Biomarkers Discovery Validation and Implementation using Proteomic Techniques for Cancer Detection

This essay discusses the use of proteomic techniques for biomarkers discovery, validation and implementation in cancer detection. It explains the role of biomarkers in disease diagnosis and treatment, and highlights the potential of proteomics in identifying drug targets and pathways related to uncontrolled cell growth. The essay also covers the limitations of proteomics and the different technologies used for the separation and identification of proteins.

Biomarkers Discovery Validation and
Implementation

Table of Contents
INTRODUCTION...........................................................................................................................1
MAIN BODY...................................................................................................................................1
CONCLUSION................................................................................................................................4
REFERENCES ...............................................................................................................................5

INTRODUCTION
Biomarkers are defined as biological molecule, gene or any other specific characteristic
by which any pathological disorder or process is rectified. It is present in the blood on any other
biological fluid which gives the sign of abnormal and normal biological functioning. It is used to
analyse if the body is responding to the treatment or not. Common methods applied for
evaluating biomarkers are cancer screening, surrogate endpoint, prognostic and predictive. In this
essay proteomic techniques are introduced for biomarkers discovery. The discussion will be
based on how this method is used in biomarkers validation and implementation for detection of
diseases. In this report, the chosen biotechnological method used in biomarker discovery is
proteomic method and it is implemented for the detection of cancer.
MAIN BODY
Recently, the understanding of living being is propelled through advancement of genome
sequencing. Proteomic technology is used for the development and improvement of biology.
Proteomic biotechnology is used for the identification of potential biomarkers and also
applicable to assess tumour prognosis. Proteomic experiments are conducted with the aim of
development of health and clinical science. Proteomic technologies characterize protein
present in the body and monitor the changes in production. The proteomic biomarkers is
applicable for the detection of cardiovascular disease, AIDS, cancer and renal diseases. It is
applicable for identification of drug target by using protein interaction and chemical proteomics.
Over the last decade the application of proteomic technologies has been increased for the
identification of diseases and their treatment. This approach has became so popular in
detection and treatment of cancer. This makes identify biomarkers and protein expression
which is used to identify tumours and helps to classify the tumours. This technique is also
helpful to rectify potential responders for the particular treatment. This techniques helps
to identify and quantify the overall protein present in an organism. Cancer proteomics
analyses different expressed proteins of a cancer patient and further compared with
healthy tissue at various stage of cancer. Proteomics has became very famous as it is used for
the identification and modification of proteins (Uzozie and Aebersold, 2018).
Cancer is a disease which is identified by the uncontrolled cell growth and causes
tumours. Glycomic, epigenetic, imaging and genetic biomarkers are applicable for the
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identification and diagnosis of cancer. Abnormal growth of blood protein is selected as
biomarker for identification of cancer to detect and treat the cancer selected
biotechnological method is proteomic biotechnology. Proteomic biotechnology involves
three steps including separation and extraction of proteins as a biomarker in cancer,
identification of biomarker proteins and verification of biomarker protein. Normally, old
cells are replaced by the formation of new cells but in cancer, old cells do not die and grow
abnormally and spread to other parts of the body. This abnormal growth of cells make mass of
the tissue which is also known as tumour. Proteomic has a crucial tool for detection of biological
changes during tumour. Malignant tumours not only shows uncontrolled growth of the cells but
also resist medicines administered during the treatment (Xu and et. al., 2021). Proteomics
biotechnology is applicable for gathering informations about drug targets and pathways which is
related to uncontrolled cell growth. Proteomics based approaches are used for the detection and
analysis of biomarkers for the uncontrolled growth of the cancer. Hepatitis B virus which is
related to hepatocellular carcinoma is studied by using proteomics techniques by using patient
patient cell sample in liver tumours and further it is compared to the healthy tissue. This
technique is effective for the various treatment for hepatocellular carcinoma. To perform
proteomics, metabolic analysis and transcriptomics primary pancreatic models and genetically
engineered mouse models are being used in case of pancreatic cancer. With the help of
proteomics it has been analysed that in case of oncogenicity KRAS gets activated where as
there is loss of LKB1. LKB1 is responsible for regulating pathways related to DNA
methylation, serine metabolism and glycolysis. It is discovered by using proteomics that
NNMT expression get increased in omental metastases of patients. By using proteomics the
tumour and the stromal compartment can be differentiated. Proteomics is being used for
discovering the cause of enhanced metastasis in cancer. To examine a patient deprived xenograft
mouse model phospho-proteomics , proteomics and transcriptomics are being used. It is
discovered that level of stress hormone increases in case of breast cancer and leads to activation
of glucocorticoid receptor at metastatic region which makes the survival rate decreased. Due to
increased glucocorticoid receptor activity level of kinase ROR1 get elevated. Both
imbalance makes survival difficult and depletion of ROR1 causes reduction in metastatic
growth and delays survival. Multi-Omics analysis of transcriptome and proteome it is
detected that expression of Bach 1 is being increased. Accumulation of Bach 1 causes loss of
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keap1 and decreases patient survival rate. Proteomics biotechnology explains the crucial role of
target molecules in cancer metastasis which helps to get brief information about diagnosis,
treatments and prognosis. Sometimes cancer may have uncontrolled cells which are resistant to
anti cancerous drugs and proteomic approaches are used to identify those cells which are
resistant to anti cancerous cells (Shah and et. al., 2019). This also helps to discover the drug
targets which can overcome the drug resistance during the treatment. In certain cases it is
observed that uncontrolled cells which survive the treatment by administering anti cancer drugs
in pancreatic, breast and lung cancer demonstrate particular molecular mechanism and protein
expression and makes the survival rate poor for the cancer patients. By using such technology
the effect of chemotherapy can be maximized. In case of breast cancer the uncontrolled cell
shows drug resistance and proteomics helps to target new specific markers as well as therapeutic
targets for CSCs (Kubota, Funabashi and Ogura, 2019). In case of acute myeloid leukaemia the
reason behind poor clinical outcome is only targeting leukaemic stem cells. IL3RA and CD99
are biomarkers of the leukaemia stem cells and it is also used for the diagnosis. Alteration
of lipid and carbon metabolism is closely related to increment of CSCs. Those cancer cells
which are drug resistance can not be treated and interfere with the treatment process. Cases in
which cells become resistant to drugs are know as intractable cancers. Anti cancerous drugs are
not sufficient to deal with such cases. A special therapy is required for the identification of
particular proteins and discovers new therapeutic targets (Huang and et. al., 2020).
Proteomics biotechnology is applicable for studying molecular level cancer
treatments and discovery of new ways to treat cancer. Immunotherapy also became so
popular as alternative treatment. Immunotherapy activates immune cells in order to active
defence mechanism but in case of anti cancer drugs and chemotherapy there is no such activation
and cell become resistant to drug. It is very crucial to use biomarkers to evaluate prognosis and
cancer therapy by using immunotherapy. Analysis of protein present in the body receiving
immunotherapy gives the sign whether the therapy is responded by the body or not. Proteomics
are used for alteration of expression in response to various signals, diagnostic markers,
candidates for vaccine production and helps to understand pathogenicity mechanism. It is also
applicable for food technology and drug target identification. Main activities of proteomics
includes bioinformatics to analyse MS data, rectify specific proteins and it is a process to
simplify complex protein or peptide mixtures. There are certain limitation of proteomics
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includes risk of high false positivity, lack of standardization, complexity in identification and it is
very difficult to estimate low abundance of proteins. Proteomic tools used in the treatment or
identification of bio marks includes comet, blast, delta mass, chemCalc and entrez. Process
which are used for the separation and identification of proteins in proteomics includes two
dimensional gel electrophoresis, high performance liquid chromatography, denaturing
polyacrylamide gel electrophoresis or sodium dodecyl. A proteomics scientist apply a number of
quantitative proteomic approaches to evaluate analysis of proteins and their modifications to
ensure the development of high quality proteomics data. Different between proteomics and
genomics is that genomics refers to the study of genes and their modification where as
proteomics refers to study of protein for the identification of bio marks for the treatment and
diagnosis. Certain technologies are also available for such cases where proteomics are not
applicable (Johnson and et. al., 2020).
CONCLUSION
From the above essay, it is concluded that biomarker refers to measurement of protein
present in the body for ensuring disease state. Concentration of proteins reflects the presence of
disease state. Several techniques are used to detect the biomarkers and proteomics is one of
them . It is very helpful for the identification of cardiovascular, pancreatic and kidney diseases. It
is highly applicable in case of cancer identification specially in case of leukaemia. It made the
analysis of potential biomarkers accessible and alteration of protein expression indicates the
presence of uncontrolled cell growth. It is helpful for the identification of body response for the
particular treatment therapies. In such cases where cells become drug resistant and
chemotherapies do not work proteomic technologies are very useful because immunotherapy
activates the immune cells and helps to activate defence mechanism fights with cancerous cells.
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REFERENCES
Books and Journals
Huang and et. al., 2020. Mass spectrometry-based proteomic capture of proteins bound to the
MACC1 promoter in colon cancer. Clinical & experimental metastasis, 37(4), pp.477-487.
Johnson and et. al., 2020. Systematic review and analysis of human proteomics aging studies
unveils a novel proteomic aging clock and identifies key processes that change with
age. Ageing research reviews, 60, p.101070.
Kubota, K., Funabashi, M. and Ogura, Y., 2019. Target deconvolution from phenotype-based
drug discovery by using chemical proteomics approaches. Biochimica et Biophysica Acta
(BBA)-Proteins and Proteomics, 1867(1), pp.22-27.
Shah and et. al., 2019. LFQ-analyst: an easy-to-use interactive web platform to analyze and
visualize label-free proteomics data preprocessed with MaxQuant. Journal of proteome
research, 19(1), pp.204-211.
Uzozie, A.C. and Aebersold, R., 2018. Advancing translational research and precision medicine
with targeted proteomics. Journal of Proteomics, 189, pp.1-10.
Xu and et. al., 2021. Simultaneous and quantitative monitoring transcription factors in human
embryonic stem cell differentiation using mass spectrometry–based targeted
proteomics. Analytical and Bioanalytical Chemistry, 413(8), pp.2081-2089.
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