Optimizing immunofluorescence with high-dynamic-range imaging to enhance PD-L1 expression evaluation for 3D pathology assessment from NSCLC tumor tissue.

Assessing programmed death ligand 1 (PD-L1) expression through immunohistochemistry (IHC) is the golden standard in predicting immunotherapy response of non-small cell lung cancer (NSCLC). However, observation of heterogeneous PD-L1 distribution in tumor space is a challenge using IHC only. Meanwhile, immunofluorescence (IF) could support both planar and three-dimensional (3D) histological analyses by combining tissue optical clearing with confocal microscopy. We optimized clinical tissue preparation for the IF assay focusing on staining, imaging, and post-processing to achieve quality identical to traditional IHC assay. To overcome limited dynamic range of the fluorescence microscope's detection system, we incorporated a high dynamic range (HDR) algorithm to restore the post imaging IF expression pattern and further 3D IF images. Following HDR processing, a noticeable improvement in the accuracy of diagnosis (85.7%) was achieved using IF images by pathologists. Moreover, 3D IF images revealed a 25% change in tumor proportion score for PD-L1 expression at various depths within tumors. We have established an optimal and reproducible process for PD-L1 IF images in NSCLC, yielding high quality data comparable to traditional IHC assays. The ability to discern accurate spatial PD-L1 distribution through 3D pathology analysis could provide more precise evaluation and prediction for immunotherapy targeting advanced NSCLC.

Comparative transcriptomic and proteomic kinetic analysis of adeno-associated virus production systems.

Recombinant adeno-associated virus (rAAV) is a major gene delivery vehicle. We have constructed a stable rAAV producer cell line by integrating essential rAAV genome, viral and helper genes into the genome of HEK293 cell under the control of inducible promoters. Upon induction, the cell line produces transducing rAAV. To gain insight into enhancing rAAV productivity and vector quality, we performed a comparative transcriptomic and proteomic analysis of our synthetic cell line GX2 and two wild-type AAV (wtAAV) production systems, one by virus co-infection and the other by multi-plasmid transfection. The three systems had different kinetics in viral component synthesis but generated comparable copies of AAV genomes; however, the capsid titer of GX2 was an order of magnitude lower compared to those two wtAAV systems, indicating that its capsid production may be insufficient. The genome packaging efficiency was also lower in GX2 despite it produced higher levels of Rep52 proteins than either wtAAV systems, suggesting that Rep52 protein expression may not limit genome packaging. In the two wtAAV systems, VP were the most abundant AAV proteins and their levels continued to increase, while GX2 had high level of wasteful cargo gene expression. Furthermore, upregulated inflammation, innate immune responses, and MAPK signaling, as well as downregulated mitochondrial functions, were commonly observed in either rAAV or wtAAV systems. Overall, this comparative multi-omics study provided rich insights into host cell and viral factors that are potential targets for genetic and process intervention to enhance the productivity of synthetic rAAV producer cell lines. KEY POINTS: • wtAAV infection was more efficient in producing full viral particles than the synthetic cell GX2. • Capsid protein synthesis, genome replication, and packaging may limit rAAV production in GX2. • wtAAV infection and rAAV production in GX2 elicited similar host cell responses.

Tuning capsid formation dynamics in recombinant adeno-associated virus producing synthetic cell lines to enhance full particle productivity.

Recombinant adeno-associated virus (rAAV) is widely used as an in vivo delivery vector for gene therapy. It is used in a very large dose, and the large quantities required for broad applications present manufacturing challenges. We have developed a synthetic biology platform of constructing cell lines integrated with essential viral genes which can be induced to produce rAAV without plasmid transfection or virus transduction. Through iterative design-construct-characterization cycles, we have showcased the potential of this synthetic cell production system. Systems characterization of the dynamics of viral transcripts and proteins as well as virus assembly and packaging revealed that the expression level and balance of viral genome and capsid protein are keys to not only the productivity but also the full particle content, an important product quality attribute. Boosting cap gene expression by sequential transfection and integration of multiple copies of the cap gene elevated the rAAV titer to levels on a par with traditional plasmid transfection and virus infection. However, overexpression of the cap gene shifted the balance and kinetics of the genome and capsid. We independently tuned the dynamics of genome amplification and capsid protein synthesis by modulating the induction concentration as well as the time profile, and significantly enhanced full particle content while maintaining a high productivity. This strategy of constructing an inducible stable producer cell line is readily adaptable to rAAV vectors of different serotypes and payloads. It can greatly facilitate scalable production of gene therapy vectors.

Synthetic Cell Lines for Inducible Packaging of Influenza A Virus.

Influenza A virus (IAV) is a negative-sense RNA virus that causes seasonal infections and periodic pandemics, inflicting huge economic and human costs on society. The current production of influenza virus for vaccines is initiated by generating a seed virus through the transfection of multiple plasmids in HEK293 cells followed by the infection of seed viruses into embryonated chicken eggs or cultured mammalian cells. We took a system design and synthetic biology approach to engineer cell lines that can be induced to produce all viral components except hemagglutinin (HA) and neuraminidase (NA), which are the antigens that specify the variants of IAV. Upon the transfection of HA and NA, the cell line can produce infectious IAV particles. RNA-Seq transcriptome analysis revealed inefficient synthesis of viral RNA and upregulated expression of genes involved in host response to viral infection as potential limiting factors and offered possible targets for enhancing the productivity of the synthetic cell line. Overall, we showed for the first time that it was possible to create packaging cell lines for the production of a cytopathic negative-sense RNA virus. The approach allows for the exploitation of altered kinetics of the synthesis of viral components and offers a new method for manufacturing viral vaccines.

An unusual uterine papillary serous carcinoma with post therapy disseminating metastasis presenting as primary renal malignancy: a case report.

Introduction: Uterine papillary serous carcinoma (UPSC) is a highly aggressive endometrial carcinoma that often presents as a high-stage disease. UPSC has a high propensity for metastasis and recurrence, even with little or no myometrial invasion. It usually metastasizes to the pelvis, retroperitoneal lymph nodes, upper abdomen, or peritoneum. However, renal metastasis of UPSC is extremely rare. Case presentation: The authors reported a unique UPSC case in a 75-year-old unmarried woman. Twenty years ago, she had a history of right breast cancer and underwent a modified radical mastectomy. Three years ago, she was diagnosed with endometrial carcinoma, and six courses of chemotherapy and radiotherapy were administered. Computed tomography and retrograde pyelography revealed a right renal pelvic tumor, and a right nephroureterectomy was performed. Renal metastatic UPSC was diagnosed. The patient was administered adjuvant chemotherapy. Clinical discussion: Metastatic UPSCs initially presenting at distant sites are uncommon manifestations. This tumor should be differentially diagnosed in patients presenting with metastatic high-grade serous papillary carcinoma of unknown primary origin. Conclusion: Diagnosing metastatic renal UPSC, based on preoperative and imaging examinations, is often challenging. Thus, a review of the past history, histopathology, and immunohistochemical evaluation plays a crucial and valuable role in the definite and differential diagnosis of this tumor type.

Inertial Measurement Unit-Based Romberg Test for Assessing Adults With Vestibular Hypofunction.

This work aims to explore the utility of wearable inertial measurement units (IMUs) for quantifying movement in Romberg tests and investigate the extent of movement in adults with vestibular hypofunction (VH). A cross-sectional study was conducted at an academic tertiary medical center between March 2021 and April 2022. Adults diagnosed with unilateral vestibular hypofunction (UVH) or bilateral vestibular hypofunction (BVH) were enrolled in the VH group. Healthy controls (HCs) were recruited from community or outpatient clinics. The IMU-based instrumented Romberg and tandem Romberg tests on the floor were applied to both groups. The primary outcomes were kinematic body metrics (maximum acceleration [ACC], mean ACC, root mean square [RMS] of ACC, and mean sway velocity [MV]) along the medio-lateral (ML), cranio-caudal (CC), and antero-posterior (AP) axes. A total of 31 VH participants (mean age, 33.48 [SD 7.68] years; 19 [61%] female) and 31 HCs (mean age, 30.65 [SD 5.89] years; 18 [58%] female) were recruited. During the eyes-closed portion of the Romberg test, VH participants demonstrated significantly higher maximum ACC and increased RMS of ACC in head movement, as well as higher maximum ACC in pelvic movement along the ML axis. In the same test condition, individuals with BVH exhibited notably higher maximum ACC and RMS of ACC along the ML axis in head and pelvic movements compared with HCs. Additionally, BVH participants exhibited markedly increased maximum ACC along the ML axis in head movement during the eyes-open portion of the tandem Romberg test. Conversely, no significant differences were found between UVH participants and HCs in the assessed parameters. The instrumented Romberg and tandem Romberg tests characterized the kinematic differences in head, pelvis, and ankle movement between VH and healthy adults. The findings suggest that these kinematic body metrics can be useful for screening BVH and can provide goals for vestibular rehabilitation.

A novel computer-assisted tool for 3D imaging of programmed death-ligand 1 expression in immunofluorescence-stained and optically cleared breast cancer specimens.

BACKGROUND: Programmed death-1 (PD-1) and programmed death-ligand 1 (PD-L1) are the two most common immune checkpoints targeted in triple-negative breast cancer (BC). Refining patient selection for immunotherapy is non-trivial and finding an appropriate digital pathology framework for spatial analysis of theranostic biomarkers for PD-1/PD-L1 inhibitors remains an unmet clinical need. METHODS: We describe a novel computer-assisted tool for three-dimensional (3D) imaging of PD-L1 expression in immunofluorescence-stained and optically cleared BC specimens (n = 20). The proposed 3D framework appeared to be feasible and showed a high overall agreement with traditional, clinical-grade two-dimensional (2D) staining techniques. Additionally, the results obtained for automated immune cell detection and analysis of PD-L1 expression were satisfactory. RESULTS: The spatial distribution of PD-L1 expression was heterogeneous across various BC tissue layers in the 3D space. Notably, there were six cases (30%) wherein PD-L1 expression levels along different layers crossed the 1% threshold for admitting patients to PD-1/PD-L1 inhibitors. The average PD-L1 expression in 3D space was different from that of traditional immunohistochemistry (IHC) in eight cases (40%). Pending further standardization and optimization, we expect that our technology will become a valuable addition for assessing PD-L1 expression in patients with BC. CONCLUSION: Via a single round of immunofluorescence imaging, our approach may provide a considerable improvement in patient stratification for cancer immunotherapy as compared with standard techniques.

Polyhydroxyalkanoates bioproduction from bench to industry: Thirty years of development towards sustainability.

The pursuit of carbon neutrality goals has sparked considerable interest in expanding bioplastics production from microbial cell factories. One prominent class of bioplastics, polyhydroxyalkanoates (PHA), is generated by specific microorganisms, serving as carbon and energy storage materials. To begin with, a native PHA producer, Cupriavidus necator (formerly Ralstonia eutropha) is extensively studied, covering essential topics such as carbon source selection, cultivation techniques, and accumulation enhancement strategies. Recently, various hosts including archaea, bacteria, cyanobacteria, yeast, and plants have been explored, stretching the limit of microbial PHA production. This review provides a comprehensive overview of current advancements in PHA bioproduction, spanning from the native to diversified cell factories. Recovery and purification techniques are discussed, and the current status of industrial applications is assessed as a critical milestone for startups. Ultimately, it concludes by addressing contemporary challenges and future prospects, offering insights into the path towards reduced carbon emissions and sustainable development goals.

Enhancing the production of recombinant adeno-associated virus in synthetic cell lines through systematic characterization.

Recombinant adeno-associated virus (rAAV) is among the most commonly used in vivo gene delivery vehicles and has seen a number of successes in clinical application. Current manufacturing processes of rAAV employ multiple plasmid transfection or rely on virus infection and face challenges in scale-up. A synthetic biology approach was taken to generate stable cell lines with integrated genetic modules, which produced rAAV upon induction albeit at a low productivity. To identify potential factors that restrained the productivity, we systematically characterized virus production kinetics through targeted quantitative proteomics and various physical assays of viral components. We demonstrated that reducing the excessive expression of gene of interest by its conditional expression greatly increased the productivity of these synthetic cell lines. Further enhancement was gained by optimizing induction profiles and alleviating proteasomal degradation of viral capsid protein by the addition of proteasome inhibitors. Altogether, these enhancements brought the productivity close to traditional multiple plasmid transfection. The rAAV produced had comparable full particle contents as those produced by conventional transient plasmid transfection. The present work exemplified the versatility of our synthetic biology-based viral vector production platform and its potential for plasmid- and virus-free rAAV manufacturing.

Wavefront control of subcycle vortex pulses via carrier-envelope-phase tailoring.

The carrier-envelope phase (CEP) of an ultrashort laser pulse is becoming more crucial to specify the temporal characteristic of the pulse's electric field when the pulse duration becomes shorter and attains the subcycle regime; here, the pulse duration of the intensity envelope is shorter than one cycle period of the carrier field oscillation. When this subcycle pulse involves a structured wavefront as is contained in an optical vortex (OV) pulse, the CEP has an impact on not only the temporal but also the spatial characteristics owing to the spatiotemporal coupling in the structured optical pulse. However, the direct observation of the spatial effect of the CEP control has not yet been demonstrated. In this study, we report on the measurement and control of the spatial wavefront of a subcycle OV pulse by adjusting the CEP. To generate subcycle OV pulses, an optical parametric amplifier delivering subcycle Gaussian pulses and a Sagnac interferometer as a mode converter were integrated and provided an adequate spectral adaptability. The pulse duration of the generated OV pulse was 4.7 fs at a carrier wavelength of 1.54 µm. To confirm the wavefront control with the alteration of the CEP, we developed a novel [Formula: see text]-2[Formula: see text] interferometer that exhibited spiral fringes originating from the spatial interference between the subcycle OV pulse and the second harmonic of the subcycle Gaussian pulse producing a parabolic wavefront as a reference; this resulted in the successful observation of the rotation of spiral interference fringes during CEP manipulation.

HeapMS: An Automatic Peak-Picking Pipeline for Targeted Proteomic Data Powered by 2D Heatmap Transformation and Convolutional Neural Networks.

The process of peak picking and quality assessment for multiple reaction monitoring (MRM) data demands significant human effort, especially for signals with low abundance and high interference. Although multiple peak-picking software packages are available, they often fail to detect peaks with low quality and do not report cases with low confidence. Furthermore, visual examination of all chromatograms is still necessary to identify uncertain or erroneous cases. This study introduces HeapMS, a web service that uses artificial intelligence to assist with peak picking and the quality assessment of MRM chromatograms. HeapMS applies a rule-based filter to remove chromatograms with low interference and high-confidence peak boundaries detected by Skyline. Additionally, it transforms two histograms (representing light and heavy peptides) into a single encoded heatmap and performs a two-step evaluation (quality detection and peak picking) using image convolutional neural networks. HeapMS offers three categories of peak picking: uncertain peak picking that requires manual inspection, deletion peak picking that requires removal or manual re-examination, and automatic peak picking. HeapMS acquires the chromatogram and peak-picking boundaries directly from Skyline output. The output results are imported back into Skyline for further manual inspection, facilitating integration with Skyline. HeapMS offers the benefit of detecting chromatograms that should be deleted or require human inspection. Based on defined categories, it can significantly reduce human workload and provide consistent results. Furthermore, by using heatmaps instead of histograms, HeapMS can adapt to future updates in image recognition models. The HeapMS is available at: https://github.com/ccllabe/HeapMS.

Decoding the prognostic significance of integrator complex subunit 9 (INTS9) in glioma: links to TP53 mutations, E2F signaling, and inflammatory microenvironments.

INTRODUCTION: Gliomas, a type of brain neoplasm, are prevalent and often fatal. Molecular diagnostics have improved understanding, but treatment options are limited. This study investigates the role of INTS9 in processing small nuclear RNA (snRNA), which is crucial to generating mature messenger RNA (mRNA). We aim to employ advanced bioinformatics analyses with large-scale databases and conduct functional experiments to elucidate its potential role in glioma therapeutics. MATERIALS AND METHODS: We collected genomic, proteomic, and Whole-Exon-Sequencing data from The Cancer Genome Atlas (TCGA) and Chinese Glioma Genome Atlas (CGGA) for bioinformatic analyses. Then, we validated INTS9 protein expression through immunohistochemistry and assessed its correlation with P53 and KI67 protein expression. Gene Set Enrichment Analysis (GSEA) was performed to identify altered signaling pathways, and functional experiments were conducted on three cell lines treated with siINTS9. Then, we also investigate the impacts of tumor heterogeneity on INTS9 expression by integrating single-cell sequencing, 12-cell state prediction, and CIBERSORT analyses. Finally, we also observed longitudinal changes in INTS9 using the Glioma Longitudinal Analysis (GLASS) dataset. RESULTS: Our findings showed increased INTS9 levels in tumor tissue compared to non-neoplastic components, correlating with high tumor grading and proliferation index. TP53 mutation was the most notable factor associated with upregulated INTS9, along with other potential contributors, such as combined chromosome 7 gain/10 loss, TERT promoter mutation, and increased Tumor Mutational Burden (TMB). In GSEA analyses, we also linked INTS9 with enhanced cell proliferation and inflammation signaling. Downregulating INTS9 impacted cellular proliferation and cell cycle regulation during the function validation. In the context of the 12 cell states, INTS9 correlated with tumor-stem and tumor-proliferative-stem cells. CIBERSORT analyses revealed increased INTS9 associated with increased macrophage M0 and M2 but depletion of monocytes. Longitudinally, we also noticed that the INTS9 expression declined during recurrence in IDH wildtype. CONCLUSION: This study assessed the role of INTS9 protein in glioma development and its potential as a therapeutic target. Results indicated elevated INTS9 levels were linked to increased proliferation capacity, higher tumor grading, and poorer prognosis, potentially resulting from TP53 mutations. This research highlights the potential of INTS9 as a promising target for glioma treatment.

Apoptotic Cell-Derived CD14(+) Microparticles Promote the Phagocytic Activity of Neutrophilic Precursor Cells in the Phagocytosis of Apoptotic Cells.

Membranous CD14 is crucial in the phagocytic activity of neutrophils. However, the role of CD14(+) microparticles (MPs) derived from apoptotic neutrophils (apo-MP) during the phagocytic process is not clear. All trans-retinoic acid (ATRA) induces acute promyelocytic leukemic NB4 cells along granulocytic differentiation. In this study, we investigated the role of CD14(+)apo-MP in the cell-cell interaction during the phagocytic process of apoptotic cells by viable ATRA-NB4 cells. We firstly demonstrate that CD14 expression and phagocytic activity of NB4 cells were upregulated simultaneously after ATRA treatment in a time-dependent manner, and both were significantly enhanced via concurrent lipopolysaccharide treatment. The phagocytic activity of ATRA-NB4 cells and lipopolysaccharide-treated ATRA-NB4 cells were both significantly attenuated by pre-treating cells with an antibody specific to either CD14 or TLR4. Further flow cytometric analysis demonstrates that apoptotic ATRA-NB4 cells release CD14(+)apo-MP in an idarubicin dosage-dependent manner. Both CD14 expression and the phagocytic activity of viable ATRA-NB4 cells were significantly enhanced after incubation with apo-MP harvested from apoptotic ATRA-NB4 cells, and the apo-MP-enhanced phagocytic activity was significantly attenuated by pre-treating apo-MP with an anti-CD14 antibody before incubation with viable cells. We conclude that CD14(+)apo-MP derived from apoptotic ATRA-NB4 cells promotes the phagocytic activity of viable ATRA-NB4 cells in engulfing apoptotic cells.

The deubiquitinase Leon/USP5 interacts with Atg1/ULK1 and antagonizes autophagy.

Accumulating evidence has shown that the quality of proteins must be tightly monitored and controlled to maintain cellular proteostasis. Misfolded proteins and protein aggregates are targeted for degradation through the ubiquitin proteasome (UPS) and autophagy-lysosome systems. The ubiquitination and deubiquitinating enzymes (DUBs) have been reported to play pivotal roles in the regulation of the UPS system. However, the function of DUBs in the regulation of autophagy remain to be elucidated. In this study, we found that knockdown of Leon/USP5 caused a marked increase in the formation of autophagosomes and autophagic flux under well-fed conditions. Genetic analysis revealed that overexpression of Leon suppressed Atg1-induced cell death in Drosophila. Immunoblotting assays further showed a strong interaction between Leon/USP5 and the autophagy initiating kinase Atg1/ULK1. Depletion of Leon/USP5 led to increased levels of Atg1/ULK1. Our findings indicate that Leon/USP5 is an autophagic DUB that interacts with Atg1/ULK1, negatively regulating the autophagic process.

Unusually aggressive primary testicular diffuse large B-cell lymphoma initially presenting as systemic disseminating metastases in older adult men: a case report.

Primary testicular lymphoma (PTL) accounts for 1-2% of all nonHodgkin lymphomas (NHL), 4% of extranodal nonHodgkin lymphomas, and ~9% of testicular malignancies. A rare subtype of PTL is primary testicular diffuse large B-cell lymphoma (PT-DLBCL), which may initially present as disseminating metastasis in older adult males and has a poor prognosis. Case presentation: Herein, the authors describe the case of a 64-year-old man with the chief complaint of a painless unilateral scrotal mass. Computed tomography scans of the abdomen and a pelvic examination demonstrated a left testicular tumor with multiple lymphadenopathies partially aggregated in the para-aortic area and disseminated to multiple soft tissues and organs. Subsequently, the patient underwent a left radical orchiectomy. Pathological and immunohistochemical examinations confirmed the diagnosis of left PT-DLBCL with systemic disseminating metastases. Clinical discussion: PTL often aggressively spreads to other extranodal organs, such as the contralateral testis, central nervous system, lung, pleura, Waldeyer's ring, and soft tissues. In men over 60 years of age, PT-DLBCL is the most common testicular malignancy. However, extensive systemic metastasis as the initial presentation is extremely rare. PT-DLBCL has a dismal prognosis and requires radical orchiectomy followed by multimodal therapy and central nervous system prophylaxis or systemic intervention to improve survival. Conclusion: The diagnosis of PT-DLBCL through preoperative and imaging examinations is often challenging. Thus, histopathology and immunohistochemical markers play a crucial and valuable role in the definite diagnosis and differential diagnosis of PTLs.

Panoramic Tissue Examination That Integrates 3-Dimensional Pathology Imaging and Gene Mutation: Potential Utility in Non-Small Cell Lung Cancer.

Novel therapeutics have significantly improved the survival and quality of life of patients with malignancies in this century. Versatile precision diagnostic data were used to formulate personalized therapeutic strategies for patients. However, the cost of extensive information depends on the consumption of the specimen, raising the challenges of effective specimen utilization, particularly in small biopsies. In this study, we proposed a tissue-processing cascaded protocol that obtains 3-dimensional (3D) protein expression spatial distribution and mutation analysis from an identical specimen. In order to reuse the thick section tissue evaluated after the 3D pathology technique, we designed a novel high-flatness agarose-embedded method that could improve tissue utilization rate by 1.52 fold, whereas it reduced the tissue-processing time by 80% compared with the traditional paraffin-embedding method. In animal studies, we demonstrated that the protocol would not affect the results of DNA mutation analysis. Furthermore, we explored the utility of this approach in non-small cell lung cancer because it is a compelling application for this innovation. We used 35 cases including 7 cases of biopsy specimens of non-small cell lung cancer to simulate future clinical application. The cascaded protocol consumed 150-µm thickness of formalin-fixed, paraffin-embedded specimens, providing 3D histologic and immunohistochemical information approximately 38 times that of the current paraffin-embedding protocol, and 3 rounds of DNA mutation analysis, offering both essential guidance for routine diagnostic evaluation and advanced information for precision medicine. Our designed integrated workflow provides an alternative way for pathological examination and paves the way for multidimensional tumor tissue assessment.

Incidental finding of multiple diffuse large B-cell lymphomas masquerading as jejunojejunal intussusception with unexplained pleural effusion: a case report.

Primary non-Hodgkin's lymphoma of the gastrointestinal (GI) tract is rare. It is aggressive and necessitates early diagnosis and management. Simultaneous primary GI lymphomas are unusual with rarely reported cases. Case presentation: This novel case report describes an 84-year-old man with multiple primary diffuse large B-cell lymphomas (DLBCLs) of the jejunum with disseminating pleural and multiple regional lymph nodes involvement presenting as intestinal obstruction and segments of jejunojejunal intussusception. The patient underwent surgical intervention and adjuvant chemotherapy. Unfortunately, the patient suffered from multiple organ failure and died 4 months after surgery. Clinical discussion: Obstruction and perforation are rare and life-threatening complications of GI lymphoma. Multiple DLBCLs of the jejunum are rare. Moreover, primary GI-DLBCL that initially presents with pleural effusion or with intestinal perforation is uncommon. This report aims to remind clinicians that lymphoma should be considered when assessing the cause of unexplained pleural effusion, especially when the available examination data cannot be confirmed by clinical manifestations. Conclusion: Through this case report, the authors learn that clinical manifestations, morphological characteristics, immunophenotypes, and molecular biological characteristics are vastly different and important. This poses the biggest challenge before surgery and should not be ignored.

Ancient ubiquitous protein 1 (AUP1) is a prognostic biomarker connected with TP53 mutation and the inflamed microenvironments in glioma.

INTRODUCTION: Glioblastoma (GBM) is the most common and lethal brain tumor. The current treatment is surgical removal combined with radiotherapy and chemotherapy, Temozolomide (TMZ). However, tumors tend to develop TMZ resistance which leads to therapeutic failure. Ancient ubiquitous protein 1 (AUP1) is a protein associated with lipid metabolism, which is widely expressed on the surface of ER and Lipid droplets, involved in the degradation of misfolded proteins through autophagy. It has recently been described as a prognostic marker in renal tumors. Here, we aim to use sophisticated bioinformatics and experimental validation to characterize the AUP1's role in glioma. MATERIAL AND METHODS: We collected the mRNA, proteomics, and Whole-Exon-Sequencing from The Cancer Genome Atlas (TCGA) for bioinformatics analyses. The analyses included the expression difference, Kaplan-Meier-survival, COX-survival, and correlation to the clinical factors (tumor mutation burden, microsatellite instability, and driven mutant genes). Next, we validated the AUP1 protein expression using immunohistochemical staining on the 78 clinical cases and correlated them with P53 and KI67. Then, we applied GSEA analyses to identify the altered signalings and set functional experiments (including Western Blot, qPCR, BrdU, migration, cell-cycle, and RNAseq) on cell lines when supplemented with small interfering RNA targeting the AUP1 gene (siAUP1) for further validation. We integrated the single-cell sequencing and CIBERSORT analyses at the Chinese Glioma Genome Atlas (CGGA) and Glioma Longitudinal AnalySiS (GLASS) dataset to rationale the role of AUP1 in glioma. RESULTS: Firstly, the AUP1 is a prognostic marker, increased in the tumor component, and correlated with tumor grade in both transcriptomes and protein levels. Secondly, we found higher AUP1 associated with TP53 status, Tumor mutation burden, and increased proliferation. In the function validation, downregulated AUP1 expression merely impacted the U87MG cells' proliferation instead of altering the lipophagy activity. From the single-cell sequencing and CIBERSORT analyses at CGGA and GLASS data, we understood the AUP1 expression was affected by the tumor proliferation, stromal, and inflammation compositions, particularly the myeloid and T cells. In the longitudinal data, the AUP1 significantly dropped in the recurrent IDH wildtype astrocytoma, which might result from increased AUP1-cold components, including oligodendrocytes, endothelial cells, and pericytes. CONCLUSION: According to the literature, AUP1 regulates lipophagy by stabilizing the ubiquitination of lipid droplets. However, we found no direct link between AUP1 suppression and altered autophagy activity in the functional validation. Instead, we noticed AUP1 expression associated with tumor proliferation and inflammatory status, contributed by myeloid cells and T cells. In addition, the TP53 mutations seem to play an important role here and initiate inflamed microenvironments. At the same time, EGFR amplification and Chromosome 7 gain combined 10 loss are associated with increased tumor growth related to AUP1 levels. This study taught us that AUP1 is a poorer predictive biomarker associated with tumor proliferation and could report inflamed status, potentially impacting the clinical application.

Deep-learning based breast cancer detection for cross-staining histopathology images.

Hematoxylin and eosin (H&E) staining is the gold standard for tissue characterization in routine pathological diagnoses. However, these visible light dyes do not exclusively label the nuclei and cytoplasm, making clear-cut segmentation of staining signals challenging. Currently, fluorescent staining technology is much more common in clinical research for analyzing tissue morphology and protein distribution owing to its advantages of channel independence, multiplex labeling, and the possibility of enabling 3D tissue labeling. Although both H&E and fluorescent dyes can stain the nucleus and cytoplasm for representative tissue morphology, color variation between these two staining technologies makes cross-analysis difficult, especially with computer-assisted artificial intelligence (AI) algorithms. In this study, we applied color normalization and nucleus extraction methods to overcome the variation between staining technologies. We also developed an available workflow for using an H&E-stained segmentation AI model in the analysis of fluorescent nucleic acid staining images in breast cancer tumor recognition, resulting in 89.6% and 80.5% accuracy in recognizing specific tumor features in H&E- and fluorescent-stained pathological images, respectively. The results show that the cross-staining inference maintained the same precision level as the proposed workflow, providing an opportunity for an expansion of the application of current pathology AI models.