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Address of Correspondence:  
Dr Usman Hassan 

Email: drusmanhassan256@gmail.com 

 
 

 Role of Molecular Biology in Histopathology 

Usman Hassan 

Consultant Histopathologist, Shaukat Khanum Cancer Hospital and Research Center, Lahore

 

Pathology has evolved significantly in the past 50 years. 

Even I can feel lot of changes in last 10 years of my 

histopathology practice starting from my residency days 

till the present day and things are now developing even at 

a greater pace. It is very difficult to keep up the pace with 

these ever-changing and developing diagnostic 

modalities.  

Light microscopy was the sole examination technique at 

first and pathology was comparatively simple. However, 

with increasing tumor diagnosis and tumor burden across 

the globe, a strong need was felt to strengthen the 

classification systems so that diseases could be put into 

specific categories and hence treated in a more specified 

and accurate manner. This need gave birth to the 

technique of immunohistochemistry, which was based on 

the principle of antigen retrieval and binding of specific 

antibodies designed for a particular antigen. Nowadays 

well-developed histopathology departments use hundreds 

of antibodies in order to diagnose different kinds of 

diseases particularly several kinds of neoplastic diseases 

including benign and malignant tumors. We can very 

confidently classify tumors broadly into categories of 

carcinoma, lymphoma, sarcoma, neuroendocrine tumor, 

melanoma, perivascular epithelioid cell tumor, metastatic 

tumor etc. Each of these broad groups can be further 

classified into specific categories based on histological 

and immunohistochemical features. This has 

revolutionized the treatment options for patients. 

However, every technique has a limitation. After immense 

and colossal research in the field of 

immunohistochemistry, it is now very much known that 

immunohistochemistry has got its own limitations. 

Despite, for example, cytokeratins which are meant to 

stain carcinomas can also be expressed in sarcomas. 

Likewise, melanocytic markers which are known to 

diagnose melanoma can also show positivity in 

perivascular epithelioid cell tumors. CD99 initially 

considered a very specific marker for Ewing’s sarcoma is 

now known to show expression in osteosarcoma (small 

cell variant), lymphoblastic lymphoma and synovial 

sarcoma. CD56 also shows its positivity in a number of 

tumors including carcinomas, lymphomas, and sarcomas. 

Therefore, we cannot overemphasize the fact that a single 

technique is not enough to diagnose a particular disease. 

It is the combination of clinical features, radiological 

features, histological findings and immunohistochemical 

results that is important for an accurate diagnosis.  

Researchers long ago started feeling that even classifying 

tumors based on histology and immunohistochemistry 

was not enough. The reason was the observation that 

patients having same age, gender, type, and stage of 

disease behaved differently. For instance, patients having 

lung adenocarcinoma, breast carcinoma, malignant 

melanoma, colorectal adenocarcinoma, thyroid 

carcinoma, sarcomas, gastrointestinal stromal tumor 

(GIST), ovarian carcinoma, lymphoma behaved very 

much differently even if they belonged to the same group 

of disease and shared similar demographic details and 

same type and stage of the disease. These findings led 

and compelled investigation, exploration, analysis, testing, 

and experimentation of genetics of disease. I can assure 

you that in future genetics will be the part and parcel of 

every field related to diagnostics, especially pathology. 

At this point of time, fluorescence in situ hybridization 

(FISH), PCR, next-generation sequencing (NGS) and 

tissue microarrays are the genetic techniques used in 

combination with histology and immunohistochemistry for 

diagnosing and classifying malignancies. Now it is 

established that malignancies having similar histological 

E D I T O R I A L  



 

                           120 J I M D C   2 0 1 7  120 

and immunohistochemical features and belonging to the 

same group can behave differently on account of their 

different genetic phenotypes. Using this fact, scientists 

are working very hard to develop targeted therapies 

against different types of genetic aberrations e.g. 

identification of many oncogenes and tumor suppressor 

genes.  

NGS has particularly helped a lot in understanding the 

genetics of a large number of diseases and malignancies 

as it has the capability of sequencing and analyzing 

millions of DNA molecules at reduced rates. Some of the 

genetic aberrations are of prognostic and other are of 

therapeutic interest. With the help of NGS, mutations of 

interest are studied for their prognostic and therapeutic 

values and few are selected to develop targeted 

therapies. NGS is not available routinely in Pakistan and 

very rarely used for research purposes at very few 

centers. I would like to give you few examples of the role 

of genetic studies in finding out molecules of treatment 

and prognostic significance. Lung adenocarcinomas can 

look alike histologically but have different genetic 

makeups. Few genes of interest in lung adenocarcinoma 

are EGFR, ALK and ROS1 against which targeted 

therapies have been developed e.g. erlotinib against 

EGFR mutation and crizotinib in ALK and ROS1 mutated 

adenocarcinomas. GIST having KIT and PDGFRA 

mutations can benefit from imatinib or sunitinib therapy 

whereas SDH deficient GISTs do not benefit from this 

therapy and require second line drug regime. Colorectal 

carcinomas having KRAS mutations behave and respond 

to therapy differently than colorectal carcinomas having 

microsatellite instability (MSI). Breast carcinomas which 

are ER and PR positive are given different therapy than 

those which are triple negative for ER, PR and HER-2/neu 

or which are only HER-2/neu positive. These are very few 

basic examples of very common tumors like a drop in the 

ocean. Unfortunately, the discovery of genetic aberrations 

has outpaced the development of targeted therapies.  

PCR technique is cheaper and very much simpler than 

NGS. The particular gene of interest can be tested in 

tumor tissue and treatment can be based on the results. 

Of course, only limited number of genes can be studied 

as compared to NGS in which millions of molecules can 

be assessed. The ability of the molecular department to 

run PCR tests on formalin fixed tumor tissue is a big 

advantage for the pathologists and treating oncologists 

and every effort should be made to acquire this expertise. 

FISH technique is another very useful and very simple 

technique which works on the principle of binding of the 

fluorescent probe to a complementary antigen of interest. 

We use quite a few FISH tests in our department. We use 

HER-2/neu amplification studies in breast carcinomas, 

FISH break apart probes for Ewing’ sarcoma (EWSR1 

gene rearrangement), synovial sarcoma (X;18) and 

alveolar rhabdomyosarcoma (FOXO1 gene 

rearrangement), N-myc and MDM2 amplifications studies 

for neuroblastoma and liposarcoma respectively, break 

apart probe for ALK gene rearrangement in lung 

adenocarcinoma and 1p and 19q co-deletion studies in 

oligodendrogliomas. Some of these results have 

therapeutic and some have prognostic value for the 

patient. 

Every institute can tailor these techniques according to 

their own needs. Pathologists should assess the tumor 

burden and tumor types being diagnosed in their institutes 

and discuss the need to develop different molecular 

techniques with oncologists and molecular biologists. This 

not only helps to diagnose tumors with accuracy but also 

help oncologists to assess prognosis and treatment plan 

of different tumors.  

I think we have entered the era in our lives where 

genetics has gained an utmost importance in diagnostics 

and therapeutics of diseases and nobody can deny the 

importance of genetics. Therefore, in spite of avoiding the 

understanding of genetics, every university and college 

should make genetics a compulsory part of their 

curriculum as it has already been included in the 

curriculum of undergraduate and postgraduate students in 

the developed world so that doctors have the basic 

knowledge of genetic techniques by the time they become 

qualified pathologists.