Face verification and recognition for digital forensics and information security

In this paper, we present an extensive evaluation of face recognition and verification approaches performed by the European COST Action MULTI-modal Imaging of FOREnsic SciEnce Evidence (MULTI-FORESEE). The aim of the study is to evaluate various face recognition and verification methods, ranging from methods based on facial landmarks to state-of-the-art off-the-shelf pre-trained Convolutional Neural Networks (CNN), as well as CNN models directly trained for the task at hand. To fulfill this objective, we carefully designed and implemented a realistic data acquisition process, that corresponds to a typical face verification setup, and collected a challenging dataset to evaluate the real world performance of the aforementioned methods. Apart from verifying the effectiveness of deep learning approaches in a specific scenario, several important limitations are identified and discussed through the paper, providing valuable insight for future research directions in the field.

General information

Publication status: Published
MoE publication type: A4 Article in a conference publication
Organisations: Computing Sciences, Inst. of Info. Sci. and Technol. of the Natl. Res. Cncl. of Italy (ISTI-CNR), University of Milan Bicocca, Department of Informatics, Aristotle University of Thessaloniki, University of Applied Sciences of Southern Switzerland
Contributors: Amato, G., Falchi, F., Gennaro, C., Massoli, F. V., Passalis, N., Tefas, A., Trivilini, A., Vairo, C.
Publication date: 1 Jun 2019

Host publication information

Title of host publication: 7th International Symposium on Digital Forensics and Security, ISDFS 2019
Publisher: IEEE
Editors: Varol, A., Karabatak, M., Varol, C., Teke, S.
ISBN (Electronic): 9781728128276
ASJC Scopus subject areas: Health Informatics, Pathology and Forensic Medicine, Computer Networks and Communications, Computer Science Applications, Safety, Risk, Reliability and Quality
Keywords: Deep learning, Face verification, Forensics, Security, Surveillance

Bibliographical note

EXT="Tefas, Anastasios"

Source: Scopus
Source ID: 85070520041

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Deep Learning in Image Cytometry: A Review

Artificial intelligence, deep convolutional neural networks, and deep learning are all niche terms that are increasingly appearing in scientific presentations as well as in the general media. In this review, we focus on deep learning and how it is applied to microscopy image data of cells and tissue samples. Starting with an analogy to neuroscience, we aim to give the reader an overview of the key concepts of neural networks, and an understanding of how deep learning differs from more classical approaches for extracting information from image data. We aim to increase the understanding of these methods, while highlighting considerations regarding input data requirements, computational resources, challenges, and limitations. We do not provide a full manual for applying these methods to your own data, but rather review previously published articles on deep learning in image cytometry, and guide the readers toward further reading on specific networks and methods, including new methods not yet applied to cytometry data.

General information

Publication status: Published
MoE publication type: A2 Review article in a scientific journal
Organisations: Faculty of Biomedical Sciences and Engineering, Uppsala University, BioImage Informatics Facility of SciLifeLab
Contributors: Gupta, A., Harrison, P. J., Wieslander, H., Pielawski, N., Kartasalo, K., Partel, G., Solorzano, L., Suveer, A., Klemm, A. H., Spjuth, O., Sintorn, I. M., Wählby, C.
Pages: 366-380
Publication date: Apr 2019
Peer-reviewed: Yes
Early online date: 2018

Publication information

Journal: Cytometry Part A
Volume: 95
Issue number: 4
ISSN (Print): 1552-4922
Original language: English
ASJC Scopus subject areas: Pathology and Forensic Medicine, Histology, Cell Biology
Keywords: biomedical image analysis, cell analysis, convolutional neural networks, deep learning, image cytometry, machine learning, microscopy
Electronic versions: 
Source: Scopus
Source ID: 85058853028

Research output: Contribution to journalReview ArticleScientificpeer-review

Extraprostatic extension (pT3a) in prostate biopsy is an under-recognized feature indicating high risk disease

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Materials Science, Tampere University Hospital, Satakunta Central Hospital
Contributors: Tolonen, T. T., Riikonen, J., Tammela, T. L., Koivusalo, L., Haapasalo, H., Kujala, P., Kaipia, A.
Number of pages: 5
Pages: 80-84
Publication date: 1 Aug 2018
Peer-reviewed: Yes

Publication information

Journal: Annals of Diagnostic Pathology
Volume: 35
ISSN (Print): 1092-9134
Ratings: 
  • Scopus rating (2018): CiteScore 1.73 SJR 0.633 SNIP 0.753
Original language: English
ASJC Scopus subject areas: Pathology and Forensic Medicine
Keywords: Extraprostatic extension, Fat infiltration, Prognosis, Prostate biopsy, Prostate cancer, Prostatic needle biopsy, pT3a

Bibliographical note

int=mol,"Koivusalo, Laura"

Source: Scopus
Source ID: 85048078125

Research output: Contribution to journalArticleScientificpeer-review

Feasibility of Prostate PAXgene Fixation for Molecular Research and Diagnostic Surgical Pathology: Comparison of Matched Fresh Frozen, FFPE, and PFPE Tissues

Advances in prostate cancer biology and diagnostics are dependent upon high-fidelity integration of clinical, histomorphologic, and molecular phenotypic findings. In this study, we compared fresh frozen, formalin-fixed paraffin-embedded (FFPE), and PAXgene-fixed paraffin-embedded (PFPE) tissue preparation methods in radical prostatectomy prostate tissue from 36 patients and performed a preliminary test of feasibility of using PFPE tissue in routine prostate surgical pathology diagnostic assessment. In addition to comparing histology, immunohistochemistry, and general measures of DNA and RNA integrity in each fixation method, we performed functional tests of DNA and RNA quality, including targeted Miseq RNA and DNA sequencing, and implemented methods to relate DNA and RNA yield and quality to quantified DNA and RNA picogram nuclear content in each tissue volume studied. Our results suggest that it is feasible to use PFPE tissue for routine robot-assisted laparoscopic prostatectomy surgical pathology diagnostics and immunohistochemistry, with the benefit of significantly improvedDNA and RNA quality and RNA picogram yield per nucleus as compared with FFPE tissue. For fresh frozen, FFPE, and PFPE tissues, respectively, the average Genomic Quality Numbers were 7.9, 3.2, and 6.2, average RNA Quality Numbers were 8.7, 2.6, and 6.3, average DNA picogram yields per nucleus were 0.41, 0.69, and 0.78, and average RNA picogram yields per nucleus were 1.40, 0.94, and 2.24. These findings suggest that where DNA and/or RNA analysis of tissue is required, and when tissue size is small, PFPE may provide important advantages over FFPE. The results also suggest several interesting nuances including potential avenues to improve RNA quality in FFPE tissues and confirm recent suggestions that some DNA sequence artifacts associated with FFPE can be avoided.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Signal Processing, BioMediTech Institute, Tampere University Hospital, Oulu University Hospital, University of Helsinki, Helsinki University Central Hospital
Contributors: Högnäs, G., Kivinummi, K., Kallio, H. M., Hieta, R., Ruusuvuori, P., Koskenalho, A., Kesseli, J., Tammela, T. L., Riikonen, J., Ilvesaro, J., Kares, S., Hirvikoski, P. P., Laurila, M., Mirtti, T., Nykter, M., Kujala, P. M., Visakorpi, T., Tolonen, T., Bova, G. S.
Number of pages: 13
Pages: 103-115
Publication date: 2018
Peer-reviewed: Yes
Early online date: 2017

Publication information

Journal: American Journal of Surgical Pathology
Volume: 42
Issue number: 1
ISSN (Print): 0147-5185
Ratings: 
  • Scopus rating (2018): CiteScore 6.06 SJR 2.794 SNIP 2.384
Original language: English
ASJC Scopus subject areas: Anatomy, Surgery, Pathology and Forensic Medicine
Keywords: DNA quality, DNA yield, histology, immunostaining, PAXgene, prostate cancer, RNA quality, RNA yield, tissue fixation, tissue processing

Bibliographical note

EXT="Kivinummi, Kati"
EXT="Kesseli, Juha"
EXT="Nykter, Matti"

Source: Scopus
Source ID: 85039151675

Research output: Contribution to journalArticleScientificpeer-review

In Vivo Expression of miR-32 Induces Proliferation in Prostate Epithelium

miRNAs are important regulators of gene expression and are often deregulated in cancer. We have previously shown that miR-32 is an androgen receptor–regulated miRNA overexpressed in castration-resistant prostate cancer and that miR-32 can improve prostate cancer cell growth in vitro. To assess the effects of miR-32 in vivo, we developed transgenic mice overexpressing miR-32 in the prostate. The study indicated that transgenic miR-32 expression increases replicative activity in the prostate epithelium. We further observed an aging-associated increase in the incidence of goblet cell metaplasia in the prostate epithelium. Furthermore, aged miR-32 transgenic mice exhibited metaplasia-associated prostatic intraepithelial neoplasia at a low frequency. When crossbred with mice lacking the other allele of tumor-suppressor Pten (miR-32xPten+/− mice), miR-32 expression increased both the incidence and the replicative activity of prostatic intraepithelial neoplasia lesions in the dorsal prostate. The miR-32xPten+/− mice also demonstrated increased goblet cell metaplasia compared with Pten+/− mice. By performing a microarray analysis of mouse prostate tissue to screen downstream targets and effectors of miR-32, we identified RAC2 as a potential, and clinically relevant, target of miR-32. We also demonstrate down-regulation of several interesting, potentially prostate cancer–relevant genes (Spink1, Spink5, and Casp1) by miR-32 in the prostate tissue. The results demonstrate that miR-32 increases proliferation and promotes metaplastic transformation in mouse prostate epithelium, which may promote neoplastic alterations in the prostate.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Signal Processing, Research group: Data-analytics and Optimization, Prostate cancer research center (PCRC), Tampere University Hospital, Turun Yliopisto/Turun Biomateriaalikeskus
Contributors: Latonen, L., Scaravilli, M., Gillen, A., Hartikainen, S., Zhang, F. P., Ruusuvuori, P., Kujala, P., Poutanen, M., Visakorpi, T.
Number of pages: 12
Pages: 2546-2557
Publication date: 1 Nov 2017
Peer-reviewed: Yes

Publication information

Journal: American Journal of Pathology
Volume: 187
Issue number: 11
ISSN (Print): 0002-9440
Ratings: 
  • Scopus rating (2017): CiteScore 3.83 SJR 2.139 SNIP 1.151
Original language: English
ASJC Scopus subject areas: Pathology and Forensic Medicine
Source: Scopus
Source ID: 85032703667

Research output: Contribution to journalArticleScientificpeer-review

Metastasis detection from whole slide images using local features and random forests

Digital pathology has led to a demand for automated detection of regions of interest, such as cancerous tissue, from scanned whole slide images. With accurate methods using image analysis and machine learning, significant speed-up, and savings in costs through increased throughput in histological assessment could be achieved. This article describes a machine learning approach for detection of cancerous tissue from scanned whole slide images. Our method is based on feature engineering and supervised learning with a random forest model. The features extracted from the whole slide images include several local descriptors related to image texture, spatial structure, and distribution of nuclei. The method was evaluated in breast cancer metastasis detection from lymph node samples. Our results show that the method detects metastatic areas with high accuracy (AUC=0.97-0.98 for tumor detection within whole image area, AUC=0.84-0.91 for tumor vs. normal tissue detection) and that the method generalizes well for images from more than one laboratory. Further, the method outputs an interpretable classification model, enabling the linking of individual features to differences between tissue types.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Faculty of Biomedical Sciences and Engineering, Research area: Microsystems, Research group: Computational Systems Biology, Signal Processing, BioMediTech, BioMediTech and Faculty of Medicine and Life SciencesUniversity of TampereTampere
Contributors: Valkonen, M., Kartasalo, K., Liimatainen, K., Nykter, M., Latonen, L., Ruusuvuori, P.
Pages: 555-565
Publication date: 2017
Peer-reviewed: Yes

Publication information

Journal: Cytometry Part A
Volume: 91
Issue number: 6
ISSN (Print): 1552-4922
Ratings: 
  • Scopus rating (2017): CiteScore 2.64 SJR 1.557 SNIP 0.926
Original language: English
ASJC Scopus subject areas: Pathology and Forensic Medicine, Histology, Cell Biology
Keywords: Breast cancer, Computer aided diagnosis, Digital pathology, Machine learning, Metastasis detection, Random forest, Sentinel lymph nodes, Whole slide images

Bibliographical note

INT=tut-bmt,"Valkonen, Mira"

Source: Scopus
Source ID: 85018639694

Research output: Contribution to journalArticleScientificpeer-review

Method for 3D fibre reconstruction on a microrobotic platform

Automated handling of a natural fibrous object requires a method for acquiring the three-dimensional geometry of the object, because its dimensions cannot be known beforehand. This paper presents a method for calculating the three-dimensional reconstruction of a paper fibre on a microrobotic platform that contains two microscope cameras. The method is based on detecting curvature changes in the fibre centreline, and using them as the corresponding points between the different views of the images. We test the developed method with four fibre samples and compare the results with the references measured with an X-ray microtomography device. We rotate the samples through 16 different orientations on the platform and calculate the three-dimensional reconstruction to test the repeatability of the algorithm and its sensitivity to the orientation of the sample. We also test the noise sensitivity of the algorithm, and record the mismatch rate of the correspondences provided. We use the iterative closest point algorithm to align the measured three-dimensional reconstructions with the references. The average point-to-point distances between the reconstructed fibre centrelines and the references are 20–30 μm, and the mismatch rate is low. Given the manipulation tolerance, this shows that the method is well suited to automated fibre grasping. This has also been demonstrated with actual grasping experiments.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Department of Automation Science and Engineering, Research area: Microsystems, Research area: Measurement Technology and Process Control, University of Jyväskylä
Contributors: Hirvonen, J., Myllys, M., Kallio, P.
Number of pages: 14
Pages: 20-33
Publication date: 1 Jul 2016
Peer-reviewed: Yes

Publication information

Journal: Journal of Microscopy: Oxford
Volume: 263
Issue number: 1
ISSN (Print): 0022-2720
Ratings: 
  • Scopus rating (2016): CiteScore 1.9 SJR 0.746 SNIP 0.846
Original language: English
ASJC Scopus subject areas: Histology, Pathology and Forensic Medicine
Keywords: 3D reconstruction, Computer vision, fibres, manipulation, microrobotics
Source: Scopus
Source ID: 84974717573

Research output: Contribution to journalArticleScientificpeer-review

Elevated levels of StAR-related lipid transfer protein 3 alter cholesterol balance and adhesiveness of breast cancer cells: Potential mechanisms contributing to progression of HER2-positive breast cancers

The STARD3 gene belongs to the minimal amplicon in HER2-positive breast cancers and encodes a cholesterol-binding membrane protein. To study how elevated StAR-related lipid transfer protein 3 (StARD3) expression affects breast cancer cells, we generated MCF-7 cells stably overexpressing StARD3-green fluorescent protein. We found that StARD3-overexpressing cells exhibited nonadherent morphological features, had increased Src levels, and had altered cholesterol balance, as evidenced by elevated mRNA levels of the cholesterol biosynthesis rate-limiting enzyme 3-hydroxy-3-methylglutaryl-coenzyme A reductase, and increased plasma membrane cholesterol content. On removal of serum and insulin from the culture medium, the morphological characteristics of the StARD3-overexpressing cells changed, the cells became adherent, and they developed enlarged focal adhesions. Under these conditions, the StARD3-overexpressing cells maintained elevated Src and plasma membrane cholesterol content and showed increased phosphorylation of focal adhesion kinase. In two Finnish nationwide patient cohorts, approximately 10% (212/2220) breast cancers exhibited high StARD3 protein levels, which was strongly associated with HER2 amplification; several factors related to poor disease outcome and poor breast cancer-specific survival. In addition, high StARD3 levels in breast cancers were associated with elevated 3-hydroxy-3-methylglutaryl-coenzyme A reductase mRNA levels and anti-Src-Tyr416 immunoreactivity. These results provide evidence that StARD3 overexpression results in increased cholesterol biosynthesis and Src kinase activity in breast cancer cells and suggest that elevated StARD3 expression may contribute to breast cancer aggressiveness by increasing membrane cholesterol and enhancing oncogenic signaling.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Integrated Technologies for Tissue Engineering Research (ITTE), FIN-00014 University of Helsinki, University of Helsinki, Minerva Foundation Institute for Medical Research Helsinki, University of Tampere Institute of Medical Technology, Helsinki University Central Hospital
Contributors: Vassilev, B., Sihto, H., Li, S., Hölttä-Vuori, M., Ilola, J., Lundin, J., Isola, J., Kellokumpu-Lehtinen, P. L., Joensuu, H., Ikonen, E.
Number of pages: 14
Pages: 987-1000
Publication date: 1 Apr 2015
Peer-reviewed: Yes

Publication information

Journal: American Journal of Pathology
Volume: 185
Issue number: 4
ISSN (Print): 0002-9440
Ratings: 
  • Scopus rating (2015): CiteScore 4.57 SJR 2.687 SNIP 1.298
Original language: English
ASJC Scopus subject areas: Pathology and Forensic Medicine
Source: Scopus
Source ID: 84925308543

Research output: Contribution to journalArticleScientificpeer-review

Automatic quantification of mitochondrial fragmentation from two-photon microscope images of mouse brain tissue

The morphology of mitochondria can inform about their functional state and, thus, about cell vitality. For example, fragmentation of the mitochondrial network is associated with many diseases. Recent advances in neuronal imaging have enabled the observation of mitochondria in live brains for long periods of time, enabling the study of their dynamics in animal models of diseases. To aid these studies, we developed an automatic method, based on supervised learning, for quantifying the degree of mitochondrial fragmentation in tissue images acquired via two-photon microscopy from transgenic mice, which exclusively express Enhanced cyan fluorescent protein (ECFP) under Thy1 promoter, targeted to the mitochondrial matrix in subpopulations of neurons. We tested the method on images prior to and after cardiac arrest, and found it to be sensitive to significant changes in mitochondrial morphology because of the arrest. We conclude that the method is useful in detecting morphological abnormalities in mitochondria and, likely, in other subcellular structures as well.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Department of Signal Processing, Research group: Laboratory of Biosystem Dynamics-LBD, Multi-scaled biodata analysis and modelling (MultiBAM), Neurotar LTD, University of Helsinki
Contributors: Lihavainen, E., Kislin, M., Toptunov, D., Khiroug, L., S. Ribeiro, A.
Pages: 338–351
Publication date: 2015
Peer-reviewed: Yes

Publication information

Journal: Journal of Microscopy: Oxford
Volume: 206
Issue number: 3
ISSN (Print): 0022-2720
Ratings: 
  • Scopus rating (2015): CiteScore 2.37 SJR 0.962 SNIP 1.085
Original language: English
ASJC Scopus subject areas: Histology, Pathology and Forensic Medicine
Keywords: Beta regression, Image analysis, Intravital imaging, Mitochondrial fragmentation, Mitochondrial morphology, Two-photon microscopy

Research output: Contribution to journalArticleScientificpeer-review

Length of prostate biopsies is not necessarily compromised by pooling multiple cores in one paraffin block: An observational study

Background: Individually submitted prostatic needle biopsies are recommended by most guidelines because of their potential advantage in terms of core quality. However, unspecified bilateral biopsies are commonly submitted in many centers. The length of the core is the key quality indicator of prostate biopsies. Because there are few recent publications comparing the quality of 12 site-designated biopsies versus pooled biopsies, we compared the lengths of the biopsies obtained by both methods. Methods: The material was obtained from 471 consecutive subjects who underwent prostatic needle biopsy in the Tampere University Hospital district between January and June 2013. Biopsies from 344 subjects fulfilled the inclusion criteria. The total number of cores obtained was 4047. The core lengths were measured on microscope slides. Extraprostatic tissue was subtracted from the core length. Results: The aggregate lengths observed were 129.5∈±∈21.8 mm (mean∈±∈SD) for site-designated cores and 136.9∈±∈26.4 mm for pooled cores (p∈=∈0.09). The length of the core was 10.8∈±∈1.8 mm for site-designated cores and 11.4∈±∈2.2 mm for pooled cores (p∈=∈0.87). The median length for pooled cores was 11 mm (range 5 mm - 18 mm). For individual site-designated cores, the median length was 11 mm (range 7 mm -15 mm). The core length was not correlated with the number of cores embedded into one paraffin block (r∈=∈0.015). There was no significant difference in cancer detection rate (p∈=∈0.62). Conclusions: Our results suggest that unspecified bilateral biopsies do not automatically lead to reduced core length. We conclude that carefully embedded multiple (three to nine) cores per block may yield cores of equal quality in a more cost-efficient way and that current guidelines favoring individually submitted cores may be too strict.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Department of Materials Science, University of Tampere, Tampere University Hospital, Tampere University of Technology
Contributors: Tolonen, T. T., Isola, J., Kaipia, A., Riikonen, J., Koivusalo, L., Huovinen, S., Laurila, M., Porre, S., Tirkkonen, M., Kujala, P.
Publication date: 2015
Peer-reviewed: Yes

Publication information

Journal: BMC Clinical Pathology
Volume: 15
Issue number: 4
ISSN (Print): 1472-6890
Ratings: 
  • Scopus rating (2015): CiteScore 1.88 SJR 0.782 SNIP 0.772
Original language: English
ASJC Scopus subject areas: Pathology and Forensic Medicine, Histology
Keywords: Biopsy quality, Guidelines, Prostate cancer, Prostatic needle biopsies

Bibliographical note

INT=mol,"Koivusalo, Laura"

Source: Scopus
Source ID: 84925387933

Research output: Contribution to journalArticleScientificpeer-review

Twist predicts poor outcome of patients with astrocytic glioma

Aims and methods Epithelial-mesenchymal transition (EMT) has previously been linked to glioma invasion and progression. To determine whether EMT regulators, Twist and Zeb1, had clinical significance in astrocytic gliomas, the association of Twist and Zeb1 with clinicopathological and molecular factors was studied in 269 astrocytoma samples. Results Twist and Zeb1 were widely expressed in astrocytic gliomas, but the expression of the former did not correlate with that of the latter. Stronger Twist expression levels were associated with higher WHO grades (p=0.001), whereas Zeb1 did not correlate with WHO grades. We found no association between Twist and proliferation activity (Ki67/MIB-1), p53 status, epidermal growth factor receptor (EGFR) amplification or neural cell adhesion molecule (NCAM) expression. There was no significant difference in Twist or Zeb1 expression when primary and secondary gliomas were analysed. Tumours with high Twist expression were IDH1 negative (p=0.009). High hypoxia-inducible factor-1a expression correlated significantly with positive Twist expression (p<0.001), whereas it was not associated with Zeb1 expression. Zeb1 expression did not correlate with proliferation, EGFR or IDH1. Nevertheless, we did find a correlation between high Zeb1 expression and low p53 expression levels (p=0.027). Positive NCAM expression was significantly associated with Zeb1 positivity (p=0.022). Zeb1 had no association with patient survival, whereas positive Twist expression predicted poor survival for patients in both univariate (p<0.001) and multivariable analyses (p=0.027). Conclusions EMT regulators, Twist and Zeb1, are common features of infiltrating astrocytomas, and Twist is upregulated in glioblastomas in particular. Twist may be a novel marker for poor prognosis in glioma patients.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Department of Signal Processing, Research group: Computational Systems Biology, BioMediTech, Multi-scaled biodata analysis and modelling (MultiBAM), Tampere University Hospital, Macquarie University, Australian School of Advanced Medicine, Ita-Suomen yliopisto
Contributors: Nordfors, K., Haapasalo, J., Mäkelä, K., Granberg, K. J., Nykter, M., Korja, M., Paavonen, T., Haapasalo, H., Soini, Y.
Number of pages: 8
Pages: 905-912
Publication date: 2015
Peer-reviewed: Yes

Publication information

Journal: Journal of Clinical Pathology
Volume: 68
Issue number: 11
ISSN (Print): 0021-9746
Ratings: 
  • Scopus rating (2015): CiteScore 2.45 SJR 1.247 SNIP 1.244
Original language: English
ASJC Scopus subject areas: Pathology and Forensic Medicine
Source: Scopus
Source ID: 84945439157

Research output: Contribution to journalArticleScientificpeer-review

A core needle biopsy provides more malignancy-specific results than fine-needle aspiration biopsy in thyroid nodules suspicious for malignancy

Background and aims: The most commonly used diagnostic method for the preoperative diagnosis of thyroid nodules is ultrasound-guided fine-needle aspiration biopsy (FNA), which often yields non-diagnostic or non-definitive results and seldom produces definite malignant diagnoses. To improve upon the malignancy-specific sensitivity, we tested core needle biopsies (CNBs) of thyroid lesions taken from surgical specimens. Material and methods: 52 consecutive patients with malignant or malignant-suspicious thyroid nodules were referred to Tampere University Hospital between May 2010 and December 2011. Preoperative FNAs were categorised as follicular neoplasm (48%), suspicion for malignancy (46%) or malignancy (6%). Intraoperative FNA and CNB samples were acquired from surgical specimens removed during surgery. The results of the needle biopsies were compared with the final pathological diagnosis. Results: CNBs had a high definitive sensitivity for malignancy (61%, CI 41% to 78%) whereas the definitive sensitivity for malignancy of FNAs was significantly lower (22%, CI 10% to 42%). CNB was not bene ficial in the diagnosis of follicular thyroid lesions. When all suspected follicular tumours were excluded, the definitive sensitivity of CNB rose to 70% (CI 48% to 86%). Conclusions: CNB may be beneficial for the diagnosis of papillary thyroid carcinoma and other non-follicular thyroid lesions. CNB may be considered as an additional diagnostic procedure in cases with FNA suspicious for malignancy.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Integrated Technologies for Tissue Engineering Research (ITTE), Department of Surgery, Tampere University Hospital, School of Management (JKK), Division of Surgery, Gastroenterology and Oncology
Contributors: Hakala, T., Kholová, I., Sand, J., Saaristo, R., Kellokumpu-Lehtinen, P.
Number of pages: 5
Pages: 1046-1050
Publication date: Dec 2013
Peer-reviewed: Yes

Publication information

Journal: Journal of Clinical Pathology
Volume: 66
Issue number: 12
ISSN (Print): 0021-9746
Ratings: 
  • Scopus rating (2013): CiteScore 2.35 SJR 1.162 SNIP 1.147
Original language: English
ASJC Scopus subject areas: Pathology and Forensic Medicine, Medicine(all)
Source: Scopus
Source ID: 84892789695

Research output: Contribution to journalArticleScientificpeer-review

STAT5A/B gene locus undergoes amplification during human prostate cancer progression

The molecular mechanisms underlying progression of prostate cancer (PCa) to castrate-resistant (CR) and metastatic disease are poorly understood. Our previous mechanistic work shows that inhibition of transcription factor Stat5 by multiple alternative methods induces extensive rapid apoptotic death of Stat5-positive PCa cells in vitro and inhibits PCa xenograft tumor growth in nude mice. Furthermore, STAT5A/B induces invasive behavior of PCa cells in vitro and in vivo, suggesting involvement of STAT5A/B in PCa progression. Nuclear STAT5A/B protein levels are increased in high-grade PCas, CR PCas, and distant metastases, and high nuclear STAT5A/B expression predicts early disease recurrence and PCa-specific death in clinical PCas. Based on these findings, STAT5A/B represents a therapeutic target protein for advanced PCa. The mechanisms underlying increased Stat5 protein levels in PCa are unclear. Herein, we demonstrate amplification at the STAT5A/B gene locus in a significant fraction of clinical PCa specimens. STAT5A/B gene amplification was more frequently found in PCas of high histologic grades and in CR distant metastases. Quantitative in situ analysis revealed that STAT5A/B gene amplification was associated with increased STAT5A/B protein expression in PCa. Functional studies showed that increased STAT5A/B copy numbers conferred growth advantage in PCa cells in vitro and as xenograft tumors in vivo. The work presented herein provides the first evidence of somatic STAT5A/B gene amplification in clinical PCas.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Prostate cancer research center (PCRC), Lombardi Comprehensive Cancer Center, Thomas Jefferson University, Haartman Institute, University of Basel, University of Tampere Institute of Medical Technology
Contributors: Haddad, B. R., Gu, L., Mirtti, T., Dagvadorj, A., Vogiatzi, P., Hoang, D. T., Bajaj, R., Leiby, B., Ellsworth, E., Blackmon, S., Ruiz, C., Curtis, M., Fortina, P., Ertel, A., Liu, C., Rui, H., Visakorpi, T., Bubendorf, L., Lallas, C. D., Trabulsi, E. J., McCue, P., Gomella, L., Nevalainen, M. T.
Number of pages: 12
Pages: 2264-2275
Publication date: Jun 2013
Peer-reviewed: Yes

Publication information

Journal: American Journal of Pathology
Volume: 182
Issue number: 6
ISSN (Print): 0002-9440
Ratings: 
  • Scopus rating (2013): CiteScore 5.06 SJR 2.902 SNIP 1.364
Original language: English
ASJC Scopus subject areas: Pathology and Forensic Medicine
Source: Scopus
Source ID: 84878221509

Research output: Contribution to journalArticleScientificpeer-review

Expression of ERG oncoprotein is associated with a less aggressive tumor phenotype in Japanese prostate cancer patients

To investigate and characterize ERG oncoprotein expression in Japanese patients with prostate cancer (PCa), we evaluated 92 index tumors from Japanese patients who had undergone radical prostatectomy for PCa, using an antibody-based detection method to determine ERG expression. Expression status was compared with clinicopathological findings including patient age, body mass index and preoperative prostate-specific antigen (PSA) levels, specimen Gleason score, pathological stage, positive surgical margin, size of index tumor, prostatic volume, zonal origin of index tumor and biochemical failure. Overall, ERG protein was expressed in 16.3% (15/92) of the index tumors, but not in benign glands. Younger patient age, lower Gleason score and negative surgical margins were found to be independently associated with its expression in the multivariate analysis (P= 0.015, 0.003 and 0.038, respectively). ERG expression was not associated with biochemical failure. Though not statistically significant, ERG expression was more frequently observed in peripheral zone than in transition zone cancers (28.2% vs 10%, respectively). In conclusion, ERG protein was less frequently expressed in this Japanese PCa cohort compared with Western reports. ERG expression was associated with a less aggressive tumor phenotype, and its biological significance needs to be further investigated.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Prostate cancer research center (PCRC), Jikei University School of Medicine, Josephine Nefkens Institute - JNI, University of Tampere Institute of Medical Technology
Contributors: Kimura, T., Furusato, B., Miki, J., Yamamoto, T., Hayashi, N., Takahashi, H., Kamata, Y., van Leenders, G. J. H. L., Visakorpi, T., Egawa, S.
Number of pages: 7
Pages: 742-748
Publication date: Nov 2012
Peer-reviewed: Yes

Publication information

Journal: PATHOLOGY INTERNATIONAL
Volume: 62
Issue number: 11
ISSN (Print): 1320-5463
Ratings: 
  • Scopus rating (2012): CiteScore 1.82 SJR 0.757 SNIP 1.076
Original language: English
ASJC Scopus subject areas: Pathology and Forensic Medicine
Keywords: ERG, Immunohistochemistry, Prostate cancer, Racial difference
Source: Scopus
Source ID: 84868319404

Research output: Contribution to journalArticleScientificpeer-review

Routine dual-color immunostaining with a 3-antibody cocktail improves the detection of small cancers in prostate needle biopsies

We performed dual-color immunostaining with a 3-antibody cocktail (α-methylacyl coenzyme-A racemase, CK34betaE12, and p63) on prostate biopsies from 200 patients. Current practice (hematoxylin and eosin staining followed by dual-color immunostaining on selected cases) was compared with a protocol in which routine dual-color immunostaining was provided in all cases. In the original pathology reports, adenocarcinoma was diagnosed in 87/200 (43%) patients. Small foci interpreted as putative cancers were detected with dual-color immunostaining in 14/113 patients who were originally diagnosed with a nonmalignant lesion. All of the suggested cancerous foci were independently reevaluated by 5 pathologists. A diagnosis of adenocarcinoma was assessed by consensus in 8 cases, and atypical small acinar proliferation was diagnosed in 1 case. Consensus was not reached in 5 cases. Six of the foci reclassified as cancer were of Gleason score 3 + 3 = 6, while 2 were graded as Gleason score 4 + 4 = 8. The feasibility of routine dual-color immunostaining was also tested by analyzing the time spent on microscopic assessment. Because small, atypical lesions expressing α-methylacyl coenzyme-A racemase (blue chromogen) were easy to detect using dual-color immunostaining, the microscopic analysis of dual-color immunostaining and hematoxylin-eosin staining was faster than that of hematoxylin-eosin staining alone that was later followed by dual-color immunostaining in selected cases (median 251 seconds versus 299 seconds, P

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Prostate cancer research center (PCRC), University of Tampere Institute of Medical Technology, School of Management (JKK)
Contributors: Tolonen, T. T., Kujala, P. M., Laurila, M., Tirkkonen, M., Ilvesaro, J., Tuominen, V. J., Tammela, T. L. J., Isola, J.
Number of pages: 8
Pages: 1635-1642
Publication date: Nov 2011
Peer-reviewed: Yes

Publication information

Journal: HUMAN PATHOLOGY
Volume: 42
Issue number: 11
ISSN (Print): 0046-8177
Ratings: 
  • Scopus rating (2011): CiteScore 3.01 SJR 1.591 SNIP 1.478
Original language: English
ASJC Scopus subject areas: Pathology and Forensic Medicine
Keywords: AMACR, Immunostaining, Needle biopsy, Prostate cancer, Sensitivity
Source: Scopus
Source ID: 80054686065

Research output: Contribution to journalArticleScientificpeer-review

Immunohistochemical ETS-related gene detection in a Japanese prostate cancer cohort: Diagnostic use in Japanese prostate cancer patients

Chromosomal rearrangements that result in high expression levels of the ETS-related gene (ERG) present in approximately 50% of prostate cancer (PCa) patients, making this one of the most common oncogenic alterations in PCa. However, ERG overexpression at the protein level has not been rigorously evaluated in Japanese PCa patients. In this study, we evaluated ERG expression using antibody-based detection in 230 prostate specimens in a Japanese PCa cohort. Overall, we identified 20.1% ERG-positive PCa cases. ERG was not detected in benign glands. The specificity of ERG staining for detecting PCa was almost 100%; all of the ERG-positive samples were also diagnosed as PCa. The expression level of the ERG protein correlated with clinicopathological variables, including grade (P= 0.038), stage (P= 0.005), and metastatic status (P= 0.014). No correlation was observed with age (P= 0.196) or with preoperative prostate-specific antigen level (P= 0.322). Although the frequency of ERG-positive cases in Japanese PCa patients (20.1%) was lower than that reported in a PCa cohort in Western countries (approximately 50%), our study demonstrates that the clinical utility of ERG detection at the protein level can serve as an ancillary tool for diagnosing PCa in the Japanese population.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Prostate cancer research center (PCRC), International Pathology Laboratory Company Ltd., Josephine Nefkens Institute - JNI, Jikei University School of Medicine, Departments of Pathology, University of Tampere Institute of Medical Technology
Contributors: Furusato, B., van Leenders, G. J. H. L., Trapman, J., Kimura, T., Egawa, S., Takahashi, H., Furusato, M., Visakorpi, T., Hano, H.
Number of pages: 6
Pages: 409-414
Publication date: Jul 2011
Peer-reviewed: Yes

Publication information

Journal: PATHOLOGY INTERNATIONAL
Volume: 61
Issue number: 7
ISSN (Print): 1320-5463
Ratings: 
  • Scopus rating (2011): CiteScore 1.86 SJR 0.764 SNIP 1.039
Original language: English
ASJC Scopus subject areas: Pathology and Forensic Medicine
Keywords: Asian, ERG, Immunohistochemistry, Japanese, Prostate cancer, Race
Source: Scopus
Source ID: 79959637195

Research output: Contribution to journalArticleScientificpeer-review