1
|
Punjabi LS, Lim KL, Chow CY, Mantoo S, Takano A. Three shades of an unusual mediastinal tumour. Diagn Cytopathol 2023; 51:716-723. [PMID: 37587908 DOI: 10.1002/dc.25212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 07/27/2023] [Accepted: 07/31/2023] [Indexed: 08/18/2023]
Abstract
Thoracic SMARCA4-deficient undifferentiated tumour (SMARCA4-UT) is an unusual and aggressive tumour. While there are approximately 100 cases of this tumour reported in the literature, there are very few detailed descriptions of its cytomorphologic characteristics, and only rare cases in which primary diagnosis was made on cytologic material. Herein we present a case with a detailed description of the appearance on three specimen types: transbronchial needle aspiration (TBNA) cytology, transbronchial needle biopsy (TBNB) and effusion cytology. Thoracic SMARCA4-UT is an important diagnosis to clinch in modern pathology because of its prognostic and therapeutic implications. We discuss an integrated approach to clinching the diagnosis with reference to clinical, radiographic, morphologic and immunohistochemical features. We also discuss possible differential diagnoses, and how they can be excluded. Cytologic and/or small biopsy diagnosis is valuable in these cases as these tumours are typically not amenable to surgical resection. With the correct diagnosis, the patient may instead be a candidate for immune checkpoint inhibitors or experimental therapy targeting SWI/SNF deficiency.
Collapse
Affiliation(s)
- Lavisha S Punjabi
- Department of Anatomical Pathology, Singapore General Hospital, Singapore, Singapore
| | - Kah Ling Lim
- Department of Anatomical Pathology, Singapore General Hospital, Singapore, Singapore
| | - Chun Yuen Chow
- Department of Anatomical Pathology, Singapore General Hospital, Singapore, Singapore
| | - Sangeeta Mantoo
- Department of Anatomical Pathology, Singapore General Hospital, Singapore, Singapore
| | - Angela Takano
- Department of Anatomical Pathology, Singapore General Hospital, Singapore, Singapore
| |
Collapse
|
2
|
Fielding D, Dalley AJ, Singh M, Nandakumar L, Lakis V, Chittoory H, Fairbairn D, Patch AM, Kazakoff SH, Ferguson K, Bashirzadeh F, Bint M, Pahoff C, Son JH, Ryan K, Hodgson A, Sharma S, Pearson JV, Waddell N, Lakhani SR, Hartel G, Simpson PT, Nones K. Discrepancies in tumor mutation burden reporting from sequential endobronchial ultrasound transbronchial needle aspiration samples within single lymph node stations - brief report. Front Oncol 2023; 13:1259882. [PMID: 37927461 PMCID: PMC10620689 DOI: 10.3389/fonc.2023.1259882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 09/29/2023] [Indexed: 11/07/2023] Open
Abstract
Introduction Tumour Mutation Burden (TMB) is a potential biomarker for immune cancer therapies. Here we investigated parameters that might affect TMB using duplicate cytology smears obtained from endobronchial ultrasound transbronchial needle aspiration (EBUS TBNA)-sampled malignant lymph nodes. Methods Individual Diff-Quik cytology smears were prepared for each needle pass. DNA extracted from each smear underwent sequencing using large gene panel (TruSight Oncology 500 (TSO500 - Illumina)). TMB was estimated using the TSO500 Local App v. 2.0 (Illumina). Results Twenty patients had two or more Diff-Quik smears (total 45 smears) which passed sequencing quality control. Average smear TMB was 8.7 ± 5.0 mutations per megabase (Mb). Sixteen of the 20 patients had paired samples with minimal differences in TMB score (average difference 1.3 ± 0.85). Paired samples from 13 patients had concordant TMB (scores below or above a threshold of 10 mutations/Mb). Markedly discrepant TMB was observed in four cases, with an average difference of 11.3 ± 2.7 mutations/Mb. Factors affecting TMB calling included sample tumour content, the amount of DNA used in sequencing, and bone fide heterogeneity of node tumour between paired samples. Conclusion TMB assessment is feasible from EBUS-TBNA smears from a single needle pass. Repeated samples of a lymph node station have minimal variation in TMB in most cases. However, this novel data shows how tumour content and minor change in site of node sampling can impact TMB. Further study is needed on whether all node aspirates should be combined in 1 sample, or whether testing independent nodes using smears is needed.
Collapse
Affiliation(s)
- David Fielding
- Department of Thoracic Medicine, The Royal Brisbane & Women’s Hospital, Brisbane, QLD, Australia
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Andrew J. Dalley
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Mahendra Singh
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
- Pathology Queensland, The Royal Brisbane & Women’s Hospital, Brisbane, QLD, Australia
| | - Lakshmy Nandakumar
- Pathology Queensland, The Royal Brisbane & Women’s Hospital, Brisbane, QLD, Australia
| | - Vanessa Lakis
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Haarika Chittoory
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - David Fairbairn
- Pathology Queensland, The Royal Brisbane & Women’s Hospital, Brisbane, QLD, Australia
| | - Ann-Marie Patch
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | | | - Kaltin Ferguson
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Farzad Bashirzadeh
- Department of Thoracic Medicine, The Royal Brisbane & Women’s Hospital, Brisbane, QLD, Australia
| | - Michael Bint
- Department of Thoracic Medicine, Sunshine Coast University Hospital, Birtinya, QLD, Australia
| | - Carl Pahoff
- Department of Respiratory Medicine, Gold Coast University Hospital, Southport, QLD, Australia
| | - Jung Hwa Son
- Department of Thoracic Medicine, The Royal Brisbane & Women’s Hospital, Brisbane, QLD, Australia
| | - Kimberley Ryan
- Department of Thoracic Medicine, The Royal Brisbane & Women’s Hospital, Brisbane, QLD, Australia
| | - Alan Hodgson
- Pathology Queensland, The Royal Brisbane & Women’s Hospital, Brisbane, QLD, Australia
| | - Sowmya Sharma
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- ACL Pathology, Sydney, NSW, Australia
| | - John V. Pearson
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Nicola Waddell
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Sunil R. Lakhani
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
- Pathology Queensland, The Royal Brisbane & Women’s Hospital, Brisbane, QLD, Australia
| | - Gunter Hartel
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Peter T. Simpson
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Katia Nones
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| |
Collapse
|
3
|
Fielding DI, Dalley AJ, Singh M, Nandakumar L, Lakis V, Chittoory H, Fairbairn D, Patch AM, Kazakoff SH, Ferguson K, Bashirzadeh F, Bint M, Pahoff C, Son JH, Hodgson A, Sharma S, Waddell N, Lakhani SR, Hartel G, Nones K, Simpson PT. Evaluating Diff-Quik cytology smears for large-panel mutation testing in lung cancer-Predicting DNA content and success with low-malignant-cellularity samples. Cancer Cytopathol 2023. [PMID: 36938641 DOI: 10.1002/cncy.22690] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/13/2022] [Accepted: 12/20/2022] [Indexed: 03/21/2023]
Abstract
BACKGROUND Cytology smears are commonly collected during endobronchial ultrasound-guided transbronchial needle aspiration (EBUS TBNA) procedures but are rarely used for molecular testing. Studies are needed to demonstrate their great potential, in particular for the prediction of malignant cell DNA content and for utility in molecular diagnostics using large gene panels. METHODS A prospective study was performed on samples from 66 patients with malignant lymph nodes who underwent EBUS TBNA. All patients had air-dried, Diff-Quik cytology smears and formalin-fixed, paraffin-embedded cell blocks collected for cytopathology and molecular testing. One hundred eighty-five smears were evaluated by microscopy to estimate malignant cell percentage and abundance and to calculate smear size and were subjected to DNA extraction. DNA from 56 smears from 27 patients was sequenced with the TruSight Oncology 500 assay (Illumina). RESULTS Each microscopy parameter had a significant effect on the DNA yield. An algorithm was developed that predicted a >50-ng DNA yield of a smear with an area under the curve of 0.86. Fifty DNA samples (89%) with varying malignant yields were successfully sequenced. Low-malignant-cell content (<25%) and smear area (<15%) were the main reasons for failure. All standard-of-care mutations were detected in replicate smears from individual patients, regardless of malignant cell content. Tier 1/2 mutations were discovered in two cases where standard-of-care specimens were inadequate for sequencing. Smears were scored for tumor mutation burden. CONCLUSIONS Microscopy of Diff-Quik smears can triage samples for comprehensive panel sequencing, which highlights smears as an excellent alternative to traditional testing with cell blocks.
Collapse
Affiliation(s)
- David I Fielding
- Department of Thoracic Medicine, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
- UQ Centre for Clinical Research, Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Andrew J Dalley
- UQ Centre for Clinical Research, Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Mahendra Singh
- UQ Centre for Clinical Research, Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
- Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Lakshmy Nandakumar
- Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Vanessa Lakis
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Haarika Chittoory
- UQ Centre for Clinical Research, Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - David Fairbairn
- Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Ann-Marie Patch
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Stephen H Kazakoff
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Kaltin Ferguson
- UQ Centre for Clinical Research, Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Farzad Bashirzadeh
- Department of Thoracic Medicine, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Michael Bint
- Department of Thoracic Medicine, Sunshine Coast University Hospital, Birtinya, Queensland, Australia
| | - Carl Pahoff
- Department of Respiratory Medicine, Gold Coast University Hospital, Southport, Queensland, Australia
| | - Jung Hwa Son
- Department of Thoracic Medicine, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Alan Hodgson
- Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Sowmya Sharma
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- ACL Pathology, Bellavista, New South Wales, Australia
| | - Nicola Waddell
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Sunil R Lakhani
- UQ Centre for Clinical Research, Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
- Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Gunter Hartel
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Katia Nones
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- School of Biomedical Sciences, University of Queensland, St Lucia, Queensland, Australia
| | - Peter T Simpson
- UQ Centre for Clinical Research, Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
| |
Collapse
|