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Molecular Oncology Jun 2024Endometrioid ovarian cancers (EOvC) are usually managed as serous tumors. In this study, we conducted a comprehensive molecular investigation to uncover the distinct...
Endometrioid ovarian cancers (EOvC) are usually managed as serous tumors. In this study, we conducted a comprehensive molecular investigation to uncover the distinct biological characteristics of EOvC. This retrospective multicenter study involved patients from three European centers. We collected clinical data and formalin-fixed paraffin-embedded (FFPE) samples for analysis at the DNA level using panel-based next-generation sequencing and array-comparative genomic hybridization. Additionally, we examined mRNA expression using NanoString nCounter® and protein expression through tissue microarray. We compared EOvC with other ovarian subtypes and uterine endometrioid tumors. Furthermore, we assessed the impact of molecular alterations on patient outcomes, including progression-free survival (PFS) and overall survival (OS). Preliminary analysis of clinical data from 668 patients, including 86 (12.9%) EOvC, revealed more favorable prognosis for EOvC compared with serous ovarian carcinoma (5-year OS of 60% versus 45%; P = 0.001) driven by diagnosis at an earlier stage. Immunohistochemistry and copy number alteration (CNA) profiles of 43 cases with clinical data and FFPE samples available indicated that EOvC protein expression and CNA profiles were more similar to endometrioid endometrial tumors than to serous ovarian carcinomas. EOvC exhibited specific alterations, such as lower rates of PTEN loss, mutations in DNA repair genes, and P53 abnormalities. Survival analysis showed that patients with tumors harboring loss of PTEN expression had worse outcomes (median PFS 19.6 months vs. not reached; P = 0.034). Gene expression profile analysis confirmed that EOvC differed from serous tumors. However, comparison to other rare subtypes of ovarian cancer suggested that the EOvC transcriptomic profile was close to that of ovarian clear cell carcinoma. Downregulation of genes involved in the PI3K pathway and DNA methylation was observed in EOvC. In conclusion, EOvC represents a distinct biological entity and should be regarded as such in the development of specific clinical approaches.
PubMed: 38923749
DOI: 10.1002/1878-0261.13679 -
Current Protocols Jun 2024Fluorescence in situ hybridization (FISH) is a cytogenetic assay that is widely used in both clinical and research settings to validate genetic aberrations. Simple in...
Fluorescence in situ hybridization (FISH) is a cytogenetic assay that is widely used in both clinical and research settings to validate genetic aberrations. Simple in principle, it is based on denaturation and hybridization of a DNA probe and its complementary sequence; however, it is subject to continuous optimization. Here we share how in-house FISH can be optimized using different control tissues to visualize and ultimately validate common and novel genetic abnormalities unearthed by next-generation sequencing (NGS). Seven specific FISH probes were designed and labeled, and conditions for eight tissue types and one patient-derived tumor organoid were optimized. Formalin-fixed paraffin-embedded (FFPE) tissue slides were used for each experiment. Slides were first deparaffinized, then placed in a pretreatment solution followed by a digestion step. In-house FISH probes were then added to the tissue to be denatured and hybridized, and then washed twice. To obtain optimal results, probe concentration, pepsin incubation time, denaturation, and the two post-hybridization washes were optimized for each sample. By modifying the above conditions, all FISH experiments were optimized in separate tissue types to investigate specific genomic alterations in tumors arising in those tissues. Signals were clear and distinct, allowing for visualization of the selected probes. Following this protocol, our lab has quickly optimized 11 directly labeled in-house FISH probes to support genetic aberrations nominated by NGS, including most recent discoveries through whole-genome sequencing analyses. We describe a robust approach of how to advance in-house labeled FISH probes. By following these guidelines, reliable and reproducible FISH results can be obtained to interrogate FFPE slides from benign, tumor tissues, and patient-derived tumor organoid specimens. This is of most relevance in the era of NGS and precision oncology. © 2024 Wiley Periodicals LLC. Basic Protocol 1: Metaphase FISH optimization Support Protocol 1: In-house probe labeling and preparation Support Protocol 2: Metaphase spread preparation Basic Protocol 2: Optimization of FISH on formalin-fixed paraffin-embedded tissue.
Topics: In Situ Hybridization, Fluorescence; Humans; Precision Medicine; Paraffin Embedding; Neoplasms; High-Throughput Nucleotide Sequencing; DNA Probes
PubMed: 38923415
DOI: 10.1002/cpz1.1093 -
Pathophysiology : the Official Journal... Jun 2024Vaginal agenesis (VA) is frequently associated with mullerian agenesis. VA treatments include mechanical dilation and surgical vaginoplasty. We created a vaginal...
Vaginal agenesis (VA) is frequently associated with mullerian agenesis. VA treatments include mechanical dilation and surgical vaginoplasty. We created a vaginal expansion sleeve (VES) as a novel device to progressively lengthen the vaginal canal. This study evaluated the histologic effects of the VES on rat vaginal tissue. The VES is a spring-like device made of proprietary woven cylindrical material and flat resin caps. The VESs were constructed as 25-30 mm, pre-contracted springs, which were secured into the vaginas of six Sprague Dawley rats and allowed to re-expand post-surgically. After one week, the VESs were removed, and the vaginas were harvested and measured in length. Test ( = 6) and control ( = 4) formalin-fixed paraffin-embedded tissues were stained with hematoxylin and eosin (H&E), Masson's trichrome, and anti-Desmin antibodies. The VESs achieved significant vaginal lengthening. The mean vaginal canal length increased from 20.0 ± 2.4 mm to 23.8 ± 1.2 mm after removal of the VESs ( = 6, < 0.001), a 19% increase. There was a positive correlation between the expander/tension generated in the vagina and the amount of acute and chronic inflammation. H&E staining revealed increased submucosal eosinophilia in five of the six test tissues. One VES sample that was lengthened to 30 mm long showed evidence of lymphocytic and neutrophilic inflammation. Desmin immunostaining and Masson's trichrome stain revealed a thinner muscularis with more infiltrative fibrous tissue between muscle fibers in the test tissue compared to the control tissue. Although effective, the VES may provoke at least a transient increase in eosinophils consistent with a localized immune reaction during muscularis remodeling.
PubMed: 38921727
DOI: 10.3390/pathophysiology31020022 -
Current Issues in Molecular Biology May 2024The Asteraceae are widely distributed throughout the world, with diverse functions and large genomes. Many of these genes remain undiscovered and unstudied. In this...
The Asteraceae are widely distributed throughout the world, with diverse functions and large genomes. Many of these genes remain undiscovered and unstudied. In this study, we discovered a new gene in and studied its function. In this study, bioinformatics, RT-qPCR, paraffin sectioning, and tobacco transgenics were utilized to bioinformatically analyze and functionally study the three variable splice variants of the unknown gene cloned from . The results showed that and had selective 3' splicing and selective 5' splicing, and had selective 5' splicing. When the corresponding transgenic tobacco plants were subjected to abiotic stress treatment, in the tobacco seedlings, the gene and the gene enhanced salt and low-temperature tolerance and the gene enhanced low-temperature tolerance; in mature tobacco plants, the gene was able to enhance salt and low-temperature tolerance, and the and genes were able to enhance low-temperature tolerance. In summary, there are differences in the functions of the different splice variants and the different seedling stages of transgenic tobacco, but all of them enhanced the resistance of tobacco to a certain extent. The analysis and functional characterization of the gene provided new potential genes and research directions for abiotic resistance breeding in .
PubMed: 38920986
DOI: 10.3390/cimb46060314 -
Current Issues in Molecular Biology May 2024The expression and function of podoplanin (PDPN) in the normal human placenta has been debated in placental evaluation. This study emphasizes the importance of a...
Combining RNAscope, Immunohistochemistry (IHC) and Digital Image Analysis to Assess Podoplanin (PDPN) Protein and PDPN_mRNA Expression on Formalin-Fixed Paraffin-Embedded Normal Human Placenta Tissues.
The expression and function of podoplanin (PDPN) in the normal human placenta has been debated in placental evaluation. This study emphasizes the importance of a multimodal approach of PDPN expression in normal human placentas. A complete examination is performed using immunohistochemistry, RNAscope and automated Digital Image examination (DIA) interpretation. QuPath DIA-based analysis automatically generated the stromal and histological scores of PDPN expression for immunohistochemistry and RNAscope stains. The umbilical cord's isolated fibroblasts and luminal structures expressed PDPN protein and PDPN_mRNA. RNAscope detected PDPN_mRNA upregulation in syncytial placental knots trophoblastic cells, but immunohistochemistry did not certify this at the protein level. The study found a significant correlation between the IHC and RNAscope H-Score ( = 0.033) and Allred Score ( = 0.05). A successful multimodal strategy for PDPN assessment in human placentas confirmed PDPN expression heterogeneity in the full-term human normal placenta and umbilical cord at the protein and mRNA level. In placental syncytial knots trophoblastic cells, PDPN showed mRNA overexpression, suggesting a potential role in placenta maturation.
PubMed: 38920982
DOI: 10.3390/cimb46060310 -
Biosensors Jun 2024An integrated and high-throughput device for pathogen detection is crucial in point-of-care testing (POCT), especially for early diagnosis of infectious diseases and...
An integrated and high-throughput device for pathogen detection is crucial in point-of-care testing (POCT), especially for early diagnosis of infectious diseases and preventing the spread of infection. We developed an on-site testing platform that utilizes a centrifugal microfluidic chip and automated device to achieve high-throughput detection. The low-power (<32 W), portable (220 mm × 220 mm × 170 mm, 4 kg) device can complete bacterial lysis, nucleic acid extraction and purification, loop-mediated isothermal amplification (LAMP) reaction, and real-time fluorescence detection. Magnetic beads for nucleic acid adsorption can be mixed by applying electromagnetic fields and centrifugal forces, and the efficiency of nucleic acid extraction is improved by 60% compared to the no-mixing group. The automated nucleic acid extraction process achieves equivalent nucleic acid extraction efficiency in only 40% of the time consumed using the kit protocol. By designing the valve system and disc layout, the maximum speed required for the centrifugal microfluidic chip is reduced to 1500 rpm, greatly reducing the equipment power consumption and size. In detecting , our platform achieves a limit of detection (LOD) of 10 CFU/mL in 60 min. In summary, our active centrifugal microfluidic platform provides a solution for the integration of complex biological assays on turntables, with great potential in the application of point-of-care diagnosis.
Topics: Lab-On-A-Chip Devices; Nucleic Acid Amplification Techniques; Escherichia coli; Humans; Biosensing Techniques; Limit of Detection; Centrifugation; Molecular Diagnostic Techniques
PubMed: 38920617
DOI: 10.3390/bios14060313 -
CEN Case Reports Jun 2024Crystalglobulin-induced nephropathy is a rare disease that causes the deposition of crystallized monoclonal immunoglobulins into the glomerular capillary and arteriole...
Crystalglobulin-induced nephropathy is a rare disease that causes the deposition of crystallized monoclonal immunoglobulins into the glomerular capillary and arteriole spaces. Here, we report the case of a patient who presented with skin ulcers, urinary protein, and renal dysfunction. The patient underwent renal and skin biopsies, and the biopsy tissue samples were subjected to mass spectrometry. The patient was diagnosed with crystalglobulin-induced nephropathy. A literature review suggested that pathological examinations using electron microscopy, mass spectrometry, and immunofluorescent staining of paraffin-embedded biopsy samples treated with pronase may be useful for the diagnosis of this condition.
PubMed: 38918330
DOI: 10.1007/s13730-024-00906-x -
Radiation Research Jun 2024Strontium-90 is a radionuclide found in high concentrations in nuclear reactor waste and nuclear fallout from reactor accidents and atomic bomb explosions. In the 1950s,...
Strontium-90 is a radionuclide found in high concentrations in nuclear reactor waste and nuclear fallout from reactor accidents and atomic bomb explosions. In the 1950s, little was known regarding the health consequences of strontium-90 internalization. To assess the health effects of strontium-90 ingestion in infancy through adolescence, the Atomic Energy Commission and Department of Energy funded large-scale beagle studies at the University of California-Davis. Conducted from 1956 to 1989, the strontium-90 ingestion study followed roughly 460 beagles throughout their lifespans after they were exposed to strontium-90 in utero (through feeding of the mother) and fed strontium-90 feed at varying doses from weaning to age 540 days. The extensive medical data and formalin-fixed paraffin-embedded tissues were transferred from UC Davis to the National Radiobiology Archive in 1992 and subsequently to the Northwestern University Radiobiology Archive in 2010. Here, we summarize the design of the strontium-90 ingestion study and give an overview of its most frequent recorded findings. As shown before, radiation-associated neoplasias (osteosarcoma, myeloproliferative syndrome and select squamous cell carcinomas) were almost exclusively observed in the highest dose groups, while the incidence of neoplasias most frequent in controls decreased as dose increased. The occurrence of congestive heart failure in each dose group, not previously assessed by UC Davis researchers, showed a non-significant increase between the controls and lower dose groups that may have been significant had sample sizes been larger. Detailed secondary analyses of these data and samples may uncover health endpoints that were not evaluated by the team that conducted the study.
PubMed: 38917999
DOI: 10.1667/RADE-24-000022.1 -
Translational Oncology Jun 2024Pancreatic ductal adenocarcinoma (PDAC) is associated with poor prognosis, wherefore targeted therapies have experienced increasing interest. Zolbetuximab is a novel...
PURPOSE
Pancreatic ductal adenocarcinoma (PDAC) is associated with poor prognosis, wherefore targeted therapies have experienced increasing interest. Zolbetuximab is a novel targeted therapy under investigation in patients with PDAC and targets Claudin 18.2 (CLDN18.2), which is a component of tight junctions and is of significance in various solid tumors. As its role in PDAC is not definitively elucidated, this study aims to clarify the significance of CLDN18.2 expression in PDAC in a real-world setting.
METHODS
All patients (n = 309) were recruited at one of the PANCALYZE study centers and received pancreatic resection with curative intention. Paraffin samples were analyzed using an antibody against CLDN18.2, which is known to be comparable to the antibody used by the SPOTLIGHT and GLOW studies.
RESULTS
94 PDACs are positive for CLDN18.2 (30.4 %). Positive CLDN 18.2 expression was associated with significantly better cancer differentiation (p < 0.001). Patients with positive CLDN18.2 expression showed significantly better overall survival when compared to patients with negative expression (median OS: 30 versus 18 months, p = 0.003). Additionally, in multivariable analyses, CLDN18.2 expression was identified as an independent factor for better survival in patients with PDAC (HR = 0.686, 95 %CI = 0.492-0.956, p = 0.026).
CONCLUSION
Significant improvement in survival could be demonstrated by adding Zolbetuximab to known chemotherapy regimes in patients with gastro-esophageal junction adenocarcinoma with at least 75 % CLDN18.2 positive cancer cells. Our findings demonstrate, that 30.4 % of the included patients with PDAC would potentially be eligible for therapy with Zolbetuximab in a real-world patient cohort. Results of trials targeting Claudin 18.2 are pending in patients with PDAC.
PubMed: 38917592
DOI: 10.1016/j.tranon.2024.102044 -
Thyroid : Official Journal of the... Jun 2024While the impact of tumor-immune infiltrate has been reported on differentiated thyroid cancer behavior (DTC), the expression of immune checkpoints [programmed cell...
BACKGROUND
While the impact of tumor-immune infiltrate has been reported on differentiated thyroid cancer behavior (DTC), the expression of immune checkpoints [programmed cell death protein 1 (PD-1) and its ligand (PD-L1)] alone has not been able to predict response to immunotherapies. We aimed to identify tumor-infiltrating immune cells and checkpoints associated with DTC.
METHODS
We performed multiplex immunofluorescence on de-paraffinized thyroid tissue collected at thyroidectomy from 17 adults with DTC to characterize the tumor immune microenvironment for leukocytes (CD45+), T cells (CD3+), T regulatory cells (Tregs) (CD3+FOXP3+), CD4+ T cells (CD3+CD4+), CD8+ T cells (CD3+CD8+), macrophages (CD68+), M2 macrophages (CD68+CD163+), M1 Macrophages (CD68+iNOS+) and immune checkpoints PD-1 and PD-L1. We compared the mean percentage expression of immune markers between tumor and adjacent thyroid tissue from the same patient by paired t-test and performed spatial analysis along the tumor's leading edge.
RESULTS
Immune checkpoints PD-1 and PD-L1 showed a significant increase in expression intratumorally as compared to adjacent thyroid tissue (p<0.05). A higher trend for M2 macrophages was observed intratumorally compared to adjacent tissue. Along the leading edge, PD-L1 expression correlated negatively with CD45 and positively with CD163 intratumorally. On exploratory analysis, there was a non-significant trend for higher FOXP3 but less CD8 and iNOS expression in tumor from DTC with (n=3) versus without distant metastases (n=14). There was a non-significant trend for higher CD58 and iNOS expression in DTC with (n=7) than without thyroiditis (n=10).
CONCLUSIONS
Higher tumoral PD-1 and PD-L1 expression indicate their role in DTC occurrence. A trend for more Tregs and M2 macrophages but less M1 macrophages intratumorally in patients with distant metastatic DTC, suggests their potential role as prognostic biomarkers. Future studies with larger sample sizes are needed to compare various clinicopathologic severities to harness tumor microenvironment for cancer prognostication and therapy.
PubMed: 38916182
DOI: 10.1089/thy.2024.0072