Formalin-fixed Tissue Research Articles

Subcellular expression of CD30 in cutaneous mastocytosis-An important factor for targeted treatment.

The subcellular distribution of CD30 on mast cells and the presence of eosinophils in cutaneous mastocytosis require further investigation, especially as the cell surface expression of CD30 is critical for the therapeutic response of systemic mastocytosis to brentuximab vedotin. Investigation of 147 biopsy specimens from 143 patients with cutaneous mastocytosis for mast cell density and distribution, frequency of CD30 expression, CD30 staining patterns, and presence and distribution of eosinophils. Correlation with clinical patterns. Retrospective multicenter immunohistochemical study of CD30 expression, eosinophils and basic clinical data in cutaneous mastocytosis. CD30 expression was found in all samples (cut-off: ≥1%), whereby the staining was predominantly cytoplasmic in 99% of the samples. Additional membrane staining was detected in 62% of the samples. Surface expression of CD30 was more common in biopsy specimens with a high mast cell burden and in biopsy specimens with a higher CD30 expression rate. Eosinophils were admixed in 58% of the samples. Females and older patients showed a trend of a lower mast cell burden. Retrospective study on formalin-fixed and paraffin-embedded tissue without functional analysis. Most cases of cutaneous mastocytosis show cell surface expression of CD30 expression and is, therefore, in principle, accessible for therapy with antibodies against CD30, provided the overall situation of the patient warrants.

Evaluation of a targeted anti-αvβ3 integrin near-infrared fluorescent dye for fluorescence-guided resection of naturally occurring soft tissue sarcomas in dogs.

Complete resection is a key prognostic factor for survival in patients with soft tissue sarcoma (STS), in humas and companion animals alike. Fluorescence-guided surgery could improve resection accuracy. As dogs are frequently affected by STS, they serve as a model to test an anti-αvβ3 integrin targeting near-infrared fluorescent (NIRF) dye (AngiostampTM800) for fluorescence-guided surgery in STS to evaluate its safety and feasibility in dogs, and if it translates into a clinically relevant benefit compared to the standard of care with regards to completeness of surgery and local recurrence. Furthermore, we aimed to correlate target expression and NIRF-signal intensity. Twenty dogs with STS were randomly allocated to either receive Angiostamp™ (NIRF group) or physiologic saline (control group) preoperatively. The researchers were blinded for treatment, and resections were adapted based on the NIRF-signal, if needed. Margin status was histologically determined at the 1 and 3cm margin. The tumor-to-background ratio was measured in native tissue biopsies and formalin-fixed tissue. The fluorescent area was compared to the corresponding tumor areas as confirmed by histology using the Dice coefficient. Target expression was quantified by immunohistochemistry and correlated to NIRF-signal ratios. A fluorescent signal was detected in all 10 tumors of the NIRF group, with a tumor-to-background ratioof 7.4 ± 5.8 in native biopsies and 13.5 ± 10.9 in formalin-fixed tissue. In the NIRF group, resection margins were adapted in 5/10 cases, leading to complete resection and preventing R1 in four of these cases. In the NIRF and control group 9/10 and 8/10 resections were R0, with one local recurrence in each group and one sarcoma-related death in the NIRF group. The NIRF-signal correlated with the histologically confirmed tumor area (Dice coefficient 0.75 ± 0.17). Target expression was higher in tumor compared to peritumoral tissue (p < 0.0003) and showed a moderate correlation with the NIRF-signal (r = 0.6516, p < 0.0001). Fluorescence-guided surgery using Angiostamp™ can pinpoint residual disease in the tumor bed and contributes to an improved resection accuracy in canine STS.

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.

Use of Carrot Oil, Olive Oil, Pine Oil, Rose Oil in Comparison to Xylene as Clearing Agent During Tissue Processing: an in Vitro Study

ABSTRACT: Background: Clearing plays a vital role in histological section preparation. Xylene has long been valued for its ability to efficiently deparaffinize and clear tissue samples. However, its hazardous properties have raised health and environmental concerns, leading researchers to seek alternative solvents for tissue processing. This study utilized safer substitutes to address these concerns. Aim: To assess the clearing ability of four different oils i.e., Carrot oil, Olive oil, Pine oil, and Rose oil in comparison with that of xylene. Materials and Methods: Thirty different formalin-fixed tissue samples were cut into five parts and cleared using Carrot oil, Olive oil, Pine oil, Rose oil, and xylene followed by routine processing, sectioning, and staining steps. Presence or absence of shrinkage, ease of cutting, nucleus, cytoplasm details and staining quality were assesed and comparison was done between each of them cleared with the 4 different oils with that cleared using xylene. Results: The results showed that all four oils cleared tissues as effectively as xylene, with Pine oil superior in nucleus and cytoplasm details, as well as staining quality insignificant number of samples. Conclusion: These oils not only more affordable and eco-friendly than xylene but can also serve as effective clearing agents.

204. ALTERATIONS IN LOCAL OESOPHAGEAL MICROBIOTA AND OUTCOMES AFTER OESOPHAGECTOMY FOR OESOPHAGO-GASTRIC CANCER: A PILOT STUDY

Abstract Oesophageal cancer is a global health burden, with an estimated 600,000 new cases and 550,000 deaths per year. It is the 9th most common cancer yet is ranked fifth for cancer mortality. The current gold standard curative strategy includes oesophagectomy, which is a morbid procedure. In particular, anastomotic leaks are a feared complication postoperatively that result in significant morbidity. Studies of patients undergoing colorectal cancer surgery show that alterations in the local microbiota can contribute to complications including anastomotic leak. Furthermore, some pathogenic bacterial species have been implicated in shorter recurrence-free survival periods after curative oncologic surgery. Unlike bacterial culture, which requires viable bacteria to be preserved from the time of sampling through to processing, 16S RNA sequencing can be performed on both fresh and fixed tissues. However, there are few studies using either tissue source and to date, none that compare results from the same patient. The aims of this pilot study were to: 1. Assess the feasibility of testing archived histological specimens (i.e. formalin fixed) that in turn facilitates retrospective analysis of patients with known clinical outcomes (i.e. anastomotic leaks) 2. Identify any difference (variance, reduce or over-abundance) between the microbiota of patients who suffered anastomotic leak and those who did not 3. Generate preliminary data to inform sample sizes, statistical methods, workflow and cost of a future prospective trial Using an established Upper GI Cancer Surgery Database, we performed propensity score matching to identify 15 patients who had a clinically evident anastomotic leak to be matched with 15 patients who did not have an anastomotic leak. Known predictors of anastomotic leak (e.g. neoadjuvant radiotherapy, smoking status, COPD, chronic kidney disease, diabetes mellitus, chronic liver disease) have been controlled for. Fresh frozen and formalin-fixed samples for the same patients were available. The formalin-fixed tissue was comprised of the "anastomotic doughnuts" created at the time of the circular stapled anastomosis. This tissue was chosen because of its immediate proximity to the anastomosis. All samples were analysed using 16S RNA sequencing to obtain a full microbial profile. Sequencing data was analysed by scientific investigators blinded to the clinical outcome (i.e. anastomotic leak vs. no leak) using a pre-existing workflow and bioinformatics pipeline.

Genomic landscape of early-stage prostate adenocarcinoma in Mexican patients: an exploratory study

BackgroundHealth disparities have been highlighted among patient with prostate adenocarcinoma (PRAD) due to ethnicity. Mexican men present a more aggressive disease than other patients resulting in less favorable treatment outcome. We aimed to identify the mutational landscape which could help to reduce the health disparities among minority groups and generate the first genomics exploratory study of PRAD in Mexican patients.MethodsParaffin-embedded formalin-fixed tumoral tissue from 20 Mexican patients with early-stage PRAD treated at The Instituto Nacional de Cancerología, Mexico City from 2017 to 2019 were analyzed. Tumoral DNA was prepared for whole exome sequencing, the resulting files were mapped against h19 using BWA-MEM. Strelka2 and Lancet packages were used to identify single nucleotide variants (SNV) and insertions or deletions. FACETS was used to determine somatic copy number alterations (SCNA). Cancer Genome Interpreter web interface was used to determine the clinical relevance of variants.ResultsPatients were in an early clinical stage and had a mean age of 59.55 years (standard deviation [SD]: 7.1 years) with 90% of them having a Gleason Score of 7. Follow-up time was 48.50 months (SD: 32.77) with recurrences and progression in 30% and 15% of the patients, respectively. NUP98 (20%), CSMD3 (15%) and FAT1 (15%) were the genes most frequently affected by SNV; ARAF (75%) and ZNF419 (70%) were the most frequently affected by losses and gains SNCA’s. One quarter of the patients had mutations useful as biomarkers for the use of PARP inhibitors, they comprise mutations in BRCA, RAD54L and ATM. SBS05, DBS03 and ID08 were the most common mutational signatures present in this cohort. No associations with recurrence or progression were identified.ConclusionsThis pilot study reveals the mutational landscape of early-stage prostate adenocarcinoma in Mexican men, providing a first approach to understand the mutational patterns and actionable mutations in early prostate cancer can inform personalized treatment approaches and reduce the underrepresentation in genomic cancer studies.

Hepatic angiotensin-converting enzyme 2 expression in metabolic dysfunction-associated steatotic liver disease and in patients with fatal COVID-19.

Metabolic dysfunction-associated steatotic liver disease (MASLD), characterised by hepatic lipid accumulation, causes inflammation and oxidative stress accompanied by cell damage and fibrosis. Liver injury (LI) is also frequently reported in patients hospitalised with coronavirus disease 2019 (COVID-19), while pre-existing MASLD increases the risk of LI and the development of COVID-19-associated cholangiopathy. Mechanisms of injury at the cellular level remain unclear, but it may be significant that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which causes COVID-19, uses angiotensin-converting expression enzyme 2 (ACE2), a key regulator of the 'anti-inflammatory' arm of the renin-angiotensin system, for viral attachment and host cell invasion. To determine if hepatic ACE2 levels are altered during progression of MASLD and in patients who died with severe COVID-19. ACE2 protein levels and localisation, and histological fibrosis and lipid droplet accumulation as markers of MASLD were determined in formalin-fixed liver tissue sections across the MASLD pathological spectrum (isolated hepatocellular steatosis, metabolic dysfunction-associated steatohepatitis (MASH) +/- fibrosis, end-stage cirrhosis) and in post-mortem tissues from patients who had died with severe COVID-19, using ACE2 immunohistochemistry and haematoxylin and eosin and picrosirius red staining of total collagen and lipid droplet areas, followed by quantification using machine learning-based image pixel classifiers. ACE2 staining is primarily intracellular and concentrated in the cytoplasm of centrilobular hepatocytes and apical membranes of bile duct cholangiocytes. Strikingly, ACE2 protein levels are elevated in non-fibrotic MASH compared to healthy controls but not in the progression to MASH with fibrosis and in cirrhosis. ACE2 protein levels and histological fibrosis are not associated, but ACE2 and liver lipid droplet content are significantly correlated across the MASLD spectrum. Hepatic ACE2 levels are also increased in COVID-19 patients, especially those showing evidence of LI, but are not correlated with the presence of SARS-CoV-2 virus in the liver. However, there is a clear association between the hepatic lipid droplet content and the presence of the virus, suggesting a possible functional link. Hepatic ACE2 levels were elevated in nonfibrotic MASH and COVID-19 patients with LI, while lipid accumulation may promote intra-hepatic SARS-CoV-2 replication, accelerating MASLD progression and COVID-19-mediated liver damage.

A scalable 3D spatial multi-omics method for high-plex morpho-molecular imaging of millimeter-thick tissues.

162 Background: Tissues are three-dimensional (3D). However, current histopathology only allows 2D and single-marker tissue views. Methods: We utilized tissue clearing, supramolecular histochemistry, light-sheet microscopy, and image processing algorithms to compile an end-to-end multi-modality pipeline for 3D digital pathology and oncology diagnostics development. Results: Our end-to-end solution allow parallelized, fully automated processing of formalin-fixed or paraffin-embedded tissues of 1cm3 size. With a tissue-to-image time of 6 days, the whole intact tissue block can be non-destructively imaged with our newly developed 3D HnE (Hematoxylin-analogue &amp; Eosin stain) and 4-plex immunohistochemistry (IHC). Deep and homogeneous penetration of staining was achieved such that all stained markers can be quantified as ground truth. The stained and cleared tissue can be recycled for subsequent FFPE 2D histology over multiple cycles for higher-plex imaging, and is also applicable to simultaneous survey of mRNA with multiplexed fluorescent in situ hybridization (FISH), post-translational modifications such as histone modifications via IHC, and glycosylation profiling with lectins. Image analysis readily allows high-dimensional clustering of cells based on their multi-modal biomolecular expression profiles, morphology, spatial locations, and neighborhoods. The method is applicable to a wide variety of human and murine tissues. Conclusions: Our 3D digital pathology platform enables maximal information extracted for precision diagnostics and advanced biomedical research.

Dia-PASEF Proteomics of Tumor and Stroma LMD Enriched from Archived HNSCC Samples.

We employed laser microdissection to selectively harvest tumor cells and stroma from the microenvironment of formalin-fixed, paraffin-embedded head and neck squamous cell carcinoma (HNSCC) tissues. The captured HNSCC tissue fractions were analyzed by quantitative mass spectrometry-based proteomics using a data independent analysis approach. In paired samples, we achieved excellent proteome coverage having quantified 6,668 proteins with a median quantitative coefficient of variation under 10%. We observed significant differences in relevant functional pathways between the spatially resolved tumor and stroma regions. Our results identified extracellular matrix (ECM) as a major component enriched in the stroma, including many cancer associated fibroblast signature proteins in this compartment. We demonstrate the potential for comparative deep proteome analysis from very low starting input in a scalable format that is useful to decipher the alterations in tumor and the stromal microenvironment. Correlating such results with clinical features or disease progression will likely enable identification of novel targets for disease classification and interventions.

Development of a peptide-generated antibody to rabbit hemorrhagic disease virus 2 VP60 and its immunohistochemical application in natural cases.

Rabbit hemorrhagic disease virus 2 (RHDV2) has spread across the United States infecting and causing death in domestic and wild rabbits. Immunohistochemistry (IHC) would be a useful tool for the detection of RHDV2 antigen in tissues as it is inexpensive and readily achievable in most diagnostic laboratories. However, there is no readily available antibody for this purpose. To fill this void, we generated an RHDV2 capsid protein VP60-specific antibody in chicken eggs and validated the antibody using formalin-fixed tissues from 5 domestic rabbits naturally infected with RHDV2. Viral antigen was detected immunohistochemically in various tissues, most prominently in hepatocytes and macrophages in liver, and in macrophages in spleen and cecal lymphoid tissue. Intravascular mononuclear cells in lung and renal tubular and biliary epithelium also were immunolabeled. Both nuclear and cytoplasmic immunolabeling were observed. This peptide-generated antibody is a potentially useful tool as an adjunct to reverse-transcription PCR or in situ hybridization for detection of RHDV2 in tissues.

Analysis of IDH and EGFR as biomarkers in glioblastoma multiforme: A case-control study

BackgroundGlioblastoma multiforme (GBM) is a very aggressive primary central nervous system (CNS) tumor with limited therapeutic options and poor prognosis. This study aimed to analyze the association between single nucleotide polymorphisms (SNPs), including IDH1 rs121913500C > T, IDH2 rs11540478G > A, and EGFR rs1468727C > T, and their association on the risk and overall survival of GBM patients in Jordan. MethodsUsing a case-control study design involving 63 GBM patients and 226 healthy controls was conducted at King Abdullah University Hospital in Jordan. DNA extraction was performed using formalin-fixed and paraffin-embedded tissue for GBM samples and blood samples for controls. SNPs analysis was performed using the Sequenom iPLEX assay sequencing technique. Survival outcomes were assessed using Cox models and hazard ratios (HR), and single-cell RNA (scRNA) analysis was performed from GSE70630. ResultsThe study showed a significant association between genotype frequency in GBM cases and controls for specific SNPs, including IDH1 rs121913500C > T, and EGFR rs1468727C > T. The G/G genotype of rs11540478 (IDH2) was associated with better prognostic outcomes in GBM patients. The scRNA analysis demonstrated the differential expression of IDH1, IDH2, and EGFR in GBM, with enrichment in central carbon metabolism in cancer. ConclusionOur findings suggest that SNPs, particularly in IDH1 and IDH2 genes and EGFR, may serve as diagnostic and prognostic biomarkers for GBM. While the study underscores the clinical relevance of these genetic variants, further investigations with larger and more diverse populations are essential to validate and extend these associations.

Identification of monoclonal antibodies from naive antibody phage-display libraries for protein detection in formalin-fixed paraffin-embedded tissues

Most antibodies used in immunohistochemistry (IHC) have been developed by animal immunization. We wanted to explore naive antibody repertoires displayed on filamentous phages as a source of full-length antibodies for IHC on Formalin-Fixed and Paraffin-Embedded (FFPE) tissues. We used two isogenic mouse fibroblast cell lines that express or not human HER2 to generate positive and negative FFPE pseudo-tissue respectively. Using these pseudo-tissues and previously described approaches based on differential panning, we isolated very efficient antibody clones, but not against HER2. To optimize HER2 targeting and tissue specificity, we first performed 3–4 rounds of in vitro panning using recombinant HER2 extracellular domain (ECD) to enrich the phage library in HER2 binders, followed by one panning round using the two FFPE pseudo-tissues to retain binders for IHC conditions. We then analyzed the bound phages using next-generation sequencing to identify antibody sequences specifically associated with the HER2-positive pseudo-tissue. Using this approach, the top-ranked clone identified by sequencing was specific to the HER2-positive pseudo-tissue and showed a staining pattern similar to that of the antibody used for the clinical diagnosis of HER2-positive breast cancer. However, we could not optimize staining on other tissues, showing that specificity was restricted to the tissue used for selection and screening. Therefore, future optimized protocols must consider tissue diversity early during the selection by panning using a wide collection of tissue types.

A Diagnostic Algorithm for Detection of Leishmania spp. in Human Fresh and Fixed Tissue Samples.

Leishmaniasis is an important travel-related parasitic infection in the United States. Treatment regimens vary by Leishmania species and require an accurate diagnosis. The sensitivity and specificity of diagnostic methods depend on the type and condition of specimen analyzed. To identify the best algorithm for detection of parasites in fresh and fixed tissue samples, we evaluated parasite cultures, two PCR methods, and Leishmania immunohistochemistry (IHC) in samples received by the CDC from 2012 through 2019. The sensitivity and specificity of IHC assays were evaluated in fresh specimens tested. Diagnostic accuracy for formalin-fixed tissue was evaluated by using PCR-based methods and IHC. Of 100 suspected cases with fresh tissue available, Leishmania spp. infection was identified by PCR in 56% (56/100) of specimens; from these, 80% (45/56) were positive by parasite culture and 59% (33/56) by IHC. Of 420 possible cases where only fixed specimens were available, 58% (244/420) were positive by IHC and/or PCR. Of these, 96% (235/420) were positive by IHC and 84% (204/420) by PCR-based methods. Overall parasite detection using all methodologies was similar for fresh and formalin-fixed tissue specimens (56% versus 58%, respectively). Although PCR-based methods were superior for diagnosis of leishmaniasis and species identification in fresh samples, IHC in combination with PCR increased the accuracy for Leishmania spp. detection in fixed samples. In conclusion, PCR is the most effective method for detecting Leishmania infection in fresh tissue samples, whereas for formalin-fixed samples, IHC and PCR-based methods should be used in combination.

Whole-exome sequencing reveals novel cancer genes and actionable targets in biliary tract cancers in primary sclerosing cholangitis.

People with primary sclerosing cholangitis (PSC) have a 20% lifetime risk of biliary tract cancer (BTC). Using whole-exome sequencing, we characterized genomic alterations in tissue samples from BTC with underlying PSC. We extracted DNA from formalin-fixed, paraffin-embedded tumor and paired nontumor tissue from 52 resection or biopsy specimens from patients with PSC and BTC and performed whole-exome sequencing. Following copy number analysis, variant calling, and filtering, putative PSC-BTC-associated genes were assessed by pathway analyses and annotated to targeted cancer therapies. We identified 53 candidate cancer genes with a total of 123 nonsynonymous alterations passing filtering thresholds in 2 or more samples. Of the identified genes, 19% had not previously been implicated in BTC, including CNGA3, KRT28, and EFCAB5. Another subset comprised genes previously implicated in hepato-pancreato-biliary cancer, such as ARID2, ELF3, and PTPRD. Finally, we identified a subset of genes implicated in a wide range of cancers such as the tumor suppressor genes TP53, CDKN2A, SMAD4, and RNF43 and the oncogenes KRAS, ERBB2, and BRAF. Focal copy number variations were found in 51.9% of the samples. Alterations in potential actionable genes, including ERBB2, MDM2, and FGFR3 were identified and alterations in the RTK/RAS (p = 0.036), TP53 (p = 0.04), and PI3K (p = 0.043) pathways were significantly associated with reduced overall survival. In this exome-wide characterization of PSC-associated BTC, we delineated both PSC-specific and universal cancer genes. Our findings provide opportunities for a better understanding of the development of BTC in PSC and could be used as a platform to develop personalized treatment approaches.

Beyond the surface: how ex-vivo diffusion-weighted imaging reveals large animal brain microstructure and connectivity.

Diffusion-weighted Imaging (DWI) is an effective and state-of-the-art neuroimaging method that non-invasively reveals the microstructure and connectivity of tissues. Recently, novel applications of the DWI technique in studying large brains through ex-vivo imaging enabled researchers to gain insights into the complex neural architecture in different species such as those of Perissodactyla (e.g., horses and rhinos), Artiodactyla (e.g., bovids, swines, and cetaceans), and Carnivora (e.g., felids, canids, and pinnipeds). Classical in-vivo tract-tracing methods are usually considered unsuitable for ethical and practical reasons, in large animals or protected species. Ex-vivo DWI-based tractography offers the chance to examine the microstructure and connectivity of formalin-fixed tissues with scan times and precision that is not feasible in-vivo. This paper explores DWI's application to ex-vivo brains of large animals, highlighting the unique insights it offers into the structure of sometimes phylogenetically different neural networks, the connectivity of white matter tracts, and comparative evolutionary adaptations. Here, we also summarize the challenges, concerns, and perspectives of ex-vivo DWI that will shape the future of the field in large brains.

Immune profiling of mouse lung adenocarcinoma paraffin tissues using multiplex immunofluorescence panel: a pilot study

BackgroundImmune profiling has become an important tool for identifying predictive, prognostic and response biomarkers for immune checkpoint inhibitors from tumor microenvironment (TME). We aimed to build a multiplex immunofluorescence (mIF) panel to apply to formalin-fixed and paraffin-embedded tissues in mice tumors and to explore the programmed cell death protein 1/ programmed cell death 1 ligand 1 (PD-1/PD-L1) axis.ResultsAn automated eight-color mIF panel was evaluated to study the TME using seven antibodies, including cytokeratin 19, CD3e, CD8a, CD4, PD-1, PD-L1, F4-80 and DAPI, then was applied in six mice lung adenocarcinoma samples. Cell phenotypes were quantified by software to explore the co-localization and spatial distribution between immune cells within the TME. This mice panel was successfully optimized and applied to a small cohort of mice lung adenocarcinoma cases. Image analysis showed a sparse degree of immune cell expression pattern in this cohort. From the spatial analysis we found that T cells and macrophages expressing PD-L1 were close to the malignant cells and other immune cells.ConclusionsComprehensive immune profiling using mIF in translational studies improves our ability to correlate the PD-1/PD-L1 axis and spatial distribution of lymphocytes and macrophages in mouse lung cancer cells to provide new cues for immunotherapy, that can be translated to human tumors for cancer intervention.

Age-dependent increase of perineuronal nets in the human hippocampus and precocious aging in epilepsy.

Perineuronal nets (PNN) are specialized extracellular matrix (ECM) components of the central nervous system, frequently accumulating at the surface of inhibitory GABAergic interneurons. While an altered distribution of PNN has been observed in neurological disorders including Alzheimer's disease, schizophrenia and epilepsy, their anatomical distribution also changes during physiological brain maturation and aging. Such an age-dependent shift was experimentally associated also with hippocampal engram formation during brain maturation. Our aim was to histopathologically assess PNN in the hippocampus of adult and pediatric patients with temporal lobe epilepsy (TLE) compared to age-matched post-mortem control subjects and to compare PNN-related changes with memory impairment observed in our patient cohort. Sixty-six formalin-fixed and paraffin-embedded tissue specimens of the human hippocampus were retrieved from the European Epilepsy Brain Bank. Twenty-nine patients had histopathologically confirmed hippocampal sclerosis (HS), and eleven patients suffered from TLE without HS. PNN were immunohistochemically visualized using an antibody directed against aggrecan and manually counted from hippocampus subfields and the subiculum. PNN density increased with age in both human controls and TLE patients. However, their density was significantly higher in all HS patients compared to age-matched controls. Intriguingly, TLE patients presented presurgically with better memory when their hippocampal PNN density was higher (p < 0.05). Our results were compatible with age-dependent ECM specialization in the human hippocampus and its precocious aging in the epileptic condition. These observations confirm recent experimental animal models and also support the notion that PNN play a role in memory formation in the human brain. "Perineuronal nets" (PNN) are a specialized compartment of the extracellular matrix (ECM), especially surrounding highly active neurons of the mammalian brain. There is evidence that PNN play a role in memory formation, brain maturation, and in some pathologies like Alzheimer's disease, schizophrenia or epilepsy. In this study, we investigated the role of PNN in patients suffering from drug-resistant focal epilepsy compared to controls. We found that with increasing age, more neurons are surrounded by PNN. Similarly, all epilepsy patients but especially patients with better memory performance also had more PNN. This study raises further interest in studying ECM molecules in the human brain under physiological and pathophysiological conditions.

Robotic-Assisted Bronchoscopy for the Diagnosis of Lung Lesions: Experience With the Use of Frozen Sections as an Aid to Confirm the Localization of Lesions During the Procedure.

Robotic-assisted navigation bronchoscopy (R-ANB) is used to target peripheral pulmonary nodules that are difficult to biopsy using conventional approaches. Frozen sections are requested to confirm these lesions have been localized and/or to diagnose neoplasms that can be immediately resected. To estimate diagnostic concordance between frozen section diagnosis (FSD) and formalin-fixed tissue diagnosis (FFTD) in biopsies obtained with R-ANB, calculate the sensitivity and specificity of FSD and FFTD for a diagnosis of malignancy, and evaluate whether the residual tissue that can be fixed in formalin after frozen section still has sufficient material for molecular studies. The results of consecutive FSD rendered on biopsies performed with R-ANB during a 30-month period were used to calculate the metrics listed above. FFTD and/or the diagnoses rendered on computed tomography-guided core biopsy subsequently performed in patients with negative R-ANB and/or lung resections in patients with malignancies were used as true-positive results. The overall concordance between FSD and FFTD in 226 lesions from 203 patients was 72%. Frozen section diagnosed 76 of 123 malignancies with 100% specificity and 68% sensitivity. Adequate material was available in 92% of biopsies where next-generation sequencing and other molecular studies were requested. Intraoperative consultations are helpful to diagnose a variety of lung lesions and help surgeons confirm that targets have been accurately reached by R-ANB. Malignancies can be diagnosed with 100% specificity but only 68% sensitivity. The performance of frozen section did not interfere with the subsequent analysis of tissue with molecular studies in most cases.

Bacterial septicemia and herpesvirus infection in Antarctic fur seals (Arctocephalus gazella) stranded in the São Paulo coast, Brazil

In August 2021, two juvenile male Antarctic fur seals (Arctocephalus gazella) stranded in the southeastern Brazilian coast and were referred to rehabilitation centers. The animals presented increased body temperature, prostration, respiratory distress and despite treatment died. A necropsy following a standardized protocol was performed, and formalin-fixed tissues were processed for microscopic examination. Samples were screened for morbillivirus, herpesvirus, and Brucella spp. by molecular analyses (PCR, RT-PCR). Bacteriological culture was performed in samples collected from the lungs, trachea, and lymph nodes of both cases. The main histopathologic findings were of infectious nature, including multifocal necrotizing and fibrinous mixed interstitial pneumonia, bronchiolitis, and bronchitis, with intralesional myriad bacteria associated with vascular fibrinoid necrosis. Pseudomonas aeruginosa was isolated from tracheal and lung swabs of Case 1, and Klebsiella oxytoca was found in nostril swabs, tracheobronchial lymph nodes, and lung of Case 2. Gammaherpesvirus infection was detected in both cases, and the sequences retrieved were classified into the genus Percavirus. All tested samples were PCR-negative for Brucella spp. and morbillivirus. We hypothesize that the deficient immunological status in association with starvation predisposed the reactivation of herpesvirus and secondary bacterial co-infections. To the authors’ knowledge, this is the first molecular detection of herpesvirus in an Antarctic pinniped. These findings reinforce that Otariid gammaherpesvirus circulating in the Southern Hemisphere are likely endemic in the Arctocephalus genus. This report contributes to the current knowledge of health aspects affecting wild pinnipeds, especially in the poorly studied Antarctic species.

INSIHGT: A scalable and homogeneous 3D multiplexed molecular mapping platform for spatial biology and precision medicine.

e15180 Background: The dynamic interplay between cancer cells and their microenvironment is a determinant of disease evolution and response to treatment. However, the current state of three-dimensional (3D) tumor microenvironment analysis is hindered by inadequate penetration of antibodies into thick tissue sections, leading to a substantial gap in acquiring unbiased, precise 3D multiplexed immunohistochemistry (IHC) images. Methods: We developed INSIHGT to surmount these limitations by enabling multi-round, multiplexed 3D IHC in standard formalin-fixed tissues. This fully automatable, fast-track method requires a simple series of chemical cocktail exchanges, translating to a tissue-to-image time of 6 days for 1 cm³ samples and as little as 6 hours for biopsy specimens. INSIHGT offers a scalable and efficient solution for detailed 3D spatial mapping of cancerous cells and their interactions within their native context. Results: 3D IHC with INSIHGT shows ideal penetration homogeneity, which quantitatively matches reference signals in 1cm3 samples. We further validated INSIHGT with 309 commercially available primary antibodies and is compatible with simultaneous fluorescent in situ hybridization (FISH) to detect RNA transcripts or DNA chromosomal abnormalities. Notably, the quality of post-INSIHGT traditional histological analyses, such as H&amp;E and standard IHC, was not altered. We demonstrated a 3D mapping of over 20 markers in a 1 mm-thick tumor sample across seven INSIHGT cycles, and an atlas of multiple tumour samples with 3D IHC &amp; H&amp;E. The large datasets seamlessly integrates with single-cell segmentation and analysis workflows, yielding comprehensive maps that elucidate protein expression, cell morphology, spatial positioning, and potential cell-cell interactions. Conclusions: INSIHGT provides an unparalleled level of visualization and analytical detail concerning the spatial dynamics within the tumor microenvironment at a single-cell resolution. As a transformative next generation histopathology platform, it can uncover new structural and molecular details within clinical specimens, accelerating biomarker discovery and novel diagnostic assays development, thereby enriching the field of tumor biology and propelling the progress of personalized oncology treatments.