Paraffin-embedded Tissue Sections Research Articles

Modification of the hi-c technology for molecular genetic analysis of formalin-fixed paraffin-embedded sections of tumor tissues

Molecular genetic analysis of tumor tissues is the most important step towards understanding the mechanisms of cancer development, and it is also necessary for the choice of targeted therapy. Hi-C (high-throughput chromatin conformation capture) technology can be used to detect various types of genomic variants, including balanced chromosomal rearrangements: inversions and translocations. In this work, we propose a modification of the Hi-C method for the analysis of chromatin contacts in formalin-fixed paraffin-embedded (FFPE) sections of tumor tissues. Our results demonstrate that this protocol allow to generate high-quality Hi-C data and detect all types of chromosomal rearrangements. We have analyzed various databases to compile a comprehensive list of translocations that hold clinical importance for targeted therapy selection. The practical value of molecular genetic testing is its ability to influence patient treatment strategies and provide prognostic insights. Detecting specific chromosomal rearrangements can guide the choice of targeted therapies, which is a critical aspect of personalized medicine in oncology.

Spatial Analysis of Gene Expression by In Situ Hybridization.

The analysis of the spatial expression patterns of genes is important for deciphering their functions. In situ hybridization provides insight into gene expression patterns at the cellular level. Here we describe a procedure for performing in situ hybridization on sections of paraffin-embedded tissue, including synthesis of labeled RNA probes, hybridization of the probes with target mRNAs, and immunological detection of the signals. The method enables evaluation of the expression patterns of genes in a variety of tissues of rice.

The relationship between the Prognostic Nutritional Index and lymphovascular and perineural invasion of the tumor in patients diagnosed with gastric cancer, and its effect on overall survival.

A low Prognostic Nutritional Index (PNI) value, lymphovascular invasion (LVI), and perineural invasion (PeNI) have been identified as indicators of poor prognosis for many malignancies. We aimed to evaluate the relationship between PNI and LVI/PeNI, their prognostic significance, and their effect on overall survival in gastric cancer patients who underwent curative gastrectomy. A cutoff value of 39.8 was taken for the PNI, and PNI < 39.8 was defined as moderate to severe malnutrition. Patients were grouped as PNI-low (PNI < 39.8) and PNI-high (PNI ≥ 39.8). Paraffin-embedded tissue sections of surgical specimens were used to evaluate PeNI as defined by previously reported criteria. The study included 270 patients with ages ranging from 23 to 90 years. The mean PNI was calculated as 39.8 ± 6.35. PeNI was detected in 232 patients (85.93%), and LVI was identified in 248 patients (91.85%). It was observed that the PNI value of patients with an expired status in the PNI < 39.8 group was lower compared to those who survived, and in patients with PNI > 39.8, those without PeNI had better survival. The presence of PeNI in patients with PNI > 39.8 increased the mortality risk by 2.088 units, while in patients with PNI > 39.8, it was found that those without LVI had better survival, and the presence of LVI increased the mortality risk by 3.171 units. Mortality developed in 166 patients (61.48%) during the five-year follow-up period. The five-year overall survival was found to be 31.02 ± 21.73 months. In patients with gastric cancer, the PNI, LVI, and PeNI are independent prognostic factors for overall survival in postoperative patients. A low PNI score is an inherently poor prognostic factor. In patients with a high PNI score, the presence of positive LVI and PeNI negatively impacts survival. We found that in patients with a low PNI, the rates of PeNI and LVI are higher compared to those with a high PNI, and this significantly affects mortality.

Single cell spatial profiling of FFPE splenic tissue from a humanized mouse model of HIV infection

BackgroundLatency remains a major obstacle to finding a cure for HIV despite the availability of antiretroviral therapy. Due to virus dormancy, limited biomarkers are available to identify latent HIV-infected cells. Profiling of individual HIV-infected cells is needed to explore potential latency biomarkers and to study the mechanisms of persistence that maintain the HIV reservoir.MethodsSingle cell spatial transcriptomic characterization using the CosMx Spatial Molecular Imager platform was conducted to analyze HIV-infected cells in formalin-fixed paraffin-embedded sections of splenic tissue surgically obtained from an HIV-infected humanized mouse model. Regulation of over a thousand human genes was quantified in both viremic and aviremic specimens. In addition, in situ hybridization and immunohistochemistry were performed in parallel to identify HIV viral RNA- and p24-containing cells, respectively. Finally, initial findings from CosMx gene profiling were confirmed by isolating RNA from CD4 + T cells obtained from a person living with HIV on antiretroviral therapy following either PMA/Ionomycin or DMSO treatment. RNA was quantified using qPCR for a panel of targeted human host genes.ResultsSupervised cell typing revealed that most of the HIV-infected cells in the mouse spleen sections were differentiated CD4 + T cells. A significantly higher number of infected cells, 2781 (1.61%) in comparison to 112 (0.06%), and total HIV transcripts per infected cell were observed in viremic samples compared to aviremic samples, respectively, which was consistent with the data obtained from ISH and IHC. Notably, the expression of 55 genes was different in infected cells within tissue from aviremic animals compared to viremic. In particular, both spleen tyrosine kinase (SYK) and CXCL17, were expressed approximately 100-fold higher. This data was further evaluated against bulk RNA isolated from HIV-infected human primary CD4 + T cells. A nearly 6-fold higher expression of SYK mRNA was observed in DMSO-treated CD4 + T cells compared to those stimulated with PMA/Ionomycin.ConclusionThis study found that the CosMx SMI platform is valuable for assessing HIV infection and providing insights into host biomarkers associated with HIV reservoirs. Higher relative expression of the SYK gene in aviremic-infected cells from the humanized mouse HIV model was consistent with levels found in CD4 + T cells of aviremic donors.

Association of spleen cells with stem cell traits with the development of hematogenous metastases

BACKGROUND: Spleen status is associated with survival in carcinomas. One of the mechanisms may be related to the effects of immunosuppressive hematopoietic cells originating from the spleen. AIM: To study the composition and quantity of hematopoietic cells with stem cell traits in the spleen and their association with hematogenous metastasis in patients with different nosological forms of carcinomas. MATERIAL AND METHODS: The study included 40 patients with stomach cancer, cardioesophageal junction cancer, cancer of pancreas, splenic flexure of the colon, sigmoid colon, kidney, ovary and uterus. The subgroup with hematogenous metastases (15 patients) included 7 cases of stomach cancer, 1 case of cardioesophageal junction cancer, 4 cases of colon cancer, 1 case of pancreatic cancer, 1 case of kidney cancer, and 1 case of ovarian cancer. The subgroup without hematogenous metastases (13 patients) included 6 cases of stomach cancer, 4 cases of cardioesophageal junction cancer, 1 case of colon cancer, 1 case of pancreatic cancer, and 1 case of uterine cancer. Formalin-fixed and paraffin-embedded spleen tissue sections served as the study material. The method of multiplex tyramide signal amplification — modified immunohistochemistry of tissue sections was applied, using antibodies to CD45, CD34, CD133, TIE2, VEGFR1, CD90, CD11b. The studied parameters were described as median (Me) and interquartile range (Q1–Q3). Differences in parameters were assessed using the Mann–Whitney criterion. ROC analysis was used to assess the prognostic value of the parameters. Differences were considered significant at a significance level of p 0.05. RESULTS: The study of spleen tissue with simultaneous determination of several markers on each cell allowed us to identify 20 phenotypes related to representatives of the continuum of hematopoietic stem cells and the continuum of stem cells with hematopoietic/angiogenic potentials, characterized by pronounced phenotypic diversity. In the general group, including all the studied nosological forms, the number of stem cells with the CD45–CD34+CD133–TIE2–VEGFR1– phenotype found in the lymphoid follicles of the spleen was lower in cases with hematogenous metastases: 43.313 (0.00–85.393) and 110.034 (83.050–197.915) (p=0.03), respectively. In the group of gastric cancer patients with hematogenous metastases, a lower number of stem cells with the CD45–CD34+CD133–TIE2–VEGFR1– phenotype [31.092 (0.000–37.987)] compared to the group without hematogenous metastases [119.962 (103.486–258.533)] (p=0.001), a higher number of stem progenitor cells with the CD45+CD34–CD133+TIE2–VEGFR1– phenotype determined in the lymphoid follicle [7901.164 (5705.314–8563.807) versus 4670.894 (3328.607–6473.649)] (p=0.035), as well as a higher number of cells with phenotype CD45+CD34–CD133+TIE2+VEGFR1+, identified in the red pulp of the spleen [131.396 (35.701–167.521) versus 21.524 (6.123–30.117)] (p=0.02), were found. CONCLUSION: The number of spleen cells with the phenotypes CD45–CD34+CD133–TIE2–VEGFR1–, CD45+CD34–CD133+TIE2–VEGFR1– and CD45+CD34–CD133+TIE2+VEGFR1+ is associated with hematogenous metastasis.

Telomere Length Measurement in Human Tissue Sections by Quantitative Fluorescence In Situ Hybridization (Q-FISH).

Telomeres in most somatic cells shorten with each cell division, and critically short telomeres lead to cellular dysfunction, cell cycle arrest, and senescence. Thus, telomere shortening is an important hallmark of human cellular senescence. Quantitative fluorescence in situ hybridization (Q-FISH) using formalin-fixed paraffin-embedded (FFPE) tissue sections allows the estimation of telomere lengths in individual cells in histological sections. In our Q-FISH method, fluorescently labelled peptide nucleic acid (PNA) probes are hybridized to telomeric and centromeric sequences in FFPE human tissue sections, and relative telomere lengths (telomere signal intensities relative to centromere signal intensities) are measured. This chapter describes our Q-FISH protocols for assessing relative telomere lengths in FFPE human tissue sections.

Genetic Signatures: CD44 Single-Nucleotide Polymorphisms Affect Cell Surface Expression and Elevate Risk in Head and Neck Squamous Cell Carcinoma.

This study aimed to investigate the impact of single-nucleotide polymorphisms (SNPs) in the CD44 gene, specifically in the 3'UTR region (rs13347) and intronic region (rs187115), on the cell surface expression of CD44 protein and the risk of development of head and neck squamous cell carcinoma (HNSCC). The study involved analysis of 85 samples and 85 healthy controls. Immunohistochemistry (IHC) and flow cytometry were used to assess cell surface protein expression using CD44 antibody. DNA from formalin-fixed paraffin-embedded tissue sections was isolated and amplified using targeted primers. Sanger sequencing of the resultant amplified products was performed to determine the genotypes of the CD44 rs13347 and rs187115 SNPs. GTEx and RegulomeDB were queried to evaluate the genotypic effects of these variants on target gene expression and regulation. A comparison between patients with HNSCC and healthy controls revealed a significant association between CD44 rs13347 and an increased risk of HNSCC in all the analyzed models, especially the TT genotype showed a significantly higher risk with an odds ratio of 8.69 (95% CI, 2.35 to 32.09; P = .0003). However, no significant association was found between CD44 rs187115 and HNSCC in any of the models analyzed (all P > .05). Other notable findings included significant associations between CD44 rs13347 genotype and age (P = .031), number of CD44-positive tumor cells (P = .049), CD44 staining intensity (SI; P = .039), and CD44 immunoreactivity score (IRS) status (P = .019). The T allele and homozygous TT genotype of CD44 rs13347 SNP were associated with increased susceptibility to HNSCC and decreased proportion of CD44-positive tumor cells, low SI, and reduced IRS.

Combining Data Independent Acquisition With Spike-In SILAC (DIA-SiS) Improves Proteome Coverage and Quantification

Data-independent acquisition (DIA) is increasingly preferred over data-dependent acquisition due to its higher throughput and fewer missing values. Whereas data-dependent acquisition often uses stable isotope labeling to improve quantification, DIA mostly relies on label-free approaches. Efforts to integrate DIA with isotope labeling include chemical methods like mass differential tags for relative and absolute quantification and dimethyl labeling, which, while effective, complicate sample preparation. Stable isotope labeling by amino acids in cell culture (SILAC) achieves high labeling efficiency through the metabolic incorporation of heavy labels into proteins invivo. However, the need for metabolic incorporation limits the direct use in clinical scenarios and certain high-throughput experiments. Spike-in SILAC (SiS) methods use an externally generated heavy sample as an internal reference, enabling SILAC-based quantification even for samples that cannot be directly labeled. Here, we combine DIA-SiS, leveraging the robust quantification of SILAC without the complexities associated with chemical labeling. We developed DIA-SiS and rigorously assessed its performance with mixed-species benchmark samples on bulk and single cell-like amount level. We demonstrate that DIA-SiS substantially improves proteome coverage and quantification compared to label-free approaches and reduces incorrectly quantified proteins. Additionally, DIA-SiS proves effective in analyzing proteins in low-input formalin-fixed paraffin-embedded tissue sections. DIA-SiS combines the precision of stable isotope-based quantification with the simplicity of label-free sample preparation, facilitating simple, accurate, and comprehensive proteome profiling.

Periodic Acid Schiff Staining to Detect Mott Cells, Aberrant Plasma Cells Containing Immunoglobulin Inclusions Called Russell Bodies.

Hematoxylin and eosin staining is widely used for routine histopathological analysis under light microscopic examination to determine alterations of tissue architecture and cellular components in animal studies. Aside from hematoxylin/eosin staining, periodic acid Schiff (PAS) staining is used to detect polysaccharides and carbohydrate-rich macromolecules, and is essential in immunological fields for evaluation of glomerular lesions of kidneys in autoimmune animals. Since erythrocytes are not stained by PAS, this stain is also helpful for identifying changes in immune cells in the red pulp of the spleen, which is filled with erythrocytes. This article describes a protocol to detect Mott cells, bizarre plasma cells containing immunoglobulin inclusion bodies (Russell bodies) in the cytoplasm. The protocol can be used for formalin-fixed, paraffin-embedded tissue sections, frozen tissue sections, tissue-touch preparations, blood films, and cytocentrifuged cell smears. © 2024 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Detection of Mott cells by PAS staining in formalin-fixed, paraffin-embedded tissue sections Basic Protocol 2: Detection of Mott cells by PAS staining in frozen tissue sections, touch preparations, blood films, and cytocentrifuged cell smears.

Making Multiplexed Imaging Flexible: Combining Essential Markers With Established Antibody Panels.

Multiplexed immunofluorescence (IF) can be achieved using different commercially available platforms, often making use of conjugated antibodies detected in iterative cycles. A growing portfolio of pre-conjugated antibodies is offered by the providers, as well as the possibility for in-house conjugation. For many conjugation methods and kits, there are limitations in which antibodies can be used, and conjugation results are sometimes irreproducible. The conjugation process can limit or slow down the progress of studies requiring conjugation of essential markers needed for a given project. Here, we demonstrate a protocol combining manual indirect immunofluorescence (IF) of primary antibodies, followed by antibody elution and staining with multiplexed panels of commercially pre-conjugated antibodies on the PhenoCycler platform. We present detailed protocols for applying the workflow on fresh frozen and formalin fixed paraffin embedded tissue sections. We also provide a ready to use workflow for coregistration of the images and demonstrate this for two examples.

Gene and Protein Expression of MAGE and Associated Immune Landscape Elements in Non-Small-Cell Lung Carcinoma and Urothelial Carcinomas.

Melanoma-associated antigen-A (MAGE-A) is expressed in multiple cancers with restricted expression in normal tissue. We sought to assess the MAGE-A3/A6 expression profile as well as immune landscape in urothelial (UC) and non-small cell lung carcinoma (NSCLC). We also assessed co-expression of immune-associated markers, including programmed cell death ligand 1 (PD-L1) in tumor and/or immune cells, and assessed the effect of checkpoint inhibitor treatment on these markers in the context of urothelial carcinoma. We used formalin-fixed paraffin-embedded (FFPE) tissue sections from a variety of tumor types were screened by IHC for MAGE-A and PD-L1 expression. Gene expression analyses by RNA sequencing were performed on RNA extracted from serial tissue sections. UC tumor samples from patients treated with checkpoint inhibitors were assessed by IHC and NanoString gene expression analysis for MAGE-A and immune marker expression before and after treatment. Overall, 84 samples (57%) had any detectable MAGE-A expression. Detectable MAGE-A expression was present at similar frequencies in both tumor tissue types, with 41 (50%) NSCLC and 43 (64%) UC. MAGE-A expression was not significantly changed before and after checkpoint inhibitor therapy by both IHC and NanoString mRNA sequencing. Other immune markers were similarly unchanged post immune checkpoint inhibitor therapy. Stable expression of MAGE-A3/A6 pre and post checkpoint inhibitor treatment indicates that archival specimens harvested after checkpoint therapy are applicable to screening potential candidates for MAGE therapies.

TRICHINELLA AND AT LEAST THREE SPECIES OF SARCOCYSTIS PARASITIZE THE MUSCLES OF BOBCATS (LYNX RUFUS) FROM MISSISSIPPI.

Muscles of 25 bobcats (Lynx rufus) from remote areas of Mississippi in 2017 were tested for parasites. Testing for Sarcocystis infections included microscopic examination of fresh unstained muscle squashes, pepsin digestion of hearts and tongues, and histological sections of paraffin-embedded tissues. Sarcocystis spp. infections were detected in the muscles of 21 (84%) by a combination of methods. Sarcocysts were detected in the unstained tongue squashes of 2 bobcats. Sarcocystis sp. bradyzoites were detected in the pepsin digests of 3 of 19 hearts, and 12 of 19 tongues. In paraffin-embedded histological sections, sarcocysts were detected in 7 of 25 hearts, 17 of 25 tongues, and 5 of 23 limb muscles. Based on the character of the cyst wall, at least 3 morphologic types of sarcocysts were detected: those with small spikes on the cyst wall, corresponding to Sarcocystis felis, those with long villar protrusions, corresponding to Sarcocystis neurona, and those lacking visible cyst wall protrusions, representing an unidentified type of sarcocyst. Myositis associated with sarcocysts was seen in the tongues of 3, and in the limb muscles of 1 bobcat. Multilocus genotyping of the DNA extracted from paraffin-embedded sections from 2 bobcats, employing 18S, 28S, COI, ITS-1, and 5.8S and rpoB genes, diagnosed Sarcocystis caninum, S. felis, Sarcocystis lutrae, and S. neurona. An encapsulated species of Trichinella was identified in the tongue of 1; it represents the first documented occurrences in bobcats from Mississippi. Taken together, these observations suggest intensive exposure of these wild carnivores to Trichinella tissue cysts, implies predation or scavenging on these tissues promotes parasite transmission, and raises caution concerning zoonotic risk when such meat is rendered for human consumption.

Exploring Therapeutic Challenges in Patients with HER2-Positive Breast Cancer-A Single-Center Experience.

Breast cancer is one of the most common forms of neoplasia worldwide. The purpose of our observational study was to evaluate the status of HER2 overexpression among new cases of breast neoplasia with an impact on the natural history of breast cancer disease and therapeutic personalization according to staging. This study included 45 breast cancer patients which have an overexpression of HER2 through the mutation of the EGFR-ERBB2 receptor. Immunohistochemical staining was performed on sections of formalin-fixed paraffin-embedded breast tissue. The patients were evaluated demographically and therapeutically in all stages. The post-surgical histopathological examination revealed complete pathological responses in 19 patients and pathological responses with residual disease either at the tumor level or lymphatic or both variants in a percentage of 44% (15 cases). The disease-free interval (DFI) under anti-HER2 therapy was recorded in 41 patients, representing 91% of the study group. Anti-HER2 therapy in any therapeutic stage has shown increased efficiency in blocking these tyrosine kinase receptors, evidenced by the high percentage of complete pathological responses, as well as the considerable percentage (47%) of complete remissions and stationary disease, in relation to the HER2-positive patient group.

Molecular and ultrastructural morphological analyses of highly metamorphosed Aspergillus fumigatus on human formalin-fixed paraffin-embedded tissue.

Invasive fungal infections including invasive pulmonary aspergillosis (IPA) generally have a poor prognosis, because the fungi spread throughout various organs. Therefore, it is important to accurately identify the fungal species for treatment. In this article, we present the results of pathological and molecular morphological analyses that were performed to elucidate the cause of respiratory failure in a patient who died despite suspicion of IPA and treatment with micafungin (MCFG). Pathological analysis revealed the existence of cystic and linear fungi in lung tissue. The fungi were identified as Aspergillus fumigatus (A. fumigatus) by partial sequencing of genomic DNA. Correlative light microscopy and electron microscopy (CLEM) analysis confirmed that fungi observed with light microscopy can also be observed with scanning electron microscopy (SEM) using formalin-fixed paraffin-embedded tissue sections. SEM revealed an atypical ultrastructure of the fungi including inhomogeneous widths, rough surfaces, and numerous cyst-like structures of various sizes. The fungi showed several morphological changes of cultured A. fumigatustreated with MCFG that were previously reported. Our results indicate that integrated analysis of ultrastructural observation by SEM and DNA sequencing may be an effective tool for analyzing fungi that are difficult to identify by conventional pathological analysis.

Aspergillosis coinfection in patients with proven mucormycosis.

Although research on aspergillosis and mucormycosis confection is important to optimize antifungal therapy, data on this issue is scarce. Thus, we systematically investigated aspergillosis coinfection in patients with proven mucormycosis. Medical records of adult patients with proven mucormycosis whose formalin-fixed paraffin-embedded (FFPE) tissue sections were available, in a tertiary hospital from August 2007 to July 2023 were retrospectively reviewed to assess coinfection with aspergillosis. We noted cultures of fungi from sterile and non-sterile sites and performed polymerase chain reaction (PCR) assays on FFPE tissues to detect Aspergillus- and Mucorales-specific DNA. Sixty-seven patients with proven mucormycosis, including 12 (18%) with a positive culture of the mucormycosis agent from sterile site cultures, were enrolled. Fungal cultures from sterile and non-sterile sites revealed Aspergillus spp. growth in nine (13%) of the 67 patients, including two sterile and seven non-sterile cultures. The fungal PCR analysis from the FFPE sections was positive for Aspergillus-specific PCR in five (7%) and positive for both Aspergillus- and Mucorales-specific PCR results in eight (12%). Overall, 21 (31%) of the 67 patients with proven mucormycosis had microbiologic and/or molecular evidence of aspergillosis coinfection. Positive blood or bronchoalveolar lavage fluid galactomannan results were more common in the coinfection group (67% [14/21]) than in the mucormycosis group (37% [17/46], P=.024). No significant difference in mortality between the two groups was observed. Approximately one-third of patients with proven mucormycosis exhibited molecular and/or microbiologic evidence of aspergillosis coinfection. Further research is needed to identify patients with aspergillosis and mucormycosis coinfections, for optimal antifungal therapy.

Association of Epstein-Barr virus (EBV) with nasopharyngeal carcinoma: Experience from a North Indian tertiary care hospital

IntroductionNasopharyngeal carcinoma (NPC), arising from nasopharyngeal epithelium is caused by Epstein-Barr virus (EBV). It is common in South China, South East Asia and North East India. The aim and objectives of this study were to determine the prevalence of EBV in formalin-fixed paraffin-embedded (FFPE) tissue sections of clinically suspected NPC patients, correlate the results of polymerase chain reaction (PCR) with histopathology findings, and to determine the utility of tissue EBV DNA as a diagnostic bio-marker. Materials and methods31 FFPE tissue samples were collected from clinically suspected NPC patients from April 2018–December 2019. Histopathological diagnosis was done by examination of Hematoxylin and Eosin stained slides. Presence of EBV was detected by EBNA-1 PCR. IHC was performed using EBV Latent Membrane Protein 1. ResultsOf the 31 clinically suspected NPC cases, 15 (48.4 %) were histopathological confirmed NPC. Of these15, 13 (86.6 %) were non-keratinising undifferentiated NPC, and one each were keratinising NPC and non-keratinising differentiated NPC respectively.EBV EBNA1 PCR was positive in 35.5 % (11/31) of clinically suspected NPC cases. Of the 11 PCR positive cases, 9 (81.8 %) were histopathological confirmed NPC.Of the 31 clinically suspected NPC cases, IHC was indicated in 23 biopsies. Of which, 12 (52.2 %) were positive for LMP1 in the abnormal cells. Of the 12 IHC positive samples, 10 were NPC cases. ConclusionEBV DNA as an indicator towards NPC among clinically suspected cases had a sensitivity of 60 % and specificity of 87.5 %. In this study, addition of EBV DNA detection by PCR from FFPE tissue sections could confirm EBV association in 20 % of cases where it was not detected by EBV LMP1 IHC, thus helped in increasing the detection of EBV positivity in NPC cases. Early diagnosis of NPC will improve the cure rate and hence reduce the morbidity and mortality rates.

Decreased expression of galectin-3 in the epidermis of psoriasis patients.

Conventional histopathological features of psoriasis and atopic dermatitis often overlap. We aimed to investigate Galectin-3 (Gal-3) expression in psoriatic skin lesions and its potential as an immunohistochemical marker for distinguishing between psoriasis and atopic dermatitis on a pathological basis. Based on immunohistochemical analysis, we assessed Gal-3 expression in formalin-fixed, paraffin-embedded tissue sections from 21 patients with psoriasis and 15 patients with atopic dermatitis. Quantitative analysis of expression intensity was performed using the average density (average optical density) method. We analysed the relationship between Gal-3 expression and clinical characteristics, as well as conventional histopathological features. Patients with psoriasis exhibited significantly decreased Gal-3 expression in the epidermis (0.11±0.05) compared to the atopic dermatitis group (0.36±0.15) and healthy controls (0.49±0.13) (p<0.0001). Reduction in Gal-3 expression in the psoriatic epidermis around areas of neutrophil aggregation was more pronounced than around areas of non-neutrophil aggregation (0.07±0.02 vs 0.16±0.05, p<0.01). In both psoriasis (r=-0.48, p<0.05) and atopic dermatitis groups (r=-0.70, p<0.01), Gal-3 expression negatively correlated with epidermal thickness. When epidermal thickness was matched between the two groups, the decrease in epidermal Gal-3 expression remained significant in the psoriasis group compared to the atopic dermatitis group (0.14±0.05 Vs 0.30±0.07, p<0.01). Patients with psoriasis show specific downregulation of epidermal Gal-3, correlating with epidermal thickness and neutrophil-related factors. Gal-3 may serve as an auxiliary discriminative marker between psoriasis and atopic dermatitis, potentially associated with keratinocyte proliferation and neutrophil function.

Differential Abundance of DNA Damage Sensors and Innate Immune Signaling Proteins in Inositol Polyphosphate 4-Phosphatase Type II–Negative Triple-Negative Breast Cancer Classified by Immunotype

The influence of neoplastic cells on the tumor microenvironment is poorly understood. In this study, eight patient samples representing two immunotypes of triple-negative breast cancer (TNBC), defined by quantitative histologic criteria as T-cell desert and T-cell infiltrated (TCI), were compared via label-free quantitative protein mass spectrometry of material extracted directly from targeted regions of formalin-fixed, paraffin-embedded tissue sections. Of 2934 proteins quantitated, 439 were significantly differentially abundant, among which 361 were overabundant in TCI-TNBC. The 361-protein group included proteins involved in major histocompatibility complex-I antigen processing and presentation, viral defense, DNA damage response, and innate immune signaling. Immunohistochemical validation of selected proteins showed good positive correlation between neoplastic cell histoscores and label-free quantitation. Extension of immunohistochemical analysis to a total of 58 inositol polyphosphate 4-phosphatase type II-negative TNBC confirmed elevated levels of the DNA damage sensor interferon-γ-inducible protein 16, inflammasome adaptor ASC, and pore-forming protein gasdermin D in TCI-TNBC neoplastic cells. By contrast, cGMP-AMP synthase inhibitor BAF was elevated in the neoplastic cells of T-cell desert TNBC. These findings demonstrate a previously unknown correlation between the degree of T-cell infiltration in inositol polyphosphate 4-phosphatase type II-negative TNBC and the levels, in cognate neoplastic cells, of proteins that modulate innate immune signaling in response to DNA damage.

Sensitive Multiplexed MicroRNA Spatial Profiling and Data Classification Framework Applied to Murine Breast Tumors.

MicroRNAs (miRNAs) are small RNAs that are often dysregulated in many diseases, including cancers. They are highly tissue-specific and stable, thus, making them particularly useful as biomarkers. As the spatial transcriptomics field advances, protocols that enable highly sensitive and spatially resolved detection become necessary to maximize the information gained from samples. This is especially true of miRNAs where the location their expression within tissue can provide prognostic value with regard to patient outcome. Equally as important as detection are ways to assess and visualize the miRNA's spatial information in order to leverage the power of spatial transcriptomics over that of traditional nonspatial bulk assays. We present a highly sensitive methodology that simultaneously quantitates and spatially detects seven miRNAs in situ on formalin-fixed paraffin-embedded tissue sections. This method utilizes rolling circle amplification (RCA) in conjunction with a dual scanning approach in nanoliter well arrays with embedded hydrogel posts. The hydrogel posts are functionalized with DNA probes that enable the detection of miRNAs across a large dynamic range (4 orders of magnitude) and a limit of detection of 0.17 zeptomoles (1.7 × 10-4 attomoles). We applied our methodology coupled with a data analysis pipeline to K14-Cre Brca1f/fTp53f/f murine breast tumors to showcase the information gained from this approach.

Integrated On-Slide Positive Controls for Immunocytochemistry on Cytology Slides.

Integrated on-slide positive controls are a standard quality assurance and quality control measure for immunohistochemistry on formalin-fixed paraffin-embedded tissue sections. They ensure identical analytical conditions for the control and patient samples. Our aim was to develop a procedure for preparing integrated on-slide positive controls for immunocytochemistry (ICC) on methanol-fixed cytospins. Leftover diagnostic cytology samples with sufficient cells and confirmed expression of Calretinin, MOC31, TTF1, and hormone receptors were used as control samples. Cells from the control samples were deposited on the peripheral part of objective slides using standard cytocentrifuge equipment. Cytospins were immediately fixed in methanol for at least 30 min and then covered with polyethylene glycol (PEG). Completely dry and solid PEG was removed from the central part of the objective slides and stored at room temperature. Patient samples were subsequently added to the central part of a PEG-protected slide, with an appropriate positive control placed on the peripheral part, and then fixed in methanol. ICC was performed on the Ventana/Roche automated platform ULTRA, using optimized and validated protocols for TTF1, hormone receptors, and double immunostaining for Calretinin/MOC31. The quality of ICC reactions for both deposits on the same slide and potential cell carryover was evaluated retrospectively. In the period from October 2021 to December 2023, the majority of integrated positive controls (364/368, 99%) consistently exhibited unequivocally positive reactions for TTF-1 (n = 93), hormone receptors (n = 84), and double staining for Calretinin/MOC31 (n = 191), with easily interpretable ICC reactions on corresponding patient samples. No obvious carryover of cells from the control sample to the patient sample was observed during this period. A novel approach developed for preparing integrated on-slide positive controls for ICC on methanol-fixed cytospins using standard cytocentrifugation is low-cost and can be widely applied in diagnostic cytology laboratories. Simultaneous ICC procedures for the control and patient samples on the same slide ensure identical analytical conditions for both samples, providing the highest level of quality control while reducing costs. Interpreting both ICC reactions on the same slide is time-efficient and convenient.