Progress Test & CAP PDF

PROGRESS YOU CAN DO IT! TEST & CAP THINK SIMPLE Abhilashini Gunaseelan HEAD IN THE GAME! A++++ 1 ...

PROGRESS YOU CAN DO IT! TEST & CAP THINK SIMPLE Abhilashini Gunaseelan HEAD IN THE GAME! A++++ 1  PROSTHETIC JOINT INFECTIONS............................................................................................ 86 NEW HORIZONS........................................................................................................ 4 PSYCHOLOGY..................................................................................................................89 CLINICAL MICROBIOLOGY...............................................................................................4 SMOKING COUNSELLING......................................................................................................... 89 INTRODUCTIONI TO PATHOGEN GENOMICS........................................................................... 4 EVOLUTION OF DIAGNOSTICS IN CLINICAL MICROBIOLOGY................................................ 5 PERSONAL PROFESSIONALISM IN DEVELOPMENT...................................................90 ANTIMICROBIAL RESISTANCE AND ONE HEALTH IMPLICATIONS......................................... 7 CARE Series................................................................................................................................ 90 HEALTH-CARE ASSOCIATED INFECTION AND MODES OF TRANSMISSION......................... 9 ACTIVE CONSTRUCTIVE RESPONDING.................................................................................. 94 PATHOGEN SURVEILLANCE..................................................................................................... 10 LEADERSHIP AND DECISION MAKING.................................................................................... 94 WORKING IN HEALTHCARE.......................................................................................................11 PATHOLOGY......................................................................................................................96 CYSTIC FIBROSIS.............................................................................................................13 MULTIPLE MYELOMA................................................................................................................. 96 INTRODUCTION TO CYSTIC FIBROSIS.................................................................................... 13 SKIN PATHOLOGY...................................................................................................................... 98 CLINICAL TRIALS PROCESS IN CF........................................................................................... 18 CANCER-ASSOCIATED THROMBOSIS................................................................................... 102 EPILEPSY..........................................................................................................................19 MEDICINE........................................................................................................................105 SEIZURES................................................................................................................................... 19 CHRONIC KIDNEY DISEASE................................................................................................... 105 EPILEPSY OVERVIEW................................................................................................................ 20 INTERSTITIAL LUNG DISEASE................................................................................................ 109 ANTI-EPILEPTICS DRUGS......................................................................................................... 21 AORTIC STENOSIS...................................................................................................................110 REFRACTORY EPILEPSY.......................................................................................................... 23 VENTRICULAR TACHYCARDIA................................................................................................ 111 EEG IN EPILEPSY....................................................................................................................... 23 COPD..........................................................................................................................................112 DIAGNOSTIC GENOMIC TOOLS IN NEUROLOGICAL DISEASE............................................. 25 LUNG CANCER..........................................................................................................................113 ARTIFICIAL INTELLIGENCE IN EPILEPSY................................................................................ 26 COMMUNITY ACQUIRED PNEUMONIA...................................................................................113 ISCHAEMIC HEART DISEASE...................................................................................................115 BREAST CANCER.............................................................................................................27 TRANSIENT ISCHAEMIC ATTACK............................................................................................116 INTRODUCTION TO BREAST CANCER GENETICS................................................................. 27 ASTHMA.....................................................................................................................................119 CURRENT AND FUTURE APPROACHES TO TARGETING GENETIC AND TRANSCRIPTOMIC DIABETES................................................................................................................................. 120 ABBERRATIONS......................................................................................................................... 27 INFLAMMATORY BOWEL DISEASE......................................................................................... 122 CURRENT PATHOLOGY APPROACHES TO GENETIC DIAGNOSIS....................................... 29 OSTEOPEROSIS....................................................................................................................... 123 BREAST CANCER AND AI.......................................................................................................... 31 PARKINSON’S........................................................................................................................... 124 DEMENTIA................................................................................................................................. 126 ARTIFICAL INTELLIGENCE.............................................................................................32 OBESITY.................................................................................................................................... 127 INTRODUCTION TO AI................................................................................................................ 32 OBSTRUCTIVE SLEEP APNOEA............................................................................................. 129 LINEAR REGRESSION............................................................................................................... 34 CHRONIC LIVER DISEASE...................................................................................................... 129 LOGISTIC REGRESSION........................................................................................................... 35 ALCOHOL WITHDRAWAL SYNDROME................................................................................... 133 AI IN HEALTHCARE.................................................................................................................... 37 MULTIPLE SCLEROSIS............................................................................................................ 133 PUBLIC HEALTH...............................................................................................................39 HYPOTONIC HYPONATREMIA................................................................................................ 134 EPIDEMIOLOGY.......................................................................................................................... 39 SURGERY........................................................................................................................136 PARASITOLOGY......................................................................................................................... 39 THYROID DISEASE.................................................................................................................. 136 MALARIA..................................................................................................................................... 39 ACUTE URINARY RETENTION................................................................................................ 137 HIV / AIDS.................................................................................................................................... 42 RENAL CALCULI....................................................................................................................... 138 OPPORTUNISTIC INFECTIONS IN HIV..................................................................................... 45 RENAL CELL CARCINOMA...................................................................................................... 139 GENOMICS........................................................................................................................47 BLADDER CANCER.................................................................................................................. 140 NOVEL GENETIC TECHNOLOGIES........................................................................................... 47 BREAST CANCER..................................................................................................................... 141 EPIGENOMICS............................................................................................................................ 48 BOWEL OBSTRUCTION........................................................................................................... 142 BULK VS SINGLE CELL PROCESSING..................................................................................... 49 HERNIA...................................................................................................................................... 143 INTERPRETING GENOMIC DATA.............................................................................................. 49 LOWER GI BLEED – Colorectal Cancer.................................................................................... 144 GENETIC VARIANT PATHOGENECITY AND ACMG GUIDELINES........................................... 51 UPPER GI BLEED..................................................................................................................... 145 BIOINFORMATICS...................................................................................................................... 51 JAUNDICE................................................................................................................................. 146 PERIPHERAL ARTERIAL DISEASE.......................................................................................... 148 CLINICAL MEDICINE & SURGERY......................................................................... 52 ABDOMINAL AORTIC ANEURYSM........................................................................................... 149 ORTHOPAEDICS...............................................................................................................52 VARICOSE VEINS..................................................................................................................... 150 ARTHRITIS.................................................................................................................................. 52 PULMONARY EMBOLISM......................................................................................................... 150 THE HIP....................................................................................................................................... 54 POST-SURGICAL COMPLICATIONS........................................................................................ 151 THE KNEE................................................................................................................................... 57 THE SHOULDER......................................................................................................................... 60 THE ELBOW................................................................................................................................ 63 THE SPINE.................................................................................................................................. 64 THE HAND AND WRIST.............................................................................................................. 68 THE FOOT AND ANKLE.............................................................................................................. 70 ORTHOPAEDIC TRAUMA........................................................................................................... 72 PAEDIATRIC ORTHOPAEDICS................................................................................................... 75 FRACTURE MANAGEMENT....................................................................................................... 79 BONE AND SOFT TISSUE TUMOURS....................................................................................... 80 MICROBIOLOGY...............................................................................................................86 2 3  o Next generation sequencing: § Rapidly predicts if bacteria are resistant to antibiotics based on NEW HORIZONS presence/absence of (1) known resistance genes, (2) groups of genes and (3) mobile genetic elements (plasmids) § Combining epidemiological data and NGS helps: (1) understand prevalence of CLINICAL MICROBIOLOGY resistance, (2) alerts authorities, (3) links illness to environment or animal INTRODUCTIONI TO PATHOGEN GENOMICS source § Current and future roles Genetics: study of genes and their role in inheritance; describes certain traits Clinical diagnostics: provides genotypic AMR prediction and o Reads: DNA sequence from one fragment; combination of base pairs polymicrobial infections o Short read sequencing: amplifies fragment DNA and then sequence Environmental metagenomics: as an unbiased representation for future o Long read sequencing: reading the nucleotide sequences at the single nucleotide surveillance level AMR gene or plasmid tracking: detect sources of transmission of AMR Genomics: study of all genes in organism (genome); and its interaction with the Machine learning: predicts resistance phenotypes from genomes and environment future trends in AMR o In healthcare: diagnosis, research, surveillance, prognosis, personalised treatment, Global Antimicrobial Resistance and Use Surveillance System (GLASS): standardizes AMR prediction surveillance to inform policies and IPC responses o Human vs pathogen Human Pathogen 3 billion base pairs 170k – 4.6 million base pairs EVOLUTION OF DIAGNOSTICS IN CLINICAL MICROBIOLOGY Diploid chromosome Haploid circular & mobile genetic element 10-7 to 10-8 mutation 10-3 to 10-4 mutation rate Glossary rate (better stability) o Phenotype: observable characteristics o Genomic sequencing: decoding the genetic material o Genotype: genetic constitution § Identify o Polymerase Chain Reaction: makes copies of DNA rapidly § Similarity o Next Generation Sequencing: parallel sequencing of millions of DNA strands § Phylogeny (mapping out hereditary) simultaneously § Protein structure § Virulence factors o Metagenomics: study of genetic material (from environment or clinical samples) via o Roadmap: pathogenà extractionà sequencingàdata analysisàinterpretation NGS o Types Role of clinical microbiology lab: Diagnosis, Treatment, Protection/Prevention § Whole genomic sequencing determines the entirety of the genome o Why send a sample: diagnosis and guide therapy § Next generation sequencing allows parallel sequencing of millions of DNA o What is the ideal report: § Amplicon sequencing for genetic variations § Informative § Metagenomic sequencing evaluates bacterial diversity § Accurate Pathogen genomics o Bioinformatics (information about DNA and amino acids) § Timely (turn-around time); Why does time matter? o Sequencing outputs SEPSIS treatment § FASTA File Antimicrobial stewardship § FASTQ File (same as FASTA but has a quality score) Prevent emergence of resistance o Pipeline (a set of complex. Algorithms used to extract and produce bioinformatics) Patient length of stay o Process: genomic dataà bioinformatic analysisà data visualisation o Phylogenetic tree: Node à Branch à Tip Koch’s Postulates (whether a microorganism causes a disease) o Min spanning trees: o Found in abundance § Labels: o Grown in pure culture Node labels: isolate ID o Cause disease Distances (no of differences between two isolates) o Reisolated and being identified as causative agent for diseased host Size of nodes: proportional to no. of sample Reasons cannot isolate pathogens § Outbreak appearance o Fastidious growth requirements (need for specific nutrients, pH, temp) Colour adds help o Previous antimicrobials Circles closer together = more similar isolates Larger circles = multiple isolates indistinguishable by sequencing o Safety Lines between circles = how many differences (alleles/SNPs) between o Technical difficulty (viruses) samples Traditional vs Molecular testing 4 5  Options Traditional Molecular Benefits Challenges Grow it Yes No Decrease human error Capital Detect it Yes Yes Enhance efficiency Operator training Phenotypic test Yes No Higher throughput Burden of maintenance Biochemical tests Yes ? Free lab staff for other tasks Deskilling workforce Genomic tests Yes Yes o NGS (Clinical metagenomics) Susceptibility tests Yes No § Simultaneously sequence millions of small fragments of DNA Detect mechanism AMR Yes Yes § Identifies all microorganisms, their susceptibilities and human nucleic acid Time 48 hours – weeks… 1 - 6 hours § Usage: avoids need for culture, able to understand entire community of pathogen, analyse host response to infection. o Molecular testings Benefits Challenges § PCR based tests Hypothesis-free, unbiased Sample turn-around time long Detects antimicrobial resistance (genotype) Detection of non-culturable organisms No standardisation Pros: Rapid result (faster than culture) Detect all potential pathogens Regulatory considerations Cons: Rely on knowing the genes, No MIC (min inhibitory Predicts infection Result interpretation complex concentration), Possible multiple mechanisms of resistance Diagnostic and surveillance application Expensive Laboratory techniques o Artificial Intelligence o Catheter Specimen Urine (CSU) § Computational models interpret visual results (gram stains, cultures) § Light microscope (squamous epithelial cells indicate contamination) § Potential roles: accurate prediction of multidrug resistance, personalised § Culture: antibiotic prescriptions, develop support systems Quantitative plating (UTI if ≥105CFU/ml of microorganism) Benefits Challenges Culture media Increase workforce capacity Process unknown § MALDI-TOF: Benchtop mass spectrometer (species level) Increase efficiency of lab Require extensive certification § NAAT: Targeted AMR detection for specific genes capable of resistance Reduce some costs Trust of system § Susceptibility testing (standardize inoculum and growth conditions) helps with Escalates cases for technical review phenotypic susceptibility (observing the organism’s actual behaviour when exposed to antimicrobial) o Blood Culture ANTIMICROBIAL RESISTANCE AND ONE HEALTH IMPLICATIONS § Automated blood culture machine: incubated at 37ºC up to 5 days; automated Definitions detection of bacteria by machine o Attributable mortality: mortality directly exposure § Gram stain (guides therapy) o Associated mortality: mortality directly/ indirectly related to exposure § Culture (blood from positive bottles inoculated onto culture media AMR threatens global security & development, health and delivery of healthcare, mainly Genotypic vs Phenotypic resistance affecting low and middle income countries. 70% of AMR infections occur in healthcare Genotypic Phenotypic facilities Genetic mutations bring about Microorganism survives and grows in Clinical impact of AMR resistance antibiotic o Increased length of stay in hospital / ICU admission PCR, NGS Culture-based: Broth microdilution, o Prolonged recovery time disc diffusion o Disruption to routine rpoB gene via PCR m.Tuberculosis grows in rifampicin o Loss of function / Morbidity / Disability / Mortality Surveillance screening samples (provides IPC practice guidelines) o Financial stress o On patient: rectum, nostrils, groin, axillae o Reliance on 2nd or 3rd line agents à Treatment complicationsàmore AMR o Environment: high touch surfaces, sanitary ware (sinks, toilets, showers) OneHealth o Screening whole samples is more sensitive than individual isolate samples at o Definitions identifying low within-sample prevalences of resistance. § Multidisciplinary and multisectoral approach; health of humans, animals and Benefits and Challenges of integrating emerging diagnostic techniques in labs ecosystems are interlinked and facilitate the development and spread of o Laboratory automation disease. 6 7  § Human activities (population overgrowth, climate change, land use change) § Concerns about profiteering from data collected that stresses ecosystems lead to disease emergence and spread. o Joint Programming Initiative AMR (JPIAMR) innovation themese o Approach to AMR § Prevention and mitigation § Decreasing use of antibiotics § Therapeutics § Optimizing consumption of antibiotics § Diagnostics o Examples of OneHealth issues § Surveillance § Zoonotic diseases § Transmission and evolution § Vector borne diseases § Food animal diseases § Contamination of water / sanitation HEALTH-CARE ASSOCIATED INFECTION AND MODES OF TRANSMISSION § AMR Glossary: Drivers of AMR o Fomite: an inanimate object that, when contaminated with or exposed to infectious agents can transmit disease to a new host o Healthcare related o CLABSI: Central-line associated bloodstream infection § Misuse / overuse antimicrobials Healthcare Associated Infection: Infections acquired at hospital or healthcare setting which § Poor access to medications were not present at time of admission. § Limited awareness and knowledge o Types: respiratory (PNEUMONIA), gastrointestinal (c.difficile), Skin/soft tissue § Suboptimal IPC (catheter/IV), SURGICAL SITE INFECTIONS, Device associated infections (dialysis, § Poor access to vaccination VAP), URINARY TRACT (CATHETER ASSOCIATED UTI) § Poor antimicrobial stewardship in veterinary medicine o European Centre for Disease Prevention and Control collects, collates, evaluates and disseminates relevant scientific and technical data o Non-healthcare related o Clinical features: § Poor Infection, Prevention and Control (IPC) measures § Onset >48 hours post admission § Mass migration § Signs of infection § Lack of access to clean water § Risk factor/exposure § Contamination of natural environment § Diagnostic criteria o Food production-related o Pathogen types § Antimicrobial agents § Endogenous: normal microbial flora (harder to prevent); due to decreased mobility, endotracheal tube, IV catheter, urinary catheter § Exposure of animals or crops to contaminations § Exogenous: from the surrounding environment; due to contaminated surfaces, § Insufficient biosecurity healthcare worker, infected patient o Natural environment-related o Transmission modes: § Climate change (higher temperatures, floods, storms) § Contact (physical) § Biodiversity loss § Respiratory droplets (2 meters); TB, measles, chickenpox; FFP2/N95 mask o Risk factors: International data sharing for AMR § Advantageous microbial adaptation: treatment resistance, virulence, biofilm, o Data operability: data can be accurately interpreted between different organizations spore and systems; not ambiguous; formatted correctly § Vulnerable host: underlying illness, immunosuppression, extremes of age, o Disease preparedness: broad-range of surveillance medical devices, surgery o Data is widely available and shared between regions and countries by § Sub-optimal environment: poor IPC practices, hygiene, infrastructure, § Standardizing processing methods antimicrobial stewardship § Track and evaluate epidemiology o Standard precautions: Hand hygiene, single-use equipment, PPE, Respiratory hygiene and cough etiquette, Safe handling and disposal of sharps, aseptic o Importance technique, environmental controls, appropriate handling of waste § Expansion of genomic data Outbreak classification § Strengthens and allows actions to be taken o >2 linked, same illnesses or, § Decision making for security and resilience o Number of cases exceeds expected number or, § Warns of potential spill-over transmissions o Single case of disease caused by a significant pathogen o Risks § Privacy of donors: collecting data with consent § Confidentiality: prevent unauthorized breach of data 8 9 PATHOGEN SURVEILLANCE Evolution of pathogen surveillance o More automated (digital database) Disease surveillance: collection, analysis and interpretation of large volumes of data i.e. o More discriminatory (highly discriminatory e.g. NGS) clinical, laboratory, epidemiological, resource use o Application of Artificial Intelligence Case definitions Whole genome sequencing Case Possible Probable Confirmed o Gold standard in terms of surveillance and outbreak investigations. Described in case Yes Yes No o Entire genome is sequenced definition o Purpose: tracks lineage; understands circulating variants; provide up-to-date Clinical criteria Yes Yes Yes genomic epidemiological data Epidemiology No Yes No o Highest discriminatory power (ability to distinguish between different strains based Lab confirmation No Partial Yes on genetic information) Sensitivity High - Low Waste-water based epidemiology Specificity Low - High o Analysis of sewage and wastewater to monitor presence, distribution and prevalence Detection Most cases Lab test Miss cases of diseases (false positives) for some (false negatives) o RNA from fecal matter can be analysed and identified o Helps facilitate clear communication o Process: pathogens excreted à conveyed to sewage à sample collected in lab à o Standardises basis for epidemiologic research samples are processed à detect pathogen à report results o Allows identification of outbreaks, and enables comparison and analysis of trends Expanding pathogen surveillance program beyond centers o Standardise what is a case (same language) WORKING IN HEALTHCARE o Ensure cases are reported (mandatory reporting) The Tuckman Model: Forming, Storming, Norming, Performing, Adjourning o Have somewhere central to report cases (national/international sys) The LaFasto and Larson Model: o Analyse data (expertise and resources) o Organisational environment, Team leadership, Team problem solving, Team o Disseminate data (communication networks) relationships, Team member Notifiable diseases o Characteristics of team excellence: clear goal, result driven structure, competent, o Legal requirement to notify a designated public health official commitment, collaborative, support, recognition, principled leadership o Information used to: (1) initiate investigation and prevent further cases, (2) early Characteristics of effective teams: Interdependent, who share common goals and must identification of outbreaks, (3) monitor the burden and changing levels of disease, (4) coordinate with key characteristics being: evidence for public health interventions (immunisations) o Dynamic teaming Purpose of surveillance data o Psychological safety o Early identification of outbreaks o Diversity o Monitoring trends in AMR o Inclusivity o Evaluating effectiveness of IPC measures The Hackman Model o Identify high risk populations o Enabling conditions of Group Effectiveness o Support planning of resources § Compelling purpose o Archive of disease activity (future reference) § Right people o Benchmarking against other facilities § Real team o Informing empiric antimicrobial guidelines § Clear norms of conduct Analysis of results § Supportive o Single dataset: identify species, antimicrobial susceptibilities, allows national and § Team focused coaching international reporting on trends o Five factors of team effectiveness o Multiple dataset: multiple patient data allows comparisons § Consistent defined group (depends on each other) Surveillance § Compelling direction (unified mission) o Levels § Enabling structure (shared habits that help work happen) § Local: hospital laboratory, surveillance scientist § Supportive context (access to tools and resources) § National: Reference laboratories, HPSC (Health Protection Surveillance § Expert coaching (develops the team) Centre, Ireland) Purpose of effective teams § International: ECDC, GLASS, EARS-Net (European AMR Surveilance o Increase complexity and specialisation of care Network is the largest AMR surveillance in Europe. o Reduce hospitalisation and associated costs o Why screen asymptomatic patients? o Improve levels of innovative care § Isolate patient to prevent / reduce onward spread o Enhance patient satisfaction § Determine choice of appropriate antimicrobial treatment o Mental well-being o Programmes: AMR-gene confirmed à Notify à Data provided to o Reduce sickness absence national/international surveillance o Reduce error rates 10 11 o Reduce violence and aggression CYSTIC FIBROSIS o Lower patient mortality INTRODUCTION TO CYSTIC FIBROSIS Progressive, autosomal recessive disease affecting lungs, pancreas, GI tract o Clinical features § Thick mucus production § Bacterial infection (CFTR gene also seen in neutrophils and macrophages disable these cells from phagocytosis and lysing mechanism) § Chronic inflammation/ bronchiectasis Pathophysiology o Mutations in CF transmembrane conductance regulator (CFTR gene) o CFTR protein at apical membrane becomes dysfunctional o Unable to move chloride to the cell surface o Reduced volume and increased hyperviscosity of mucus o Organ damage CFTR protein (ATP-binding cassette (ABC) transporter superfamily) o At apical membrane of polarised epithelial cells o Cyclic AMP-regulated (phosphorylated by Protein Kinase A) o Acts as chloride channel o Process: CFTR moves Cl from inside to outside of cell. Chloride outside will attract a layer of water. This helps tiny cilia to move in a sweeping motion to remove mucus up and out. CFTR mutations o If both parents are carriers of CF then 25% chance of having CF o F508del is the commonest cause of CF (70% of CF patients carry at least one copy) Minimal function (95%) : Severe Residual function (5%): Mild MF 1 2 3 4 5 6 7 Reduced Cl- CFTR X protein X protein Channel level of conductance stability No mRNA synthesis folding dysregulation CFTR reduced reduced protein - F508del G551D - - - - Manifestations in early childhood: o Birth/Infancy: failure to thrive, meconium ileus, intestinal obstruction o Childhood: failure to reach growth milestone, recurrent chest infections, abdominal cramps, diarrhoea o Lung disease in early childhood (3-month old) § 81% on abnormal CT (mucus plugging, air trapping, bronchial wall thickening) § BAL (inflammation (IL-8) and bacterial infection) Manifestations in adults o Lung disease in adults: onset few days-weeks § Productive cough § Sputum volume, purulence and viscosity increase § Wheezing § Haemoptysis 12 13  o Pancreas § Pancreatic insufficiency (test for Fecal Elastase) § Fatty infiltration of pancreas (fat replaces pancreatic cells) § Recurrent pancreatitis o Gastrointestinal § Conditions: Malabsorption, GERD, Rectal prolapse, DIOS (distal intestinal obstruction syndrome), Meconium ileus § Sites: Large bowel (constipation, colonic ca) Small bowel (DIOS – recurrent abd pain) Upper GI (Vomiting, GERD) o Liver § Focal biliary cirrhosis, fatty infiltration, cirrhosis with splenomegaly, varices § Jaundice, itch, abdominal pain, gallstones, haematemesis o CF-related diabetes: polyuria, polydipsia, lack of energy, failure to gain weight o Osteoporosis o Delayed puberty / growth retardation o Obstructive azoospermia [CBAVD (Congenital Bilateral Absence of Vas Deferens)] o CF-renal disease: compounded by aminoglycoside usage and diabetes Respiratory complications o Infectious: Physical findings § Obstructive airway disease o General inspection § Respiratory failure § Reduced BMI, Delayed puberty § Mucus plugging § Clubbed ± cyanosis, ± oxygen o Non-infectious: § Tremor § Haemoptysis, § Tachypnoea (using accessory muscles) § Pneumothorax (pleuradiesis contraindicated) o Chest: Hyperinflation ± portacath, Crepitations, Wheeze § Allergic bronchopulmonary aspergillosis o Abdomen: Hepatospelnomegaly ± PEG tube Wheeze o Diabetes o Diagnosis of acute exacerbations Unresponsive to antibiotics § Increased cough/sputum/congestion/dyspnoea/fatigue Thick mucus plus § Decreased appetite/ FEV1 Raised IgE § Change in sputum § Atelectasis Outpatient Monitoring: FEV1, BMI, Sputum CF culture Mucus plugging Annual measurements: Acute SOB o OGTT (HbA1C) Hypoxemia o Liver US § Advanced disease o Vitamin levels Type 2 respiratory failure o Bone densitometry (DEXA scan) Pulm hypertension with Cor Pulmonale o CXR o IgE, RAST Aspergillus Diagnosis of CF o FBC, U&E, LFT’s, Ca/Phos, Protein, Albumin o Step 1: New Born Screening CF scoring system: ABLE score o Step 2: Sweat Chloride o A – Age < 24 o Step 3: CFTR Genetic Analysis (if mutation of varying clinical consequence then o B – BMI < 20.1 proceed to step 4) o L – Lung function < 52.8% o Step 4: Physiologic testing o E – Exacerbations needing IV antibiotics in last 3 months > 1 § NPD : Nasal potential difference Management : To slow/stop disease progression & prevent/treat complications § ICM : Intestinal current measurements o Potentiators: improve CFTR function at cell surface (facilitates Cl- flux) § Ivacaftor § Need one copy of G551D mutation (class 3 mutation) § Binds to CFTR protein at cell surface à opening the channel § Starting in utero has been shown to delay/ prevent end organ damage. s 14 15  o Corrector: improve CFTR protein folding and trafficking (support movement of CFTR o P.aeruginosa (aggressive treatment) proteins to cell surface) § 2 weeks tobramycin IV with o Examples either ticarcillin/clavulanate or ceftazidime Kalydeco Ivacaftor G551D; gating mechanism § Then, 2 months of tobramycin per neb Orkambi Lumacaftor (cor) + Ivacaftor homozygous F508del § Then, 1 month of ciprofloxacin PO Symdeko Tezacaftor (cor) + Ivacaftor homozygous F508del Trikafta 1 Potentiator (Ivacaftor) + homozygous F508del o Anti-inflammatories for CF pts > 6yoa (>40kg) (ETI) 2 Correctors F508del + MF mutations § Azithromycin 3 x 500mg/week PO (alternate days) (Tezacaftor & Elexacaftor) Single F508del mutation § High dose ibuprofen (peak plasma concentration of 50-100ng/ml) TRIKAFTA has the greatest efficacy with min S/E; o CF mutations without therapies § Improved lung function and QoL; § Gene therapies (RNA, DNA) § Approved for anyone with ≥1 copy of F508del mutation; § Gene editing (CRISPR, Base editing) § Improves chronic rhinosinusitis and resp symptoms; § Read through § Decrease pulm exacerbations; § Anti-sense oligonucleotides § AAT (a1-antitrypsin), IL-6 and TNFaR (tumor necrosis factor alpha receptor) levels decrease Follow-Up Lifestyle therapies o Review every 3 months with sputum or spirometry o Dietary supplements: o Every 6 moths – nutritional screen § pancreatic enzymes (Creon) o 1 year evaluation – CXR, Abd US § fat soluble vitamins (Aquadek) § high fat diet § PPI § PEG feeds (Perative, Nutrison) § Insulin (diabetes) § Ursofalk (liver disease) o Physical therapies: airway clearance, physio, exercise Mucolytics: o rhDNAse = Dornase Alpha (Pulmozyme) OD per neb o Mannitol (Bronchitol) BD o Bronchodilators: Salbutamol, Ipratropium (per neb) o Hypertonic saline (3% - 7%) BD/TDS § Decreases hyperviscosity of mucus § Breaks ionic bonds (Disrupts structure of mucus) § Increases depth of airway surface § Stimulates cilia movement § Induce cough to clear sputum § Absorbs mucus from mucosa and submucosa, reducing oedema in airway wall. § FEV and FVC increases o Non-invasive Positive Pressure Ventilation (NIPPV) o Antibiotics Pathogen Treatment H.Influenza, S.aureus Co-amoxiclav (PO) P.aeruginosa Tobramycin, Colistin, Aztreonam (per neb) Aspergillus Prednisolone (PO OD) (Allergic …or… Bronchopulmonary Methylprednisolone (IV monthly) ± Aspergillosis) Itraconazole (PO, 12-18 months) Strenotrophomonas Sulphamethoxazole / Trimethoprim-Septrin MRSA Vancomycin or Linezolid MSSA Flucloxacillin Infections o Staph Aureus in first few years of life à Cephalexin PO § Decreases S.aureus § But increases P.aeruginosa P.aeruginosa 16 17 1. Resistant to antibiotics 2. Virulence factor a. Elastase b. Alkaline Phospatase 3. Pro-inflammatory CLINICAL TRIALS PROCESS IN CF EPILEPSY SEIZURES Transient occurrence of signs / symptoms due to abnormal excessive/ synchronous neuronal activity in brain New onset seizures happen in pts over 65 yoa Classification of Seizures: o Focal epilepsies: focal aware, focal impaired awareness, progression to tonic- clonic FIA Absence (focal impaired awareness) Duration < 10 secs 2 – 3 mins Automatisms Doing something Simple Complex unconsciously Post-event Normal Fatigue Generalised Spike and Wave EEG Focal seizure onset (3Hz spike wave) Imaging Normal Normal / lesion Valproate, Lamotrigine, Treatment AEDs / Surgery Topiramate o Generalised epilepsies: absence, myoclonic, tonic-clonic, tonic/atonic (drop seizure), atypical absence Subtle seizures: focal aware, focal with impaired awareness, absence, myoclonic jerks (during wakefulness) Not all events are seizure: o Convulsive syncope: § Neurally mediated reflex syncope Vasovagal syncope (cardioinhibitory, vasodepressor) Carotid sinus syncope Reflex syncope (micturition) § Postural hypotension § Cardiac outflow obstruction § Arrhythmia o Non-epileptic psychogenic seizure: § beware of frontal lobe seizure § requires EEG monitoring Not all seizures are due to epilepsy (Acute Symptomatic Seizure) o Causes: Hypoglycaemia, Eclampsia, Alcohol Withdrawal Syndrome, Acute CNS insult, Encephalopathy, Medications (therapeutic/overdose), Environmental toxin, Multi-system disorder, Cancer-associated o Treatment: short term Localisation o Praecuneus: altered visual perception o Primary visual cortex: flashing lights o Hypothalamus: gelastic seizure o Mesial prefrontal / ant. cingulate: hyperkinetic, ictal fear, vocalisation 18 19  o DLPFC/ Orbitofrontal: complex automatisms, dialeptic o Treatment: Epidyolex (cannabidiol), Felbamate ± Rufinamide o Frontal eyefields: head / eye version (Glutamergic NT reducers) o Precentral: clonic, tonic (face, arm) DRAVET SYNDROME (Development and Epileptic Encephalopathy) o Post-central: tingling/ numbness o Severe myoclonic epilepsy of infancy, intellectual disability, o Superior parietal lobule: altered body perception typical gait disorder o Parieto-occipital junction: eye version, nystagmus o SCN1A gene (80%) o Temporal neocortex (Heschi’s): auditory aura o ASM: Valproate, Levetiracetam, Clobazam, Stiripentol o Frontal operculum: hypersalivation o Na channel blockers worsen condition in loss of function o Broca’s: expressive languageI mutations, but better in gain of function. o Insula: nausea, abd aura, pain, sweating o Gene therapy: STK-001 o Amygdala: tachycardia, apnoea Epilepsy syndromes o Mesiotemporal: behavioural arrest, gustatory/psychic aura o Refers to combination of cause, EEG, image findings, course, drug responsiveness and prognosis o Childhood epilepsy syndromes EPILEPSY OVERVIEW § West syndrome Characterised by 2 recurrent unprovoked seizures within 24 hours § Epilepsy-aphasia syndrome o Risk of premature death 2-3 times higher § Tuberous sclerosis complex o 4-fold increase risk of additional co-morbidities § Rasmussen’s syndrome Aetiology: Unknown (40%), Structural (tumour, vascular, trauma), Genetic, Infectious o Adult epilepsy syndrome (encephalitis, abscess, meningitis), Metabolic (Pyridoxine-dependent seizure, porphyria) § Syndrome of pure MTS Processes associated with Epileptogenesis (when the brain gradually develops epilepsy): Gliosis, § Juvenile Myoclonic Epilepsy Inflammation, Neuronal loss, Neurogenesis, Plasticity o Status Epilepticus – Medical Emergency! Classification § Epileptic activity > 5 minutes o Focal: Acquired, Unilateral/focal, MRI abnormal § > 30 minutes: long term damage, high death rate § Symptomatic: Driving: Lobar, lesional, unifocal, multifocal o Stable and free of functionally disabling seizures during wakefulness for >1year. Temporal Lobe Epilepsy (acquired after precipitating injury); most o Can drive Group1 vehicle with anti-epileptics, not Group 2 common (60-70% in adults); involves limbic system, prone to drug o Self-declare to the insurance company and NDLS refractory Diagnosis: History, Collateral, Risk factors, Family History, Precipitating injury, Examination § Idiopathic: self-limited usually normal Self-limited epilepsy with autonomic seizure 1-14yoa Imaging modalities: CT, MRI, PET, MEG, SPECT Group 1 Multifocal high volt spike Treatment decisions: (SeLEAS) (3-6 peak) Self-limited epilepsy with centrotemporal 3-14yoa o 15% recurrence à no meds Centrotemporal spikes 1 TC seizure + normal EEG + normal MRI + no focal onset spikes (SeLECTS) (7 peak) Childhood occipital visual epilepsy (COVE) 1-19yoa o 30-50% recurrence à treat / no treat Group 2 Occipital spikes 1 TC seizure + one abnormality (8-9 peak) Photosensitive occipital lobe epilepsy 1-50yoa o 80% recurrence à meds Occipital spikes 1 TC seizure + three abnormalities (POLE) (4-17 peak) o Generalised: Genetic, Bilateral, Normal MRI Surgery: § Unknown o Focal ablation (laser heat destroys cell) § Idiopathic: o Focal resective surgery Primary generalised o Callostomy Epilepsy with tonic-clonic seizure (grand mal upon awakening) o Vagal nerve stimulation JUVENILE MYOCLONIC EPILEPSY (common) o Stereotactic Laser ablation of Hippocampus (SLAH) o Myoclonus (100%), Generalised TC seizure (95%), Absence (40%) ANTI-EPILEPTICS DRUGS o Frequently underdiagnosed § Symptomatic: Principle LENNOX-GASTAUT SYNDROME (Genetic) o Neurotransmitters: mediate rapid, synaptic actions; eg. Glutamate (excitatory) & o Spike and slow wave on EEG (40% relapse and develop treatment resistant metastatic disease intelligence without explicit programming o Mutations o Reinforcement learning: utilises rewarding desired behaviour and punishes § Family Hx 10% undesired behavior § Li-fraumeni-like syndrome (germline mutation in T53) o Deep learning: utilises artificial neural networks and big data to uncover complex § PALB2, p53 (tumour suppressor) relationships and enable complex tasks § BRCA1/2 (DNA damage) o Machine learning: utilises statistics-based algorithms to enable computers to predict Molecular subtypes patterns and improve tast with each experience o Luminal A (40%): ER+, PR+, HER2- Challenges in diagnosis: § Low-level Ki-67; most-prevalent o Variability in seizure presentation § Best prognosis; slow growth o Limitation of diagnostic tool: Scalp EEG (limited sensitivity), intracranial EEG § Hormone therapy (invasive), Surgical planning (difficulty in localising seizure onset zone) o Normal-like (8%): ER+, PR+, HER2- o Individualised assessment (no tool to predict risk of assessment, no tool to § Low-level Ki-67; slightly worse prognosis than luminal A accurately assess risk of recurrence) § Endocrine tx o Lifestyle modification challenge o Luminal B (20%): ER+, PR±, HER2± Application in Epilepsy: (1) Neuroimaging interpretation, (2) EEG interpretation, (3) Surgical § High-level Ki-67 planning, (4) Medical device applications, (5) Drug discovery, (6)Image quality § Hormone therapy + Herceptin (if HER2+). Chemo also be used. enhancement, (7) Personalised treatment o HER2 Enriched (10-15%): ER-, PR-, HER2+ Challenges of implementing AI in epilepsy: § Amplification of HER2 receptor o Data quality and availability § Faster growth, more spread and higher recurrence o Integration with clinical workflows § Poor prognosis, better than TNBC o Real-time data processing § Chemo + HER2 therapy o Model drift (requires continuous monitoring) o Triple Negative (15%): ER-, PR-, HER2- o Trust and Liability § Most aggressive; Worst prognosis; Likely recurrence o Data Privacy and Security § BRCA1 mutations o Black Box (Interpretability) § Chemo tx o Workforce barriers Current therapies o ER+ § Tamoxifen: modulate estrogen receptors § Aromatase inhibitors: reduce circulating estrogen o HER2+ § Monoclonal antibodies: Trastuzumab (Herceptin) § Monoclonal AB with payload: Trastuzumab emtansine (T-DM1) § Small molecule inhibitors: Lapatinib, Neratinib Breast cancer metastasis: Brain, bone, lung, liver Diagnostic methods and NGS tools o NGS: rapidly sequence known or suspected hereditary cancer risk-related genes; detect mutations at once; identify novel germline variants o WGS: comprehensive picture of germline mutations across the entire cancer genome o Targeted sequence studies: assess only genes that have known associations with cancer predisposition (reducing sequencing costs and data analysis burdens) CURRENT AND FUTURE APPROACHES TO TARGETING GENETIC AND TRANSCRIPTOMIC ABBERRATIONS Druggable targets for breast cancer o To exploit cancer vulnerability o Inhibit crucial pathways for cancer development 26 27  o Targets: proteins (mass spect.), genes (WGS, RNA-seq), epigenetic markers o RET (methyl-seq, ChIP-seq, ATAC-seq) § RET (Rearrange during Transfection) Multiomics: identify the genes, proteins, metabolites and epigenetic markers is a protooncogene encoding Receptor Tyrosine Kinase o Identify the best potential target found in the central and peripheral nervous system § Can rank genes, protein, metabolites and epigenetic markers RTKs: Phosphorylation by these TKs regulate signal transduction in § Based on their differential expression/regulation, network centrality, functional response to intra/extracellular stimuli annotation, etc. § RET (gain-of-function) mutations exhibit resistance to SERMs o Data integration: interactions between these groups § Dysregulation of RTK is common in all cancers. o Intraindividual variability of drug responses (how individuals respond) § TK inhibitors (Lapatinib, Cabozantinib): block abnormal signal transduction o Classifying patients (cluster individuals based on their molecular signatures of drug pathways for cell proliferation response) Treatment for HER+ enriched breast cancer o Predict the optimal drug response (estimate efficacy, safety, toxicity, adverse effects, o Monoclonal antibody: Trastuzumab (Herceptin) resistance, sensitivity, etc) o Drug conjugates (ADCs): Ado-Trastuzumab Emtansine (T-DM1) o Single Cell Multiomics: improves our understanding by uncovering cellular § ADC attacks cancer cells expressing HER2 on cell surface heterogeneity; maps interactions; characterise spatial organisation within cells § Then phagocytosing, to release cytotoxic payload à death Molecular characteristics of breast cancer o Combined with Derutexan (chemo drug) for HER2-low phenotype o Genetic: mutations / amplifications in proliferating genes (inhibition of tumour Mutations in Triple Negative Breast Cancer (subtype-specific) suppressor or activation of tumour promoter) o LAR (Luminal Androgen Receptor): PI3Ki, Trastuzumab o Epigenetic: global hypomethylation (gene activation), hypermethylation (gene o BLIS (Basal-like Immune Suppressed): Immunotherap, p53, cell cycle-i silencing) – to methyl, is to silence o IM (Immunomodulatory): RETi o Post-translational modifications: tumour suppressor protein (p53) ubiquitination o MES (Mesenchymal-like): EGFRi, RETi ER+ breast cancer (Estrogen Signalling) o BRCA: PARPi (Olaparib) o Uses ER-alpha and ER-beta nuclear receptors § PARP repairs single-stranded (SSB) DNA breaks § Ligand dependent transcriptional regulation § BRCA repairs double-stranded (DSB) DNA breaks § Ligand independent activation (consequence of downstream tyrosine kinase § When PARP enzyme is inhibited, the SS is not repaired signalling) § Unrepaired SSB evolves to DSB § Ligand dependent non-genomic mechanism § In cells with BRCA mutation, DSB cannot be repaired à instability à death o Therapies (anti-estrogen) Cancer epigenetics (more in Genomics) § 1. SERM (Selective Estrogen Receptor Modulators, tamoxifen): inhibit binding o DNA methylation à DNMT of oestradiol to ER; 1/3 will relapse § DNA MethylTransferase for drug resistance § 2. AI (Aromatase Inhibitor, anastrozole): reduce estrogen production; prevent § MOA: Gene hypermethylation = silencing (tumour suppressor) aromatase from converting testosterone to oestradiol o Histone methylation à EZH1-EZH2 dual inhibitor (Valemetostat) § 3. SERD (Selective Estrogen Receptor Downregulator, Fulvestrant): ERD-ER o Histone acetylation à HDACi (Tucidinostat) complex is unable to translocate to the nucleus and induce gene transcription § Changes the transcriptional activity of genes via, Resistance to endocrine therapy (intrinsic or acquired) § HDACs (histone deacetylase) & HATs(histone acetyltransferase) o ESR1 mutations o RNA methylation: m6A modifiers (biomarker) § Encodes ER-alpha (binds to estrogen to promote gene expression; blocked § Aberrant expression of m6A modifiers cause tx resistance and impaired using SERMs in cancer tx) antitumour immunity § ESR1 mutations found in circulating tumour DNA for metastatic breast cancer § However, is also a predictive value for diagnosis and treatment after relapse using AI. Combining epigenetics with resistance in ER+ cancers o PI3KCA signalling in cancer o PI3K/AKT phosphorylates DNMT1 à stabilise chromatin à DNA hypermethylation § Found in ER+/HER2- pts maintained § PI3K is a fam of lipid-kinase enzymes; involved in proliferation, apoptosis, cell o HDAC + ESR1 promoter à reduced H3K27ac à DNMT-1 mediated promoter à signalling and metabolism downregulate ESR1 à DNA hypermethylation § No estrogen à PI3K reactivates ER transcription o Tamoxifen (which induces autophagy of ER+ breast cancer cells) can become § PI3K inhibitor: Alpelisib (with Fulvestrant) resistant to cells, but when combined with HDACi redirects cell to apoptosis. § Screening: Therascreen o CDK4/6 role § Cyclin D-CDK4/6 complex controlled by extracellular proliferative/ inhibitory CURRENT PATHOLOGY APPROACHES TO GENETIC DIAGNOSIS signals Immunohistochemistry (key markers as below) § In cancer, this complex is hyperactivated and is independent of mitotic Oestrogen receptor (ER) detected stimulation o Becomes activated after oestrogen binding à translocate into nucleus § CDK4/6 inhibitors (Palbociclib): stimulate antitumour immune response (T cell o 70-80% of invasive cancers express ER activation) o Positive if ≥1% of tumour cells show staining 28 29  o ER+ better prognosis § STK11 (Peutz-Jagher) Progesterone receptor (PR) detected Risk management o Positive if ≥1% of tumour cells show staining o Increase surveillance (more mammograms, MRIs, breast exams) o PR+ better prognosis o Chemoprevention HER2 detected o Prophylactic surgery (preventative mastectomy/oophorectomy) o HER2 is transmembrane GF receptor (regulates cell growth); located on chromosome 17 o Gene amplification in 12-18% of invasive breast ca à HER2 overexpression à BREAST CANCER AND AI proliferation, angiogenesis and cell survival 2D mammography (gold standard for screening) o Membranous straining (0 to +3) o Challenges à missed / late-st