Molecular Analysis Of Tissues Research Articles

Oral Hedgehog Inhibitor, Vismodegib, for Locally Advanced Periorbital and Orbital Basal Cell Carcinoma: A Report by the American Academy of Ophthalmology

To review the efficacy and safety of oral vismodegib (Erivedge; Genentech) in the management of locally advanced orbital and periorbital basal cell carcinoma (BCC). A literature search was conducted last in September 2023 in the PubMed database for English language original research that evaluated the effect of oral vismodegib on orbital and periorbital BCC. Sixty articles were identified and 16 met the inclusion criteria. Most studies demonstrated high response rates, with up to 100% of patients responding to the medication in individual studies and initial complete regression occurring in up to 88% of patients. Vismodegib treatment resulted in significant reductions in tumor volume, resulting in globe preservation for most patients. However, in 12% of patients, the response was partial. Recurrences also occurred with substantial frequency, even after an initial complete response. As such, up to 79.4% of patients required surgical intervention, and up to 23% of patients still required exenteration. Use of these agents resulted in reductions in tumor volume that may delay or prevent the need for exenteration in some, but not all, patients. Importantly, molecular analysis of tissue excised after vismodegib therapy revealed persistent tumor in all patients, with frequent accumulation of mutations that may confer resistance to further hedgehog inhibitor therapy. Although most adverse events were rated as level I or II, side effects were common, with up to 100% of patients in studies experiencing at least 1 event. Muscle cramps, alopecia, weight loss, fatigue, and dysgeusia were the most common adverse events, and several patients discontinued therapy because of them. Furthermore, 1 patient died of sepsis that may have resulted from the therapy. Although level I and II evidence are lacking, most studies indicate a benefit from the use of oral vismodegib to treat orbital and periorbital BCC tumor volume. However, patients should be cautioned about the adverse side effects of treatment and the persistence of tumor cells with mutations that may cause long-term resistance. Use of vismodegib as short-term neoadjuvant therapy may be effective in shrinking tumor volume to reduce surgical morbidity while reducing the frequency and severity of side effects. The author(s) have no proprietary or commercial interest in any materials discussed in this article.

Abstract 4708: Application of spatially resolved transcriptomics to screen multiple tumor biospecimens using tissue microarrays

Abstract The tumor microenvironment is composed of highly heterogeneous structures and cell types that dynamically influence and communicate with each other. Although examination of singular biospecimens is sufficient for diagnostic purposes, it is inadequate and cost prohibitive when scaling for complex and overarching studies. Thus, high density multi-tumor tissue microarrays (TMAs) have been a practical and effective solution for high-throughput molecular analysis of tissues. Introduced more than a decade ago, TMAs have been instrumental in the recent study of tumor biology, the development of diagnostic tests, the establishment of quality control, and the investigation and identification of oncological biomarkers. Here, we demonstrate the pairing of the 10x Genomics Visium Cytassist Spatial Gene Expression Solution and Xenium In-Situ Platform on multi-tumor TMAs to screen for common biomarkers among a cohort of samples. Spatial transcriptomics technology has proven valuable in mapping the whole transcriptome with spatial context (Visium), whereas In Situ (Xenium) enables high-throughput cellular characterization at single-cell resolution. With the addition of our CytAssist platform, we expand on the pre-existing standard Visium solution by facilitating the retrieval of RNA transcriptomic information from tissues placed on standard or archival slides. On the other hand, the novel Xenium platform compliments whole transcriptome Visium data by unlocking the potential to assign transcripts to a particular cell with spatial context and subcellular resolution. The combination of spatial transcriptomics and targeted in situ data with FFPE TMAs promotes a high-throughput method to accelerate the uncovering of molecular signatures suitable to understanding the tumor microenvironment. We showcase the ability to spatially and comprehensively resolve individual oncogene and tumor suppressor genes associated with multiple tumors from a cohort of cancer patients and from multiple different tumor samples. In addition, these markers are mapped back to distinct morphological features within each tissue core, and use differential gene expression data to identify distinct cell types throughout the different patient tissues. By combining the throughput of TMA samples and depth of the Visium and Xenium platforms, the strategy enables greater insights into cell-type specifics while also expanding the spectrum of biospecimen types that can be analyzed. Citation Format: Syrus Mohabbat, Hardeep Singh, Stephen R. Williams, Lauren M M. Gutgesell, David J. Sukovich, Govinda M. Kamath, Hanyoup Kim, Amanda Janesick, Robert Shelansky, Ghezal Beliakoff, Augusto M. Tentori, Albert Kim, Cedric R. Uytingco, Sarah Taylor. Application of spatially resolved transcriptomics to screen multiple tumor biospecimens using tissue microarrays. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4708.

Liquid biopsy and glioblastoma.

Glioblastoma is the most common and malignant primary brain tumor. Despite a century of research efforts, the survival of patients has not significantly improved. Currently, diagnosis is based on neuroimaging techniques followed by histopathological and molecular analysis of resected or biopsied tissue. A recent paradigm shift in diagnostics ranks the molecular analysis of tissue samples as the new gold standard over classical histopathology, thus correlating better with the biological behavior of glioblastoma and clinical prediction, especially when a tumor lacks the typical hallmarks for glioblastoma. Liquid biopsy aims to detect and quantify tumor-derived content, such as nucleic acids (DNA/RNA), circulating tumor cells (CTCs), or extracellular vesicles (EVs) in biofluids, mainly blood, cerebrospinal fluid (CSF), or urine. Liquid biopsy has the potential to overcome the limitations of both neuroimaging and tissue-based methods to identify early recurrence and to differentiate tumor progression from pseudoprogression, without the risks of repeated surgical biopsies. This review highlights the origins and time-frame of liquid biopsy in glioblastoma and points to recent developments, limitations, and challenges of adding liquid biopsy to support the clinical management of glioblastoma patients.

From morbid anatomy to molecular analysis: the evolution of anatomical pathology in Australia

The practice of anatomical pathology in Australia has evolved rapidly in the past two centuries, from the morbid anatomy performed in the early 1800s to the highly specialised histological, immunohistochemical and even molecular analysis of tissues performed today. While some literature exists on the development of anatomical pathology as a specialty worldwide, there is minimal formal literature on the history of this specialty in Australia. This poster examines key events that have shaped modern Australian anatomical pathology. Against the backdrop of global advances in medicine, we discuss the transition from macroscopic to microscopic observation forming the basis of the pathologist’s daily work, the significance of the establishment of a college, and the economic forces that have influenced the growth of anatomical pathology. In doing so, we elucidate the origin of contemporary issues facing the specialty, and to explore the implications of such developments as digital pathology for its future.

Comparing MS imaging of lipids by WALDI and MALDI: two technologies for evaluating a common ground truth in MS imaging.

In this study, we conducted a direct comparison of water-assisted laser desorption ionization (WALDI) and matrix-assisted laser desorption ionization (MALDI) mass spectrometry imaging, with MALDI serving as the benchmark for label-free molecular tissue analysis in biomedical research. Specifically, we investigated the lipidomic profiles of several biological samples and calculated the similarity of detected peaks and Pearson's correlation of spectral profile intensities between the two techniques. We show that, overall, MALDI MS and WALDI MS present very close lipidomic analyses and that the highest similarity is obtained for the norharmane MALDI matrix. Indeed, for norharmane in negative ion mode, the lipidomic spectra revealed 100% similarity of detected peaks and over 0.90 intensity correlation between both technologies for five samples. The MALDI-MSI positive ion lipid spectra displayed more than 83% similarity of detected peaks compared to those of WALDI-MSI. However, we observed a lower percentage (77%) of detected peaks when comparing WALDI-MSI with MALDI-MSI due to the rich WALDI-MSI lipid spectra. Despite this difference, the global lipidomic spectra showed high consistency between the two technologies, indicating that they are governed by similar processes. Thanks to this similarity, we can increase datasets by including data from both modalities to either co-train classification models or obtain cross-interrogation.

Inoperable de novo metastatic colorectal cancer with primary tumour in situ: Evaluating discordant responses to upfront systemic therapy of the primary tumours and metastatic sites and complications arising from primary tumours (experiences from an Irish Cancer Centre).

Systemic therapy is the mainstay of treatment for de novo metastatic colorectal cancer (mCRC). Heterogeneity between primary tumours and metastases may lead to discordant responses to systemic therapy at these sites. The aim of the present study was to examine these discrepancies and to evaluate the rates of complications arising from the primary tumour and the strategies employed to manage these complications. Electronic medical records were screened for patients eligible for data analysis between January 1st, 2014 and December 31st, 2019. All patients diagnosed with de novo mCRC with primary tumour in situ at the time of initial systemic therapy were included in data analysis. Responses in primary tumour and metastatic sites (according to the Response Evaluation Criteria In Solid Tumours v1.1), discrepancies in these responses and rates of complications arising from primary tumours were assessed along with patient, pathological or molecular factors that may be associated with these discrepant responses or primary tumour complications. A total of 50 patients were identified (median age, 62 years). Right-colon, left-colon and rectal primary tumours comprised 34, 44 and 22% of CRC cases, respectively. All patients received 5-fluorouracil-based chemotherapy (either alone or in combination with oxaliplatin or irinotecan). Disease response (DR), stable disease (SD) and progressive disease (PD) were observed as the first response to systemic therapy in 24, 62 and 12% of primary tumours and in 36, 18 and 44% of metastatic sites, respectively. Only 36% of patients demonstrated concordant responses between the primary tumours and metastases, while the remaining 62% demonstrated discordant responses between the primary tumour and distant metastases (22% had DR with SD; 36% had DR or SD with PD; and 4% had PD with SD in the primary tumour and metastases, respectively). Restaging images were not available for 2% of the patients. Approximately 30% of patients developed complications from primary tumours, including bowel obstruction (6.12%), perforation (6%), rectal pain (6%) and rectal bleeding (10%). Approximately 10% of patients underwent palliative stoma creation. Additionally, 12% required palliative radiotherapy to the primary tumour (due to localized complications arising from the tumour). Discordant responses to systemic therapy between primary tumours and metastases occurred in 60% of patients with de novo mCRC (with primary tumour in situ at the time of first systemic therapy). The observations of the present study have potential implications for molecular tissue analysis to help guide systemic therapy. Tissue from metastatic sites may be preferable to confirm biomarker status in mCRC based on this study.

Alcoholic fixation over formalin fixation: A new, safer option for morphologic and molecular analysis of tissues.

Formalin is a widely used fixative but there is potential public health risks to exposure. Besides, alcoholic fixation is advantageous over formalin fixation because of faster fixation, optimal preservation and safer workplace environment. Following fixation by EMA and 10% neutral buffered formalin (NBF), we analyzed the tissue morphology, antigenic stability, DNA and RNA quantity with quality (OD value). The findings of EMA fixing on both the tissue morphology and molecular characterization, were satisfactory. Specially, EMA was faster in penetration of tissues than NBF, fixed ideally as early as 8 h of fixation whereas improper fixation was evident for NBF. In Hematoxylin and Eosin (H & E) staining, better cellular details with stronger affinity for staining were observed. In immunohistochemistry, better antigenic stability was reported for EMA-fixed tissues. The nucleic acid analysis revealed that total genomic DNA and RNA yield from EMA fixed tissues were significantly higher (P < 0.05) with superior quality than NBF fixed tissues. Our results suggest that EMA could be a potential alternative to NBF for fixation and preservation of tissues. These data provide new insights into an option for a safer working environment to support study and research.

Real Time Tissue Identification From Diathermy Smoke by Differential Mobility Spectrometry

Current methods for intraoperative surgical margin assessment are inadequate in terms of diagnostic accuracy, ease-of-use, and speed of analysis. Molecular analysis of tissues could potentially overcome these issues. A system based on differential ion mobility spectrometry (DMS) analysis of surgical smoke has been proposed as one potential method, but to date, it has been able to function in a relatively slow and heavily controlled manner that is inadequate for clinical use. In this study, we present an integrated sensor system that can measure a surgical smoke sample in seconds and relay the information of the tissue type to the user in near real time in simulated surgical use. The system was validated by operating porcine adipose tissue and muscle tissue. The differentiation of these tissues based on their surgical smoke profile with a cross-validated linear discriminant analysis model produced a classification accuracy of 93.1% (N = 1059). The measurements were also classified with a convolutional neural network model, resulting in a classification accuracy of 93.2%. These results indicate that the DMS-based smoke analysis system is capable of rapid tissue identification from surgical smoke produced in freehand surgery.

Acute vitamin B12 supplementation evokes antidepressant response and alters Ntrk-2

Depression is the leading cause of disability worldwide. Although most research into risk factors focuses on stress, dietary factors also have a strong link with depression. For instance, chronic vitamin B12-supplementation may reduce depression risk and helps to reverse the prodepressive effects of early life stress in animal models. However, it is still unclear whether a single acute dose of vitamin B12 is sufficient to induce antidepressant effects on molecular or behavioral levels. Based on pharmacological work and CRISPR-dCas9 epigenome editing in Neuro2A-cells we provide in vitro evidence for a link between vitamin B12, gene expression and DNA methylation of the antidepressant-associated gene Ntrk-2, which codes for the BDNF-receptor TRKB. Using stress-induction protocols in C57Bl/6 J mice combined with behavioral testing and subsequent molecular tissue analysis, we establish in vivo evidence for antidepressant effects of vitamin B12. Acute supplementation with vitamin B12, but not folic acid, selectively altered DNA methylation and gene expression of Ntrk-2 in vitro, albeit DNA methylation and Ntrk-2 gene expression do not correlate in vivo. Importantly, one acute vitamin B12 injection improved multiple behavioral measures in tests for antidepressant action and at the same time reversed the effects of chronic and acute stress on Ntrk-2 levels in vivo, however causality has not been proven at this stage. Taken together, acute vitamin B12 supplementation can reverse stress effects on Ntrk-2 gene expression and improve behaviors that are associated with depression-like behavior in mice. Our findings encourage further investigation of vitamin B12-supplementation as a novel model for antidepressant action.

A molecular biomarker for prediction of clinical outcome in children with ASD, constipation, and intestinal inflammation

In children with autism spectrum disorder (ASD) who present to the gastroenterologist with chronic constipation on a background of colonic inflammation, we have identified two distinct clinical subtypes: (1) patients who experience a sustained state of GI symptomatic remission while on maintenance anti-inflammatory therapy (fast responders) and, (2) those with recurrent right-sided fecal loading requiring regular colon cleanouts during treatment for enterocolitis (slow responders). We hypothesized that a detailed molecular analysis of tissue from the affected region of the colon would provide mechanistic insights regarding the fast versus slow response to anti-inflammatory therapy. To test this, ascending colon biopsy tissues from 35 children with ASD (20 slow responders and 15 fast responders) were analyzed by RNAseq. Hierarchical cluster analysis was performed to assign samples to clusters and gene expression analysis was performed to identify differentially expressed transcripts (DETs) between samples within the clusters. Significant differences were found between the two clusters with fast responder-predominant cluster showing an upregulation of transcripts involved in the activation of immune and inflammatory response and the slow responder-predominant cluster showing significant over-representation of pathways impacting colonic motility (e.g. genes involved in tryptophan and serotonin degradation and mitochondrial dysfunction). Regression analysis identified a single long non-coding RNA that could predict cluster assignment with a high specificity (0.88), sensitivity (0.89) and accuracy (0.89). Comparison of gene expression profiles in the ascending colon from a subset of patients with ASD, chronic right-sided fecal loading constipation and a slow versus fast response to therapy has identified molecular mechanisms that likely contribute to this differential response following the primary therapeutic intervention (i.e. treatment for colonic inflammation with brief induction immunosuppression followed by maintenance non-steroidal anti-inflammatory therapy). Importantly, we have identified a transcript that, if validated, may provide a biomarker that can predict from the outset which patients will be slow responders who would benefit from an alternate therapeutic strategy in treating their constipation.

Somatic mutations in benign breast disease tissue and risk of subsequent invasive breast cancer

BackgroundInsights into the molecular pathogenesis of breast cancer might come from molecular analysis of tissue from early stages of the disease.MethodsWe conducted a case–control study nested in a cohort of women who had biopsy-confirmed benign breast disease (BBD) diagnosed between 1971 and 2006 at Kaiser Permanente Northwest and who were followed to mid-2015 to ascertain subsequent invasive breast cancer (IBC); cases (n = 218) were women with BBD who developed subsequent IBC and controls, individually matched (1:1) to cases, were women with BBD who did not develop IBC in the same follow-up interval as that for the corresponding case. Targeted sequence capture and sequencing were performed for 83 genes of importance in breast cancer.ResultsThere were no significant case–control differences in mutation burden overall, for non-silent mutations, for individual genes, or with respect either to the nature of the gene mutations or to mutational enrichment at the pathway level. For seven subjects with DNA from the BBD and ipsilateral IBC, virtually no mutations were shared.ConclusionsThis study, the first to use a targeted multi-gene sequencing approach on early breast cancer precursor lesions to investigate the genomic basis of the disease, showed that somatic mutations detected in BBD tissue were not associated with breast cancer risk.

The Use of Liquid Biopsies in Patients With NSCLC

The Use of Liquid Biopsies in Patients With NSCLC

Pathology interface for the molecular analysis of tissue by mass spectrometry

Background: Imaging mass spectrometry (IMS) generates molecular images directly from tissue sections to provide better diagnostic insights and expand the capabilities of clinical anatomic pathology. Although IMS technology has matured over recent years, the link between microscopy imaging currently used by pathologists and MS-based molecular imaging has not been established. Methods: We adapted the Vanderbilt University Tissue Core workflow for IMS into a web-based system that facilitates remote collaboration. The platform was designed to perform within acceptable web response times for viewing, annotating, and processing high resolution microscopy images. Results: We describe a microscopy-driven approach to tissue analysis by IMS. Conclusion: The Pathology Interface for Mass Spectrometry is designed to provide clinical access to IMS technology and deliver enhanced diagnostic value.

An ALK translocation positive carcinoma of the lung presenting as uremia due to bilateral

We describe an unusual presentation of metastatic lung adenocarcinoma as malignant retroperitoneal fibrosis (MRPF). The diagnostic challenge, due to the small solitary lung mass and absence of a discrete retroperitoneal mass, was overcome by diagnostic laparoscopy. Molecular analysis of tissue acquired was positive for ALK gene rearrangement. Treatment of the patient with crizotinib reversed MRPF. He was weaned off the nephrostomy tubes and is with stable renal function 11 months after diagnosis.

Vascular endothelial growth factor receptor-2 inhibition in experimental murine colitis

BackgroundIn the setting of inflammatory bowel disease, inflammation is associated with a simultaneous increase in angiogenesis; moreover, elevated vascular endothelial growth factor (VEGF) levels implicate angiogenesis as a pathologic contributor to disease severity. We hypothesize that selectively inhibiting vascular endothelial growth factor receptor-2 (VEGFR2) in a model of murine colitis will reduce angiogenesis, resulting in decreased inflammation and disease severity, providing mechanistic insight into the role of pathologic angiogenesis in IBD. Materials and methodsIn a dextran sodium sulfate model of murine colitis, anti-VEGFR2 monoclonal antibody (DC101) or placebo was administered. Clinical assessments followed by histologic and molecular tissue analysis were performed to quantify inflammation, microvessel density (MVD), VEGF and VEGFR2 gene expression, and phosphorylated mitogen-activated protein kinase protein expression. ResultsWeight loss began after d 6 with the treatment group demonstrating a more favorable percent weight change. Inflammation and MVD were similar between cohorts, both increasing in parallel toward a plateau. VEGF and VEGFR2 messenger RNA expression were not significantly different, but phosphorylated mitogen-activated protein kinase was elevated in the DC101 cohort (P = 0.03). ConclusionsDespite a more favorable weight change profile in the treated group, no difference was observed between cohorts regarding clinical disease severity. However, a parallel rise in inflammation and MVD was observed coinciding with weight loss, suggesting their relationship in IBD. VEGFR2 downstream signaling was significantly elevated in the treated cohort, possibly by VEGF-independent signal transduction. Early and effective inhibition of angiogenesis by limiting downstream VEGF signaling or targeting multiple angiogenic pathways may block angiogenesis, thereby reducing disease severity and provide evidence toward the mechanism and clinical benefit of antiangiogenics in the setting of IBD.

Direct Molecular Tissue Analysis by MALDI Imaging Mass Spectrometry in the Field of Gastrointestinal Disease

*Institute of Pathology, Research Unit Analytical Pathology, Helmholtz Zentrum Munchen, German Research Center for Environmental Health, Neuherberg, Germany; ‡ § Department of Medicine II, Klinikum rechts der Isar, Technische Universitat Munchen, Munich, Germany; Department of Medicine II, Universitatsklinikum Mannheim, University of Heidelberg, Mannheim, Germany; and Institute of Pathology, Technische Universitat Munchen, Munich, Germany

Fast quantification of immunohistochemistry tissue microarrays in lung carcinoma

Tissue microarrays (TMAs) are an effective tool for high-throughput molecular analysis of tissues to help identify new diagnostic and prognostic markers and targets in human cancers. We have developed a fully automated method for rapid, continuous and quantitative analysis of TMAs based on immunohistochemistry. The method deals with complex and varying tissue architectures, segments tumour cells from normal cells, conducts cell compartmentalisation, identifies nuclei and cytoplasm and produces three different continuous measurements of marker expression levels within tumour cell nuclei, tumour cell cytoplasm and total tumour cell protein expression. We have demonstrated this method using three independent protein markers (BAK, BAX and a novel biomarker, named KS) over 7 TMAs, involving 2 BAK stained TMAs with 229 tumour tissue cores, 2 BAX stained TMAs with 229 tumour tissue cores and 3 KS stained TMAs with 373 tumour cores of lung carcinomas. We validated the automated method, showing that the automated scoring is significantly correlated with the pathologist-based scoring.

Hepatitis-Related Renal Disease

Many glomerular diseases can be caused by viral infections based on the diagnostic criteria, including clinical and laboratory data, and molecular analysis of tissue. Operative pathogenetic mechanisms include kidney tropism of the virus, immune complex formation, direct cytopathogenic effect, and multi-organ failure. Chronic infection with hepatitis virus is etiologically linked to well-defined glomerulopathies. In endemic areas, HBV is associated with both membranous nephropathy and mesangiocapillary glomerulonephritis, while HCV is known to cause cryoglobulinemia-mediated glomerulonephritis and other forms of glomerulonephritis. Renal biopsy with appropriate serological and molecular testing helps to define virus-related glomerular lesions and provides a prognostic and therapeutic guide. Antiviral agents remain the mainstay of treatment.

Coronary arterioles in type 2 diabetic (db/db) mice undergo a distinct pattern of remodeling associated with decreased vessel stiffness

Little is known about the impact of type 2 diabetes mellitus (DM) on coronary arteriole remodeling. The aim of this study was to determine the mechanisms that underlie coronary arteriole structural remodeling in type 2 diabetic (db/db) mice. Passive structural properties of septal coronary arterioles isolated from 12- to 16-week-old diabetic db/db and control mice were assessed by pressure myography. Coronary arterioles from 12-week-old db/db mice were structurally similar to age-matched controls. By 16weeks of age, coronary wall thickness was increased in db/db arterioles (p<0.01), while luminal diameter was reduced (control: 118±5μm; db/db: 102±4μm, p<0.05), augmenting the wall-to-lumen ratio by 58% (control: 5.9±0.6; db/db: 9.5±0.4, p<0.001). Inward hypertrophic remodeling was accompanied by a 56% decrease in incremental elastic modulus (p<0.05, indicating decreased vessel coronary wall stiffness) and a ~30% reduction in coronary flow reserve (CFR) in diabetic mice. Interestingly, aortic pulse wave velocity and femoral artery incremental elastic modulus were increased (p<0.05) in db/db mice, indicating macrovascular stiffness. Molecular tissue analysis revealed increased elastin-to-collagen ratio in diabetic coronaries when compared to control and a decrease in the same ratio in the diabetic aortas. These data show that coronary arterioles isolated from type 2 diabetic mice undergo inward hypertrophic remodeling associated with decreased stiffness and increased elastin-to-collagen ratio which results in a decreased CFR. This study suggests that coronary microvessels undergo a different pattern of remodeling from macrovessels in type 2 DM.

Imaging mass spectrometry revealed the production of lyso-phosphatidylcholine in the injured ischemic rat brain

To develop an effective neuroprotective strategy against ischemic injury, it is important to identify the key molecules involved in the progression of injury. Direct molecular analysis of tissue using mass spectrometry (MS) is a subject of much interest in the field of metabolomics. Most notably, imaging mass spectrometry (IMS) allows visualization of molecular distributions on the tissue surface. To understand lipid dynamics during ischemic injury, we performed IMS analysis on rat brain tissue sections with focal cerebral ischemia. Sprague–Dawley rats were sacrificed at 24 h after middle cerebral artery occlusion, and brain sections were prepared. IMS analyses were conducted using matrix-assisted laser desorption/ionization time-of-flight mass spectrometer (MALDI-TOF MS) in positive ion mode. To determine the molecular structures, the detected ions were subjected to tandem MS. The intensity counts of the ion signals of m/z 798.5 and m/z 760.5 that are revealed to be a phosphatidylcholine, PC (16:0/18:1) are reduced in the area of focal cerebral ischemia as compared to the normal cerebral area. In contrast, the signal of m/z 496.3, identified as a lyso-phosphatidylcholine, LPC (16:0), was clearly increased in the area of focal cerebral ischemia. In IMS analyses, changes of PC (16:0/18:1) and LPC (16:0) are observed beyond the border of the injured area. Together with previous reports—that PCs are hydrolyzed by phospholipase A2 (PLA2) and produce LPCs,—our present results suggest that LPC (16:0) is generated during the injury process after cerebral ischemia, presumably via PLA2 activation, and that PC (16:0/18:1) is one of its precursor molecules.