Laboratory Investigation; a Journal of Technical Methods and Pathology

Primary gastrointestinal (GI) T- and NK- cell lymphomas / lymphoproliferative disorders (LPD) are uncommon and they are usually aggressive in nature. However, T- and NK-cell lymphoma / LPD of the GI tract with indolent clinical course have been reported over the past two decades. Indolent T-cell LPD was formally proposed a decade ago in 2013, and 4 years later recognized as a provisional entity by the revised 4th Edition of WHO Classification of Tumors of Haematopoietic and Lymphoid Tissue in 2017. Indolent T-cell LPD of the GI tract has been changed to indolent T-cell lymphoma of the GI tract (ITCL-GI) as a distinct entity by the 5th edition of WHO Haematolymphoid Tumors, but the International Consensus Classification (ICC) of mature lymphoid neoplasms prefers indolent clonal T-cell LPD of the GI tract instead...

Diffuse large B-cell lymphoma (DLBCL) is the most common non-Hodgkin lymphoma. New therapeutic strategies are needed for the treatment of refractory DLBCL. 4-Hydroxy-2-nonenal (4-HNE) is a cytotoxic lipid peroxidation marker, which alters intracellular signaling and induces genetic mutations. Lipid peroxidation is associated with nonapoptotic cell death, called ferroptosis. However, the relationship between 4-HNE accumulation and feroptotic regulators in DLBCL has not been fully evaluated. Here, we aimed to evaluate the accumulation of lipid peroxide and the expression of ferroptosis suppressor protein 1 (FSP1) in DLBCL using immunohistochemistry...

Mutation detection for therapy monitoring in cell-free DNA (cfDNA) is used clinically for some malignancies. Gallbladder carcinoma (GBC) presents a diagnostic challenge and has limited late-stage treatment options. To our knowledge, this novel study examines, for the first time, genomic alterations in cfDNA from GBC to assess diagnostic accuracy and therapeutic options. The concordance of somatic genomic changes in cfDNA and DNA from paired tumor tissue was analyzed. Paired serum and tissue samples from 40 histologically proven GBC, 20 cholecystitis, and 4 normal (noninflamed gallbladder) controls were included...

Formalin-fixed paraffin-embedded (FFPE) tissues are the primary source of DNA for companion diagnostics (CDx) of cancers. Degradation of FFPE tissue DNA and inherent tumor heterogeneity constitute serious challenges in current CDx assays. To address these limitations, we introduced sequence artifact elimination and mutation enrichment to MeltArray, a highly multiplexed PCR approach, to establish an integrated protocol that provides accuracy, ease of use, and rapidness. Using PIK3CA mutations as a model, we established a MeltArray protocol that could eliminate sequence artifacts completely and enrich mutations from 23...

The pathogenesis of malignant mesothelioma (MM) has been extensively investigated, focusing on stress derived from reactive oxygen species. We aimed to identify diagnostic biomarkers of MM by analyzing proteins in formalin-fixed paraffin-embedded specimens using liquid chromatography-mass spectrometry. We extracted proteins from formalin-fixed paraffin-embedded sections of MM tissues (n = 7) and compared their profiles with those of benign mesothelial tissues (n = 4) and alveolar tissue (n = 1)...

The epithelial-mesenchymal transition (EMT) is a fundamental process in developing fibrotic diseases, including forming epiretinal membranes (ERMs). ERMs can result in irreversible vision loss. Previous research has demonstrated that vitreous derived from patients with proliferative diabetic retinopathy can stimulate angiogenesis through the Axl/PI3K/Akt pathway. Building upon this knowledge, we aimed to explore the influence of vitreous from patients with macular membranes in ARPE-19 cells. Our findings reveal that patient-derived vitreous from individuals with macular membranes promotes EMT and PI3K δ expression in ARPE-19 cells...

Growth differentiation factor-15 (GDF15), a stress sensitive cytokine, and a distant member of the TGF-β superfamily, has been shown to exhibit increased levels with aging, and in various age-related pathologies. Although GDF15 levels are elevated in the aqueous humor (AH) of glaucoma (optic nerve atrophy) patients, the possible role of this cytokine in modulation of intraocular pressure (IOP) or AH outflow is unknown. The current study addresses this question using transgenic mice expressing human GDF15 and GDF15 null mice, and by perfusing enucleated mouse eyes with recombinant human GDF15...

Ki-67 is a nuclear protein associated with proliferation, and a strong potential biomarker in breast cancer, but is not routinely measured in current clinical management due to a lack of standardization. Digital image analysis (DIA) is a promising technology that could allow high throughput analysis and standardization. There is a dearth of data on the clinical reliability as well as intra- and inter-algorithmic variability of different DIA methods. In this study, we scored and compared a set of breast cancer cases in which manually counted Ki-67 has already been demonstrated to have prognostic value (n=278) to five DIA methods; namely, Aperio ePathology, Definiens Tissue Studio, Qupath, an unsupervised IHC color histogram (IHCCH) algorithm and a deep learning pipeline piNET...

Chronic kidney disease (CKD) progresses through the replacement of functional tissue compartments with fibrosis, a maladaptive repair process. Shifting kidney repair towards a physiologically intact architecture, rather than fibrosis, is key to blocking CKD progression. Much research into the mechanisms of fibrosis is performed in rodent models with less attention to the human genetic context. Recently, human induced pluripotent stem cell (iPSC)-derived organoids have shown promise in overcoming the limitation...

Atherosclerosis is a chronic inflammatory cardiovascular disease with a high morbidity and mortality rate. An increasing number of studies have addressed the crucial contribution of Gasdermin D (GSDMD)-mediated pyroptosis, which is triggered by the inflammasomes to the development of atherosclerosis. However, the underlying mechanism is still unclear. This study aimed to uncover the detailed role of GSDMD in the development of atherosclerosis. An atherosclerotic model was established in Gsdmd-/- /Ldlr-/- mice and Gsdmd+/+ /Ldlr-/- mice fed with a high-fat diet...

Intestinal microbiota confers susceptibility to diet-induced obesity, yet many probiotic species that synthesize tryptophan (trp) actually attenuate this effect, though the underlying mechanisms are unclear. We monocolonized germ-free (GF) mice with a widely consumed probiotic Lacticaseibacillus rhamnosus GG (LGG) under trp-free or -sufficient dietary conditions. We obtained untargeted metabolomics from the mouse feces and serum using liquid chromatography-mass spectrometry and obtained intestinal transcriptomic profiles via bulk-RNA sequencing...

Impaired endometrial decidualization is the primary cause of recurrent implantation failure (RIF). RNA methylation modification, especially NSUN family mediated m5 C, is crucial for various physiological events, such as maternal-to-zygotic transition, gametogenesis, embryonic development, organismal lifespan, and cell cycle. However, the regulatory mechanisms between NSUN family mediated m5 C modification and RIF remain unknown. We acquired NSUN2 expression data of 15 human endometrium samples at proliferative and secretory stages from reproductive cell atlas...

Metabolic syndrome (MetS) is a worldwide challenge that is closely associated with obesity, non-alcoholic liver disease, insulin resistance, and type 2 diabetes. Boosting nicotinamide adenine dinucleotide (NAD+ ) presents a great potential in preventing MetS. However, the function of nuclear NAD+ in the development of MetS remains poorly understood. In this study, hepatocyte-specific Nmnat1 knockout (KO) mice were used to determine a possible link between nuclear NAD+ and high-fat diet (HFD)-induced MetS. We found that Nmnat1 knockout significantly reduced hepatic nuclear NAD+ levels but did not exacerbate high-fat diet (HFD)-induced obesity and hepatic triglycerides (TG) accumulation...

In order to better understand the pathogenesis of acute type A aortic dissection (ATAAD), high-sensitivity LC-MS/MS-based proteomics and phosphoproteomics approaches were used to identify differential proteins. Heat shock protein family B (small) member 6 (HSPB6) in aortic dissection, was significantly reduced in human and mouse aortic dissection samples by RT-PCR, Western blotting, and immunohistochemical staining techniques. Using an HSPB6-knockout mouse, we investigated the potential role of HSPB6 in β- aminopropionitrile monofumarate -induced aortic dissection...

The risk of developing cervical squamous lesions in women with multiple high risk human papilloma virus (hrHPV) infections is uncertain. The aim of this retrospective study is to investigate the type-specific attribution and phylogenetic effects of single and multiple hrHPV subtypes in cervical squamous lesions. All cases with cervical histopathologic diagnosis and HPV genotyping results in the six months preceding biopsy from October 2018 to December 2022 were studied and analyzed. Over the study period, 70,361 cases with histopathologic follow-up and prior HPV genotyping were identified...

Meningiomas rank among the most common intracranial tumors, and surgery stands as the primary treatment modality for meningiomas. The precise subtyping and diagnosis of meningiomas, both before and during surgery, play a pivotal role in enabling neurosurgeons to choose the optimal surgical program. In this study, we utilized multiphoton microscopy (MPM) based on two-photon excited fluorescence and second-harmonic generation to identify five common meningioma subtypes. The morphological features of these subtypes were depicted using the MPM multi-channel mode...

Formalin-fixed paraffin-embedded (FFPE) tissues stored in biobanks and pathology archives are a vast but underutilized source for molecular studies on different diseases. Beyond being the gold standard for preservation of diagnostic human tissues, FFPE samples retain similar genetic information as matching blood samples, which could make FFPE samples an ideal resource for genomic analysis. However, research on this resource has been hindered by the perception that DNA extracted from FFPE samples is of poor quality...

Recent studies have described several molecular subtypes and deregulation of immune-oncologic signalling pathways in angiosarcoma. Interestingly, mast cells were enriched in subsets of angiosarcoma, although their significance remains unknown. In this study, we aim to verify this observation using immunohistochemistry (H-scores) and NanoString transcriptomic profiling, as well as to explore the association between mast cells with clinical and biological features. In the study cohort (n=60), H-scores showed a significant moderate correlation with NanoString mast cell scores (r=0...

Formalin-fixed paraffin-embedded (FFPE) samples represent the cornerstone of tissue-based analysis in precision medicine. Targeted next-generation sequencing panels are routinely used to analyze a limited number of genes to guide treatment decision-making for advanced-stage patients. The number and complexity of genetic alterations to be investigated are rapidly growing; in several instances, a comprehensive genomic profiling analysis is needed. The poor quality of genetic material extracted from FFPE samples may impact the feasibility/reliability of sequencing data...

Cutaneous neurofibromas (cNFs) are characteristic of neurofibromatosis 1 (NF1), yet their immune microenvironment is incompletely known. A total of 61 cNFs from 10 patients with NF1 were immunolabeled for different types of T cells and macrophages, and the cell densities were correlated with clinical characteristics. Eight cNFs and their overlying skin were analyzed for T cell receptor CDR domain sequences, and mass spectrometry of 15 cNFs and the overlying skin was performed to study immune-related processes...