Pathology Archives - InnoHEALTH magazine

Evolving Biomarkers in Pathology: Unveiling new avenues for disease detection and prognosis

InnoHEALTH magazine digital team — Fri, 04 Aug 2023 05:08:29 +0000

Biological markers might be either present or absent; or might be increased or decreased; or might be present in a changed form.

With the increasing importance and awareness of healthcare, the quality of care and patient safety have gained global concern. In this context, the need for biomarkers cannot be denied at all.

What are biomarkers?

The term “biomarker” is a merged/blended word of “biological marker”. Biomarkers indicate the underlying biological processes/events, either normal or abnormal taking place in one’s body. Biological markers might be either present or absent; or might be increased or decreased; or might be present in a changed form. They serve as indicators of an underlying disease process, determining the risk factors associated with a disease process. They provide crucial clues about one’s current health or to future health status.

Biomarkers can be found in blood, urine, stool, tumor tissue or body fluids. They are produced by the normal cells in response to a disease process or cancer or by the cancer cells itself. Biomarkers are available for various diseases: heart diseases, neurological diseases, renal diseases, infective disorders, genetic disorders, cancers etc.

What are the characteristics of an ideal biomarker?

An ideal biomarker should have the following characteristics:

It should be sensitive.
It should correlate with the severity of disease/damage.
It should express itself early in the disease progression.
It should be measurable in blood/urine.
It should be stable in a tissue so that it can be measured even after sometime has passed.
It should be visible prior to the histopathological changes.
It should give reproducible results.
It should be portable, reliable, and immediate.
It should be precise, sensitive and specific.

What are the types of biomarkers?

A. Molecular, histologic, radiographic or physiologic biomarkers.
B. Molecular biomarkers can be:

DNA (genes)
Proteins
Hormones

C. The other type of classification is:

1. Diagnostic biomarkers: Detects/ confirms the presence /absence of a disease condition. Also helps in identifying the disease subtype and helps in differentiating between different diseases. Example: High sensitivity Troponin assay helps in diagnosing myocardial necrosis.
2. Predictive/ prognostic biomarker: Helps to indicate how a disease may develop in an individual when a disorder is already diagnosed. Also helps to determine which patients might be benefitted from a specific treatment plan. To identify the likelihood of a clinical event, disease recurrence, or disease progression in patients with a disease.
3. Monitoring biomarker: This type of biomarker can be measured serially in order to assess the status of a disease. Example: Measurement of HbA1C, LDL cholesterol levels, INR (to adjust the dose of anticoagulants) etc.
4. Susceptibility biomarker: It indicates the risk for developing a disease in an individual who is currently not having any disease.
5. Safety biomarker: It is measured before/ after an exposure to a medical intervention to indicate the likelihood, presence or extent of toxicity as an adverse event.
6. Treatment- response biomarker: Helpful to differentiate patients on the basis of their outcomes related to efficacy and side effects (responders/non-responders and patients with/without adverse drug reactions).

Macromolecules such as nucleic acids, genetic alterations, and protein molecules as well as intact cells are utilized as diagnostic biomarkers in breast cancer.

Emerging biomarkers in various fields of Pathology:

Myeloid neoplasms biomarkers:

Immunohistochemistry (IHC) plays an indispensable role in analyzing biomarkers that play an important role in treatment of patients with myeloid neoplasms.
Cluster of differentiation markers or CD markers are the most commonly used leukemia biomarkers. CD marker specific antibodies are used for cell sorting, identification and leukemia diagnosis.
Genetic abnormalities have been correlated with Chronic myeloid leukemia (CML) in the blast phase. The genes involved are as follows:

In regulation of cell apoptosis and proliferation: Epidermal growth factor receptor (EGFR), tumor protein p53 (TP53)
In cell adhesion: Catenin beta 1 (CTNNB1),
Genes associated with TGF Beta: Transforming growth factor beta 1 and 2 (TGFB1, TGFB2)
TNF-alpha pathways: Tumor necrosis factor-alpha (TNFA), Nuclear factor kappa B subunit 1 (NFKB1)
MicroRNAs are also involved in CML: miRNA -451 nad miRNA -21

Breast cancer biomarkers:

As we all are aware, the three most important markers for breast cancer are:

Estrogen receptor (ER)
Progesterone receptor (PR)
HER 2 neu
Ki-67
P53

Some of the single blood-based biomarkers in detecting breast cancer are: Human epidermal growth factor receptor 2 (HER2), Cancer Antigen 15-3 (CA 15-3), Carcinoembryonic Antigen (CEA), MUC1.

Macromolecules such as nucleic acids, genetic alterations, and protein molecules as well as intact cells are utilized as diagnostic biomarkers in breast cancer. Recently it is found that aberrant DNA methylation is linked to breast cancer. MAST1, PRDM14, ZNF177 irregular DNA methylation variants were found and verified as prospective breast cancer molecular indicators. Circulating proteins are used as screening biomarkers such as Trefoil factor TFF1, 2, 3. Micro RNA such as miR-145, 221 and 21 are found in the blood of breast cancer individuals.

Colorectal cancers (CRC) biomarkers:

Tumor based biomarkers: Microsatellite instability (MSI) analysis, BRAF and KRAF mutation analysis. Micro RNAs also contribute to oncogenesis in CRC.
Stool biomarkers: Fecal blood tests (gFOBT) is based on the detection of pseudoperoxidase activity of heme in stool samples due to bleeding in adenomatous / neoplastic lesions. Stool immunohistochemical test (FIT) and detection of Vimentin methylation.
DNA based tests: Mutations in key genes TP53 and APC
RNA based tests: Detection of tumor mRNA transcripts such as PTGS2 and MMP7.
Blood based biomarkers: CEA

Endometrial cancer biomarker: K-RAS, HER2/neu, EGFR, PI3KCA, FGFR2, PTEN, p53.
Neurodegenerative disease biomarkers: Amyloid beta, Total tau protein, Phosphorylated Tau Protein.
Biomarkers in diabetes: HbA1C, fasting plasma glucose (FGP), Oral glucose tolerance test (OGTT). Adiponectin, C-reactive protein (CRP), ferritin and interleukin-2 receptor A.

The use of biomarkers is not only limited to cancer but has a widespread use in all the major fields of medicine and research. “The biomarkers are undoubtedly a boon to clinical practice.”

“Composed by: Dr. Shubha.H.V is a Consultant Pathologist/Lab Head, SRL Diagnostics, Fortis Hospital, Rajajinagar, Bangalore. “

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Hospitals designing bats for a fresh look

InnoHEALTH Magazine — Tue, 01 May 2018 05:49:51 +0000

Planning and Designing Healthcare Facilities
A lean, innovative, and evidence-based approach
Book written by Dr. V.K. Singh & Prof. Paul Lilrank

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Hitting newsstands in the United States of America and India simultaneously, A New Book–Planning and Designing Healthcare Facilities: A Lean, Innovative and Evidence based approach by Dr V.K. Singh and Prof. Paul Lillrank call for a fresh approach in designing new age hospitals in the wake of emerging new normal in the healthcare sector.

Authors say modern medicine is founded on the scientific pursuit for knowledge about the human body and its pathologies. Science builds theories and tests them against evidence. The scientific method should now be applied to the design of hospitals and health service systems. This is the rationale for evidence – based design.

According to authors, lean and innovation complement each other. Lean means creating more value for customers with fewer resources. Innovation is a process of translating an idea into goods or services that create value for which customer is ready to pay. The General Hospital is still a valid concept and is not going to disappear anytime soon, particularly in parts of the world where public health is poor, resources are scarce, and a majority of people is underserved. While visions are always welcome, the task at hand, and the theme of this book, is to improve on the Dominant Design, the standard General Hospital.

Evidence-based design (EBD) emphasizes credible evidence to influence design. It works on well-defined problems, applies a multidisciplinary perspective, involves users and customers, establishes quantitative performance measures for critical variables, and uses tests and simulations throughout the design process.

Prof. Lillrank along with Riikka-Leena Leskelä and Olli Tolkki say the hospital has traditionally been seen as a production site like a factory where flows of material, people, energy and information combine with fixed assets. In modern manufacturing, the factory has evolved into supply networks. In a similar vein, the modern hospital is seen as a node in a regional service system. A hospital design initiative should therefore begin with a master plan that defines the hospital’s place and role in a broader health service system.

Dr. Singh in a chapter on ‘Patient First, Functions Next and Design Later’ along with Mr. S K Biswas says the evolution of hospital design principles has gone through stages.

The first was ‘functions follow design’, as services had to be adapted to whatever structures were available. Next came ‘design follows functions’. Various professional groups lined out their requirements in terms of floor space and layout. More recently, the concept ‘Design follows first patients, then functions’ has been adopted. The emphasis now is on integrating the needs of patients, hospital functions, and functionaries in hospital design.

In a chapter, ‘Green Hospitals and Sustainable solution to Healthcare Facility’, Mr. Rajeev Boudhankar says as important parts of the modern urban landscape, hospitals must adopt environmentally friendly and sustainable designs and technologies. Green hospitals use energy, water, materials and land more efficiently than conventional buildings.

With more natural light and better air quality, green buildings contribute to improved health, comfort, and productivity. The LEED 2009 for Healthcare Green Building Rating System is a set of performance standards for certifying healthcare facilities.

In ‘Designing a Patient-centric Healthcare Facility Using Lean Methodology’, Mr. John Gallagher, Kim Chaney and Ron Kwon say 2P (Process Preparation) is a Lean design tool that helps to organize the flow of activity in a way that results in the least amount of waste. This chapter details how it worked when Concord Hillside Medical Associates, a multi-specialty group practice part of Harvard Vanguard Medical Associates near Boston, applied it in a major facility design project.

Likewise, in an article on ‘Creating safer healthcare environments using an evidence-based design process, Dr. Anjali Joseph, Ellen Taylor and Xiaobo Quan say a growing body of research shows that the healthcare built environment impacts safety outcomes such as infections, medication errors, falls, and staff injuries. Latent conditions that adversely impact patient safety are built into the physical environment during the planning, design, and construction phases. Design decisions should be proactively evaluated by engaging users from different disciplines such as infection control, nursing, risk managers, and environmental services. Emerging tools such as the Safety Risk Assessment (SRA) toolkit provide a structured way to apply evidence-based design to improve patient safety.

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Dr. Singh and Dr. Biswas in another chapter on ‘Evidence Based Design in Hospitals – Theory to Implementation’ opine that the principles of Lean Healthcare support Evidence Based Design. Lean calls for the identification of all major stakeholders and specifying what they consider valuable. Stakeholder value can be grouped into the basic categories tangibility, reliability, responsiveness, assurance and empathy. When these requirements are not met, processes create waste.

EBD analyze the constraints that need to be addressed. The design process covers several stages, initial hypothetical design, process design, service design, and empirical design. These principles are detailed in a case in a hospital in Kolkata.

On Virtual Hospitals of Future, IT expert Sachin Gaur says the Information and Communication Technologies (ICT), particularly smart and wearable devices, have the potential to break constraints of time and location. Physical installations may turn virtual, and centralized services may be decentralized. Assessing the potential of new technologies, the CIMO -methodology of Evaluation Science can be employed. It asks the questions, what is the context in which technology is applied through what kinds of interventions, and which mechanisms are activated to produce which outcomes?

On ‘Redefining Healthcare of Tomorrow in Smart City’, Dr Singh and Ms. Nimisha Singh say the three pillars of the smart city are-people, process, technology, and the information flows that bind them together as an optimized whole. The Smart Cities Mission under the leadership of Prime Minister Narendra Modi is an initiative towards urbanization. Smart cities require smart healthcare.

With the Internet of things (IoT), layers of smartness are being added to the hospitals, such as remote monitoring, chronic disease management, medication management, patient self-management, and workflow management.

In a Chapter titled ‘Delivering Inclusive Intelligent Healthcare’ by Innovative and Comprehensive e-Health System, Dr. Kuo Shou-Jen and Lai Chien-Wen aver that the chapter is based on a case study of Changhua Christian Healthcare System (CCH), Taiwan. CCH has been a pioneer in implementing sophisticated new technologies. The case emphasizes the importance of the combination of high tech with human touch.

In a chapter on ‘Planning Safe Hospitals’, Ms. Sushma Guleria says that the Hyogo Framework for Action 2005-2015 (HFA) spells out the challenge to substantially reduce the impact of disasters and to make risk reduction an essential component of development policies and programs. Risk reduction planning should be integrated into the health sector to make hospitals safe from disasters and strengthen their capacity to remain functional in disaster situations. Hospitals need to have disaster management plans and to evaluate their performance by implementing the Hospital Safety Index used widely to gather information for sound decision making.

In an article on ‘Designing Innovative Facilities: Contamination & Security Hazards at Hospitals’, Dr. Singh along with Dr. Raman Chawala emphasis on the danger of chemical, biological, radiological, nuclear and explosive (CBRNE) related terrorism which pose a contamination threat to healthcare institutions. Designing innovative resilience can provide long term and effective solutions by establishing a rigorous framework that can accelerate adaptation and ability to recover from any known and unknown contamination security and safety hazards.

‘Adapt or Obsolesce: The evolution of the Singapore Health System’, Matthew Saunders said Singapore is an advanced country of small size with a single party dominated political system. This has made it agile and able to respond quickly to changing circumstance in ways that differ from larger and more complex polities. Singapore faces the same challenges as other developing countries, including ageing society, non-communicable diseases and healthcare cost inflation, while it is well positioned to implement advanced technologies, such as electronic patient records and smart solutions. Singapore highlights the systemic nature of healthcare, where service production, facility design, finance, and regulation require innovative approaches to integration.

Dr. B. R. Shetty, Founder and Chairman, NMC Healthcare, Abu Dhabi, United Arab Emirates in his foreword said, “The book is a timely effort to discuss various concepts and tools to reduce delivery costs and maintain high quality by the means of planning a hospital with an eye on operations. It details experiences from around the globe. The authors strive to integrate several strains of thought: Lean, Innovation, Patient Centricity, and Evidence–based designs. This is what the healthcare industry needs.

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Read all the issues of InnoHEALTH magazine:
InnoHEALTH Volume 1 Issue 1 (July to September 2016) – https://goo.gl/iWAwN2
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InnoHEALTH Volume 2 Issue 1 (January to March 2017) – https://goo.gl/DEyKnw
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InnoHEALTH Volume 2 Issue 3 (July to September 2017) – https://goo.gl/MCVjd6
InnoHEALTH Volume 2 Issue 4 (October to December 2017) – http://amzn.to/2B2UMLw
InnoHEALTH Volume 3 Issue 1 (January to March 2018) – https://goo.gl/fksdQx
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HOW GENETIC TESTING CAN INNOVATE HEALTHCARE DELIVERY

InnoHEALTH Magazine — Tue, 02 May 2017 06:16:23 +0000

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How Genetic Testing can Innovate Healthcare Delivery

Dr. V.L Ramprasad holds a Master’s Degree and Ph.D. from BITS, Pilani. He has worked as Scientist (Molecular Genetics) at Vision Research Foundation, Sankara Nethralaya and was handling Affymetrix and Illumina technologies at Spinco Biotech. He also worked as Principal Scientist at SciGenom Labs. He has 17 peer-reviewed publications to his credit.

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Though in a nascent stage, precision medicine is evolving at a fast pace. There are many labs set across the country and world which offer genetic testing at an affordable fee. Moving from a traditional medical model of treating pathologies to an individualized predictive and preventive model of personalized medicine promises to reduce the healthcare cost on an overburdened and overwhelmed system. The increasing number of catalogs of causative and risk genes will provide a foundation for Personalized Medicine and pharmacogenomics. The advent of NGS has helped in bringing down the cost of genome sequencing to less than $1000. However, there are many other new technologies on development that will make the sequencing even faster and more economical.

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The current medical model focuses on the detection and treatment of pathologies. Treating disorders, especially on advanced states, is very expensive for patients and society in general. The Human Genome Project not only provided the essential reference map for the human genome but also stimulated the development of technology and analytic tools to process massive quantities of genomic data. Thus, accelerated the early detection of disorders and the identification of pharmacogenetic markers to customize treatments. Furthermore, the Human Genome Project has significantly contributed to the discovery of numerous genetic markers, several human disease-specific genomes, including cancers. Because of increased discovery rate of clinically relevant biomarkers, the relevant application of conventional molecular diagnostic methods like low- and/or medium-throughput sanger sequencing is restricted as they cannot screen such a huge number of genetic markers with a limited tumor/disease specific material. The advent of next-generation sequencing (NGS) technologies has not only reduced sequencing cost by orders of magnitude, but also significantly increased the throughput with just a few or single cell. One such new development in pre-natal genetic testing is “pre-implantation genetic screening”.

Pre-Implantation Genetic Screening

Chromosome segregation during female meiosis is particularly error prone in humans. These chromosomal abnormalities also called as Aneuploidy, worsen with advancing age. Many of recent studies have demonstrated that aneuploidy rates in the oocytes of women over 40 are over 75%, whereas approximately a quarter of oocytes from women in their early 30s are chromosomally abnormal.[1] A majority of human embryos produced from such oocytes using in vitro fertilization (IVF) techniques are aneuploid and has been shown that they fail to implant in the uterus, although a minority do succeed in forming a pregnancy only to later miscarry.[2] Hence, reliable identification of euploid (healthy) embryos is inevitable, but the main obstacle to testing human embryos for aneuploidy is the extremely limited amount of tissue available for analysis. Thus, most methods currently available for the genetic analysis of pre-implantation embryos may not be suitable and suffer from shortcomings which limit their clinical applicability. A few chromosome screening methods applicable to single cells biopsied from pre-implantation embryos are available, but the high cost of testing has restricted their usage.[3] New advancements in NGS technology provided an excellent alternative tool for the identification of chromosomal abnormalities using a few or single cell.

Next Generation Sequencing (NGS)

Next-generation sequencing popularly referred to as ‘high-throughput sequencing’. The advent of next-generation sequencing (NGS) technologies in the context of pre-natal genetic testing provides highly accurate, low-cost diagnosis of aneuploidy in cells from human pre-implantation embryos and is rapid enough to allow testing without embryo cryopreservation. Many reports indicated NGS improves IVF success rates. Thus, NGS becomes a reliable aneuploidy screening method and has the potential to revolutionize pre-implantation genetic screening (PGS).[4]

Furthermore, NGS becomes an integral part of precision medicine as it provides a viable alternative for characterizing genomic aberrations in tumors/other human disease for predictive and prognostic purposes with its massively parallel sequencing capability. This specific advantage of NGS technology enables testing of multiple genes/clinically relevant biomarkers per tumor as the standard-of-care, which may not be feasible with low- and medium-throughput traditional techniques such as Sanger sequencing, pyrosequencing, allele-specific polymerase chain reaction (PCR).[5,6,7]

The predominantly used NGS technologies are from:
• Illumina (HiSeq 2500/4000/X Ten etc.)
• Roche Applied Science/454 Life Sciences
• Life Technologies (Ion Torrent/Proton)
• Pacific Biosciences (Sequel)

The application of NGS technology in genetic testing is enormously increasing because it requires a single input of relatively low-quantity DNA or RNA for the screening of multiple markers, in contrast to traditional sequencing technologies, which need cumulatively larger quantities of input nucleic acid. NGS can provide simultaneous screening of a variety of genomic aberrations such as single-nucleotide variants (SNVs), multiple-nucleotide variants (MNVs), small and large insertions and deletions, and copy number variation (CNVs) of the genes. However, the benefits offered by these NGS technologies come with several challenges that must be adequately addressed before they can be transformed from research tools to routine clinical practices. Integrating NGS into a clinical diagnostic setting requires thorough validation with respect to consistent performance and accuracy, as per the stringent regulations and guidelines established by the regulatory agencies governing the clinical laboratories.[8]

Genetic Testing is Now More Accessible

More than a thousand genetic tests are available today and the number is still increasing. Genetic test panels give patients an insight into diseases which they may have inherited and give them an understanding of what preventive measures need to be taken. The results help understand the chances of a person liable to get inflicted by a genetic disorder and passing it on to someone else and vice versa. An expert in genetics is the best person to seek advice from, for those wanting to take a genetic test as such tests include risks and have their limitations as well. There are many labs set across the country and world which offer genetic testing at an affordable fee. Though many test labs have been established and it has been made more accessible, it continues to remain an expensive affair for the middle and lower middle sections of society in India.

Precision Medicine

Precision medicine or ‘specific treatment’ helps researchers and doctors to understand the exact treatment they need to offer to the patients. The advent of precision medicine is moving us closer to more precise, predictable and powerful health care that is customized for the individual patient. The approach of personalized therapy involves having a deep understanding of the unpredictability in a person’s genes, his/her environment and lifestyle. A complete bespoke treatment with appropriate decisions customized to a person’s medical condition. The therapies adopted range from imaging to molecular diagnostics and analytics/software and will be in accordance with the person’s genetic analysis. As mentioned previously, NGS becomes an integral part of precision medicine because of its high throughput and multiplexing capabilities which enables to analyze many clinically relevant markers across many samples.

The Future

Though it’s a nascent stage, precision medicine is evolving at a fast pace. Moving from a traditional medical model of treating pathologies to an individualized predictive and preventive model of personalized medicine promises to reduce the healthcare cost on an overburdened and overwhelmed system. The increasing number of catalogs of causative and risk genes will provide a foundation for Personalized Medicine and pharmacogenomics. The advent of NGS has helped in bringing down the cost of genome sequencing to less than $1000. However, there are many other new technologies on development that will make the sequencing even faster and more economical, such as Oxford Nanopore technologies (GridION™ System based on nanopore-based sensing). The future perspective of this advanced technology may reduce the cost of screening diseases specific gene panel to $100 within a time-frame of an hour. Research is proving that the therapies which are intended for one type of cancer could, in the future, be used to treat other types of cancers, on the premise of changes occurring in a person’s DNA. Discovery of mutations via sequencing and optional treatments are some of the findings through the process of sequencing and these may offer much hope towards better customized treatments for individuals.

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Refernces:
[1] Fragouli E, Alfarawati S, Goodall NN, Sánchez-García JF, Colls P, Wells D. The cytogenetics of polar bodies: insights into female meiosis and the diagnosis of aneuploidy. Mol Hum Reprod, 2011;17:286–95.
[2] Scott RT, Ferry K, Su J, Tao X, Scott K, Treff NR. Comprehensive chromosome screening is highly predictive of the reproductive potential of human embryos: a prospective, blinded, nonselection study.Fertil Steril,2012;97:870-5.
[3] Fragouli E, Alfarawati S, Daphnis DD, Goodall NN, Mania A, Griffiths T, Gordon A, Wells D. Cytogenetic analysis of human blastocysts with the use of FISH, CGH and aCGH: scientific data and technical evaluation. Hum Reprod 2011;26:480–90.
[4] Hong KH, Taylor DM, Forman E, Tao X, Treff NR. Development of a novel next-gen sequencing (NGS) methodology for accurate characterization of genome-wide mitochondrial heteroplasmy in human embryos. Fertil Steril 2012;98:S58–9.
[5] Roychowdhury S, Chinnaiyan AM. Translating genomics for precision cancer medicine. Annu Rev Genomics Hum Genet. 2014; 15():395-415.
[6] Previati M, Manfrini M, Galasso M, Zerbinati C, Palatini J, Gasparini P, Volinia S. Next generation analysis of breast cancer genomes for precision medicine. Cancer Lett. 2013 Oct 1; 339(1):1-7.
[7] Roper N, Stensland KD, Hendricks R, Galsky MD. The landscape of precision cancer medicine clinical trials in the United States. Cancer Treat Rev. 2015 May; 41(5):385-90.
[8] Jennings L, Van Deerlin VM, Gulley ML, College of American Pathologists Molecular Pathology Resource Committee. Recommended principles and practices for validating clinical molecular pathology tests. Arch Pathol Lab Med. 2009 May; 133(5):743-55.

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