Tissue Sections Research Articles

Multiplexed in situ RNA imaging by combFISH.

Multiplexed in situ RNA imaging offers new opportunities for gene expression profiling by providing high-throughput spatial information. In this work, we present a cyclic combinatorial fluorescent in situ hybridization (combFISH) assay to achieve multiplexed detection of RNA in cell cultures and tissues. Specifically, multiplexing is achieved through cyclic interrogation of barcode sequences on the rolling circle amplicons generated from the padlock probe assay by using sets of combinatorial detection probes. Theoretically, combFISH can detect 64 genes in three hybridization cycles by combinatorial barcoding using 12 fluorescently labeled detection probes. Our method eliminates sequencing-by-ligation (SBL) chemistry in the in situ sequencing protocol and directly uses RNA as targets for ligation, making it more straightforward. We showed that our method works in fresh-frozen and formalin-fixed paraffin-embedded tissue sections. With its straightforward protocols, we expect our method to be adopted by the scientific community and extended to clinical settings.

Multiplex Imaging for Cell Phenotyping of Early Human Atherosclerosis.

Previous studies using animal models and cultured cells suggest that vascular smooth muscle cells (SMCs) and inflammatory cytokines are important players in atherogenesis. Validating these findings in human disease is critical to designing therapeutics that target these components. Multiplex imaging is a powerful tool for characterizing cell phenotypes and microenvironments using biobanked human tissue sections. However, this technology has not been applied to human atherosclerotic lesions and needs to first be customized and validated. For validation, we created an 8-plex imaging panel to distinguish foam cells from SMC and leukocyte origins on tissue sections of early human atherosclerotic lesions (n=9). The spatial distribution and characteristics of these foam cells were further analyzed to test the association between SMC phenotypes and inflammation. Consistent with previous reports using human lesions, multiplex imaging showed that foam cells of SMC origin outnumbered those of leukocyte origin and were enriched in the deep intima, where the lipids accumulate in early atherogenesis. This new technology also found that apoptosis or the expression of pro-inflammatory cytokines were not more associated with foam cells than with nonfoam cells in early human lesions. More CD68+ SMCs were present among SMCs that highly expressed interleukin-1β. Highly inflamed SMCs showed a trend of increased apoptosis, whereas leukocytes expressing similar levels of cytokines were enriched in regions of extracellular matrix remodeling. The multiplex imaging method can be applied to biobanked human tissue sections to enable proof-of-concept studies and validate theories based on animal models and cultured cells.

Key aspects of papillomavirus infection influence the host cervicovaginal microbiome in a preclinical murine papillomavirus (MmuPV1) infection model.

Human papillomaviruses (HPVs) are the most common sexually transmitted infection in the United States and are a major etiological agent of cancers in the anogenital tract and oral cavity. Growing evidence suggests changes in the host microbiome are associated with the natural history and ultimate outcome of HPV infection. We sought to define changes in the host cervicovaginal microbiome during papillomavirus infection, persistence, and pathogenesis using the murine papillomavirus (MmuPV1) cervicovaginal infection model. Cervicovaginal lavages were performed over a time course of MmuPV1 infection in immunocompetent female FVB/N mice and extracted DNA was analyzed by qPCR to track MmuPV1 viral copy number. 16S ribosomal RNA (rRNA) gene sequencing was used to determine the composition and diversity of microbial communities throughout this time course. We also sought to determine whether specific microbial communities exist across the spectrum of MmuPV1-induced neoplastic disease. We, therefore, performed laser-capture microdissection to isolate regions of disease representing all stages of neoplastic disease progression (normal, low- and high-grade dysplasia, and cancer) from female reproductive tract tissue sections from MmuPV1-infected mice and performed 16S rRNA sequencing. Consistent with other studies, we found that the natural murine cervicovaginal microbiome is highly variable across different experiments. Despite these differences in initial microbiome composition between experiments, we observed that MmuPV1 persistence, viral load, and severity of disease influenced the composition of the cervicovaginal microbiome. These studies demonstrate that papillomavirus infection can alter the cervicovaginal microbiome.IMPORTANCEHuman papillomaviruses (HPVs) are the most common sexually transmitted infection in the United States. A subset of HPVs that infect the anogenital tract (cervix, vagina, anus) and oral cavity cause at least 5% of cancers worldwide. Recent evidence indicates that the community of microbial organisms present in the human cervix and vagina, known as the cervicovaginal microbiome, plays a role in HPV-induced cervical cancer. However, the mechanisms underlying this interplay are not well-defined. In this study, we infected the female reproductive tract of mice with a murine papillomavirus (MmuPV1) and found that key aspects of papillomavirus infection and disease influence the host cervicovaginal microbiome. This is the first study to define changes in the host microbiome associated with MmuPV1 infection in a preclinical animal model of HPV-induced cervical cancer. These results pave the way for using MmuPV1 infection models to further investigate the interactions between papillomaviruses and the host microbiome.

First report of Macrophomina phaseolina causing сharcoal rot in soybean (Glycine max (L.) Merr.) plants in Uzbekistan.

The soybean production area is expanding in Uzbekistan. Soybeans were planted on an area of 10 thsd ha and the harvest amounted to 30 thsd metric tons in 2023 (IPAD, https://ipad.fas.usda.gov/countrysummary). Macrophomina phaseolina (Mp) is a soil- and seed-borne fungal pathogen causing economically important diseases of legume crops (Pennerman et al. 2024). Drought stress and a warm climate are favorable to this pathogen (Irulappan et al. 2022). Under these conditions, its microsclerotia survive for a longer period and become more virulent (Chamorro et al. 2015). In August 2022, typical symptoms of charcoal rot were observed in about 25% of "Orzu" soybean cultivar affecting 6 ha located on the experimental base "Durmon" of our institute. Diseased plants displayed the following charcoal rot symptoms: leaves turn yellow, then wilt, die, and remain attached to the plant; the lower portion of the stem and tap root have a light gray or ashy black discoloration; tiny black specks on the lower stem and root; after splitting the stem, it has the appearance of fine charcoal powder. In order to determine the causal agent of these symptoms, a total of 17 diseased plants were collected from focal lesions in soybean plantings. From each plant, twelve sections of stem and root tissue were selected, cut into small 5-mm pieces, and surface sterilized with 1% sodium hypochlorite for four minutes, then rinsed three times with sterile distilled water. The disinfected tissues were dried on sterile filter paper for 5 min and placed on PDA Petri plates, which were incubated in an incubation chamber for 3 days (16 h light (26oC) and 8 h dark (18oC)). Fungi were subsequently subcultured on PDA and incubated for 7 days to obtain pure cultures. Six monohyphal colonies were purified. The colonies showed dense growth, with a gray initial mycelium becoming darker with aging. After 8 days on PDA, black-colored microsclerotia with spherical to oblong shapes were observed. On average, they measured 60 µm in width and 130 µm in length (n = 30). From six isolated monohyphal colonies, one has been chosen for molecular-genetic identification. Molecular-genetic analysis was conducted by amplification and sequencing of the ITS region with the ITS1 and ITS4 primers (White et al. 1990). The resulting sequence was deposited in the NCBI database under accession number OQ073450. After BLAST analysis (Altschul et al. 1990) it was 100% identical with the reference sequences of Mp (accession MT039671, MT039663 and MH496040) isolated in sugar beet, maize and sunflower, respectively, from Serbia. In order to verify the pathogenicity, soybean seedlings (cv. Orzu) were dipped into spore suspension (1 × 107 spores/ml) of sequenced strain R-17 for 1 minute and transferred to a 15 cm diameter plastic pot with 350 g of sterilized soil mix. After 25 days, the inoculated plants showed classic charcoal rot symptoms, while the control plants remained healthy. The pathogen was successfully reisolated from the infected seedlings onto PDA, fulfilling Koch's postulate. The identity of the re-isolated strain was confirmed by morphological features and sequencing of the ITS region. It should be noted that in Uzbekistan, Mp has not been documented in any plants. Therefore, according to our knowledge, this is the first report of this fungus affecting soybean plants in Uzbekistan. Since molecular-genetic analysis of the R-17 strain showed clustering with strains from Serbia, we speculate that there may have been a recent introduction of Mp from Serbia into Uzbekistan. This assumption is additionally confirmed by the fact that Serbia is the largest seed exporter in Uzbekistan. The increase in charcoal rot disease poses a major challenge to soybean production in Uzbekistan. Understanding the genetic diversity of Mp can be utilized to manage this disease, improve soybean yield, and help soybean breeding programs in Uzbekistan.

Intracranial angioleiomyoma: a case series of seven patients and review of the literature.

Angioleiomyoma, predominantly arising from the extremities, is a benign soft tissue tumor. Reports on its intracranial location are rare. We assessed clinical, radiological, and pathological features of intracranial angioleiomyoma (iALM) treated at our neurosurgical institution. We consecutively enrolled all patients with neuropathologically confirmed iALM treated at a single neurosurgical institution between 2013 and 2021. Clinical and imaging data were collected, and histological tissue sections were analyzed. A review of the literature on iALM was conducted. Seven patients with iALM (four female) with a median age of 45 years (range: 32-76 years) were identified. In three cases, the lesion was found incidentally. In magnetic resonance imaging (MRI), all tumors were hypo- to isointense on T1-weighted, hyperintense on T2-weighted sequences, and gadolinium-enhancing. A strong FLAIR signal was seen in six patients. Surgery consisted of gross total resection in all cases without perioperative complications. Neuropathological staining was positive for smooth muscle actin (SMA) in all lesions. Mature smooth muscle cells arranged around blood vessels were typically observed. The Ki-67 index was ≤ 3%. The patients were discharged after a median of 6 days (range: 4-9 days). During a median follow-up time of 14 months (range: 4-41 months), no tumor recurrence occurred. In the current literature, 42 additional cases of iALM were identified. Intracranial angioleiomyoma is a benign soft tissue tumor treated by gross total resection. Tumor morphology and positive staining for SMA lead to the neuropathological diagnosis.

First Report of Bacterial Leaf Spot Disease on Sesame (Sesamum indicum L.) Caused by Pseudomonas syringae pv. sesami in North Carolina.

In July 2022, dark brown to black, angular, water-soaked lesions were observed on sesame leaves (Sesamum indicum L.) in a research plot established to assess yield potential for eight varieties at the North Carolina (NC) Sandhills Research Station (Chavez 2023). Symptoms were indicative of a bacterial leaf spot (BLS). At early flowering stage, leaf spots were present on scattered plants; varieties ES108, SS3301, and ES201 exhibited up to 75% disease prevalence, with lower frequency in ES103, S39, S4302, S3251, and S3276. Symptomatic leaves from 3-4 plants were collected on four different dates from July through September. A section of symptomatic tissue was excised and macerated in sterile deionized water (SDW). A 10 µL aliquot was streaked onto SPA medium (15 g sucrose, 5.0 g proteose peptone, 0.50 g MgSO4 7H2O, 0.25 g K2HPO4, 15 g agar per liter of SDW) and incubated at 28ºC. After 72 h, numerous, smooth, white-cream colored, convex-shaped, colonies were individually isolated. Five randomly selected isolates from the different collection dates, designated as AHP108-AHP111 and AHP116, were genotyped. The 16S rRNA, gyrB, rpoD, and gapA genes were sequenced (Heuer et al. 1997; Hwang et al. 2005) and deposited to NCBI (GenBank Accessions: P213467- PP213470; OQ628040-OQ628042; PP214983-PP214994; and PP255798). These five isolates shared 100% sequence identity for gyrB and rpoD. AHP108-AHP111 shared 100% sequence identity for 16S rRNA and gapA, with 99.7% and 90.8% identity, respectively, for AHP116. A phylogenetic tree was inferred from a maximum-likelihood analysis of concatenated gyrB, rpoD, and gapA sequences of the five isolates and the top 11 hts from a blastn search of the NCBI nucleotide database. Those hits included closely related sequences from Pseudomonas syringae pv. sesami type strains ICMP 763T and ICMP 7459T. Based on this phylogenetic analysis AHP108-AHP111 and AHP116 are P. syringae pv. sesami. Recent genomic analysis suggests this pathovar is part of P. amygdali (Gomila et al. 2017), but an official name change has not been proposed. Each of the five isolates were infiltrated into leaves of sesame varieties ES108, ES103, and S327, consistently resulting in similar symptoms. Thus, strain AHP116, as a representative, was used to fulfill Koch's postulates using five, 30-day-old potted sesame plants (var. S3301). Plants were spray-inoculated with a bacterial suspension of ~108 CFU/ml until runoff; plants were incubated in moist chambers 24 h pre and post inoculation at 28ºC with 80% relative humidity and a 12 h photoperiod. At 13 days post inoculation, symptoms resembling those on plants at the Sandhills Research Stations in 2022 were evident. Reisolated bacteria were confirmed to be AHP116 through 16S rRNA and gyrB amplification and sequencing. No symptoms were observed on the five water-inoculated plants. BLS of sesame has been reported in Asia and is thought to be seedborne (Firdous et al. 2009; Prathuangwong and Yowabutra 1997). To our knowledge, this is the first report of P. syringae pv. sesami causing BLS on sesame in North Carolina. Sesame cultivation in the state increased from approximately 2,000 acres in 2022 to 13,000 acres in 2023 and there is interest in cultivating sesame as a rotational and alternative crop because it requires minimal input costs. Potential outbreaks of BLS in this warm, humid region could negatively affect sesame production, where little is known about the economic impact of the disease.

Extracellular Matrix Mimicking Wound Microenvironment Responsive Amyloid-Heparin@TAAgNP Co-Assembled Hydrogel: An Effective Conductive Antibacterial Wound Healing Material.

Bioengineered composite hydrogel platforms made of a supramolecular coassembly have recently garnered significant attention as promising biomaterial-based healthcare therapeutics. The mechanical durability of amyloids, in conjunction with the structured charged framework rendered by biologically abundant key ECM component glycosaminoglycan, enables us to design minimalistic customized biomaterial suited for stimuli responsive therapy. In this study, by harnessing the heparin sulfate-binding aptitude of amyloid fibrils, we have constructed a pH-responsive extracellular matrix (ECM) mimicking hydrogel matrix. This effective biocompatible platform comprising heparin sulfate-amyloid coassembled hydrogel embedded with polyphenol functionalized silver nanoparticles not only provide a native skin ECM-like conductive environment but also provide wound-microenvironment responsive on-demand superior antibacterial efficacy for effective diabetic wound healing. Interestingly, both the cytocompatibility and antibacterial properties of this bioinspired matrix can be fine-tuned by controlling the mutual ratio of heparin sulfate-amyloid and incubated silver nanoparticle components, respectively. The designed biomaterial platform exhibits notable effectiveness in the treatment of chronic hyperglycemic wounds infected with multidrug-resistant bacteria, because of the integration of pH-responsive release characteristics of the incubated functionalized AgNP and the antibacterial amyloid fibrils. In addition to this, the aforementioned assemblage shows exceptional hemocompatibility with significant antibiofilm and antioxidant characteristics. Histological evidence of the incised skin tissue sections indicates that the fabricated composite hydrogel is also effective in controlling pro-inflammatory cytokines such as IL6 and TNFα expressions at the wound vicinity with significant upregulation of angiogenesis markers like CD31 and α-SMA.

Characteristics of mast cell infiltration in lung adenocarcinoma and its impact on prognosis

BackgroundThe role of mast cells in malignancies remains unclear, and there is no clear correlation between mast cells and tumor microvessels, tumor growth, or lung adenocarcinoma (LUAD) prognosis. This study aims to explore the association between mast cell density (MCD) and intratumoral microvessel density (MVD), clinicopathological parameters, and prognosis in LUAD, by evaluating mast cell infiltration characteristics and their prognostic significance.MethodsThis retrospective investigation involved 238 patients with LUAD undergoing complete resection. Tumor and normal lung tissue sections outside the tumor were immunohistochemically stained for MCD in the intratumoral and outside regions, respectively. CD34 polyclonal antibody was used to measure intratumoral MVD.ResultsIntratumoral regions of LUAD had a higher MCD (P < 0.001) than normal lung tissue. In the intratumoral region, MCD and CD34-MVD were positively correlated (r = 0.411, P < 0.001). Intratumoral MCD correlated with sex, smoking history, tumor differentiation, pathological subtype, and tumor size. Female sex (P = 0.012), no smoking history (P = 0.002), acinar predominant type (P = 0.012), and tumor size ≤ 3 cm (P = 0.009) were associated with a higher MCD, whereas poorly differentiated (P = 0.039) and solid/micropapillary predominant types (P = 0.001) were associated with a lower MCD. Higher intratumoral MCD exhibited a marginally improved overall survival, and individuals with higher MCD infiltration ratios (intratumoral MCD/outside the MCD) had higher disease-free and overall survival rates (log-rank P < 0.001). A high MCD infiltration ratio was associated with decreased risk of tumor progression and death following complete resection.ConclusionThe tumor microenvironment controls mast cell infiltration in LUAD, and patients with increased intratumoral mast cell infiltration have better prognosis.

In Situ Structural Characterization of Cardiomyocyte Microenvironment by Multimodal STED Microscopy

Within the myocardium, cardiomyocytes reside in a complex and dynamic extracellular matrix (ECM) consisting of a basement membrane (BM) and interstitial matrix. The interactions between cardiomyocytes and the myocardial ECM play a critical role in maintaining cardiac geometry and function throughout cardiac development and in adult hearts. Understanding how the structural changes of the myocardial ECM affect cardiomyocyte function requires knowledge of pericellular structures. These structures are of a size beyond the resolution of conventional optical microscopy. Here, we demonstrated multi-scale and multi-aspect characterization of the cardiomyocyte microenvironment in myocardial tissue sections using multimodal stimulated emission depletion (STED) microscopy. Second harmonic generation and autofluorescence facilitated multiplexed imaging, enabling the interpretation of protein distribution in 3D. STED imaging modality revealed BM structures of cardiomyocytes and myocardial capillaries at the subdiffractional level. Moreover, meaningful measurements retrieved from acquired images, such as sarcomere length and capillary density, enabled quantitative assessment of myocardial structures.

A gain-of-function mutation in BnaIAA13 disrupts vascular tissue and lateral root development in Brassica napus.

Rapeseed (Brassica napus) is an important oilseed crop worldwide. Plant vascular tissues are responsible for material transport and provide mechanical support. The lateral roots (LRs) absorb sufficient water and nutrients. The genetic basis of vascular tissues and LRs development in rapeseed remains unknown. This study characterized an EMS-mutagenized rapeseed mutant, T16, which showed dwarf stature, reduced LRs, and leaf wilting. Scanning electron microscopy observations showed that the internode-cell shortened. Observations of the tissue sections revealed defects in the development of vascular bundles in the stems and petioles. Genetic analysis revealed that the phenotypes of T16 were controlled by a single semi-dominant nuclear gene. Map-based cloning and genetic complementarity confirmed that BnaA03.IAA13 is the functional gene, a G-to-A mutation in second exon changed the glycine at the 79th position to glutamic acid, disrupting the conserved degron motif VGWPP. Transcriptome analysis in roots and stems showed that auxin and cytokinin signaling pathways were disordered in T16. Evolutionary analysis showed that AUXIN/INDOLE-3-ACETIC ACID was conserved during plant evolution. The heterozygote of T16 significantly reduced the plant height while maintaining other agronomic traits. Our findings provide novel insights into the regulatory mechanisms of vascular tissues and LRs development, and provide a new germplasm resource for rapeseed breeding.

A universal pipeline to combine spatial transcriptomics, proteomics, and diagnostic H&amp;E assays on a single tissue section to study tissue microenvironment.

e14657 Background: Spatial multi-omics approaches, including spatial transcriptomics (ST) and spatial proteomics (SP), that elucidate the complex tissue microenvironment (TME) are gaining traction in cancer research studies. However, combining these approaches onto one tissue section remains challenging. ST methods visualize, locate and quantify RNA targets, evaluating the transcriptome of the TME at the subcellular level while SP methods stain and visualize protein biomarkers at the cellular level. Here we show a pipeline that combines these ST and SP methods with Hematoxylin and Eosin (H&amp;E) approach on a single tissue section to achieve single slide multi-omics data with high resolution tissue morphology images. Methods: 5µm formalin-fixed paraffin-embedded sections of human lung cancer samples were placed on a Xenium (10x Genomics, Pleasanton, CA) slides and treated to expose RNA molecules. Probe hybridization was performed with a human lung panel kit containing 289 barcoded DNA padlock probes. Downstream ligation and amplification generated copies of the barcode and thereafter, the Xenium Analyzer performed imaging and data collection. The same tissue section was then stained and imaged in COMET (Lunaphore Technologies SA, Switzerland) using sequential immunofluorescence (seqIF) method to detect 40 protein targets in situ. Serial sections of the specimens were used for direct H&amp;E and seqIF staining for comparative validation. Results: Multi-omics images generated from Xenium and COMET were overlayed, jointly analyzed and interpreted. Staining specificity of the protein targets for the post-Xenium slides remain comparable with the direct COMET-stained slide. 40-plex COMET staining intensity in post-Xenium slide was minimally weaker compared to direct COMET-stained slide. Additionally, H&amp;E staining of the post-Xenium/COMET slide and direct COMET-stained slide were comparable to the direct H&amp;E-stained section, demonstrating discernable tissue landscape features despite a fainter hematoxylin stain. Overall, tissue integrity and cell morphology were well-preserved across the different workflows performed on each section, and the protein targets remain relatively stable for labelling after in situ RNA detection process. Conclusions: We present a pipeline that combines two spatial omics approaches with the diagnostic standard H&amp;E staining on a single tissue section, allowing the same cells to be assessed for their histological, proteomic, and transcriptomic information. A visual comparison of images showed minimal compromise to cellular morphology and protein stability at the end of the pipeline compared to direct staining of serial sections. This pipeline could be potentially generalized to most of the ST and SP approaches, thus advancing multi-omics cancer research and potentially clinical diagnostics in the future.

Automated Whole Slide Imaging for Label-Free Histology Using Photon Absorption Remote Sensing Microscopy.

Pathologists rely on histochemical stains to impart contrast in thin translucent tissue samples, revealing tissue features necessary for identifying pathological conditions. However, the chemical labeling process is destructive and often irreversible or challenging to undo, imposing practical limits on the number of stains that can be applied to the same tissue section. Here we present an automated label-free whole slide scanner using a PARS microscope designed for imaging thin, transmissible samples. Peak SNR and in-focus acquisitions are achieved across entire tissue sections using the scattering signal from the PARS detection beam to measure the optimal focal plane. Whole slide images (WSI) are seamlessly stitched together using a custom contrast leveling algorithm. Identical tissue sections are subsequently H&E stained and brightfield imaged. The one-to-one WSIs from both modalities are visually and quantitatively compared. PARS WSIs are presented at standard 40x magnification in malignant human breast and skin samples. We show correspondence of subcellular diagnostic details in both PARS and H&E WSIs and demonstrate virtual H&E staining of an entire PARS WSI. The one-to-one WSI from both modalities show quantitative similarity in nuclear features and structural information. PARS WSIs are compatible with existing digital pathology tools, and samples remain suitable for histochemical, immunohistochemical, and other staining techniques. This work is a critical advance for integrating label-free optical methods into standard histopathology workflows.

Advancing rare cancer research by MALDI mass spectrometry imaging: Applications, challenges, and future perspectives in sarcoma.

MALDI mass spectrometry imaging (MALDI imaging) uniquely advances cancer research, by measuring spatial distribution of endogenous and exogenous molecules directly from tissue sections. These molecular maps provide valuable insights into basic and translational cancer research, including tumor biology, tumor microenvironment, biomarker identification, drug treatment, and patient stratification. Despite its advantages, MALDI imaging is underutilized in studying rare cancers. Sarcomas, a group of malignant mesenchymal tumors, pose unique challenges in medical research due to their complex heterogeneity and low incidence, resulting in understudied subtypes with suboptimal management and outcomes. In this review, we explore the applicability of MALDI imaging in sarcoma research, showcasing its value in understanding this highly heterogeneous and challenging rare cancer. We summarize all MALDI imaging studies in sarcoma to date, highlight their impact on key research fields, including molecular signatures, cancer heterogeneity, and drug studies. We address specific challenges encountered when employing MALDI imaging for sarcomas, and propose solutions, such as using formalin-fixed paraffin-embedded tissues, and multiplexed experiments, and considerations for multi-site studies and digital data sharing practices. Through this review, we aim to spark collaboration between MALDI imaging researchers and clinical colleagues, to deploy the unique capabilities of MALDI imaging in the context of sarcoma.

Using sample reinterrogation to guide high-parameter, spatially resolved tissue biomarker discovery.

e15182 Background: High-parameter, spatially resolved phenotyping can accelerate the discovery of tissue biomarkers as well as reveal emergent disease indicators like cellular neighborhood architecture. These spatial biology techniques hold high potential as diagnostic and prognostic indicators yet can be challenging to deploy due to high cost and lack of standardization. We have developed a powerful spatial biology workflow based on multiplex cyclic immunofluorescent (IF) staining using validated markers and assay kits that allows the researcher to adjust the markers included in the assay with feedback from marker expression in previous rounds. We term this sample re-interrogation. Here we present an illustration of this new workflow. Methods: Three FFPE lung biopsy specimens were repeatedly assayed for biomarker expression using CellScape™ Precise Spatial Multiplexing paired with VistaPlex™ Assay Kits. In this workflow, tissues are mounted in enclosed fluidic chambers. IF Staining and imaging were conducted on the CellScape instrument as iterative rounds. Between each imaging round, we conducted analyses on data from previously collected rounds. Conclusions drawn between staining rounds then guided decisions of whether and how to continue the experiment. Results: Each sample provided evidence for the utility of staged rounds of tissue staining, analysis, and rational assay planning. Two FFPE lung samples from the biopsy were not considered for further iterative staining after initial interrogation for consensus markers resulted in poor expression ( e.g.: CD4, CD20, CD45, pan-cytokeratin). One of these two samples was stained with markers indicative of cell death pathways and fibrosis to provide a positive explanation for initial poor staining. A third lung tissue showed punitive indication of tertiary lymphoid structure (TLS) inclusion. Further rounds of staining were conducted to iteratively explore the nature of these punitive TLS structures. Each round of additional stains was chosen based on data derived from the previous staining series following analysis and deliberation among the biomarker team. Conclusions: The data illustrate that even among tissue sections taken from the same biopsy, a specimen’s unique biomarker expression profile may require adjustments to assay parameters. Two of the FFPE sections proved unacceptable for further investigation after only a handful of stains. This finding highlights the benefit of rational reinterrogation, as the saved resources in not staining these tissues could measure in the thousands of dollars in reagents alone. The third lung tissue specimen offers an example of a tailored spatial biology assay through iterative reinterrogation. All included biomarkers were judged best suited to elucidate the next round of staining, representing an optimized and flexible spatial biology workflow.

Exploration and prognostic analysis of two types of high-risk ovarian cancers: clear cell vs. serous carcinoma: a population-based study

BackgroundOvarian clear cell carcinoma (OCCC) is a rare pathological histotype in ovarian cancer, while the survival rate of advanced OCCC (Stage III-IV) is substantially lower than that of the advanced serous ovarian cancer (OSC), which is the most common histotype. The goal of this study was to identify high-risk OCCC by comparing OSC and OCCC, with investigating potential risk and prognosis markers.MethodsPatients diagnosed with ovarian cancer from 2009 to 2018 were identified from the Surveillance, Epidemiology, and End Results (SEER) Program. Logistic and Cox regression models were used to identify risk and prognostic factors in high-risk OCCC patients. Cancer-specific survival (CSS) and overall survival (OS) were assessed using Kaplan-Meier curves. Furthermore, Cox analysis was employed to build a nomogram model. The performance evaluation results were displayed using the C-index, calibration plots, receiver operating characteristic (ROC) curve, and decision curve analysis (DCA). Immunohistochemically approach was used to identify the expression of the novel target (GPC3).ResultsIn the Cox analysis for advanced OCCC, age (45–65 years), tumor numbers (total number of in situ/malignant tumors for patient), T3-stage, bilateral tumors, and liver metastases could be defined as prognostic variables. Nomogram showed good predictive power and clinical practicality. Compared with OSC, liver metastases had a stronger impact on the prognosis of patients with OCCC. T3-stage, positive distant lymph nodes metastases, and lung metastases were risk factors for developing liver metastases. Chemotherapy was an independent prognostic factor for patient with advanced OCCC, but had no effect on CSS in patients with liver metastases (p = 0.0656), while surgery was significantly related with better CSS in these patients (p < 0.0001) (p = 0.0041). GPC3 expression was detected in all tissue sections, and GPC3 staining was predominantly found in the cytoplasm and membranes.ConclusionAdvanced OCCC and OCCC with liver metastases are two types of high-risk OCCC. The constructed nomogram exhibited a satisfactory survival prediction for patients with advanced OCCC. GPC3 immunohistochemistry is expected to accumulate preclinical evidence to support the inclusion of GPC3 in OCCC targeted therapy.

Nilgai antelope display no signs of infection upon experimental challenge with a virulent Babesia bovis strain

BackgroundBovine babesiosis is caused by infection with the protozoal parasite Babesia bovis, which is transmitted by Rhipicephalus (Boophilus) spp. It can cause mortality rates up to 90% in immunologically naive Bos taurus cattle. In south Texas, R. (B.) microplus is known to infest nilgai antelope (Boselaphus tragocamelus); however, their susceptibility to infection with B. bovis and their role in the transmission of the parasite remain unknown. In this study, we challenged nilgai antelope with B. bovis and evaluated their susceptibility to infection.MethodsNilgai were needle inoculated with ≈108B. bovis-parasitized erythrocytes (merozoites) or a homogenate of B. bovis-infected larval ticks (sporozoite) delivered intravenously. Bos taurus beef calves were inoculated in parallel, as this strain of B. bovis is lethal to cattle. Temperature and hematocrit were monitored daily over the course of each study, and whole blood was collected for molecular [polymerase chain reaction (PCR)] and serological [indirect enzyme-linked immunosorbent assay (ELISA)] diagnostic evaluation. Histological sections of nilgai cerebral tissue were examined for evidence of infection. Recipient bovine calves were sub-inoculated with blood from nilgai challenged with either stage of the parasite, and they were monitored for clinical signs of infection and evaluated by a PCR diagnostic assay. Red blood cells (RBCs) from prechallenged nilgai and B. taurus beef cattle were cultured with an in vitro B. bovis merozoite culture to examine colonization of the RBCs by the parasite.ResultsNilgai did not display clinical signs of infection upon inoculation with either the merozoite or sporozoite stage of B. bovis. All nilgai were PCR-negative for the parasite, and they did not develop antibodies to B. bovis. No evidence of infection was detected in histological sections of nilgai tissues, and in vitro culture analysis indicated that the nilgai RBCs were not colonized by B. bovis merozoites. Cattle subinoculated with blood from challenged nilgai did not display clinical signs of infection, and they were PCR-negative up to 45 days after transfer.ConclusionsNilgai do not appear to be susceptible to infection with a strain of B. bovis that is lethal to cattle. Tick control on these alternative hosts remains a critical priority, especially given their potential to disseminate ticks over long distances.Graphical

Prediction of immune-related adverse events in urological cancer during checkpoint inhibitor immunotherapy through immunohistochemical analysis of tumorous LCP1/ADPGK.

e14699 Background: The expanded utilization of immune checkpoint inhibitors (ICIs) have successfully improved the outcome of cancer patients, yet the concomitant immune-related adverse events (irAEs) can lead to fulminant unfavorable consequences. Currently, a comprehensive approach to predict irAEs is lacking. Some relevant biomarkers derived from database analyses are still in the early stages of investigation and lack robust validation in clinical samples, including LCP1/ADPGK. Herein, we validated the performance of LCP1 and ADPGK in a retrospective patient cohort with advanced urological cancers undergoing ICIs treatment, while comparing the predictive efficacy between different algorithmic models. Methods: We retrospectively collected clinical data of patients with renal cell carcinoma (RCC), upper urinary tract epithelial carcinoma (UTUC), bladder cancer (BC) receiving anti-PD-1/PD-L1 treatment from 2020 to 2023 in Peking University First Hospital. Patients were categorized into irAEs and non-irAEs groups, with irAE assessments conducted by two expert urological oncologists. Immunohistochemistry (IHC) was performed on 5-µm-thick pre-treated FFPE tumor tissue sections. Results: A total of 112 patients were included in the study, comprising 60 with RCC, 21 with UTUC, and 31 with BC. Among them, 51 (45.5%) patients experienced irAEs, with 9 exhibiting severe irAEs of grade III-IV. Immunohistochemical analysis revealed higher expression levels of LCP1 and ADPGK in patients with irAEs compared to those without irAEs. The area under the receiver-operating characteristic curve (AUC) for predicting irAEs using LCP1 and ADPGK individually was 0.82 (p &lt; 0.0001, 95%CI = 0.74-0.90) and 0.86 (p &lt; 0.0001, 95%CI = 0.80-0.93), respectively. The combination of LCP1 and ADPGK demonstrated an improved AUC of 0.89 (p &lt; 0.0001, 95%CI = 0.83-0.95). Among different algorithms, the bivariate linear-regression and the geometric mean model show similar prediction effects. Notably, the combined LCP1+ADPGK model successfully predicted irAEs in RCC (AUC = 0.89, p &lt; 0.0001, 95%CI = 0.81-0.98), UTUC (AUC = 0.81, p = 0.0063, 95%CI = 0.63-0.99), and BC (AUC = 0.88, p = 0.0004, 95%CI = 0.75-1.00). The expression of LCP1/ADPGK was not associated with the type of cancers. Conclusions: The bivariate linear-regression model of LCP1 and ADPGK could accurately predict irAEs in patients with urological cancers, which may allow us to improve the risk-benefit balance for individuals considered for ICIs therapy.

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.

Nanobodies against the myelin enzyme CNPase as tools for structural and functional studies.

2',3'-cyclic nucleotide 3'-phosphodiesterase (CNPase) is an abundant constituent of central nervous system non-compact myelin, frequently used as a marker antigen for myelinating cells. The catalytic activity of CNPase, the 3'-hydrolysis of 2',3'-cyclic nucleotides, is well characterised in vitro, but the in vivo function of CNPase remains unclear. CNPase interacts with the actin cytoskeleton to counteract the developmental closure of cytoplasmic channels that travel through compact myelin; its enzymatic activity may be involved in adenosine metabolism and RNA degradation. We developed a set of high-affinity nanobodies recognizing the phosphodiesterase domain of CNPase, and the crystal structures of each complex show that the five nanobodies have distinct epitopes. One of the nanobodies bound deep into the CNPase active site and acted as an inhibitor. Moreover, the nanobodies were characterised in imaging applications and as intrabodies, expressed in mammalian cells, such as primary oligodendrocytes. Fluorescently labelled nanobodies functioned in imaging of teased nerve fibers and whole brain tissue sections, as well as super-resolution microscopy. These anti-CNPase nanobodies provide new tools for structural and functional biology of myelination, including high-resolution imaging of nerve tissue.

Newly synthesized acridone derivatives targeting lung cancer: A toxicity and xenograft model study.

AKT is one of the overexpressed targets in nonsmall cell lung cancer (NSCLC) and plays an important role in its progression and offers an attractive target for the therapy. The PI3K/AKT/mTOR pathway is upregulated in NSCLC. Acridone is an important heterocycle compound which treats cancer through various mechanisms including AKT as a target. In the present work, the study was designed to evaluate the safety profile of three acridone derivatives (AC-2, AC-7, and AC-26) by acute and repeated dose oral toxicity. In addition to this, we also checked the pAKT overexpression and its control by these derivatives in tumor xenograft model. The results from acute and repeated dose toxicity showed these compounds to be highly safe and free from any toxicity, mortality, or significant alteration in body weight, food, and water intake in the rats. In the repeated dose toxicity, compounds showed negligible variations in a few hematological parameters at 400 mg/kg. The histopathology, biochemical, and urine parameters remained unchanged. The xenograft model study demonstrated AC-2 to be inhibiting HOP-62 induced tumor via reduction in p-AKT1 (Ser473) expression significantly. In immunofluorescence staining AC-2 treated tissue section showed 2.5 fold reduction in the expression of p-AKT1 (Ser473). Histopathology studies showed the destruction of tumor cells with increased necrosis after treatment. The study concluded that AC-2 causes cell necrosis in tumor cells via blocking the p-AKT1 expression. The findings may provide a strong basis for further clinical applications of acridone derivatives in NSCLC.