Limbic-predominant age-related TDP-43 encephalopathy in the oldest old: a population-based study.

Population-based cohort studies are essential for understanding the pathological basis of dementia in older populations. Previous studies have shown that limbic-predominant age-related TDP-43 encephalopathy neuropathological change (LATE-NC) increases with age, but there have been only a few studies, which have investigated this entity in a population-based setting. Here we studied the frequency of LATE-NC and its associations with other brain pathologies and cognition in a population aged ≥ 85 years. The population-based Vantaa 85+ study cohort includes all 601 individuals aged ≥ 85 years who were living in Vantaa, Finland in 1991. A neuropathological examination was performed on 304 subjects (50.5%) and LATE-NC staging was possible in 295 of those. Dementia status and Mini-Mental State Examination (MMSE) scores were defined in the baseline study and 3 follow-ups (1994-99). The LATE-NC stages were determined based on TDP-43 immunohistochemistry, according to recently updated recommendations. Arteriolosclerosis was digitally assessed by calculating the average sclerotic index of five random small arterioles in amygdala and hippocampal regions, and frontal white matter. The association of LATE-NC with arteriolosclerosis and previously determined neuropathological variables including Alzheimer's disease neuropathological change (ADNC), Lewy-related pathology (LRP), hippocampal sclerosis (HS), and cerebral amyloid angiopathy (CAA), and cognitive variables were analysed by Fisher's exact test, linear and logistic regression (univariate and multivariate) models. LATE-NC was found in 189 of 295 subjects (64.1%). Stage 2 was the most common (28.5%) and stage 3 the second most common (12.9%), whereas stages 1a, 1b and 1c were less common (9.5%, 5.1% and 8.1%, respectively). Stages 1a (P < 0.01), 2 (P < 0.001) and 3 (P < 0.001) were significantly associated with dementia and lower MMSE scores. LATE-NC was associated with ADNC (P < 0.001), HS (P < 0.001), diffuse neocortical LRP (P < 0.002), and arteriolosclerosis in amygdala (P < 0.02). In most cases LATE-NC occurred in combination alongside other neuropathological changes. There were only six subjects with dementia who had LATE-NC without high levels of ADNC or LRP (2% of the cohort, 3% of the cases with dementia), and five of these had HS. In all multivariate models, LATE-NC was among the strongest independent predictors of dementia. When LATE-NC and ADNC were assessed in a multivariate model without other dementia-associated pathologies, the attributable risk was higher for LATE-NC than ADNC (24.2% vs. 18.6%). This population-based study provides evidence that LATE-NC is very common and one of the most significant determinants of dementia in the general late-life aged population.

Deep Learning-Based Image Analysis of Liver Steatosis in Mouse Models.

The incidence of nonalcoholic fatty liver disease is a continuously growing health problem worldwide, along with obesity. Therefore, novel methods to both efficiently study the manifestation of nonalcoholic fatty liver disease and to analyze drug efficacy in preclinical models are needed. The present study developed a deep neural network-based model to quantify microvesicular and macrovesicular steatosis in the liver on hematoxylin-eosin-stained whole slide images, using the cloud-based platform, Aiforia Create. The training data included a total of 101 whole slide images from dietary interventions of wild-type mice and from two genetically modified mouse models with steatosis. The algorithm was trained for the following: to detect liver parenchyma, to exclude the blood vessels and any artefacts generated during tissue processing and image acquisition, to recognize and differentiate the areas of microvesicular and macrovesicular steatosis, and to quantify the recognized tissue area. The results of the image analysis replicated well the evaluation by expert pathologists and correlated well with the liver fat content measured by EchoMRI ex vivo, and the correlation with total liver triglycerides was notable. In conclusion, the developed deep learning-based model is a novel tool for studying liver steatosis in mouse models on paraffin sections and, thus, can facilitate reliable quantification of the amount of steatosis in large preclinical study cohorts.

MYC protein is a high-risk factor in mantle cell lymphoma and identifies cases beyond morphology, proliferation and TP53/p53 - a Nordic Lymphoma Group study.

The transcription factor MYC is a well-described oncogene with an important role in lymphomagenesis, but its significance for clinical outcome in mantle cell lymphoma (MCL) remains to be determined. We performed an investigation of the expression of MYC protein in a cohort of 251 MCL patients complemented by analyses of structural aberrations and mRNA, in a sub-cohort of patients. Fourteen percent (n=35) of patients showed high MYC protein expression with >20% positive cells (MYChigh), among whom only one translocation was identified, and 86% (n=216) of patients showed low MYC protein expression. Low copy number gains of MYC were detected in ten patients, but with no correlation to MYC protein levels. However, MYC mRNA levels correlated significantly to MYC protein levels with a R2 value of 0.76. Patients with a MYChigh tumor had both an independent inferior overall survival and an inferior progression-free survival (hazard ratio [HR]=2.03, 95% confidence interval [95% CI]: 1.2-3.4 and HR=2.2, 95% CI: 1.04-4.6, respectively) when adjusted for additional high-risk features. Patients with MYChigh tumors also tended to have additional high-risk features and to be older at diagnosis. A subgroup of 13 patients had concomitant MYChigh expression and TP53/p53 alterations and a substantially increased risk of progression (HR=16.9, 95% CI: 7.4-38.3) and death (HR=7.8, 95% CI: 4.4-14.1) with an average overall survival of only 0.9 years. In summary, we found that at diagnosis a subset of MCL patients (14%) overexpressed MYC protein, and had a poor prognosis but that MYC rearrangements were rare. Tumors with concurrent MYC overexpression and TP53/p53 alterations pinpointed MCL patients with a dismal prognosis with a median overall survival of less than 3 years. We propose that MYC needs to be assessed beyond the current high-risk factors in MCL in order to identify cases in need of alternative treatment.

Mechanistic insights into antifungal potential of Alexidine dihydrochloride and hexachlorophene in Candida albicans: a drug repurposing approach.

Candida albicans has been listed in the critical priority group by the WHO in 2022 depending upon its contribution in invasive candidiasis and increased resistance to conventional drugs. Drug repurposing offers an efficient, rapid, and cost-effective solution to develop alternative therapeutics against pathogenic microbes. Alexidine dihydrochloride (AXD) and hexachlorophene (HCP) are FDA approved anti-cancer and anti-septic drugs, respectively. In this study, we have shown antifungal properties of AXD and HCP against the wild type (reference strain) and clinical isolates of C. albicans. The minimum inhibitory concentrations (MIC50) of AXD and HCP against C. albicans ranged between 0.34 and 0.69 µM and 19.66-24.58 µM, respectively. The biofilm inhibitory and eradication concentration of AXD was reported comparatively lower than that of HCP for the strains used in the study. Further investigations were performed to understand the antifungal mode of action of AXD and HCP by studying virulence features like cell surface hydrophobicity, adhesion, and yeast to hyphae transition, were also reduced upon exposure to both the drugs. Ergosterol content in cell membrane of the wild type strain was upregulated on exposure to AXD and HCP both. Biochemical analyses of the exposed biofilm indicated reduced contents of carbohydrate, protein, and e-DNA in the extracellular matrix of the biofilm when compared to the untreated control biofilm. AXD exposure downregulated activity of tissue invading enzyme, phospholipase in the reference strain. In wild type strain, ROS level, and activities of antioxidant enzymes were found elevated upon exposure to both drugs. FESEM analysis of the drug treated biofilms revealed degraded biofilm. This study has indicated mode of action of antifungal potential of alexidine dihydrochloride and hexachlorophene in C. albicans.

Friedelin: Structure, Biosynthesis, Extraction, and Its Potential Health Impact.

Pharmaceutical companies are investigating more source matrices for natural bioactive chemicals. Friedelin (friedelan-3-one) is a pentacyclic triterpene isolated from various plant species from different families as well as mosses and lichen. The fundamental compounds of these friedelane triterpenoids are abundantly found in cork tissues and leaf materials of diverse plant genera such as Celastraceae, Asteraceae, Fabaceae, and Myrtaceae. They possess many pharmacological effects, including anti-inflammatory, antioxidant, anticancer, and antimicrobial activities. Friedelin also has an anti-insect effect and the ability to alter the soil microbial ecology, making it vital to agriculture. Ultrasound, microwave, supercritical fluid, ionic liquid, and acid hydrolysis extract friedelin with reduced environmental impact. Recently, the high demand for friedelin has led to the development of CRISPR/Cas9 technology and gene overexpression plasmids to produce friedelin using genetically engineered yeast. Friedelin with low cytotoxicity to normal cells can be the best phytochemical for the drug of choice. The review summarizes the structural interpretation, biosynthesis, physicochemical properties, quantification, and various forms of pharmacological significance.

Correlation of HbA1c with Serum Iron & Transferrin Saturation in Non-Diabetic Patients with Iron Deficiency.

Objective: To determine correlation of HbA1c with serum iron and transferrin saturation in non-diabetic patients with iron deficiency. Methods: This cross-sectional comparative study was conducted at Dr Ruth KM Pfau Civil Hospital Karachi from 15th September 2021 to 14th March 2022, on non-diabetic patients based on fasting blood sugar (FBS) of <100 mg/dl. Patients were divided into two groups. Group one included patients having iron deficiency anemia (ID), whereas group two included same number of age and sex matched healthy subjects taken as controls, without ID. Blood sample was taken for HbA1c, CBC, serum iron and total iron binding capacity. Transferrin saturation (TSAT) was calculated. Comparison of quantitative variables with ID and non-ID group was done by Student's t-test. Correlation of HbA1c with iron &TSAT was done in both groups using Kendal tau-b test, as data was not normally distributed. Results: Out of 230 patients, 83 (36.1%) were males while 147(63.9%) were females. Mean age of patients was 43.7±13.28 years. Mean HbA1c level was significantly high in ID group (5.89±0.43) as compared to non-ID group (5.52±0.50) with a p-value <.001. The HbA1c levels correlated negatively with hemoglobin, serum iron levels and transferrin saturation with a p-value <.001. Conclusion: Low serum Iron and TSAT was related to elevation in HbA1c value. Iron deficiency needs to be corrected before HbA1c interpretation.

Wide-Range Humidity-Temperature Hybrid Flexible Sensor Based on Strontium Titanate and Poly 3,4 Ethylenedioxythiophene Polystyrene Sulfonate for Wearable 3D-Printed Mask Applications.

In this paper, we report a fast, linear wide-range hybrid flexible sensor based on a novel composite of strontium titanate (SrTiO3) and poly 3,4 ethylenedioxythiophene polystyrene sulfonate (PEDOT: PSS) as a sensing layer. Inter-digitate electrodes (IDEs) were printed for humidity monitoring (finger: 250 µm; spacing: 140 µm; length: 8 mm) whilst a meander-based pattern was printed for the temperature measurement (meander thickness: 180 µm; spacing: 400 µm) on each side of the PET substrate using silver ink. Moreover, active layers with different concentration ratios were coated on the electrodes using a spray coating technique. The as-developed sensor showed an excellent performance, with a humidity measurement range of (10-90% RH) and temperature measurement range of (25-90 °C) with a fast response (humidity: 5 s; temperature: 4.2 s) and recovery time (humidity: 8 s; temperature: 4.4 s). The reliability of the sensor during mechanical bending of up to 5.5 mm was validated with a reliable performance. The sensor was also used in real-world applications to measure human respiration. For this, a suggested sensor-based autonomous wireless node was included in a 3D-printed mask. The manufactured sensor was an excellent contender for wearable and environmental applications because of its exceptional performance, which allowed for the simultaneous measurement of both quantities by a single sensing device.

Pharmacogenetics of sulfonylurea: Presence of CYP2C9*2, CYP2C9*3 and a novel allele, CYP2C9*61, in Type 2 diabetes patients under sulfonylurea therapy.

CYP2C9 is an important member of the cytochrome P450 gene family involved in the metabolism of 15% of the drugs including an oral antidiabetic agent sulfonylurea. This study aims to investigate the frequency of CYP2C9*2 and CYP2C9*3 alleles of the gene in the sulfonylurea treated diabetic subjects in Pakistan. Briefly, total 105 patients were included in the study and segregated as control (24) and test (81) based on the clinical manifestations after taking sulfonylurea. Genomic DNA was extracted from blood of the subjects and amplified using CYP2C9 specific primers for exon 3 and exon 7 and then subjected to DNA sequencing. Alignment of the sequences with the reference sequence shows presence of CYP2C9*3/*3, CYP2C9*1/*3 and CYP2C9*1/*2 genotypes in the test cases but only the latter two were found in the control cases. In addition a novel allele, CYP2C9*61 in the heterozygous state, was also identified frequently in the test cases. Molecular structure comparison also showed variations in the structural features of protein encoded by the allelic variants. To the best of our knowledge, the present data is the first report for CYP2C9 allelic variations in the indigenous diabetic subjects and also report the existence of novel allelic variant of CYP2C9, CYP2C9*61.

Microscopy Image Browser: A Platform for Segmentation and Analysis of Multidimensional Datasets.

Understanding the structure-function relationship of cells and organelles in their natural context requires multidimensional imaging. As techniques for multimodal 3-D imaging have become more accessible, effective processing, visualization, and analysis of large datasets are posing a bottleneck for the workflow. Here, we present a new software package for high-performance segmentation and image processing of multidimensional datasets that improves and facilitates the full utilization and quantitative analysis of acquired data, which is freely available from a dedicated website. The open-source environment enables modification and insertion of new plug-ins to customize the program for specific needs. We provide practical examples of program features used for processing, segmentation and analysis of light and electron microscopy datasets, and detailed tutorials to enable users to rapidly and thoroughly learn how to use the program.

Vacuum Assisted Closure- utilization as home based therapy in the management of complex diabetic extremity wounds.

OBJECTIVE: Vacuum assisted closure is a reported technique to manage complex wounds. We have utilized this technique by using simple locally available material in the management of our patients on outpatient basis. The objective of this study is to present our experience. METHODS: This study was conducted from June 2011 to June 2013 at Dow University Hospital and Aga Khan University Hospital, Karachi. There were 38 patients managed with vacuum assisted closure. Mean age was 56±7.8 years. Twenty three patients presented with necrotizing fasciitis and 15 patients with gangrene. Lower limbs were involved in majority of the patients. Debridement or amputations were done. Vacuum dressing was changed twice weekly in outpatient department. Wounds were closed secondarily if possible or covered with split thickness skin graft in another admission. RESULTS: All the wounds were successfully granulated at the end of vacuum therapy. Mean hospital stay was 7.5 days. Vacuum dressing was applied for a mean of 20 days. There was reduction in the size of the wound. Thirteen patients underwent secondary closure of the wound under local anesthesia, 18 patients required coverage with split thickness skin graft and 7 patients healed with secondary intention. CONCLUSION: Vacuum assisted closure appeared to be an effective method to manage complex diabetic wounds requiring sterile wound environment.

Glomerular diseases outcome at one year in a tertiary care centre.

OBJECTIVES: To determine outcome in primary and secondary glomerular diseases at one year follow up. METHODS: Study design is observational cohort, done in out-patient department, Dow Iinternational Medical College, DUHS. All information gathered on a proforma. All patients with dipstick positive proteinuria and clinical glomerular disease were included in study. Patients with no proteinuria were excluded so were patients with stage 5 CKD. Patients were followed for proteinuria and renal insufficiency at completion of one year follow up. Statistical analysis was done on SPSS version 16. RESULT: Total number of patients who completed one year follow up was 173. Mean age of patients was 51.67+ 10.16 (range 15 to 75 years). Ninety two (53.2%), were males and 81(46.8%) were females, ratio being 1.1: 1.0. Mean weight of our patients was 67.43+ 14.13 Kg, (35 to 107 kg). Commonest cause of glomerular disease in our patient was diabetic nephropathy which was seen in 94.2% patients. Commonest associated problem with glomerular disease was hypertension seen in 66.5% of patients. Four out of 173 patients had stage 5 CKD at end of follow up at one year while quantitativ proteinuria remained same at one year follow up. CONCLUSION: One year follow up is critical for patients with glomerular disease associated with stage 4 CKD as progression to end stage renal failure may be seen within one year in these patients.

Pyuric diabetic patients: A tertiary centre experience from Karachi.

OBJECTIVES: (1) To determine frequency of urinary tract infection among pyuric diabetic patients. (2) To determine sterile pyuria frequency among pyuric diabetic patients. (3) To determine factors predisposing to urinary tract infection. METHODS: This is a non randomized, prospective observational study done in tertiary care set up of Dow University of Health Sciences, Karachi. Data collection done from June 2013 till August 2013. Sampling was done by convenient method, sample size of 97. Inclusion criteria was all adult (above 16) patients with diabetes mellitus and pyuria (more than 4 pus cells /HPF) whose urine culture report was also available. Verbal consent was sought from patients. All data was collected on a Performa. Data was maintained and analyzed on SPSS version 16. RESULTS: Total number of pyuric diabetic patients in study was 97. Frequency of Urinary tract infection was 59/97 (60.82%), prevalence of culture negative sterile pyuria was found 38/97 (39.17%). Urinary tract infection was found to be more in females with lower urinary tract symptoms and flank pains. Stone disease, obstructed pelvicalyceal system, proteinuria, high serum creatinine and positive nitrites were found more in culture positive patients than in culture negative pyuric patients. CONCLUSIONS: Pyuric diabetic patients in our study population were found to have culture positive UTI in 60.82% and culture negative sterile pyuria among 39.17% of patients. UTI was found more in females, in symptomatic patient and with abnormal urinary tract anatomy and function.

Utilizing deep learning model for assessing melanocytic density in resection margins of lentigo maligna.

BACKGROUND: Surgical excision with clear histopathological margins is the preferred treatment to prevent progression of lentigo maligna (LM) to invasive melanoma. However, the assessment of resection margins on sun-damaged skin is challenging. We developed a deep learning model for detection of melanocytes in resection margins of LM. METHODS: In total, 353 whole slide images (WSIs) were included. 295 WSIs were used for training and 58 for validation and testing. The algorithm was trained with 3,973 manual pixel-wise annotations. The AI analyses were compared to those of three blinded dermatopathologists and two pathology residents, who performed their evaluations without AI and AI-assisted. Immunohistochemistry (SOX10) served as the reference standard. We used a dichotomized cutoff for low and high risk of recurrence (≤ 25 melanocytes in an area of 0.5 mm for low risk and > 25 for high risk). RESULTS: The AI model achieved an area under the receiver operating characteristic curve (AUC) of 0.84 in discriminating margins with low and high recurrence risk. In comparison, the AUC for dermatopathologists ranged from 0.72 to 0.90 and for the residents in pathology, 0.68 to 0.80. Additionally, with aid of the AI model the performance of two pathologists significantly improved. CONCLUSIONS: The deep learning showed notable accuracy in detecting resection margins of LM with a high versus low risk of recurrence. Furthermore, the use of AI improved the performance of 2/5 pathologists. This automated tool could aid pathologists in the assessment or pre-screening of LM margins.

Manually pressurized droplet digital PCR chip for rapid SARS-CoV-2 diagnostics.

Droplet digital PCR (ddPCR) is a technique in which PCR reaction is divided into thousands of nanoliter-sized droplets and has proven to be a great tool in virus diagnostics. Compared to the gold standard system quantitative real-time PCR (RT-qPCR), ddPCR functions particularly well when dealing with samples with low template counts, such as viral concentration. This feature makes the technique suitable for early detection of the virus. In this study, a novel portable PDMS ddPCR chip is introduced. The chip functions without external pumps using manual pressurization with a multichannel pipet. The created droplets are monodispersed and form a monolayer on the chip's collection chamber, from where they can be effortlessly imaged. Droplets were analyzed and counted using artificial intelligence. The use of the manually pressurized chip was demonstrated for a SARS-CoV-2 assay, which takes advantage of isothermal strand invasion-based amplification (SIBA) technology, allowing quick and accurate, even point-of-care analysis of the sample. The results demonstrate that SIBA assays can be divided into nanoliter-sized droplets and used as quantitative assays, giving an approximation of the samples' viral count.

A deep-learning-based model for assessment of autoimmune hepatitis from histology: AI(H).

Histological assessment of autoimmune hepatitis (AIH) is challenging. As one of the possible results of these challenges, nonclassical features such as bile-duct injury stays understudied in AIH. We aim to develop a deep learning tool (artificial intelligence for autoimmune hepatitis [AI(H)]) that analyzes the liver biopsies and provides reproducible, quantifiable, and interpretable results directly from routine pathology slides. A total of 123 pre-treatment liver biopsies, whole-slide images with confirmed AIH diagnosis from the archives of the Institute of Pathology at University Hospital Basel, were used to train several convolutional neural network models in the Aiforia artificial intelligence (AI) platform. The performance of AI models was evaluated on independent test set slides against pathologist's manual annotations. The AI models were 99.4%, 88.0%, 83.9%, 81.7%, and 79.2% accurate (ratios of correct predictions) for tissue detection, liver microanatomy, necroinflammation features, bile duct damage detection, and portal inflammation detection, respectively, on hematoxylin and eosin-stained slides. Additionally, the immune cells model could detect and classify different immune cells (lymphocyte, plasma cell, macrophage, eosinophil, and neutrophil) with 72.4% accuracy. On Sirius red-stained slides, the test accuracies were 99.4%, 94.0%, and 87.6% for tissue detection, liver microanatomy, and fibrosis detection, respectively. Additionally, AI(H) showed bile duct injury in 81 AIH cases (68.6%). The AI models were found to be accurate and efficient in predicting various morphological components of AIH biopsies. The computational analysis of biopsy slides provides detailed spatial and density data of immune cells in AIH landscape, which is difficult by manual counting. AI(H) can aid in improving the reproducibility of AIH biopsy assessment and bring new descriptive and quantitative aspects to AIH histology.

CD163+ macrophages in mantle cell lymphoma induce activation of prosurvival pathways and immune suppression.

ABSTRACT: Mantle cell lymphoma (MCL) is dependent on a supportive tumor immune microenvironment (TIME) in which infiltration of CD163+ macrophages has a negative prognostic impact. This study explores how abundance and spatial localization of CD163+ cells are associated with the biology of MCL, using spatial multiomic investigations of tumor and infiltrating CD163+ and CD3+ cells. A total of 63 proteins were measured using GeoMx digital spatial profiling in tissue microarrays from 100 diagnostic MCL tissues. Regions of interest were selected in tumor-rich and tumor-sparse tissue regions. Molecular profiling of CD163+ macrophages, CD20+ MCL cells, and CD3+ T-cells was performed. To validate protein profiles, 1811 messenger RNAs were measured in CD20+ cells and 2 subsets of T cells. Image analysis was used to extract the phenotype and position of each targeted cell, thereby allowing the exploration of cell frequencies and cellular neighborhoods. Proteomic investigations revealed that CD163+ cells modulate their immune profile depending on their localization and that the immune inhibitory molecules, V-domain immunoglobulin suppressor of T-cell activation and B7 homolog 3, have higher expression in tumor-sparse than in tumor-rich tissue regions and that targeting should be explored. We showed that MCL tissues with more abundant infiltration of CD163+ cells have a higher proteomic and transcriptional expression of key components of the MAPK pathway. Thus, the MAPK pathway may be a feasible therapeutic target in patients with MCL with CD163+ cell infiltration. We further showed the independent and combined prognostic values of CD11c and CD163 beyond established risk factors.

Visualizing Arc protein dynamics and localization in the mammalian brain using AAV-mediated in situ gene labeling.

The activity-regulated cytoskeleton-associated (Arc) protein is essential for synaptic plasticity and memory formation. The Arc gene, which contains remnants of a structural GAG retrotransposon sequence, produces a protein that self-assembles into capsid-like structures harboring Arc mRNA. Arc capsids, released from neurons, have been proposed as a novel intercellular mechanism for mRNA transmission. Nevertheless, evidence for intercellular transport of Arc in the mammalian brain is still lacking. To enable the tracking of Arc molecules from individual neurons in vivo, we devised an adeno-associated virus (AAV) mediated approach to tag the N-terminal of the mouse Arc protein with a fluorescent reporter using CRISPR/Cas9 homologous independent targeted integration (HITI). We show that a sequence coding for mCherry can successfully be knocked in at the 5' end of the Arc open reading frame. While nine spCas9 gene editing sites surround the Arc start codon, the accuracy of the editing was highly sequence-dependent, with only a single target resulting in an in-frame reporter integration. When inducing long-term potentiation (LTP) in the hippocampus, we observed an increase of Arc protein highly correlated with an increase in fluorescent intensity and the number of mCherry-positive cells. By proximity ligation assay (PLA), we demonstrated that the mCherry-Arc fusion protein retains the Arc function by interacting with the transmembrane protein stargazin in postsynaptic spines. Finally, we recorded mCherry-Arc interaction with presynaptic protein Bassoon in mCherry-negative surrounding neurons at close proximity to mCherry-positive spines of edited neurons. This is the first study to provide support for inter-neuronal in vivo transfer of Arc in the mammalian brain.

Comparative Evaluation of Breast Ductal Carcinoma Grading: A Deep-Learning Model and General Pathologists' Assessment Approach.

Breast cancer is the most prevalent neoplasia among women, with early and accurate diagnosis critical for effective treatment. In clinical practice, however, the subjective nature of histological grading of infiltrating ductal adenocarcinoma of the breast (DAC-NOS) often leads to inconsistencies among pathologists, posing a significant challenge to achieving optimal patient outcomes. Our study aimed to address this reproducibility problem by leveraging artificial intelligence (AI). We trained a deep-learning model using a convolutional neural network-based algorithm (CNN-bA) on 100 whole slide images (WSIs) of DAC-NOS from the Cancer Genome Atlas Breast Invasive Carcinoma (TCGA-BRCA) dataset. Our model demonstrated high precision, sensitivity, and F1 score across different grading components in about 17.5 h with 19,000 iterations. However, the agreement between the model's grading and that of general pathologists varied, showing the highest agreement for the mitotic count score. These findings suggest that AI has the potential to enhance the accuracy and reproducibility of breast cancer grading, warranting further refinement and validation of this approach.

RTN4B interacting protein FAM134C promotes ER membrane curvature and has a functional role in autophagy.

The endoplasmic reticulum (ER) is composed of a controlled ratio of sheets and tubules, which are maintained by several proteins with multiple functions. Reticulons (RTNs), especially RTN4, and DP1/Yop1p family members are known to induce ER membrane curvature. RTN4B is the main RTN4 isoform expressed in nonneuronal cells. In this study, we identified FAM134C as a RTN4B interacting protein in mammalian, nonneuronal cells. FAM134C localized specifically to the ER tubules and sheet edges. Ultrastructural analysis revealed that overexpression of FAM134C induced the formation of unbranched, long tubules or dense globular structures composed of heavily branched narrow tubules. In both cases, tubules were nonmotile. ER tubulation was dependent on the reticulon homology domain (RHD) close to the N-terminus. FAM134C plays a role in the autophagy pathway as its level elevated significantly upon amino acid starvation but not during ER stress. Moreover, FAM134C depletion reduced the number and size of autophagic structures and the amount of ER as a cargo within autophagic structures under starvation conditions. Dominant-negative expression of FAM134C forms with mutated RHD or LC3 interacting region also led to a reduced number of autophagic structures. Our results suggest that FAM134C provides a link between regulation of ER architecture and ER turnover by promoting ER tubulation required for subsequent ER fragmentation and engulfment into autophagosomes.

REEP3 and REEP4 determine the tubular morphology of the endoplasmic reticulum during mitosis.

The endoplasmic reticulum (ER) is extensively remodeled during metazoan open mitosis. However, whether the ER becomes more tubular or more cisternal during mitosis is controversial, and dedicated factors governing the morphology of the mitotic ER have remained elusive. Here, we describe the ER membrane proteins REEP3 and REEP4 as major determinants of ER morphology in metaphase cells. REEP3/4 are specifically required for generating the high-curvature morphology of mitotic ER and promote ER tubulation through their reticulon homology domains (RHDs). This ER-shaping activity of REEP3/4 is distinct from their previously described function to clear ER from metaphase chromatin. We further show that related REEP proteins do not contribute to mitotic ER shaping and provide evidence that the REEP3/4 carboxyterminus mediates regulation of the proteins. These findings confirm that ER converts to higher curvature during mitosis, identify REEP3/4 as specific and crucial morphogenic factors mediating ER tubulation during mitosis, and define the first cell cycle-specific role for RHD proteins.