Chapter 13 Flow cytometry, molecular analysis, and other special techniques
The purpose of this chapter is to summarize the application of these molecular and other special techniques to effusion fluids.SURFACE MARKER FLOW CYTOMETRY
Serous effusion is an appropriate specimen for surface marker flow cytometric analysis to confirm the diagnosis of malignant lymphoid neoplasm. However, unlike the role of flow cytometry in the diagnosis of lymphoid lesions by fine-needle aspiration or biopsies, which is well-accepted, its use in serous fluids is limited. However, recently its use in body fluid analysis is increasing significantly. 
It is usually difficult to differentiate between reactive lymphocytosis and malignant lymphoma in serous effusions, especially in low-grade malignant lymphomas, on morphology alone. Flow cytometric analysis can be useful in this situation.1
FLOW CYTOMETRY AND HEMATOPOIETIC NEOPLASMS
When the diagnosis of lymphoma/leukemia is suspected on cytopathologic examination and/or the patient has had a previous history of lymphoma/leukemia, cell surface flow cytometry can be helpful in the diagnosis and the classification of these tumors. 
The algorithms in Figures 13.1 and 13.2 and Table 13.1 summarize the approaches of using flow cytometry data for aiding in the diagnosis of hematopoietic lesions.
Table 13.1 Flow cytometry immunophenotyping of leukemias
| ALL | AML | |
|---|---|---|
| B-cell | T-cell | CD13+ |
| CD19+ | CD2, 3, 5, 7 + | CD33+ |
| CD20+/− | CD4/CD8 + | CD34+/−* |
| TdT+ | Dual CD4/CD8 – | HLA-DR +/− |
| CD34+/− | Dual TdT+ | CD41, Megakaryocytic differentiation |
| CD34+/− | CD71, Glycophorin A: Erythroid differentiation | |
| CD64, CD4, CD14: Monocytic differentiation | ||
* HLA-DR/34 -: Acute promyelocytic leukemia. ALL, acute lymphoblastic leukemia; AML, acute myeloid leukemia.
The main differential diagnoses when one encounters small lymphocytes are usually between low-grade lymphomas and reactive chronic effusion. Flow cytometry is usually the most helpful in this setting. The encountering of large neoplastic cells usually brings up the diagnostic consideration of other large cell tumors such as poorly differentiated carcinomas, melanomas, and sarcomas.2–4 Flow cytometric analysis is often less helpful in this circumstance, whereas immunocytochemistry on cell block sections is more useful (see Figures 13.1, 13.2 and Table 13.1; see also Chapter 12).
UNIQUENESS OF SURFACE MARKER FLOW CYTOMETRIC STUDIES OF HEMATOPOIETIC NEOPLASMS IN SEROUS EFFUSIONS
Use of flow cytometry as a screening tool
Questions usually arise if all serous effusion specimens with numerous small, mature-appearing lymphoid cells should be sent for flow cytometry. A few prospective studies investigating flow cytometry as a screening tool in serous effusion specimens are reported.1,5,6 Finch et al6 evaluated flow cytometric analysis in pleural lymphocytosis, which was defined as specimens containing a majority of small, mature-appearing, small lymphocytes or cytologically atypical lymphoid cells. By flow cytometry, 73.9% of pleural fluids were categorized as reactive and 12.3% were positive for non-Hodgkin lymphoma. But when patients did not have a prior history of non-Hodgkin lymphomas, only 4% of pleural effusions were positive for lymphoma by flow cytometry. The above data did not suggest the use of flow cytometry as a screening tool to diagnose non-Hodgkin lymphomas in pleural lymphocytosis.5 In contrast, Wells and Jorgensen7 presented a study in an abstract form that included 309 pleural effusions from 281 patients. The majority of these cases were without a known history of a lymphoproliferative disease. The specimen was triaged for flow cytometric analysis based on cytologic examination. Eight percent (26/309) of all cases evaluated by the flow cytometric analysis demonstrated a new positive diagnosis. The authors concluded that 8% of all cases was a significant number and may be a valuable way to confirm the primary diagnosis of lymphoid malignancy.
In our opinion, the decision to send the specimen for flow cytometric analysis should be based primarily on cytomorphologic evaluation, clinical context, and patient population.
The usefulness of flow cytometry in selected patient populations
When flow cytometry is performed in a selected patient population that has a known history of or is suspected of malignant lymphoma either clinically or cytomorphologically, flow cytometry is proved to be a more valuable tool.1,6 Czader and Ali performed a retrospective study on 115 serous effusions from pleural (n = 86), peritoneal (n = 20), and pericardial (n = 9) fluids. In these cases, the main indication for flow cytometric analysis was the presence of spontaneous serous effusions in patients with known histories of malignant lymphoma. The application of flow cytometry and morphology together were able to assign all but one case that was originally diagnosed as atypical/suspicious (16% of specimens studies) to either benign or malignant categories resulting in appropriate clinical staging and management in the majority of the cases.1 In the same study, 4 cases with benign morphology were reclassified to the atypical/suspicious category after flow cytometric studies demonstrated an aberrant population. Another study by Finch et al showed that, in 34.2% of patients with a previous history of malignant lymphoma and 33.3% of patients with cytologically atypical lymphoid cells in their pleural fluid, the diagnosis was confirmed by using flow cytometric studies.6
Significance of an aberrant or monoclonal lymphoid population by flow cytometry
The finding of an aberrant or monoclonal lymphoid popu-lation by flow cytometry in serous effusions is not equal to a diagnosis of malignant lymphoma. 
The presence of mono-clonality by flow cytometry without appropriate clinical context and morphologic findings should be interpreted cautiously and does not always equate with a diagnosis of malignant lymphoma. In other types of cytology specimens such as fine-needle aspirations, studies of flow cytometric analysis of reactive lymph nodes with follicular hyperplasia and lym-phoid follicles of Hashimoto’s thyroiditis, patients have shown that germinal center (GC) B-cells (CD10+/CD20+) can show upwardly skewed kappa-to-lambda light chain (K/L) ratios, giving the false impression of monoclonality.8 Likewise, a monoclonal lymphoid population in a serous effusion may be identified but does not always mean a diagnosis of malignant lymphoma. For example, a case in Czader’s study1 showed a kappa restricted B-cell population in the setting of a chronic hepatitis C infection without evidence of lymphoma.
FLOW CYTOMETRY AND NON-HEMATOPOIETIC NEOPLASM
Unlike the flow cytometry role in hematologic neoplasm, the application of these techniques in non-hematopoietic neoplasm is not well-accepted in clinical practice and is still under investigation. There have been studies using flow cytometry on non-hematopoietic neoplasms on bench fine-needle aspiration specimens9 and paraffin-embedded tissue.10 However, such applications on serous effusions have not been reported in the literature.
Instead of using cell surface markers to identify malignant cells, the percentage of CD16+, CD56+, and CD3–natural killer lymphocytes by flow cytometry may be helpful in identifying metastatic adenocarcinoma in serous effusion.11,12 An association of a higher percentage of natural killer (NK) cells (12–33%12 and 29–68%11) with metastatic adenocarcinoma has been reported. In contrast to this, mesotheliomas, lymphomas, leukemias, malignant melanomas, and reactive mesothelial hyperplasia showed a lower percentage of NK cells (1–16%12 and 2–20%11). 
It was further suggested that the presence of ≥12% NK cells should make the cytopathologist suspect the presence of metastatic adenocarcinoma.12
ELECTRON MICROSCOPY
With an increasing use of immunohistochemistry, there has been a decreasing use of electron microscopy in the diagnosis of malignant neoplasm. The main usefulness of electron microscopy in serous effusion fluid is in the differential diagnosis between malignant mesothelioma and metastatic adenocarcinoma after cytopathologic confirmation of malignancy. The presence of slender and elongated microvilli, abundant intermediate filaments, and lack of secretory granules favored mesothelioma, whereas short stubby microvilli and secretory granules suggested a diagnosis of adenocarcinoma.13,14 Nonetheless, overlapping features may exist and cause difficulty in interpretation.13 
The main challenge with serous fluid specimens as compared to tissue biopsy is to locate and identify the malignant cell unequivocally for ultrastructural evaluation. Spuriously, the reactive mesothelial cells in the background may be evaluated and misinterpreted as mesothelioma. Furthermore, in clinical practice, electron microscopic studies are considered expensive, laborious, lengthy, and, nowadays, the diagnosis is usually reached with the help of immunocytochemistry.
FLUORESCENCE IN-SITU HYBRIDIZATION AND METASTATIC SEROUS EFFUSION
Application of the interphase fluorescence in-situ hybridization (FISH) technique has not become a standard practice in serous effusion analysis; nonetheless, recent studies have demonstrated the possible role of this method for detecting malignant cells in effusions with higher sensitivity.15–22 The potential uses of FISH using different centromere-specific probes on chromosomes 1, 3, 7, 8, 9, 10, 11, 12, 17, and 18 (with different combinations) have been examined in serous effusions for detecting pleural malignant mesothelioma,15 metastatic breast cancer,16 and metastatic carcinoma.16–21 The studies suggested that FISH can be helpful in cytologically negative or ambiguous effusions and yielded highly sensitive and specific results when used together with cytologic examination.15–22 Diagnostic superiority was demonstrated in metastatic effusions from the breast, lung, pancreas, gynecologic, and gastrointestinal carcinomas.18 Furthermore, cases with known primary tumors associated with abnormal FISH patterns would facilitate the appropriate choice of centromic probes for detection of metastasis.20 However, the limitation of FISH has been observed in cases consisting of a small population of malignant cells hidden against a background of inflammatory or reactive cells.21
It should be highlighted that cytomorphologic examination is still the gold standard for tumor staging and is the only method accepted in the classical AJCC cancer staging.18,23 Prospective studies are needed to demonstrate the clinical benefit of FISH to detect disseminated tumor cells in correlation with clinical outcomes.18
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