In-Depth Notes on Cancer Screening and Detection

PHAR44002 – Advanced Therapies: Cancer Screening and Detection/Biomarkers Notes

  • Intended Learning Outcomes:

  • Understanding of cancer screening and detection methods.

  • Knowledge of cancer biomarkers, their definitions, classifications, and technologies for detection.

  • Familiarity with various genomic fields: genomics, proteomics, metabolomics, transcriptomics, and epigenetics.

Cancer Screening: Purpose and Guidelines

  • Definition: Identification of preclinical diseases through simple tests to reduce mortality and improve quality of life.

  • Key Indicators of Validity:

  • Sensitivity: Proportion of true positives in those with the disease.

  • Specificity: Proportion of true negatives in those without the disease.

  • Evaluation of Screening: Success evaluated by reduced cancer mortality among the screened population.

Biases in Screening

  • Healthy Volunteer Bias: Participants tend to be healthier, wealthier, and more educated, affecting study validity.

  • Lead-Time Bias: Earlier diagnoses do not necessarily lead to longer survival times.

  • Length-Biased Sampling: Screening preferentially detects slow-growing lesions, leading to potential misrepresentation of survival benefits.

  • Overdiagnosis: Identification of benign tumors that do not require treatment but may be falsely classified as cancerous.- or cancerous tumours that are so slow growing that it is more likely for something else to kill the patient instead.

Cancer Detection: Screening Methods

  • Imaging Techniques:

  • CT, MRI, PET scans, and ultrasounds.

  • Histological Examination:

  • Biopsy and tissue analysis.

  • Molecular Diagnostics:

  • Blood and liquid biopsies, focusing on circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA).

Common Cancer Screening Methods

  • Cervical Screening:

  • Offered to individuals with a cervix aged 25-64, every 3 years (ages 25-49) or 5 years (ages 50-64).

  • Bowel Cancer Screening:

  • Offered to individuals aged 50-74 every 2 years.

  • Breast Screening:

  • Offered to women aged 50-70, with self-referral available for those over 70.


CTCS- circulating tumour cells- shed into bloodstream from primary or metastatic tumour sites transported via circulation to distant organs. Clincially significant for those with metastatic disease and implementatin of precision medicine. CTCs correlate with metastasis, poor prognosis and the chance of recurrence.


Cancer cells release free DNA molecules into circulation= ctDNA. cell free DNA , or cfDNA, in the plasma of cancer parients can be sued as an indicator for early detection, can guide treatment and monitoring response to therapy, including drug resistance.

Cancer Biomarkers: Definition and Classification

  • Definition: Biological molecules indicative of normal or abnormal processes in various body fluids, or tissues.

  • Clinical Relevance: Essential for early detection, diagnosis, prognosis, and monitoring treatment responses.

  • Can be used for the early detection of cancer using non/minimally invasive tests.

Types of Biomarkers

  • Predictive: Indicate likelihood of therapy success (e.g., MDSs with del(5q) mutation).

  • Prognostic: Estimate overall survival (e.g., TP53 mutations).

  • Diagnostic: Help diagnose cancers (e.g., Philadelphia chromosome in CML).

  • Molecular, physiologic, histologic and radiographic - identifying specific DNA/RNA or protein associated with a disorder.

Technologies for Detection of Biomarkers

  • Fluorescent Immunoassay: Utilizes specific immunological response and fluorescence sensitivity.

  • Radioimmunoassay: Detects antigen-antibody reactions through radioactive tracers.

  • Molecular Hybridization: Detects DNA/RNA sequences through hybrid formation.

  • DNA sequencing-analysis of base sequence of DNA fragments to detect any tumour markers.

  • PCR- amplify specific DNA fragments.

  • Immunohistochemistry- detects the distribution of antigens/ antibodies on tissue sections.

  • Liquid Biopsy: Tests tumor biomarkers in body fluids (cfDNA, cfRNA, CTCs, ctDNA).

  • Electron microscopy - visualise ultrastructure of cells and tissues

  • CRISPR/Cas9- gene editing tool based on bacterial immune system w ,ow cost, high efficiency.

Examples of Cancer Biomarkers

  • Alpha-fetoprotein (AFP): Liver cancer | Beta-2-microglobulin (B2M): Multiple myeloma.Found by blood test

  • CA15-3/CA27.29: Breast cancer | CA19-9: Pancreatic and gallbladder cancers. Found by blood test

  • Thyroglobulin: Thyroid cancer | Chromogranin A (CgA): Neuroendocrine tumors. found by blood test.

Importance of Genomics, Proteomics, Metabolomics, and Epigenetics

  • Genomics: Understanding genomic sequencing and variants for personalized medicine.

  • Proteomics: Study of proteomes for disease understanding and therapeutic insights.

  • Metabolomics: Characterization of metabolites for precision medicine applications.

  • Epigenetics: Role of modifications in DNA and histones affecting gene expression, critical in oncogenesis and genetic therapy.

  • Genomic medicine-

  • discovery research- assesses genotype-phenotype associations, idetifies people at increased risk of disease, finds all variants related to phenotype or disease and characterise variation of genes known to disease/ treatment response.

  • clinical validation- assess outcomes after use of genomics to direct therapy, assess effects of genomic info on health outcomes- using this for pts, families, providers/ care systems. can identify causes of rare / undiagnosed disease and validate drug targets and develop therapeutic agents.

  • clinical implementation- using results in critical care, develop clinical informatics for reporting genomic results and decision support. educate clinicians and patients of results.


FUNCTIONAL GENOMICS- investifation of large datasets given by genome sequencing to determine the function of genes, RNA and proteins.


COMPARATIVE GENOMICS- compares fenome sequences of different species- can lead to identification of regions of similarity and difference and help to improve disease treatment.


NEXT GENERATION SEQUENCING

NGS= powerful DNA technology allowinf the analysis of large amounts of genetic information quickly and accurately.


Sanger sequencing- amplification of specific DNA region by PCR, chain termination PCR uses fluorescently labelled dideoxynucleotides- each one stops DNA synthesis at different points. fragments are separated by size and sequence is read based on fluorescent signals- shows DNA sequence. Gives a chromatogram with peaks showimg the different nuceotides.

Is accurste bit slow- onyl sequences one dna fragment at a time, therefore suitable for small scale sequencing.


Second generation sequencing / NGS- genomic DNA broken into fragments and adapters attached to both ends. they are hybridised to a solid surface and amplified- form clusters. Incorporates fluorescently labelled nucleotides and cameras- they detect the light signals each time a base is added.

Data output - assembled into sequences for entire genomes or large regions.

Can sequence entire genomes/ many at once. Fast, cost effective, detects nucleotide substitutions, small insertions, deletions, copy number chromosomal rearrangements etc.


Proteomics- large scale study of proteomes (set of proteins produced in an organism). Proteome is not constant, differs between cells and over time. Can reflect underlying transcriptome. But protein activity is modulated by many factors and the expression level of relevant genes.


Metabolomics- comprehensive analysis of metabolites in biological specimen. Detailed characterisation of metabolic phenotypes - enables precision medicine .can be used to discover biomarkers that can then be used to diagnose and /or monitor therapeutics.


Histones- proteins that organise the genetic material. High % of basic AAs- overall positive charge.

pos charged AAs associated w overall neg charge of DNA. Histone modification influences association with DNA and gene expression.


Epigenetics important as genomics and proteomics are not enough.

Epigenetics - the study of heritable changes in gene expression that do not involve alterations to the underlying DNA sequence, playing a crucial role in cancer development and progression.

epigenetic changes affects gene expression.

DNA methylation controls how genes are turned on or off. Carried out by DNA methyltransferases. These enzymes found in higher amounts in cancers such as leukemias, brain tumours, breast, stomach, colon, liver, pancreatic, prostate, lung.

DNA methylation as a biomarker.

Methylation of CpG sites linked to poor outcomes in cancer patients.

GSTP1 gene methylation is potential diagnostic marker for liver cancer.

Methylation of NMDAR2B and PGP9.5 genes linked to poor survival in oesophagous squamous cell carcinoma.


Epigenetics and cancer

  • epigenetic modifications can lead to tumourgenesis

  • 3 main epigenetic mechanisms:

  • - DNA methylation by dna methyltransferase. Abnormal methylation patterns can silence tumour suppressor genes / activate oncogenes, leading to cancer

  • Histone modifications by Histone acetyletransferase (adds acetyl groups, activating gene expression), Histone lysine methyltransferase (adds methyl groups), histone deacetylase (removes acetyl groups, can silence genes) . These modifications affect how tightly DNA is wound around histones, influencing Gene expression.

  • miRNAs= microRNAs - small RNAs that regulate gene expression post transcriptionally, can silence target genes by binding to mRNA and causing degradation or blocking translation. Dyregulated miRNAs can silence tumour suppressor genes/ fail to suppress oncogenes- promoting cancer.

Conclusion

  • Comprehensive understanding of cancer screening, detection methods, biomarkers, and biological analyses can improve early diagnosis and treatment outcomes, benefiting patient care.

Future Outlook

  • Continuous developments in genomics and proteomics will enhance personalized treatments and precision medicine, improving healthcare outcomes for cancer patients.