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Ko SW, Jo IH, Yoon SB. Feasibility and clinical utility of endoscopic ultrasound-guided tissue acquisition for comprehensive genomic profiling in pancreatic cancer: A systematic review and meta-analysis. Pancreatology 2025; 25:89-97. [PMID: 39732591 DOI: 10.1016/j.pan.2024.12.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Revised: 11/09/2024] [Accepted: 12/21/2024] [Indexed: 12/30/2024]
Abstract
BACKGROUND Endoscopic ultrasound-guided tissue acquisition (EUS-TA) has become essential for diagnosing pancreatic ductal adenocarcinoma (PDAC) and is increasingly utilized for comprehensive genome profiling (CGP) to advance precision medicine. This systematic review and meta-analysis assess the feasibility and clinical utility of EUS-TA samples for CGP in PDAC. METHODS We conducted a thorough systematic literature search in PubMed, EMBASE, and the Cochrane Library up to October 2023. Key outcomes included sequencing success rates, detection rates of four major driver genes and actionable genes, and concordance rates with other sample types or methodologies. RESULTS A total of 23 studies met the inclusion criteria. The pooled sequencing success rate was 83.9 % [95 % confidence interval (CI): 75.8-89.7 %]. No significant difference was observed in sequencing success rates between fine needle aspiration and biopsy (odds ratio 1.77, 95 % CI 0.70-4.47). Meta-regression analysis revealed that the minimum DNA requirement for CGP significantly influenced sequencing success rates. The pooled mutation rate for K-ras was 86.4 % (95 % CI 83.6-88.8), while potentially actionable mutations had a pooled rate of 17.7 % (95 % CI 12.8-23.8). The concordance rate between CGP results from EUS-guided samples and surgical specimens was 81.6 % (95 % CI 68.2-90.1). CONCLUSION Comprehensive genomic profiling of PDAC using EUS-TA-derived samples demonstrated feasibility in clinical settings. Approximately 18 % of patients undergoing CGP exhibited potentially actionable mutations, highlighting the potential for personalized therapeutic approaches.
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Affiliation(s)
- Sung Woo Ko
- Department of Internal Medicine, Eunpyeong St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Ik Hyun Jo
- Department of Internal Medicine, St. Vincent's Hospital, College of Medicine, The Catholic University of Korea, Suwon, South Korea
| | - Seung Bae Yoon
- Department of Internal Medicine, Eunpyeong St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, South Korea.
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Pan Y, Ran T, Zhang X, Qin X, Zhang Y, Zhou C, Zou D. Adequacy of EUS-guided fine-needle aspiration and fine-needle biopsy for next-generation sequencing in pancreatic malignancies: A systematic review and meta-analysis. Endosc Ultrasound 2024; 13:366-375. [PMID: 39802109 PMCID: PMC11723693 DOI: 10.1097/eus.0000000000000097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/16/2025] Open
Abstract
Background and Objectives A majority of pancreatic malignancies are unresectable at the time of presentation and require EUS-guided fine-needle aspiration or fine-needle biopsy (EUS-FNA/FNB) for diagnosis. With the advent of precision therapy, there is an increasing need to use EUS-FNA/FNB sample for genetic analysis. Next-generation sequencing (NGS) is a preferred technology to detect genetic mutations with high sensitivity in small specimens. We performed a meta-analysis to evaluate the adequacy of EUS-FNA/FNB for NGS in pancreatic malignancies. Methods PubMed, Embase, Cochrane Library, and Web of Science were searched from database inception to November 11, 2023. The primary outcome was the proportion of sufficient sample acquired by EUS-FNA/FNB in pancreatic malignancies for NGS. Secondary outcomes were the proportion of sufficient sample for NGS in pancreatic ductal adenocarcinoma (PDAC) and the detection rates of mutations in KRAS, TP53, CDKN2A, and SMAD4 and actionable mutations in PDAC. The pooled proportions were calculated using a random-effects model. Potential sources of heterogeneity were investigated with subgroup analyses and meta-regression. Results Twenty studies with 881 samples were included. The pooled adequacy of EUS-FNA/FNB sample for NGS was 89.9% (95% CI, 80.8%-96.7%) in pancreatic malignancies and 92.0% (95% CI, 81.3%-98.8%) in PDAC. Screening sample suitability before NGS testing was associated with lower adequacy in subgroup analysis (79.7% vs. 98.4%, P = 0.001). The pooled prevalences of mutations in KRAS, TP53, CDKN2A, and SMAD4 in PDAC were 87.4% (95% CI, 83.2%-91.2%), 62.6% (95% CI, 53.2%-71.7%), 20.6% (95% CI, 11.9%-30.8%), and 19.4% (95% CI, 11.2%-29.1%), respectively. The pooled prevalence of potentially actionable mutations in PDAC was 14.5% (95% CI, 8.2%-22.0%). Conclusions In the majority of cases, EUS-FNA/FNB can acquire adequate sample for NGS and identify tumor-specific mutations in patients with pancreatic malignancies. Strict pre-analysis screening criteria may negatively impact the sample adequacy and the success rate for NGS.
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Affiliation(s)
| | | | | | | | | | - Chunhua Zhou
- Department of Gastroenterology, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China
| | - Duowu Zou
- Department of Gastroenterology, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China
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Seyfedinova SS, Freylikhman OA, Sokolnikova PS, Samochernykh KA, Kostareva AA, Kalinina OV, Solonitsyn EG. Fine-needle aspiration technique under endoscopic ultrasound guidance: A technical approach for RNA profiling of pancreatic neoplasms. World J Gastrointest Oncol 2024; 16:2663-2672. [PMID: 38994174 PMCID: PMC11236257 DOI: 10.4251/wjgo.v16.i6.2663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/18/2024] [Accepted: 04/07/2024] [Indexed: 06/14/2024] Open
Abstract
BACKGROUND Early diagnosis of pancreatic ductal adenocarcinoma (PDAC) has been a longstanding challenge. The prognosis of patients with PDAC depends on the stage at diagnosis. It is necessary to identify biomarkers for the detection and differentiation of pancreatic tumors and optimize PDAC sample preparation procedures for DNA and RNA analysis. Most molecular studies are done using paraffin-embedded blocks; however, the integrity of DNA and RNA is often compromised in this format. Moreover, RNA isolated from human pancreatic tissue samples is generally of low quality, in part, because of the high concentration of endogenous pancreatic RNAse activity present. AIM To assess the potential of endoscopic ultrasound-guided fine-needle aspiration (EUS-FNA) to obtain specimens from pancreatic neoplasms for subsequent RNA molecular profiling, including next-generation sequencing (NGS). METHODS Thirty-four EUS-FNA samples were included in this study: PDAC (n = 15), chronic pancreatitis (n = 5), pancreatic cysts (n = 14), mucinous cysts (mucinous cystic neoplasia/intraductal papillary mucinous neoplasia) n = 7, serous cystic neoplasms n = 5, and pseudocysts n = 2. Cyst material consisted of cyst fluid and cyst wall samples obtained by through-the-needle biopsy (TTNB). Samples were stored at -80 °C until analysis. RNA purity (A260/230, A260/280 ratios), concentration, and integrity (RIN) were assessed. Real-time polymerase chain reaction was conducted on all samples, and small RNA libraries were prepared from solid mass samples. RESULTS RNA was successfully extracted from 29/34 (85%) EUS-FNA samples: 100% pancreatic adenocarcinoma samples, 100% chronic pancreatitis samples, 70% pancreatic fluid cyst samples, and 50% TTNB samples. The relative expression of GAPDH and HPRT were obtained for all successfully extracted RNA samples (n = 29) including low-quality RNA specimens. Low concentration and nonoptimal RIN values (no less than 3) of RNA extracted from EUS-FNA samples did not prevent NGS library preparation. The suitability of cyst fluid samples for RNA profiling varied. The quality of RNA extracted from mucinous cyst fluid had a median RIN of 7.7 (5.0-8.2), which was compatible with that from solid neoplasms [6.2 (0-7.8)], whereas the quality of the RNA extracted from all fluids of serous cystic neoplasms and TTNB samples had a RIN of 0. CONCLUSION The results demonstrate the high potential of EUS-FNA material for RNA profiling of various pancreatic lesions, including low-quality RNA specimens.
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Affiliation(s)
| | | | - Polina Sergeevna Sokolnikova
- Research Laboratory of Molecular and Cellular Modeling and Gene Therapy, Almazov Medical Research Centre, Saint-Petersburg 197341, Russia
| | - Konstantin Aleksandrovich Samochernykh
- Head of Russian Neurosurgical Institute Named after Prof. A. L. Polenova, Russian Neurosurgical Institute Named after Prof. A. L. Polenova, Saint-Petersburg 191014, Russia
| | - Anna Aleksandrovna Kostareva
- Head of Institute of Molecular Biology and Genetics, Almazov National Medical Research Centre, Saint-Petersburg 197341, Russia
| | - Olga Viktorovna Kalinina
- Research Laboratory of Autoimmune and Autoinflammatory Diseases, Almazov National Medical Research Centre, Saint-Petersburg 197341, Russia
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4
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Seyfedinova SS, Freylikhman OA, Sokolnikova PS, Samochernykh KA, Kostareva AA, Kalinina OV, Solonitsyn EG. Fine-needle aspiration technique under endoscopic ultrasound guidance: A technical approach for RNA profiling of pancreatic neoplasms. World J Gastrointest Oncol 2024; 16:2651-2660. [DOI: 10.4251/wjgo.v16.i6.2651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/18/2024] [Accepted: 04/07/2024] [Indexed: 06/13/2024] Open
Abstract
BACKGROUND Early diagnosis of pancreatic ductal adenocarcinoma (PDAC) has been a longstanding challenge. The prognosis of patients with PDAC depends on the stage at diagnosis. It is necessary to identify biomarkers for the detection and differentiation of pancreatic tumors and optimize PDAC sample preparation procedures for DNA and RNA analysis. Most molecular studies are done using paraffin-embedded blocks; however, the integrity of DNA and RNA is often compromised in this format. Moreover, RNA isolated from human pancreatic tissue samples is generally of low quality, in part, because of the high concentration of endogenous pancreatic RNAse activity present.
AIM To assess the potential of endoscopic ultrasound-guided fine-needle aspiration (EUS-FNA) to obtain specimens from pancreatic neoplasms for subsequent RNA molecular profiling, including next-generation sequencing (NGS).
METHODS Thirty-four EUS-FNA samples were included in this study: PDAC (n = 15), chronic pancreatitis (n = 5), pancreatic cysts (n = 14), mucinous cysts (mucinous cystic neoplasia/intraductal papillary mucinous neoplasia) n = 7, serous cystic neoplasms n = 5, and pseudocysts n = 2. Cyst material consisted of cyst fluid and cyst wall samples obtained by through-the-needle biopsy (TTNB). Samples were stored at -80 °C until analysis. RNA purity (A260/230, A260/280 ratios), concentration, and integrity (RIN) were assessed. Real-time polymerase chain reaction was conducted on all samples, and small RNA libraries were prepared from solid mass samples.
RESULTS RNA was successfully extracted from 29/34 (85%) EUS-FNA samples: 100% pancreatic adenocarcinoma samples, 100% chronic pancreatitis samples, 70% pancreatic fluid cyst samples, and 50% TTNB samples. The relative expression of GAPDH and HPRT were obtained for all successfully extracted RNA samples (n = 29) including low-quality RNA specimens. Low concentration and nonoptimal RIN values (no less than 3) of RNA extracted from EUS-FNA samples did not prevent NGS library preparation. The suitability of cyst fluid samples for RNA profiling varied. The quality of RNA extracted from mucinous cyst fluid had a median RIN of 7.7 (5.0-8.2), which was compatible with that from solid neoplasms [6.2 (0-7.8)], whereas the quality of the RNA extracted from all fluids of serous cystic neoplasms and TTNB samples had a RIN of 0.
CONCLUSION The results demonstrate the high potential of EUS-FNA material for RNA profiling of various pancreatic lesions, including low-quality RNA specimens.
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Affiliation(s)
| | | | - Polina Sergeevna Sokolnikova
- Research Laboratory of Molecular and Cellular Modeling and Gene Therapy, Almazov Medical Research Centre, Saint-Petersburg 197341, Russia
| | - Konstantin Aleksandrovich Samochernykh
- Head of Russian Neurosurgical Institute Named after Prof. A. L. Polenova, Russian Neurosurgical Institute Named after Prof. A. L. Polenova, Saint-Petersburg 191014, Russia
| | - Anna Aleksandrovna Kostareva
- Head of Institute of Molecular Biology and Genetics, Almazov National Medical Research Centre, Saint-Petersburg 197341, Russia
| | - Olga Viktorovna Kalinina
- Research Laboratory of Autoimmune and Autoinflammatory Diseases, Almazov National Medical Research Centre, Saint-Petersburg 197341, Russia
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Buchberg J, de Stricker K, Pfeiffer P, Mortensen MB, Detlefsen S. Mutational profiling of 103 unresectable pancreatic ductal adenocarcinomas using EUS-guided fine-needle biopsy. Endosc Ultrasound 2024; 13:154-164. [PMID: 39318643 PMCID: PMC11419524 DOI: 10.1097/eus.0000000000000072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 05/27/2024] [Indexed: 09/26/2024] Open
Abstract
Background and Objective Pancreatic ductal adenocarcinoma (PDAC) is among the most lethal cancers, with a 5-year survival rate of around 9%. Only 20% are candidates for surgery. Most unresectable patients undergo EUS-guided fine-needle biopsy (EUS-FNB) for diagnosis. Identification of targetable mutations using next-generation sequencing (NGS) is increasingly requested. Data on feasibility of EUS-FNB for NGS and knowledge regarding mutational profile of unresectable PDAC are scarce. We evaluated the "technical yield" of EUS-FNB for NGS in unresectable PDAC: relative fraction of diagnostic EUS-FNBs meeting technical criteria. We also investigated the "molecular yield": relative fraction of EUS-FNBs included in NGS containing sufficient DNA for detection of at least one mutation. Furthermore, we determined the relative frequency of cancer-associated mutations in unresectable PDAC. Patients and Methods Formalin-fixed and paraffin-embedded EUS-FNBs diagnostic of unresectable PDAC and fulfilling these criteria were included (n = 105): minimum 3-mm2 tissue, minimum of 2-mm2 tumor area, and minimum 20% relative tumor area. NGS was performed using Ion GeneStudio S5 Prime System and Oncomine™ Comprehensive Assay v.3 including 161 cancer-related genes. Results Technical yield was 48% (105/219) and molecular yield was 98% (103/105). Most frequently mutated genes were KRAS (89.3%) and TP53 (69.9%), followed by CDKN2A (24.3%), ARID1A (9.7%), SMAD4 (7.8%), TSC2 (7.8%), and CCND3 (6.8%). Conclusion EUS-FNB for NGS of unresectable PDAC is feasible. Our technical criteria for NGS, using leftovers in formalin-fixed and paraffin-embedded blocks after routine pathology diagnosis, were met by around half of EUS-FNBs. Almost all EUS-FNBs fulfilling the technical criteria yielded a successful NGS analysis.
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Affiliation(s)
- Julie Buchberg
- Department of Pathology, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | - Karin de Stricker
- Department of Pathology, Odense University Hospital, Odense, Denmark
| | - Per Pfeiffer
- Department of Clinical Research, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
- Department of Oncology, Odense University Hospital, Odense, Denmark
- Odense Pancreas Center (OPAC), Odense University Hospital, Odense, Denmark
| | - Michael Bau Mortensen
- Department of Clinical Research, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
- Odense Pancreas Center (OPAC), Odense University Hospital, Odense, Denmark
- Department of Surgery, Upper GI and HPB Section, Odense University Hospital, Odense, Denmark
| | - Sönke Detlefsen
- Department of Pathology, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
- Odense Pancreas Center (OPAC), Odense University Hospital, Odense, Denmark
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6
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Lisotti A, Cominardi A, Conti Bellocchi MC, Crinò SF, Larghi A, Facciorusso A, Arcidiacono PG, De Angelis C, Di Matteo FM, Fabbri C, Bertani H, Togliani T, Rizzatti G, Brancaccio M, Grillo A, Fantin A, Pezzoli A, D'Errico F, Amato A, Antonini F, Montale A, Pisani A, Forti E, Manno M, Carrara S, Petrone MC, Binda C, Zagari RM, Fusaroli P. Repeated endoscopic ultrasound-guided fine-needle biopsy of solid pancreatic lesions after previous nondiagnostic or inconclusive sampling. Dig Endosc 2024; 36:615-624. [PMID: 37712906 DOI: 10.1111/den.14686] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 09/12/2023] [Indexed: 09/16/2023]
Abstract
OBJECTIVES Repeated endoscopic ultrasound (EUS)-guided tissue acquisition represents the standard practice for solid pancreatic lesions after previous nondiagnostic or inconclusive results. Since data are lacking, we aimed to evaluate the diagnostic performance of repeated EUS fine-needle biopsy (rEUS-FNB) in this setting. The primary outcome was diagnostic accuracy; sample adequacy, sensitivity, specificity, and safety were secondary outcomes. METHODS Consecutive patients undergoing rEUS-FNB for solid pancreatic lesions at 23 Italian centers from 2019 to 2021 were retrieved. Pathology on the surgical specimen, malignant histology together with ≥6-month follow-up, and benign pathology together with ≥12-month follow-up were adopted as gold standards. RESULTS Among 462 patients, 56.5% were male, with a median age of 68 (59-75) years, malignancy prevalence 77.0%. Tumor size was 26 (20-35) mm. Second-generation FNB needles were used in 89.6% cases. Diagnostic accuracy, sensitivity, and specificity of rEUS-FNB were 89.2%, 91.4%, and 81.7%, respectively (19 false-negative and 12 false-positive results). On multivariate analysis, rEUS-FNB performed at high-volume centers (odds ratio [OR] 2.12; 95% confidence interval [CI] 1.10-3.17; P = 0.03) and tumor size (OR 1.03; 95% CI 1.00-1.06; P = 0.05) were independently related to diagnostic accuracy. Sample adequacy was 94.2%. Use of second-generation FNB needles (OR 5.42; 95% CI 2.30-12.77; P < 0.001) and tumor size >23 mm (OR 3.04; 95% CI 1.31-7.06; P = 0.009) were independently related to sample adequacy. CONCLUSION Repeated EUS-FNB allowed optimal diagnostic performance after nondiagnostic or inconclusive results. Patients' referral to high-volume centers improved diagnostic accuracy. The use of second-generation FNB needles significantly improved sample adequacy over standard EUS-FNB needles.
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Affiliation(s)
- Andrea Lisotti
- Gastroenterology Unit, Hospital of Imola, University of Bologna, Imola, Italy
| | - Anna Cominardi
- Gastroenterology Unit, Hospital of Imola, University of Bologna, Imola, Italy
- Gastroenterology Unit, Hospital of Piacenza, Piacenza, Italy
| | | | | | - Alberto Larghi
- Digestive Endoscopy Unit, Fondazione Policlinico Universitario A. Gemelli, IRCCS, Rome, Italy
| | - Antonio Facciorusso
- Gastroenterology Unit, Department of Surgical and Medical Sciences, University of Foggia, Foggia, Italy
| | | | - Claudio De Angelis
- Department of General and Specialist Medicine, Gastroenterologia-U, Città della Salute e della Scienza di Torino, Turin, Italy
| | | | - Carlo Fabbri
- Gastroenterology and Digestive Endoscopy Unit, Forlì-Cesena Hospitals, AUSL Romagna, Forli, Italy
| | - Helga Bertani
- Gastroenterology and Digestive Endoscopy Unit, Azienda Ospedaliero Universitaria di Modena, Modena, Italy
| | - Thomas Togliani
- Gastroenterology and Digestive Endoscopy Unit, University Hospital Borgo Trento, Verona, Italy
| | - Gianenrico Rizzatti
- Digestive Endoscopy Unit, Fondazione Policlinico Universitario A. Gemelli, IRCCS, Rome, Italy
| | - Mario Brancaccio
- Unit of Gastroenterology, Santa Maria delle Croci Hospital, AUSL Romagna, Ravenna, Italy
| | - Antonino Grillo
- Gastroenterology and Digestive Endoscopy Unit, Rimini "Infermi" Hospital, AUSL Romagna, Rimini, Italy
| | - Alberto Fantin
- Gastroenterology Unit, Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
| | - Alessandro Pezzoli
- Department of Gastroenterology and GI Endoscopy, University Hospital, Ferrara, Italy
| | - Francesca D'Errico
- Gastroenterology and Endoscopy Unit, Ente Ecclesiastico F. Miulli, Acquaviva delle Fonti, Bari, Italy
| | - Arnaldo Amato
- Division of Digestive Endoscopy and Gastroenterology, Valduce Hospital, Como, Italy
| | - Filippo Antonini
- Gastroenterology and Interventional Endoscopy Unit, "C. e G. Mazzoni" Hospital, Ascoli Piceno, Italy
| | - Amedeo Montale
- Division of Gastroenterology, E.O. Galliera Hospital, Genoa, Italy
| | - Antonio Pisani
- National Institute of Gastroenterology IRCCS Saverio de Bellis, Castellana Grotte, Bari, Italy
| | - Edoardo Forti
- Digestive Endoscopy Unit, ASST Niguarda, Milan, Italy
| | - Mauro Manno
- Gastroenterology and Digestive Endoscopy Unit, Azienda USL Modena, Modena, Italy
| | - Silvia Carrara
- Endoscopic Unit, Department of Gastroenterology, IRCCS Humanitas Research Hospital, Milan, Italy
| | - Maria Chiara Petrone
- IRCCS San Raffaele Scientific Institute, Vita-Salute San Raffaele University, Milan, Italy
| | - Cecilia Binda
- Gastroenterology and Digestive Endoscopy Unit, Forlì-Cesena Hospitals, AUSL Romagna, Forli, Italy
| | - Rocco Maurizio Zagari
- SSD "Patologie organiche esofago-gastriche", IRCCS Azienda Ospedaliero-Universitaria di Bologna, S. Orsola Hospital, Bologna, Italy
- Department of Medical and Surgical Sciences - DIMEC, University of Bologna, Bologna, Italy
| | - Pietro Fusaroli
- Gastroenterology Unit, Hospital of Imola, University of Bologna, Imola, Italy
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Souza da Silva R, Pina MJ, Cirnes L, Gouveia L, Albergaria A, Schmitt F. Comprehensive Genomic Studies on the Cell Blocks of Pancreatic Cancer. Diagnostics (Basel) 2024; 14:906. [PMID: 38732320 PMCID: PMC11083533 DOI: 10.3390/diagnostics14090906] [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: 03/21/2024] [Revised: 04/15/2024] [Accepted: 04/20/2024] [Indexed: 05/13/2024] Open
Abstract
Pancreatic cancer is one of the deadliest malignancies, characterized by late-stage diagnosis and limited treatment options. Comprehensive genomic profiling plays an important role in understanding the molecular mechanisms underlying the disease and identifying potential therapeutic targets. Cell blocks (CBs), derived from EUS-FNA, have become valuable resources for diagnosis and genomic analysis. We examine the molecular profile of pancreatic ductal adenocarcinoma (PDAC) using specimens obtained from CB EUS-FNA, across a large gene panel, within the framework of next-generation sequencing (NGS). Our findings revealed that over half (55%) of PDAC CB cases provided adequate nucleic acid for next-generation sequencing, with tumor cell percentages averaging above 30%. Despite challenges such as low DNA quantification and degraded DNA, sequencing reads showed satisfactory quality control statistics, demonstrating the detection of genomic alterations. Most cases (84.6%) harbored at least one gene variant, including clinically significant gene mutation variants such as KRAS, TP53, and CDKN2A. Even at minimal concentrations, as long as the extracted DNA is of high quality, performing comprehensive molecular profiling on PDAC samples from cell blocks has remained feasible. This strategy has yielded valuable information about the diagnosis, genetic landscape, and potential therapeutic targets, aligning closely with a precision cytopathology approach.
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Affiliation(s)
- Ricella Souza da Silva
- IPATIMUP Diagnostics, IPATIMUP—Institute of Molecular Pathology and Immunology of Porto University, 4200-135 Porto, Portugal; (R.S.d.S.)
| | - Maria João Pina
- IPATIMUP Diagnostics, IPATIMUP—Institute of Molecular Pathology and Immunology of Porto University, 4200-135 Porto, Portugal; (R.S.d.S.)
| | - Luís Cirnes
- IPATIMUP Diagnostics, IPATIMUP—Institute of Molecular Pathology and Immunology of Porto University, 4200-135 Porto, Portugal; (R.S.d.S.)
| | - Luís Gouveia
- Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
| | - André Albergaria
- IPATIMUP Diagnostics, IPATIMUP—Institute of Molecular Pathology and Immunology of Porto University, 4200-135 Porto, Portugal; (R.S.d.S.)
- Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
- I3S—Instituto de Investigação e Inovação em Saúde, University of Porto, 4200-135 Porto, Portugal
| | - Fernando Schmitt
- IPATIMUP Diagnostics, IPATIMUP—Institute of Molecular Pathology and Immunology of Porto University, 4200-135 Porto, Portugal; (R.S.d.S.)
- Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
- CINTESIS@RISE (Health Research Network), Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
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8
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Feng H, Li H, Chen M, Zhang T, Zhou Y, Xu Y, Zhang W, Zhang T. Editorial: New insights into molecular mechanisms and targeted therapy for gastrointestinal tumors. Front Cell Dev Biol 2023; 11:1289530. [PMID: 37842088 PMCID: PMC10569337 DOI: 10.3389/fcell.2023.1289530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 09/20/2023] [Indexed: 10/17/2023] Open
Affiliation(s)
- Haoran Feng
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Haosheng Li
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mengdi Chen
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tao Zhang
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - YiMing Zhou
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Ye Xu
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Wei Zhang
- Department of Colorectal Surgery, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Tao Zhang
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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9
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Pecciarini L, Brunetto E, Grassini G, De Pascali V, Ogliari FR, Talarico A, Marra G, Magliacane G, Redegalli M, Arrigoni G, Lazzari C, Gregorc V, Bulotta A, Doglioni C, Cangi MG. Gene Fusion Detection in NSCLC Routine Clinical Practice: Targeted-NGS or FISH? Cells 2023; 12:cells12081135. [PMID: 37190044 DOI: 10.3390/cells12081135] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/05/2023] [Accepted: 04/10/2023] [Indexed: 05/17/2023] Open
Abstract
The ability to identify the broadest range of targetable gene fusions is crucial to facilitate personalized therapy selection for advanced lung adenocarcinoma (LuADs) patients harboring targetable receptor tyrosine kinase (RTK) genomic alterations. In order to evaluate the most effective testing approach for LuAD targetable gene fusion detection, we analyzed 210 NSCLC selected clinical samples, comparing in situ (Fluorescence In Situ Hybridization, FISH, and ImmunoHistoChemistry, IHC) and molecular (targeted RNA Next-Generation Sequencing, NGS, and RealTime-PCR, RT-PCR) approaches. The overall concordance among these methods was high (>90%), and targeted RNA NGS was confirmed to be the most efficient technique for gene fusion identification in clinical practice, allowing the simultaneous analysis of a large set of genomic rearrangements at the RNA level. However, we observed that FISH was useful to detect targetable fusions in those samples with inadequate tissue material for molecular testing as well as in those few cases whose fusions were not identified by the RNA NGS panel. We conclude that the targeted RNA NGS analysis of LuADs allows accurate RTK fusion detection; nevertheless, standard methods such as FISH should not be dismissed, as they can crucially contribute to the completion of the molecular characterization of LuADs and, most importantly, the identification of patients as candidates for targeted therapies.
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Affiliation(s)
- Lorenza Pecciarini
- Pathology Unit, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Emanuela Brunetto
- Pathology Unit, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Greta Grassini
- Pathology Unit, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Valeria De Pascali
- Pathology Unit, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | | | - Anna Talarico
- Pathology Unit, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Giovanna Marra
- Pathology Unit, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Gilda Magliacane
- Pathology Unit, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Miriam Redegalli
- Pathology Unit, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Gianluigi Arrigoni
- Pathology Unit, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Chiara Lazzari
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Turin, Italy
| | - Vanesa Gregorc
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Turin, Italy
| | - Alessandra Bulotta
- Department of Oncology, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Claudio Doglioni
- Pathology Unit, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Maria Giulia Cangi
- Pathology Unit, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
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10
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Locally Performed HRD Testing for Ovarian Cancer? Yes, We Can! Cancers (Basel) 2022; 15:cancers15010043. [PMID: 36612041 PMCID: PMC9817883 DOI: 10.3390/cancers15010043] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/13/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022] Open
Abstract
Assessment of HRD status is now essential for ovarian cancer patient management. A relevant percentage of high-grade serous carcinoma (HGSC) is characterized by HRD, which is caused by genetic alterations in the homologous recombination repair (HRR) pathway. Recent trials have shown that not only patients with pathogenic/likely pathogenic BRCA variants, but also BRCAwt/HRD patients, are sensitive to PARPis and platinum therapy. The most common HRD test is Myriad MyChoice CDx, but there is a pressing need to offer an alternative to outsourcing analysis, which typically requires high costs and lengthy turnaround times. In order to set up a complete in-house workflow for HRD testing, we analyzed a small cohort of HGSC patients using the CE-IVD AmoyDx HRD Focus Panel and compared our results with Myriad's. In addition, to further deepen the mechanisms behind HRD, we analyzed the study cohort by using both a custom NGS panel that analyzed 21 HRR-related genes and FISH analysis to determine the copy numbers of PTEN and EMSY. We found complete concordance in HRD status detected by the Amoy and the Myriad assays, supporting the feasibility of internal HRD testing.
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