Translate this page into:
Molecular testing on serous effusion: An update
-
Received: ,
Accepted: ,
How to cite this article: Sahu S, Gupta P, Dey P. Molecular testing on serous effusion: An update. CytoJournal 2021;18:35.
Abstract
Cytological examination of the effusion fluid provides valuable information regarding the presence of malignancy. At times, it is challenging to diagnose malignant cells in serous effusion. The various ancillary techniques are available to solve the problem including immunocytochemistry, DNA ploidy, and multicolored flow cytometry. At present, the molecular tests on the effusion sample are of growing interest. The effusion sample is rich in cells and cell-free fluid that contains free DNA, cytokines, and extracellular vesicles. Molecular tests in effusion sample not only provide a diagnosis of malignancy but can also give valuable information that may be essential for the individualized therapy, management, and prognostic assessment. In this paper, we reviewed the application of the different molecular tests in the effusion sample.
Keywords
Molecular testing
Serous effusion
Cytology
Genetic markers
Diagnosis
Polymerase chain reaction
Fluorescent in situ hybridization
Next-generation sequencing
Comparative genomic hybridization
INTRODUCTION
There are three major sources of serous effusions in the body: Pleural, peritoneal, and pericardial. Both neoplastic and non-neoplastic lesions may be responsible for the effusion. Out of the neoplastic causes, metastatic carcinomas are the far more frequent than mesothelioma. Cytological examination of the effusion fluid provides valuable information regarding the presence of malignancy. However, the sensitivity and specificity of cytological examination to detect malignancy are widely variable from 67% to 90% and 90 to 100%, respectively.[1,2] It is mainly due to the overlapping cytological features of reactive mesothelial cells and malignant cells.[3] The various ancillary techniques are available to solve the problem including immunocytochemistry,[4] DNA ploidy, and multicolored flow cytometry. At present, the molecular tests on the effusion sample are of growing interest. The effusion sample is rich in cells and cell-free fluid that contains free DNA, cytokines, and extracellular vesicles. Molecular tests in effusion sample not only provide a diagnosis of malignancy but can also give valuable information that may be essential for the individualized therapy, management, and prognostic assessment. In this paper, we reviewed the different molecular tests that are done in the effusion sample.
CYTOLOGY SAMPLE FROM THE EFFUSION FLUID
Several different types of cytology sample preparation are available for the molecular tests from the effusion fluid that includes (1) cell block, (2) direct smear, (3) cytospin preparation, (4) cell pellet, (5) liquid-based cytology (LBC), and (6) liquid biopsy.
Cell block
It is the most widely used preparation for the molecular tests. The material for the cell block should be fixed in 10% neutral buffered formalin, and any fixative containing heavy metal should be avoided.[5,6] The cellularity in the cell block preparation should always be assessed on the hematoxylin and eosin-stained smear. The cell block material can be used for future tests, and various immunocytochemistry can be done on cell block sections. The significant disadvantages of cellblock are as follows: (1) Immediate assessment of the cellularity is difficult as the cell block preparation takes at least 1 day time, (2) the absence of the whole nuclei and fragmentation of DNA, and (3) the formation of cross-linking of between nucleic acid and proteins.
Direct smear
In the absence of cell block preparation, the Diff-Quik stained slide or Papanicolaou’s stained slide can be used for the molecular tests. The Diff-Quik stained smears provide better quality DNA compared to Papanicolaou’s stained smear.[7]
The cells from the slide are collected by the scraping by scalpel or by lifting the cells with the help of Pinpoint solution.[8,9] The direct smear has several advantages such as (1) quick assessment of cellularity, (2) less formalin interference, and (3) the dispersed tumor cells are easy to locate. However, direct smear needs the sacrifice of the slide and may have medicolegal consequence.
LBC (supernatant of effusion fluid)
Slides prepared from LBC platform provide a good source of DNA. The cells can be scrapped from the LBC slide for molecular tests or DNA can be extracted from the LBC solution.[10] The CytoLyt fixative solution used in ThinPrep LBC platform (Hologic Inc., Marlborough, USA) usually provides several times the higher yield of DNA than the CytoRich fixative solution used in SurePath LBC platform (Becton, Dickinson and Company, NJ, USA).[11]
Hence, it is necessary to choose the proper fixative in LBC platform. The main advantages of LBC are as follows: (1) Rapid preparation of the slide, (2) direct visualization of the cells, and (3) intact cell nuclei.
Cytospin
The cytospin preparation provides multiple slides in a small predetermined area. The cells are concentrated and provide higher DNA yield.[8]
Cell pellet
It is the preliminary preparation for the cell block or smear preparation.
The cell pellet in the centrifuged specimen of effusion sample also contains an optimum amount of DNA material for the molecular tests.[12]
Liquid biopsy (supernatant of effusion fluid)
The cf-DNA may be present in the effusion sample. The DNA is derived from both the normal cells and also from the circulating cell-free tumor DNA (ct-DNA). Therefore after centrifugation, the supernatant fluid of the effusion can be used as a liquid biopsy specimen and various molecular tests such as sensitive polymerase chain reaction (PCR) and next-generation sequencing (NGS).[13]
Table 1 shows the relative advantages and disadvantages of the different preparation of effusion sample for the molecular tests.
| Types of preparation | Advantages | Disadvantages | Comments |
|---|---|---|---|
| Cell block | (1) The cellularity and cell morphology can be visualized from the hematoxylin and eosin stained section of the cell block,(2) the nature of the cells can be assessed by immunocytochemistry | (1) Immediate assessment of the cellularity is difficult, (2) the absence of the whole nuclei, (3) the formation of cross-linking between nucleic acid and proteins | The most common preparation for molecular tests |
| Direct smear | (1) Immediate cellularity assessment, (2) whole nuclei available, (3) better quality of DNA, (4) malignant cells can be seen in microscope | (1) The slide has to be sacrificed, (2) strict validation needed, (3) cover slip removal takes time | The cells are obtained for molecular tests by scarping, lifting, or transferring |
| Liquid-based cytology | (1) Intact whole nuclei, (2) the better quality DNA or RNA, (3) multiple slide preparation can be done | CytoRich fixative gives suboptimal DNA | SurePath and ThinPrep preparations are available |
| Cell pellet | (1) Whole nuclei present, (2) direct transfer of the cells for molecular tests | The slide has to be made for evaluation of cellularity and cell viability | The supernatant fluid can also be used as liquid biopsy |
THE ADEQUACY OF THE REPRESENTATIVE TUMOR CELLS IS AFFTECTED BY TWO WAYS
The total cellularity of the sample: The overall cellularity of the sample is directly proportional to the DNA yield for the molecular test. Hence, high cellular usually reassures that the molecular tests will be effective
Tumor fraction: The contamination of reactive mesothelial cells and inflammatory cells may affect the proportion of the tumor cells in the sample. The low tumor fraction is a challenge to the cytologist as it may decrease the sensitivity of the molecular test because the DNA molecules may have come from the nonneoplastic cells. It has been noted that 20% tumor cells is the minimum threshold to avoid the false-negative molecular test.[14]
THE ROLE OF CYTOPATHOLOGISTS IN MOLECULAR TESTING
The cytologists have several vital responsibilities in the execution of the molecular tests [Figure 1]. The primary duty of the cytologist is to examine the stained cytology smear or section of the cellblock to assess the cytomorphology and to have a provisional diagnosis. It is also essential to find out the slide/smear for an adequate number of viable tumor cells. The area of the slide can be marked for future use. Next step is to decide the exact molecular tests for the diagnosis/typing/primary source of the tumor. In the case of management of the tumor, the decision of the precise molecular analysis should be taken by the combined team consisting of oncologist, molecular pathologist, and cytopathologist.
- Schematic diagram showing the duties and responsibilities of the cytologist in the execution of molecular tests on effusion sample.
MOLECULAR TESTS
Several molecular tests can be done in the effusion fluid.
PCR
PCR can be done in the very tiny amount of DNA or RNA. This technique is mainly target based, and therefore, only selected genetic alterations are detected by PCR. With the help of real-time PCR, we can quantitate DNA or RNA of the sample. The specific gene mutation can be detected in the extremely minute amount of DNA or RNA with the help of the various sophisticated PCR techniques that include droplet digital PCR, allele-specific PCR, amplification refractory mutation system, and single-stranded conformation polymorphism (SSCP).[15-17] With the help of PCR, single gene mutation in the cell or cell-free DNA can be detected.[18]
Fluorescent in situ hybridization (FISH)
FISH uses DNA probes labeled with fluorescent dyes. FISH can be used in the archival material, and no culture of the cell is needed for this test. It requires a fluorescent microscope for the interpretation of the signals. However, if the chromogen tagged DNA probe is used, then the signal can be interpreted by the light microscope. As the specific DNA probe is used in FISH, so only the selected chromosomal changes can be interpreted by this technique. The various genetic mutational changes have been studied in effusion sample by FISH.[19,20] The signal in FISH can be interpreted along with the cytomorphology of the cells.
Gene sequencing
In this process, the sequential order of nucleotides in the DNA (or RNA) is assessed. The earliest and the classical method of gene sequencing is Sanger’s sequencing. In this method, the nucleotide incorporation is terminated by the addition of 2’, 3’-dideoxynucleotides (dATP, dTTP, dCTP, and dGTP). Each terminated fragment of DNA is recorded at a time, and from that data, ultimately whole DNA sequence is generated. Sanger sequencing platform is, therefore, a slow process as only a fragment of DNA is sequenced in each reaction. However, in the case of NGS, a large number of DNA fragments are simultaneously analyzed. Hence, it is also called as NGS which is also called as high-throughput sequencing. The different types of NGS include pyrosequencing, microelectrophoretic methods, hybridization sequencing, and real-time observation of single molecules. Overall, the basic steps of NGS are (a) to make a library of DNA, (b) simultaneous huge millions of parallel sequence, (c) analysis of data by bioinformatics, and (d) the data interpretation. NGS has been used successfully in effusion samples of various metastatic carcinomas.[21,22]
MICROARRAY OF DNA AND RNA
Comparative genomic hybridization (CGH) is a laborious and tedious technique that helps to identify the loss, gain, or amplification of the chromosome. In CGH, a test DNA from the patient and a reference DNA from a healthy female are tagged with red and green fluorescence. The admixture of this DNA (1:1 ratio) is then incubated with the metaphasic plate (along with cot-1-DNA), and the red and green fluorescence is measured to find out the loss (excess red) and gain (excess green) of the chromosome. The array-based CGH (a-CGH) technique uses c-DNA or genomic bacterial artificial chromosome (which is known as “chip”) instead of the metaphasic plate. The test and reference DNA is then hybridized on this “chip.” Both CGH and a-CGH are successfully used in the effusion sample specimen.[23,24]
Table 2 highlights the basic principles, merits and demerits of different molecular techniques that are used in the effusion sample.
| Tests | Basic principle | Advantages | Disadvantages | Comments | |
|---|---|---|---|---|---|
| Polymerase chain reaction (PCR) | Target DNA is amplified with the help of primer, DNA polymerase, and nucleotides | Very minute quantity of DNA needed It is highly sensitive and specific |
Only specific target DNA can be studied | The different sophisticated PCR techniques include droplet digital PCR, amplification refractory mutation system, and single-stranded conformation polymorphism | |
| Fluorescent in situhybridization | Fluorescent tagged DNA probes are incubated with the test DNA to find out the signal in case of complimentary DNA present in the test | Archival material can be used It can be correlated with cytomorphology |
Target specific | ||
| Next-generation sequencing (NGS) | In a single assay, massive parallel sequencing of DNA occurs | Large number of target DNAs can be studied in a single test Extremely rapid sequencing in comparison to Sanger sequence Whole-genome can be studied, and it is not target specific |
High cost Sophisticated |
The different types of NGS include pyrosequencing, microelectrophoretic methods, hybridization sequencing, and real-time observation of single molecules | |
| Comparative genomic hybridization (CGH) | Here, the test (tagged with red fluorescence) and reference (tagged with green fluorescence) in equal proportion are incubated on the metaphase plate followed by the measurement of red and green fluorescence to find out gene deletion or amplification | It works as virtual karyotyping Genome-wide analysis can be done |
Relatively large amount of DNA is needed | Array-based CGH gives better resolution and large number of DNA sequences can be studied in a precise way | |
APPLICATIONS OF MOLECULAR TECHNIQUES IN EFFUSION FLUID
The molecular tests in the effusion sample can be applied for the diagnosis of malignancy, the detection of types and primary sites, the management of individual cases in personalized therapy, and follow-up of the cases.
DIAGNOSIS
Diagnosis of mesothelioma
The mesothelioma-related genes are BAP1 and CDKN2A. “BRCA-1-associated protein” (BAP1) gene is located at 3p21 chromosome. BAP1 gene is preserved in the reactive mesothelial cells and is lost in majority of the cases of mesothelioma. The demonstration of loss of BAP1 in an effusion sample is highly specific (100%) for mesothelioma. FISH can detect the mutational changes of these genes in mesothelioma[25] Walts et al. demonstrated BAP1 loss and mutational changes of CDKN2A in the cell block sections of effusion sample.[26] They suggested that these are the specific diagnostic makers of mesothelioma. Illei et al. also demonstrated homozygous deletion of CDKN2A by FISH in ThinPrep preparation of effusion sample.[27] They noted that FISH in effusion sample increased the diagnostic sensitivity of malignant mesothelioma cases.
Diagnosis of metastatic carcinomas
Mucin (MUC)
The different mucin genes such as MUCI, MUC2, and MUC5AC are quantitated in effusion sample by quantitative RT-PCR technique.[28] It was noted that the expression of MUC1 MUC2 and MUC5AC genes was higher in malignant effusion than that of benign effusion. The sensitivity and specificity to detect malignancy in effusion by quantitative estimation of MUC genes by RT-PCR were 86.1% and 91.5%, respectively.
EpCAM, CEA, Cadherin, MUC1, and mammaglobin
The expression of a panel of genes consisting of EpCAM, CEA, cadherin, MUC1, and mammaglobin was studied in the effusion sample with the help of RT-PCR.[29] It was noted that RT-PCR analysis of CEA and Ep-CAM significantly increased diagnostic sensitivity in effusion sample.
The panel of genes
Leichsenring et al. studied a large panel of genes from the cell block of 20 effusion samples with the help of NGS. Somatic mutations were detected all the samples, and it was suggested that NGS in the effusion sample might help in the diagnosis.[22]
Microsatellite marker
Woenckhaus et al. studied microsatellite markers in the 20 effusion samples by PCR and noted genetic alterations of microsatellite genes in the tumor samples only. The combination of cytological and microsatellite analysis raised the sensitivity of the detection of malignancy from 57% to 79%. It was suggested that in challenging cases, microsatellite markers might help in the diagnosis of malignancy.[30]
K-ras and p53
Dai et al. performed PCR -based single-stranded conformation polymorphism (PCR-SSCP) in 16 cases of pleural effusion to detect K-ras and p53 gene mutation.[31] Interestingly, they used the stained cytology slides for these tests. At first, the cellular areas of the slide were identified and then those areas were marked. The microdissection of the cell was done with the help of micromanipulator system. The PCR-SSCP was done in the microdissected cells to find out mutational changes. There were identical mutational changes in the cells of the effusion sample and resected specimen. The authors suggested that p-53 and K-ras mutation patterns are useful markers to diagnose lung carcinoma in pleural effusion sample.
Claudin 4
Mohamed et al. did RT-PCR from the cell pellet of 75 effusion sample and noted that mRNA of claudin 4 is high in the malignant effusion compared to the benign sample. They suggested that the detection of claudin 4 gene upregulation may help in the diagnosis of malignancy.[32]
Human telomerase reverse transcriptase (h-TERT)
Shu et al. studied mRNA of h-TERT in 96 effusion samples and noted that mRNA of h-TERT is frequently present in the malignant pleural effusion.[33] The sensitivity and specificity of mRNA of telomerase reverse transcriptase are 90 and 95%, respectively. The detection of mRNA of hTERT may help to diagnose malignancy in effusion sample.
Micro-RNAs (mi-RNA) as a diagnostic marker
mi-RNAs are the non-coding RNA of single-stranded RNA of short-length nucleotides. They regulate the expression of oncogenes or suppressor genes. Therefore, mi-RNAs are indirectly linked with carcinogenesis.[34] The study of miRNA is easy to do, economically feasible with high sensitivity and specificity. The studies on miRNA as a diagnostic marker in the identification of metastatic carcinoma are promising. Shin et al. noted reduced expression of miRNA-134, miRNA-185, and miRNA-22 in malignant effusion compared to that of benign effusion.[35] Wang et al. showed that nine miRNAs (miRNA-200c-3p, miRNA-200b-3p, miRNA-200a-3p, miRNA-429 and miRNA-141-3p, miRNA-205-5p, miRNA-483-5p, miRNA-375, and miRNA-203a-3p) were most frequently associated with metastatic carcinoma in effusion.[36] Altered profile of mi-RNA may be a helpful in distinguishing mesothelioma from the metastatic carcinoma in effusion sample. The expression of mi-RNA-200 is reduced in mesothelioma than that of metastatic adenocarcinoma of lung.[37] Table 3 highlights the applications of molecular tests in effusion in the diagnosis.
| Genetic marker/s | Number of samples | Sample preparation | Molecular tests | Results | Comments |
|---|---|---|---|---|---|
| BAP1 and CDKN2A (p16) |
|||||
| BAP1 and CDKN2A (p16)[26] | 67 samples;32 MM, 35 atypical reactive mesothelial cells | Cell block section of effusion | Immunocytochemistry for BAP1 and FISH for CDKN2A | Homozygous deletion of CDKN2A (p16) by FISH is more sensitive than loss of BAP1 immunostaining. | Good diagnostic markers of malignant mesothelioma |
| CDKN2A[27] | 32 total samples; 19 benign and 7 MM and 6 cytological suspicious | ThinPrep | Dual color FISH | Homozygous CDKN2A deletion was noted in 6/7 MM and 6/6 specimens with suspicious cytology | FISH increased diagnostic sensitivity of MM |
| MUC1 MUC2, and MUC5AC[28] | 89 total samples; 54 malignant, 35 benign | Cell pellet | QT-RT-PCR | The expression of MUC1 MUC2, and MUC5AC genes are higher in malignant effusion | The sensitivity and specificity of to detect malignancy in effusion are 86.1% and 91.5%, respectively |
| CEA, Ep-CAM, E-cadherin, mammaglobin, MUC1[29] | 114 total cases; 71 malignancy, 43 benign | Cell pellet | RT-PCR | The combined application of cytology and RT-PCR of CEA and Ep-CAM had high sensitivity and specificity (90.1%) | RT-PCR analysis of CEA and Ep-CAM significantly increased diagnostic sensitivity |
| A large panel of genes (161 genes)[22] | 20 samples | Cell block | NGS | Somatic mutations were detected all these cases | The genetic markers assessment may have diagnostic importance |
| Microsatellite markers[30] | 20 samples; 14 malignant and 6 benign | Cell Pellet | PCR | Genetic alterations of microsatellites were noted in tumor patients only | A combination of cytological and microsatellite analysis may help in the diagnosis of difficult cases |
| P53 and k-RAS[31] | 16 cases | Microdissected cells from the glass slide | PCR-single-stranded conformation polymorphism | The same mutational changes were noted in the cytology sample and resected specimen | Mutational changes of p53 and k-RAS may help in the diagnosis of malignancy in effusion sample |
| Claudin 4[32] | 75 total cases; 56 malignant and 19 benign | Cell pellet | RT-PCR | mRNA of claudin 4 detected in cells of effusion samples in malignant cases | The detection of claudin 4 gene upregulation may help in the diagnosis of malignancy |
| Telomerase reverse transcriptase[33] | 96 total cases; 41 malignant and 55 benign | Cell pellet | RT-PCR | mRNA of telomerase reverse transcriptase is frequently present in malignant effusion sample than the benign sample | The sensitivity and specificity of mRNA of telomerase reverse transcriptase are 90% and 95%, respectively, and the detection of TERT may help in the diagnosis of malignancy |
MM: Malignant mesothelioma, CEA: Carcinoembryonic antigen, EpCAM: Epithelial cell adhesion molecule, MUC1: Mucin 1, RT-PCR: Real-time reverse transcriptase-polymerase chain reaction
MANAGEMENT AND PROGNOSIS
In the era of personalized medicine, molecular tests can be used extensively in the effusion samples.
EGFR and ALK
Introduction of targeted therapy for EGFR and ALK has changed the scenario of the management of lung adenocarcinoma.[38,39]
Several studies have demonstrated EGFR and ALK mutation in pleural fluid samples.[33-38] PCR and NGS have been applied from either cell block or cell pellet material of effusion fluid for the demonstration of EFGR mutation.[40-45] Less than 5% of tumor cells were sufficient for the detection of EGFR mutation by NGS.[40] There was a high concordance between the result of the resected specimen and the effusion sample.[40] EGFR mutational analysis from effusion sample was successful in more than 90% of cases, and various studies concluded that EGFR mutational status from the effusion sample could be used for targeted therapy.[40-42]
EML4-ALK gene fusion was demonstrated in the effusion sample by FISH or RT-PCR, and the majority of the studies were done successfully on the cell block material of effusion sample and concluded that the demonstration of ALK gene rearrangement in effusion could be used for targeted therapy instead of a tissue section from the biopsy material.[43-45]
Her2/neu
Her2/neu gene amplification is successfully demonstrated by FISH technique in effusion sample by various researchers.[46,47] Nizzoli et al. successfully showed Her2/ neu gene amplification in the archival May-GrünwaldGiemsa (MGG) stained slide.[47] FISH in the archival MGG stained slide is particularly useful in cases that need pre-operative chemotherapy, but tissue section or cell block is not available.
BRCA1 and BRCA2
Mutational changes of BRCA1 and BRCA2 have been demonstrated by NGS in effusion samples.[48,49] There was complete concordance of mutation results between histopathology sections and effusion samples. Fumagalli et al. performed NGS on archival MGG slides by scrapping the representative cytology smear. They concluded that BRCA test is reproducible in effusion fluid sample of ovarian cancer and a useful tool for clinical decision-making.[49]
Cancer stem cell markers
Sherman-Samis et al. performed quantitative RT-PCR of various cancer stem cell markers (NANOG, OCT4, SOX2, SOX4, SOX9, LIN28A, and LIN28B) in a large number of effusion samples.[50] They noted that higher SOX2 and SOX9 protein expressions were associated with overall shorter survival. Table 4 highlights the applications of molecular tests in effusion in the management and prognostic assessments.
| Molecular markers | Specimen preparation | Tests | Results and comments |
|---|---|---|---|
| EGFR | |||
| EGFR[40] | Cell pellet from fresh sample | NGS | Less than 5% tumor cells can also be processed. There was high concordance of the result of pleural effusion and biopsy sample from tumor. The molecular analysis by NGS can be used for targeted therapy |
| EGFR[41] | Cell block | NGS | Clinically relevant genetic alterations can be detected in effusion sample for the targeted therapy |
| EGFR, ALK, and ROS1[42] | Cell block | PCR for EGFR and K-ras; FISH for ALK | Molecular tests were successful in 91% samples. Molecular tests in effusion sample can be used for targeted therapy |
| ALK | |||
| ALK[43] | Cell block | RT-PCR and FISH | EML4-ALK fusion Gene can be demonstrated successfully in pleural effusion sample. Both RT-PCR and FISH are specific and can be used for targeted therapy |
| ALK[44] | Cell block | FISH | ALK rearrangement can be successfully demonstrated in cell block of pleural effusion |
| ALK[45] | Cell block | FISH and RT-PCR | Cell block of effusion had good performance for ALK detection and can be used instead of tumor tissue. |
| Her2/neu | |||
| Her2/neu[46] | Cytospin | FISH | Her2 gene amplification can be detected in effusion sample even in the small amount of cells. |
| Her2/neu[47] | Archival May-Grünwald-Giemsa stained smear | FISH | HER-2/neu gene amplification can be demonstrated by FISH from May-Grünwald-Giemsa stain |
| BRCA1 and BRCA2 | |||
| BRCA1 and BRCA2[48] | Cell pellet | NGS | There was complete concordance (100%) of mutation result between effusion cytology and histology samples. |
| BRCA1 and BRCA2[49] | Archival May-Grünwald-Giemsa stained smear | NGS | BRCA test was reproducible in effusion fluid sample of ovarian cancer and a useful tool for clinical decision-making |
| Cancer stem cell markers | |||
| NANOG, OCT4, SOX2, SOX4, SOX9, LIN28A, and LIN28B[50] | Cell pellet | QRT-PCR | Higher SOX2 and SOX9 protein expression were associated with overall shorter survival |
CONCLUSION AND FUTURE PERSPECTIVES
Serous effusion provides enough material for all the tests that can be done on tissue biopsy. All the molecular analyses, including a-CGH, FISH, PCR, and NGS, can be done successfully from the serous fluid sample. For the diagnostic purpose, immunocytochemistry on the effusion sample is highly useful in the majority of the cases. The molecular tests are costly and time consuming. Therefore, it is not recommended for diagnostic purposes in a routine situation. However, the molecular tests can be done in undiagnosed effusion cases when the combined clinical information, radiological investigations, and immunocytochemistry are not helpful. The selection of molecular tests largely depends on the clinical setup. In the case of diagnosis of malignancy, the expression of EpCAM, CEA, telomerase reverse transcriptase, or microsatellite gene mutation may be helpful. The molecular tests should be selectively chosen to identify the source of metastasis.
mi-RNA is a promising biomarker in effusion sample because of relative more stability in the biological sample, high sensitivity and specificity, and economically feasible to evaluate. However, it is associated with certain limitation. The one specific mRNA is often regulated by several miRNA. Hence, it is often difficult to specify the target molecule. Hence, the derangement of a particular mi-RNA may be linked with two different malignancies. More extensive study in this area is required to find out the exact panel of miRNA in the diagnosis and even prognosis of the metastatic diseases in the effusion sample.
The information on selected gene mutational changes in effusion sample may be immensely helpful to introduce targeted therapy. The array-based CGH can give information on molecular changes of a large number of genes and may be very helpful for therapeutic purpose. Another less explored area is cell-free DNA of the supernatant fluid of the effusion sample. NGS of the supernatant fluid of the effusion may work as a liquid biopsy and may provide us with a plethora of information.
In the era of molecular technology, the cytopathologist plays many vital roles. The cytologist may provide the provisional cytological diagnosis to guide the clinicians for ordering the molecular tests. He can also assess the cellularity of the samples for the selection of the slide for the molecular analyses. Finally, the cytologist may take part the central role of integrating the molecular data, clinical history, and cytological features for the ultimate conclusion.
Data sharing
Only the published data were used in this paper.
COMPETING INTEREST STATEMENT BY ALL AUTHORS
There is no competing of interest in this paper as declared by all the authors.
AUTHORSHIP STATEMENT BY ALL AUTHORS ETHICS STATEMENT BY ALL AUTHORS
Dr. Saumya Sahu: Collected references, analyzed data, and wrote the manuscript.
Parikshaa Gupta: Collected references and analyzed data.
Pranab Dey: Concept of the work, data analysis, and drafting the manuscript.
LIST OF ABBREVIATIONS (In alphabetic order)
ARMS-Amplification refractory mutation system
BAP1-BRCA-1-associated protein’
BRCA1-Breast Cancer 1
CEA-Carcinoembryonic antigen
CF-Cell free
CGH-Comparative genomic hybridization
CDKN2A-Cyclin-dependent kinase inhibitor 2A
DNA-Deoxy ribonucleic acid
dd-droplet digital
EGFR-Epidermal growth factor receptor
EpCAM-Epithelial cell adhesion molecule
FISH-Fluorescent in situ hybridization
h-TERT-Human telomerase reverse transcriptase
LBC-Liquid-based cytology
mi RNA-Micro RNA
NGS-Next generation sequencing
PCR-Polymerase chain reaction
RT-PCR-Reverse transcriptase polymerase chain reaction
SSCP-Single stranded conformation polymorphism.
EDITORIAL/PEER-REVIEW STATEMENT
To ensure the integrity and highest quality of CytoJournal publications, the review process of this manuscript was conducted under a double-blind model (authors are blinded for reviewers and vice versa) through automatic online system.
References
- Cytohistological correlation in serous effusions using the newly proposed international system for reporting serous fluid cytopathology: Experience of an oncological center. Diagn Cytopathol. 2021;49:596-605.
- [CrossRef] [PubMed] [Google Scholar]
- Are we ready to develop a tiered scheme for the effusion cytology? A comprehensive review and analysis of the literature. Diagn Cytopathol. 2019;47:1145-59.
- [CrossRef] [PubMed] [Google Scholar]
- Approach to diagnostic cytopathology of effusions In: Shidham VB, Atkinson BF, eds. Cytopathologic Diagnosis of Serous Fluids (1st ed. Ch. 3). Amsterdam: Elsevier, W B Saunders Company; 2007. p. :31-42.
- [Google Scholar]
- Immunocytochemistry of effusion fluids: Introduction to the SCIP approach In: Shidham VB, Atkinson BF, eds. Cytopathologic Diagnosis of Serous Fluids (1st ed. Ch. 5). Elsevier, W B Saunders Company; 2007. p. :55-78.
- [Google Scholar]
- CellBlockistry: Chemistry and art of cell-block making-a detailed review of various historical options with recent advances. Cytojournal. 2019;16:12.
- [CrossRef] [PubMed] [Google Scholar]
- Novel modification of HistoGel-based cell block preparation method: Improved sufficiency for molecular studies. Arch Pathol Lab Med. 2018;142:529-35.
- [CrossRef] [PubMed] [Google Scholar]
- Archival fine-needle aspiration cytopathology (FNAC) samples: Untapped resource for clinical molecular profiling. J Mol Diagn. 2010;12:739-45.
- [CrossRef] [PubMed] [Google Scholar]
- Optimizing the DNA yield for molecular analysis from cytologic preparations. Cancer Cytopathol. 2016;124:254-60.
- [CrossRef] [PubMed] [Google Scholar]
- Application of immunocytochemistry and BRAF mutational analysis to direct smears of metastatic melanoma. Cancer Cytopathol. 2012;120:52-61.
- [CrossRef] [PubMed] [Google Scholar]
- EGFR and KRAS mutations detection on lung cancer liquid-based cytology: A pilot study. J Clin Pathol. 2012;65:87-91.
- [CrossRef] [PubMed] [Google Scholar]
- Preparation of DNA from cytological material: Effects of fixation, staining, and mounting medium on DNA yield and quality. Cancer Cytopathol. 2013;121:344-53.
- [CrossRef] [PubMed] [Google Scholar]
- Using “residual” FNA rinse and body fluid specimens for next-generation sequencing: An institutional experience. Cancer Cytopathol. 2016;124:324-9.
- [CrossRef] [PubMed] [Google Scholar]
- Detection of EGFR gene mutation status from pleural effusions and other body fluid specimens in patients with lung adenocarcinoma. Thorac Cancer. 2019;10:2218-24.
- [CrossRef] [PubMed] [Google Scholar]
- How to prepare cytological samples for molecular testing. J Clin Pathol. 2017;70:819-26.
- [CrossRef] [PubMed] [Google Scholar]
- Clinical utility of circulating tumor DNA for molecular assessment and precision medicine in pancreatic cancer. Adv Exp Med Biol. 2016;924:13-7.
- [CrossRef] [PubMed] [Google Scholar]
- Allele specific locked nucleic acid quantitative PCR (ASLNAqPCR): An accurate and cost-effective assay to diagnose and quantify KRAS and BRAF mutation. PLoS One. 2012;7:e36084.
- [CrossRef] [PubMed] [Google Scholar]
- Molecular techniques and methods applied in cytology In: Yang B. Rao J, editors. Molecular Cytopathology. Switzerland: Springer; 2016. p. :17-26.
- [CrossRef] [Google Scholar]
- KRAS and BRAF mutations in circulating tumour DNA from locally advanced rectal cancer. Sci Rep. 2018;8:1445.
- [CrossRef] [PubMed] [Google Scholar]
- Clinical significance of the detection of the homozygous deletion of p16 gene in malignant pleural effusion. Intern Med. 2017;46:1161-6.
- [CrossRef] [PubMed] [Google Scholar]
- Fluorescence in situ hybridization in the definitive diagnosis of malignant mesothelioma in effusion cytology. Chest. 2010;138:137-44.
- [CrossRef] [PubMed] [Google Scholar]
- Comprehensive mutation profiling by next-generation sequencing of effusion fluids from patients with high-grade serous ovarian carcinoma. Cancer Cytopathol. 2015;123:289-97.
- [CrossRef] [PubMed] [Google Scholar]
- Targeted deep sequencing of effusion cytology samples is feasible, informs spatiotemporal tumor evolution, and has clinical and diagnostic utility. Genes Chromosomes Cancer. 2018;57:70-9.
- [CrossRef] [PubMed] [Google Scholar]
- Fluorescence in situ hybridization, comparative genomic hybridization, and other molecular biology techniques in the analysis of effusions. Diagn Cytopathol. 2005;33:294-9.
- [CrossRef] [PubMed] [Google Scholar]
- The potential value of comparative genomic hybridization analysis in effusion and fine needle aspiration cytology. Mod Pathol. 2002;15:818-25.
- [CrossRef] [PubMed] [Google Scholar]
- Fluorescence in situ hybridization (FISH) provides estimates of minute and interstitial BAP1, CDKN2A, and NF2 gene deletions in peritoneal mesothelioma. Mod Pathol. 2020;33:217-27.
- [CrossRef] [PubMed] [Google Scholar]
- BAP1 immunostain and CDKN2A (p16) FISH analysis: Clinical applicability for the diagnosis of malignant mesothelioma in effusions. Diagn Cytopathol. 2016;44:599-606.
- [CrossRef] [PubMed] [Google Scholar]
- The use of CDKN2A deletion as a diagnostic marker for malignant mesothelioma in body cavity effusions. Cancer. 2003;99:51-6.
- [CrossRef] [PubMed] [Google Scholar]
- Application of mucin quantitative competitive reverse transcription polymerase chain reaction in assisting the diagnosis of malignant pleural effusion. Am J Respir Crit Care Med. 2001;164:1312-8.
- [CrossRef] [PubMed] [Google Scholar]
- Evaluation of a panel of molecular markers for the diagnosis of malignant serous effusions. Clin Cancer Res. 2005;11:6862-7.
- [CrossRef] [PubMed] [Google Scholar]
- Microsatellite analysis of pleural supernatants could increase sensitivity of pleural fluid cytology. J Mol Diagn. 2005;7:517-24.
- [CrossRef] [Google Scholar]
- Application of the p53 and K-ras gene mutation patterns for cytologic diagnosis of recurrent lung carcinomas. Cancer. 2000;90:258-63.
- [CrossRef] [Google Scholar]
- Improvement of malignant serous effusions diagnosis by quantitative analysis of molecular claudin 4 expression. Biomarkers. 2010;15:315-24.
- [CrossRef] [PubMed] [Google Scholar]
- Diagnostic accuracy of human telomerase reverse transcriptase mRNA in malignant pleural effusions: A preliminary report for in situ hybridization detection. Clin Chim Acta. 2007;381:131-5.
- [CrossRef] [PubMed] [Google Scholar]
- MicroRNAs-novel biomarkers for malignant pleural effusions. Contemp Oncol (Pozn). 2019;23:133-40.
- [CrossRef] [PubMed] [Google Scholar]
- Diagnostic value of circulating extracellular miR-134, miR-185, and miR-22 levels in lung adenocarcinoma-associated malignant pleural effusion. Cancer Res Treat. 2014;46:178-85.
- [CrossRef] [PubMed] [Google Scholar]
- Identification of differential expressed PE exosomal miRNA in lung adenocarcinoma, tuberculosis, and other benign lesions. Medicine (Baltimore). 2017;96:e8361.
- [CrossRef] [PubMed] [Google Scholar]
- Downregulated microRNAs in the differential diagnosis of malignant pleural mesothelioma. Int J Cancer. 2010;127:2859-69.
- [CrossRef] [PubMed] [Google Scholar]
- Erlotinib versus chemotherapy as first-line treatment for patients with advanced EGFR mutation-positive non-small-cell lung cancer (OPTIMAL, CTONG-0802): A multicentre, open-label, randomized, phase 3 study. Lancet Oncol. 2011;12:735-42.
- [CrossRef] [Google Scholar]
- First-line crizotinib versus chemotherapy in ALK-positive lung cancer. N Engl J Med. 2014;371:2167-77.
- [CrossRef] [PubMed] [Google Scholar]
- Next generation sequencing-based molecular profiling of lung adenocarcinoma using pleural effusion specimens. J Thorac Dis. 2018;10:2631-7.
- [CrossRef] [PubMed] [Google Scholar]
- Comprehensive genomic profiling of malignant effusions in patients with metastatic lung adenocarcinoma. J Mol Diagn. 2018;20:184-94.
- [CrossRef] [PubMed] [Google Scholar]
- Identification of EGFR mutation, KRAS mutation, and ALK gene rearrangement in cytological specimens of primary and metastatic lung adenocarcinoma. Cancer Cytopathol. 2013;121:500-7.
- [CrossRef] [PubMed] [Google Scholar]
- Detection of EML4-ALK in lung adenocarcinoma using pleural effusion with FISH, IHC, and RT-PCR methods. PLoS One. 2015;10:e0117032.
- [CrossRef] [PubMed] [Google Scholar]
- Detection of ALK rearrangements in malignant pleural effusion cell blocks from patients with advanced non-small cell lung cancer: A comparison of Ventana immunohistochemistry and fluorescence in situ hybridization. Cancer Cytopathol. 2015;123:117-22.
- [CrossRef] [PubMed] [Google Scholar]
- Cell block samples from malignant pleural effusion might be valid alternative samples for anaplastic lymphoma kinase detection in patients with advanced non-small-cell lung cancer. Histopathology. 2015;66:949-54.
- [CrossRef] [PubMed] [Google Scholar]
- Combined detection of Her2/neu gene amplification and protein overexpression in effusions from patients with breast and ovarian cancer. J Cancer Res Clin Oncol. 2010;136:1389-400.
- [CrossRef] [PubMed] [Google Scholar]
- HER-2/neu evaluation by fluorescence in situ hybridization on destained cytologic smears from primary and metastatic breast cancer. Acta Cytol. 2005;49:27-30.
- [CrossRef] [PubMed] [Google Scholar]
- Cytology material is equivalent to tumor tissue in determining mutations of BRCA 1/2 genes in patients with tubo-ovarian high grade serous carcinoma. BMC Cancer. 2019;19:296.
- [CrossRef] [PubMed] [Google Scholar]
- Next-generation sequencing-based BRCA testing on cytological specimens from ovarian cancer ascites reveals high concordance with tumour tissue analysis. J Clin Pathol. 2020;73:1 SSCP 68-71
- [CrossRef] [PubMed] [Google Scholar]
- SOX2 and SOX9 are markers of clinically aggressive disease in metastatic high-grade serous carcinoma. Gynecol Oncol. 2019;153:651-60.
- [CrossRef] [PubMed] [Google Scholar]
