Different Types Of Cancer Research Articles

A computational workflow for analysis of missense mutations in precision oncology

Every year, more than 19 million cancer cases are diagnosed, and this number continues to increase annually. Since standard treatment options have varying success rates for different types of cancer, understanding the biology of an individual's tumour becomes crucial, especially for cases that are difficult to treat. Personalised high-throughput profiling, using next-generation sequencing, allows for a comprehensive examination of biopsy specimens. Furthermore, the widespread use of this technology has generated a wealth of information on cancer-specific gene alterations. However, there exists a significant gap between identified alterations and their proven impact on protein function. Here, we present a bioinformatics pipeline that enables fast analysis of a missense mutation’s effect on stability and function in known oncogenic proteins. This pipeline is coupled with a predictor that summarises the outputs of different tools used throughout the pipeline, providing a single probability score, achieving a balanced accuracy above 86%. The pipeline incorporates a virtual screening method to suggest potential FDA/EMA-approved drugs to be considered for treatment. We showcase three case studies to demonstrate the timely utility of this pipeline. To facilitate access and analysis of cancer-related mutations, we have packaged the pipeline as a web server, which is freely available at https://loschmidt.chemi.muni.cz/predictonco/.Scientific contributionThis work presents a novel bioinformatics pipeline that integrates multiple computational tools to predict the effects of missense mutations on proteins of oncological interest. The pipeline uniquely combines fast protein modelling, stability prediction, and evolutionary analysis with virtual drug screening, while offering actionable insights for precision oncology. This comprehensive approach surpasses existing tools by automating the interpretation of mutations and suggesting potential treatments, thereby striving to bridge the gap between sequencing data and clinical application.

Comparing the photodynamic treatment of OSCC between natural and artificial photosensitizers

Purpose: Since Verteporfin is the generally accepted photosensitizer for OSCC and other forms of skin cancer. Its synthetic structure and broad range in absorption has made it harmful to both tumor and healthy cells and tissues. The study aims to see whether a natural and herbal extract like Chlorophyllin, used in primarily bladder cancer, can become an alternative to Verteporfin. Methods: This study uses HSC-2 cell lines and mice models. The cancer cells in vitro and in vivo will be treated with increasing amounts and various durations of Chlorophyllin and Verteporfin. Killing in vitro is measured by MTT assay and in vivo is measured by xenograft tumor size. Positive control is Verteporfin, and negative control is DMSO in vitro or saline solution for the xenograft experiment. Possible results: The three main possible results: (1) Chlorophyllin kills more cancer cells in vitro and in vivo and it has less killed normal tissue. (5) Verteporfin kills more cancer cells but also has more damage to normal tissues when compared to Chlorophyllin. (8) Verteporfin kills more cancer cells in vitro and in vivo and it has less killed normal tissue. Conclusion: The results of the study will determine if natural alternatives are worth investing research into as they can be low-cost extraction, low toxicity, and high selectivity of cells to kill. Chlorophyllin can pave the way to more intensive research of natural photosensitizers in different types of cancers.

In Silico Analysis of the Missense Variants of Uncertain Significance of CTNNB1 Gene Reported in GnomAD Database.

CTNNB1 pathogenic variants are related to the improper functioning of the WNT/β-catenin pathway, promoting the development of different types of cancer of somatic origin. Bioinformatics analyses of genetic variation are a great tool to understand the possible consequences of these variants on protein structure and function and their probable implication in pathologies. The objective of this study is to describe the impact of the missense variants of uncertain significance (VUS) of the CTNNB1 gene on structure and function of the β-catenin protein. The CTNNB1 variants were obtained from the GnomAD v2.1.1 database; subsequently, a bioinformatic analysis was performed using the VarSome, UCSC Genome Browser, UniProt, the Kinase Library database, and DynaMut2 platforms to evaluate clinical significance, gene conservation, consensus sites for post-translational modifications, and the dynamics and stability of proteins. The GnomAD v2.1.1 database included 826 variants of the CTNNB1 gene, of which 385 were in exons and exon/intron boundaries. Among these variants, 214 were identified as missense, of which 146 were classified as VUS. Notably, 12 variants were in proximity to consensus sites for post-translational modifications (PTMs). The in silico analysis showed a slight tendency towards probably pathogenic for c.59C>T (p.Ala20Val) and c.983T>C (p.Met328Thr) missense VUS. These findings provide possible functional implications of these variants in some types of cancer.

Prevalence of KRAS amplification in patients with metastatic cancer: Real-world next-generation sequencing analysis

BackgroundThe Kirsten rat sarcoma virus (KRAS) is a prominent proto-oncogene. Several treatments for KRAS mutations have been developed. However, KRAS amplification, a KRAS alteration, is poorly understood, and there is currently no appropriate treatment other than conventional chemotherapy. This study aimed to elucidate the role of KRAS amplification in different types of cancers. MethodsFrom October 2019 to June 2023, we performed next-generation sequencing using Trusight Oncology 500 on 3895 patients with 37 different cancer types at the Samsung Medical Center. We analyzed the distribution of KRAS amplification according to cancer type and its correlation with tumor mutation burden (TMB). Concomitant KRAS mutations were also identified. ResultsOf the total 3895 patients, 99 (2.5 %) had KRAS amplification. The highest frequency of KRAS amplification was detected in 2 % (27/1350) of patients with colorectal cancer, followed by 3.48 % (32/920) of patients with gastric cancer and 3.88 % (9/232) patients with of pancreatic cancer. MSI-High was not detected in patients with KRAS amplification. There was no correlation between KRAS copy number variation and TMB status. Among patients with KRAS amplification, 27.3 % (27/99) had a concomitant KRAS mutation. More than 50 % of patients had G12D or G12V mutations. In gastric cancer, patients with both KRAS amplification and mutation were extremely rare at 3.1 % (1/32); however, in colorectal cancer, more than half of the patients had KRAS amplification and mutation (51.9 %, 14/27). KRAS amplification and mutations are associated with mutations in tumor suppressor genes TP53, BRCA2, ARID1B, and PTCH1. ConclusionsOf the 3895 patients with metastatic solid tumors, 99 (2.5 %) had KRAS amplification, and next-generation sequencing analysis provided a deeper understanding of KRAS amplification.

Construction of pan-cancer regulatory networks based on causal inference

The pan-cancer initiative aims to study the origin patterns of cancer cell, the processes of carcinogenesis, and the signaling pathways from a perspective that spans across different types of cancer. The construction of the pan-cancer related gene regulatory network is helpful to excavate the commonalities in regulatory relationships among different types of cancers. It also aids in understanding the mechanisms behind cancer occurrence and development, which is of great scientific significance for cancer prevention and treatment. In light of the high dimension and large sample size of pan-cancer omics data, a causal pan-cancer gene regulation network inference algorithm based on stochastic complexity is proposed. With the network construction strategy of local first and then global, the stochastic complexity is used in the conditional independence test and causal direction inference for the candidate adjacent node set of the target nodes. This approach aims to decrease the time complexity and error rate of causal network learning. By applying this algorithm to the sample data of seven types of cancers in the TCGA database, including breast cancer, lung adenocarcinoma, and so on, the pan-cancer related causal regulatory networks are constructed, and their biological significance is verified. The experimental results show that this algorithm can eliminate the redundant regulatory relationships effectively and infer the pan-cancer regulatory network more accurately (https://github.com/LindeEugen/CNI-SC).

Extracellular vesicles in tumor-adipose tissue crosstalk: key drivers and therapeutic targets in cancer cachexia

Cancer cachexia is a complex metabolic syndrome characterized by unintentional loss of skeletal muscle and body fat. This syndrome is frequently associated with different types of cancer and negatively affects the prognosis and outcome of these patients. It involves a dynamic interplay between tumor cells and adipose tissue, where tumor-derived extracellular vesicles (EVs) play a crucial role in mediating intercellular communication. Tumor cells release EVs containing bioactive molecules such as hormones (adrenomedullin, PTHrP), pro-inflammatory cytokines (IL-6), and miRNAs (miR-1304-3p, miR-204-5p, miR-155, miR-425-3p, miR-146b-5p, miR-92a-3p), which can trigger lipolysis and induce the browning of white adipocytes contributing to a cancer cachexia phenotype. On the other hand, adipocyte-derived EVs can reprogram the metabolism of tumor cells by transporting fatty acids and enzymes involved in fatty acid oxidation, resulting in tumor growth and progression. These vesicles also carry leptin and key miRNAs (miR-155-5p, miR-10a-3p, miR-30a-3p, miR-32a/b, miR-21), thereby supporting tumor cell proliferation, metastasis formation, and therapy resistance. Understanding the intricate network underlying EV-mediated communication between tumor cells and adipocytes can provide critical insights into the mechanisms driving cancer cachexia. This review consolidates current knowledge on the crosstalk between tumor cells and adipose tissue mediated by EVs and offers valuable insights for future research. It also addresses controversial topics in the field and possible therapeutic approaches to manage cancer cachexia and ultimately improve patient outcomes and quality of life.

Categorizing Dermatological Malignancies Via Computational Methods

In this study, a machine learning model is developed to classify different types of cancer using convolutional neural networks (CNNs) for image processing. The core objective is to achieve a performance level comparable to that of dermatologists. The model is trained on a substantial dataset of medical images, enabling it to learn and recognize various characteristics indicative of different cancer types. By leveraging the power of CNNs, the model can process these images effectively, identifying subtle patterns and features that are often challenging to detect with the naked eye. The training process involves feeding the CNN with labelled images, enabling it to differentiate between benign and malignant cases with high accuracy. Through rigorous testing, the model demonstrates competence on par with experienced dermatologists, both in terms of sensitivity and specificity. This equivalence in performance is particularly significant as it underscores the model's potential to aid in clinical settings, providing reliable second opinions and enhancing diagnostic workflows. A user interface is also developed to allow input images to be analysed by the trained CNN model. This interface not only displays the model’s predictions but also provides essential metrics such as confidence scores and probability distributions. These metrics offer valuable insights into the model's decision-making process, aiding clinicians in understanding and trusting the AI's assessments. Overall, the findings suggest that convolutional neural networks hold substantial promise for improving cancer diagnosis. The model's high performance in classification tasks demonstrates its viability as a tool for supporting dermatologists in clinical practice. By reducing diagnostic errors and accelerating the identification process, this technology has the potential to significantly impact patient outcomes and advance the field of medical imaging and diagnostics. Keywords: Convolutional Neural Networks (CNNs); Cancer Classification; Medical Image Processing; Dermatology AI; Diagnostic Accuracy

Interference with PLA2G16 promotes cell cycle arrest and apoptosis and inhibits the reprogramming of glucose metabolism in multiple myeloma cells by modulating the Hippo/YAP signaling pathway.

Multiple myeloma, which is a clonal plasma cell tumor, derives from a postmitotic lymphoid B-cell lineage and remains untreatable. Group XVI phospholipase A2 (PLA2G16) can either be a tumor suppressor or an oncogene in different types of cancer. This study was intended to explore the role of PLA2G16 in multiple myeloma and to reveal the reaction mechanism. The mRNA and protein expressions of PLA2G16 in human bone marrow stromal cell line HS-5 and multiple myeloma cells were assessed using reverse transcription-quantitative PCR and western blot. The transfection efficacy of sh-PLA2G16 and oe-YAP was examined using reverse transcription-quantitative PCR and western blot. Through cell counting kit-8 assay and 5-ethynyl-2'- deoxyuridine staining, multiple myeloma cell viability and proliferation were detected. Flow cytometry was used to measure cell apoptosis and cell cycle distribution. Oxygen consumption rate, the activities of mitochondrial respiratory chain complexes I-V, and the activity of caspase-3 were estimated with Seahorse XF24 analyzer, oxidative phosphorylation activity assay kit, and caspase-3 assay kit, respectively. Lactate production and glucose consumption were evaluated usingcorresponding assay kits. Western blot was employed to meaure proteins associated with cell cycle, glycolysis, pentose phosphate pathway as well as Hippo/YAP signaling pathway. In this study, PLA2G16 expression was greatly increased in multiple myeloma cells and PLA2G16 silence inhibited cell proliferation, promoted cell apoptosis, facilitated cell cycle arrest, and suppressed the reprogramming of glucose metabolism in multiple myeloma. It was also identified that PLA2G16 depletion inhibited the Hippo/YAP signaling pathway. Further experiments revealed that the overexpression of YAP partially reversed the inhibitory effects of PLA2G16 silence on multiple myeloma cell malignant development and the reprogramming of glucose metabolism. Collectively, PLA2G16 silence impeded multiple myeloma progression and inhibited glucose metabolism reprogramming by blocking the Hippo/YAP signaling pathway.

Socioeconomic Disparities in Six Common Cancer Survival Rates in South Korea: Population-Wide Retrospective Cohort Study.

In South Korea, the cancer incidence rate has increased by 56.5% from 2001 to 2021. Nevertheless, the 5-year cancer survival rate from 2017 to 2021 increased by 17.9% compared with that from 2001 to 2005. Cancer survival rates tend to decline with lower socioeconomic status, and variations exist in the survival rates among different cancer types. Analyzing socioeconomic patterns in the survival of patients with cancer can help identify high-risk groups and ensure that they benefit from interventions. The aim of this study was to analyze differences in survival rates among patients diagnosed with six types of cancer-stomach, colorectal, liver, breast, cervical, and lung cancers-based on socioeconomic status using Korean nationwide data. This study used the Korea Central Cancer Registry database linked to the National Health Information Database to follow up with patients diagnosed with cancer between 2014 and 2018 until December 31, 2021. Kaplan-Meier curves stratified by income status were generated, and log-rank tests were conducted for each cancer type to assess statistical significance. Hazard ratios with 95% CIs for any cause of overall survival were calculated using Cox proportional hazards regression models with the time since diagnosis. The survival rates for the six different types of cancer were as follows: stomach cancer, 69.6% (96,404/138,462); colorectal cancer, 66.6% (83,406/125,156); liver cancer, 33.7% (23,860/70,712); lung cancer, 30.4% (33,203/109,116); breast cancer, 91.5% (90,730/99,159); and cervical cancer, 78% (12,930/16,580). When comparing the medical aid group to the highest income group, the hazard ratios were 1.72 (95% CI 1.66-1.79) for stomach cancer, 1.60 (95% CI 1.54-1.56) for colorectal cancer, 1.51 (95% CI 1.45-1.56) for liver cancer, 1.56 (95% CI 1.51-1.59) for lung cancer, 2.19 (95% CI 2.01-2.38) for breast cancer, and 1.65 (95% CI 1.46-1.87) for cervical cancer. A higher deprivation index and advanced diagnostic stage were associated with an increased risk of mortality. Socioeconomic status significantly mediates disparities in cancer survival in several cancer types. This effect is particularly pronounced in less fatal cancers such as breast cancer. Therefore, considering the type of cancer and socioeconomic factors, social and medical interventions such as early cancer detection and appropriate treatment are necessary for vulnerable populations.

"That Was an Eye Opener for Me": Mixed-Methods Outcomes Educating Texas Community Health Workers on HPV Vaccination Using Project ECHO®.

Human papillomavirus (HPV) is known to cause six different types of cancer. HPV vaccination can prevent over 90% of these cancers. Community health workers (CHWs) have the potential to drive HPV vaccination demand through education and navigation by addressing vaccine hesitancy and dis/misinformation and by reaching non-English speaking, vulnerable, or rural populations. Despite their possible reach, there is limited research on HPV vaccination education programs for CHWs. In 2020-2021, the American Cancer Society (ACS) HPV Cancer Free Texas (HPVCFT) Project implemented the eight-session Mission: HPVCFT Vaccination ECHO-CHW Program ten times. This manuscript details the program's implementation processes and outcomes. The program used the Project ECHO model and was offered in both English and Spanish. One hundred and forty-six Texan CHWs completed pre- and post-training surveys. The participants demonstrated significant HPV vaccination knowledge increases and desirable shifts in their foundational HPV vaccination beliefs, including the belief that the HPV vaccine is for cancer prevention. The participants also reported increased confidence in communicating about the HPV vaccine in the community. Improving knowledge, beliefs, and confidence in HPV vaccination is the first step in addressing concerns and increasing uptake. Future research and interventions are needed to better understand how CHWs can be more systematically linked to vaccination opportunities or provided with clearer paths for directing patients to providers that vaccinate.

A Multi-Omics Analysis of an Exhausted T Cells' Molecular Signature in Pan-Cancer.

T cells are essential tumor suppressors in cancer immunology, but their dysfunction induced by cancer cells can result in T cell exhaustion. Exhausted T cells (Tex) significantly influence the tumor immune environment, and thus, there is a need for their thorough investigation across different types of cancer. Here, we address the role of Tex cells in pan-cancer, focusing on the expression, mutations, methylation, immune infiltration, and drug sensitivity of a molecular signature comprising of the genes HAVCR2, CXCL13, LAG3, LAYN, TIGIT, and PDCD1across multiple cancer types, using bioinformatics analysis of TCGA data. Our analysis revealed that the Tex signature genes are differentially expressed across 14 cancer types, being correlated with patient survival outcomes, with distinct survival trends. Pathway analysis indicated that the Tex genes influence key cancer-related pathways, such as apoptosis, EMT, and DNA damage pathways. Immune infiltration analysis highlighted a positive correlation between Tex gene expression and immune cell infiltration in bladder cancer, while mutations in these genes were associated with specific immune cell enrichments in UCEC and SKCM. CNVs in Tex genes were widespread across cancers. We also highlight high LAYN methylation in most tumors and a negative correlation between methylation levels and immune cell infiltration in various cancers. Drug sensitivity analysis identified numerous correlations, with CXCL13 and HAVCR2 expressions influencing sensitivity to several drugs, including Apitolisib, Belinostat, and Docetaxel. Overall, these findings highlight the importance of reviving exhausted T cells to enhance the treatment efficacy to significantly boost anti-tumor immunity and achieve better clinical outcomes.

Delineation of gastrointestinal tumors biopsies using a fluorescence lifetime imaging optical fiber probe.

Autofluorescence spectroscopy has emerged in recent years as a powerful tool to report label-free contrast between normal and diseased tissues, both in vivo and ex-vivo. We report the application of an instrument employing an optical fiber probe and capable of performing real-time autofluorescence lifetime imaging at a macroscopic scale, under bright background conditions. We validate and demonstrate the practicality of this technology to discriminate healthy against neoplastic tissue in freshly excised tumor biopsies. The capability of delineating tumor margins through processing the fluorescence decays in the phasors domain was demonstrated on four different types of cancer, highlighting the broad range of potential clinical applications for the proposed approach. The presented results suggest that our autofluorescence lifetime imaging probe, together with phasor analysis, can offer a real-time tool to observe lifetime contrast on tissues and, thus, is a suitable candidate for improving in situ tissue diagnostics during surgery.

A review on macrocyclic kinase inhibitors in clinical trials

Macrocyclic kinase inhibitors have high binding affinity and selectivity towards a variety of kinases including mammalian target of rapamycin complex 1/2, janus kinases/ Fms like tyrosine kinase, cyclin-dependent kinases and anaplastic lymphoma kinase1. Recently, few macrocyclic kinase inhibitors have entered clinical trial for treatment different types of cancers including leukemia, non-small cell lung cancer, myelofibrosis, breast cancer, glioblastoma and lymphoma. Of them, ridaforomilus has completed Phase III clinical trial and is waiting to be approved for treatment of breast cancer and advanced leukemia. Pacritinib is also currently being tested in phase III clinical trial for treatment of myelofibrosis and, loratinib is being evaluated for advanced ALK gene positive nonsmall cell lung carcinoma. The broad-spectrum cyclin-dependent kinases inhibitor, TGO2, has also entered phase II clinical trial for treatment of glioblastoma and advanced leukemia.

Extended Synaptotagmins 1 and 2 Are Required for Store-Operated Calcium Entry, Cell Migration and Viability in Breast Cancer Cells.

Extended synaptotagmins (E-Syts) are endoplasmic reticulum (ER)-associated proteins that facilitate the tethering of the ER to the plasma membrane (PM), participating in lipid transfer between the membranes and supporting the Orai1-STIM1 interaction at ER-PM junctions. Orai1 and STIM1 are the core proteins of store-operated Ca2+ entry (SOCE), a major mechanism for Ca2+ influx that regulates a variety of cellular functions. Aberrant modulation of SOCE in cells from different types of cancer has been reported to underlie the development of several tumoral features. Here we show that estrogen receptor-positive (ER+) breast cancer MCF7 and T47D cells and triple-negative breast cancer (TNBC) MDA-MB-231 cells overexpress E-Syt1 and E-Syt2 at the protein level; the latter is also overexpressed in the TNBC BT20 cell line. E-Syt1 and E-Syt2 knockdown was without effect on SOCE in non-tumoral MCF10A breast epithelial cells and ER+ T47D breast cancer cells; however, SOCE was significantly attenuated in ER+ MCF7 cells and TNBC MDA-MB-231 and BT20 cells upon transfection with siRNA E-Syt1 or E-Syt2. Consistent with this, E-Syt1 and E-Syt2 knockdown significantly reduced cell migration and viability in ER+ MCF7 cells and the TNBC cells investigated. To summarize, E-Syt1 and E-Syt2 play a relevant functional role in breast cancer cells.

MiR-584-5p is a New Potential Prognostic Biomarker in Head and Neck Squamous Cell Carcinoma.

MicroRNA-584-5p (miR-584-5p) plays an important role in certain types of cancer. However, its precise role in head and neck squamous cell carcinoma (HNSC) remains unknown. Our aim was to investigate how miR-584-5p influences HNSC. The Cancer Genome Atlas (TCGA) provided samples for the study. We use statistical methods to evaluate the diagnostic value, the prognostic value, and the correlation with the clinical features of miR-584-5p. We analyze the target genes and the regulatory network of miR- 584-5p. Quantitative reverse transcriptase PCR (qRT-PCR) confirmed the expression of miR- 584-5p in HNSC cell lines. MiR-584-5p expression of miR-584-5p varied significantly among different types of cancer. A notable correlation was observed between elevated miR-584-5p expression and gender (p < 0.001) and histological grade (p < 0.001). Furthermore, high levels of miR-584-5p were found to be associated with a decrease in overall survival (HR: 1.44; 95% CI: 1.10-1.88; p = 0.007), progression-free survival (HR: 1.35; 95% CI: 1.02-1.79; p = 0.035) and disease-specific survival (HR: 1.54; 95% CI: 1.09-2.18; p = 0.016) in the context of HNSC. miR-584-5p demonstrated independent prognostic significance in HNSC and potentially contributes to disease progression through multiple pathways, such as dilated cardiomyopathy and hypertrophic cardiomyopathy. In particular, HNSC cell lines exhibited a substantial upregulation of miR-584-5p compared to normal epithelial cells. It is possible that miR-584-5p could serve as a promising patent for a therapeutic target and prognostic biomarker for people with HNSC.

Canonical WNT/β-catenin signaling upregulates aerobic glycolysis in diverse cancer types.

Despite many efforts, a comprehensive understanding and clarification of the intricate connections within cancer cell metabolism remain elusive. This might pertain to intracellular dynamics and the complex interplay between cancer cells, and cells with the tumor stroma. Almost a century ago, Otto Warburg found that cancer cells exhibit a glycolytic phenotype, which continues to be a subject of thorough investigation. Past and ongoing investigations have demonstrated intricate mechanisms by which tumors modulate their functionality by utilizing extracellular glucose as a substrate, thereby sustaining the essential proliferation of cancer cells. This concept of "aerobic glycolysis," where cancer cells (even in the presence of enough oxygen) metabolize glucose to produce lactate plays a critical role in cancer progression and is regulated by various signaling pathways. Recent research has revealed that the canonical wingless-related integrated site (WNT) pathway promotes aerobic glycolysis, directly and indirectly, thereby influencing cancer development and progression. The present review seeks to gather knowledge about how the WNT/β-catenin pathway influences aerobic glycolysis, referring to relevant studies in different types of cancer. Furthermore, we propose the concept of impeding the glycolytic phenotype of tumors by employing specific inhibitors that target WNT/β-catenin signaling.

New insights into the role of tetraspanin 6, 7, and 8 in physiology and pathology.

The tetraspanin (TSPAN) family comprises 33 membrane receptors involved in various physiological processes in humans. Tetrasapanins are surface proteins expressed in cells of various organisms. They are localised to the cell membrane by four transmembrane domains (TM4SF). These domains bind several cell surface receptors and signalling proteins to tetraspanin-enriched lipid microdomains (TERM or TEM). Tetraspanins play a critical role in anchoring many proteins. They also act as a scaffold for cell signalling proteins. To summarise how tetraspanins 6, 7 and 8 contribute to the carcinogenesis process in different types of cancer. To provide a comprehensive review of the role of tetraspanins 6, 7 and 8 in cancer biology, we conducted a thorough search in PubMed, Embase and performed manual search of reference list to collect and extract data. The assembly of tetraspanins covers an area of approximately 100-400 nm. Tetraspanins are involved in various biological processes such as membrane fusion, aggregation, proliferation, adhesion, cell migration and differentiation. They can also regulate integrins, cell surface receptors and signalling molecules. Tetraspanins form direct bonds with proteins and other members of the tetraspanin family, forming a hierarchical network of interactions and are thought to be involved in cell and membrane compartmentalisation. Tetraspanins have been implicated in cancer progression and have been shown to have multiple binding partners and to promote cancer progression and metastasis. Clinical studies have documented a correlation between the level of tetraspanin expression and the prediction of cancer progression, including breast and lung cancer. Tetraspanins are understudied in almost all cell types and their functions are not clearly defined. Fortunately, it has been possible to identify the basic mechanisms underlying the biological role of these proteins. Therefore, the purpose of this review is to describe the roles of tetraspanins 6, 7 and 8.

ARID1A is involved in DNA double-strand break repair in gastric cancer.

Defects in DNA damage repair can cause genetic mutations, which in turn can cause different types of cancers. Chromatin remodeling complexes, which help repair damaged DNA, can cause the chromatin structure to change as a result of DNA damage. ARID1A may play a role in the process of DNA damage repair, and arid1a may be related to the occurrence and development of gastric cancer (GC). This study aimed to investigate the mechanism of ARID1A regulating the DNA damage repair of gastric adenocarcinoma cell lines AGS and SGC-7901 and its effect on migration, proliferation and apoptosis. The expression of ARID1A plasmid was detected by Western blot and real-time polymerase chain reaction (PCR). The effect of etoposide (ETO) on the survival rate of AGS and SGC-7901 gastric adenocarcinoma cell lines was detected by MTT assay. The DNA double-strand break model was established by ETO and then passed through the comet assay and immunofluorescence co-localization to observe DNA damage; western blot method was used to detect the effect of ARID1A on the expression of related proteins in DNA damage repair pathway in gastric adenocarcinoma cells; scratch test and colony formation experiments were used to observe ARID1A migration and proliferation of gastric adenocarcinoma cells. The flow cytometry was used to detect the effect of ARID1A on apoptosis of gastric adenocarcinoma cells. The expression of mRNA and protein was increased after transfection of ARID1A plasmid. ETO was confirmed by MTT assay to inhibit cell survival in a dose-dependent manner. After the DNA double-strand break model was established by ETO, the expression levels of phospho-ataxia telangiectasia mutated (p-ATM) protein increased in the overexpressed ARID1A group. Meanwhile, the overexpressed ARID1A group had a shortened tail moment, and γ-H2AX and ARID1A co-localized in the DNA damage site of the nucleus. The over-expressed ARID1A group had weaker wound healing ability, reduced number of clone formation, and increased apoptosis rate. ARID1A may repair DNA double-strand breaks caused by ETO by p-ATM pathway; ARID1A can inhibit the migration and proliferation of gastric adenocarcinoma cells and promote apoptosis. Our findings indicate that ARID1A could serve as a therapeutic target and biomarker for GC patients.

PiRNAs and PIWI-like proteins in cancer and their future as biomarkers and therapy targets in breast cancer

Globally, breast cancer (BC) is the most common type of cancer, with 2.296.840 new cases in 2020 with almost 700.000 related deaths. Due to the high burden this represents, it is imperative to expand horizons to be able to find novel biomarkers and therapeutic targets that can be used to improve prognosis, treatment, and survival of breast cancer patients. In recent years, numerous studies have been conducted looking for the association between piRNAs (PIWI – interacting RNAs) and the development, pathogenesis, metastasis, and progression of different types of cancer, including BC. PiRNAs are small molecules (24-31 nucleotides) that interact with the PIWI-protein complex (PIWI-like proteins - HIWI/HILI in humans) performing regulatory functions by inducing transcriptional, post-transcriptional, translational, and post-translational epigenetic changes, which has been observed to contribute to cancer development through modifications in cell proliferation, transposon silencing, genome rearrangement, epigenetic regulation, protein regulation, and stem cell maintenance. In breast cancer, a strong association has been found between the expression of some piRNAs, PIWI-like proteins and tumor development. If a specific piRNA could be associated with a distinct type of cancer, it could then be used as an early biomarker which would allow for a better prognosis. Findings surrounding these molecular mechanisms could also spark interest in studies focusing on the modification of the expression of piRNAs in cancer cells. In this article, we intend to review in a straightforward manner the current information about piRNAs/PIWI-like proteins focusing on their expression in BC.

Identification of a prognostic DNA repair gene signature in esophageal cancer.

DNA repair plays a crucial role in the development and progression of different types of cancers. Nevertheless, little is known about the role of DNA repair-related genes (DRRGs) in esophageal cancer (EC). The present study aimed to identify a novel DRRGs prognostic signature in EC. Gene set enrichment analysis (GSEA) was performed to screen 150 genes related to DNA repair, which is the most important enrichment gene set in EC. Univariate and multivariate Cox regression analyses were used to screen DRRGs closely associated with prognosis. The difference in the expression of hub DRRGs between tumor and normal tissues was analyzed. Combined with clinical indicators (including age, gender, and tumor stage), we evaluated whether the 4-DRRGs signature was an independent prognostic factor. In addition, we evaluated the prediction accuracy using a receiver operating characteristic (ROC) curve and visualized the model's performance via a nomogram. Four-DRRGs (NT5C3A, TAF9, BCAP31, and NUDT21) were selected by Cox regression analysis to establish a prognostic signature to effectively classify patients into high- and low-risk groups. The area under the curve (AUC) of the time-dependent ROC of the prognostic signature for 1- and 3-year was 0.769 and 0.720, respectively. Compared with other clinical characteristics, the risk score showed a robust ability to predict the prognosis in EC, especially in the early stage of EC. Furthermore, we constructed a nomogram to interpret the clinical application of the 4-DRRGs signature. In conclusion, we identified a prognostic signature based on the DRRGs for patients with EC, which can contribute independent value in identifying clinical outcomes that complement the TNM system in EC.