients essential for ATP production Cristae: folds within the inner membrane → provides large surface area → increased capacity for ATP production Matrix: internal space that contains DNA, ribosomes, enzymes used for energy production Mitochondrial DNA: circular chromosome separate to the DNA found in the nucleus  Leigh Syndrome Neurometabolic disorder as progressive loss of muscle function Difficulty swallowing and failure to thrive MT-ATP6 Weak muscle tone and involuntary contractions Neurological symptoms Involuntary eye movements Optic nerve atrophy Peripheral neuropathy Mutation in mtDNA gene MT-ATP6 which encodes for ATP synthase membrane unit 6 MT-ATP6 vital component of the proton channel DOI:10.3389/fgene.2021.698825 Mutation in nuclear gene COX which encodes for cytochrome c oxidase COX COX vital component of the electron transport chain  MELAS Mitochondrial Encephalopathy, Lactic Acidosis, and Stroke-like episodes (MELAS) Caused by mutations in genes encoded by mtDNA MT-ND1 and MT-ND5: encode parts of the NADH dehydrogenase enzyme MT-TH, MT-TL1, MT-TV: encode for mitochondrial specific transfer RNAs  Plasma Membrane Semi-permeable membrane that forms the principal barrier of the cell Alberts et al Essential Cell Biology 5th Edition  Cystic Fibrosis Cystic Fibrosis is caused by dysfunctional chloride channels Mutations in the CFTR gene G551D prevents correct channel opening F508del produces a truncated protein resulting in fewer functional channels at the cell surface No movement of Cl- resulting in thick sticky mucous through unrestrained Na+ absorption resulting in dehydration of the mucous layer DOI: 10.1038/482145a Alberts et al Essential Cell Biology 5th Edition  Organelle-Based Diseases Nuclear Envelope: Cytoplasm: Progeria Sickle cell anaemia Emery-Dreifuss muscular dystrophy Endoplasmic Reticulum: Lysosome: Phenylketonuria (PKU) Lysosomal storage diseases Endoplasmic storage disease Tay-Sachs Hurler Syndrome Niemann-Pick Pompe Disease Plasma Membrane: Cystic Fibrosis (CF) Cytoskeleton: Hereditary spherocytosis Epidermolysis bullosa Muscular dystrophy Golgi Apparatus: Congenital disorders of Mitochondria: glycosylation Leigh Syndrome Alzheimer’s disease MELAS Adapted from DOI: 10.1016/j.jddst.2020.102315  Learning Objectives Discuss the genetic origins of a range of organelle-based diseases Review exemplar diseases of different organelles in the cell Relate changes in protein structure and function to the pathology of organelle-based diseases Discuss possible interventions as therapies for the discussed diseases Discussion Question: Why have we spent the last 10 weeks learning the basic details of how the various compartments of the cell function? Questions?