Current applications of molecular testing on body cavity fluids

Minimally Invasive, Maximally Effective: The Power of Precision Cytoanalysis on Effusion Samples-A Comprehensive Exploration from Traditional Methods to Innovative Approaches

Precision medicine translates through molecular assays and in minimally invasive diagnosis, evident in analyses of effusions that serve therapeutic and diagnostic purposes. This cost-effective and low-risk approach provides advantages, playing a pivotal role in late-stage oncology and frequently standing as the primary resource for cancer diagnosis and treatment pathways. This article outlines the workflow for managing serous fluid and explores how cytology effusion analysis extends beyond immunocytological diagnosis. Combined with current molecular tests it showcases the potential to be a skillful tool in precision cytopathology.

Liposarcoma Involving Serous Fluid Cavities-A Case Series Illustrating Clinical Implications and the Diagnostic Role of Exfoliative Cytology

Introduction: Cytological diagnosis of sarcomas requires detailed cytomorphological assessment and integration of immunocytochemistry and/or molecular testing. The role of exfoliative cytology, as compared to aspiration cytology, is less understood. This case series describes well-differentiated/dedifferentiated liposarcomas in effusions, with cytomorphological features, ancillary test results and clinical outcomes detailed. Methods: A computerized search of the department pathology archives was performed for sarcomatous effusions with histological diagnosis or clinical history of well-differentiated/dedifferentiated liposarcoma. Clinical progress, cytology slides, immunocytochemistry and molecular test results were reviewed. Results: Six patients were identified. In 5 patients with clinical follow up, 4 (80%) were deceased within 5 months of malignant effusion. One patient was alive with 12 years disease-free survival after radical resection with adjuvant radiotherapy. Three patients showed dedifferentiation on histology, and high-grade (dedifferentiated) tumor cells were present in effusion cytology of 2 patients. Two showed well-differentiated components only on biopsy, but high-grade (dedifferentiated) tumor cells were identified in cytology. The high-grade tumor cells displayed marked nuclear irregularity, enlargement, size variation, with macronucleoli and multinucleation. Well-differentiated lipomatous components were demonstrated in 4 patients (66.7%), comprising of multivacuolated lipoblasts and atypical lipocytes. CDK4 and MDM2 immunoreactivity in all 3 cases with cell blocks, and CDK4 and MDM2 amplification in one were successfully demonstrated. Conclusion: Lipomatous and dedifferentiated components can be sampled and cytomorphologically identified on effusion fluids of liposarcomas, with sufficient cellularity for immunocytochemistry and molecular testing. Although generally associated with poor prognosis, long disease-free survival with sarcomatous effusion is possible with radical surgery and adjuvant treatment.

Impact of serous fluid volume on next-generation sequencing: a significant step forward for optimization of serous fluid sample collection

Current literature lacks data regarding the influence of serous fluid volume (SFV) on next-generation sequencing (NGS) performed on malignant cases. In this study, we highlight the impact of SFV and other parameters influencing the outcome of NGS analysis. We evaluated 827 samples of serous fluids from 607 patients. Of these, 72 samples underwent NGS analysis. Effusion volume, tumor cellularity, DNA, and RNA quality metrics, as well as clinicopathologic and molecular data were evaluated. Pleural fluid accounted for 56.3% of the fluid samples collected. The most common primary tumor site was gastrointestinal/pancreatobiliary, adenocarcinoma was the most common histologic type. Overall mean volume was 293 mL. The mean Qubit DNA of the 72 effusion samples that underwent NGS analysis was 14.3 ng/μL and mean Qubit RNA was 28.2 ng/μL. The mean Qubit DNA concentration increases in SFV up to 100 mL only. No correlation exists between SFV and mean tumor cellularity. In addition, 74.6% (50 of 67) of sequenced samples showed oncogenic drivers; KRAS was the most common driver followed by EGFR. Three cases displayed ALK fusions, and 1 case displayed NTRK1 fusion. The DNA yield is higher in SFV of 100 mL as a cutoff. Beyond 100 mL, there is no impact of SFV on DNA yield. SFV does not impact RNA yield and mean tumor cellularity. Effusion samples should be submitted for molecular testing despite low tumor cellularity. Our results as a pilot study are important in optimization of SFV for both diagnosis as well as NGS analysis for improving management.

Overcoming Pitfalls in Breast Fine-Needle Aspiration Cytology: A Practical Review

BACKGROUND

Fine-needle aspiration cytology (FNAC) is a cornerstone technique for the initial assessment of breast lesions, offering a rapid and minimally invasive option for cytological evaluation. While FNACs can forego the need for core needle biopsies (CNBs), variations in technique, subjective interpretation, and intrinsic limitations present diagnostic challenges. The International Academy of Cytology (IAC) established the Yokohama system and is developing the WHO Reporting System for Breast Cytopathology jointly with IARC, to standardize diagnostic criteria, aiming to enhance diagnostic precision and consistency. Due to the preference for CNBs, expertise in breast FNAC is low in the developed world.

SUMMARY

This review assesses common pitfalls in breast cytopathology. These common and uncommon entities may easily lead to false-negative or false-positive diagnoses, due to morphological overlap or misleading clinical and radiological contexts. For instance, pauci-cellular lesions, such as lobular carcinomas, often lead to false-negative diagnoses, whereas complex sclerosing lesions, fibroadenomas, and papillary lesions may show concerning features, resulting in a false positive. The same is true for some benign inflammatory pathologies, such as steatonecrosis, and uncommon lesions, such as collagenous spherulosis. Ductal carcinoma in situ can lead to both false-negative and false-positive diagnoses, and high-grade lesions are impossible to tell apart from invasive carcinomas. These are discussed in detail. Procedural and preanalytical conditions, and the role of ancillary testing, are also briefly addressed.

KEY MESSAGES

Breast FNAB is a powerful diagnostic technique, fast and minimally invasive. Even in contexts which lack expertise, this technique can be successfully adopted with a cautious approach and as long as pitfalls are kept in mind, benefiting patients and healthcare systems.

Challenging the concept of "risk of malignancy" in cytology

Several standardized systems for nongynecological cytopathology have been published following the successful implementation of The Bethesda System for Reporting Cervical Cytology. Each of these systems comprises a set of reporting categories accompanied by a risk of malignancy. However, in most cases, these risk of malignancy estimates have not been based on high-quality evidence and often may not be consider proper "risks" (because they have been estimated based on cross-sectional studies). This commentary discusses the problems related to the data used to generate these risks. To make nongynecological cytopathology reporting more evidence-based, large-scale prospective cohort studies and randomized trials, in addition to high-quality systematic reviews and meta-analyses, should be performed.

Evaluating Diagnostic Clarity: The Comparative Efficacy of BlueStain in Serous Effusion Cytology under the International System for Reporting Serous Fluid Cytopathology Reporting Framework

Serous effusion cytology is a pivotal diagnostic and staging tool in clinical pathology, valued for its simplicity and cost-effectiveness. Staining techniques such as Giemsa and Papanicolaou are foundational, yet the search for rapid and efficient alternatives continues. Our study assesses the efficacy of an in-house-developed BlueStain, a toluidine blue variant, within the International System for Reporting Serous Fluid Cytopathology (TIS), aiming to optimize diagnostic clarity and resource use.

MATERIALS AND METHODS

This section provides details on the cohort of 237 patients with serous effusions, the ethical approval process, sample collection, and staining procedures with BlueStain, Papanicolaou, and Giemsa. It also describes the microscopic evaluation criteria, scoring system, and statistical methods used to compare the stains.

RESULTS

BlueStain demonstrated notable performance, particularly in identifying malignant cells, presenting a competitive alternative to the Papanicolaou stain, which, despite higher quality indices in other categories, requires more resources and time. The study revealed that BlueStain might offer a valuable balance between quality and efficiency, especially in cases where rapid diagnostic turnaround is essential.

CONCLUSIONS

Our findings suggest that BlueStain is a viable staining method in the context of serous effusions, capable of providing detailed cytomorphological analysis. While traditional stains hold their place for their established diagnostic clarity, BlueStain offers a rapid and resource-optimized alternative. The absence of definitive diagnostic criteria in the atypical category and the inherent sample heterogeneity underscores the necessity for adaptable staining methods like BlueStain. The study highlights the potential trade-offs between detail and practicality in staining techniques, advocating for further research into innovative methods that do not compromise diagnostic precision for cost and time efficiency.

Review of the impact of the International System for Serous Fluid Cytopathology

The International System for Reporting Serous Fluid Cytology (TIS) has been proposed by an expert working team composed of the International Academy of Cytology and the American Society of Cytopathology, following an international survey. Since its introduction, the TIS has gained worldwide acceptance, and this review aims to assess its global impact. A literature search revealed 25 studies which have presented data on the impact of the TIS. Most of them provide data, including risk of malignancy (ROM) for each diagnostic category, separately for pleural, peritoneal and pericardial effusions, while a few do not separate them. A few studies focus on specific diagnoses like mesothelioma on specific types of fluids or more specific issues like the optimal fluid volume for cytology or interobserver variability. A synopsis of the data from the literature search is presented in four tables. The ROM assessment is discussed, as well as interobserver variability and the use of ancillary diagnostic immunochemistry. In conclusion, our review of the published data suggests that the TIS is a valid classification scheme that has been widely accepted by pathologists globally, is highly reproducible and makes a valuable contribution to clinical therapeutic management.

Lymphoproliferative disorder involving body fluid: diagnostic approaches and roles of ancillary studies

Lymphocyte-rich effusions represent benign reactive process or neoplastic condition. Involvement of lymphoproliferative disease in body cavity is not uncommon, and it often causes diagnostic challenge. In this review, we suggest a practical diagnostic approach toward lymphocyte-rich effusions, share representative cases, and discuss the utility of ancillary tests. Cytomorphologic features favoring neoplastic condition include high cellularity, cellular atypia/pleomorphism, monomorphic cell population, and frequent apoptosis, whereas lack of atypia, polymorphic cell population, and predominance of small T cells usually represent benign reactive process. Involvement of non-hematolymphoid malignant cells in body fluid should be ruled out first, followed by categorization of the samples into either small/medium-sized cell dominant or large-sized cell dominant fluid. Small/medium-sized cell dominant effusions require ancillary tests when either cellular atypia or history/clinical suspicion of lymphoproliferative disease is present. Large-sized cell dominant effusions usually suggest neoplastic condition, however, in the settings of initial presentation or low overall cellularity, ancillary studies are helpful for more clarification. Ancillary tests including immunocytochemistry, in situ hybridization, clonality test, and next-generation sequencing can be performed using cytologic preparations. Throughout the diagnostic process, proper review of clinical history, cytomorphologic examination, and application of adequate ancillary tests are key elements for successful diagnosis.

Reassessing the optimal volume for malignancy detection in serous fluid cytology

BACKGROUND

The international system for reporting serous fluid cytopathology (TIS) recommends submitting at least 50-75 mL of serous fluid to decrease false-negative results. However, prior studies did not agree on specific volume requirements or consensus adequacy criteria. Our study aims to assess whether fluid volume affects the adequacy rate and to assess the minimum volume necessary for optimal adequacy in pleural and peritoneal fluids.

METHODS

A total of 8530 serous fluid cytology cases were identified in the laboratory information system. Differences in mean fluid volume received in the laboratory were compared using an ANOVA Games-Howell test based on TIS category. The percentage of malignant diagnoses across the volume ranges of 0 to 5 mL, 5 to 10 mL, 10 to 25 mL, 25 to 50 mL, 50 to 75 mL, 75 to 100 mL, 100 to 150 mL, 150 to 250 mL, 250 to 500 mL, 500 to 2000 mL was compared in pleural and peritoneal fluids using a chi-square test, and a SiZer analysis was performed.

RESULTS

Mean fluid volume in inadequate, atypical, and negative cases was significantly lower compared to positive cases. A SiZer analysis showed a positive relationship between the malignancy fraction of pleural and peritoneal fluids and fluid volume. The percentage of malignant diagnoses in pleural and peritoneal fluid samples increased significantly up to a volume range of 75-100 mL.

CONCLUSIONS

There is a significant relationship between fluid volume, adequacy and detection of malignancy in serous effusion cytopathology. The malignancy fraction increases with larger fluid volumes but at least 75-100 mL of fluid should be submitted for optimal diagnosis of malignancy in pleural and peritoneal fluids.

Optimization of pre-analytical and analytical steps for DNA and RNA analysis of fresh cytology samples

BACKGROUND

Different cytology preparations can be used for molecular diagnostics, however the influence of pre-analytical and analytical steps on the results are not yet well defined. We aimed to determine optimal steps for efficient extraction of DNA and RNA from fresh cells for molecular diagnostics.

METHODS

MCF7 and FaDu human cell lines, were used as a model to determine fresh cells storage conditions (temperature: 25°C, 4°C, -20°C, -80°C; duration: 0 h, 4 h, 12 h, 24 h, 48 h) and optimal nucleic acids extraction method. Besides, the minimal number of total cells and minimal percentage of mutated cells needed for successful extraction of nucleic acids and subsequent determination of present mutation were evaluated.

RESULTS

Extraction of nucleic acids using spin columns yielded the highest quantity and quality of nucleic acids. Isolation of nucleic acids was feasible in all storage conditions, however higher temperature and longer duration of fresh cells storage were associated with lower quality of isolated nucleic acids and similar quantification cycle of housekeeping genes. Successful molecular testing was feasible with least 10⁴ cells, while specific mutation was detected in as low as 5% of mutated cells.

CONCLUSIONS

Our cell line model, mimicking fresh cytology samples, showed that quantity of extracted either DNA or RNA declined with higher temperatures and longer duration of storage but regardless of the storage conditions, we successfully detected both housekeeping genes and mutated gene using qPCR.

Application of the International System for Reporting Serous Fluid Cytopathology (TIS): A Retrospective Institutional Study

BACKGROUND

Cytology of serous effusions is an important diagnostic tool for the diagnosis of cancer, staging and prognosis of the patient. Herein, we retrospectively applied the TIS on reporting serous cytopathology and provided the corresponding risk of malignancy (ROM).

METHODS

Pleural, pericardial and peritoneal effusion samples were retrieved from the archives of our department and reclassified according to the TIS. The ROM for each category was calculated based on available surgical follow-up.

RESULTS

A total 3790 effusions were available for the study. 1292 pleural samples were reclassified: 27 (2.1%) non-diagnostic (ND), 1014 (78.5 %) negative for malignancy (NFM), 86 (6.6 %) atypia of undetermined significance (AUS), 29 (2.3 %) suspicious of malignancy (SFM) and 136 (10.5%) malignant (M). 241 pericardial samples were reclassified: 4 (1.6 %) as ND, 173 (71.8 %) as NFM, 10 (4.1 %) as AUS, 7 (3 %) as SFM, and 47 (19.5%) as M. 2257 peritoneal cases were re-categorized as follows: 31 (1.4 %) as ND, 1897 (84 %) as NFM, 39 (1.7 %) as AUS, 53 (2.4 %) as SFM, and 237 (10.5 %) as M. The ROM was, respectively, for each of the aforementioned categories, 18.5%, 15%, 45.3%, 93%, 100% in pleural effusions, 25%, 13.2%, 35%, 100%, 100% in pericardial effusions and 19.3%, 10.4%, 43.5%, 100%, 100% in peritoneal effusions.

CONCLUSIONS

Pleural, pericardial, and peritoneal cytology show high specificity and moderate sensitivity in the evaluation of serous effusions. The ROM reported in our study was mostly concordant with ROM published by the TIS.

Application of the International System for Reporting Serous Fluid Cytopathology with Cytohistological Correlation and Risk of Malignancy Assessment

The International System for Reporting Serous Fluid Cytopathology (TIS) classifies serous effusions into five categories: non-diagnostic (ND), negative for malignancy (NFM), atypia of unknown significance (AUS), suspicious for malignancy (SFM) and malignant (MAL). The main objectives of this classification comprise the establishment of a universal code of communication between cytopathologists and clinicians and histopathologists, as well as between different laboratories worldwide, paving the way for the setting of clinical management guidelines based on the risk of malignancy assessment for each diagnostic category. We retrieved the total number of pleural and peritoneal effusion cases of our department for the three-year time period between 2018 and 2020, yielding a total of 528 and 500 cases, respectively. We then proceeded to reclassify each specimen according to TIS guidelines and calculate the risk of malignancy (ROM) for each category by searching each patients’ histology records, medical history and clinical follow-up. For pleural effusions, 3 (0.57%) cases were classified as ND, 430 (81.44%) cases as NFM, 15 (2.84%) as AUS, 15 (2.84%) as SFM and 65 (12.31%) as MAL. ROM amounted to 0%, 5.3%, 33.33%, 93.33% and 100% for each category, respectively. As far as peritoneal effusions are concerned, 6 (1.2%) were categorized as ND with ROM estimated at 16.66%, 347 (69.4%) as NFM (ROM = 9%), 13 (2.6%) as AUS (ROM = 38.46%), 12 (2.4%) as SFM (ROM = 83.33%) and 122 (24.4%) as MAL (ROM = 100%). Our results underline the utility of the current classification, both as a means of communication between doctors of different specialties and as general guidelines for the further clinical management of patients.

Direct next-generation sequencing analysis using endometrial liquid-based cytology specimens for rapid cancer genomic profiling

BACKGROUND

Genomic examination of cytology specimens is often performed on cell blocks or conventional smears rather than on liquid-based cytology (LBC) specimens. Since LBC specimens preserve high-quality DNA, cancer genome profiling using next-generation sequencing (NGS) is also attainable from residual LBC specimens. One of the advantages of using LBC specimens for NGS is that it allows direct extraction of DNA from residual specimens, avoiding a sacrifice of smear slides and minimizing genomic profiling processing time.

METHODS

Endometrial LBC specimens were subjected to NGS analysis to validate the practicality of rapid cancer genomic profiling in a pathology laboratory. The extracted DNA was subjected to NGS using a customized cancer gene panel comprising 56 genes and 17 microsatellite regions. The workflow strategy was defined, and the processing time estimated for specimen sampling, cell counting, NGS run, and genome profiling.

RESULTS

NGS analysis of most LBC specimens revealed somatic mutations, tumor mutation burden, and microsatellite instability, which were almost identical to those obtained from formalin-fixed paraffin-embedded tissues. The processing time for direct NGS analysis and cancer genomic profiling of the residual LBC specimens was approximately 5 days.

CONCLUSION

The residual LBC specimens collected using endometrial cytology were verified to carry a high tumor fraction for NGS analysis and could serve as an alternate source for rapid molecular classification and diagnosis of endometrial cancers, as a routine process in a pathology laboratory.

Cytohistological Correlation in Pleural Effusions Based on the International System for Reporting Serous Fluid Cytopathology

The International System for Reporting Serous Fluid Cytology (TIS) was recently developed. Given its novelty, most studies looking into the risk of malignancy (ROM) of serous effusion diagnostic categories were published before the development of TIS. We searched the database of our department for pleural effusions diagnosed in the last five years, excluding those without a corresponding pleural biopsy. Cases were reviewed and reclassified according to the TIS. A cytohistological correlation was performed. In total, 350 pleural effusion specimens with one or more corresponding pleural biopsies were included. After reclassification, 5 (1.43%) were nondiagnostic (ND), 253 (72.29%) were negative for malignancy (NFM), 7 (2.00%) had atypia of unknown significance (AUS), 14 (4.00%) were suspicious for malignancy (SFM), and 71 (20.57%) were malignant (MAL). Calculated ROM was 40% for ND, 20.16% for NFM, 42.86% for AUS, 78.57% for SFM, and 100% for MAL. Effusion cytology sensitivity and specificity were 60.29% and 98.56%, respectively. This is the first publication looking into the cytohistological correlation of a retrospective cohort of pleural effusions based on the TIS. We add to the body of data regarding the ROM for TIS categories, highlighting areas of potential future research.

The value of cytology in distinguishing malignant mesothelioma: An institutional experience of 210 cases reclassified according to the International System for Reporting Serous Fluid Cytopathology (ISRSFC)

OBJECTIVE

Malignant mesothelioma (MM) is usually diagnosed by histological examination of tissue samples; however, effusion cytology offers an opportunity to identify a strong possibility for mesothelioma diagnosis at an early stage. We conducted a retrospective analysis of cytological specimens from a large series of histologically proven MM diagnosed over 19 years. The cases were reviewed and reclassified according to the International System for Reporting Serous Fluid Cytopathology (ISRSFC).

METHODS

A total of 450 cases were identified. Cytological analysis was present in 210 patients (164 pleural and 46 peritoneal effusions). All cases were reviewed and reclassified according to the proposed ISRSFC scheme. A comparison among the cytomorphological features was made throughout the different diagnostic categories.

RESULTS

The 210 cases were histologically diagnosed as follows: 192 (91.4%) cases had an epithelioid type and 18 (8.6%) had a sarcomatoid subtype of MM. The cytological cases were reclassified as follows: 2 (0.9%) as non-diagnostic (ND), 81 (38.6%) as negative for malignancy (NFM), 4 (1.9%) as atypia of undetermined significance (AUS), 11 (5.2%) as suspicious for malignancy (SFM), 112 (53.4%) as malignant (MAL). Sarcomatoid cells in the MAL category were characterised cytomorphologically by more pronounced discohesion. In comparison with the epithelioid subtype, the tumour cells appeared solitary with moderate or marked nuclear pleomorphism, and irregular chromatin.

CONCLUSIONS

It is important to recognise the cytological characteristics of this aggressive entity to suggest an early and precise possible diagnosis. Morphological features, coupled with clinico-radiological data may help the clinicians in adequately managing the patients.

A retrospective analysis of pleural effusion specimens based on the newly proposed International System for Reporting Serous Fluid Cytopathology

BACKGROUND

Recently, the International System for Reporting Serous Fluid Cytopathology (TIS) has been established, with an aim to standardize reporting and guide clinical decision making.

METHODS

The cytological and clinicopathological data of pleural effusions were retrieved from the pathology database and electronic medical records. All specimens were evaluated and reclassified in accordance with the TIS recommendations. Finally, the risk of malignancy (ROM) and performance parameters were measured.

RESULTS

A total of 2454 pleural effusion specimens were included, among which 30 (1.2%), 1670 (68.1%), 151 (6.2%), 54 (2.2%) and 549 (22.4%) patients were classified into non-diagnostic (ND), negative for malignancy (NFM), atypia of undetermined significance (AUS), suspicious for malignancy (SFM) and malignancy (MAL) groups, respectively. The most commonly diagnosed malignancies were lung cancer (48.4%), ovary cancer (10.2%), breast cancer (7.5%), and 21.3% unknown primary site (UPS). Among the 36 UPS patients, the most common site of origin was lung (36.1%), followed by ovary (13.9%) and breast (11.1%) via immunocytochemistry of cell block. The calculated ROM values were 26.7%, 12%, 62.3%, 77.8% and 100% for ND, NFM, AUS, SFM and MAL groups, respectively. When considering MAL as the only positive group, the diagnostic accuracy, sensitivity, specificity, positive and negative predictive values were determined to be 95.2%, 81.9%, 100%, 100% and 93.6%, respectively.

CONCLUSION

The newly proposed TIS is an easy-to-master, user-friendly, and standardized classification system, especially when applying on pleural effusions. An adequate serous sample, application of immunocytochemistry, review of cytomorphological data and past medical history could enhance the accuracy of cytological diagnosis.

The International System for Reporting Serous Fluid Cytopathology: How to Incorporate Molecular Data in Cytopathology Reports

Serous effusion cytology is widely employed in the initial evaluation of the etiology of effusions with a high diagnostic sensitivity. To standardize practices, The International System for Reporting Serous Fluid Cytology (TIS) was developed following best international practices, the most up-to-date literature, and expert consensus. In the context of this system, ancillary techniques play an important role. Besides defining basic principles in laboratory specimen handling, adequacy criteria, and a standardized reporting terminology with five diagnostic categories, TIS provides an actionable framework for using immunohistochemical and molecular testing in effusion samples, namely, in atypical, suspicious of malignant samples. For diagnostic purposes, these tests may be employed to distinguish between a primary and secondary neoplasm, to confirm a diagnosis of malignant mesothelioma vs. reactive mesothelial hyperplasia, and to correctly classify and determine the primary location of a metastasis. Theranostic molecular tests may also be used for these samples to evaluate potential therapeutic targets. Pathologists play a central role in guiding this process by determining adequacy and selecting appropriate ancillary tests. The activity in this area of research should increase in the near future as new therapeutic targets are discovered and new drugs enter the clinical practice.

A Simple and Practical Guide for Triaging Lymphocyte-rich Effusions for Ancillary Studies

Lymphocyte-rich effusions of the body cavities may represent a reactive/benign condition, primary effusion lymphoma, or systemic lymphoma with secondary malignant effusion, either as initial presentation or as a late complication. Cytomorphologic examination is essential and fundamental for diagnosis and may provide important clues to the nature of diseases. However, based on morphology alone, cytologic diagnosis of lymphocyte-rich effusions could be very challenging, particularly when the lymphocytes are small. Cytologists/cytopathologists might be uncertain when a lymphocyte-rich effusion specimen warrants a comprehensive hematopathologic workup. Herein we present a simple and practical algorithmic approach. On the basis of the cytomorphology of lymphocytes (small vs. large cells), presence or absence of cellular atypia, and clinical information (an earlier history or current lymphoma), the lymphocyte-rich effusion samples could be triaged for ancillary studies including immunophenotyping and molecular assays if indicated. Incorporation of cytomorphology, correlation with clinical information, and appropriate application of various ancillary techniques is mandatory for a correct diagnosis of lymphocyte-rich effusion specimens.

Diagnostic mesothelioma biomarkers in effusion cytology

Malignant mesothelioma is a rare malignancy with a poor prognosis whose development is related to asbestos fiber exposure. An increasing role of genetic predisposition has been recognized recently. Pleural biopsy is the gold standard for diagnosis, in which the identification of pleural invasion by atypical mesothelial cell is a major criterion. Pleural effusion is usually the first sign of disease; therefore, a cytological specimen is often the initial or the only specimen available for diagnosis. Given that reactive mesothelial cells may show marked atypia, the diagnosis of mesothelioma on cytomorphology alone is challenging. Accordingly, cell block preparation is encouraged, as it permits immunohistochemical staining. Traditional markers of mesothelioma such as glucose transporter 1 (GLUT1) and insulin-like growth factor 2 mRNA-binding protein 3 (IMP3) are informative, but difficult to interpret when reactive proliferations aberrantly stain positive. BRCA1-associated protein 1 (BAP1) nuclear staining loss is highly specific for mesothelioma, but sensitivity is low in sarcomatoid tumors. Cyclin-dependent kinase inhibitor 2A (CDKN2A)/p16 homozygous deletion, assessed by fluorescence in situ hybridization, is more specific for mesothelioma with better sensitivity, even in the sarcomatoid variant. The surrogate marker methylthioadenosine phosphorylase (MTAP) has been found to demonstrate excellent diagnostic correlation with p16. The purpose of this review is to provide an essential appraisal of the literature regarding the diagnostic value of many of these emerging biomarkers for malignant mesothelioma in effusion cytology.

Cytology samples and molecular biomarker testing in lung cancer-advantages and challenges

This review presents an overview on molecular diagnostic in lung cancer using cytologic samples. Every patient with advanced non-small cell lung cancer (NSCLC) should be tested for targetable driver mutations and gene arrangements. If a mutation is found, this may open an option for targeted therapy. As most of the NSCLC patients in advanced stage of disease are no candidates for surgery, these tests have to be performed on small biopsies or cytology samples. The most common and treatable gene alterations should be tested in every patient: EGFR, ALK, ROS1. A growing number of other genetic changes with targetable mutations may become treatable in the near future. To find patients who might profit from inclusion into clinical studies, relevant additional markers may be tested in an appropriate context. Another important approach for treatment is immunotherapy of lung cancer, which is guided by status of PD-L1 expression on tumour cells. The use of cytology samples carries considerable advantages: often, DNA of high quality is extracted thus enabling easy and precise analysis, and samples may be easily obtained. In case of effusions, effusion fluid seldom is not aspirated for immediate patient relief, so no additional dedicated procedure is needed. Some challenges exist: If the tumour cell count is low, mutations with a low allelic frequency may be missed. In cellblocks formalin-induced DNA, damage may obviate any DNA analysis. In very cellular smears, FISH may be impossible due to massive overlapping of nuclei. Autofluorescence may impede FISH analysis. Although there is no real universal test for genomic profiling for lung cancer, the pathology laboratory must be prepared to offer different assays on different specimens in order to address turnaround time and optimise detections of difficult tumour alterations such as gene fusions. The data from the literature demonstrate that cytology show consistent results, and it is a good alternative for lung cancer molecular testing.

Molecular Profiling of Malignant Pleural Effusions with Next Generation Sequencing (NGS): Evidence that Supports Its Role in Cancer Management

Malignant pleural effusions (MPEs) often develop in advanced cancer patients and confer significant morbidity and mortality. In this review, we evaluated whether molecular profiling of MPEs with next generation sequencing (NGS) could have a role in cancer management, focusing on lung cancer. We reviewed and compared the diagnostic performance of pleural fluid liquid biopsy with other types of samples. When applied in MPEs, NGS may have comparable performance with corresponding tissue biopsies, yield higher DNA amount, and detect more genetic aberrations than blood-derived liquid biopsies. NGS in MPEs may also be preferable to plasma liquid biopsy in advanced cancer patients with a MPE and a paucicellular or it could be difficult to obtain tissue/fine-needle aspiration biopsy. Of interest, post-centrifuge supernatant NGS may exhibit superior results compared to cell pellet, cell block or other materials. NGS in MPEs can also guide clinicians in tailoring established therapies and identifying therapy resistance. Evidence is still premature regarding the role of NGS in MPEs from patients with cancers other than lung. We concluded that MPE processing could provide useful prognostic and theranostic information, besides its diagnostic role.

How the COVID-19 Pandemic Impacted Oncological Molecular Diagnosis: A Picture from a National Reference Center for Molecular Pathology

Introduction

The Portuguese healthcare system had to adapt at short notice to the COVID-19 pandemic. We implemented workflow changes to our molecular pathology laboratory, a national reference center, to maximize safety and productivity. We assess the impact this situation had on our caseload and what conclusions can be drawn about the wider impact of the pandemic in oncological therapy in Portugal. Material and Methods. We reviewed our database for all oncological molecular tests requested between March and April of 2019 and 2020. For each case, we recorded age, sex, region of the country, requesting institution, sample type, testing method, and turnaround time (TAT). A comparison between years was made.

Results

The total number of tests decreased from 421 in 2019 to 319 in 2020 (p = 0.0027). The greatest reduction was in clinical trial-related cases. Routine cases were similar between years (267 vs. 256). TAT was higher in 2019 (mean 15 days vs. 12.3 days; p = 0.0003). Medium- to large-sized public hospitals in the north of the country were mostly responsible for the reduction in cases (p = 0.0153).

Conclusions

Case reduction was observed at hospitals that have mostly been involved in the treatment of COVID-19 and in the north of the country, the region worst-hit by the pandemic. Similar to other studies, our TAT decreased, even with a similar number of routine cases. Thus, we conclude that it is possible to successfully adapt the workflow of a molecular pathology laboratory to new safety standards without losing efficiency.

The international system for reporting serous fluid cytopathology-diagnostic categories and clinical management

INTRODUCTION

Effusions can develop inside serous cavities in several pathologic states, both neoplastic and non-neoplastic. They are easy to drain and can provide useful diagnostic information. However, the reported diagnostic efficacy of these specimens has not been uniform across different laboratories. To standardize practices, the international system for reporting serous fluid cytology (TIS) was developed in accordance with the best international practices, the most up-to-date reported data, and expert consensus.

RESULTS

TIS has set the basic principles for laboratory handling of serous effusion specimens, defined the adequacy criteria, and set a standardized reporting terminology with well-defined criteria for each diagnostic category. These include nondiagnostic, negative for malignancy, atypia of undetermined significance, suspicious for malignancy, and malignant. Each can provide useful inherent information for appropriate clinical management and follow-up, with a defined expected diagnostic category incidence and risk of malignancy.

CONCLUSIONS

TIS applies to serous fluids collected from the pleura, peritoneal, and pericardial cavities. Using TIS, indeterminate categories are presented as either preliminary or as options of last resource. TIS has emphasized the role of ancillary tests in arriving at the correct interpretation within each category. It also has emphasized the importance of a malignant diagnosis as a definitive diagnosis, comparable to histologic examinations. Because of the well-documented outcomes in the adoption of uniform cytology terminology for other organ systems, we recommend the use of the upcoming TIS and believe its use will be paramount to improving the diagnostic yield in this area of cytology.

Next-generation sequencing in residual liquid-based cytology specimens for cancer genome analysis

BACKGROUND

Cancer genome profiling of cytology specimens using next-generation sequencing (NGS) requires adequate and good-quality DNA. Genomic examination of cytology samples was conventionally performed on cell block (CB) or smear specimens than on residual liquid-based cytology (LBC) specimens, which are high-quality DNA sources even after long-term storage.

METHODS

We estimated tumor fractions of 37 residual LBC specimens, including 30 fine needle aspiration (FNA) samples from the thyroid (12 papillary thyroid carcinomas and two malignant lymphomas), lymph node (13 metastatic carcinomas and one malignant lymphoma), and breast cancer (one phyllodes tumor and one invasive ductal carcinoma), two pancreatic carcinoma samples, and five liquid (ascites, pleural effusion, and cerebrospinal fluid) samples. The DNA was extracted from all samples and subjected to NGS using a customized cancer gene panel comprising 28 cancer-related genes.

RESULTS

NGS analysis revealed somatic mutations corresponding to pathological diagnosis with adequate variant allele frequency (VAF) in 24 LBC specimens, which had significantly higher tumor fraction (72.5% ± 4.9%). Ten cases, including the five fluid samples, had very small tumor fractions (7.5% ± 2.3%) to obtain sufficient VAF. Other two samples had high tumor fractions but showed very low VAF, indicating the presence of fusion genes. The remaining one sample yielded no DNA recovery.

CONCLUSION

The residual LBC specimens collected by FNA from the thyroid gland and lymph node were verified to carry high tumor fraction and could serve as an alternate source for molecular testing to screen and diagnose cancers without the use of CB or smears.