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Exosomes, small extracellular vesicles (sEVs) secreted by various cell types, play crucial roles in intercellular communication and are increasingly recognized as valuable biomarkers for disease diagnosis and therapeutic targets. Meanwhile, machine learning (ML) techniques have revolutionized biomedical research by enabling the analysis of complex datasets and highly accurate prediction of disease outcomes. Exosomes, with their diverse cargo of proteins, nucleic acids, and lipids, offer a rich source of molecular information reflecting the physiological state of cells. Integrating exosome analysis with ML algorithms, including supervised and unsupervised learning techniques, allows for identifying disease-specific biomarkers and predicting disease outcomes based on exosome profiles. Integrating exosome biology with ML presents a promising avenue for advancing biomedical research and clinical practice. This review explores the intersection of exosome biology and ML in biomedicine, highlighting the importance of integrating these disciplines to advance our understanding of disease mechanisms and biomarker discovery.

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Oral Lichen Planus (OLP) presents a significant challenge in diagnosis due to its varied clinical manifestations and the absence of specific biomarkers. Timely and accurate diagnosis is crucial, particularly given its association with oral squamous cell carcinoma (OSCC). This review aims to explore the potential role of exosomes, small extracellular vesicles, in the pathogenesis of OLP and their utility as diagnostic biomarkers. Exosomes facilitate the exchange of information between cells and modulate immune responses by carrying various bioactive molecules such as proteins, lipids, and nucleic acids. In the context of OLP, exosomes derived from affected tissues or immune cells are thought to contribute to disease progression by mediating the transfer of pro-inflammatory molecules, including cytokines like interleukin-6 and tumour necrosis factor-alpha and chemokines such as CCL2, CCL5 and microRNAs such as miR-155, miR-146a, miR-21, and miR-34a, etc. Additionally, the distinct molecular contents of exosomes derived from OLP lesions may accurately represent the pathological changes occurring in these tissues. This suggests the potential of exosomes to be used as non-invasive biomarkers for diagnosing and tracking the progression of the disease. Understanding the immune microenvironment of OLP and the role of exosomes within this context is critical for advancing our knowledge of OLP pathogenesis and identifying new diagnostic and therapeutic strategies. However, challenges remain in identifying and characterising exosomes and their clinical translation. Further research is warranted to address these challenges and fully exploit exosomes' diagnostic and therapeutic potential in OLP and other inflammatory oral diseases.

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Breast cancer (BC) is the most prevalent malignancy affecting women worldwide. Although conventional treatments such as chemotherapy, surgery, hormone therapy, radiation therapy, and biological therapy are commonly used, they often entail significant side effects. Therefore, there is a critical need to investigate more cost-effective and efficient treatment modalities in BC. Extracellular vesicles (EVs), including exosomes, microvesicles, and apoptotic bodies, play a crucial role in modulating recipient cell behaviour and driving cancer progression. Among the EVs, exosomes provide valuable insights into cellular dynamics under both healthy and diseased conditions. In cancer, exosomes play a critical role in driving tumor progression and facilitating the development of drug resistance. BC-derived exosomes (BCex) dynamically influence BC progression by regulating cell proliferation, immunosuppression, angiogenesis, metastasis, and the development of treatment resistance. Additionally, BCex serve as promising diagnostic markers in BC which are detectable in bodily fluids such as urine and saliva. Targeted manipulation of BCex holds significant therapeutic potential. This review explores the therapeutic and diagnostic implications of exosomes in BC, underscoring their relevance to the disease. Furthermore, it discusses future directions for exosome-based research in BC, emphasizing the necessity for further exploration in this area.

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BRCA1 mutation carriers have a greater risk of developing cancers in hormone-responsive tissues like breasts and ovaries. However, this tissue-specific incidence of BRCA1 related cancers remains elusive. The majority of the BRCA1 mutated breast cancers exhibit typical histopathological features of high-grade tumors, with basal epithelial phenotype, classified as triple-negative molecular subtype and have a higher percentage of DNA damage and chromosomal abnormality. Though there are many studies relating BRCA1 with ER-α (Estrogen receptor-α), it has not been reported whether E2 (Estrogen) -ER-α signaling can modulate the DNA repair activities of BRCA1. The present study analyzes whether deregulation of ER-α signaling, arising as a result of E2/ER-α deficiency, could impact the BRCA1 dependent DDR (DNA Damage Response) pathways, predominantly those of DNA-DSB (Double Strand break) repair and oxidative damage response. We demonstrate that E2/E2-stimulated ER-α can augment BRCA1 mediated high fidelity repairs like HRR (Homologous Recombination Repair) and BER (Base Excision Repair) in breast cancer cells. Conversely, a condition of ER-α deficiency itself or any interruption in ligand-dependent ER-α transactivation resulted in delayed DNA damage repair, leading to persistent activation of γH2AX and retention of unrepaired DNA lesions, thereby triggering tumor progression. ER-α deficiency not only limited the HRR in cells but also facilitated the DSB repair through error prone pathways like NHEJ (Non Homologous End Joining). ER-α deficiency associated persistence of DNA lesions and reduced expression of DDR proteins were validated in human mammary tumors.

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The lack of traditional cancer treatments has resulted in an increased need for new clinical techniques. Standard two-dimensional (2D) models used to validate drug efficacy and screening have a low in vitro-in vivo translation potential. Recreating the in vivo tumor microenvironment at the three-dimensional (3D) level is essential to resolve these limitations in the 2D culture and improve therapy results. The physical and mechanical environments of 3D culture allow cancer cells to expand in a heterogeneous manner, adopt different phenotypes, gene and protein profiles, and develop metastatic potential and drug resistance similar to human tumors. The current application of 3D scaffold culture systems based on synthetic polymers or selected extracellular matrix components promotes signalling, survival, and cancer cell proliferation. This review will focus on the recent advancement of numerous 3D-based scaffold models for cancer tissue engineering, which will increase the predictive ability of preclinical studies and significantly improve clinical translation.

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Neuroblastoma (NB), a developmental cancer, is often fatal, emphasizing the need to understand its pathogenesis and identify new therapeutic targets. The heterogeneous pathological and clinical phenotype of NB underscores the cryptic biological and genetic features of this tumor that result in outcomes ranging from rapid progression to spontaneous regression. Despite recent genome-wide mutation analyses, most primary NBs do not harbor driver mutations, implicating epigenetically-mediated gene regulatory mechanisms in the initiation and maintenance of NB. Aberrant epigenomic mechanisms, as demonstrated by global changes in DNA methylation signatures, acetylation, re-distribution of histone marks, and change in the chromatin architecture, are hypothesized to play a role in NB oncogenesis. This paper reviews the evidence for, putative mechanisms underlying, and prospects for therapeutic targeting of NB oncogenesis related to DNA methylation.

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Osteosarcoma (OS) is the most common primary bone cancer in children and adolescents, but its pathogenesis has been difficult to establish because of its well-known heterogeneous nature. OS has been associated with genetic and cytogenetic abnormalities, which include function-impairing mutations in tumor suppressors and the activation of oncogenes. OS tumorigenesis has been linked to alterations of several genes characterized by a high level of genetic instability and recurrent DNA amplifications and deletions. MicroRNAs (miRNAs), 18-25-nucleotide noncoding RNAs, are critical for various biological processes like differentiation, cell growth and cell death. Dysregulation of miRNA expression leads to phenotypic and genotypic changes in cells, which leads to cancer. Studies on miRNAs have initiated a significant effect in both diagnosis and treatment of cancer. This review focuses on the current knowledge of clinical applications of miRNAs for the better diagnosis and management of OS.

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BACKGROUND: Osteosarcoma is a rare but highly malignant cancer of the bone. As a consequence, the number of established cell lines used for experimental in vitro and in vivo osteosarcoma research is limited and the value of these cell lines relies on their stability during culture. Here we investigated the stability in gene expression by microarray analysis and array genomic hybridization of three low metastatic cell lines and derivatives thereof with increased metastatic potential using cells of different passages. PRINCIPAL FINDINGS: The osteosarcoma cell lines showed altered gene expression during in vitro culture, and it was more pronounced in two metastatic cell lines compared to the respective parental cells. Chromosomal instability contributed in part to the altered gene expression in SAOS and LM5 cells with low and high metastatic potential. To identify metastasis-relevant genes in a background of passage-dependent altered gene expression, genes involved in "Pathways in cancer" that were consistently regulated under all passage comparisons were evaluated. Genes belonging to "Hedgehog signaling pathway" and "Wnt signaling pathway" were significantly up-regulated, and IHH, WNT10B and TCF7 were found up-regulated in all three metastatic compared to the parental cell lines. CONCLUSIONS: Considerable instability during culture in terms of gene expression and chromosomal aberrations was observed in osteosarcoma cell lines. The use of cells from different passages and a search for genes consistently regulated in early and late passages allows the analysis of metastasis-relevant genes despite the observed instability in gene expression in osteosarcoma cell lines during culture.

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BACKGROUND: ΔNp63, a splice variant of p63, is overexpressed and exhibits oncogenic activity in many cancers including pancreatic and breast cancer and promotes cell survival by inhibiting apoptosis. Despite its role in tumorigenesis, mechanistic activity of ΔNp63 mediated oncogenic function in osteosarcoma is poorly understood. METHODS: The expression levels of p63 isoforms in osteosarcoma cell lines were identified using quantitative techniques. Expression profiling using microarray, siRNA mediated loss-of-function, and chromatin immunoprecipitation assays were employed to identify novel ΔNp63α targets in p63-null osteosarcoma SaOS-2 cells that were engineered to express ΔNp63α. The phenotype of SaOS-2-ΔNp63α cells was assessed using wound-healing, colony formation, and proliferation assays. RESULTS: The comparative expression analyses identified ΔNp63α as the predominant p63 isoform expressed by invasive OS cell lines. Phenotypic analyses of SaOS-2-ΔNp63α cells in vitro indicate that ΔNp63α imparted tumorigenic attributes upon tumor cells. Further, we show that in osteosarcoma cells ΔNp63α directly regulated the transcription factor GLI2, which is a component of the hedgehog signaling pathway, and that functional interactions between ΔNp63α and GLI2 confer oncogenic properties upon OS cells. CONCLUSIONS: Here, we report that GLI2 is the novel target gene of ΔNp63α and that ΔNp63α-GLI2 crosstalk in osteosarcoma cells is a necessary event in osteosarcoma progression. Defining the exact mechanisms involved in this interaction that mediate the pathogenesis of osteosarcoma promises to identify targets for drug therapy.

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Metastasis is the major cause of death of osteosarcoma patients and its diagnosis remains difficult. In preclinical studies, however, forced expression of reporter genes in osteosarcoma cells has remarkably improved the detection of micrometastases and, consequently, the quality of the studies. We recently showed that Dunn cells equipped with a lacZ reporter gene disseminated from subcutaneous primary tumors as frequently as their highly metastatic subline LM8, but only LM8 cells grew to macrometastases. In the present time-course study, tail-vein-injected Dunn and LM8 cells settled within 24 h at the same frequency in the lung, liver, and kidney of mice. Furthermore, Dunn cells also grew to macrometastases, but, compared to LM8, with a delay of two weeks in lung and one week in liver and kidney tissue, consistent with prolonged survival of the mice. Dunn- and LM8-cell-derived ovary and spine metastases occurred less frequently. In vitro, Dunn cells showed less invasiveness and stronger contact inhibition and intercellular adhesion than LM8 cells and several cancer- and dormancy-related genes were differentially expressed. In conclusion, Dunn cells, compared to LM8, have a similar capability but a longer latency to form macrometastases and provide an interesting new experimental system to study tumor cell dormancy.

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Osteosarcoma (OS) is a rare bone neoplasm that affects mainly adolescents. It is associated with poor prognosis in case of metastases formation. The search for metastasis predicting markers is therefore imperative to optimize treatment strategies for patients at risk and important for the search of new drugs for the treatment of this devastating disease. Here, we have analyzed by microarray the differential gene expression in four human and two mouse OS cell line systems consisting of parental cell lines with low metastatic potential and derivatives thereof with increased metastatic potential. Using two osteoblastic cell line systems, the most common OS phenotype, we have identified forty-eight common genes that are differentially expressed in metastatic cell lines compared to parental cells. The identified subset of metastasis relevant genes in osteoblastic OS overlapped only minimally with differentially expressed genes in the other four preosteoblast or nonosteoblastic cell line systems. The results imply an OS phenotype specific expression pattern of metastasis regulating proteins and form a basis for further investigation of gene expression profiles in patients' samples combined with survival analysis with the aim to optimize treatment strategies to develop new drugs and to consequently improve the survival of patients with the most common form of osteoblastic OS.

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OBJECTIVE: Tropical chronic pancreatitis (TCP) is a form of chronic pancreatitis seen in many tropical countries in young non-alcoholic subjects who are often malnourished. Nutritional deficiencies, either at the macro or micro level, and food toxins have been implicated in its causation, although there is no final proof to confirm this suggestion. Mutations of SPINK1 and CFTR genes have been proposed as disease modifiers, or as determinants of phenotypes. Mutations involving the calcium sensing receptor (CASR) have been suggested to increase the risk of chronic pancreatitis (CP), since high intracellular levels of calcium activate trypsinogen within the acinar cells. A combination of CASR and SPINK1 gene mutations has been proposed to predispose to idiopathic CP. The purpose of this study was to report on novel mutations in CASR, identified in TCP patients. MATERIAL AND METHODS: We screened our TCP patients for mutations in CASR and SPINK1 genes. In a cohort of 35 patients and an equivalent number of controls, genomic DNA was screened for mutations in CASR and SPINK1 by direct DNA sequencing. RESULTS: Four new mutations were found in the CASR gene. A combination of both SPINK1 (N34S) and CASR mutations was seen in 6% of the patients, while 22% harbored a single mutation. CONCLUSIONS: Our study suggests, for the first time, that CASR mutation may be a risk for TCP, and that this risk may be further increased if there is an associated SPINK1 mutation.

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