Molecular cytopathology and flow cytometry: pre-analytical procedures matter

Guidelines for Handling of Cytological Specimens in Cancer Genomic Medicine

Rapid advances are being made in cancer drug therapy. Since molecularly targeted therapy has been introduced, personalized medicine is being practiced, pathological tissue from malignant tumors obtained during routine practice is frequently used for genomic testing. Whereas cytological specimens fixed mainly in alcohol are considered to be more advantageous in terms of preservation of the nucleic acid quality and quantity. This article is aimed to share the information for the proper handling of cytological specimens in practice for genomic medicine based on the findings established in "Guidelines for Handling of Cytological Specimens in Cancer Genomic Medicine (in Japanese)" published by the Japanese Society of Clinical Cytology in 2021. The three-part practical guidelines are based on empirical data analyses; Part 1 describes general remarks on the use of cytological specimens in cancer genomic medicine, then Part 2 describes proper handling of cytological specimens, and Part 3 describes the empirical data related to handling of cytological specimens. The guidelines indicated proper handling of specimens in each fixation, preparation, and evaluation.

Tissue management in precision medicine: What the pathologist needs to know in the molecular era

Precision medicine is “an emerging approach for disease treatment and prevention that takes into account individual variability in genes, environment, and lifestyle for each person.” Among many medical specialists involved in precision medicine, the pathologists play an important and key role in the implementation and development of molecular tests that are in the center of decision of many therapeutic choices. Besides many laboratory procedures directly involved in the molecular tests, is fundamental to guarantee that tissues and cells collected for analysis be managed correctly before the DNA/RNA extraction. In this paper we explore the pivotal and interconnected points that can influence molecular studies, such as pre-analytical issues (fixation and decalcification); diagnosis and material selection, including the calculation of nuclei neoplastic fraction. The standardization of sample processing and morphological control ensures the accuracy of the diagnosis. Tissue or cytological samples constitutes the main foundation for the determination of biomarkers and development of druggable targets. Pathology and precision oncology still have a long way to go in terms of research and clinical practice: improving the accuracy and dissemination of molecular tests, learning in molecular tumor boards for advanced disease, and knowledge about early disease. Precision medicine needs pathology to be precise.

[New aspects in fine needle biopsies of the lymph nodes]

BACKGROUND

The cytology of lymph nodes is a cost-effective method with a short turnaround time and low risk to patients that delivers valuable information on the cause of the lymphadenopathies.

OBJECTIVES

To discuss the value of lymph node cytology in the diagnosis of lymph node swellings.

METHODS

Analysis of the causes of the controversially discussed aspects of lymph node cytology. Presentation of the diagnostic groups of lymph node cytology according to the Sydney system.

RESULTS

The technical aspects of lymph node sampling during fine needle biopsy, as well as the subsequent preparation of the correctly fixed direct smears and the triage of the sample for the auxiliary studies, may pose a significant challenge for some puncturers. The whole spectrum of modern pathologic auxiliary studies can be applied to correctly triaged cytologic samples. The diagnoses of fine needle biopsies of the lymph nodes can be divided into five groups according to the recently proposed Sydney reporting system: insufficient/non-diagnostic, benign, atypical, suspicious, and malignant. Further details concerning the diagnosis as well as recommendations on how to proceed are additionally included in cytologic reports.

CONCLUSIONS

The improvement of lymph node sampling as well as the technical aspects of the sample handling, including the application of auxiliary studies, considerably increase the diagnostic value of fine needle biopsy of the lymph nodes. Wide implementation of the usage of the diagnostic groups for reporting fine needle biopsies of the lymph nodes can standardize reporting and improve communication with other clinical specialists.

A Proposal for the Performance, Classification, and Reporting of Lymph Node Fine-Needle Aspiration Cytopathology: The Sydney System

BACKGROUND

The evaluation of lymph nodes (LN) by fine-needle aspiration cytology (FNAC) is routinely used in many institutions but it is not uniformly accepted mainly because of the lack of guidelines and a cytopathological diagnostic classification. A committee of cytopathologists has developed a system of performance, classification, and reporting for LN-FNAC.

METHODS

The committee members prepared a document that has circulated among them five times; the final text has been approved by all the participants. It is based on a review of the international literature and on the expertise of the members. The system integrates clinical and imaging data with cytopathological features and ancillary techniques. The project has received the endorsement and patronage of the International Academy of Cytology and the European Federation of the Cytology Societies.

RESULTS

Clinical, imaging, and serological data of lymphadenopathies, indications for LN-FNAC, technical procedures, and ancillary techniques are evaluated with specific recommendations. The reporting system includes two diagnostic levels. The first should provide basic diagnostic information and includes five categories: inadequate/insufficient, benign, atypical lymphoid cells of undetermined/uncertain significance, suspicious, and malignant. For each category, specific recommendations are provided. The second diagnostic level, when achievable, should produce the identification of specific benign or malignant entities and additional information by utilizing ancillary testing.

CONCLUSION

The authors believe that the introduction of this system for performing and reporting LN-FNAC may improve the quality of the procedure, the report, and the communication between cytopathologists and the clinicians. This system may lead to a greater acceptance and utilization of LN-FNAC and to a better interdisciplinary understanding of the results of this procedure.

Announcement: The International System for Reporting Lymph Node Cytopathology

Fine needle aspiration biopsy cytopathology (FNAC) of lymph nodes is a very common, inexpensive, and rapid diagnostic procedure and can lead to the accurate and timely diagnosis of one of the wide range of pathological processes that involve lymph nodes. These diagnoses include specific reactive processes, specific infections such as tuberculosis, metastatic carcinomas and melanomas, and some lymphomas. The FNAC effectively triages the lymph node material, but the initial diagnosis often requires ancillary testing as a second diagnostic step to make a specific diagnosis, such as the particular infectious agent, the type of lymphoma or Hodgkin lymphoma, or the specific type of metastatic malignancy. An international group of cytopathologists have begun the process of developing a system for the standardized reporting of lymph node FNAC. The group is addressing the pre-analytical issues related to the FNAC, including the role of clinical information and the use of ultrasound, and developing a structure of reporting categories based on the cytopathological findings linked to management recommendations. The basis of the system is the integration of the FNAC with the clinical setting, imaging, and ancillary tests that utilize the FNAC material, to produce a final report that will enhance patient care.

Consistency and reproducibility of next-generation sequencing in cytopathology: A second worldwide ring trial study on improved cytological molecular reference specimens

BACKGROUND

Artificial genomic reference standards in a cytocentrifuge/cytospin format with well-annotated genomic data are useful for validating next-generation sequencing (NGS) on routine cytopreparations. Here, reference standards were optimized to be stained by different laboratories before DNA extraction and to contain a lower number of cells (2 × 10⁵ ). This was done to better reflect the clinical challenge of working with insufficient cytological material.

METHODS

A total of 17 worldwide laboratories analyzed customized reference standard slides (slides A-D). Each laboratory applied its standard workflow. The sample slides were engineered to harbor epidermal growth factor receptor (EGFR) c.2235_2249del15 p.E746_A750delELREA, EGFR c.2369C>T p.T790M, Kirsten rat sarcoma viral oncogene homolog (KRAS) c.38G>A p.G13D, and B-Raf proto-oncogene, serine/threonine kinase (BRAF) c.1798_1799GT>AA p.V600K mutations at various allele frequencies (AFs).

RESULTS

EGFR and KRAS mutation detection showed excellent interlaboratory reproducibility, especially on slides A and B (10% and 5% AFs). On slide C (1% AF), either the EGFR mutation or the KRAS mutation was undetected by 10 of the 17 laboratories (58.82%). A reassessment of the raw data in a second-look analysis highlighted the mutations (n = 10) that had been missed in the first-look analysis. BRAF c.1798_1799GT>AA p.V600K showed a lower concordance rate for mutation detection and AF quantification.

CONCLUSIONS

The data show that the detection of low-abundance mutations is still clinically challenging and may require a visual inspection of sequencing reads to detect. Genomic reference standards in a cytocentrifuge/cytospin format are a valid tool for regular quality assessment of laboratories performing molecular studies on cytology with low-AF mutations.

Precision cytopathology: expanding opportunities for biomarker testing in cytopathology

Precision cytopathology refers to therapeutically linked biomarker testing in cytopatology, a dynamically growing area of the discipline. This review describes basic steps to expand precision cytopathology services. Focusing exclusively on solid tumors, the review is divided into four sections: Section 1: Overview of precision pathology- opportunities and challenges; Section 2: Basic steps in establishing or expanding a precision cytopathology laboratory; Section 3: Cytopathology specimens suitable for next generation sequencing platforms; and Section 4: Summary. precision cytopathology continues to rapidly evolve in parallel with expanding targeted therapy options. Biomarker assays (companion diagnostics) comprise a multitude of test types including immunohistochemistry, in situ hybridization and molecular genetic tests such as PCR and next generation sequencing all of which are performable on cytology specimens. Best practices for precision cytopathology will incorporate traditional diagnostic approaches allied with careful specimen triage to enable successful biomarker analysis. Beyond triaging, cytopathologists knowledgeable about molecular test options and capabilities have the opportunity to refine diagnoses, prognoses and predictive information thereby assuming a lead role in precision oncology biomarker testing.

Advances in Molecular Testing Techniques in Cytologic Specimens

There has been a paradigm shift in the practice of cytopathology with the advent of highly sensitive molecular tests using small amounts of tissue that can provide diagnostic, prognostic, and predictive information for clinical management. The cytopathologist plays a key role in providing a timely and accurate diagnosis as well as ensuring appropriate processing and handling of the specimen and judicious triaging of the tissue for molecular testing that guide therapeutic decisions. As the era of "precision medicine" continues to evolve and expand, cytopathology remains a dynamic field with advances in the practice of molecular cytopathology providing new paradigms in clinical care.

Consistency and reproducibility of next-generation sequencing and other multigene mutational assays: A worldwide ring trial study on quantitative cytological molecular reference specimens

BACKGROUND

Molecular testing of cytological lung cancer specimens includes, beyond epidermal growth factor receptor (EGFR), emerging predictive/prognostic genomic biomarkers such as Kirsten rat sarcoma viral oncogene homolog (KRAS), neuroblastoma RAS viral [v-ras] oncogene homolog (NRAS), B-Raf proto-oncogene, serine/threonine kinase (BRAF), and phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit α (PIK3CA). Next-generation sequencing (NGS) and other multigene mutational assays are suitable for cytological specimens, including smears. However, the current literature reflects single-institution studies rather than multicenter experiences.

METHODS

Quantitative cytological molecular reference slides were produced with cell lines designed to harbor concurrent mutations in the EGFR, KRAS, NRAS, BRAF, and PIK3CA genes at various allelic ratios, including low allele frequencies (AFs; 1%). This interlaboratory ring trial study included 14 institutions across the world that performed multigene mutational assays, from tissue extraction to data analysis, on these reference slides, with each laboratory using its own mutation analysis platform and methodology.

RESULTS

All laboratories using NGS (n = 11) successfully detected the study's set of mutations with minimal variations in the means and standard errors of variant fractions at dilution points of 10% (P = .171) and 5% (P = .063) despite the use of different sequencing platforms (Illumina, Ion Torrent/Proton, and Roche). However, when mutations at a low AF of 1% were analyzed, the concordance of the NGS results was low, and this reflected the use of different thresholds for variant calling among the institutions. In contrast, laboratories using matrix-assisted laser desorption/ionization-time of flight (n = 2) showed lower concordance in terms of mutation detection and mutant AF quantification.

CONCLUSIONS

Quantitative molecular reference slides are a useful tool for monitoring the performance of different multigene mutational assays, and this could lead to better standardization of molecular cytopathology procedures. Cancer Cytopathol 2017;125:615-26. © 2017 American Cancer Society.

Expectations and Projections for the Future of Nongynecolgical Cytology 10 Years Ago: Did They Materialize and How Did We Do?

In 2007, an article entitled "How Technology Is Reshaping the Practice of Nongynecologic Cytology: Frontiers of Cytology Symposium" [Bibbo: Acta Cytol 2007;51:123-152] was published. The moderator and editor was Marluce Bibbo, previous Editor-in-Chief of Acta Cytologica, and 17 participants from countries throughout the world were asked to answer how new technologies were being applied in their respective laboratories and whether future advances and challenges can be predicted. Ten years later, two previous participants in this Golden Anniversary Cytology Symposium were asked by Kari Syrjänen, current Editor-in-Chief of Acta Cytologica, to make a reappraisal of the 2007 predictions.

Analysis of Pre-Analytic Factors Affecting the Success of Clinical Next-Generation Sequencing of Solid Organ Malignancies

Application of next-generation sequencing (NGS) technology to routine clinical practice has enabled characterization of personalized cancer genomes to identify patients likely to have a response to targeted therapy. The proper selection of tumor sample for downstream NGS based mutational analysis is critical to generate accurate results and to guide therapeutic intervention. However, multiple pre-analytic factors come into play in determining the success of NGS testing. In this review, we discuss pre-analytic requirements for AmpliSeq PCR-based sequencing using Ion Torrent Personal Genome Machine (PGM) (Life Technologies), a NGS sequencing platform that is often used by clinical laboratories for sequencing solid tumors because of its low input DNA requirement from formalin fixed and paraffin embedded tissue. The success of NGS mutational analysis is affected not only by the input DNA quantity but also by several other factors, including the specimen type, the DNA quality, and the tumor cellularity. Here, we review tissue requirements for solid tumor NGS based mutational analysis, including procedure types, tissue types, tumor volume and fraction, decalcification, and treatment effects.

Factors affecting the success of next-generation sequencing in cytology specimens

BACKGROUND

The use of cytology specimens for next-generation sequencing (NGS) is particularly challenging because of the unconventional substrate of smears and the often limited sample volume. An analysis of factors affecting NGS testing in cytologic samples may help to increase the frequency of successful testing.

METHODS

This study reviewed variables associated with all in-house cytology cases (n = 207) that were analyzed by NGS with the Ion Torrent platform during a 10-month interval. A statistical analysis was performed to measure the effects of the DNA input threshold, specimen preparation, slide type, tumor fraction, DNA yield, and cytopathologist bias.

RESULTS

One hundred sixty-four of 207 cases (79%) were successfully sequenced by NGS; 43 (21%) failed because of either a low DNA yield or a template/library preparation failure. The median estimated tumor fraction and DNA concentration for the successfully sequenced cases were 70% and 2.5 ng/μL, respectively, whereas they were 60% and 0.2 ng/μL, respectively, for NGS failures. Cell block sections were tested in 91 cases, and smears were used in 116 cases. NGS success positively correlated with the DNA yield but not the tumor fraction. Cell block preparations showed a higher success rate than smears. Frosted-tip slides yielded significantly more DNA than fully frosted slides. Lowering the input DNA concentration below the manufacturer's recommended threshold of 10 ng (>0.85 ng/μL) resulted in a marked increase in the NGS success rate from 58.6% to 89.8%.

CONCLUSIONS

The failure of NGS with cytology samples is usually a result of suboptimal DNA due to multiple pre-analytical factors. Knowledge of these factors will allow better selection of cytology material for mutational analysis.

Is liquid-based cytology the magic bullet for performing molecular techniques?

OBJECTIVE

The role of pathology has evolved from the first microscopic definitions of diseases by Virchow to the new concept of molecular cytopathology. The management of diseases is now a multidisciplinary approach with the translation of morphological, imagery and molecular findings to therapeutic protocols. Obtaining the most reliable diagnostic material is the essential part of the medical management of patients.

STUDY DESIGN

Here, we try to gain a concise insight into the available data regarding the role of cytology in the application of molecular techniques, focusing on cancer cytopathology.

RESULTS

Obtaining cytological material is now feasible by different methods, and in some cases it is the only possible approach to a lesion which is not easily accessible for tissue sampling. The methods of obtaining cytological material have evolved in recent years in parallel with rapid advances in high-throughput molecular techniques, opening new windows for the diagnosis and management of diseases.

CONCLUSIONS

Different kinds of cytological material are reliable for the application of molecular techniques. Cytological material obtained in a liquid base has advantages such as the better preservation of cytomorphological features and the use of the remaining liquid for nucleic acid extraction even after long storage and the application of molecular methods.

Pre-analytic steps for molecular testing on thyroid fine-needle aspirations: The goal of good results

Fine-needle aspiration cytology (FNAC) represents a valid alternative to biopsy in a variety of clinical settings mainly based on its simplicity and less invasive clinical approach. In some cases, morphology evaluation alone is not sufficient to manage the patients, so that the application of ancillary techniques can contribute to diagnosis, prognosis and prediction of tumor behavior. These techniques include polymerase chain reaction (PCR), fluorescence in situ hybridization (FISH), in situ PCR, direct Sequencing, microarrays and proteomic methodologies. Although several recent experiences underline the superior value of deoxyribonucleic acid (DNA) quality mainly for advanced genomic high throughput platforms, very scant literature studied the role of the pre-analytical or analytical phases. Despite the high specificity of molecular techniques as a support for diagnosis, there is a need for an increased standardization of pre-analytical/analytical steps such as providing appropriate clinical history, proper collection of laboratory specimens and proper preparation of samples, adequate fixative/reagent concentrations and technical equipments. All these requirements are crucial according to the results from 42 American laboratories, which reported 0.33% of significant molecular errors with 60% of them in the pre-analytical phase. The most common error is to forget that cytological preparation requires specific molecular variables, which are different from histological specimens. Cytological samples offer the advantage of a well preserved DNA, readily extractable and reasonably stable (from 6 months to 5 years) avoiding pitfalls due to formalin-fixation. Freshly prepared, unstained direct, alcohol-fixed papanicolaou, air-dried diff-quick smears are all suitable for DNA extraction and preservation. In the specific field of thyroid FNAC, molecular analysis has been supported by the growing evidence that papillary thyroid carcinoma (PTC), the most common thyroid cancer, frequently is a diploid lesion and can display non-overlapping mutations of the v-Raf murine sarcoma viral oncogene homolog B1 (BRAF) in 46% to 70%, cases, ret proto-oncogene (RET) in 3 to 85% and Rat Sarcoma oncogene (RAS) in 0-21% cases. Recently, several cytological papers demonstrated that the combination of morphology and molecular analysis can increase the diagnostic accuracy allowing more precise prediction of malignancy regardless of the diagnostic categories. In conclusion, the correct use of the pre-analytical-analytical steps might lead to optimal results on cytology and empower the prognostic value of molecular techniques as strong indicators of cancer for their high specificity and positive predictive value.

The cytologic category of oncocytic (Hurthle) cell neoplasm mostly includes low-risk lesions at histology: an institutional experience

DESIGN

The cytological diagnosis of oncocytic/Hurthle cell neoplasms (OCN) represents a challenge with which cytopathologists face up to in their practice. The majority of these lesions undergo surgery for a definitive characterization of the nature mainly due to their more aggressive behavior than other malignant follicular lesions. In this study, we aimed at the evaluation of the effective malignant rate in a large cohort of OCNs.

METHODS

From January 2008 to December 2011, we analyzed 150 cyto-histological OCNs and 64 benign oncocytic/Hurthle lesions (BOL). Both groups of patients were analyzed for clinical and cyto-histological parameters. All the nodules were sampled under sonographic guidance and processed with the liquid-based cytological method.

RESULTS

In agreement with literature, we found a significant correlation only with female gender in both OCN (P=0.0160) and BOL groups. The 64 BOLs were histologically diagnosed as 15 Hashimoto thyroiditis (HT), 45 hyperplastic nodules in HT, and four papillary thyroid carcinomas (PTC, 6.2%). The 150 OCNs resulted in 141 (94%) oncocytic adenomas and nine (6%) malignant lesions. The latter group included five oncocytic carcinomas (OCC), three oncocytic variants of PTC, and one macrofollicular PTC featured by mild nuclear clearing with a dispersive cellular pattern. The malignant rate was respectively 6.2% in BOLs without any OCC whereas 3.3% OCC diagnosed in the OCN category.

CONCLUSIONS

Our OCNs mostly resulted in histological adenomas with a lower rate of malignancy than in other series. Some morphological parameters (nuclear clearing, dysplasia, and dispersive cellular pattern) might be helpful in stratifying OCN patients into different risks of malignancy.

Diagnostic and prognostic value of immunocytochemistry and BRAF mutation analysis on liquid-based biopsies of thyroid neoplasms suspicious for carcinoma

OBJECTIVE

In the field of fine-needle aspiration cytology, the category of suspicious for malignancy (SM) thyroid lesions, that bears 55-85% risk of malignant histology, is a challenging topic in which morphology alone is not always able to make a correct diagnosis. Recently, immunocytochemistry (ICC) has been referred to as helpful in differentiating low- and high-malignant risk lesions and BRAF activating mutations have been identified in a significant amount of papillary thyroid carcinomas (PTC). The introduction of the liquid-based cytology (LBC) may simplify the application of these techniques to thyroid cytology.

DESIGN

Our aim is to evaluate the diagnostic and prognostic role of both ICC and BRAF mutation for the SM category on LBC.

METHODS

From October 2010 through June 2011, 113 LBC cytological cases (including 37 SM and 76 PTC) underwent surgery. All cases were studied for BRAF mutation and ICC.

RESULTS

ICC resulted positive in 26 (86.6%) histologically malignant SM with 15 of which (40.5%) expressing a BRAF mutation. Overall, 63 cases showed a BRAF mutation resulting in PTC. Concerning the prognostic role of BRAF mutation for the two categories, we reported a significant correlation with multifocality, nodal involvement and extra-capsular invasion (P<0.0001).

CONCLUSIONS

Special techniques such as ICC and molecular markers might be successfully carried out on LBC-processed material. For both categories, ICC is more sensitive whereas BRAF analysis is an interesting support due to its high specificity adding a prognostic value in both SM and PTCs.