Benign Tissue Research Articles

Evaluation of Machine Learning Classification Models for False-Positive Reduction in Prostate Cancer Detection Using MRI Data.

In this work, several machine learning (ML) algorithms, both classical ML and modern deep learning, were investigated for their ability to improve the performance of a pipeline for the segmentation and classification of prostate lesions using MRI data. The algorithms were used to perform a binary classification of benign and malignant tissue visible in MRI sequences. The model choices include support vector machines (SVMs), random decision forests (RDFs), and multi-layer perceptrons (MLPs), along with radiomic features that are reduced by applying PCA or mRMR feature selection. Modern CNN-based architectures, such as ConvNeXt, ConvNet, and ResNet, were also evaluated in various setups, including transfer learning. To optimize the performance, different approaches were compared and applied to whole images, as well as gland, peripheral zone (PZ), and lesion segmentations. The contribution of this study is an investigation of several ML approaches regarding their performance in prostate cancer (PCa) diagnosis algorithms. This work delivers insights into the applicability of different approaches for this context based on an exhaustive examination. The outcome is a recommendation or preference for which machine learning model or family of models is best suited to optimize an existing pipeline when the model is applied as an upstream filter.

Extracellular vesicles carry transcriptional 'dark matter' revealing tissue-specific information.

From eukaryotes to prokaryotes, all cells secrete extracellular vesicles (EVs) as part of their regular homeostasis, intercellular communication, and cargo disposal. Accumulating evidence suggests that small EVs carry functional small RNAs, potentially serving as extracellular messengers and liquid-biopsy markers. Yet, the complete transcriptomic landscape of EV-associated small RNAs during disease progression is poorly delineated due to critical limitations including the protocols used for sequencing, suboptimal alignment of short reads (20-50nt), and uncharacterized genome annotations-often denoted as the 'dark matter' of the genome. In this study, we investigate the EV-associated small unannotated RNAs that arise from endogenous genes and are part of the genomic 'dark matter', which may play a key emerging role in regulating gene expression and translational mechanisms. To address this, we created a distinct small RNAseq dataset from human prostate cancer & benign tissues, and EVs derived from blood (pre- & post-prostatectomy), urine, and human prostate carcinoma epithelial cell line. We then developed an unsupervised data-based bioinformatic pipeline that recognizes biologically relevant transcriptional signals irrespective of their genomic annotation. Using this approach, we discovered distinct EV-RNA expression patterns emerging from the un-annotated genomic regions (UGRs) of the transcriptomes associated with tissue-specific phenotypes. We have named these novel EV-associated small RNAs as 'EV-UGRs' or "EV-dark matter". Here, we demonstrate that EV-UGR gene expressions are downregulated by ∼100 fold (FDR<0.05) in the circulating serum EVs from aggressive prostate cancer subjects. Remarkably, these EV-UGRs expression signatures were regained (upregulated) after radical prostatectomy in the same follow-up patients. Finally, we developed a stem-loop RT-qPCR assay that validated prostate cancer-specific EV-UGRs for selective fluid-based diagnostics. Overall, using an unsupervised data driven approach, we investigate the 'dark matter' of EV-transcriptome and demonstrate that EV-UGRs carry tissue-specific Information that significantly alters pre- and post-prostatectomy in the prostate cancer patients. Although further validation in randomized clinical trials is required, this new class of EV-RNAs hold promise in liquid-biopsy by avoiding highly invasive biopsy procedures in prostate cancer.

Machine learning and experimental analyses identified miRNA expression models associated with metastatic osteosarcoma

Osteosarcoma (OS), as the most common primary bone cancer, has a high invasiveness and metastatic potential, therefore, it has a poor prognosis. This study identified early diagnostic biomarkers using miRNA expression profiles associated with osteosarcoma metastasis. In the first step, we used RNA-seq and online microarray data from osteosarcoma tissues and cell lines to identify differentially expressed miRNAs. Then, using seven feature selection algorithms for ranking, the first-ranked miRNAs were selected as input for five machine learning systems. Using network analysis and machine learning algorithms, we developed new diagnostic models that successfully differentiated metastatic osteosarcoma from non-metastatic samples based on newly discovered miRNA signatures. The results showed that miR-34c-3p and miR-154-3p act as the most promising models in the diagnosis of metastatic osteosarcoma. Validation for this model by RT-qPCR in benign tissue and osteosarcoma biopsies confirmed the lower expression of miR-34c-3p and miR-154-3p in OS samples. In addition, a direct correlation between miR-34c-3p expression, miR-154-3p expression and tumor grade was discovered. The combined values of miR-34c-3p and miR-154-3p showed 90 % diagnostic power (AUC = 0.90) for osteosarcoma samples and 85 % (AUC = 0.85) for metastatic osteosarcoma. Adhesion junction and focal adhesion pathways, as well as epithelial-to-mesenchymal transition (EMT) GO terms, were identified as the most significant KEGG and GO terms for the top miRNAs. The findings of this study highlight the potential use of novel miRNA expression signatures for early detection of metastatic osteosarcoma. These findings may help in determining therapeutic approaches with a quantitative and faster method of metastasis detection and also be used in the development of targeted molecular therapy for this aggressive cancer. Further research is needed to confirm the clinical utility of miR-34c-3p and miR-154-3p as diagnostic biomarkers for metastatic osteosarcoma.

Pediatric intramuscular hemangioma in the submandibular triangle and other musculoskeletal presentations: A pediatric case series

BackgroundIntramuscular hemangiomas (IMH) account for 0.8 % or less of all benign soft tissue tumors in the general population. Due to their uncommon nature, especially in the head and neck, they are often misdiagnosed and not included in the differential diagnosis. MethodsThis study describes a case series of eleven pediatric patients with a diagnosis of IMH through a retrospective review of the electronic health records and archival records in the Department of Pathology at Children's Hospital of Colorado (CHCO). ResultsThe index case had a unique presentation in the submandibular triangle, while the remaining ten cases are appendicular and thoracolumbar in nature. ConclusionsThis case series contributes to the sparse scientific literature available regarding IMH, particularly in its head and neck presentation as relevant to otolaryngologists.

The expression of c-MYC, Cyclin D1 and Ki-67/MIB-1 in benign and malignant thyroid tissues: is there any diagnostic value?

To investigate the immunohistochemical (IHC) expression and the diagnostic value of c-MYC, Cyclin D1, and Ki-67∕MIB-1 in follicular adenomas (FAs), follicular carcinomas (FCs), and anaplastic carcinomas (ACs) of the thyroid gland, as well as in their corresponding adjacent, non-neoplastic thyroid tissue (NNTT). We conducted a retrospective study of patients who were pathologically diagnosed with FA, FC, or AC after total thyroidectomy. Tissue microarrays with cores taken from neoplastic and adjacent NNTT were constructed. Immunohistochemistry for anti-c-MYC, anti-Cyclin D1, and anti-Ki-67∕MIB-1 antibodies was performed, and the positivity was evaluated. Twenty-eight specimens were included. Nuclear c-MYC positivity was observed in 4∕11 FCs, and 3∕4 ACs, whereas cytoplasmic c-MYC positivity was found in 16∕24 NNTTs. Globally, there were statistically significant differences between neoplasms and NNTTs, with higher nuclear c-MYC and Cyclin D1 expression observed in neoplasms (p=0.017 and p=0.001, respectively). In contrast, cytoplasmic positivity was seen solely in NNTTs (p=0.001). Cyclin D1 positivity was noted in 11∕13 FAs, 7∕11 FCs, 2∕4 ATCs, and only in one NNTT. A statistically significant correlation was found between MIB1 and c-MYC nuclear positivity (p=0.040). Our findings exhibit a clear difference in the IHC expression of c-MYC and Cyclin D1 between different types of thyroid tumors, as well as between the neoplastic and NNTT. Nuclear c-MYC positivity excludes the benign nature of a thyroid lesion, in contrast to cytoplasmic positivity, which demonstrates normal or hyperplastic nature.

The Current Role of Contrast-Enhanced Ultrasound (CEUS) in the Diagnosis and Staging of Bladder Cancer: A Review of the Available Literature.

Contrast-enhanced ultrasound (CEUS) is an advanced imaging technique that integrates conventional US with the intravenous injection of specific US contrast agents (UCAs), combining the non-invasiveness of US with the higher accuracy of contrast-enhanced imaging. In contrast with magnetic resonance imaging (MRI), computed tomography (CT) and cystoscopy, CEUS has few contraindications, and UCAs are non-nephrotoxic agents that can be safely used in patients with kidney failure. CEUS is a well-established method for the detection of liver lesions and for echocardiography, and its indications are expanding. The updated 2018 WFUMB-EFSUMB guidelines have added the urinary bladder under non-hepatic applications of CEUS. The technique is able to distinguish between benign tissue, such as clots or hematoma, and malignant lesions by perfusing the mass with contrast agent. Thanks to the different perfusion rates of the various layers of the bladder wall, CEUS is also able to predict tumor invasion depth and stage. Despite that, current urological guidelines do not include CEUS as a plausible imaging technique for bladder urothelial carcinoma. The main reason for this omission might be the presence of scarce randomized evidence and the absence of large validated series. In this review, we describe the rationale behind the use of CEUS in bladder cancer and the added value of this imaging technique in the detection and staging of bladder lesions. In addition, we researched the available literature on the topic and then described the results of randomized clinical trials and a meta-analysis investigating the accuracy of CEUS in bladder cancer diagnosis and staging. The reported studies show that CEUS is a highly accurate diagnostic and staging tool for BC, reaching levels of specificity and sensitivity in differentiating between Ta-T1, or low-grade BC, and T2, or high-grade BC, that are comparable to those shown by the reference standard methods. Nonetheless, several limitations were found and are highlighted in this review. The aim of this study is to further validate and promote the use of CEUS as a quick, economic and effective diagnostic tool for this high-impact disease.

Epidemiología de los tumores musculoesqueléticos en una unidad de referencia

ObjectiveThe objective of this study was to perform an epidemiological analysis of patients presented to the Musculoskeletal Tumors Committee of a reference hospital. Material and methodA retrospective analysis of patients with sarcomas treated in a reference Sarcoma Unit between 2009 and 2022 was carried out. ResultsA total of 1978 patients were analyzed, of which 1477 (74.67%) were diagnosed as sarcomas. They were divided into 446 (30.20%) bone tumors and 1.031 (69.80%) soft tissue tumors. The most common benign bone tumor was enchondroma (27.23%), giant cell tumor (59.21%) was the most common tumor of intermediate malignancy and the malignant one was osteosarcoma (24.78%). The most frequently observed benign soft tissue tumor was lipoma (50.74%), the atypical lipomatous tumor (53.25%) was the most frequent tumor of intermediate malignancy and the malignant one was sarcoma of uncertain differentiation (38.10%). ConclusionOur study represents the first work on the epidemiology of sarcomas and other musculoskeletal tumors in our country, being very useful to adapt the resources destined for their diagnosis and treatment.

Vascular Leiomyoma of oral cavity: A case report in young male patient

Abstract Vascular Leiomyoma of the oral cavity is an uncommon benign soft tissue neoplasia arising from the tunica media of the smooth muscle cells. We reported a rare case of Vascular Leiomyoma involving the retromolar trigone area of a young man. A 24-year-old male presented with a slowly growing mass in the retromolar area, which was associated with pain and difficulty in opening of mouth and eating and drinking. A punch biopsy was taken and sent for histopathological examination which revealed a benign angiomatous lesion. The mass was excised, and the adjoining area was curetted. Histopathological examination confirmed the diagnosis of Vascular Leiomyoma. The immunohistochemistry of cells shows: alpha-smooth muscle (+); vimentin (+), Desmin, actin (+), and S100 (−). Angioleiomyomas are benign lesions, but malignant transformation is a possibility so careful histologic inspection is necessary to distinguish these lesions from their malignant counterpart.

Proteomic and Phosphoproteomic analysis of thyroid papillary carcinoma: Identification of potential biomarkers for metastasis

Thyroid cancer has emerged as the most rapidly proliferating solid neoplasm. In this study, we included a cohort of patients who underwent sonographic assessment and surgical intervention at the Sir Run Run Shaw Hospital, associated with the School of Medicine at Zhejiang University, spanning from January 2019 to June 2020. Stratification of cases was based on a combination of preoperative ultrasonographic evaluations and postoperative histopathological diagnoses, resulting in three distinct groups: high-risk papillary thyroid carcinoma (PTC) labeled as C1, low-risk PTC designated as C2, and a control group (N) composed of benign thyroid tissue adjacent to the carcinoma. Proteomic and phosphoproteomic analyses were conducted on PTC specimens. The comparative assessment revealed that proteins up-regulated in the C1/N and C2/N groups were predominantly involved in functions such as amino acid binding, binding of phosphorylated compounds, and serine protease activity. Notably, proteins like NADH dehydrogenase, ATP synthase, oxidoreductases, and iron ion channels were significantly elevated in the C1 versus C2 comparative group. Through meticulous analysis of differential expression multiples, statistical significance, and involvement in metabolic pathways, this study identified eight potential biomarkers pertinent to PTC metastasis diagnostics, encompassing phosphorylated myosin 10, phosphorylated proline-directed protein kinase, leucine tRNA synthetase, 2-oxo-isovalerate dehydrogenase, succinic semialdehyde dehydrogenase, ADP/ATPtranslocase, pyruvate carboxylase, and fibrinogen. Therapeutic assays employing metformin, an AMP-activated protein kinase (AMPK) activator, alongside the phosphorylation-specific inhibitor ML-7 targeting Myosin10, demonstrated attenuated cellular proliferation, migration, and invasion capabilities in thyroid cancer cells, accompanied by a reduction in amino acid pools. Cellular colocalization and interaction studies elucidated that AMPK activation imposes an inhibitory influence on Myosin10 levels. The findings of this research corroborate the utility of proteomic and phosphoproteomic platforms in the identification of metastatic markers for PTC and suggest that modulation of AMPK activity, coupled with the inhibition of Myosin10 phosphorylation, may forge novel therapeutic avenues in the management of thyroid carcinoma. SignificanceThe significance of our research lies in its potential to transform the current understanding and management of thyroid papillary carcinoma (PTC), particularly in its metastatic form. By integrating both proteomic and phosphoproteomic analyses, our study not only sheds light on the molecular alterations associated with PTC but also identifies eight novel biomarkers that could serve as indicators of metastatic potential.

Vaginal Cellular Angiofibroma: Report of a Rare Case with Literature Review

ABSTRACT Cellular angiofibroma (CA) is a relatively recently described, rare, benign soft tissue tumor that predominantly occurs in the vulvoperineal region. It was first described in 1997 as a mesenchymal-origin tumor composed of connective (fibrous) tissue and blood vessels. We report a case of vaginal CA in a 40-year-old woman who presented with pressure symptoms, incidentally diagnosed with a vaginal mass and clinically suspected as vaginal myoma. This case was diagnosed based on histomorphology and immunohistochemistry and underwent surgical treatment. This tumor was a diagnostic dilemma for other benign and aggressive spindle cell tumors in the same area, such as endometrial stromal nodule, spindle cell lipoma, solitary fibrous tumors, and mixed tumors of the vagina.

A prospective evaluation of the prostate microbiome in malignant and benign tissue using transperineal biopsy.

The link between the prostate microbiome and prostate cancer remains unclear. Few studies have analyzed the microbiota of prostate tissue, and these have been limited by potential contamination by transrectal biopsy. Transperineal prostate biopsy offers an alternative and avoids fecal cross-contamination. We aim to characterize the prostate microbiome using transperineal biopsy. Patients with clinical suspicion for prostate cancer who were to undergo transperineal prostate biopsy with magnetic resonance imaging(MRI) fusion guidance were prospectively enrolled from 2022 to 2023. Patients were excluded if they had Prostate Imaging Reporting and Data System lesions with scores ≤ 3, a history of prostate biopsy within 1 year, a history of prostate cancer, or antibiotic use within 30 days of biopsy. Tissue was collected from the MRI target lesions and nonneoplastic transitional zone. Bacteria were identified using 16S ribosomal RNA gene sequencing. Across the 42 patients, 76% were found to have prostate cancer. Beta diversity indices differed significantly between the perineum, voided urine, and prostate tissue. There were no beta diversity differences between cancerous or benign tissue, or between pre- and postbiopsy urines. There appear to be unique genera more abundant in cancerous versus benign tissue. There were no differences in alpha diversity indices relative to clinical findings including cancer status, grade, and risk group. We demonstrate a rigorous method to better characterize the prostate microbiome using transperineal biopsy and to limit contamination. These findings provide a framework for future large-scale studies of the microbiome of prostate cancer.

Evaluation of Parameters Affecting Intrinsic Uniformity to Perform Best Optimum Daily QC

Nuclear Medicine plays a vital role in the diagnosis of benign and malignant cancer tissues. The quality assurance program of gamma cameras in nuclear medicine provides an artifact-free diagnosis. One of the most important quality control (QC) is to test the response of detectors to a uniform distributed source called as uniformity test. The QC of image uniformity test includes intrinsic uniformity (IU) and Differential uniformity (DU) of CFOV (Central Field of View) and UFOV (Useful Field of View). The purpose of this study is to evaluate the best value of parameters for getting the best uniformity results and set as a benchmark for checking the performance of gamma cameras in the future. It is analyzed that using an energy window placed at 140 KeV at 20%, with a matrix size of 256 x 256, acquiring 60 million counts and the source activity close to 500 µC obtained images are good and both uniformities are within the manufacturer’s requirements, however, increasing the number of acquired counts and by mounting a source at a distance larger than 2m, images become better.

GRIN3A: A biomarker associated with a cribriform pattern and poor prognosis in prostate cancer

Prostate cancer with a cribriform pattern, including invasive cribriform carcinoma (ICC) and/or intraductal carcinoma (IDC) is associated with a poor prognosis, and the underlying mechanisms are unclear. Therefore, we aimed to identify biomarkers for this feature. Using a radical prostatectomy cohort, we performed within-patient differential expression analyses with RNA sequencing data to compare samples with a cribriform pattern to those with non-cribriform Gleason pattern 4 (NcGP4; n=13). ACSM1, GRIN3A, PCDHB2, and REG4 were identified as differentially expressed, and validation was performed using real-time reverse transcription polymerase chain reaction (n=99; 321 RNA samples) and RNA in situ hybridization on tissue microarrays (n=479; 2047 tissue cores). GRIN3A was significantly higher expressed in cribriform pattern vs. NcGP4, when assessed within the same patient (n=27; p=0.005) and between different patients (n=83; p=0.001). Tissue cores with IDC more often expressed GRIN3A compared to ICC, NcGP4, and benign tissue (52 % vs. ≤ 32 %). When IDC and NcGP4 was compared within the same patient (173 pairs of tissue cores; 54 patients), 38 (22 %) of the tissue microarray core pairs had GRIN3A expression in only IDC, 33 (19 %) had expression in both IDC and NcGP4, 14 (8 %) in only NcGP4 and 88 (51 %) were negative in both entities (p=0.001). GRIN3A was as well associated with biochemical recurrence (log-rank, p=0.002). In conclusion, ectopic GRIN3A expression is an RNA-based biomarker for the presence of cribriform prostate cancer, particularly for IDC.

HMAGEA2 Accelerates the Progression of Prostate Cancer via the EFNA3-Erk1/2 Signaling Pathway.

Human melanoma-associated antigen A2 (hMAGEA2) family members play several roles in many types of cancer and have been explored as potential prognostic markers. In this study, we investigated the molecular mechanism underlying hMAGEA2-mediated tumorigenesis of prostate cancer. Immunohistochemistry and western blot were used to assess protein expression whereas microarray and quantitative reverse transcription-PCR determined mRNA expression. CCK-8 assay was used to determine cell proliferation. Colony formation assay was used to examine tumorigenesis. Migration and invasion were examined using a transwell assay. Propidium iodide (PI)/Annexin V double staining was performed to measure apoptosis. Transcriptional activity was measured using Dual-luciferase reporter assay. hMAGEA2 was highly over-expressed in human prostate cancer tissues compared to benign prostatic hyperplasia tissues. To elucidate its biological function in prostate cancer, we established two stable hMAGEA2-knockdown prostate cancer cell lines, PC3M and 22RV1, and found that they presented significantly decreased proliferation, anchorage-independent colony formation, migration, and invasion. As hMAGEA2 knockdown suppressed prostate cancer cell growth, we examined its potential influence on tumor apoptosis. hMAGEA2-knockdown cell lines displayed early apoptosis. Moreover, knockdown of hMAGEA2 resulted in the down-regulation of EFNA3 expression. Luciferase assay showed that hMAGEA2 bound to the EFNA promoter region and regulated its transcription. Down-regulation of EFNA3 expression led to decreased Ras/Braf/MEK/Erk1/2 phosphorylation and, consequently, inhibited prostate cancer progression. hMAGEA2 promotes prostate cancer growth, metastasis, and tumorigenesis by regulating the EFNA3-Erk1/2 signaling pathway, indicating its potential as a therapeutic marker for prostate cancer.

Endometriosis: A Narrative Review

Although much progress has been made since endometriosis was first scientifically described centuries ago, numerous unanswered questions still surround this chronic, inflammatory condition. For instance, one theory on the pathogenesis of endometriosis suggests that the condition begins from retrograde menstrual flow implanting on surfaces in the abdomen and pelvis (Samson’s theory), which is a logical mechanism given the high rates of endometriosis in patients with obstructive anomalies of the lower genital tract and significant retrograde flow. This explanation has many shortcomings however, as retrograde menstruation occurs more commonly than the reported 10% prevalence of endometriosis. Additionally, endometriosis lesions can be found in areas quite remote from the pelvis, such as the thoracic cavity. As such, research has been increasingly focused on identifying immune, genetic, and local environmental factors that likely play critical roles in the development of endometriosis. This growth of benign endometrial-like tissue outside of the uterus can sometimes be asymptomatic, but it can also cause debilitating pain, infertility, ovarian cysts (endometriomas), and can invade surrounding organs such as the bowel or bladder. There are three main phenotypes of endometriosis: superficial lesions, deeply infiltrating endometriosis (including nodules), and ovarian endometriomas. While the exact etiology may be obscure, the societal and economic impacts of this condition are undeniable. Patients diagnosed with endometriosis are at a significantly higher risk of absenteeism from work or school, lower quality of life, chronic pelvic pain, and are more likely to receive a mental health diagnosis such as depression or anxiety. Apart from direct and indirect incurred costs to patients (estimated at approximately $5000 per patient annually), at a national level the economic burden of endometriosis exceeds $2 billion annually in Canada, and approaches $80 billion in the USA.

Differentiation of Cutaneous Metastatic Breast Cancer from Cutaneous Adnexal Tumors Using Wnt9b Polyclonal Antibody Stain

Objective: The histologic diagnosis of cutaneous metastatic breast cancer can be challenging as the differentials can include primary cutaneous glandular neoplasms and metastases from other glandular neoplasms which present very similar on H&amp;E. Many immunohistological markers including GATA3 and CK7 have been employed to screen for primary or metastatic breast cancer cells and because of this, we wanted to develop a stain capable of differentiating these diagnoses quickly and accurately. Methods: We utilized 61 archived dermatopathology laboratory specimens of various benign and malignant cutaneous adnexal and breast tissues for analysis with a polyclonal Wnt9b antibody stain. Results: The average staining in benign categories (cutaneous adnexal and benign breast tissue) as well as metastases from non-breast carcinomas was negative. Among the malignant cutaneous adnexal and metastatic breast tissues, a significant difference was observed in staining as adnexal carcinomas were weakly positive (0.53+) and primarily seen in the outer layer of glandular structures, while metastatic breast tissues were strongly positive (3.63+) (P&lt;0.01). The specificity in both adnexal and metastatic breast tissues was 100% while the sensitivity for adnexal carcinomas was 37% and metastatic breast was 94%. A larger sample size could greatly improve these values. Conclusion: These results demonstrate that Wnt9b has specific staining for cutaneous metastatic breast cell nuclei and could be utilized as a diagnostic to differentiate from cutaneous adnexal tumors in routine dermatopathological applications. Keywords: Metastatic Breast Carcinomas; Cutaneous Adnexal Tumor; Staining; Polyclonal Antibody; Histological Markers

Differentiation of malignant from benign soft tissue tumors using radiomics based on pharmacokinetic parameter maps obtained from dynamic contrast-enhanced magnetic resonance imaging data

Differentiation of malignant from benign soft tissue tumors using radiomics based on pharmacokinetic parameter maps obtained from dynamic contrast-enhanced magnetic resonance imaging data

An unusual case of nodular fasciitis presenting as an intra-tendinous mass.

Nodular fasciitis is a benign soft tissue pseudotumour typically occurring in the upper extremities, head and neck, thigh and trunk. It is most commonly seen in subcutaneous locations but also can be present in intramuscular and intermuscular (fascial) locations. Its occurrence in the hand is rare, and while it can occur in close proximity to tendons, its presentation as an intra-tendinous mass has not been previously described. We present a unique and rare case of nodular fasciitis arising within the flexor digitorum profundus (FDP) tendon of the hand in a 16-year-old female. The patient presented with a painful swelling in the volar aspect of the base of her left middle finger, with progressive flexion deformity of the finger. Ultrasound and magnetic resonance imaging revealed a mass within the FDP tendon of the middle finger. An ultrasound-guided biopsy revealed a diagnosis of nodular fasciitis. Given the self-limiting nature of the condition, she was managed conservatively with close clinical and imaging follow-up. This case highlights the importance of considering nodular fasciitis in the differential diagnosis of an intra-tendinous lesion in the hand, even though it is a rare occurrence in this location. The clinical presentation, diagnostic workup, and management of this unique case are discussed, emphasising the potential for its misdiagnosis as a malignancy which can have important implications in management.

Integrative analysis of ultra-deep RNA-seq reveals alternative promoter usage as a mechanism of activating oncogenic programmes during prostate cancer progression.

Transcription factor (TF) proteins regulate gene activity by binding to regulatory regions, most importantly at gene promoters. Many genes have alternative promoters (APs) bound by distinct TFs. The role of differential TF activity at APs during tumour development is poorly understood. Here we show, using deep RNA sequencing in 274 biopsies of benign prostate tissue, localized prostate tumours and metastatic castration-resistant prostate cancer, that AP usage increases as tumours progress and APs are responsible for a disproportionate amount of tumour transcriptional activity. Expression of the androgen receptor (AR), the key driver of prostate tumour activity, is correlated with elevated AP usage. We identified AR, FOXA1 and MYC as potential drivers of AP activation. DNA methylation is a likely mechanism for AP activation during tumour progression and lineage plasticity. Our data suggest that prostate tumours activate APs to magnify the transcriptional impact of tumour drivers, including AR and MYC.

Vision transformer-convolution for breast cancer classification using mammography images: A comparative study

Breast cancer is a significant global health concern, highlighting the critical importance of early detection for effective treatment of women’s health. While convolutional networks (CNNs) have been the best for analysing medical images, recent interest has emerged in leveraging vision transformers (ViTs) for medical data analysis. This study aimed to conduct a comprehensive comparison of three systems a self-attention transformer (VIT), a compact convolution transformer (CCT), and a tokenlearner (TVIT) for binary classification of mammography images into benign and cancerous tissue. Thorough experiments were performed using the DDSM dataset, which consists of 5970 benign and 7158 malignant images. The performance accuracy of the proposed models was evaluated, yielding results of 99.81% for VIT, 99.92% for CCT, and 99.05% for TVIT. Additionally, the study compared these results with the current state-of-the-art performance metrics. The findings demonstrate how convolution-attention mechanisms can effectively contribute to the development of robust computer-aided systems for diagnosing breast cancer. Notably, the proposed approach achieves high-performance results while also minimizing the computational resources required and reducing decision time.