Path Exam 2 Notes PDF

Saturday, November 16, 2024 Path Exam 2 Notes Week 1 - Human genome 23 pairs of chromosomes - Diploid - 3 billion base pairs of DNA - ~20000 protein coding genes - Central dogma DNA replication —(transcription)—> RNA —(translation)—...

Saturday, November 16, 2024 Path Exam 2 Notes Week 1 - Human genome 23 pairs of chromosomes - Diploid - 3 billion base pairs of DNA - ~20000 protein coding genes - Central dogma DNA replication —(transcription)—> RNA —(translation)—> protein - Chromosome aneuploidy Loss or gain of individual chromosomes - Structural variation Abnormally formed chromosome - Translocation Chromosome segments swapped with one another - May be balanced/reciprocal or unbalanced Results in gain and or loss of genomic material Variants - Robertsonian translocation Breakage at the centrosome and infusion gives a hybrid chromosome - Long chromosome - During pregnancy which 1   gives rise to abnormal gametes and can lead to miscarriages or infertility in males - Isochromosomes Centromere divided horizontally with 2 Q’s 2 arms are the same - Ring chromosome May form after deletions of both ends of a chromosome - Inversion Segment of a chromosome is in an inverted orientation - Copy number variant Deletion - Loss of a portion of a chromosome Gain - Gain of a portion of a chromosome Duplication Ampli cation - Multiple copies of a portion of chromosome Most commonly in neoplasia - Chromosomal rearrangements Structural chromosome changes - Translocations - Inversions - Insertions - Deletions - Duplications - Ring chromosomes 2  fi  Aneuploidy - Occurs when 1 of the chromosomes is present in an abnormal number of copies - Trisomy Three copies of any chromosome 2n + 1 - Monosomy A single copy of any chromosome 2n -1 Polyploidy - Involve 3n or 4n chromosomes or some exact multiple of the haploid chromosome number - Genomic abnormalities Deletion Duplication Inversion Insertion/substitution Translocation Sequence variants - DNA break Double strand Blunt ends/sticky ends - Fast repairs no abnormalities - If no repair Structural rearrangements Terminal deletion at end if single stranded break 3   Interstitial deletion - Double stranded break Terminal deletion - Double stranded break - Ring chromosomes Double stranded break - Balanced variants Inversion Reciprocal translocation - Unbalanced variants Insertion Deletion Non reciprocal translocation Tandem duplication Dispersed duplication - Deletions Terminal Seen at chromosome level - Cri du chat (5p15) - Wolf-hirschhorn (4p36) Interstitial Not seen at chromosome level - Williams (7q11.2) Micro deletion (FISH) - Retinoblastoma (13q14) - Prader-willi (15q11.2) 4   - Angelman (15q11.2) - Digeorge (22q11.2) - Double minutes and homogeneously staining regions are the cytogenetic hallmarks of genomic ampli cation in cancer - Di erent mechanisms have been proposed to explain their genesis - Cytogenetics Chromosome abnormalities - Aneuploidies - Structural variants Week 2 - Molecular genetics Sequence variants Copy number variants - Karyotype analysis Requires cell culture to stimulate cells to divide Arrest cells in metaphase - Longer chromosomes - Increased resolution Identify metaphases Cut out individual chromosomes Align in pairs Look for abnormalities Resolution - 5-10 million base pairs (5-10Mb) Smaller changes can be missed 5  ff fi  Breakpoints are approximate - Cant evaluate gene content near breakpoint Indications - Suspect aneuploidy - Family history of structural variant - Hematological malignancies - Numerical x structural - Karyotype Representation of entire metaphase chromosomes in a cell arranged in order of size and structure -Diagnosis examples 6   - Fluorescence in situ hybridization Targeted analysis need probe for speci c region/abnormality Recurrent CNV detection, fusion or CNV detection in neoplasia are indications Metaphase FISH - Requires culture - Visualize probe on chromosomes - Identify location Interphase FISH - Direct analysis - Count number of signals - Enumerate target - FISHing for Ewing sarcoma Paediatric small round cell tumours - Begin as a growth of cells in the bones and the soft tissue around the bones and the soft tissue around the bones 5 year survival Translocation resulting in gene fusion EWS/ FLI1 - t(11;22)(q24;q12) - Diagnostics 7  fi  ~90% of Ewing sarcomas Results in oncogenic EWS/FLI fusion protein FISH is most e cient diagnostic assay - Chromosomal microarray (CMA) Two types - Array comparative genomic hybridization (aCGH) - SNP microarrays Can determine more precise breakpoints and gene content Doesn’t tell us about the structure of the chromosome Can nd unbalanced changes - Chromosomal aneuploidies - Copy number variants - Doesn’t detect translocations Inversions Sequence variants Copy number of millions of loci across genome compared to controls High density coverage over genes - Platform speci c Identi cations - First tier test for children with multiple congenital anomalies and/or developmental delays - Oncology for prognostic CNVs 8  fi fi fi ffi  -Immune system The body’s defence mechanism against microorganisms and their products (toxins) - Innate immunity Born with Not speci c Does not require previous exposure to an antigen/stimulant Epithelial barriers - Skin - Mucosal surfaces Phagocytes - Neutrophils - Macrophages - Recognize microbes via toll-like receptors Natural killer cells - Recognize and destroy virus-infected cells as well as other damaged cells and tumor cells Damaged cells/tumour cells may not express normal MHCI, and NK cells will destroy them 9  fi  Damaged/stressed cells may bind to activating receptors on NK cells - Have innate ability to lyse viral infected cells and tumor cells without previous sensitization - Recognize self via MHC class I molecules Expressed on normal healthy cells Inhibitory signals Complement system - Adaptive immunity Acquired Speci c and requires previous exposure to a stimulant Lymphocytes - B cells - T cells Antigen presenting cells - Dendritic cells - Macrophages Human major histocompatibility complex - Complete system Recognition - Normal self - Altered or injured self 10  fi  - Non self (foreign) Speci city - Ability to inactivate, destroy, and remove invaders without harming self Regulation - Type - Duration - Intensity of reaction Ampli cation - Synergistic reactions between systems to reach optimal e ect Memory - Remember the rst exposure and accelerate reaction on second exposure Hormonal immunity - Antibody immunoglobulin mediated Targets extracellular microbes - Antibodies are produced by plasma cells and are speci cally directed against a particular antigen - Antibodies can neutralize microbes Promote their phagocytosis and destruction Activated the complement system Cell mediated immunity - Reaction of T cells to attack cell associated microbes T lymphocytes - Originate from primitive stem cells Yolk sac in the embryo and in the bone marrow after birth - Mature in the thymus - Di erentiate into helper/inducer cells (CD4) 11  ff fi fi fi fi ff  Help other cell types to defend - B cells - Macrophages Suppressor/cytotoxic cells (CD8) - Direct killing of infected cells - Constitute 60-70% of peripheral blood lymphocytes - Programmed to recognize antigen by antigen speci c T cell receptor - TCR are linked to cluster of polypeptide chains called CD3 complex Doesn’t directly bind antigen but involved in transduction of signals to T cells - Helper T cell production IFN gamma - Stimulates B cells to produce Ig and activates macrophages IL2 - Stimulates proliferation of T cells Utilize CD40 ligand to stimulate macrophages to produce microbicidal substance - Utilize to activate B cells - APCs Antigen presenting cells - Dendritic cells Phagocytic cells - Preserve antigens for potential presentation Have cytoplasmic processes with which to capture antigens Express MHC II and T cell co stimulatory molecules Can also display antigen via MHC I - Macrophages 12  fi  Phagocytic cells Display peptides via MHC II for T cell recognition - B cells Also display peptides via MHC II for T cell recognition - Major histocompatibility complex (MHC) Highly pleomorphic membrane proteins derived from the human leukocyte antigen complex (HLA) - Cluster of genes on chromosome 6 Three major classes I-III - MHC I Present on all nucleated cells and recognized by cytotoxic T cells - Also by NK cells Mostly bind peptide antigen derived from intracellular proteins for display to cytotoxic T cells - MHC II Expressed on antigen presenting cells and B cells for display to helper T cells Mostly bind peptide antigen derived from extracellular bacteria - MHC III Not part of peptide display system Extracellular portion binds antigen for presentation to T cells (I and II only) - B lymphocytes Originate from primitive stem cell 13   - Yolk sac in the embryo and bone marrow after birth Reach full maturation in bone marrow Migrate into peripheral blood and lymphoid tissue Constitute 10-20% peripheral blood lymphocytes Recognize antigens via B cell antigen receptor complex which includes a speci c immunoglobulin Can recognize peptides, lipids, polysaccharides, nucleic acids in their native conformations Diversity of antibodies is generated via somatic Ig gene rearrangements T cells activate B cells via CD40 - Induces isotope switching of antibody class to allow diversity of antibody function - Promote a nity maturation Production of antibodies with greater a nity for an antigen When stimulated di erentiate into plasma cells Plasma cells secrete large amount of immunoglobulin - Immunoglobulins Neutralize microbes and toxins Damage cells using complement system Facilitate phagocytosis by macrophages or neutrophils Facilitate killing cells by antibody 14  ffi ff fi ffi  dependent cell mediated cytotoxicity by NK cells - IgM/A/G/D/E IgM - First produced in response to infection - Found in blood and lymphatic uid - Activate complement IgA - Found in mucosal areas - Protects mucosal surfaces by preventing pathogens from adhering to cells IgD - Found in small amounts in the blood - Plays role in initiating B cell activation IgE - Involved in allergic responses and defence against parasitic infections - Binds to allergens and triggers the release of histamine from mast cells an basophils - Coats various parasites to target them for destruction by mast cells and eosinophils IgG is the only Ig capable of crossing the placenta - Protecting the infant during maturation of the immune system - Opsonize microbes to target them from phagocytosis - Activate complement 15  fl  - Cross the placenta to protect the fetus and neonate - Tissues of immune system Primary lymphoid organs - Where lymphoid cells originate and mature Bone marrow Thymus Secondary lymphoid organs - Peripheral Organized to maximize interaction between lymphocytes, antigen presenting cells, and to capture antigen - Lymph nodes Sample lymph - Spleen Sample blood - Mucosal, cutaneous lymphoid tissues Surveillance against breaches of epithelia - Hypersensitivity reaction Excessive or pathological reaction of the immune system - Immune response might not be adequately controlled - Inappropriately targeted against self tissue - Results in tissue damage Causes - Loss of self tolerance Autoimmune disease - Excessive reaction to microbes and cross reaction with microbial products - Reactions to environmental antigens 16   Subtypes - Humoral (antibody mediated ) Type I - IgE mediated - Allergy Immediate reaction occurring within minutes after interaction of the antigen and IgE bound to mast cells Late reaction causes tissue damage May result in an anaphylactic reaction leading to shock and death if not treated immediately Degranulation of mast cells - Histamine —> vasodilation —> increase vascular permeability, smooth muscle contraction, and increase in mucus secretion - Adenosine —> bronchoconstriction and inhibition of platelet aggregation - Chemotactic factors for neutrophils and eosinophils Production of lipid mediators - Prostaglandins and leukotrienes Severe bronchospasm Most potent vasoactive and spasmogenic agents Increased mucin production Cytokine production - TNF, IL4/5/13 Recruit and activated leukocytes Important in ampli cation of response and in late phase reaction 17  fi  Type II - Antibody mediated - Antibodies directed against target antigens xed on cell surfaces or other tissue components - Antigens may be normal molecules intrinsic to cell membranes or adsorbed exogenous antigens Examples - Autoimmune hemolytic anemia - Autoimmune thrombocytopenic purpura - Graves disease Antibodies against thyroid stimulating hormone receptor - Stimulate thyroid epithelial cells to secrete thyroid hormones - Hyperthyroidism - Myasthenia gravis 18  fi  Antibodies against acetylcholine receptors inhibit neuromuscular transmission - Opsonization and phagocytosis - Complement activation and tissue in ammation Cell lysis - Antibody mediated cellular dysfunction Type III - Immune complex mediated - Antigen and antibody complexes are formed in the circulation - Complement activation and acute in ammation - Exogenous antigens Microbial proteins - Endogenous antigens Nucleoproteins - Antigen/antibody complexes deposit in blood vessels and surrounding connective tissues Some organs and joints - e.g SLE, PAN, PSG Type IV - T cell mediated - Cellular reactions Delayed type hypersensitivity initiated by CD4 T cells - Cytokine mediated - Tuberculin reaction 19  fl fl  CD4 T cells recognize an antigen presented on antigen presenting cell in associated with class II MHC Memory CD4 cells will be recruited upon second exposure along with macrophages Cytokines are produced which increases vascular permeability, brin deposition, and in ammation Prolonged reaction causes the formation of a granuloma - T cell mediated cytotoxicity mediated by CD8 cells CD8 T cells kill antigen bearing target cells Antigen presenting cells with MHC class I will stimulate cytotoxic T lymphocytes Killing mechanism is dependent on perforin-granzyme system Involved in solid organ transplant rejection May be involved in type I diabetes - Autoimmunity Failure of self tolerance - Central tolerance is programmed death of self reactive T cells and B cells during their maturation in the thymus and bone marrow respectively Thymic APCs present processed self antigen to immature T cells Most T cells that recognize self antigen undergo apoptosis - Some survive to become regulatory T cells B cells recognize self antigen may undergo apoptosis or receptor editing 20  fl fi  - Peripheral tolerance is the inactivation or deletion of self reactive lymphocytes in the peripheral blood and tissues Anergy - Functional inactivation or failure to respond - Both B and T cells Suppression by regulatory suppressor T cells - Immunosuppressive cytokine production Apoptosis - Both B and T cells may undergo apoptosis when recognizing self antigen Factors - Genetic susceptibility Family associations Speci c HLA allele associations Genetic polymorphisms linked to AI disease - Infections Some infections may trigger AI disease Cross reaction of epitopes with self antigens Tissue damage results in up regulation of APC co stimulatory molecules - Tissue injury 21  fi  - Gender Women > men - Environmental exposures UV radiation Smoking - SLE Systemic lupus erythematosus - Multi-system disease Acute or chronic - F/M = 9/1 - 1/700 in child bearing age - A ects joints, kidney, heart, serial membranes Failure of self tolerance Results in production of autoantibodies - Anti nuclear antibodies Anti DNA Anti histones Anti nucleolar antigens - Antibodies against blood cells Anemia Thrombocytopenia - Anti phospholipid antibodies Blood clotting abnormalities Immune complex formation results in organ and skin damage - Type III hypersensitivity - Immune complex deposition and complement activation 22  ff  Opsonization and phagocytosis in antibodies against blood cells - Type II hypersensitivity - Anemia - Thrombocytopenia Manifestations - Malar rash - Lupus nephritis - Swelling - Pericarditis - CNS involvement - Immunode ciency Primary - Inherited defects of the immune system - Innate immunity Phagocytes NK cells Complement proteins - Adaptive immunity Humoral Cell mediated - Types Bruton disease - X linked agammaglobulinemia - Non functional tyrosine kinase - Failure of pre-B cells to di erentiate into B cells 23  fi ff  - Marked decrease of B cells in peripheral blood and lymphoid tissue - Absent plasma cells throughout the entire body - Absent immunoglobulins in the blood - Normal T cell functions - Clinical manifestations Recurrent bacterial infections - Lack of antibody mediated opsonization - Chronic pharyngitis - Sinusitis - Otitis media - Bronchitis - Pneumonia Certain viral infections Intestinal protozoan Treatment through IV of immunoglobulins Common variable immunode ciency - Group of immune disorders - Equally a ect both males and females - Cause indicates block in antigen stimulated B cell di erentiation - Mature B cells are present but no plasma cells Intrinsic B cell defect De cient helper T cell Increased suppression by suppressor T cell - Hypogammaglobulinemia - Impaired antibody response to infections - Increased susceptibility to infections 24  fi ff fi ff  - Both sexes are e ected equally - Diagnosis is made by exclusion after other causes of immune de ciency are excluded - Patients have higher incidence of developing autoimmune diseases Isolated IgA de ciency - Most common primary immunode ciency - Weakened mucosal immunity due to lack of IgA production secondary to lack of IgA secreting plasma cells Block in their terminal di erentiation - Susceptible to sinopulmonary infections and diarrhea Hyper IgM syndrome - Defect in isotype class switching resulting in lack of production of IgG/A/E antibody subtypes - 70% are X linked Mutation of CD40L on helper T-cells cannot activate B cells to class switch - Also cell mediated defect Cannot activate phagocytes via CD40 - Recurrent infections secondary to low levels of opsonizing IgG antibodies - Also susceptible to intracellular pathogens due to defect in cell mediated immunity - 30% secondary to other mutations CD40 or other molecules necessary for class switching 25  fi ff ff fi fi  DiGeorge syndrome - Thymic hypoplasia Congenital malformation a ecting the third and fourth pharyngeal pouches Defect in the development of thymus, parathyroid glands, portions of the face and aortic arch Absent T cells in lymphoid tissue and peripheral blood due to lack of maturation in the thymus Infants are extremely vulnerable to viral, fungal, protozoal, intracellular bacterial infections - Defect in cell mediated immunity Immunity might improve with age in those partial defects - Hypocalcemia Tetany - Muscle spasms - Secondary to parathyroid gland hypoplasia Midline developmental abnormalities 90% deletion of 22q11 Treatment - Thymic transplant for some patients Severe combined immunode ciency - Group of distinct disorders with common feature being defects in both humoral and cell mediated immunity - Two major abnormalities result in B and T cell defects Mutation in gamma chain of common cytokine receptors - IL2/4/7/9/15 - X linked 26  ff fi  - IL7 most important due to its role in stimulating survival and expansion of immature B and T cell precursor Adenosine deaminase de ciency - Autosomal recessive - Accumulation of adenosine and metabolites resulting in inhibition of DNA synthesis and are toxic to lymphocytes - Clinical features Hypoplastic thymus Atrophic lymphoid tissue Severe infections with variable organisms Treatment with stem cell transplant or fatal in rst year of life Wiscott-Aldrich syndrome Secondary - De ciency of immune function secondary to another disease process Infection Immunosuppression Aging Malnutrition - Genetic de ciencies of innate immunity Hereditary de ciency of complements - Decreased C3 causes susceptibility for bacterial infections - Decreased C1q, C2, and C4 causes increased risk of autoimmune disease 27  fi fi fi fi fi  Defects in the phagocyte oxidase enzyme - Chronic granulomatous disease Defects in integrins and selectin - De ciencies in leukocyte adhesion - Acquired immunode ciency Malnutrition Infection - Acquired immunode ciency syndrome (AIDS) Human immunode ciency virus (HIV) Depletion of CD4+ lymphocytes Immunosuppression - Most common cause of secondary immunode ciency Chemotherapy Radiotherapy Suppressive drugs such as corticosteroids Autoimmune diseases Malignancy Aging - Genetic variation Permanent changes to the nucleotide sequence - Mutations Variants causing disease - Single nucleotide variants Missense Nonsense Silent 28  fi fi fi fi fi  - Deletions, duplications, insertions In frame Frameshift Copy number variants - > 500 bp to several Kb deletions/duplications One or many genes involved Dynamic mutations - Microsatellite instability Repeats of 1-6 nucleotides - Trinucleotide expansion Ampli cation of a simple nucleotide repeat sequence - Unstable May be expanded during gametogenesis Somatic mutations - Mutation found only in cancer tissue Related to tumor progression - Oncogenic mutations are clinical actionable Diagnostic Prognosis or predictive value - Not at risk to o spring Hereditary/germline mutations - Mutation found in all tissues - Hereditary susceptibility to cancer Increases risk for cancer by many folds - Mendelian pattern of inheritance - Risk to transmit variant to o spring 29  fi ff ff  - Genetic counselling - Polymorphisms Common variants - Alleles Alternative versions of DNA sequence at a locus - Gene mutation signi cance Loss of function mutations - Nonsense - Frameshift - Missense - Gene deletion - Inactivation of tumor repressor gene - Majority of hereditary cancers Gain of function mutations - Missense/ampli cation - Activation of oncogene - Single gene disorders Caused by a mutation in a single locus Follow classic mendelian pattern of inheritance - Autosomal recessive Cystic brosis - Caused by mutation in the CFTR gene (ion transporter) - Mutation result in loss of function - Parents are una ected carriers Heterozygous - Each parent has a 50% chance of passing mutated allele 30  fi fi ff fi  25% chance of having an a ected child - Homozygous - CF transmembrane conductance regulator gene Involved in hydration of airway and other organs that secret mucus - Pancreas - Bile - Male genitalia - Sweat glands - Intestines - Variable expressivity and genotype phenotype correlation is observed - Allelic heterogeneity Many disease causing mutations in CFTR identi ed - Autosomal dominant Familial hypercholesterolemia - Caused by mutations in LDLR LDL receptor - Usually inherited from an a ected parent Heterozygous - Child has 50% chance of inheriting mutation from a ected parent - Shows incomplete dominance Phenotype of homozygous for the mutation is more sever than heterozygous - Early onset 31  ff ff ff fi  - Mutations result in loss of function Haploinsu cieecy - Mutations in other genes can also cause this ApoB and PCSKo - Genetic heterogeneity - Results in increase plasma cholesterol and coronary artery disease ABO blood group system - Codominance - 3 alleles IA, IB, i IA and IB are codominant alleles - Dominant to i - X linked recessive Hemophilia A - Heterozygous female Una ected - Each son has 50% chance of beings a ected Hemizygous - Each daughter has 50% chance of being a heterozygous carrier - Mutation in clotting factor VIII (F8) in X chromosome - Male disease - Skewed x inactivation in females WT X chromosome expressed - X linked dominant Rett syndrome 32  ff fi ff  - Female heterozygous are a ected - Homozygous małe lethality - Early onset progressive neurodevelopmental disorder - Loss of function mutation I MECP2 gene Epigenetic regulation and transcriptional silencing - Highly expressed in brain - Molecular basis of disease Complex inheritance - Genetic variants that alter susceptibility to disease Polymorphisms Multifactorial origin - Genetic variants combined with environmental exposures may trigger disease process Familial aggregation Heritability - Proportion of phenotypic variation within a population that is due to genetic variation Liability - All genetic and environmental factors that contribute to the development of a multifactorial disorder Risk of having the a ected phenotype as a result of a particular phenotype Environmental factors play a role in determining if individuals with genetic liability close to threshold will end up being a ected - Epigenetic's Heritable changes in gene expression that occur with no modi cations to the DNA sequence 33  ff ff ff fi  - Are reversible - Environmentally responsive DNA methylation - Covalent modi cation of DNA - Methylation of cytosines at CpG nucleotides (5-meC) Enriched in gene promoters - DNMT1 DNA methyltransferase 1 - Hypermethylation of gene promoter results in gene silencing - Important role in genomic imprinting and X chromosome inactivation X chromosome inactivation - Dosage compensation in females - Random X inactivation during early embryonic development - Heterochromatic chromsome form Barr body structures Inactive - Inactivation is regulated by IncRNA X inactivation speci c transcript (Xist) interacts with histone modi cation and DMT methylation enzymes Genomic imprinting - Only one of two alleles is expressed Other is silenced - Monoallelic expression - Refers to parent of origin speci c gene expression - Epigenetically mediated repression of one allele DNA methylation at imprinting control region (ICR) - Genes with role in embryonic and placental growth and development 34  fi fi fi fi  - Methylated state is reset prior to meiosis - Disorders Imprinting defects are caused by gentian or epigenetic alteration - Deletion, mutation, uniparental disomy - Epimutation UPD - Two copies of the same chromosome are abnormally inherited from just one parent Angelman syndrome - Chr15q11-13 - Deletion is maternally inherited - Symptoms are due to lack of function of UBE3A Prader willi syndrome - Chr15q11-q13 - Deletion is paternally inherited - Symptoms are due to lack of function of SNRPN - Triplet repeat expansion Dynamic mutations - Expansion of unstable repeat sequences Mechanism - Slipped mispairing during DNA replication Repeat expansion can occur in coding or non coding regions of a gene and result in loss or gain of protein function > 20 diseases described 35   Fragile X syndrome - Molecular mechanism Trinucleotide repeat (CGG) expansion in the 5’UTR of FMR1 gene - Located on X chromosome Associated with DNA hyper methylation of gene promoter and repression of gene expression Normal size allele - 5-44 repeats - FMR1 disorders Occurs in individuals with an FMR1 full mutation Characterized in a ected males by developmental delay and intellectual disability along with a variety of behavioural issues - Some females present symptoms Tremor/ataxia syndrome - Individuals with an FMR1 premutation Late onset Progressive cerebellar ataxia and intention tremor followed by cognitive impairment - More common in males - Primary ovarian insu ciency Hypergonadotropic hypogonadism before age 40 - Observed in 20% of women who carry a permutation allele - Mitochondrial disorders mtDNA - Each human cell contains thousands of copies Small circular double strand DNA 36  ff ffi  37 genes - 13 protein coding - 2 rRNA - 22 tRNA Homoplasmy x heteroplasmy Replicative segregation Maternal inheritance Highly mutable Disorders - Involve neurodegenerative, cardiovascular, neurometabolic, visual, auditory, muscular disorders - Nuclear genes encoding for oxidative phosphorylation proteins also cause mitochondrial disorders Follow mendelian inheritance - Methods of molecular genetics PCR - Polymerase chain reaction Denaturation Annealing Extension - Variations Allele speci c PCR PCR + digestion Real time PCR qfPCR GAP-PCR 37  fi  - Advantages Fast Use small amounts of DNA Can multiplex Detect a variety of mutations - Deletions - Insertions - Point mutations - Limitations Must know size of interest - Need to know what mutation is Size of allele that can be quanti ed - Fast - Use small amounts of DNA - Can multiplex Many mutations or samples - Detect a variety of mutations Deletions Insertions Point mutations Sanger sequencing - Targeted approach BRCA1: 24 exons; BRCA: 27 exons - Screen mutations - Labor intensive 38  fi  - Detect SNV Small insertion/deletions - Cheap and fast - Good for testing single gene/single variant conformation - Steps PCR ampli cation of target regions Puri cation Sequencing reaction using FW and RV primers Cycles sequencing with ddNTPs Capillary electrophoresis - Identify single nucleotide changes - Historic gold standard for mutation detection - Lower limit of detection Next generation sequencing - High throughout method - Whole genome sequencing - Whole exam sequencing - Targeted sequencing Gene panels - Ability to detect both SNV and CNV Exon/gene deletion or duplications - Analysis Alignment of reference genome Variant calling 39  fi fi  - SNVs - CNVs - INDELs Classi cation of variants and reporting - Due to a higher error rate compared to Sanger sequencing each region of interest must be sequenced hundreds of times - Coverage Number of times a single base is sequenced Also known as sequencing depth - Variant allele fraction The percentage of reads supporting a given variant - Genetic counselling Evaluation risk for disease in probing and relatives Adress psychosocial issues Collect family and medical history O er genetic testing Continuous clinical assessment Provide appropriate treatment and management options - Germline mutations Can result in predisposition to cancer Mutation is present in all cells Test blood 40  ff fi  - Looking for heterozygous or homozygous mutations - Somatic mutations In tumor suppressors and oncogenes result in uncontrolled cell proliferation Mutation is in subset of cells - Looking for mosaic or sub clonal mutations - Need lower limit of detection Test tumor - Solid tumors Test blood for hematological cancers Mutation only found in cancer tissue Oncogenic mutations are clinically actionable - Diagnostic - Prognosis - Predictive No risk to o spring - Sporadic cancers Many mutations build up in cells over time eventually leading to cancer - Hereditary cancers First mutation is inherited and already present at birth - Additional mutations build up over time leading to cancer Syndromes - Caused by pathogenic variant in a cancer associated gene 41  ff  - Follow mendelian inheritance Autosomal dominant - Multiple generations a ected with cancer - Earlier age of onset compared to sporadic cancers - Higher risk of multiple primary cancers and multifocal tumours - Similar cancer types within the family Possibly including very rare tumours - Variable penetrance Not all carriers will develop cancer Test peripheral blood for germline variants Increases risk for cancer by many folds Genetic counselling to discuss risks, prevention, treatment, test family - Genomic alterations in neoplasia WAGR syndrome - 11p13 minimal 650kb deletion including WT1 and PAX6 - Phenotype is a result of both dosage sensitive genes WT1 predisposes to Wilm’s tumor PAX6 results in remaining phenotypes Wilms tumor - Most common paediatric primary tumour of the kidney - Germline Increased risk of Wilms tumour 42  ff  - WAGR syndrome due to deletion of the WT1 gene - Denys Drash syndrome due to sequence variant in WT1 gene - Beckwith Wiedemann syndrome Imprinting disorder of the 11p15.5 locus - Screening Abdominal screening every 3 months - Somatic Certain CNVs are known unfavourable biomarkers - Copy number deletions of 1p and 16q Copy number gain of 1q - Patients with these abnormalities may have therapy modi cations - Technique Microarray is best approach for a solid tumor - Myeloid malignancies Malignant clonal disorders of the hematopoietic progenitor/stem cells Chronic phase - Myeloproliferative neoplasms - Myelodysplastic disorders Acute phase - Acute myeloid leukaemia Decreased circulating mature peripheral blood cells Lethal without treatment Historically de ned by karyotype and FISH Cytogenetics and molecular genetics are necessary at diagnosis - FISH/PCR Fast answer for recurrent/actionable mutations 43  fi fi  - Karyotype Longer TAT Detects aneuploidies and rearrangements Clonal evolution - Microarray Can support karyotype and provide better resolution for CNVs Evaluate LOH - NGS DNA and fusion panel DNA panel provides gene level mutation information RNA panel can detect cryptic gene fusions missed by cytogenetics - FLT3 ITD detection Allele speci c PCR with fragment size analysis for two speci c FLT3 variants ITD - Internal tandem duplication - 3-200 bases TKD - Tyrosine kinase domain - Single nucleotide variant - Results in resistance to targeted therapy - NPM1 indel detection Allele speci c PCR with fragment size analysis by mass spectrometry for three speci c NPM1 insertion deletion variants - De nes a separate AML entity - In the absence of FLT3 variant associated with good prognosis - Fusion NGS panel 44  fi fi fi fi fi  Gene fusion detection by NGS uses same work ow as DNA sequencing First step is to convert RNA to complementary DNA Same library preparation strategy with PCR primers targeting speci c genes commonly involved in fusions DNA and cDNA libraries can optionally be combined for sequencing steps - Fusion NGS panel negative LHSC fusion myeloid panel includes 30 fusion driver gene with >200 partners - Rules out vast majority of translocations associated with AML FLT3-ITD with NPM1 are typically observed with normal karyotypes - DNA NGS panel 50 genes involved in myeloid neoplasms Limit of detection - 5% variant allele fraction No additional variants detected - Can resolve sequence of FLT3-ITD 45  fl fi  Week 3 - Metabolism Range of biochemical processes that occur within humans to sustain life Consists of anabolism and catabolism of substances - Build up - Break down Commonly used to refer to the breakdown of food and its transformation into energy Genetic - inborn errors of metabolism - Relatively rare - Phenylketonuria (PKU) Abnormality in amino acid metabolism 1/12000 live births (white>other) Autosomal recessive Commonest variant has severe decrease in phenylalanine hydroxylase (PAH) which leads to increased phenylalanine but no tyrosine - Phenylalanine is needed for production of neurotransmitters (dopamine and norepinephrine) - Tyrosine is required for melanin production Baby is normal at birth but accumulation of blood phenylalanine causes impaired brain development Screening test during rst week of life - Blood phenylalanine levels - De nitive genetic testing to determine speci c mutation Clinical manifestations - Decreased skin/hair pigmentation - Abnormal body oder 46  fi fi fi  Sweat and urine - Intellectual disability - Inability to talk/walk - Seizures - Hyperactivity - Maternal PKU syndrome 75-90% infants born to treat adult female PKU patients have intellectual disability due to maternal phenylalanine crossing placenta during fetal development - Teratogen - Treatment Diet restriction of natural protein at least until adulthood and during pregnancy - Restriction of phenylalanine intake with tyrosine Eliminate all high protein foods - Meat, sh, eggs, dairy, nuts, whole grains, beans, gelatine, plant algae Eliminate diet drinks and foods containing aspartame Usually requires supplementation with medical foods containing phenylalanine free protein substitutes - Galactosemia De ciency of galactose 1 phosphate uridyl transferase (GLAT) Autosomal recessive Normally lactose —> glucose and galactose (in small bowl) Galactose —> glucose (involves GLAT) De eceny of GLAT results in increased galactose 1 phosphate Clinical manifestations - Accumulation of galactose and metabolites in many organs/tissues 47  fi fi fi  Eyes - Cataracts Liver - Hepatomegaly Early fatty change Later cirrhosis like - Jaundice - Liver failure Kidney - Renal failure Brain - Neurological defects - Failure to thrive Vomiting Diarrhea upon milk ingestion Diagnosis - Newborn screening test Fluorometric assay of GLAT enzyme activity on a spot of dried blood - Positive screening test followed by GLAT level assay in red cells Treatment - Dietary control Restriction of galactose for at least two years of life - Lysosomal storage disease Autosomal recessive disorder 48   - Results in decreased hydrolytic enzymes found normally in lysosomes Lysosomes - Autophagy Resulting from fusion with autophagosome - Immunity Fuse with phagosomes - Membrane repair Through fusion with plasma membrane Failure to metabolize complex intra/extracellular substrates - Sphingolipids - Mucopolysaccharides Approximately 70 lysosomal storage diseases have been identi ed A ect mainly infants and young children Storage of insoluble intermediates in lysosomes of mononuclear phagocytes - Hepatosplenomegaly - CNS involvement leads to brain damage - Tay Sachs disease (Gm2 gangliosidosis) Commonest gangliosidosis - De ciency of enzyme hexosamindase A Common in ashkenazi jews - 1/30 heterozygotes Accumulation of gangliosides occurs in the CNS 49  ff fi fi  - Autonomic nervous system and retina Abnormal storage disease of Gm2 (ganglioside) in neurons, axons, glial cells, leads to cell swelling - Lysosomal accumulations are seen by electron microscopy Antenatal diagnosis and carrier detection - Enzyme assays and DNA based analysis Infants appear normal at birth - Signs and symptoms begin to appear by 6 months - Neurological impairment, mental retardation, increasing dementia - Motor and mental deterioration, resulting in motor incoordination, intellectual disability - Muscular accidity - Blindness Eyes - Ganglion cells in retina are swollen - Cherry red spots Choroidal circulation shows through red in fovea where all retinal ganglion cells are normally pushed aside to increase visual acuity Only normal part of retina seen Death 2-3 years after birth Prominent lysosomes with whorled con gurations - Gaucher disease A cluster of autosomal recessive disorders resulting from mutations in the gene encoding glucocerebrosidase Most common lysosomal storage disorder Glucocerebrosidase cleaves glucose residue from ceramide Defect results in glucocerbrosides accumulation in phagocytes 50  fl fi  - In some subtypes also in the central nervous system Glucocerbrosides are continually formed from the catabolism of glycolipids derived mainly from cell membranes of senescent leukocytes and red cells Pathologic changes are caused by the burden of storage material and also by activation of macrophages and the consequent secretion of cytokines such as interleukin and tumor necrosis factor - IL1/6 - TNF Type I - Most common - Chronic non-neuronopathic form - Occurs mainly in jews of European heritage - Reduced but detectable levels of glucocerebrosidase activity - Storage glucocerebrosidase limited to mononuclear phagocytes throughout the body without involving the brain - Spleen and skeletal involvement dominate - Longevity is shortened but not markedly Type II - Acute neuronopathic - Infantile acute cerebral pattern - Virtually no detectable glucocerebrosidase activity in tissues - Hepatosplenomegaly seen but clinical picture is dominated by progressive central nervous system involvement leading to death at an early age Type III - Intermediate between I and II - Systemic involvement characteristic of type I but has progressive CNS disease that usually begins in adolescence or early adulthood 51   Glucocerbrosides accumulate in massive amounts in phagocytic cells throughout the body Distended phagocytic cells found in spleen, liver, bone marrow, lymph nodes, tonsils, thymus, Peyer patches - Similar cells may be found in alveolar septa and air spaces in the lung - In contrast to other lipid storage diseases these cells rarely appear vacuolated but have brillary type of cytoplasm resembling crumpled tissue paper - Necrotic bone Mutation of glucocerebrosidase gene is most common known genetic risk factor for development of Parkinson disease - Patients have a 20 fold higher risk of developing it - 5-10% of patients with it have mutations in the gene encoding glucocerebrosidase Diagnosis - Level of glucocerbrosides in leukocytes or cultured rborblasts is helpful in diagnosis and in detection of heterozygote carriers - DNA testing available in select populations - Niemann-pick disease (NPD) Autosomal recessive - De ciency of enzyme sphingomyelinase (in NPD types A and B) - No man picks his nose using his sphinger - Common in ashkenazi jews - Accumulation of sphingomyelin (lipids) in phagocytic cells and neurons Diagnosis - Biochemical assay for sphingomyelinase activity in leukocytes or bone marrow biopsy - Individuals a ected with types A and B as well as carriers can be detected by DNA analysis 52  fi ff fi fi  Type A - Severe infantile form - Mostly severely a ects spleen, liver, bone marrow, lymph nodes, lungs Due to phagocytic cell content Resulting in organomegaly - CNS impairment - Progressive wasting - Death within the rst 3 years of life Type B - Organomegaly - No CNS involvement - Survive into adulthood - Familial hypercholesterolemia Autosomal dominant Mutations in the LDL receptor gene Inadequate removal of plasma LDL by liver - Acute intermittent porphyria Autosomal dominant De ciency of enzyme porphobilinogen deaminase Symptoms triggered by hormones, drugs, dietary changes Impaired heme synthesis Accumulation of intermediate porphyrin - Diabetes insipidus X linked recessive or autosomal dominant ADH de ciency 53  fi fi fi ff  Excessive urination due to n inability of the kidney to resorb water properly from urine - Polyuria - Lesch-nyhan syndrome X linked recessive De ciency of hypoxanthine guanine phosphoribosyl transferase Accumulation of uric acid in all body uid Secondary gout Acquired metabolic disorders - Very common - Related to dyslipidemia and other factors Atherosclerosis - Related to abnormal glucose metabolism Diabetes mellitus - Atherosclerosis Pathogenesis - Formation of atheroma on inner aspect of large and medium sized arteries Fibrofatty plaques on intima - Narrowing of artery lumen results in reduced blood ow and ultimately can result in damage to or necrosis of organs Stenosis leading to ischemia Modi able major risk factors - Hyperlipidemia Hypercholesterolemia - Hypertension - Cigarette smoking 54  fi fi fl fl  - Diabetes mellitus Other risk factors - Genetics, age, gender - Obesity - Stress - Elevated serum homocysteine levels From vitamin B de ciencies and cardiovascular disease - Elevated C reactive protein CRP - Maker of in ammation Lesion prone are - Reversible fatty streak formed which can progress to atherosclerosis Compensatory enlargement initially prevents reduction of blood ow through vessel Plaque can become - Thin cap plaque Unstable Vulnerable Most prone to plaque rupture - Can lead to sudden cardiac death - Thick cap plaque Stable - Fibrotic plaque Stable - Stable plaques can undergo surface erosion and thrombosis Rapidly expanding leading to more prominent calci cations 55  fl fi fi fl  - Can lead to sudden cardiac cardiac death - Extensive narrowing of luminal diameter from large plaques generally results in critical stenosis Reducing blood supply to the heart and resulting in angina Plaque formation begins early in life but remains clinically silent until it has progressed to the point resulting in disease - Fatty streaks - Atherosclerotic plaques - Stenosis - Ischemia - Plaque rupture - Thrombosis Consequences - Large elastic arteries Aorta Carotid Iliac arteries - Large and medium sized muscular arteries Coronary and popliteal arteries - Myocardial infarction - Cerebral infarction 56   - Aortic aneurysms - Peripheral vascular disease - Diabetes mellitus Group of metabolic derangements that are characterized by hyperglycaemia Due to absolute lack of insulin, or relative lack/defect in insulin action Diagnosis - Normal blood glucose 70-120 mg/dL - Fasting plasma glucose ≥ 126 mg/dL - Random plasma glucose ≥ 200 mg/dL - 2h plasma glucose ≥ 200 mg/dL during oral glucose tolerance test with loading 75g dose - Glutted hemoglobin ≥ 6.5% Normal glucose regulation - Glucose production in liver - Glucose uptake and utilization by peripheral tissues Mostly skeletal muscle - Actions of insulin and other hormones that counter regulate insulate Do the opposite of what insulin does - Insulin Synthesized by pancreatic beta cells Production is stimulated by blood glucose levels 57   Role - Anabolic function Increases synthesis and decreases degradation of glycogen, lipid, protein - Increases rate of glucose transport into certain cells in the body Striated muscle cells, fat cells - Promotes protein synthesis Type 1 - Absolute insulin de ciency - Due to pancreatic beta cell destruction - Pathogenesis Decreased function of beta cells in pancreas leads to substantially reduced insulin secretion Autoimmune - Islet destruction by immune e ector cells reacting against endogenous beta cell antigens leading to reduced insulin secretion Genetic susceptibility - 90-95% express HLA-DR3 or DR4 Class II MHC molecules Mechanisms of beta cell destruction - Failure of self tolerance in T cells speci c for islet antigens Develops most commonly during childhood Type 2 - Relative insulin de ciency - Peripheral resistance to insulin and beta cell dysfunction Inadequate compensatory response 58  fi fi ff fi  - 80-90% of cases - Pathogenesis Peripheral resistance to insulin action and inadequate response of insulin secretion Genetic factors Environmental factors - Sedentary lifestyle - Poor dietary habits - Obesity Metabolic defects in type 2 diabetes - Insulin resistance Liver Skeletal muscle Adipose tissue - Beta cell dysfunction Relative insulin de ciency Mid 40s, but increasing at a younger age due to obesity Both types can get chronic hyperglycaemia resulting in damage to many organs - Kidney - Eye Retina - Nerves Peripheral neuropathy - Blood vessels 59  fi  Artherosclerosis Microangiopathy Signs/symptoms - Hyperglycaemia - Glucosuria, polyuria - Polydipsia, polyphagia - Weight loss despite eating more - Diabetic ketoacidosis Body fat gets metabolized as a source of energy and the oxidation products of ketone bodies lead to metabolic acidosis More common and severe in type 1 Fatigue, nausea, vomiting, severe abdominal pain, fruity odour, deep laboured breathing - Nonketotic hypersmolar coma More common in type 2 Complications - Macrovascular damage Atherosclerosis leads to myocardial infarction, ischemic limbs, brain stroke Large and medium sized artery - Microvascular disease Nephropathy - Kidney Retinopathy - Retina Neuropathy - Nerves 60   - Pain, tingling, loss of feeling in legs and feet - Heart Accelerated atherosclerosis leading to coronary artery disease and then a myocardial infarct - Extremities Atherosclerosis in extremities leading to ischemic limb/gangrene and then lower leg amputation - Kidney Atherosclerosis of renal artery Glomeruli a ected - Capillary basement membrane thickening leading to proteinuria, end stage renal failure and dialysis with renal transplantation - Eye Diabetic retinopathy leading to retinal hemorrhages, exudates, thickening of BM of retinal capillaries and then blindness Cataract formation Glaucoma - Nervous system Peripheral neuropathy - Pain, tingling, loss of sensation in extremities Prone to injury and infection Autonomic neuropathy - Bowel, bladder, erectile dysfunction - Immune system Prone to infection 61  ff  Pathogenesis of complications - Non enzymatic glycosylation Advanced glycosylation end products Alter function of a ected proteins - Activation of second messenger pathways Protein kinase C leading to activation of pro-angiogenic molecules - Metabolism of glucose by polyol pathway Accumulation of intracellular sorbitol - Nutrients Macro - Large amounts - Carbs - Proteins - Fats Micro - Vitamins Water soluble - B - C Fat soluble - A - D - E - K Water - Main component of body uids 62  ff fl  - Carrier - Regulation of body temperature - Causes and factors of malnutrition Genetic diseases Malabsorption syndromes Poverty Chronic alcoholism Ignorance and failure of diet supplementation Self imposed dietary restriction Speci c drug therapies Inadequate total parenteral nutrition Acute and chronic illness Gastrointestinal diseases - Severe acute malnutrition (SAM) Weight for height ratio that is 3 standard deviations below the normal range Results from dietary de ciencies of proteins and calories Used to be called protein energy malnutrition Marasmus - Inadequate total intake of calories/all nutrients Skin and bones - Severe reduction in total caloric intake - Weight falls to 60% of normal for sex, height, age - Growth retardation and loss of muscle mass by catabolism of somatic (muscle) protein to use amino acids for energy - Visceral (non muscle) protein compartment mostly spared so serum albumin is normal or minimally reduced 63  fi fi  Structural proteins, organs, blood cells, other blood proteins - Extremities are emaciated - Head appears too large for body - Anemia - Multi vitamin de ciencies - Immune de ciency Concurrent infections Kwashiorkor - Inadequate intake of protein with normal or near normal total calorie intake - Child is weaned too early and given a carbohydrate diet - Protein deprivation is relatively greater than the reduction in calories - Relatively severe protein deprivation associated with severe loss of visceral protein compartment with resultant hypoalbuminemia leading to uid retention Edema Ascites - Relative sparing of subcutaneous fat and muscle mass - Enlarged fatty liver occurs due to reduced synthesis of carrier protein component of lipoprotein Fat storage in liver - Skin and hair changes Alternating zones of hyperpigmentation, desquamation, hypopigmentation Alternating pale and dark colour - Vitamin de ciencies - Infections - Self induced malnutrition Anorexia nervosa 64  fi fi fi fl  - Primarily in previously healthy young women - Obsession with body image and thinness - Self induced starvation - Marked weight loss - Endocrine abnormalities Amenorrhea Decreased thyroid hormone - Gelatinous transformation of bone marrow Pathognomonic Decreased bone density - Low estrogen Anemia - Electrolyte abnormalities Hypokalemia Cardia arrhythmia Sudden death Bulimia nervosa - Binging and vomiting - Primarily in previously healthy young women who have developed an obsession with body image and thinness - Weight and gonadotropin levels remain near normal - Electrolyte imbalance Hypokalemia - Cardiac arrhythmias - Pulmonary aspiration of gastric contents - Esophageal and gastric tears 65   Secondary PEM - Chronic illness - AIDs - Vitamins Fat soluble - Storage in liver and fatty tissues - Excess > de ciency - A, D, E, K Water soluble - Need to constantly replenish - De ciency > excess - B1, B2, B6, B12, C, niacin, folic acid, pantothenic acid, biotin Vitamin A de ciency - Sources Animal derived - Liver, sh, eggs, milk, butter Vegetables - Carrots, squash, spinach - Functions Maintenance of normal vision Regulation of cell growth and di erentiation Regulation of lipid metabolism Enhancing immunity to infections - Actions of vitamin A Mediates normal vision 66  fi fi fi fi ff  - Required for rhodopsin synthesis - Retinol —> retinal —> rhodopsin De ciency results in blindness Leading cause of blindness worldwide Maintains normal epithelial cell di erentiation - Required for di erentiation of mucus secreting epithelium - De ciency leads to squamous metaplasia of epithelial cells Xerophthalmia - Dryness of corn and conjunctiva Bitot’s spots Keratomalacia - Softening of the cornea Cornea eventually becomes ulcerated/infected - Leads to total blindness - Has lysosome stabilizing functions and enhances resistance to infection Vitamin D - Sources UV radiation of skin Cod liver oil Forti ed milk Cereal Anti-rachitic vitamin A ects calcium homeostasis 67  ff ff fi fi fi ff  - Synthesis and metabolism Produced from 7-dehydrocholesterol in skin or ingested from diet Converted in liver to 25(OH)D and in kidney to 1,25(OH)2D - Active form is 1,25 dihydroxyvitamin D 1,25(OH)2D stimulates expression of RANKL on osteoblasts and increases intestinal absorption of calcium and phosphorus - Hypovitaminosis D Serum calcium levels remain normal - Parathyroid e ect - Early stage Serum phosphate levels are decreased due to urinary excretion Serum alkaline phosphatase levels are increased in an attempt to form new bone - Osteoblastic activity Vitamin D de ciency - Serum levels of calcium are normal or nearly normal - Phosphate is low Mineralization is impaired - Rickets Vitamin D de ciency causes this in children Inadequate sunlight blocking of cholecalciferol production in skin Deformity - Softened occipital bones and frontal bossing - Failure of endochondral ossi cation resulting in continued cartilage growth at epiphysis causing nodular enlargement of joints Rachitic rosary in childhood - Costo-chondral joints 68  fi fi ff fi  - Anterior protrusion of the sternum Pigeon breast deformity - Lumbar lordosis - Bowed legs Fractures Teeth a ected - Poor dentin formation - Osteomalacia After epiphyseal closure Defective calci cation of bones leads to fractures and deformities - Vitamin B9 de ciency Folate/folic acid is essential for transfer and use of one carbon units in DNA synthesis Megaloblastic anemia - Due to impaired DNA synthesis Neural tube defects - Spina bi da - Vitamin B12 de ciency Required for red blood cell formation, neurological function, and DNA synthesis Cheese, eggs, leafy greens, liver, milk, nuts, red meat, salmon, whole cereals Decreased intake - Inadequate diet Vegetarians, aged people, alcoholics Impaired absorption - Intrinsic factor de ciency 69  ff fi fi fi fi fi  - Pernicious anemia Autoimmune T cell and antibody mediated condition resulting in gastric atrophy with lack of intrinsic factor and achlorhydria - Interference with absorption and malabsorption states Gastrectomy Alcoholics Di use intestinal disease - Chrons disease - Colitis - Lymphoma - Systemic sclerosis IIeal resection - Ileitis Medications - Proton pump inhibitors for acid re ux - Clinical manifestations Anemia - Low RBC count - Microcytic - Normochromic Clinical signs - Anemia Low blood count Macrocytic Normochromic - Folate de ciency has the same blood results 70  ff fi fl  - Serum and folate to distinguish between them - Degradation of spinal cord due to defect in myelin formation Paresthesia and numbness of toes and ngers Ataxia - Later paraplegia - Atrophy and ulceration of oral mucosa - Treatment Dietary or intramuscular B12 injections - Vitamin C Ascorbic acid Antioxidant Facilitates iron uptake in the GIT It is important in the formation of intracellular ground substance of bone, dentin, and other connective tissues such as blood vessels Cofactor in activation of proline/lysine hydroxylase - Allows cross linking of proline and lysine residues in collagen - De ciency results in defective collagen formation Scurvy - Limeys Due to consumption of citrus fruits - Limes and lemons which are high in vitamin C - Most animals synthesize their own vitamin C Exceptions are man, monkeys, and guinea pigs 71  fi fi  - Defective collagen around blood vessels Hemorrhages in skin, joints, gum - Defective collagen Poor bone formation in kids and poor wound healing - Toxicity Vitamin A - Acute Headache, dizziness, vomiting, stupor, and blurred vision - Chronic Weight loss, anorexia, nausea, vomiting, bone and joint pain - Teratogenic Due to e ects on cell di erentiation Vitamin D - Elevated serum calcium - Nausea, vomiting, diarrhea, headache - Calci cations of tissues - Muscle weakness, bone pain - May impair renal function - Obesity Accumulation of adipose tissue that is of su cient magnitude to impair health Caloric intake exceeds caloric expenditure Measure by body mass index Genetic, environmental, psychological factors Disorder of energy homeostasis 72  fi ff ff ffi  - Two sides of energy equation, intake and expenditure, regulated by neural and hormonal mechanisms so that body weight is maintained within a narrow range for many years - Controls lipostat Senses quantity of energy stores (adipose tissue) Appropriately regulates food intake as well as energy expenditure - Hypothalamus is the master regulator of energy homeostasis - Worlds greatest health concern Complications - Type 2 diabetes mellitus - Cardiac hypertrophy - Hypertension - Hypercholesterolemia - Atherosclerosis Cerebral arteries Coronary arteries - Myocardial infarction - Gallbladder disease - Osteoarthritis - Non alcoholic fatty liver disease - Pickwickian syndrome Sleep apnea Hypoventilation - Some cancers Breast 73   Uterine Colon Week 4 - Infectious disease A disease caused by an infectious agent that can be passed on to others - Tissue damage or dysfunction caused by a bacterium, virus, protozoan, fungus Infectious = transmissible = communicable disease - Disease A pathological condition of body parts or tissues characterized by an identi able group of signs or symptoms - Any deviation from a condition of good health and well being - Infection Occurs when an infectious agent enters the host and beings to reproduce - May or may not lead to disease - Host An organism infected by another organism - Infecting dose Minimum infective dose vs minimal lethal dose - Pathogen An infectious agent that causes disease - Pathogenesis Steps or mechanisms involved in the development of a disease - Pathogenicity The ability of an infectious agent to cause disease - Virulence 74  fi  The relative ability of an agent to cause disease in a host - The degree of pathogenicity of an infectious agent - Historical perspectives Infectious agents have probably always caused disease in humans Smallpox has been discovered in ancient Egyptian and Chinese writings and Amy have been responsible for more deaths than all other diseases combined - There are no cases recorded since 1980 - Massive decline There is evidence that malaria and poliomyelitis have existed since ancient times In the 14th century the bubonic plague killed about 20 million people in Europe alone In the 20th century the 1918 in uenza may have killed up to 50 million people worldwide More than 36 million people have died of AIDS to date Most recent pandemic (COVID-19) caused by SARS-CoV-2 is responsible for 7 million deaths and counting - Bacteria and virus related pandemics - Robert Koch Bacteria were discovered in 1675 by Antony van Leeuwenhoek Robert koch rst demonstrated that speci c diseases are associated with particular microorganisms in 1876 - Developed a set of criteria to show that anthrax was caused by a speci c bacterium and that tuberculosis was caused by a di erent bacterium - Presented his discovery of mycobacterium tuberculosis in a lecture in march 1882 - Brought entire laboratory set up for audience to see - Methods were so innovative that his criteria are still used today to identify disease causing agents 75  fi fl fi ff fi  Di culties can arise for agents di cult to grow in the laboratory - Nobel prize in physiology and medicine in 1905 for work on tuberculosis Kochs postulates - Developed four criteria to demonstrate that a speci c disease is caused by a particular agent Speci c agent must be associated with every case of the disease Speci c agent must be isolated from a diseased host and grown in culture When culture grown ages is introduced into a healthy susceptible host the age must cause the same disease Same agent must again be isolated from the infected experimental host - Infectious diseases today Despite availability and use of e ective vaccines, antibiotics, antivirals, antifungals Cause death among the elderly, infants, those with chronic disease or immunosuppressed individuals Low to middle income countries - Most deaths are among children from respiratory and diarrheal infections - Tuberculosis Bacterium - Measles Virus - Malaria Protozoa - In uenza Virus - Diarrheal diseases Bacteria, virus, protozoa, helminths 76  fl ffi fi fi ff ffi