TY - JOUR AB - Precision medicine aims to provide personalized care based on individual patient characteristics, rather than guideline-directed therapies for groups of diseases or patient demographics. Images-both radiology- and pathology-derived-are a major source of information on presence, type, and status of disease. Exploring the mathematical relationship of pixels in medical imaging ("radiomics") and cellular-scale structures in digital pathology slides ("pathomics") offers powerful tools for extracting both qualitative, and increasingly, quantitative data. These analytical approaches, however, may be significantly enhanced by applying additional methods arising from fields of mathematics such as differential geometry and algebraic topology that remain underexplored in this context. Geometry's strength lies in its ability to provide precise local measurements, such as curvature, that can be crucial for identifying abnormalities at multiple spatial levels. These measurements can augment the quantitative features extracted in conventional radiomics, leading to more nuanced diagnostics. By contrast, topology serves as a robust shape descriptor, capturing essential features such as connected components and holes. The field of topological data analysis was initially founded to explore the shape of data, with functional network connectivity in the brain being a prominent example. Increasingly, its tools are now being used to explore organizational patterns of physical structures in medical images and digitized pathology slides. By leveraging tools from both differential geometry and algebraic topology, researchers and clinicians may be able obtain a more comprehensive, multi-layered understanding of medical images and contribute to precision medicine's armamentarium. AU - Levenson, R.M.* AU - Singh, Y.* AU - Rieck, B. AU - Hathaway, Q.A.* AU - Farrelly, C.* AU - Rozenblit, J.* AU - Prasanna, P.* AU - Erickson, B.* AU - Choudhary, A.* AU - Carlsson, G.* AU - Deepa, D.* C1 - 70544 C2 - 55663 TI - Advancing precision medicine: Algebraic topology and differential geometry in radiology and computational pathology. JO - Lab. Invest. VL - 104 IS - 6 PY - 2024 SN - 0023-6837 ER - TY - JOUR AB - Matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI) allows spatial analysis of proteins, metabolites, or small molecules from tissue sections. Here, we present the simultaneous generation and analysis of MALDI-MSI, whole-exome sequencing (WES), and RNA-sequencing data from the same formalin-fixed paraffin-embedded (FFPE) tissue sections. Genomic DNA and total RNA were extracted from (i) untreated, (ii) hematoxylin-eosin (HE) stained, and (iii) MALDI-MSI-analyzed FFPE tissue sections from three head and neck squamous cell carcinomas. MALDI-MSI data were generated by a time-of-flight analyzer prior to preprocessing and visualization. WES data were generated using a low-input protocol followed by detection of single-nucleotide variants (SNVs), tumor mutational burden, and mutational signatures. The transcriptome was determined using 3’-RNA sequencing and was examined for similarities and differences between processing stages. All data met the commonly accepted quality criteria. Besides SNVs commonly identified between differently processed tissues, FFPE-typical artifactual variants were detected. Tumor mutational burden was in the same range for tissues from the same patient and mutational signatures were highly overlapping. Transcriptome profiles showed high levels of correlation. Our data demonstrate that simultaneous molecular profiling of MALDI-MSI-processed FFPE tissue sections at the transcriptome and exome levels is feasible and reliable. AU - Kreutzer, L. AU - Weber, P. AU - Heider, T. AU - Heikenwaelder, M.* AU - Riedl, T.* AU - Baumeister, P.* AU - Klauschen, F.* AU - Belka, C. AU - Walch, A.K. AU - Zitzelsberger, H. AU - Hess J. AU - Unger, K. C1 - 66094 C2 - 52645 SP - 1400-1405 TI - Simultaneous metabolite MALDI-MSI, whole exome and transcriptome analysis from formalin-fixed paraffin-embedded tissue sections. JO - Lab. Invest. VL - 102 IS - 12 PY - 2022 SN - 0023-6837 ER - TY - JOUR AB - Multimodal tissue analyses that combine two or more detection technologies provide synergistic value compared to single methods and are employed increasingly in the field of tissue-based diagnostics and research. Here, we report a technical pipeline that describes a combined approach of HER2/CEP17 fluorescence in situ hybridization (FISH) analysis with MALDI imaging on the very same section of formalin-fixed and paraffin-embedded (FFPE) tissue. FFPE biopsies and a tissue microarray of human gastroesophageal adenocarcinoma were analyzed by MALDI imaging. Subsequently, the very same section was hybridized by HER2/CEP17 FISH. We found that tissue morphology of both, the biopsies and the tissue microarray, was unaffected by MALDI imaging and the HER2 and CEP17 FISH signals were analyzable. In comparison with FISH analysis of samples without MALDI imaging, we observed no difference in terms of fluorescence signal intensity and gene copy number. Our combined approach revealed adenosine monophosphate, measured by MALDI imaging, as a prognostic marker. HER2 amplification, which was detected by FISH, is a stratifier between good and poor patient prognosis. By integrating both stratification parameters on the basis of our combined approach, we were able to strikingly improve the prognostic effect. Combining molecules detected by MALDI imaging with the gene copy number detected by HER2/CEP17 FISH, we found a synergistic effect, which enhances patient prognosis. This study shows that our combined approach allows the detection of genetic and metabolic properties from one very same FFPE tissue section, which are specific for HER2 and hence suitable for prognosis. Furthermore, this synergism might be useful for response prediction in tumors. AU - Huber, K. AU - Kunzke, T. AU - Buck, A. AU - Langer, R.* AU - Luber, B.* AU - Feuchtinger, A. AU - Walch, A.K. C1 - 56198 C2 - 46889 CY - 75 Varick St, 9th Flr, New York, Ny 10013-1917 Usa SP - 1535-1546 TI - Multimodal analysis of formalin-fixed and paraffin-embedded tissue by MALDI imaging and fluorescence in situ hybridization for combined genetic and metabolic analysis. JO - Lab. Invest. VL - 99 IS - 10 PB - Nature Publishing Group PY - 2019 SN - 0023-6837 ER - TY - JOUR AB - © 2018 USCAP, Inc All rights reserved. Animal models can reproduce some model-specific aspects of human diseases, but some animal models translate poorly or fail to translate to the corresponding human disease. Here, we develop a strategy to systematically compare human and mouse tissues, and conduct a proof-of-concept experiment to identify molecular similarities and differences using patients with idiopathic pulmonary fibrosis and a bleomycin-induced fibrosis mouse model. Our novel approach employs high-throughput tissue microarrays (TMAs) of humans and mice, high-resolution matrix-assisted laser desorption/ionization-Fourier transform-ion cyclotron resonance-mass spectrometry imaging (MALDI-FT-ICR-MSI) to spatially resolve mass spectra at the level of specific metabolites, and hierarchical clustering and pathway enrichment analysis to identify functionally similar/different molecular patterns and pathways in pathological lesions of humans and mice. We identified a large number of common molecules (n=1366) and fewer exclusive molecules in humans (n=83) and mice (n=54). Among the common molecules, the 'ascorbate and aldarate metabolism' pathway had the highest similarity in human and mouse lesions. This proof-of-concept study demonstrates that our novel strategy employing a reliable and easy-to-perform experimental design accurately identifies pathways and factors that can be directly compared between animal models and human diseases. AU - Aichler, M. AU - Kunzke, T. AU - Buck, A. AU - Sun, N. AU - Ackermann, M.* AU - Jonigk, D.* AU - Gaumann, A.* AU - Walch, A.K. C1 - 52121 C2 - 43729 CY - New York SP - 141-149 TI - Molecular similarities and differences from human pulmonary fibrosis and corresponding mouse model: MALDI imaging mass spectrometry in comparative medicine. JO - Lab. Invest. VL - 98 IS - 1 PB - Nature Publishing Group PY - 2018 SN - 0023-6837 ER - TY - JOUR AU - Dislich, B.* AU - Stein, A.* AU - Seiler, C.A.* AU - Walch, A.K. AU - Berezowska, S.* AU - Zlobec, I.* AU - Galvan, J.A.* AU - Langer, R.* C1 - 47953 C2 - 39831 CY - New York SP - 170A TI - Low frequency of epithelial PD-L1 staining in esophageal and other gastrointestinal adenocarcinomas. JO - Lab. Invest. VL - 96 PB - Nature Publishing Group PY - 2016 SN - 0023-6837 ER - TY - JOUR AU - Li, J.* AU - Dawidek, T.* AU - Liegsalz, V.* AU - Tzalis, V.* AU - Feuchtinger, A. AU - Avril, S.* C1 - 47955 C2 - 39829 CY - New York SP - 53A TI - Intratumoral heterogeneity of common protein biomarkers assessed by immunohistochemistry in breast cancer tissues. JO - Lab. Invest. VL - 96 PB - Nature Publishing Group PY - 2016 SN - 0023-6837 ER - TY - JOUR AB - MALDI Imaging mass spectrometry has entered the field of tissue-based research by providing unique advantages for analyzing tissue specimen in an unprecedented detail. A broad spectrum of analytes ranging from proteins, peptides, protein modification over small molecules, drugs and their metabolites as well as pharmaceutical components, endogenous cell metabolites, lipids, and other analytes are made accessible by this in situ technique in tissue. Some of them were even not accessible in tissues within the histological context before. Thereby, the great advantage of MALDI Imaging is the correlation of molecular information with traditional histology by keeping the spatial localization information of the analytes after mass spectrometric measurement. This method is label-free and allows multiplex analysis of hundreds to thousands of molecules in the very same tissue section simultaneously. Imaging mass spectrometry brings a new quality of molecular data and links the expert discipline of pathology and deep molecular mass spectrometric analysis to tissue-based research. This review will focus on state-of-the-art of MALDI Imaging mass spectrometry, its recent applications by analyzing tissue specimen and the contributions in understanding the biology of disease as well as its perspectives for pathology research and practice. AU - Aichler, M. AU - Walch, A.K. C1 - 43182 C2 - 36272 CY - New York SP - 422-431 TI - MALDI Imaging mass spectrometry: Current frontiers and perspectives in pathology research and practice. JO - Lab. Invest. VL - 95 IS - 4 PB - Nature Publishing Group PY - 2015 SN - 0023-6837 ER - TY - JOUR AB - We performed genome-wide analysis of copy-number changes and loss of heterozygosity (LOH) in Barrett's esophageal adenocarcinoma by single nucleotide polymorphism (SNP) microarrays to identify associated genomic alterations. DNA from 27 esophageal adenocarcinomas and 14 matching normal tissues was subjected to SNP microarrays. The data were analyzed using dChipSNP software. Copy-number changes occurring in at least 25% of the cases and LOH occurring in at least 19% were regarded as relevant changes. As a validation, fluorescence in situ hybridization (FISH) of 8q24.21 (CMYC) and 8p23.1 (SOX7) was performed. Previously described genomic alterations in esophageal adenocarcinomas could be confirmed by SNP microarrays, such as amplification on 8q (CMYC, confirmed by FISH) and 20q13 or deletion/LOH on 3p (FHIT) and 9p (CDKN2A). Moreover, frequent gains were detected on 2p23.3, 7q11.22, 13q31.1, 14q32.31, 17q23.2 and 20q13.2 harboring several novel candidate genes. The highest copy numbers were seen on 8p23.1, the location of SOX7, which could be demonstrated to be involved in amplification by FISH. A nuclear overexpression of the transcription factor SOX7 could be detected by immunohistochemistry in two amplified tumors. Copy-number losses were seen on 18q21.32 and 20p11.21, harboring interesting candidate genes, such as CDH20 and CST4. Finally, a novel LOH region could be identified on 6p in at least 19% of the cases. In conclusion, SNP microarrays are a valuable tool to detect DNA copy-number changes and LOH at a high resolution. Using this technique, we identified several novel genes and DNA regions associated with esophageal adenocarcinoma. AU - Wiech, T.* AU - Nikolopoulos, E.* AU - Weis, R.* AU - Langer, R.* AU - Bartholomé, K.* AU - Timmer, J.* AU - Walch, A.K. AU - Höfler, H. AU - Werner, M.* C1 - 4984 C2 - 25766 SP - 385-397 TI - Genome-wide analysis of genetic alterations in Barrett's adenocarcinoma using single nucleotide polymorphism arrays. JO - Lab. Invest. VL - 89 IS - 4 PB - Nature Publ. Group PY - 2009 SN - 0023-6837 ER - TY - JOUR AB - Although the antiangiogenic activity of type I interferons (IFN) is well known, the mechanism by which it occurs is unclear. In the present study, we have investigated effects of short-term and long-term IFN-alpha exposure on different types of endothelial cells (EC). Short-term IFN-alpha treatment resulted in a distinct reduction of apoptosis of serum and growth factor starved HUVEC and HDMEC. This was accompanied by a strong upregulation of the IFN inducible guanylate binding protein-1 (GBP-1) whereas no consistent regulation of several known antiapoptotic proteins was evident. Stable transfection of HUVEC with an expression vector for GBP-1 mimicked the protective effect of IFN-alpha, suggesting that GBP-1 may contribute to the inhibition of apoptosis. When IFN-alpha, together with serum and EC growth factors, was present continuously a decrease of population doublings by more than 40% was observed in both HDMEC and HCAEC. In addition, the cells displayed a senescent phenotype significantly earlier than control cells and showed an increased adherence for monocytes. Our findings suggest that the antiangiogenic effect of IFN-alpha is mediated by inducing EC senescence rather than EC apoptosis. Furthermore IFN-alpha released in chronic inflammatory conditions might contribute via its prosenescent activity to the pathogenesis of atherosclerosis. AU - Pammer, J.* AU - Reinisch, C.* AU - Birner, P.* AU - Pogoda, K. AU - Stürzl, M. AU - Tschachler, E.* C1 - 4765 C2 - 25037 SP - 997-1007 TI - Interferon-alpha prevents apoptosis of endothelial cells after short-term exposure but induces replicative senescence after continuous stimulation. JO - Lab. Invest. VL - 86 IS - 10 PB - Nature Publ. Group PY - 2006 SN - 0023-6837 ER - TY - JOUR AU - Langer, S.* AU - Geigl, J.B.* AU - Gangnus, R.* AU - Speicher, M.R. C1 - 399 C2 - 22550 SP - 582-592 TI - Sequential application of interphase-FISH and CGH to single cells. JO - Lab. Invest. VL - 85 IS - 4 PY - 2005 SN - 0023-6837 ER - TY - JOUR AU - Laux, H.* AU - Tomer, R.* AU - Mader, M.T. AU - Smida, J.* AU - Budczies, J. AU - Kappler, R.* AU - Hahn, H.* AU - Blöchinger, M.* AU - Schnitzbauer, U.* AU - Eckardt-Schupp, F. AU - Höfler, H. C1 - 1205 C2 - 22080 SP - 1372-1386 TI - Tumor-associated E-cadherin mutations do not induce Wnt target gene expression, but affect E-cadherin repressors. JO - Lab. Invest. VL - 84 PY - 2004 SN - 0023-6837 ER - TY - JOUR AU - Kremer, M. AU - Spitzer, M.* AU - Mandl-Weber, S.* AU - Stecker, K.* AU - Schmidt, B.* AU - Höfler, H. AU - Quintanilla-Martinez, L. AU - Fend, F.* C1 - 10015 C2 - 20805 SP - 107-114 TI - Discordant Bone Marrow Involvement in Diffuse Large B-Cell Lymphoma : Comparative Molecular Analysis Reveals a Heterogeneous Group of Disorders. JO - Lab. Invest. VL - 83 PY - 2003 SN - 0023-6837 ER - TY - JOUR AB - SUMMARY: The importance of alterations of the Her-2/neu oncogene in the tumorigenesis of Barrett's adenocarcinoma (BCA) is discussed controversially. In the present study, we evaluated for the first time the Her-2/neu status in the metaplasia-dysplasia-adenocarcinoma sequence of BCA simultaneously at the DNA, mRNA, and protein level using resection specimens of 25 patients. The locus-specific Her-2/neu gene status was quantified by performing fluorescence in situ hybridization, and information about the ploidy status of chromosome 17 was obtained. Tissue sections from the same areas were used for quantitative RT-PCR (TaqMan RT-PCR) of laser-microdissected tumor cells and for immunohistochemistry to quantify Her-2/neu mRNA and oncoprotein expression. Her-2/neu gene amplification was observed in 35% of BCA, and all of these samples showed strong overexpression of both mRNA and oncoprotein. A polysomy 17 without Her-2/neu gene amplification was observed in 52% of BCA, showing a normal or moderately elevated mRNA expression and no or weak immunopositivity. From 13 areas of high-grade dysplasia (HGD) we found four to be amplified for the Her-2/neu locus, whereas five showed a polysomy 17. All four samples of HGD areas with Her-2/neu gene amplification displayed mRNA and strong oncoprotein overexpression; however, lower mRNA levels were seen than in the amplified BCA areas. None of the samples with low-grade dysplasia (LGD) showed a locus-specific Her-2/neu amplification, but polysomy 17 was present in four of eight cases. No changes were detected in BCA-associated intestinal metaplasia and squamous epithelium. In summary, only a locus-specific Her-2/neu gene amplification was associated with strong mRNA overexpression and strong membranous Her-2/neu immunostaining in BCA and HGD. A chromosome 17 polysomy, as found in the majority of BCA, led to no or weak mRNA overexpression and no or weak immunopositivity. In the metaplasia-dysplasia-adenocarcinoma sequence, a chromosome 17 polysomy without Her-2/neu gene amplification was already present in LGD. This may be a result of an early polyploidization, preceding the later genetic events, such as Her-2/neu gene amplification in HGD and BCA. AU - Walch, A.K. AU - Specht, K. AU - Bink, K. AU - Zitzelsberger, H. AU - Braselmann, H. AU - Bauer, M.* AU - Aubele, M. AU - Stein, H.* AU - Siewert, J.R.* AU - Höfler, H. AU - Werner, M. C1 - 23339 C2 - 31101 SP - 791-801 TI - Her-2/neu gene amplification, elevated mRNA expression, and protein overexpression in the metaplasia-dysplasia-adenocarcinoma sequence of Barrett's esophagus. JO - Lab. Invest. VL - 81 IS - 6 PB - Nature Publishing Group PY - 2001 SN - 0023-6837 ER - TY - JOUR AB - Although some impressive applications of multicolor fluorescence in situ hybridization (M-FISH) have been demonstrated on cytogenetic preparations, there are no reports of studies that carry over these advanced multitarget techniques to histological sections of tumor tissues in molecular pathology. Despite recent advances in protocols, M-FISH with a simultaneous multicolor painting tool does not seem to be a feasible approach in histological sections, mainly because of the inherent problem of the third dimension, which leads to complex overlays of both fluorescence signals and nuclei of tumor cells. To overcome these technical limitations, we introduce here an innovative and robust method for the detection of multiple targets by interphase FISH in formalin-fixed and paraffin-embedded tissue, called sequential multilocus fluorescence in situ hybridization (SML-FISH). AU - Walch, A.K. AU - Bink, K. AU - Hutzler, P. AU - Böwering, K.* AU - Letsiou, I.* AU - Zitzelsberger, H. AU - Braselmann, H. AU - Stein, H.* AU - Höfler, H.* AU - Werner, M. C1 - 23342 C2 - 31100 SP - 1457-1459 TI - Sequential multilocus fluorescence in situ hybridization can detect complex patterns of increased gene dosage at the single cell level in tissue sections. JO - Lab. Invest. VL - 81 IS - 10 PB - Nature Publishing Group PY - 2001 SN - 0023-6837 ER - TY - JOUR AU - Weninger, W.* AU - Partanen, T.A.* AU - Breiteneder-Geleff, S.* AU - Mayer, C.* AU - Kowalski, H.* AU - Mildner, M.* C1 - 20980 C2 - 19029 SP - 243-251 TI - Expression of vascular endothelial growth factor receptor-3 and podoplanin suggests a lymphatic endothelial cell origin of kaposi's sarcoma tumor cells. JO - Lab. Invest. VL - 79 PY - 1999 SN - 0023-6837 ER - TY - JOUR AB - BACKGROUND: There is general agreement that radiation effects on capillary endothelial cells are a leading event in the pathogenesis of late effects of radiation in normal tissues. The mechanism of microvascular involvement however is unclear. In the myocardium, there is not only a decrease in capillary number, but a focal loss of endothelial alkaline phosphatase. The present study addresses the question of whether radiation-induced alkaline phosphatase loss is due to cell death or to modification of cell function and ultrastructure. EXPERIMENTAL DESIGN: The time course of ultrastructural changes underlying endothelial alkaline phosphatase loss and development of myocardial degeneration was studied in two strains of rat, that differ in latent time of clinical radiation-induced cardiomyopathy. RESULTS: In both strains of rat, development of ultrastructural damage in cardiomyocytes was preceded by a focal loss of endothelial alkaline phosphatase reactivity. The absence of enzyme reaction product was neither due to endothelial cell loss, nor to a depletion in enzyme-bearing cytotic vesicles. The endothelial cell/pericyte relationship was also unchanged. Within enzyme-negative areas, there was an increased number of enlarged endothelial cells and of lymphocyte adherence to endothelial cells, which was then followed by endothelial cell rupture and extravasation of blood cells. In Wistar rats, enzyme loss started at 25 days after 20 Gy and reached its maximum extent by 90 days. In Sprague-Dawley rats, which show a significantly higher preirradiation enzyme reactivity, the onset of alkaline phosphatase loss and associated alterations was delayed by about 30 days and was significantly less extensive. CONCLUSIONS: Radiation-induced endothelial alkaline phosphatase loss is unrelated to cell death in mitosis, but nonetheless it is relevant for the development of ultimate clinical heart failure. AU - Balz, K. AU - Schultz-Hector, S. C1 - 20675 C2 - 13892 SP - 252-260 TI - Radiation-induced Loss of Endothelial Alkaline Phosphatase Activity and Development of Myocardial Degeneration: an Ultrastructural Study. JO - Lab. Invest. VL - 71 IS - 2 PB - Williams & Wilkins PY - 1994 SN - 0023-6837 ER - TY - JOUR AB - BACKGROUND: There is general agreement that radiation effects on capillary endothelial cells are a leading event in the pathogenesis of late effects of radiation in normal tissues. The mechanism of microvascular involvement however is unclear. In the myocardium, there is not only a decrease in capillary number, but a focal loss of endothelial alkaline phosphatase. The present study addresses the question of whether radiation-induced alkaline phosphatase loss is due to cell death or to modification of cell function and ultrastructure. EXPERIMENTAL DESIGN: The time course of ultrastructural changes underlying endothelial alkaline phosphatase loss and development of myocardial degeneration was studied in two strains of rat, that differ in latent time of clinical radiation-induced cardiomyopathy. RESULTS: In both strains of rat, development of ultrastructural damage in cardiomyocytes was preceded by a focal loss of endothelial alkaline phosphatase reactivity. The absence of enzyme reaction product was neither due to endothelial cell loss, nor to a depletion in enzyme-bearing cytotic vesicles. The endothelial cell/pericyte relationship was also unchanged. Within enzyme-negative areas, there was an increased number of enlarged endothelial cells and of lymphocyte adherence to endothelial cells, which was then followed by endothelial cell rupture and extravasation of blood cells. In Wistar rats, enzyme loss started at 25 days after 20 Gy and reached its maximum extent by 90 days. In Sprague- Dawley rats, which show a significantly higher pre-irradiation enzyme reactivity, the onset of alkaline phosphatase loss and associated alterations was delayed by about 30 days and was significantly less extensive. CONCLUSIONS: Radiation-induced endothelial alkaline phosphatase loss is unrelated to cell death in mitosis, but nonetheless it is relevant for the development of ultimate clinical heart failure. AU - Schultz-Hector, S. AU - Balz, K. C1 - 33262 C2 - 35482 SP - 252-260 TI - Radiation-induced loss of endothelial alkaline phosphatase activity and development of myocardial degeneration: An ultrastructural study. JO - Lab. Invest. VL - 71 IS - 2 PY - 1994 SN - 0023-6837 ER -