Research

15 pages, 3491 KiB

Open AccessArticle

A Critical Issue in Lung Cancer Cytology and Small Biopsies: DNA and RNA Extraction from Archival Stained Slides for Biomarker Detection through Real Time PCR and NGS—The Experience in Pathological Anatomy Unit

by Giuseppa Zannini, Ilaria Tedesco, Immacolata Cozzolino, Marco Montella, Eduardo Clery, Carminia Maria Della Corte, Floriana Morgillo, Marina Accardo, Renato Franco and Federica Zito Marino

Diagnostics 2023, 13(9), 1637; https://doi.org/10.3390/diagnostics13091637 - 05 May 2023

Viewed by 1224

Abstract

The handling of biomaterials is crucial for precision medicine in advanced-stage lung patients with only cytology or small biopsies available. The main purpose of the study was to evaluate the quantity and quality of nucleic acids extracted from mixed stained slides (MSSs), including [...] Read more.

The handling of biomaterials is crucial for precision medicine in advanced-stage lung patients with only cytology or small biopsies available. The main purpose of the study was to evaluate the quantity and quality of nucleic acids extracted from mixed stained slides (MSSs), including H&E, IHC and FISH, compared to the extraction from unstained slides (USs). A series of 35 lung adenocarcinoma surgical samples was selected to set up the method and the technical approach was validated in a series of 15 small biopsies and 38 cytological samples. DNA extracted from MSSs was adequate in all samples and the Real Time PCR was successful in 30/35 surgical samples (86%), 14/15 small biopsies (93%), and 33/38 cytological samples (87%). NGS using DNA extracted from MSSs was successful in 18/35 surgical samples (51%), 11/15 small biopsies (73%), and 26/38 cytological samples (68%). RNA extracted from MSSs was unsatisfactory in all cases showing an inadequate degree of fragmentation. Our technical approach based on the recovery of stained slides could represent a strategic way forward for DNA-based biomarker testing in lung cancer cases without biomaterials. The RNA extracted from MSSs did not represent a successful approach. Full article

(This article belongs to the Special Issue Tissue-Based Biomarkers of Solid Tumors in the Routine Clinical Setting 2.0)

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20 pages, 16180 KiB

Open AccessArticle

GLUT3/SLC2A3 Is an Endogenous Marker of Hypoxia in Prostate Cancer Cell Lines and Patient-Derived Xenograft Tumors

by John M. Ryniawec, Matthew R. Coope, Emily Loertscher, Vignesh Bageerathan, Diogo de Oliveira Pessoa, Noel A. Warfel, Anne E. Cress, Megha Padi and Gregory C. Rogers

Diagnostics 2022, 12(3), 676; https://doi.org/10.3390/diagnostics12030676 - 10 Mar 2022

Cited by 7 | Viewed by 2873

Abstract

The microenvironment of solid tumors is dynamic and frequently contains pockets of low oxygen levels (hypoxia) surrounded by oxygenated tissue. Indeed, a compromised vasculature is a hallmark of the tumor microenvironment, creating both spatial gradients and temporal variability in oxygen availability. Notably, hypoxia [...] Read more.

The microenvironment of solid tumors is dynamic and frequently contains pockets of low oxygen levels (hypoxia) surrounded by oxygenated tissue. Indeed, a compromised vasculature is a hallmark of the tumor microenvironment, creating both spatial gradients and temporal variability in oxygen availability. Notably, hypoxia associates with increased metastasis and poor survival in patients. Therefore, to aid therapeutic decisions and better understand hypoxia’s role in cancer progression, it is critical to identify endogenous biomarkers of hypoxia to spatially phenotype oncogenic lesions in human tissue, whether precancerous, benign, or malignant. Here, we characterize the glucose transporter GLUT3/SLC2A3 as a biomarker of hypoxic prostate epithelial cells and prostate tumors. Transcriptomic analyses of non-tumorigenic, immortalized prostate epithelial cells revealed a highly significant increase in GLUT3 expression under hypoxia. Additionally, GLUT3 protein increased 2.4-fold in cultured hypoxic prostate cell lines and was upregulated within hypoxic regions of xenograft tumors, including two patient-derived xenografts (PDX). Finally, GLUT3 out-performs other established hypoxia markers; GLUT3 staining in PDX specimens detects 2.6–8.3 times more tumor area compared to a mixture of GLUT1 and CA9 antibodies. Therefore, given the heterogeneous nature of tumors, we propose adding GLUT3 to immunostaining panels when trying to detect hypoxic regions in prostate samples. Full article

(This article belongs to the Special Issue Tissue-Based Biomarkers of Solid Tumors in the Routine Clinical Setting 2.0)

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14 pages, 1860 KiB

Open AccessArticle

Relevance of ARID1A Mutations in Endometrial Carcinomas

by Antonio De Leo, Gloria Ravegnini, Francesco Musiani, Thais Maloberti, Michela Visani, Viviana Sanza, Sabrina Angelini, Anna Myriam Perrone, Pierandrea De Iaco, Angelo Gianluca Corradini, Francesca Rosini, Marco Grillini, Donatella Santini, Claudio Ceccarelli, Claudio Zamagni, Giovanni Tallini and Dario de Biase

Diagnostics 2022, 12(3), 592; https://doi.org/10.3390/diagnostics12030592 - 25 Feb 2022

Cited by 7 | Viewed by 2648

Abstract

Since the Cancer Genome Atlas (TCGA) project identified four distinct groups based on molecular alterations, mutation analyses have been integrated into the characterization of endometrial carcinomas (ECs). ARID1A seems to be the subunit more involved in the loss of function of the SWI/SNF [...] Read more.

Since the Cancer Genome Atlas (TCGA) project identified four distinct groups based on molecular alterations, mutation analyses have been integrated into the characterization of endometrial carcinomas (ECs). ARID1A seems to be the subunit more involved in the loss of function of the SWI/SNF complex in ECs. The aim of this study is to define the relevance of ARID1A alterations in a cohort of EC, studying the possible associations between DNA mutation (genomic level), RNA expression (transcriptomic level), and protein expression (proteomic level). A total of 50 endometrial carcinomas were characterized for ARID1A mutations (using targeted DNA next-generation sequencing—NGS), ARID1A gene expression (using RNAseq and qRT-PCR), and ARID1A protein expression (using immunohistochemistry—IHC). Moreover, we have investigated if ARID1A mutations may alter the protein structure, using the Protein Data Bank sequence. We found a good correlation between ARID1A mutations and protein immunostaining, even if we did not find statistically significant differences in the ARID1A expression levels. In conclusion, our data demonstrated that the molecular characterization of ARID1A should be associated with IHC analysis, mainly in those cases harboring “novel” ARID1A mutations or in those alterations with “uncertain” pathogenic significance. Full article

(This article belongs to the Special Issue Tissue-Based Biomarkers of Solid Tumors in the Routine Clinical Setting 2.0)

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11 pages, 555 KiB

Open AccessArticle

Biomarkers Changes after Neoadjuvant Chemotherapy in Breast Cancer: A Seven-Year Single Institution Experience

by Saverio Coiro, Elisa Gasparini, Giuseppe Falco, Giacomo Santandrea, Moira Foroni, Giulia Besutti, Valentina Iotti, Roberto Di Cicilia, Monica Foroni, Simone Mele, Guglielmo Ferrari, Giancarlo Bisagni and Moira Ragazzi

Diagnostics 2021, 11(12), 2249; https://doi.org/10.3390/diagnostics11122249 - 30 Nov 2021

Cited by 7 | Viewed by 2138

Abstract

The adoption of neoadjuvant chemotherapy (NACT) for breast cancer (BC) is increasing. The need to repeat the biomarkers on a residual tumor after NACT is still a matter of debate. We verified estrogen receptors (ER), progesterone receptors (PR), Ki67 and human epidermal growth [...] Read more.

The adoption of neoadjuvant chemotherapy (NACT) for breast cancer (BC) is increasing. The need to repeat the biomarkers on a residual tumor after NACT is still a matter of debate. We verified estrogen receptors (ER), progesterone receptors (PR), Ki67 and human epidermal growth factor receptor 2 (HER2) status changes impact in a retrospective monocentric series of 265 BCs undergoing NACT. All biomarkers changed with an overall tendency toward a reduced expression. Changes in PR and Ki67 were statistically significant (p = 0.001). Ki67 changed in 114/265 (43.0%) cases, PR in 44/265 (16.6%), ER in 31/265 (11.7%) and HER2 in 26/265 (9.8%). Overall, intrinsic subtype changed in 72/265 (27.2%) cases after NACT, and 10/265 (3.8%) cases switched to a different adjuvant therapy accordingly. Luminal subtypes changed most frequently (66/175; 31.7%) but with less impact on therapy (5/175; 2.8%). Only 3 of 58 triple-negative BCs (5.2%) changed their intrinsic subtype, but all of them switched treatment. No correlation was found between intrinsic subtype changes and clinicopathological features. To conclude, biomarkers changes with prognostic implications occurred in all BC intrinsic subtypes, albeit they impacted therapy mostly in HER2 negative and/or hormone receptors negative BCs. Biomarkers retesting after NACT is important to improve both tailored adjuvant therapies and prognostication of patients. Full article

(This article belongs to the Special Issue Tissue-Based Biomarkers of Solid Tumors in the Routine Clinical Setting 2.0)

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Review

Jump to: Research, Other

14 pages, 556 KiB

Open AccessReview

Diagnostic Predictors of Immunotherapy Response in Head and Neck Squamous Cell Carcinoma

by Piero Giuseppe Meliante, Federica Zoccali, Marco de Vincentiis, Massimo Ralli, Carla Petrella, Marco Fiore, Antonio Minni and Christian Barbato

Diagnostics 2023, 13(5), 862; https://doi.org/10.3390/diagnostics13050862 - 23 Feb 2023

Cited by 5 | Viewed by 2088

Abstract

Programmed cell death ligand-1 (PD-L1) binds PD-1 on CD⁸⁺ lymphocytes, inhibiting their cytotoxic action. Its aberrant expression by head and neck squamous cell carcinoma (HNSCC) cells leads to immune escape. Pembrolizumab and nivolumab, two humanized monoclonal antibodies against PD-1, have been approved [...] Read more.

Programmed cell death ligand-1 (PD-L1) binds PD-1 on CD⁸⁺ lymphocytes, inhibiting their cytotoxic action. Its aberrant expression by head and neck squamous cell carcinoma (HNSCC) cells leads to immune escape. Pembrolizumab and nivolumab, two humanized monoclonal antibodies against PD-1, have been approved in HNSCC treatment, but ~60% of patients with recurrent or metastatic HNSCC fail to respond to immunotherapy and only 20 to 30% of treated patients have long-term benefits. The purpose of this review is to analyze all the fragmentary evidence present in the literature to identify what future diagnostic markers could be useful for predicting, together with PD-L1 CPS, the response to immunotherapy and its durability. We searched PubMed, Embase, and the Cochrane Register of Controlled Trials and we summarize the evidence collected in this review. We confirmed that PD-L1 CPS is a predictor of response to immunotherapy, but it should be measured across multiple biopsies and repeatedly over time. PD-L2, IFN-γ, EGFR, VEGF, TGF–β, TMB, blood TMB, CD73, TILs, alternative splicing, tumor microenvironment, and some macroscopic and radiological features are promising predictors worthy of further studies. Studies comparing predictors appear to give greater potency to TMB and CXCR9. Full article

(This article belongs to the Special Issue Tissue-Based Biomarkers of Solid Tumors in the Routine Clinical Setting 2.0)

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Other

Jump to: Research, Review

7 pages, 916 KiB

Open AccessInteresting Images

Giant Paratesticular Liposarcoma: Molecular Characterization and Management Principles with a Review of the Literature

by Giuliana Pavone, Chiara Romano, Federica Martorana, Lucia Motta, Lucia Salvatorelli, Antonio Maria Zanghì, Gaetano Magro and Paolo Vigneri

Diagnostics 2022, 12(9), 2160; https://doi.org/10.3390/diagnostics12092160 - 06 Sep 2022

Cited by 3 | Viewed by 1667

Abstract

Paratesticular liposarcomas are extremely rare malignant tumors originating from fat tissues, with an often-challenging diagnosis. We present here the case of a 76-year-old man with a giant paratesticular liposarcoma, initially misdiagnosed as a scrotal hernia. After two years, the progressively enlarging mass underwent [...] Read more.

Paratesticular liposarcomas are extremely rare malignant tumors originating from fat tissues, with an often-challenging diagnosis. We present here the case of a 76-year-old man with a giant paratesticular liposarcoma, initially misdiagnosed as a scrotal hernia. After two years, the progressively enlarging mass underwent surgical resection, and a diagnosis of well-differentiated liposarcoma (lipoma-like subtype) was made. Post-operative treatments were not indicated, and the patient remains relapse free. Next generation sequencing performed on the neoplastic tissue showed co-amplification of MDM2 and CDK4. These alterations are molecular hallmarks of well-differentiated liposarcomas and corroborate the histological diagnosis. Clinical and molecular features of the presented case are in line with the majority of previously published experiences. In conclusion, the presence of a liposarcoma should be taken into account during the diagnostic workup of scrotal masses, in order to minimize the rate of misdiagnosis and improper management. Molecular analysis may support histological characterization of these rare entities and potentially disclose novel therapeutic targets. Full article

(This article belongs to the Special Issue Tissue-Based Biomarkers of Solid Tumors in the Routine Clinical Setting 2.0)

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11 pages, 2992 KiB

Open AccessCase Report

Malignant Clinical Course of “Proliferative” Ovarian Struma: Diagnostic Challenges and Treatment Pitfalls

by Aleksandra Asaturova, Alina Magnaeva, Anna Tregubova, Vlada Kometova, Yevgeniy Karamurzin, Sergey Martynov, Yuliya Lipatenkova, Leila Adamyan and Andrea Palicelli

Diagnostics 2022, 12(6), 1411; https://doi.org/10.3390/diagnostics12061411 - 07 Jun 2022

Cited by 4 | Viewed by 2081

Abstract

Struma ovarii (SO) is a monodermal teratoma predominantly composed of thyroid tissue (TT) showing benign, “proliferative”, or malignant histology. By imaging, a 38-year-old patient with lower backache revealed a 6.2-cm vertebral lesion (L5). Core biopsy showed well-differentiated TT without features of papillary carcinoma. [...] Read more.

Struma ovarii (SO) is a monodermal teratoma predominantly composed of thyroid tissue (TT) showing benign, “proliferative”, or malignant histology. By imaging, a 38-year-old patient with lower backache revealed a 6.2-cm vertebral lesion (L5). Core biopsy showed well-differentiated TT without features of papillary carcinoma. A 3.5-cm left ovarian mature teratoma (lacking TT) and peritoneal nodules (showing well-differentiated TT) were also identified and surgically removed. Thyroid ultrasound and cytological examination resulted negative. Four years before, left ovarian cystectomy was performed for a histologically “proliferative” SO. According to the malignant clinical course and WHO classification, this case was overall reassessed as a recurring well-differentiated follicular carcinoma arising in SO (WD-FC-SO), despite lacking malignant histological features in any specimens. Immunophenotype: TTF-1+/PAX-8+/thyroglobulin+/CK7+/chromogranin-/synaptophysin-/inhibin-/calretinin-/HNF1B-; Ki-67 index < 5%. Polymerase chain reaction analysis resulted negative for BRAF^V^600E mutation. The patient refused further treatments, without recurrence after 17 months. The clinical behavior of SO may be unpredictable. Histologically benign or proliferative strumas extraordinarily metastasize, while SO with malignant features may not recur. The exceptional evidence of peritoneal implants of well-differentiated TT (peritoneal strumosis) in patients with histologically benign SO represents a metastasis of WD-FC-SO (like in our case). A multidisciplinary approach including clinical, laboratory, radiologic, and histopathological data is required. Full article

(This article belongs to the Special Issue Tissue-Based Biomarkers of Solid Tumors in the Routine Clinical Setting 2.0)

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12 pages, 6444 KiB

Open AccessInteresting Images

S-100 Immunohistochemical Positivity in Rhabdomyoma: An Underestimated Potential Diagnostic Pitfall in Routine Practice

by Andrea Palicelli, Antonio Ramponi, Guido Valente, Renzo Boldorini, Annalisa Balbo Mussetto and Magda Zanelli

Diagnostics 2022, 12(4), 892; https://doi.org/10.3390/diagnostics12040892 - 02 Apr 2022

Viewed by 1668

Abstract

A 66-year-old man presented with a 2.8 cm lesion of the left vocal cord. On contrast-enhanced computed tomography scans, the tumor extended to the supraglottis, subglottis, paraglottic space and anterior commissure, causing partial obstruction of the laryngeal lumen. At another hospital, a fragmented [...] Read more.

A 66-year-old man presented with a 2.8 cm lesion of the left vocal cord. On contrast-enhanced computed tomography scans, the tumor extended to the supraglottis, subglottis, paraglottic space and anterior commissure, causing partial obstruction of the laryngeal lumen. At another hospital, a fragmented incisional biopsy was diagnosed as a granular cell tumor, as to the S-100 immunohistochemical positivity. After excision, the tumor revealed to be an adult-type laryngeal rhabdomyoma. The typical cytoplasmic rod-like inclusions and cross striations were more evident in the second specimen. We confirmed the unusual S-100 immunohistochemical positivity (variable intensity, >90% of tumor cells). Muscle markers were not performed on the previous biopsy, resulting positive in our specimen (Desmin: strong, diffuse expression; Smooth Muscle Actin: strong staining in 10% of tumor cells). Melan-A, CD68, GFAP, pan-cytokeratins, CEA, calretinin and neurofilaments resulted negative. To our brief, systematic literature review, S-100 positivity (usually variable, often weak or patchy/focal) was globally found in 19/34 (56%) adult-type rhabdomyomas of the head and neck region. Especially on fragmented biopsy material, the differential diagnoses of laryngeal rhabdomyomas may include granular cell tumors, oncocytic tumors of the salivary glands or of different origin, and paragangliomas. Full article

(This article belongs to the Special Issue Tissue-Based Biomarkers of Solid Tumors in the Routine Clinical Setting 2.0)

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