Molecular Pathology

Molecular Pathology Indian Medical PG Question 1: Techniques used for protein expression proteomics study include:

• A. PolyAcrylamide Gel Electrophoresis (PAGE)
• B. Gene Expression Analysis (indirectly related to proteomics)
• C. Mass Spectrometry
• D. All of the options (Correct Answer)

Molecular Pathology Explanation: ***All of the options*** - All listed techniques—**Polyacrylamide Gel Electrophoresis (PAGE)**, **Gene Expression Analysis**, and **Mass Spectrometry**—are used in protein expression proteomics studies, either directly or indirectly, to analyze and quantify proteins. - The integration of these various techniques provides a comprehensive approach to understanding protein expression profiles. *PolyAcrylamide Gel Electrophoresis (PAGE)* - **PAGE** (including 1D and 2D-PAGE) is a fundamental technique for separating proteins based on their **molecular weight** and **isoelectric point**, which is crucial for visualizing and quantifying expressed proteins. - It often serves as an initial separation step before more detailed analysis, such as **mass spectrometry**. *Gene Expression Analysis (indirectly related to proteomics)* - Although **gene expression analysis** (e.g., using **RT-PCR** or **microarrays**) measures mRNA levels, it is indirectly related to proteomics because mRNA levels often **correlate with protein levels**. - It provides insights into the **transcriptional regulation** that influences protein expression, complementing direct protein analysis. *Mass Spectrometry* - **Mass spectrometry** is a powerful and widely used technique in proteomics for **identifying, quantifying, and characterizing proteins** and peptides by measuring their **mass-to-charge ratio**. - It can be used for both **discovery proteomics** (identifying novel proteins) and **targeted proteomics** (quantifying specific proteins).

Molecular Pathology Indian Medical PG Question 2: Which of the following is a primarily RNA based technique?

• A. Western blotting
• B. Northern blotting (Correct Answer)
• C. Southern blotting
• D. Sanger's technique

Molecular Pathology Explanation: ***Northern blotting*** - **Northern blotting** is a molecular biology technique used to study **gene expression** by detecting specific **RNA molecules** (mRNA) in a sample. - It involves separating RNA fragments by **gel electrophoresis**, transferring them to a membrane, and then detecting specific sequences using **labeled probes**. *Western blotting* - **Western blotting** is a technique used to detect specific **proteins** in a sample. - It involves separating proteins by **gel electrophoresis**, transferring them to a membrane, and then detecting specific proteins using labeled **antibodies**. *Southern blotting* - **Southern blotting** is a molecular biology method used for the detection of **specific DNA sequences** in DNA samples. - It involves separating **DNA fragments** by **gel electrophoresis**, transferring them to a membrane, and then hybridizing with a labeled probe. *Sanger's technique* - **Sanger sequencing**, or the **dideoxy chain-termination method**, is a widely used method for **DNA sequencing**. - It uses **dideoxynucleotides** to terminate DNA synthesis at specific bases, allowing the determination of the **DNA sequence**.

Molecular Pathology Indian Medical PG Question 3: Which of the following are correct with regard to lung cancer? 1. Surgical resection has a limited role in curative treatment of lung cancer. 2. Pattern of disease and prognosis of oat cell carcinoma are different to other varieties in the lungs. 3. Small cell lung cancer is a type of Neuroendocrine Tumour (NET). 4. Squamous cancer appears as a cavitating tumour in the lungs.

• A. 1, 3 and 4
• B. 2, 3 and 4 (Correct Answer)
• C. 1, 2 and 3
• D. 1, 2 and 4

Molecular Pathology Explanation: ***2, 3 and 4*** - **Oat cell carcinoma** (small cell lung cancer) is known for its **aggressive behavior**, rapid growth, early metastasis, and distinct response to chemotherapy and radiation rather than surgery, making its pattern and prognosis different from **non-small cell lung cancer (NSCLC)** types [1]. - **Small cell lung cancer (SCLC)** originates from **neuroendocrine cells** in the lung, classifying it as a type of **Neuroendocrine Tumour (NET)**, which explains its unique biological and clinical characteristics [1]. - **Squamous cell carcinoma** is often centrally located and can undergo central necrosis, leading to **cavitation** which appears as a cavitating tumor on imaging [1]. *1, 3 and 4* - This option is incorrect because statement 1, which suggests surgical resection has a limited role in curative treatment, is generally **false for non-small cell lung cancer (NSCLC)**, where surgery is the primary curative modality in early stages [1]. - While statements 3 and 4 are correct, the inclusion of incorrect statement 1 makes this option invalid. *1, 2 and 3* - This option is incorrect as statement 1 claiming a limited role for surgical resection in curative treatment is generally **false for NSCLC**, where localized tumors are ideally treated with surgery [1]. - Statements 2 and 3 are correct, but the inaccuracy of statement 1 renders this option incorrect. *1, 2 and 4* - This option is incorrect because statement 1, which states that surgical resection has a limited role in curative treatment, is generally **incorrect for early-stage NSCLC** [1]. - Although statements 2 and 4 are accurate, the error in statement 1 makes this combination incorrect.

Molecular Pathology Indian Medical PG Question 4: Which of the following is the most fundamental criterion that must be met by a disease before it is to be considered suitable for a screening programme? 1. The natural history of the disease should be adequately understood. 2. No effective treatment should exist for the disease. 3. The disease should not have a recognizable latent or asymptomatic stage. 4. There should be a test that can detect the disease prior to onset of signs and symptoms.

• A. 4. There should be a test that can detect the disease prior to onset of signs and symptoms.
• B. 3. The disease should not have a recognizable latent or asymptomatic stage.
• C. 1. The natural history of the disease should be adequately understood. (Correct Answer)
• D. 2. No effective treatment should exist for the disease.

Molecular Pathology Explanation: ***The natural history of the disease should be adequately understood.*** * This is the **most fundamental criterion** because understanding the natural history (progression from asymptomatic to symptomatic disease) allows for the identification of a **critical window** for early intervention through screening. * Without this knowledge, it's impossible to determine when to screen, what to screen for, or whether early detection will lead to a better outcome. *There should be a test that can detect the disease prior to onset of signs and symptoms.* * While important, the existence of a detectable test *before* symptoms is only useful if the **natural history** is understood, allowing for appropriate timing and interpretation of the test. * A test without understanding the disease's progression might lead to **overdiagnosis** or diagnosis at a stage where intervention is no longer effective. *The disease should not have a recognizable latent or asymptomatic stage.* * This statement is incorrect; a disease *must* have a **recognizable latent or asymptomatic stage** to be suitable for screening. * Screening aims to detect disease **before** symptoms appear, making the existence of such a stage essential for successful early intervention. *No effective treatment should exist for the disease.* * This statement is incorrect; for a screening program to be beneficial, an **effective treatment must exist** for the disease once detected. * Screening without effective treatment options would merely lead to earlier diagnosis without improving patient outcomes, causing unnecessary anxiety and burden.

Molecular Pathology Indian Medical PG Question 5: A patient has a cerebellar mass, renal tumor, and a family history of similar conditions. Which of the following mutations is most likely present in the family?

• A. VHL (Correct Answer)
• B. Neurofibromatosis (NF1)
• C. Tuberous Sclerosis Complex (TSC)
• D. Li-Fraumeni syndrome

Molecular Pathology Explanation: ***VHL*** - **Von Hippel-Lindau (VHL) disease** is an inherited disorder characterized by the development of tumors and cysts in various parts of the body, including **hemangioblastomas** in the cerebellum and retina, **renal cell carcinomas**, and pheochromocytomas [1]. - The combination of a **cerebellar mass**, renal tumor, and a family history strongly points to VHL disease, which is caused by a germline mutation in the **VHL tumor suppressor gene** [1]. *Neurofibromatosis (NF1)* - **Neurofibromatosis type 1 (NF1)** typically presents with multiple neurofibromas, **café-au-lait spots**, optic pathway gliomas, and Lisch nodules in the iris. - While NF1 can cause tumors, the specific combination of a cerebellar mass and renal tumor is not typical of NF1, and the characteristic skin findings are not mentioned. *Tuberous Sclerosis Complex (TSC)* - **Tuberous Sclerosis Complex (TSC)** is characterized by the growth of benign tumors in the brain (e.g., **subependymal giant cell astrocytomas**), kidneys (e.g., **angiomyolipomas**), heart, lungs, and skin (e.g., facial angiofibromas) [2]. - While TSC can involve brain and kidney tumors, the typical brain tumors are different (astrocytomas vs. hemangioblastomas), and hemangioblastomas are not a common feature of TSC [2]. *Li-Fraumeni syndrome* - **Li-Fraumeni syndrome** is a rare inherited cancer predisposition syndrome characterized by a high risk of developing various cancers, including **sarcomas**, breast cancer, brain tumors (often astrocytomas or medulloblastomas), and adrenocortical carcinoma. - While brain tumors are part of Li-Fraumeni syndrome, renal cell carcinoma is not a primary feature, and the classic cerebellar hemangioblastoma is not typical for this syndrome. **References:** [1] Cross SS. Underwood's Pathology: A Clinical Approach. 6th ed. Common Clinical Manifestations Of Central And Peripheral Nervous System Disease, pp. 724-727. [2] Kumar V, Abbas AK, et al.. Robbins and Cotran Pathologic Basis of Disease. 9th ed. The Central Nervous System, pp. 1318-1319.

Molecular Pathology Indian Medical PG Question 6: Knudson two-hit hypothesis is classically exemplified by

• A. Crohn disease
• B. Ulcerative colitis
• C. Retinoblastoma (Correct Answer)
• D. Melanoma

Molecular Pathology Explanation: ***Retinoblastoma*** - The **Knudson two-hit hypothesis** was **originally formulated** based on studies of **retinoblastoma** by Alfred Knudson in 1971 [1]. - It posits that **two separate mutational events** are required to inactivate **both alleles** of the **Rb tumor suppressor gene** in the same cell, leading to tumor formation [1], [2]. - This explains both **hereditary** (germline mutation + somatic mutation) and **sporadic** (two somatic mutations) forms of retinoblastoma [1], [2]. - Retinoblastoma remains the **paradigmatic example** of this hypothesis and tumor suppressor gene inactivation [2]. *Crohn disease* - This is an **inflammatory bowel disease**, not a neoplasm, with complex etiology involving genetic susceptibility, environmental factors, and immune dysregulation. - Its pathogenesis does **not follow the Knudson two-hit hypothesis**, which specifically relates to tumor suppressor gene inactivation in cancer. *Ulcerative colitis* - Similar to Crohn disease, **ulcerative colitis** is an **inflammatory bowel disease** with multifactorial etiology, not a neoplastic condition. - While chronic UC can increase colorectal cancer risk through accumulated mutations, the disease itself does **not represent the two-hit hypothesis model**. *Melanoma* - **Melanoma** is a skin cancer often linked to **UV radiation** and mutations in oncogenes like **BRAF** and tumor suppressors like **PTEN** and **CDKN2A**. [3] - While some familial melanomas involve tumor suppressor genes, melanoma is **not the classic example** used to illustrate the Knudson hypothesis—**retinoblastoma holds that distinction**. **References:** [1] Kumar V, Abbas AK, et al.. Robbins and Cotran Pathologic Basis of Disease. 9th ed. Neoplasia, p. 300. [2] Cross SS. Underwood's Pathology: A Clinical Approach. 6th ed. (Basic Pathology) introduces the student to key general principles of pathology, both as a medical science and as a clinical activity with a vital role in patient care. Part 2 (Disease Mechanisms) provides fundamental knowledge about the cellular and molecular processes involved in diseases, providing the rationale for their treatment. Part 3 (Systematic Pathology) deals in detail with specific diseases, with emphasis on the clinically important aspects., pp. 227-228. [3] Kumar V, Abbas AK, et al.. Robbins and Cotran Pathologic Basis of Disease. 9th ed. Neoplasia, pp. 297-298.

Molecular Pathology Indian Medical PG Question 7: Which of the following are criteria for cancer screening? I. Screening test should be sensitive and specific II. Screening test should be acceptable to the screened population III. The disease should be an uncommon one for screening to be effective IV. Disease should be recognisable at an early stage Select the correct answer using the code given below :

• A. II, III and IV
• B. I, III and IV
• C. I, II and III
• D. I, II and IV (Correct Answer)

Molecular Pathology Explanation: ***I, II and IV*** - A successful **screening test** should be **sensitive** (correctly identify those with the disease) and **specific** (correctly identify those without the disease) to minimize false negatives and false positives. - For a screening program to be effective, the test must be **acceptable** to the target population to ensure high participation rates. The disease should also be **recognizable at an early stage** to allow for timely and effective intervention. *II, III and IV* - This option is partially correct as it includes acceptability and early recognition, but incorrectly states that the disease should be uncommon. In reality, screening is often more impactful for diseases with a higher prevalence. - The claim that the disease should be uncommon is incorrect; screening programs are often prioritized for relatively common diseases where early detection can significantly alter outcomes. *I, III and IV* - This option correctly identifies the need for a sensitive and specific test, and early disease recognition, but it incorrectly asserts that the disease should be an uncommon one. - Screening is generally most beneficial for diseases with a significant prevalence, allowing for a substantial impact on public health. *I, II and III* - This option accurately points to the necessity of a sensitive and specific test and its acceptability to the screened population, but it mistakenly suggests that the disease should be uncommon. - Effective screening targets diseases where early detection can lead to improved outcomes, which are often diseases with a notable burden in the population.

Molecular Pathology Indian Medical PG Question 8: Which of the following statements are correct with regard to Familial Adenomatous Polyposis ? 1. It is associated with mutation of APC gene located on the long arm of chromosome 5. 2. It is inherited as an autosomal recessive condition. 3. It is associated with 100% lifetime risk for development of Colorectal carcinoma. 4. Congenital hypertrophy of retinal pigment epithelium is present in half of the cases of familial adenomatous polyposis. Select the correct answer using the code given below :

• A. 1, 2 and 3
• B. 1, 3 and 4 (Correct Answer)
• C. 2, 3 and 4
• D. 1, 2 and 4

Molecular Pathology Explanation: ***1, 3 and 4*** - Familial Adenomatous Polyposis is indeed associated with a mutation in the **APC gene** located on the **short arm of chromosome 5 (5q21-q22)** and carries a **nearly 100% lifetime risk** of developing colorectal carcinoma if left untreated [1]. - **Congenital hypertrophy of the retinal pigment epithelium (CHRPE)**, also known as bear claw lesions, is a characteristic extracolonic manifestation observed in approximately half of FAP patients, though it does not usually affect vision. *1, 2 and 3* - This option is incorrect because FAP is inherited as an **autosomal dominant** condition, not autosomal recessive. - Statement 2, claiming autosomal recessive inheritance, is false, rendering this combination incorrect. *2, 3 and 4* - This option incorrectly states that FAP is inherited as an **autosomal recessive** condition. It is an autosomal dominant disorder. - While statements 3 and 4 are correct, the inclusion of statement 2 makes this option invalid. *1, 2 and 4* - This option is incorrect due to the assertion that FAP is an **autosomal recessive** condition (statement 2). - FAP is correctly linked to the APC gene mutation (statement 1) and CHRPE (statement 4), but the inheritance pattern given here is wrong. **References:** [1] Kumar V, Abbas AK, et al.. Robbins and Cotran Pathologic Basis of Disease. 9th ed. The Gastrointestinal Tract, pp. 821-822.

Molecular Pathology Indian Medical PG Question 9: BRCA1 gene is located on which chromosome?

• A. 17q21 (Correct Answer)
• B. 13q12
• C. 12q13
• D. 21q17

Molecular Pathology Explanation: ***17q21*** - The **BRCA1 gene** is located on the long arm (q) of **chromosome 17** at region 21. - This gene plays a crucial role in **DNA repair** and is associated with an increased risk of breast and ovarian cancers. *13q12* - This location corresponds to the **BRCA2 gene**, which is also involved in DNA repair and cancer predisposition. - While both BRCA1 and BRCA2 are significant, they are distinct genes on different chromosomes. *12q13* - This is not the correct chromosomal location for either BRCA1 or BRCA2. - Various other genes are located on chromosome 12, but not BRCA1. *21q17* - This is an incorrect chromosomal designation; the "q" arm designation is typically followed by a band number, and 17 is not a standard band number for chromosome 21 in this context. - **Chromosome 21** is primarily associated with **Down syndrome** (trisomy 21).

Molecular Pathology Indian Medical PG Question 10: Agarose gel electrophoresis from DNA of a population of cells as seen under ultraviolet light is shown below. What is the correct explanation for the finding seen in the band labeled as "C"?

• A. Predominantly necrotic cells
• B. Mixed population of normal and apoptotic cells
• C. A population of viable cells
• D. Apoptotic cells (Correct Answer)

Molecular Pathology Explanation: ***Apoptotic cells*** - Band C shows a characteristic **DNA ladder pattern** with discrete bands representing fragmentation into nucleosome-sized units (multiples of ~180-200 base pairs), which is pathognomonic of **apoptosis**. [1] - During apoptosis, **endonucleases** cleave DNA at internucleosomal linker regions, creating uniform fragments that migrate as distinct bands on agarose gel electrophoresis. *Predominantly necrotic cells* - **Necrotic cell DNA** undergoes random, non-specific degradation by cellular enzymes, resulting in a continuous **smear pattern** rather than discrete bands. - The **smear appearance** reflects DNA fragments of varying sizes distributed throughout the gel, unlike the organized pattern seen in band C. *Mixed population of normal and apoptotic cells* - A mixed population would show both **intact high molecular weight DNA** (remaining near the gel origin) and the **apoptotic ladder pattern** superimposed. - Band C displays a pure ladder pattern without evidence of intact DNA, indicating a homogeneous apoptotic population. *A population of viable cells* - **Viable cells** maintain intact genomic DNA that remains as a single **high molecular weight band** near the top of the gel. - The **fragmented ladder pattern** in band C is incompatible with viable cell DNA, which should show minimal degradation. **References:** [1] Kumar V, Abbas AK, et al.. Robbins and Cotran Pathologic Basis of Disease. 9th ed. Cellular Responses to Stress and Toxic Insults: Adaptation, Injury, and Death, pp. 63-64.

Molecular Pathology Flashcard 1 of 10

Question: Which subtype under molecular classification of breast cancer has the best prognosis?_____

Answer: Luminal A

Molecular Pathology Flashcard 2 of 10

Question: Oncotype dx, mammaprint, endopredict and PAM50- Prosigna are all prognostic panels based on _____ in breast cancers

Answer: gene expression

Molecular Pathology Flashcard 3 of 10

Question: HER2-_____ cancers are most common subtype of breast cancer in patients with germline mutations in TP53 (Li Fraumeni syndrome)

Answer: positive

Molecular Pathology Flashcard 4 of 10

Question: _____ is a molecular test in breast cancer that is a 21-gene assay

Answer: Oncotype Dx

Molecular Pathology Flashcard 5 of 10

Question: In Array based Comparative Genomic Hybridization, if the test sample has amplification, then some spots on the array will flouresce _____.

Answer: red

Molecular Pathology Flashcard 6 of 10

Question: _____ is a tumor suppressor gene that encodes a negative regulator of the -catenin/WNT pathway

Answer: APC

Molecular Pathology Flashcard 7 of 10

Question: _____ syndrome is most commonly characterized by a 47,XXY karyotype

Answer: Klinefelter

Molecular Pathology Flashcard 8 of 10

Question: _____ disease is due to a deletion of the VHL gene on chromosome 3p, leading unregulated activity of HIF1a

Answer: Von Hippel-Lindau

Molecular Pathology Flashcard 9 of 10

Question: Mutations that cause _____ of the HER2 receptor can precipitate development of certain Breast* and Gastric* Cancers by amplifying the signal transduction

Answer: overexpression

Molecular Pathology Flashcard 10 of 10

Question: Over 85% of mutations in the FGFR3 gene occur _____ and are related to increased paternal age

Answer: sporadically