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Hade AC, Philips MA, Promet L, Jagomäe T, Hanumantharaju A, Salumäe L, Reimann E, Plaas M, Vasar E, Väli M. A cost-effective and efficient ex vivo, ex situ human whole brain perfusion protocol for immunohistochemistry. J Neurosci Methods 2024; 404:110059. [PMID: 38218387 DOI: 10.1016/j.jneumeth.2024.110059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 12/18/2023] [Accepted: 01/07/2024] [Indexed: 01/15/2024]
Abstract
BACKGROUND Chemical fixation of the brain can be executed through either the immersion method or the perfusion method. Perfusion fixation allows for better preservation of the brain tissue's ultrastructure, as it provides rapid and uniform delivery of the fixative to the tissue. Still, not all facilities have the expertise to perform perfusion fixation, with initial high cost and complexity of perfusion systems as the main factors limiting its widespread usage. NEW METHOD Here we present our low-cost approach of whole brain ex situ perfusion fixation to overcome the aforementioned limitations. Our self-made perfusion system, constructed utilising commercially accessible and affordable medical resources alongside laboratory and everyday items, demonstrates the capability to generate superior histological stainings of brain tissue. The perfused tissue can be stored prior to proceeding with IHC for at least one year. RESULTS Our method yielded high-quality results in histological stainings using both free-floating cryosections and paraffin-embedded tissue sections. The system is fully reusable and complies with the principles of sustainable management. COMPARISON WITH EXISTING METHODS Our whole brain perfusion system has been assembled from simple components and is able to achieve a linear flow with a pressure of 70 mmHg corresponding to the perfusion pressure of the brain. CONCLUSIONS Our ex situ method can be especially useful in research settings where expensive perfusion systems are not affordable or in any field with high time pressure, making it suitable for the field of forensic medicine or pathology in general.
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Affiliation(s)
- Andreas-Christian Hade
- Department of Pathological Anatomy and Forensic Medicine, University of Tartu, 19 Ravila Street, 50411 Tartu, Estonia; Estonian Forensic Science Institute, Tervise 20, Tallinn, Estonia
| | - Mari-Anne Philips
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia; Centre of Excellence in Genomics and Translational Medicine, University of Tartu, Tartu, Estonia.
| | - Liisi Promet
- International Max Planck Research School for Neurosciences, University of Göttingen, Göttingen, Germany
| | - Toomas Jagomäe
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia; Centre of Excellence in Genomics and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Arpana Hanumantharaju
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia; Centre of Excellence in Genomics and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Liis Salumäe
- Pathology Service, Tartu University Hospital; Tartu, Estonia
| | - Ene Reimann
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Mario Plaas
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia; Centre of Excellence in Genomics and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Eero Vasar
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia; Centre of Excellence in Genomics and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Marika Väli
- Department of Pathological Anatomy and Forensic Medicine, University of Tartu, 19 Ravila Street, 50411 Tartu, Estonia; Estonian Forensic Science Institute, Tervise 20, Tallinn, Estonia
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Vanea C, Džigurski J, Rukins V, Dodi O, Siigur S, Salumäe L, Meir K, Parks WT, Hochner-Celnikier D, Fraser A, Hochner H, Laisk T, Ernst LM, Lindgren CM, Nellåker C. Mapping cell-to-tissue graphs across human placenta histology whole slide images using deep learning with HAPPY. Nat Commun 2024; 15:2710. [PMID: 38548713 PMCID: PMC10978962 DOI: 10.1038/s41467-024-46986-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 03/15/2024] [Indexed: 04/01/2024] Open
Abstract
Accurate placenta pathology assessment is essential for managing maternal and newborn health, but the placenta's heterogeneity and temporal variability pose challenges for histology analysis. To address this issue, we developed the 'Histology Analysis Pipeline.PY' (HAPPY), a deep learning hierarchical method for quantifying the variability of cells and micro-anatomical tissue structures across placenta histology whole slide images. HAPPY differs from patch-based features or segmentation approaches by following an interpretable biological hierarchy, representing cells and cellular communities within tissues at a single-cell resolution across whole slide images. We present a set of quantitative metrics from healthy term placentas as a baseline for future assessments of placenta health and we show how these metrics deviate in placentas with clinically significant placental infarction. HAPPY's cell and tissue predictions closely replicate those from independent clinical experts and placental biology literature.
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Affiliation(s)
- Claudia Vanea
- Nuffield Department of Women's & Reproductive Health, University of Oxford, Oxford, UK.
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK.
| | | | | | - Omri Dodi
- Faculty of Medicine, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Siim Siigur
- Department of Pathology, Tartu University Hospital, Tartu, Estonia
| | - Liis Salumäe
- Department of Pathology, Tartu University Hospital, Tartu, Estonia
| | - Karen Meir
- Department of Pathology, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - W Tony Parks
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, Canada
| | | | - Abigail Fraser
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
| | - Hagit Hochner
- Braun School of Public Health, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Triin Laisk
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Linda M Ernst
- Department of Pathology and Laboratory Medicine, NorthShore University HealthSystem, Chicago, USA
- Department of Pathology, University of Chicago Pritzker School of Medicine, Chicago, USA
| | - Cecilia M Lindgren
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
- Centre for Human Genetics, Nuffield Department, University of Oxford, Oxford, UK
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Nuffield Department of Population Health Health, University of Oxford, Oxford, UK
| | - Christoffer Nellåker
- Nuffield Department of Women's & Reproductive Health, University of Oxford, Oxford, UK.
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK.
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Roht L, Laidre P, Tooming M, Tõnisson N, Nõukas M, Nurm M, Estonian Biobank Research Team, Roomere H, Rekker K, Toome K, Fjodorova O, Murumets Ü, Šamarina U, Pajusalu S, Aaspõllu A, Salumäe L, Muhu K, Soplepmann J, Õunap K, Kahre T. The Prevalence and Molecular Landscape of Lynch Syndrome in the Affected and General Population. Cancers (Basel) 2023; 15:3663. [PMID: 37509324 PMCID: PMC10377710 DOI: 10.3390/cancers15143663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/07/2023] [Accepted: 07/08/2023] [Indexed: 07/30/2023] Open
Abstract
BACKGROUND Lynch syndrome (LS) is the most frequent genetically pre-disposed colorectal cancer (CRC) syndrome, accounting for 2-3% of all CRC cases. In Estonia, ~1000 new cases are diagnosed each year. This retroactive and prospective study aimed to estimate the prevalence of LS and describe disease-causing variants in mismatch repair (MMR) genes in a diagnostic setting and in the Estonian general population. METHODS LS data for the diagnostic cohort were gathered from 2012 to 2022 and data for the general population were acquired from the Estonian Biobank (EstBB). Furthermore, we conducted a pilot study to estimate the improvement of LS diagnostic yield by raising the age limit to >50 years for immunohistochemistry analysis of MMR genes. RESULTS We estimated LS live birth prevalence between 1930 and 2003 in Estonia at 1:8638 (95% CI: 1: 9859-7588). During the study period, we gathered 181 LS individuals. We saw almost a six-fold increase in case prevalence, probably deriving from better health awareness, improved diagnostic possibilities and the implementation of MMR IHC testing in a broader age group. CONCLUSION The most common genes affected in the diagnostic and EstBB cohorts were MLH1 and PMS2 genes, respectively. The LS diagnosis mean age was 44.8 years for index cases and 36.8 years (p = 0.003) for family members. In the MMR IHC pilot study, 29% had LS.
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Affiliation(s)
- Laura Roht
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, 50406 Tartu, Estonia
- Department of Clinical Genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, 50406 Tartu, Estonia
| | - Piret Laidre
- Department of Clinical Genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, 50406 Tartu, Estonia
| | - Mikk Tooming
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, 50406 Tartu, Estonia
- Department of Laboratory Genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, 50406 Tartu, Estonia
| | - Neeme Tõnisson
- Department of Clinical Genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, 50406 Tartu, Estonia
- Estonian Biobank, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
| | - Margit Nõukas
- Estonian Biobank, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
- Institute of Molecular and Cell Biology, University of Tartu, 51010 Tartu, Estonia
| | - Miriam Nurm
- Estonian Biobank, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
| | | | - Hanno Roomere
- Department of Laboratory Genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, 50406 Tartu, Estonia
| | - Kadri Rekker
- Department of Laboratory Genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, 50406 Tartu, Estonia
| | - Kadri Toome
- Department of Laboratory Genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, 50406 Tartu, Estonia
| | - Olga Fjodorova
- Department of Laboratory Genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, 50406 Tartu, Estonia
| | - Ülle Murumets
- Department of Laboratory Genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, 50406 Tartu, Estonia
| | - Ustina Šamarina
- Department of Laboratory Genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, 50406 Tartu, Estonia
| | - Sander Pajusalu
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, 50406 Tartu, Estonia
- Department of Clinical Genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, 50406 Tartu, Estonia
- Department of Laboratory Genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, 50406 Tartu, Estonia
| | | | - Liis Salumäe
- Pathology Service, Tartu University Hospital, 50406 Tartu, Estonia
| | - Kristina Muhu
- Estonian Unemployment Insurance Fund, 10142 Tallinn, Estonia
| | - Jaan Soplepmann
- Department of Surgical and Gynecological Oncology, Surgery Clinic, Tartu University Hospital, 50406 Tartu, Estonia
- Department of Hematology and Oncology, Institute of Clinical Medicine, University of Tartu, 50406 Tartu, Estonia
| | - Katrin Õunap
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, 50406 Tartu, Estonia
- Department of Clinical Genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, 50406 Tartu, Estonia
| | - Tiina Kahre
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, 50406 Tartu, Estonia
- Department of Laboratory Genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, 50406 Tartu, Estonia
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Orumaa M, Innos K, Suurna M, Salumäe L, Veerus P. Quality Assessment of Cervical Cytology Practices in Estonia From 2007 to 2018. Cancer Control 2022; 29:10732748221141794. [PMID: 36542780 PMCID: PMC9793007 DOI: 10.1177/10732748221141794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Cervical cancer incidence and mortality in Estonia are among the highest in Europe, although the overall coverage with cervical cytology is high. This indicates potential issues with the quality of collection and/or laboratory evaluation of cervical cytology. OBJECTIVES The aim of the retrospective observational study was to assess the quality of cervical cytology specimen collection, evaluation, and reporting using laboratory reports in Estonia. METHODS The study included women with a cervical cancer diagnosis in 2017-2018. Cervical cytology and histology reports for these women in 2007-2018 were obtained from ten laboratories. We described the quality of cytology specimen collection and reporting of cytology results. Multivariate logistic regression was used to calculate odds ratios (OR) with 95% confidence intervals (CI) to identify factors associated with NILM as the last cervical cytology result within 5 or 2 years before the cervical cancer diagnosis. Also, we calculated cytology-histology correlation (CHC). RESULTS We identified 503 cytology and 100 histology reports from 138 women. The laboratories differed greatly regarding human resources, work capacity and volume. Differences between local and regional laboratories were observed in reporting specimen adequacy (P < .001). We found that local laboratories had 3 times higher odds (OR = 2.95, 95% CI: 1.05-8.33) of reporting normal results 2 years before cancer diagnosis than regional laboratories. According to the CHC, 58.9% of pairs were in agreement. CONCLUSIONS The study showed considerable heterogeneity and suboptimal performance of cervical cytology practices in Estonia, particularly at local laboratories. Efforts to improve laboratory quality assurance are crucial.
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Affiliation(s)
- Madleen Orumaa
- Department of Epidemiology and
Biostatistics, National Institute for Health
Development, Tallinn, Estonia,Department of Research, Cancer
Registry of Norway, Oslo University
Hospital, Oslo, Norway,Madleen Orumaa, Department of Epidemiology
and Biostatistics, National Institute for Health Development, Hiiu 42, 11619
Tallinn, Estonia.
| | - Kaire Innos
- Department of Epidemiology and
Biostatistics, National Institute for Health
Development, Tallinn, Estonia
| | - Maria Suurna
- Department of Epidemiology and
Biostatistics, National Institute for Health
Development, Tallinn, Estonia
| | - Liis Salumäe
- Pathology Department of Tartu
University Hospital, Tartu, Estonia
| | - Piret Veerus
- Department of Epidemiology and
Biostatistics, National Institute for Health
Development, Tallinn, Estonia
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5
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Lepland A, Malfanti A, Haljasorg U, Asciutto EK, Pickholz M, Bringas M, Đorđević S, Salumäe L, Peterson P, Teesalu T, Vicent MJ, Scodeller P. Depletion of Mannose Receptor-Positive Tumor-associated Macrophages via a Peptide-targeted Star-shaped Polyglutamate Inhibits Breast Cancer Progression in Mice. Cancer Res Commun 2022; 2:533-551. [PMID: 36923553 PMCID: PMC10010335 DOI: 10.1158/2767-9764.crc-22-0043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 05/03/2022] [Accepted: 06/03/2022] [Indexed: 12/31/2022]
Abstract
Although many studies have explored the depletion of tumor-associated macrophages (TAM) as a therapeutic strategy for solid tumors, currently available compounds suffer from poor efficacy and dose-limiting side effects. Here, we developed a novel TAM-depleting agent ("OximUNO") that specifically targets CD206+ TAMs and demonstrated efficacy in a triple-negative breast cancer (TNBC) mouse model. OximUNO comprises a star-shaped polyglutamate (St-PGA) decorated with the CD206-targeting peptide mUNO that carries the chemotherapeutic drug doxorubicin (DOX). In the TNBC model, a fluorescently labeled mUNO-decorated St-PGA homed to CD206+ TAMs within primary lesions and metastases. OximUNO exhibited no acute liver or kidney toxicity in vivo. Treatment with OximUNO reduced the progression of primary tumor lesions and pulmonary metastases, significantly diminished the number of CD206+ TAMs and increased the CD8/FOXP3 expression ratio (indicating immunomodulation). Our findings suggest the potential benefit of OximUNO as a TAM-depleting agent for TNBC treatment. Importantly, our studies also represent a novel design of a peptide-targeted St-PGA as a targeted therapeutic nanoconjugate. Significance A peptide-targeted nanoformulation of DOX exclusively eliminates mannose receptor+ TAMs in breast cancer models, generating response without off-target effects (a drawback of many TAM-depleting agents under clinical study).
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Affiliation(s)
- Anni Lepland
- Laboratory of Precision and Nanomedicine, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Alessio Malfanti
- Polymer Therapeutics Laboratory, Prince Felipe Research Centre, Valencia, Spain
| | - Uku Haljasorg
- Molecular Pathology Research Group, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Eliana K. Asciutto
- School of Science and Technology, National University of San Martin (UNSAM) ICIFI and CONICET, Buenos Aires, Argentina
| | - Monica Pickholz
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Física de Buenos Aires (IFIBA), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Mauro Bringas
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA-CONICET), C1405BWE Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Snežana Đorđević
- Polymer Therapeutics Laboratory, Prince Felipe Research Centre, Valencia, Spain
| | - Liis Salumäe
- Pathology Department, Tartu University Hospital, Tartu, Estonia
| | - Pärt Peterson
- Molecular Pathology Research Group, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Tambet Teesalu
- Laboratory of Precision and Nanomedicine, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
- Centre for Nanomedicine and Department of Cell, Molecular and Developmental Biology, University of California, Santa Barbara, California
| | - María J. Vicent
- Polymer Therapeutics Laboratory, Prince Felipe Research Centre, Valencia, Spain
| | - Pablo Scodeller
- Laboratory of Precision and Nanomedicine, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
- Corresponding Author: Pablo Scodeller, Department of Biomedicine, University of Tartu, Tartu 50411, Estonia. Phone: 372-737-4268; E-mail:
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