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NPJ Precision Oncology Jun 2024We conducted spatial immune tumor microenvironment (iTME) profiling using formalin-fixed paraffin-embedded (FFPE) samples of 25 KRAS-mutated non-small cell lung cancer...
We conducted spatial immune tumor microenvironment (iTME) profiling using formalin-fixed paraffin-embedded (FFPE) samples of 25 KRAS-mutated non-small cell lung cancer (NSCLC) patients treated with immune checkpoint inhibitors (ICIs), including 12 responders and 13 non-responders. An eleven-marker panel (CD3, CD4, CD8, FOXP3, CD68, arginase-1, CD33, HLA-DR, pan-keratin (PanCK), PD-1, and PD-L1) was used to study the tumor and immune cell compositions. Spatial features at single cell level with cellular neighborhoods and fractal analysis were determined. Spatial features and different subgroups of CD68 cells and FOXP3 cells being associated with response or resistance to ICIs were also identified. In particular, CD68 cells, CD33 and FOXP3 cells were found to be associated with resistance. Interestingly, there was also significant association between non-nuclear expression of FOXP3 being resistant to ICIs. We identified CD68 cells in the lung cancer tissues being associated with improved responses, which should be insightful for future studies of tumor immunity.
PubMed: 38898200
DOI: 10.1038/s41698-024-00626-6 -
Scientific Reports Jun 2024The increasing incidence of oropharyngeal squamous cell carcinoma (OPSCC) is primarily due to human papillomavirus, and understanding the tumor biology caused by the...
The increasing incidence of oropharyngeal squamous cell carcinoma (OPSCC) is primarily due to human papillomavirus, and understanding the tumor biology caused by the virus is crucial. Our goal was to investigate the proteins present in the serum of patients with OPSCC, which were not previously studied in OPSCC tissue. We examined the difference in expression of these proteins between HPV-positive and -negative tumors and their correlation with clinicopathological parameters and patient survival. The study included 157 formalin-fixed, paraffin-embedded tissue samples and clinicopathological data. Based on the protein levels in the sera of OPSCC patients, we selected 12 proteins and studied their expression in HPV-negative and HPV-positive OPSCC cell lines. LRG1, SDR16C5, PIP4K2C and MVD proteins were selected for immunohistochemical analysis in HPV-positive and -negative OPSCC tissue samples. These protein´s expression levels were compared with clinicopathological parameters and patient survival to investigate their clinical relevance. LRG1 expression was strong in HPV-negative whereas SDR16C5 expression was strong in HPV-positive tumors. Correlation was observed between LRG1, SDR16C5, and PIP4K2C expression and patient survival. High expression of PIP4K2C was found to be an independent prognostic factor for overall survival and expression correlated with HPV-positive tumor status. The data suggest the possible role of LRG1, SDR16C5 and PIP4K2C in OPSCC biology.
Topics: Humans; Male; Oropharyngeal Neoplasms; Female; Middle Aged; Aged; Papillomavirus Infections; Glycoproteins; Carcinoma, Squamous Cell; Biomarkers, Tumor; Squamous Cell Carcinoma of Head and Neck; Papillomaviridae; Adult; Prognosis; Cell Line, Tumor
PubMed: 38898137
DOI: 10.1038/s41598-024-64823-w -
The Tohoku Journal of Experimental... Jun 2024
Focal Light Chain Proximal Tubulopathy Complicated by Monoclonal Gammopathy of Undetermined Significance/Smoldering Multiple Myeloma Successfully Diagnosed by Immunofluorescence on Pronase-Digested Paraffin Section: Reports of Two Cases and Review of the Literature.
PubMed: 38897961
DOI: 10.1620/tjem.2024.J047 -
Materials (Basel, Switzerland) May 2024Leakage is a high-incidence disease of embankment dams, and efficiently addressing this disease guarantees the safe operation of dams. Underwater leakage self-priming...
Leakage is a high-incidence disease of embankment dams, and efficiently addressing this disease guarantees the safe operation of dams. Underwater leakage self-priming plugging technology is a new technology that utilizes the melting and solidifying characteristics of phase-change materials and the negative pressure in the leakage entry area to accurately plug the leakage. However, little is yet known about the underwater melting process of phase-change materials and how their characteristics influence the plugging effect. In this study, three kinds of phase-change materials, namely, paraffin, rosin, and stearic acid, were used to conduct underwater leakage self-priming plugging tests, observe and analyze the underwater melting process, and compare the plugging effects. The results showed that the underwater melting process of phase-change materials exhibited different plugging window periods depending on their melting points, specific heat capacities, and mobilities, which were the main factors affecting their plugging effects. In the final plugging stage, paraffin had the best plugging effect, but the material strength was low; rosin had good plugging compactness, but the fluidity performance was poor, and the material effective utilization was low; stearic acid had a low melting point but dispersed easily. Therefore, a blocking material with a suitable blocking window period can be produced by adjusting the material properties accordingly for an improved blocking effect.
PubMed: 38893910
DOI: 10.3390/ma17112647 -
Cancers May 2024Given the crucial predictive implications of microsatellite instability (MSI) in colorectal cancer (CRC), MSI screening is commonly performed in those with and at risk...
Given the crucial predictive implications of microsatellite instability (MSI) in colorectal cancer (CRC), MSI screening is commonly performed in those with and at risk for CRC. Here, we compared results from immunohistochemistry (IHC) and the droplet digital PCR (ddPCR) MSI assay on formalin-fixed paraffin-embedded tumor samples from 48 patients who underwent surgery for colon and rectal cancer by calculating Cohen's kappa measurement (), revealing high agreement between the methods ( = 0.915). We performed Kaplan-Meier survival analyses and univariate and multivariate Cox regression to assess the prognostic significance of ddPCR-based MSI and to identify clinicopathological features associated with CRC outcome. Patients with MSI-high had better overall survival (OS; = 0.038) and disease-free survival (DFS; = 0.049) than those with microsatellite stability (MSS). When stratified by primary tumor location, right-sided CRC patients with MSI-high showed improved DFS, relative to those with MSS ( < 0.001), but left-sided CRC patients did not. In multivariate analyses, MSI-high was associated with improved OS (hazard ratio (HR) = 0.221, 95% confidence interval (CI): 0.026-0.870, = 0.042), whereas the loss of DNA mismatch repair protein MutL homolog 1 (MLH1) expression was associated with worse OS (HR = 0.133, 95% CI: 0.001-1.152, = 0.049). Our results suggest ddPCR is a promising tool for MSI detection. Given the opposing effects of MSI-high and MLH1 loss on OS, both ddPCR and IHC may be complementary for the prognostic assessment of CRC.
PubMed: 38893125
DOI: 10.3390/cancers16112005 -
International Journal of Molecular... May 2024Cutaneous field cancerization (CFC) refers to a skin region containing mutated cells' clones, predominantly arising from chronic exposure to ultraviolet radiation (UVR),...
Cutaneous field cancerization (CFC) refers to a skin region containing mutated cells' clones, predominantly arising from chronic exposure to ultraviolet radiation (UVR), which exhibits an elevated risk of developing precancerous and neoplastic lesions. Despite extensive research, many molecular aspects of CFC still need to be better understood. In this study, we conducted ex vivo assessment of cell differentiation, oxidative stress, inflammation, and DNA damage in CFC samples. We collected perilesional skin from 41 patients with skin cancer and non-photoexposed skin from 25 healthy control individuals. These biopsies were either paraffin-embedded for indirect immunofluorescence and immunohistochemistry stain or processed for proteins and mRNA extraction from the epidermidis. Our findings indicate a downregulation of p53 expression and an upregulation of Ki67 and p16 in CFC tissues. Additionally, there were alterations in keratinocyte differentiation markers, disrupted cell differentiation, increased expression of iNOS and proinflammatory cytokines IL-6 and IL-8, along with evidence of oxidative DNA damage. Collectively, our results suggest that despite its outwardly normal appearance, CFC tissue shows early signs of DNA damage, an active inflammatory state, oxidative stress, abnormal cell proliferation and differentiation.
Topics: Humans; Oxidative Stress; DNA Damage; Cell Differentiation; Skin Neoplasms; Inflammation; Male; Female; Middle Aged; Ultraviolet Rays; Aged; Keratinocytes; Nitric Oxide Synthase Type II; Adult; Tumor Suppressor Protein p53; Skin; Ki-67 Antigen; Cyclin-Dependent Kinase Inhibitor p16; Interleukin-6
PubMed: 38891963
DOI: 10.3390/ijms25115775 -
International Journal of Molecular... May 2024The mechanism underlying podocyte dysfunction in minimal change disease (MCD) remains unknown. This study aimed to shed light on the potential pathophysiology of MCD...
The mechanism underlying podocyte dysfunction in minimal change disease (MCD) remains unknown. This study aimed to shed light on the potential pathophysiology of MCD using glomerular proteomic analysis. Shotgun proteomics using label-free quantitative mass spectrometry was performed on formalin-fixed, paraffin-embedded (FFPE) renal biopsies from two groups of samples: control (CTR) and MCD. Glomeruli were excised from FFPE renal biopsies using laser capture microdissection (LCM), and a single-pot solid-phase-enhanced sample preparation (SP3) digestion method was used to improve yield and protein identifications. Principal component analysis (PCA) revealed a distinct separation between the CTR and MCD groups. Forty-eight proteins with different abundance between the two groups (-value ≤ 0.05 and |FC| ≥ 1.5) were identified. These may represent differences in podocyte structure, as well as changes in endothelial or mesangial cells and extracellular matrix, and some were indeed found in several of these structures. However, most differentially expressed proteins were linked to the podocyte cytoskeleton and its dynamics. Some of these proteins are known to be involved in focal adhesion (NID1 and ITGA3) or slit diaphragm signaling (ANXA2, TJP1 and MYO1C), while others are structural components of the actin and microtubule cytoskeleton of podocytes (ACTR3 and NES). This study suggests the potential of mass spectrometry-based shotgun proteomic analysis with LCM glomeruli to yield valuable insights into the pathogenesis of podocytopathies like MCD. The most significantly dysregulated proteins in MCD could be attributable to cytoskeleton dysfunction or may be a compensatory response to cytoskeleton malfunction caused by various triggers.
Topics: Humans; Nephrosis, Lipoid; Proteomics; Podocytes; Kidney Glomerulus; Male; Female; Adult; Proteome; Laser Capture Microdissection; Middle Aged
PubMed: 38891801
DOI: 10.3390/ijms25115613 -
Animals : An Open Access Journal From... Jun 2024The objectives of the present study were to describe specific anatomical structures of the dromedary udder. Eighty-six dromedary udders were examined, taking...
The objectives of the present study were to describe specific anatomical structures of the dromedary udder. Eighty-six dromedary udders were examined, taking morphological measurements and producing injection casts using resin, gelatin, and paraffin. The udder of the dromedaries consists of four quarters. The shape of the udders and teats varies considerably between animals and is influenced by age, breeding, and lactation status. The most frequently found udder form was the globular udder (48.8%) and the most common teat form in this study was the funnel teat (44.2%). The most common teat tip shape was a smooth or a slightly rough ring teat (61.6%). Injection casts showed a complete separation of the teat canals. There is also no communication between tributary mammary complexes. Resin injections of the glandular tissue adjacent to the teat cistern showed an extensive branching into large, medium, and small milk ducts. Frozen sections of the udder revealed complete separation of the right and left mammary complex through the . The teat sections showed longitudinal folds from the tip of the teat to the base of the teat. A ring fold at the transition from the to the teat cistern was present. The results of this study increase the knowledge of the anatomical structures of the dromedary udder, which may be useful for breeding a selection of dairy dromedaries.
PubMed: 38891721
DOI: 10.3390/ani14111674 -
Foods (Basel, Switzerland) May 2024The application of organic fertilizers is one of the most important agricultural measures aimed at improving the flavor and productivity of , with the granulation and...
The application of organic fertilizers is one of the most important agricultural measures aimed at improving the flavor and productivity of , with the granulation and coating of organic fertilizers, which can reduce seepage losses of great significance to the ecosystem. In this study, Jingcai 8 tomato was selected as the test material. Headspace solid-phase microextraction and gas chromatography-mass spectrometry (HS-SPME-GC-MS) methods were used to investigate the effects of different pelletized organic fertilizers and various coating materials on the flavor profile of the tomatoes. The results indicated that 67 volatile organic compounds (VOCs) were identified in the tomato fruits and 62 volatile compounds were identified in the leaves under different fertilizer treatments. The volatile compound content of the fruits in the BP treatment group was 35.38 μg/g, which was higher than that in other treatment groups, and the volatile compound content of the leaves was lower. A differential compound analysis with log|fold change| ≥ 1 and variable important in projection (VIP) > 1 highlighted styrene, 3-methyl-1-butanol, and (E, E)-2,4-hexadienal as the major up-regulated compounds and methyl salicylate as the major down-regulated compound in the tomato fruit BCK (control) vs. BP. Moreover, the α-phellandrene content decreased in the tomato leaves. In addition, an analysis of the tomato fruit differential compounds and compounds with odor activity values (OAV) of ≥ 1, considering the OAV values of characteristic aroma compounds, identified key compounds affecting the flavor of the tomato fruits under the BP treatment. These included 2-nonenal, (E)-2-pentylfuran, trans-β-ionone, 1-penten-3-one, (E, E)-2,4-hexadienal, and 3-hexenol (fruity, floral, and herbaceous odors), (E, E)-2,4-heptadienal (fatty odor), and hexanal (green odor). The combined results analysis of the volatile compound content, differential compounds, and OAV values of characteristic aroma compounds aimed to clarify that the BP treatment group, which applied pelletized, large-grain organic fertilizer with polyurethane (pozzolanic + small-grain oil-coated + 2% paraffinic + 4% polyurethane) as a coating material, proved to be most effective in influencing the flavor of the tomato fruits. This finding lays the foundation for its potential commercial application in artificial orchards.
PubMed: 38890880
DOI: 10.3390/foods13111653 -
Open Forum Infectious Diseases Jun 2024Among combat injured, invasive fungal infections (IFIs) result in significant morbidity. Cultures and histopathology are the primary diagnostic methods for IFIs, but...
BACKGROUND
Among combat injured, invasive fungal infections (IFIs) result in significant morbidity. Cultures and histopathology are the primary diagnostic methods for IFIs, but they have limitations. We previously evaluated a panfungal polymerase chain reaction assay, which was 83% sensitive and 99% specific for angioinvasive IFIs. Here, we evaluated 3 less resource-intensive seminested assays targeting clinically relevant fungi in the order Mucorales and genera and .
METHODS
Formalin-fixed paraffin-embedded tissue specimens from a multicenter trauma IFI cohort (2009-2014) were used. Cases were US military personnel injured in Afghanistan with histopathologic IFI evidence. Controls were patients with similar injury patterns and no laboratory IFI evidence (negative culture and histopathology). Seminested assays specific to Mucorales (V4/V5 regions of 18S rDNA), (mitochondrial tRNA), and (internal transcribed spacer [ITS]/28A regions of DNA) were compared with a panfungal assay amplifying the internal transcribed spacer 2 region of rDNA and to histopathology.
RESULTS
Specimens from 92 injury sites (62 subjects) were compared with control specimens from 117 injuries (101 subjects). We observed substantial agreement between the seminested and panfungal assays overall, especially for the order Mucorales. Moderate agreement was observed at the genus level for and . When compared with histopathology, sensitivity and specificity of seminested assays were 67.4% and 96.6%, respectively (sensitivity increased to 91.7% when restricted to sites with angioinvasion).
CONCLUSIONS
Prior studies of seminested molecular diagnostics have focused on culture-negative samples from immunocompromised patients. Our findings underscore the utility of the seminested approach in diagnosing soft-tissue IFIs using formalin-fixed paraffin-embedded tissue samples, especially with angioinvasion.
PubMed: 38887475
DOI: 10.1093/ofid/ofae078