1
|
Pinheiro M, Wentzensen N, Dean M, Yeager M, Chen Z, Shastry A, Boland JF, Bass S, Burdett L, Lorey T, Mishra S, Castle PE, Schiffman M, Burk RD, Zhu B, Mirabello L. Somatic mutations in 3929 HPV positive cervical cells associated with infection outcome and HPV type. Nat Commun 2024; 15:7895. [PMID: 39266536 PMCID: PMC11393421 DOI: 10.1038/s41467-024-51713-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 08/13/2024] [Indexed: 09/14/2024] Open
Abstract
Invasive cervical cancers (ICC), caused by HPV infections, have a heterogeneous molecular landscape. We investigate the detection, timing, and HPV type specificity of somatic mutations in 3929 HPV-positive exfoliated cervical cell samples from individuals undergoing cervical screening in the U.S. using deep targeted sequencing in ICC cases, precancers, and HPV-positive controls. We discover a subset of hotspot mutations rare in controls (2.6%) but significantly more prevalent in precancers, particularly glandular precancer lesions (10.2%), and cancers (25.7%), supporting their involvement in ICC carcinogenesis. Hotspot mutations differ by HPV type, and HPV18/45-positive ICC are more likely to have multiple hotspot mutations compared to HPV16-positive ICC. The proportion of cells containing hotspot mutations is higher (i.e., higher variant allele fraction) in ICC and mutations are detectable up to 6 years prior to cancer diagnosis. Our findings demonstrate the feasibility of using exfoliated cervical cells for detection of somatic mutations as potential diagnostic biomarkers.
Collapse
Affiliation(s)
- Maisa Pinheiro
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Michael Dean
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD, USA
- Department of Biology, Hood College, Frederick, MD, USA
| | - Zigui Chen
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong, China
| | - Amulya Shastry
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Joseph F Boland
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Sara Bass
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Laurie Burdett
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Thomas Lorey
- Regional Laboratory and Women's Health Research Institute, Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Sambit Mishra
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Philip E Castle
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Division of Cancer Prevention, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Mark Schiffman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Robert D Burk
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Obstetrics & Gynecology and Women's Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA.
| |
Collapse
|
2
|
Abe H, Kawahara A, Akiba J, Yamaguchi R. Advances in diagnostic liquid-based cytology. Cytopathology 2024. [PMID: 38837293 DOI: 10.1111/cyt.13405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 05/09/2024] [Accepted: 05/20/2024] [Indexed: 06/07/2024]
Abstract
Liquid-based cytology (LBC) has changed the landscape of gynaecological cytology. A growing demand exists for LBC in diagnostic cytology, particularly for ancillary testing, such as immunocytochemistry and molecular testing. Ancillary testing solely based on conventional preparation (CP) methods remains challenging. Recently, the increased demand for specialist testing and minimally invasive techniques, such as endoscopic ultrasonography fine-needle aspiration, to obtain cellular samples has led to an increasing demand for ancillary testing on cytology LBC supernatant, slides and cell block (CB). This facilitates the diagnosis and prognosis in cytology samples enabling personalized treatment. An understanding of the history and future prospects of LBC is crucial for its application in routine diagnostics by cytopathologists and cytotechnologists. In this review, we initiated an internet search using the keyword 'liquid-based cytology', and we conducted a literature review to discuss the usefulness of combined diagnosis of LBC and CP, immunocytochemistry and molecular testing and assessed the quality of nucleic acids in diagnostic LBC. High-quality and cell-rich diagnostic LBC surpassed the CP method alone in terms of reliability and versatility of ancillary testing in cytological diagnosis. Conclusively, diagnostic LBC lends itself to various new technologies and is expected to continue evolving with innovations in the future.
Collapse
Affiliation(s)
- Hideyuki Abe
- Department of Diagnostic Pathology, Kurume University Hospital, Kurume, Japan
| | - Akihiko Kawahara
- Department of Diagnostic Pathology, Kurume University Hospital, Kurume, Japan
| | - Jun Akiba
- Department of Diagnostic Pathology, Kurume University Hospital, Kurume, Japan
| | - Rin Yamaguchi
- Department of Diagnostic Pathology, Nagasaki University Hospital, Nagasaki, Japan
| |
Collapse
|
3
|
Hoshino A, Oana Y, Ohi Y, Maeda Y, Omori M, Takada Y, Ikeda T, Sotome K, Maeda H, Yanagisawa T, Takeuchi O, Kuronuma S, Sangai T, Shibahara Y, Murakumo Y, Saegusa M, Kanomata N, Nagasawa S, Yamaguchi R, Yoshida M, Kozuka Y, Matsumoto H, Tsugawa K, Maeda I. Using the DNA Integrity Number to Analyze DNA Quality in Specimens Collected from Liquid-Based Cytology after Fine-Needle Aspiration of Breast Tumors and Lesions. Acta Cytol 2024; 68:145-152. [PMID: 38555634 DOI: 10.1159/000538071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 02/25/2024] [Indexed: 04/02/2024]
Abstract
INTRODUCTION Cancer genome analysis using next-generation sequencing requires adequate and high-quality DNA samples. Genomic analyses were conventionally performed using formalin-fixed paraffin-embedded sections rather than cytology samples such as cell block or smear specimens. Specimens collected from liquid-based cytology (LBC) have the potential to be sources of high-quality DNA suitable for genetic analysis even after long-term storage. METHODS We collected breast tumor/lesion fractions from 92 residual LBC specimens using fine-needle aspiration (FNA) biopsy, including breast carcinoma (1 invasive carcinoma and 4 ductal carcinomas in situ), papillomatous lesion (5 intraductal papillomas), and fibroepithelial lesion (19 phyllodes tumors and 53 fibroadenomas) samples, and others (1 ductal adenoma, 1 hamartoma, 1 fibrocystic disease, and 7 unknown). DNA was extracted from all samples and subjected to DNA integrity number (DIN) score analysis. RESULTS Average DIN score collected from 92 LBC specimens was significantly higher score. In addition, high-quality DNA with high DIN values (7.39 ± 0.80) was successfully extracted more than 12 months after storage of residual LBC specimens. CONCLUSION Residual LBC specimens collected from FNA of the breast were verified to carry high-quality DNA and could serve as an alternate source for genetic analysis.
Collapse
Affiliation(s)
- Akiyoshi Hoshino
- Department of Diagnostic Pathology, Kitasato University Kitasato Institute Hospital, Tokyo, Japan,
- Department of Pathology, Kitasato University School of Medicine, Tokyo, Japan,
| | - Yoshiyasu Oana
- Department of Diagnostic Pathology, Kitasato University Kitasato Institute Hospital, Tokyo, Japan
| | - Yasuyo Ohi
- Department of Pathology, Sagara Hospital, Kagoshima City, Kagoshima, Japan
| | - Yukari Maeda
- Department of Pathology, Sagara Hospital, Kagoshima City, Kagoshima, Japan
| | - Masako Omori
- Department of Pathology, Kurashiki Medical Center, Kurashiki City, Okayama, Japan
| | - Yuki Takada
- Department of Pathology, Kurashiki Medical Center, Kurashiki City, Okayama, Japan
| | - Tadashi Ikeda
- Department of Surgery, Kitasato University Kitasato Institute Hospital, Tokyo, Japan
| | - Keiichi Sotome
- Department of Surgery, Kitasato University Kitasato Institute Hospital, Tokyo, Japan
| | - Hinako Maeda
- Department of Surgery, Kitasato University Kitasato Institute Hospital, Tokyo, Japan
| | - Takako Yanagisawa
- Department of Surgery, Kitasato University Kitasato Institute Hospital, Tokyo, Japan
| | - Osamu Takeuchi
- Biomedical Laboratory, Kitasato University Kitasato Institute Hospital, Tokyo, Japan
| | - Satoshi Kuronuma
- Biomedical Laboratory, Kitasato University Kitasato Institute Hospital, Tokyo, Japan
| | - Takafumi Sangai
- Department of Surgery, Kitasato University Hospital, Sagamihara City, Sagamihara, Japan
| | - Yukiko Shibahara
- Department of Pathology, Kitasato University Hospital, Sagamihara City, Sagamihara, Japan
| | - Yoshiki Murakumo
- Department of Pathology, Kitasato University Hospital, Sagamihara City, Sagamihara, Japan
| | - Makoto Saegusa
- Department of Pathology, Kitasato University Hospital, Sagamihara City, Sagamihara, Japan
| | - Naoki Kanomata
- Department of Pathology, St. Lukes International Hospital, Tokyo, Japan
| | - Satoi Nagasawa
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa City, Chiba, Japan
| | - Rin Yamaguchi
- Department of Pathology, Nagasaki University Hospital, Nagasaki City, Nagasaki, Japan
| | - Masayuki Yoshida
- Department of Diagnostic Pathology, National Cancer Center Hospital, Tokyo, Japan
| | - Yuji Kozuka
- Department of Pathology, Mie University Hospital, Tsu, Japan
| | | | - Koichiro Tsugawa
- Divison of Breast and Endocrine Surgery, Department of Surgery, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Ichiro Maeda
- Department of Diagnostic Pathology, Kitasato University Kitasato Institute Hospital, Tokyo, Japan
- Department of Pathology, Kitasato University School of Medicine, Tokyo, Japan
| |
Collapse
|
4
|
Futane A, Jadhav P, Mustafa AH, Srinivasan A, Narayanamurthy V. Aptamer-functionalized MOFs and AI-driven strategies for early cancer diagnosis and therapeutics. Biotechnol Lett 2024; 46:1-17. [PMID: 38155321 DOI: 10.1007/s10529-023-03454-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 11/07/2023] [Accepted: 11/20/2023] [Indexed: 12/30/2023]
Abstract
Metal-Organic Frameworks (MOFs) have exceptional inherent properties that make them highly suitable for diverse applications, such as catalysis, storage, optics, chemo sensing, and biomedical science and technology. Over the past decades, researchers have utilized various techniques, including solvothermal, hydrothermal, mechanochemical, electrochemical, and ultrasonic, to synthesize MOFs with tailored properties. Post-synthetic modification of linkers, nodal components, and crystallite domain size and morphology can functionalize MOFs to improve their aptamer applications. Advancements in AI and machine learning led to the development of nonporous MOFs and nanoscale MOFs for medical purposes. MOFs have exhibited promise in cancer therapy, with the successful accumulation of a photosensitizer in cancer cells representing a significant breakthrough. This perspective is focused on MOFs' use as advanced materials and systems for cancer therapy, exploring the challenging aspects and promising features of MOF-based cancer diagnosis and treatment. The paper concludes by emphasizing the potential of MOFs as a transformative technology for cancer treatment and diagnosis.
Collapse
Affiliation(s)
- Abhishek Futane
- Department of Engineering Technology, Faculty of Electronics and Computer Technology & Engineering, Universiti Teknikal Malaysia Melaka, Hang Tuah Jaya, 76100, Durian Tunggal, Melaka, Malaysia
| | - Pramod Jadhav
- Faculty of Civil Engineering Technology, Universiti Malaysia Pahang (UMP) Lebuhraya Tun Razak, 26300, Gambang, Kuantan, Pahang, Malaysia
| | - Abu Hasnat Mustafa
- Faculty of Industrial Science and Technology, Universiti Malaysia Pahang, 26300, Gambang, Pahang, Malaysia
| | - Arthi Srinivasan
- Faculty of Chemical and Process Engineering Technology, University Malaysia Pahang (UMP), Lebuhraya Tun Razak, 26300, Gambang, Kunatan, Pahang, Malaysia
| | - Vigneswaran Narayanamurthy
- Department of Engineering Technology, Faculty of Electronics and Computer Technology & Engineering, Universiti Teknikal Malaysia Melaka, Hang Tuah Jaya, 76100, Durian Tunggal, Melaka, Malaysia.
- Department of Biotechnology, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai, India.
| |
Collapse
|
5
|
Akahane T, Isochi-Yamaguchi T, Hashiba-Ohnuki N, Bandoh N, Aimono E, Kato Y, Nishihara H, Kamada H, Tanimoto A. Cancer gene analysis of liquid-based cytology specimens using next-generation sequencing: A technical report of bimodal DNA- and RNA-based panel application. Diagn Cytopathol 2023; 51:493-500. [PMID: 37162026 DOI: 10.1002/dc.25149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 04/08/2023] [Accepted: 04/17/2023] [Indexed: 05/11/2023]
Abstract
BACKGROUND As liquid-based cytology (LBC) specimens harbor high-quality DNA, genomic analysis using LBC specimens is beneficial for integrative diagnosis. This study aimed to clarify the feasibility of LBC specimens for a bimodal application of DNA- and RNA-based next-generation sequencing (NGS) panels. METHODS LBC specimens were prepared from cultured human cancer HEC59 cells using commercially available fixatives (Cellprep, CytoRich Red, and SurePath solutions), and were subjected to NGS for a feasibility study. Clinical LBC specimens of thyroid and salivary gland tumors were prepared using CytoRich Red solution. After DNA and RNA extraction, NGS analyses were performed in a single run using combined DNA- and RNA-based custom-made cancer panels for the detection of gene mutations and fusions. RESULTS High-quality DNA and RNA were obtained, and the expected gene mutations and fusions were detected in HEC59 cells using all types of LBC fixatives. Most available clinical cases (18 out of 20) exhibited pathogenic gene mutations (15 cases) and fusion genes (3 cases) using the bimodal DNA- and RNA-based panels. Overall, 18 cases (90%) showed oncogenic mutations or fusion genes of diagnostic values. CONCLUSION Simultaneous application of bimodal DNA- and RNA-based gene panels was useful in NGS analysis using residual LBC specimens for integrative diagnosis. Residual LBC specimens for genomic analysis, including fusion gene analysis, are particularly useful for obtaining genomic information before surgical resection.
Collapse
Affiliation(s)
- Toshiaki Akahane
- Department of Pathology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
- Center for Human Genome and Gene Analysis, Kagoshima University Hospital, Kagoshima, Japan
| | - Tomomi Isochi-Yamaguchi
- Department of Pathology, Laboratory of Cancer Medical Science, Hokuto Hospital, Obihiro, Japan
| | - Natumi Hashiba-Ohnuki
- Department of Pathology, Laboratory of Cancer Medical Science, Hokuto Hospital, Obihiro, Japan
| | - Nobuyuki Bandoh
- Department of Otolaryngology-Head and Neck Surgery, Hokuto Hospital, Obihiro, Japan
| | - Eriko Aimono
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Yasutaka Kato
- Department of Biology and Genetics, Laboratory of Cancer Medical Science, Hokuto Hospital, Obihiro, Japan
| | - Hiroshi Nishihara
- Department of Biology and Genetics, Laboratory of Cancer Medical Science, Hokuto Hospital, Obihiro, Japan
- Keio Cancer Center, Keio University School of Medicine, Shinjuku-ku, Japan
- Center for the Research of Advanced Diagnosis and Therapy of Cancer, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Hajime Kamada
- Department of Neurosurgery, Hokuto Hospital, Obihiro, Japan
| | - Akihide Tanimoto
- Department of Pathology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
- Center for Human Genome and Gene Analysis, Kagoshima University Hospital, Kagoshima, Japan
- Center for the Research of Advanced Diagnosis and Therapy of Cancer, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| |
Collapse
|
6
|
Peña KB, Riu F, Hernandez A, Guilarte C, Elizalde-Horcada M, Parada D. Study of Liquid-Based Cytology Using Next-Generation Sequencing as a Liquid Biopsy Application in Patients with Advanced Oncological Disease. Biomedicines 2023; 11:1578. [PMID: 37371673 DOI: 10.3390/biomedicines11061578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/17/2023] [Accepted: 05/27/2023] [Indexed: 06/29/2023] Open
Abstract
In patients with advanced cancer, it is necessary to detect driver mutations and genetic arrangements. If a mutation is found, targeted therapy may become an option. However, in most patients with advanced cancer, obtaining material can be challenging, and these determinations must be made based on small biopsies or cytologic samples. We analyzed the ability of liquid-based cytology to determine the mutational status in patients with advanced cancer by next-generation sequencing. We studied cytologic samples from 28 patients between 1 January 2018 and 31 December 2022. All samples were processed by next-generation sequencing using the Oncomine® Precision and Comprehensive Assay Panels for Solid Tumors. Eleven male and 17 female patients with a median age of 63.75 years were included. Clinical stage IV was predominant in 21 patients. Eleven patients died, and 17 survived. The DNA and RNA concentrations were 10.53 ng/µL and 13 ng/µL, respectively. Eleven patients showed actionable mutations, and 17 showed other genomic alterations. Liquid-based cytology can be used as a component of liquid biopsy, as it allows the identification of actionable mutations in patients with advanced oncological disease. Our findings expand the utility of liquid biopsy from different body fluids or cell aspirates.
Collapse
Affiliation(s)
- Karla Beatríz Peña
- Molecular Pathology Unit, Department of Pathology, Hospital Universitari de Sant Joan, 43202 Reus, Tarragona, Spain
- Institut d'Investigació Sanitària Pere Virgili, 43202 Reus, Tarragona, Spain
- Facultat de Medicina i Ciències de la Salut, Universitat Rovira i Virgili, 43002 Reus, Tarragona, Spain
| | - Francesc Riu
- Molecular Pathology Unit, Department of Pathology, Hospital Universitari de Sant Joan, 43202 Reus, Tarragona, Spain
- Institut d'Investigació Sanitària Pere Virgili, 43202 Reus, Tarragona, Spain
- Facultat de Medicina i Ciències de la Salut, Universitat Rovira i Virgili, 43002 Reus, Tarragona, Spain
| | - Anna Hernandez
- Molecular Pathology Unit, Department of Pathology, Hospital Universitari de Sant Joan, 43202 Reus, Tarragona, Spain
- Institut d'Investigació Sanitària Pere Virgili, 43202 Reus, Tarragona, Spain
| | - Carmen Guilarte
- Molecular Pathology Unit, Department of Pathology, Hospital Universitari de Sant Joan, 43202 Reus, Tarragona, Spain
| | | | - David Parada
- Molecular Pathology Unit, Department of Pathology, Hospital Universitari de Sant Joan, 43202 Reus, Tarragona, Spain
- Institut d'Investigació Sanitària Pere Virgili, 43202 Reus, Tarragona, Spain
- Facultat de Medicina i Ciències de la Salut, Universitat Rovira i Virgili, 43002 Reus, Tarragona, Spain
| |
Collapse
|
7
|
Next-Generation Sequencing Analysis of Pancreatic Cancer Using Residual Liquid Cytology Specimens from Endoscopic Ultrasound—Guided Fine-Needle Biopsy: A Prospective Comparative Study with Tissue Specimens. Diagnostics (Basel) 2023; 13:diagnostics13061078. [PMID: 36980386 PMCID: PMC10047095 DOI: 10.3390/diagnostics13061078] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/03/2023] [Accepted: 03/09/2023] [Indexed: 03/14/2023] Open
Abstract
This study evaluated the feasibility and clinical utility of liquid-based cytology (LBC) specimens via endoscopic ultrasound–guided fine-needle biopsy (EUS-FNB) for next-generation sequencing (NGS) of pancreatic cancer (PC). We prospectively evaluated the performance of DNA extraction and NGS using EUS-FNB samples obtained from PC. Thirty-three consecutive patients with PC who underwent EUS-FNB at our hospital were enrolled. DNA samples were obtained from 96.8% of the patients. When stratified with a variant allele frequency (VAF) > 10% tumor burden, the NGS success rate was 76.7% (n = 23) in formalin-fixed paraffin-embedded (FFPE), 83.3% (n = 25) in LBC, and 76.7% (n = 23) in frozen samples. The overall NGS success rate was 86.7% (n = 26) using FFPE, LBC, or frozen samples. The detection rates for the main mutated genes were as follows: 86.7% for KRAS, 73.3% for TP53, 66.7% for CDKN2A, 36.7% for SMAD4, and 16.7% for ARID1A. LBC had the highest median value of VAF (23.5%) for KRAS and TP53. PC mutation analysis using NGS was successfully performed using LBC compared with FFPE and frozen samples. This approach provides an alternative and affordable source of molecular testing materials.
Collapse
|
8
|
Yokoyama S, Iwaya H, Akahane T, Hamada T, Higashi M, Hashimoto S, Tanoue S, Ohtsuka T, Ido A, Tanimoto A. Sequential evaluation of
MUC
promoter methylation using next‐generation sequencing‐based custom‐made panels in liquid‐based cytology specimens of pancreatic cancer. Diagn Cytopathol 2022; 50:499-507. [DOI: 10.1002/dc.25022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 07/12/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Sieya Yokoyama
- Department of Pathology Kagoshima University Graduate School of Medical and Dental Sciences Kagoshima Japan
| | - Hiromichi Iwaya
- Digestive and Lifestyle Diseases Kagoshima University Graduate School of Medical and Dental Sciences Kagoshima Japan
| | - Toshiaki Akahane
- Department of Pathology Kagoshima University Graduate School of Medical and Dental Sciences Kagoshima Japan
- Center for Human Genome and Gene Analysis Kagoshima University Hospital Kagoshima Japan
| | - Taiji Hamada
- Department of Pathology Kagoshima University Graduate School of Medical and Dental Sciences Kagoshima Japan
| | - Michiyo Higashi
- Unit of Surgical Pathology Kagoshima University Hospital Kagoshima Japan
| | - Shinichi Hashimoto
- Digestive and Lifestyle Diseases Kagoshima University Graduate School of Medical and Dental Sciences Kagoshima Japan
| | - Shiroh Tanoue
- Digestive and Lifestyle Diseases Kagoshima University Graduate School of Medical and Dental Sciences Kagoshima Japan
| | - Takao Ohtsuka
- Department of Digestive Surgery, Breast and Thyroid Surgery Kagoshima University Graduate School of Medical and Dental Sciences Kagoshima Japan
| | - Akio Ido
- Digestive and Lifestyle Diseases Kagoshima University Graduate School of Medical and Dental Sciences Kagoshima Japan
| | - Akihide Tanimoto
- Department of Pathology Kagoshima University Graduate School of Medical and Dental Sciences Kagoshima Japan
- Center for Human Genome and Gene Analysis Kagoshima University Hospital Kagoshima Japan
- Unit of Surgical Pathology Kagoshima University Hospital Kagoshima Japan
| |
Collapse
|
9
|
Performance of Idylla KRAS assay on extracted DNA and de-stained cytology smears: Can we rescue small sample? Ann Diagn Pathol 2022; 60:152023. [DOI: 10.1016/j.anndiagpath.2022.152023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 08/01/2022] [Indexed: 11/22/2022]
|
10
|
Suzuki S, Bandoh N, Goto T, Kubota A, Uemura A, Kono M, Sato R, Takeda R, Sakaue S, Yamaguchi-Isochi T, Nishihara H, Takei H, Harabuchi Y. A retrospective study of parotid gland tumors at a single institution. Oncol Lett 2022; 24:207. [PMID: 35720490 PMCID: PMC9178697 DOI: 10.3892/ol.2022.13328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 04/06/2022] [Indexed: 11/13/2022] Open
Abstract
The aim of the present study was to analyze the clinical characteristics, surgical treatments and clinical outcome of patients with parotid gland tumors and to compare the results with those cited in the literature. A retrospective study was conducted in 140 patients (male, n=77; female, n=63) with parotid gland tumors who underwent parotidectomy at Hokuto Hospital Department of Otolaryngology-Head and Neck Surgery (Obihiro, Japan) between April 2007 and December 2021. Of the 140 patients enrolled, 118 (84.3%) patients had benign tumors, including 63 (45%) patients with pleomorphic adenomas and 43 (30.7%) patients with Warthin tumors, and 22 patients (15.7%) had parotid carcinoma. Comparison of the three groups of patients with parotid gland tumors indicated that pack years as an indicator of smoking status were significantly higher in patients with Warthin tumors than in those with parotid carcinomas (P=0.011) or pleomorphic adenoma (P<0.001). Fine-needle aspiration cytology (FNAC) was non-diagnostic for only 6 (4.3%) of 140 patients. The sensitivity, specificity, positive predictive value, negative predictive value and accuracy of FNAC by both conventional smear and liquid-based cytology (LBC) for parotid carcinomas were 70, 99, 93.3, 94.4 and 82.9%, respectively. Among the 22 patients with parotid carcinoma, extended total/total and superficial parotidectomy were performed in 10 (45%) and 11 (50%) cases, respectively. Total and selective neck dissection of the area from level II to I, II and III were performed in 6 (24%) and 7 (32%) patients, respectively. Postoperative radiotherapy (50 Gy) was performed in 15 (68%) patients. The overall survival (OS) and disease-free survival (DFS) rates at 5 years were 51.5 and 76.4%, respectively. Univariate analysis revealed that age >65 years was significantly associated with poorer 5-year OS (P<0.001) and DFS (P<0.001). Multivariate analysis revealed that an age of more than 65 years combined with high-grade histologic malignancy was associated with worse DFS (P=0.02; hazard ratio, 3.628; 95% confidence interval, 1.283-9.514). In conclusion, the clinical characteristics and treatment outcomes of parotid gland tumors were consistent with the results of previous reports. Smoking may be closely related to the pathogenesis of Warthin tumors. LBC potentially provides improved accuracy in FNAC.
Collapse
Affiliation(s)
- Shiori Suzuki
- Department of Otolaryngology-Head and Neck Surgery, Hokuto Hospital, Obihiro, Hokkaido 080-0833, Japan.,Department of Otolaryngology-Head and Neck Surgery, Asahikawa Medical University, Asahikawa, Hokkaido 078-8510, Japan
| | - Nobuyuki Bandoh
- Department of Otolaryngology-Head and Neck Surgery, Hokuto Hospital, Obihiro, Hokkaido 080-0833, Japan
| | - Takashi Goto
- Department of Otolaryngology-Head and Neck Surgery, Hokuto Hospital, Obihiro, Hokkaido 080-0833, Japan
| | - Akinobu Kubota
- Department of Otolaryngology-Head and Neck Surgery, Hokuto Hospital, Obihiro, Hokkaido 080-0833, Japan.,Department of Otolaryngology-Head and Neck Surgery, Asahikawa Medical University, Asahikawa, Hokkaido 078-8510, Japan
| | - Akihiro Uemura
- Department of Otolaryngology-Head and Neck Surgery, Hokuto Hospital, Obihiro, Hokkaido 080-0833, Japan
| | - Michihisa Kono
- Department of Otolaryngology-Head and Neck Surgery, Hokuto Hospital, Obihiro, Hokkaido 080-0833, Japan.,Department of Otolaryngology-Head and Neck Surgery, Asahikawa Medical University, Asahikawa, Hokkaido 078-8510, Japan
| | - Ryosuke Sato
- Department of Otolaryngology-Head and Neck Surgery, Hokuto Hospital, Obihiro, Hokkaido 080-0833, Japan.,Department of Otolaryngology-Head and Neck Surgery, Asahikawa Medical University, Asahikawa, Hokkaido 078-8510, Japan
| | - Ryuhei Takeda
- Department of Otolaryngology-Head and Neck Surgery, Hokuto Hospital, Obihiro, Hokkaido 080-0833, Japan.,Department of Otolaryngology-Head and Neck Surgery, Asahikawa Medical University, Asahikawa, Hokkaido 078-8510, Japan
| | - Shota Sakaue
- Department of Otolaryngology-Head and Neck Surgery, Hokuto Hospital, Obihiro, Hokkaido 080-0833, Japan.,Department of Otolaryngology-Head and Neck Surgery, Asahikawa Medical University, Asahikawa, Hokkaido 078-8510, Japan
| | | | - Hiroshi Nishihara
- Genomics Unit, Keio Cancer Center, Keio University School of Medicine, Shinjukuku, Tokyo 160-8582, Japan
| | - Hidehiro Takei
- Department of Pathology and Translational Pathobiology, Louisiana State University Health Sciences Center at Shreveport, Shreveport, LA 71103, USA
| | - Yasuaki Harabuchi
- Department of Otolaryngology-Head and Neck Surgery, Hokuto Hospital, Obihiro, Hokkaido 080-0833, Japan.,Department of Otolaryngology-Head and Neck Surgery, Asahikawa Medical University, Asahikawa, Hokkaido 078-8510, Japan
| |
Collapse
|
11
|
Dolinar A, Grubelnik G, Srebotnik-Kirbiš I, Strojan Fležar M, Žlajpah M. Optimization of pre-analytical and analytical steps for DNA and RNA analysis of fresh cytology samples. Cancer Med 2022; 11:4021-4032. [PMID: 35403378 DOI: 10.1002/cam4.4728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 02/16/2022] [Accepted: 03/16/2022] [Indexed: 11/10/2022] Open
Abstract
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.
Collapse
Affiliation(s)
- Ana Dolinar
- Department of molecular genetics, Institute of Pathology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Gašper Grubelnik
- Department of molecular genetics, Institute of Pathology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Irena Srebotnik-Kirbiš
- Department of cytopathology, Institute of Pathology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Margareta Strojan Fležar
- Department of cytopathology, Institute of Pathology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Margareta Žlajpah
- Department of molecular genetics, Institute of Pathology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| |
Collapse
|
12
|
Sekita‐Hatakeyama Y, Fujii T, Nishikawa T, Mitoro A, Sawai M, Itami H, Morita K, Uchiyama T, Takeda M, Sho M, Yoshiji H, Hatakeyama K, Ohbayashi C. Evaluation and diagnostic value of next-generation sequencing analysis of residual liquid-based cytology specimens of pancreatic masses. Cancer Cytopathol 2022; 130:202-214. [PMID: 34665935 PMCID: PMC9297882 DOI: 10.1002/cncy.22525] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 09/21/2021] [Accepted: 10/01/2021] [Indexed: 12/12/2022]
Abstract
BACKGROUND Liquid-based cytology (LBC) is a widely used method for processing specimens obtained by endoscopic biopsy. This study evaluated next-generation sequencing (NGS) analysis of LBC specimens to improve the diagnostic accuracy of pancreatic lesions. METHODS Upon the diagnosis of a suspected pancreatic mass, LBC residues were used retrospectively. The quantity and quality of DNA extracted from residual LBC samples were evaluated, and an NGS analysis targeting 6 genes (KRAS, GNAS, TP53, CDKN2A, SMAD4, and PIK3CA) was performed. RESULTS The library was prepared from LBC specimens taken from 52 cases: 44 were successful, and 8 preparations failed. An analysis of DNA quantity and quality suggested that the success or failure of NGS implementation depended on both properties. The final diagnosis was achieved by a combination of the pathological analysis of the surgical excision or biopsy material with clinical information. Among the 33 cases of pancreatic ductal adenocarcinoma (PDAC), KRAS, TP53, CDKN2A, and SMAD4 mutations were identified in 31 (94%), 16 (48%), 3 (9%), and 2 (6%), respectively. Among the 11 benign cases, only a KRAS mutation was identified in 1 case. On the basis of NGS results, 18 of 33 PDACs (55%) were classified as highly dysplastic or more, and 10 of 11 benign lesions were evaluated as nonmalignant, which was consistent with the final diagnosis. CONCLUSIONS NGS analysis using LBC specimens from which DNA of appropriate quantity and quality has been extracted could contribute to improving the assessment of pancreatic tumor malignancies and the application of molecular-targeted drugs.
Collapse
Affiliation(s)
| | - Tomomi Fujii
- Department of Diagnostic PathologyNara Medical UniversityKashiharaJapan
| | - Takeshi Nishikawa
- Department of Diagnostic PathologyNara Medical UniversityKashiharaJapan
| | - Akira Mitoro
- Department of GastroenterologyNara Medical UniversityKashiharaJapan
| | - Masayoshi Sawai
- Department of GastroenterologyMinami‐Nara General Medical CenterOyodo‐ChoJapan
| | - Hiroe Itami
- Department of Diagnostic PathologyNara Medical UniversityKashiharaJapan
| | - Kouhei Morita
- Department of Diagnostic PathologyNara Medical UniversityKashiharaJapan
| | - Tomoko Uchiyama
- Department of Diagnostic PathologyNara Medical UniversityKashiharaJapan
| | - Maiko Takeda
- Department of Diagnostic PathologyNara Medical UniversityKashiharaJapan
| | - Masayuki Sho
- Department of SurgeryNara Medical UniversityKashiharaJapan
| | - Hitoshi Yoshiji
- Department of GastroenterologyNara Medical UniversityKashiharaJapan
| | - Kinta Hatakeyama
- Department of Diagnostic PathologyNara Medical UniversityKashiharaJapan
- Department of PathologyNational Cerebral and Cardiovascular CenterSuitaJapan
| | - Chiho Ohbayashi
- Department of Diagnostic PathologyNara Medical UniversityKashiharaJapan
| |
Collapse
|
13
|
ATM immunohistochemistry as a potential marker for the differential diagnosis of no specific molecular profile subtype and POLE-mutation subtype endometrioid carcinoma. Pathol Res Pract 2022; 230:153743. [DOI: 10.1016/j.prp.2021.153743] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 12/12/2021] [Accepted: 12/16/2021] [Indexed: 12/21/2022]
|
14
|
Nikas IP, Mountzios G, Sydney GI, Ioakim KJ, Won JK, Papageorgis P. Evaluating Pancreatic and Biliary Neoplasms with Small Biopsy-Based Next Generation Sequencing (NGS): Doing More with Less. Cancers (Basel) 2022; 14:cancers14020397. [PMID: 35053560 PMCID: PMC8773813 DOI: 10.3390/cancers14020397] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/05/2022] [Accepted: 01/10/2022] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Pancreatic cancer and cholangiocarcinoma are aggressive diseases mostly diagnosed at an advanced and inoperable stage. This review presents the value of next-generation sequencing (NGS) when performed on small biopsies—including fine-needle aspiration/biopsy samples, brushings, pancreatic juice and bile, and also blood—in the field of pancreatobiliary neoplasia. NGS could guide physicians while evaluating pancreatic solid and cystic lesions or suspicious biliary strictures, performing surveillance in high-risk individuals, or monitoring the disease and assessing prognosis in already diagnosed cancer patients. Evidence suggests that NGS performed on small biopsies is a robust tool for the diagnosis and pre-operative risk stratification of pancreatic and biliary lesions, whereas it also carries significant prognostic and therapeutic value. However, effective standardization of the pre-analytical and analytical assay parameters used for each clinical scenario is needed to fully implement NGS into routine practice and provide more personalized management in patients with suspected or established pancreatobiliary neoplasia. Abstract Pancreatic cancer and cholangiocarcinoma are lethal diseases mainly diagnosed at an inoperable stage. As pancreatobiliary surgical specimens are often unavailable for further molecular testing, this review aimed to highlight the diagnostic, prognostic, and therapeutic impact of next-generation sequencing (NGS) performed on distinct small biopsies, including endoscopic ultrasound fine-needle aspirations and biopsies of pancreatic solid and cystic lesions, biliary duct brushings, and also “liquid biopsies” such as the pancreatic juice, bile, and blood. NGS could clarify indeterminate pancreatic lesions or biliary strictures, for instance by identifying TP53 or SMAD4 mutations indicating high-grade dysplasia or cancer. It could also stratify pancreatic cystic lesions, by distinguishing mucinous from non-mucinous cysts and identifying high-risk cysts that should be excised in surgically fit patients, whereas the combination of cytology, elevated cystic CEA levels and NGS could improve the overall diagnostic accuracy. When NGS is performed on the pancreatic juice, it could stratify high-risk patients under surveillance. On the plasma, it could dynamically monitor the disease course and response to therapy. Notably, the circulating tumor DNA (ctDNA) levels have been associated with staging, grading, and survival. Lastly, NGS has shown potential in identifying potentially actionable molecular alterations. In conclusion, NGS applied on small biopsies could carry significant diagnostic, prognostic, and therapeutic value.
Collapse
Affiliation(s)
- Ilias P. Nikas
- School of Medicine, European University Cyprus, Nicosia 2404, Cyprus; (G.I.S.); (K.J.I.)
- Correspondence:
| | - Giannis Mountzios
- Fourth Department of Medical Oncology and Clinical Trials Unit, Henry Dunant Hospital Center, 11526 Athens, Greece;
| | - Guy I. Sydney
- School of Medicine, European University Cyprus, Nicosia 2404, Cyprus; (G.I.S.); (K.J.I.)
- Department of Internal Medicine, Southern Illinois University School of Medicine, Springfield, IL 62702, USA
| | - Kalliopi J. Ioakim
- School of Medicine, European University Cyprus, Nicosia 2404, Cyprus; (G.I.S.); (K.J.I.)
- Department of Internal Medicine, Limassol General Hospital, Limassol 4131, Cyprus
| | - Jae-Kyung Won
- Department of Pathology, Seoul National University Hospital and College of Medicine, Seoul 03080, Korea;
| | - Panagiotis Papageorgis
- Tumor Microenvironment, Metastasis and Experimental Therapeutics Laboratory, Basic and Translational Cancer Research Center, Department of Life Sciences, European University Cyprus, Nicosia 2404, Cyprus;
| |
Collapse
|
15
|
Kobayashi Y, Kitazono I, Akahane T, Yanazume S, Kamio M, Togami S, Nohara S, Sakamoto I, Yokoyama S, Tabata K, Kobayashi H, Tanimoto A. Molecular Evaluation of Endometrial Dedifferentiated Carcinoma, Endometrioid Carcinoma, Carcinosarcoma, and Serous Carcinoma Using a Custom-Made Small Cancer Panel. Pathol Oncol Res 2022; 27:1610013. [PMID: 35002543 PMCID: PMC8734147 DOI: 10.3389/pore.2021.1610013] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 10/28/2021] [Indexed: 12/18/2022]
Abstract
It is often difficult to histologically differentiate among endometrial dedifferentiated carcinoma (DC), endometrioid carcinoma (EC), serous carcinoma (SC), and carcinosarcoma (CS) due to the presence of solid components. In this study, we aimed to categorize these carcinomas according to The Cancer Genome Atlas (TCGA) classification using a small custom-made cancer genome panel (56 genes and 17 microsatellite regions) for integrated molecular diagnosis. A total of 36 endometrial cancer cases with solid components were assessed using IHC, next-generation sequencing (NGS), and the custom-made panel. Among 19 EC cases, six were categorized as MMR-deficient (MMR-d) and eight were classified as having a nonspecific molecular profile. Three EC cases were classified as POLE mutation (POLEmut)-type, which had a very high tumor mutation burden (TMB) and low microsatellite instability (MSI). Increased TMB and MSI were observed in all three DC cases, classified as MMR-d with mutations in MLH1 and POLD1. Except for one case classified as MMR-d, all SC cases exhibited TP53 mutations and were classified as p53 mutation-type. SC cases also exhibited amplification of CCND1, CCNE1, and MYC. CS cases were classified as three TCGA types other than the POLEmut-type. The IHC results for p53 and ARID1A were almost consistent with their mutation status. NGS analysis using a small panel enables categorization of endometrial cancers with solid proliferation according to TCGA classification. As TCGA molecular classification does not consider histological findings, an integrated analytical procedure including IHC and NGS may be a practical diagnostic tool for endometrial cancers.
Collapse
Affiliation(s)
- Yusuke Kobayashi
- Course of Advanced Cancer Medicine for Gynecologic Cancer, Kagoshima, Japan
| | - Ikumi Kitazono
- Department of Pathology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Toshiaki Akahane
- Department of Pathology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan.,Center for Human Genome and Gene Analysis, Kagoshima University Hospital, Kagoshima, Japan
| | - Shintaro Yanazume
- Department of Obstetrics and Gynecology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Masaki Kamio
- Department of Obstetrics and Gynecology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Shinichi Togami
- Department of Obstetrics and Gynecology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Sachio Nohara
- Department of Biomedical Informatics, Mitsubishi Space Software, Amagasaki, Japan
| | - Ippei Sakamoto
- Department of Biomedical Informatics, Mitsubishi Space Software, Amagasaki, Japan
| | - Seiya Yokoyama
- Department of Pathology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Kazuhiro Tabata
- Department of Pathology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Hiroaki Kobayashi
- Course of Advanced Cancer Medicine for Gynecologic Cancer, Kagoshima, Japan.,Department of Obstetrics and Gynecology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Akihide Tanimoto
- Department of Pathology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan.,Center for Human Genome and Gene Analysis, Kagoshima University Hospital, Kagoshima, Japan
| |
Collapse
|
16
|
Sugiyama K, Washimi K, Sato S, Hiruma T, Sakai M, Okubo Y, Miyagi Y, Yokose T. Differential diagnosis of lipoma and atypical lipomatous tumor/well-differentiated liposarcoma by cytological analysis. Diagn Cytopathol 2022; 50:112-122. [PMID: 34984861 PMCID: PMC9305447 DOI: 10.1002/dc.24928] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/23/2021] [Accepted: 12/26/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND Adipocytic tumors are the most common soft tissue tumors, with lipomas and atypical lipomatous tumor/well-differentiated liposarcomas (ALT/WDL), which comprise most cases. Preoperative differential diagnosis of lipoma or ALT/WDL can provide important information for decisions regarding treatment. We evaluated the cytological findings of 20 cases of lipoma and ALT/WDL. METHODS Fluorescence in situ hybridization (FISH) was performed on formalin-fixed paraffin-embedded specimens (FFPE) to examine mouse double minute 2 homolog (MDM2) amplification in all cases. Tissue samples were collected from the center of the surgical materials, stained with Pap, and evaluated for 12 cytological parameters by six cytotechnologists. RESULTS The findings regarding large atypical cells, multinucleated cells, and nuclear pleomorphism were highly concordant among the cytotechnologists and were associated with MDM2 amplification. Large atypical cells, considered a highly specific feature of ALT/WDL, were not observed in lipoma cases. However, the sensitivity of the large atypical cell findings was not high (67%); therefore, comprehensive evaluation of multinucleated cells and pleomorphism is crucial for predicting ALT/WDL diagnosis. FISH of MDM2 on Pap-stained specimens was performed in four cases. In two, the results were similar to those of MDM2 FISH performed on FFPE sections and were reproducible, whereas in the other two, the signal could not be evaluated because of the strong background coloration. CONCLUSIONS Cytology specimens may be useful for the preoperative diagnosis of adipocytic tumors, particularly if the FISH conditions for Pap-stained specimens and the detection accuracy of MDM2 amplification can be improved.
Collapse
Affiliation(s)
- Kana Sugiyama
- Department of Clinical Laboratory, Kanagawa Cancer Center, Yokohama, Kanagawa, Japan
| | - Kota Washimi
- Department of Pathology, Kanagawa Cancer Center, Yokohama, Kanagawa, Japan
| | - Shinya Sato
- Department of Pathology, Kanagawa Cancer Center, Yokohama, Kanagawa, Japan.,Molecular Pathology and Genetics Division, Kanagawa Cancer Center Research Institute, Yokohama, Kanagawa, Japan
| | - Toru Hiruma
- Department of Musculoskeletal Tumor Surgery, Kanagawa Cancer Center, Yokohama, Kanagawa, Japan
| | - Mai Sakai
- Department of Clinical Laboratory, Kanagawa Cancer Center, Yokohama, Kanagawa, Japan
| | - Yoichiro Okubo
- Department of Pathology, Kanagawa Cancer Center, Yokohama, Kanagawa, Japan
| | - Yohei Miyagi
- Molecular Pathology and Genetics Division, Kanagawa Cancer Center Research Institute, Yokohama, Kanagawa, Japan
| | - Tomoyuki Yokose
- Department of Pathology, Kanagawa Cancer Center, Yokohama, Kanagawa, Japan
| |
Collapse
|
17
|
Kanayama K, Izuhara J. Impact of LBC fixative type and fixation time on molecular analysis of pancreatic cancer cells: A comparative study of cell morphology, antigenicity and nucleic acids. J Cytol 2022; 39:66-71. [PMID: 35814881 PMCID: PMC9261998 DOI: 10.4103/joc.joc_13_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 04/20/2022] [Indexed: 11/04/2022] Open
Abstract
Introduction: Liquid-based cytology (LBC) has been widely used since 2000. Next-Generation Sequencing (NGS) analysis of residual specimens in LBC fixative may also be performed for pancreatic cancer in the near future. We examined cell morphology, antigenicity and nucleic acids in pancreatic cancer cells at different fixation times using two types of LBC fixatives. Methods: PANC-1 cells were fixed in 1 ml CytoRich Red (CR), CytoRich Blue (CB), 95% ethanol (95% AL) or 10% neutral buffered formalin (10% NBF) and evaluated for cell area, antigenicity and nucleic acids with fixation times of 1 hour and 1, 3, 9, and 14 days. Antigenicity was evaluated by immunocytochemical staining for p53 and CK20, and nucleic acid fragmentation was assessed by real-time PCR. Results: There was no difference in total cell area between 1 hour and 14 day fixation times for the CR group, but the CB group showed cell contraction with 9 days fixation. In immunocytochemical staining, the CR group showed high p53 and CK20 positivity even after 14 days fixation. The CB group had a lower p53 positive rate than the CR group from 1 hour fixation. For nucleic acid fragmentation, Ct values for the CR group increased with fixation time. The CB group had consistently low Ct values. Conclusion: Different LBC fixatives and fixation time can have varying effects on cell morphology, antigenicity and nucleic acids in pancreatic cancer cells. Therefore, fixative type and fixation time should be considered for molecular testing on residual samples in LBC fixatives.
Collapse
|
18
|
Tafoya M, Judd A, Chiotti K, Dearen K, Jiron K, Chabot-Richards D, Broehm CJ. Performance of a 50-gene next generation sequencing panel with post-centrifuge supernatant cytology fluid in non-small-cell lung cancer. Diagn Cytopathol 2021; 49:1173-1178. [PMID: 34339108 DOI: 10.1002/dc.24844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 07/19/2021] [Accepted: 07/22/2021] [Indexed: 11/07/2022]
Abstract
BACKGROUND Liquid based cytology (LBC) specimens are increasingly utilized for molecular analysis, as results are comparable to molecular analysis performed on traditional specimens (biopsy or cell block). However, there are few studies demonstrating the long-term viability of DNA in LBC samples. METHODS In this study, a 50-gene next generation sequencing (NGS) panel was performed on DNA isolated from post-centrifuged supernatant LBC samples of cases of non-small-cell lung carcinoma. Comparison was made to results of an identical NGS panel performed on a concurrent clinical sample (biopsy or cell block). Quality parameters including DNA concentration, total reads, amplicons with reads under 450 and 350, and variant allele fraction were also compared. For a subset of LBC samples, DNA was isolated after being held for varying extended lengths of time after collection (up to 41 days) at 5°C and results compared. RESULTS Results of NGS mutation analysis were concordant between LBC samples and clinical samples. DNA concentration was on average higher in the LBC samples compared to the clinical samples. The remaining metrics were more variable, but illustrated the adequacy of LBC samples for NGS testing. DNA isolated from LBC samples held for longer periods of time was of good concentration. NGS analysis was successfully performed on all samples, with concordance with results of clinical samples. CONCLUSION DNA isolated directly from LBC fluid is suitable for NGS analysis. DNA is also stable in LBC preservative for extended periods of time before isolation and NGS analysis can subsequently be successfully performed.
Collapse
Affiliation(s)
- Marissa Tafoya
- Department of Pathology, University of New Mexico Hospital, Albuquerque, New Mexico, USA
| | - Andrew Judd
- Department of Pathology, University of New Mexico Hospital, Albuquerque, New Mexico, USA
| | - Kelsey Chiotti
- TriCore Reference Laboratories, Albuquerque, New Mexico, USA
| | - Karen Dearen
- TriCore Reference Laboratories, Albuquerque, New Mexico, USA
| | - Kassandra Jiron
- TriCore Reference Laboratories, Albuquerque, New Mexico, USA
| | - Devon Chabot-Richards
- Department of Pathology, University of New Mexico Hospital, Albuquerque, New Mexico, USA
| | - Cory J Broehm
- Department of Pathology, University of New Mexico Hospital, Albuquerque, New Mexico, USA
| |
Collapse
|
19
|
Akahane T, Kitazono I, Kobayashi Y, Nishida-Kirita Y, Yamaguchi T, Yanazume S, Tabata K, Kobayashi H, Tanimoto A. Direct next-generation sequencing analysis using endometrial liquid-based cytology specimens for rapid cancer genomic profiling. Diagn Cytopathol 2021; 49:1078-1085. [PMID: 34319014 DOI: 10.1002/dc.24841] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 07/13/2021] [Accepted: 07/20/2021] [Indexed: 11/08/2022]
Abstract
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.
Collapse
Affiliation(s)
- Toshiaki Akahane
- Department of Pathology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan.,Center for Human Genome and Gene Analysis, Kagoshima University Hospital, Japan
| | - Ikumi Kitazono
- Unit of Surgical Pathology, Kagoshima University Hospital, Kagoshima, Japan
| | - Yusuke Kobayashi
- Advanced Cancer Medicine for Gynecologic Cancer, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | | | - Tomomi Yamaguchi
- Department of Pathology, Laboratory of Cancer Medical Science, Hokuto Hospital, Obihiro, Japan
| | - Shintaro Yanazume
- Department of Obstetrics and Gynecology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Kazuhiro Tabata
- Department of Pathology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Hiroaki Kobayashi
- Advanced Cancer Medicine for Gynecologic Cancer, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan.,Department of Obstetrics and Gynecology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Akihide Tanimoto
- Department of Pathology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan.,Center for Human Genome and Gene Analysis, Kagoshima University Hospital, Japan.,Unit of Surgical Pathology, Kagoshima University Hospital, Kagoshima, Japan
| |
Collapse
|
20
|
Dell'Aquila M, Fiorentino V, Martini M, Capodimonti S, Cenci T, Lombardi CP, Raffaelli M, Pontecorvi A, Fadda G, Pantanowitz L, Larocca LM, Rossi ED. How limited molecular testing can also offer diagnostic and prognostic evaluation of thyroid nodules processed with liquid-based cytology: Role of TERT promoter and BRAF V600E mutation analysis. Cancer Cytopathol 2021; 129:819-829. [PMID: 34076961 DOI: 10.1002/cncy.22454] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 04/17/2021] [Accepted: 04/19/2021] [Indexed: 12/30/2022]
Abstract
BACKGROUND Mutational analysis contributes to the diagnosis and prognosis of thyroid nodules analyzed with fine-needle aspiration cytology (FNAC). Although several advanced molecular tests based on multiple molecular markers are available for clinical use and have increased their impact on clinical management of patients, they are not widely available. Among them is BRAF V600E, one of the most studied mutations. Other genetic alterations, such as TERT promoter mutations, may coexist in thyroid carcinomas. Previous studies have demonstrated that this duet might be involved in the aggressiveness of thyroid cancer, although its prognostic value related to mortality remains undefined. The detection of such genetic alterations in thyroid liquid-based cytology (LBC) thus may assist with patient management. METHODS From January 2013 to June 2014, 356 thyroid FNAC samples were processed by LBC, including 174 surgical follow-up samples. BRAF V600E and TERT mutation analyses were performed on both LBC and histopathology. RESULTS The study included 119 samples categorized as atypia of undetermined significance, 42 categorized as follicular neoplasms, 61 categorized as suspicious for malignancy, and 34 categorized as positive for malignancy. BRAF V600E mutation was detected in 10.4% of all cases, whereas TERT promoter mutations were identified in 1.1%. TERT-mutated cases belonged to the positive for malignancy category, with a histologic diagnosis of tall cell variant of papillary thyroid carcinoma. These genetic alterations correlated with lymph node metastases (P = .0349) and higher disease stage. CONCLUSIONS BRAF V600E and TERT analysis can be performed on LBC. TERT mutations are rarely identified in well differentiated thyroid carcinoma but are associated with higher stage. Although a larger molecular panel may offer more information, analyzing these few point mutations is still likely to be useful for managing potentially more aggressive thyroid carcinomas.
Collapse
Affiliation(s)
- Marco Dell'Aquila
- Division of Anatomic Pathology and Histology, Fondazione Policlinico Universitario "Agostino Gemelli"-IRCCS, Rome, Italy
| | - Vincenzo Fiorentino
- Division of Anatomic Pathology and Histology, Fondazione Policlinico Universitario "Agostino Gemelli"-IRCCS, Rome, Italy
| | - Maurizio Martini
- Division of Anatomic Pathology and Histology, Fondazione Policlinico Universitario "Agostino Gemelli"-IRCCS, Rome, Italy
| | - Sara Capodimonti
- Division of Anatomic Pathology and Histology, Fondazione Policlinico Universitario "Agostino Gemelli"-IRCCS, Rome, Italy
| | - Tonia Cenci
- Division of Anatomic Pathology and Histology, Fondazione Policlinico Universitario "Agostino Gemelli"-IRCCS, Rome, Italy
| | - Celestino Pio Lombardi
- Division of Endocrine Surgery, Fondazione Policlinico Universitario "Agostino Gemelli"-IRCCS, Rome, Italy
| | - Marco Raffaelli
- Division of Endocrine Surgery, Fondazione Policlinico Universitario "Agostino Gemelli"-IRCCS, Rome, Italy
| | - Alfredo Pontecorvi
- Division of Endocrinology, Fondazione Policlinico Universitario "Agostino Gemelli"-IRCCS, Rome, Italy
| | - Guido Fadda
- Division of Anatomic Pathology and Histology, Fondazione Policlinico Universitario "Agostino Gemelli"-IRCCS, Rome, Italy
| | - Liron Pantanowitz
- Department of Pathology, University of Michigan, Ann Arbor, Michigan
| | - Luigi Maria Larocca
- Division of Anatomic Pathology and Histology, Fondazione Policlinico Universitario "Agostino Gemelli"-IRCCS, Rome, Italy
| | - Esther Diana Rossi
- Division of Anatomic Pathology and Histology, Fondazione Policlinico Universitario "Agostino Gemelli"-IRCCS, Rome, Italy
| |
Collapse
|
21
|
Hartl DM, Guerlain J, Breuskin I, Hadoux J, Baudin E, Al Ghuzlan A, Terroir-Cassou-Mounat M, Lamartina L, Leboulleux S. Thyroid Lobectomy for Low to Intermediate Risk Differentiated Thyroid Cancer. Cancers (Basel) 2020; 12:cancers12113282. [PMID: 33171949 PMCID: PMC7694652 DOI: 10.3390/cancers12113282] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/02/2020] [Accepted: 11/04/2020] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Total thyroidectomy used to be recommended for all thyroid cancers. We now know that some thyroid cancers have a relatively low risk of recurrence. Today, for some of these cancers, depending on the type of tumor, its’ size and other tumor characteristics, a thyroid lobectomy (or hemithyroidectomy) can be performed without increasing the patient’s risk of cancer recurrence. Thyroid lobectomy has the advantages of having less risk of surgical complications and a less frequent need for thyroid hormone replacement therapy. This approach is not optimal for all thyroid cancers, however, and careful tumor and patient selection are necessary. This review explains the rationale and criteria for patient selection for thyroid lobectomy for selected thyroid cancers. Abstract Many recent publications and guidelines have promoted a “more is less” approach in terms of treatment for low to intermediate risk differentiated thyroid cancer (DTC), which comprise the vast majority of thyroid cancers: less extensive surgery, less radioactive iodine, less or no thyroid hormone suppression, and less frequent or stringent follow-up. Following this approach, thyroid lobectomy has been proposed as a means of decreasing short- and long-term postoperative morbidity while maintaining an excellent prognosis for tumors meeting specific macroscopic and microscopic criteria. This article will examine the pros and cons of thyroid lobectomy for low to intermediate risk cancers and discuss, in detail, criteria for patient selection and oncological outcomes.
Collapse
Affiliation(s)
- Dana M. Hartl
- Department of Surgery, Anesthesia and Interventional Medicine Gustave Roussy, 94805 Villejuif, France; (J.G.); (I.B.)
- Correspondence:
| | - Joanne Guerlain
- Department of Surgery, Anesthesia and Interventional Medicine Gustave Roussy, 94805 Villejuif, France; (J.G.); (I.B.)
| | - Ingrid Breuskin
- Department of Surgery, Anesthesia and Interventional Medicine Gustave Roussy, 94805 Villejuif, France; (J.G.); (I.B.)
| | - Julien Hadoux
- Department of Nuclear Medicine and Endocrine Oncology, Anesthesia and Interventional Medicine Gustave Roussy, 94805 Villejuif, France; (J.H.); (E.B.); (M.T.-C.-M.); (L.L.); (S.L.)
| | - Eric Baudin
- Department of Nuclear Medicine and Endocrine Oncology, Anesthesia and Interventional Medicine Gustave Roussy, 94805 Villejuif, France; (J.H.); (E.B.); (M.T.-C.-M.); (L.L.); (S.L.)
| | - Abir Al Ghuzlan
- Department of Biology and Pathology, Anesthesia and Interventional Medicine Gustave Roussy, 94805 Villejuif, France;
| | - Marie Terroir-Cassou-Mounat
- Department of Nuclear Medicine and Endocrine Oncology, Anesthesia and Interventional Medicine Gustave Roussy, 94805 Villejuif, France; (J.H.); (E.B.); (M.T.-C.-M.); (L.L.); (S.L.)
| | - Livia Lamartina
- Department of Nuclear Medicine and Endocrine Oncology, Anesthesia and Interventional Medicine Gustave Roussy, 94805 Villejuif, France; (J.H.); (E.B.); (M.T.-C.-M.); (L.L.); (S.L.)
| | - Sophie Leboulleux
- Department of Nuclear Medicine and Endocrine Oncology, Anesthesia and Interventional Medicine Gustave Roussy, 94805 Villejuif, France; (J.H.); (E.B.); (M.T.-C.-M.); (L.L.); (S.L.)
| |
Collapse
|