Frontiers in pancreatic cancer on biomarkers, microenvironment, and immunotherapy

Pancreatic cancer remains one of the most challenging malignancies to treat due to its late-stage diagnosis, aggressive progression, and high resistance to existing therapies. This review examines the latest advancements in early detection, and therapeutic strategies, with a focus on emerging biomarkers, tumor microenvironment (TME) modulation, and the integration of artificial intelligence (AI) in data analysis. We highlight promising biomarkers, including microRNAs (miRNAs) and circulating tumor DNA (ctDNA), that offer enhanced sensitivity and specificity for early-stage diagnosis when combined with multi-omics panels. A detailed analysis of the TME reveals how components such as cancer-associated fibroblasts (CAFs), immune cells, and the extracellular matrix (ECM) contribute to therapy resistance by creating immunosuppressive barriers. We also discuss therapeutic interventions that target these TME components, aiming to improve drug delivery and overcome immune evasion. Furthermore, AI-driven analyses are explored for their potential to interpret complex multi-omics data, enabling personalized treatment strategies and real-time monitoring of treatment response. We conclude by identifying key areas for future research, including the clinical validation of biomarkers, regulatory frameworks for AI applications, and equitable access to innovative therapies. This comprehensive approach underscores the need for integrated, personalized strategies to improve outcomes in pancreatic cancer.

Multiple primary tumors in a patient with non‑small‑cell lung cancer harboring mutations in ERCC6 and LYL1: A case report

Certain types of primary tumor, particularly triple primary tumors with germline mutations, are rare. The present study reports a novel case of the metachronous occurrence of three pathological conditions, namely, non-small-cell lung cancer (NSCLC), early T cell precursor acute lymphoblastic leukemia (ETP-ALL) and SCLC. The present study used next-generation sequencing to aid diagnosis. A 44-year-old male patient presented to The First Affiliated Hospital Zhejiang University School of Medicine (Hangzhou, China) in September 2016.) with a nodule in the right lower lung during an annual checkup. Then, the patient was diagnosed with poorly differentiated NSCLC (T1N2M0; stage IIIA) and underwent surgical resection and biopsy. In September 2018, the patient was diagnosed with ETP-ALL with superficial lymphadenopathy. Germline testing demonstrated germ cell variants of ERCC excision repair 6, chromatin remodeling factor (ERCC6; c.1322A>G) and LYL1 basic helix-loop-helix family member (LYL1; c.587T>A). In November 2020, the patient was diagnosed with SCLC by bronchoscopic biopsy following allogeneic hematopoietic stem cell transplantation. The patient was diagnosed with lung cancer in October 2016 and the treatment were: surgery, chemotherapy, radiotherapy, and targeted therapy. In October 2018, the patient was diagnosed with ETP-ALL and the treatment were: chemotherapy and allogeneic hematopoietic stem cell transplantation. In November 2020, the patient was diagnosed with small cell lung cancer and received chemotherapy and radiotherapy. The patient died at September 2022. The present case highlighted the importance of monitoring germline mutations in patients and their families to facilitate early diagnosis, appropriate treatment and prognostic evolution in the face of rapid recurrent cancer.

Recent Advances in Nanodrug Delivery Systems Production, Efficacy, Safety, and Toxicity

In the last three decades, the development of nanoparticles or nano-formulations as drug delivery systems has emerged as a promising tool to overcome the limitations of conventional delivery, potentially to improve the stability and solubility of active molecules, promote their transport across the biological membranes, and prolong circulation times to increase efficacy of a therapy. Despite several nano-formulations having applications in drug delivery, some issues concerning their safety and toxicity are still debated. This chapter describes the recent available information regarding safety, toxicity, and efficacy of nano-formulations for drug delivery. Several key factors can influence the behavior of nanoparticles in a biological environment, and their evaluation is crucial to design non-toxic and effective nano-formulations. Among them, we have focused our attention on materials and methods for their preparation (including the innovative microfluidic technique), mechanisms of interactions with biological systems, purification of nanoparticles, manufacture impurities, and nano-stability. This chapter places emphasis on the utilization of in silico, in vitro, and in vivo models for the assessment and prediction of toxicity associated with these nano-formulations. Furthermore, the chapter includes specific examples of in vitro and in vivo studies conducted on nanoparticles, illustrating their application in this field.

Mechanistic Modeling the Role of MicroRNAs and Transcription Factors in Disease Progression

In this chapter, we illustrate the utilization of network analysis and mechanistic modeling, two potent branches of systems biology, to simplify the representation of intricate biological processes such as cell signaling, gene regulation, and metabolic pathways. Specifically, we demonstrate the application of a well-established method to generate a microRNA-transcription factor-gene regulatory feed-forward loop network extracted from the GEO dataset GSE163877. Furthermore, we outline a method for constructing a deterministic model using the LSODA method based on the sub-network. This model furnishes insights into the roles of crucial differentially expressed microRNAs and transcription factors in gene expression associated with Alzheimer's disease progression. Our analysis of the model reveals elevated kinetics of synthesis for EGR1, miR-6891, miR-4786, and LTBP1. The model suggests the linear upregulation of miR-8080, miR-3921, HSPB6, and downregulation MX2 gene. The rest of the miRNA, TFs, and genes shows a momentary variation in expression and if the system is undisturbed, they attain equilibrium. Thus, we elucidate how mechanistic modeling, along with perturbation studies and network analysis of expression data, can yield diverse insights into the trajectory of disease progression.

ADAR1 is required for acute myeloid leukemia cell survival by modulating post-transcriptional Wnt signaling through impairing miRNA biogenesis

Recent extensive studies on the genomic and molecular profiles of acute myeloid leukemia (AML) have expanded the treatment options, including, a range of compounds represented by fms-like tyrosine kinase 3 and isocitrate dehydrogenase 1/2 inhibitors. However, despite this progress, further treatments for AML are still required. Adenosine deaminase acting on RNA 1 (ADAR1) has been shown to play an important oncogenic role in many cancers, but its involvement in AML progression remains underexplored. In this study, we demonstrated that ADAR1 was overexpressed in AML and served as a crucial oncogenic target. Loss of ADAR1 inhibited the Wnt signaling pathway, blocked AML cell proliferation, and induced apoptosis. Importantly, we demonstrate that ADAR1, as an RNA-binding protein, interacts with pri-miR-766 independently of its editing function, regulating the maturation of miR-766-3p and enhancing the expression of WNT5B. Genetic inhibition or use of the ADAR1 inhibitor ZYS-1 significantly suppressed AML cell growth both in vitro and in vivo. Overall, these results elucidated the tumorigenic mechanism of ADAR1 and validated it as a potential drug target in AML.

Targeting cancer stem cells by TPA leads to inhibition of refractory sarcoma and extended overall survival

Refractory cancer recurrence in patients is a serious challenge in modern medicine. Tumor regrowth in a more aggressive and invasive drug-resistant form is caused by a specific sub-population of tumor cells defined as cancer stem cells (CSCs). While the role of CSCs in cancer relapse is recognized, the signaling pathways of CSCs-driven chemoresistance are less well understood. Moreover, there are no effective therapeutic strategies that involve specific inhibition of CSCs responsible for cancer recurrence and drug resistance. There is a clinical need to develop new therapies for patients with refractory sarcomas, particularly fibrosarcoma. These aggressive tumors, with poor overall survival, do not respond to conventional therapies. Standard systemic chemotherapy for these tumors includes doxorubicin (DOX). A Tyr peptide analog (TPA), developed in our laboratory, specifically targets CSCs by drastically reducing expression of the polycomb group protein enhancer of zester (EZH2) and its downstream targets, specifically ALDH1A1 and Nanog. In vivo experiments demonstrated that TPA inhibited tumor growth in nu/nu mice with relapsed DOX-treated fibrosarcoma 7-fold and led to improved overall (2-fold) survival. In an experimental metastatic model, the combination of TPA with DOX treatment extended overall survival 3-fold, suggesting that targeting CSC can become an effective strategy in the treatment of refractory/relapse fibrosarcoma.

ChiTaRS 8.0: the comprehensive database of chimeric transcripts and RNA-seq data with applications in liquid biopsy

Gene fusions are nucleotide sequences formed due to errors in replication and transcription control. These errors, resulting from chromosomal translocation, transcriptional errors or trans-splicing, vary from cell to cell. The identification of fusions has become critical as key biomarkers for disease diagnosis and therapy in various cancers, significantly influencing modern medicine. Chimeric Transcripts and RNA-Sequencing database version 8.0 (ChiTaRS 8.0; http://biosrv.org/chitars) is a specialized repository for human chimeric transcripts, containing 47 445 curated RNA transcripts and over 100 000 chimeric sequences in humans. This updated database provides unique information on 1055 chimeric breakpoints derived from public datasets using chromosome conformation capture techniques (the Hi-C datasets). It also includes an expanded list of gene fusions that are potential drug targets, and chimeric breakpoints across 934 cell lines, positioning ChiTaRS 8.0 as a valuable resource for testing personalized cancer therapies. By utilizing text mining on a curated selection of disease-specific RNA-sequencing data from public datasets, as well as patient blood and plasma samples, we have identified novel chimeras-particularly in diseases such as oral squamous cell carcinoma and glioblastoma-now catalogued in ChiTaRS. Thus, ChiTaRS 8.0 serves as an enhanced fusion transcript repository that incorporates insights into the functional landscape of chimeras in cancers and other complex diseases, based on liquid biopsy results.

Chimeric antigen receptor macrophages targeting c-MET(CAR-M-c-MET) inhibit pancreatic cancer progression and improve cytotoxic chemotherapeutic efficacy

BACKGROUND

Pancreatic ductal adenocarcinoma (PDAC) is one of the most malignant tumors. Macrophages are abundant in the tumor microenvironment, making them an attractive target for therapeutic intervention. While current immunotherapies, including immune checkpoint inhibition (ICI) and chimeric antigen receptor T (CAR-T) cells, have shown limited efficacy in pancreatic cancer, a novel approach involving chimeric antigen receptor macrophages (CAR-M) has, although promising, not been explored in pancreatic cancer. In this study, we first investigated the role of CAR-M cells targeting c-MET in pancreatic cancer.

METHODS

The effectiveness and rationality of c-MET as a target for CAR-M in pancreatic cancer were validated through bioinformatic analyses and immunohistochemical staining of samples from pancreatic cancer patients. We utilized flow cytometry and bioluminescence detection methods to demonstrate the specific binding and phagocytic killing effect of CAR-M on pancreatic cancer cells. Additionally, we observed the process of CAR-M engulfing pancreatic cancer cells using confocal microscopy and a long-term fluorescence live cell imaging system. In an in situ tumor model transplanted into NOD/SCID mice, we administered intraperitoneal injections of CAR-M to confirm its inhibitory function on pancreatic cancer. Furthermore, we validated these findings in human monocyte-derived macrophages (hMDM).

RESULTS

Bioinformatics and tumor tissue microarray analyses revealed significantly higher expression levels of c-MET in tumor tissues, compared to the paired peritumoral tissues, and higher c-MET expression correlated with worse patient survival. CAR-M cells were engineered using human monocytic THP-1 cell line and hMDM targeting c-MET (CAR-M-c-MET). The CAR-M-c-MET cells demonstrated highly specific binding to pancreatic cancer cells and exhibited more phagocytosis and killing abilities than the pro-inflammatory polarized control macrophages. In addition, CAR-M-c-MET cells synergized with various cytotoxic chemotherapeutic drugs. In a NOD/SCID murine model, intraperitoneally injected CAR-M-c-MET cells rapidly migrated to tumor tissue and substantially inhibited tumor growth, which did not lead to obvious side effects. Cytokine arrays and mRNA sequencing showed that CAR-M-c-MET produced higher levels of immune activators than control macrophages.

CONCLUSIONS

This study provides compelling evidence for the safety and efficacy of CAR-M therapy in treating pancreatic cancer. The results demonstrate that CAR-M-c-MET significantly suppresses pancreatic cancer progression and enhances the effectiveness of cytotoxic chemotherapy. Remarkably, no discernible side effects occur. Further clinical trials are warranted in human pancreatic cancer patients.

Exploring the potential of CAR-macrophage therapy

Chimeric antigen receptor T cell (CAR-T) cell therapy has achieved significant success in treating hematologic malignancies, but its efficacy in solid tumor treatment is relatively limited. Therefore, researchers are exploring other genetically modified immune cells as potential treatment strategies to address the challenges in solid tumor therapy. Chimeric antigen receptor macrophage (CAR-M) involves the genetic engineering of macrophages to express chimeric antigen receptors, enabling them to recognize and attack tumor cells. In contrast to CAR-T cells, CAR-M cells offer distinct advantages such as enhanced infiltration and survival capabilities, along with a diverse array of anti-tumor mechanisms, making them a promising immunotherapy approach that may yield better results in solid tumor treatment. This article provides an overview of the research advancements in CAR-M-mediated tumor immunotherapy, encompassing topics such as the design and transduction of CAR, cell sources, anti-tumor mechanisms and clinical applications. The future research direction in this field will involve leveraging innovative biological technologies to augment the anti-tumor efficacy of CAR-M, understand the underlying mechanisms, and enhance the safety and efficacy of CAR-M therapy.

Unlocking Immunity: Innovative prostate cancer vaccine strategies

OBJECTIVE

Prostate Cancer (PCa) is a leading cause of cancer-related mortality in men, especially in Western societies. The objective of this research is to address the unmet need for effective treatments in advanced or recurrent PCa, where current strategies fall short of offering a cure. The focus is on leveraging immunotherapy and cancer vaccines to target the tumor's unique immunological microenvironment.

MAIN RESULTS

Despite immunotherapy's success in other cancers, its effectiveness in PCa has been limited by the tumor's immunosuppressive characteristics. However, cancer vaccines that engage Tumor-Specific Antigens (TSA) and Tumor-Associated Antigens (TAA) have emerged as a promising approach. Preclinical and clinical investigations of Dendritic Cell (DC) vaccines, DNA vaccines, mRNA vaccines, peptide vaccines, and viral vectors have shown their potential to elicit anti-tumor immune responses. The exploration of combination therapies with immune checkpoint inhibitors and the advent of novel adjuvants and oral microparticle vaccines present innovative strategies to improve efficacy and compliance.

CONCLUSION

The development of cancer vaccines for PCa holds significant potential. Future directions include optimizing vaccine design, refining combination therapy strategies, and creating patient-friendly administration methods. The integration of interdisciplinary knowledge and innovative clinical trial designs is essential for advancing personalized and precision immunotherapy for PCa.

Advantage looping: Gene regulatory circuits between microRNAs and their target transcription factors in plants

The 20 to 24 nucleotide microRNAs (miRNAs) and their target transcription factors (TF) have emerged as key regulators of diverse processes in plants, including organ development and environmental resilience. In several instances, the mature miRNAs degrade the TF-encoding transcripts, while their protein products in turn bind to the promoters of the respective miRNA-encoding genes and regulate their expression, thus forming feedback loops (FBLs) or feedforward loops (FFLs). Computational analysis suggested that such miRNA-TF loops are recurrent motifs in gene regulatory networks (GRNs) in plants as well as animals. In recent years, modeling and experimental studies have suggested that plant miRNA-TF loops in GRNs play critical roles in driving organ development and abiotic stress responses. Here, we discuss the miRNA-TF FBLs and FFLs that have been identified and studied in plants over the past decade. We then provide some insights into the possible roles of such motifs within GRNs. Lastly, we provide perspectives on future directions for dissecting the functions of miRNA-centric GRNs in plants.

Transcriptional regulatory program controlled by MYB in T-cell acute lymphoblastic leukemia

The transcription factor MYB is frequently upregulated in T-cell acute lymphoblastic leukemia (T-ALL), a hematological malignancy originating from T-cell precursors. Here, we demonstrate that MYB plays a crucial role by regulating genes essential for T-ALL pathogenesis. Integrative analysis reveals a long MYB isoform, ENST00000367814.8, which is dominantly expressed and confers a proliferative advantage in T-ALL cells. Rapid depletion of MYB via dTAG-mediated protein degradation affects a large number of genes, which can be classified into early response or late response genes based on their kinetics. Early response genes include many genes involved in hematopoiesis, such as TAL1, RUNX1, GATA3, IKZF2, and CXCR4. Their expression can be recovered at later time-points, suggesting the presence of a negative feedback loop mechanism. In contrast, late response genes, which are continuously downregulated after MYB depletion, includes many genes involved in cell proliferation as well as TAL1 targets, thereby affecting the cellular phenotype.

RUNX1 expression is regulated by a super-enhancer and is a therapeutic target in adult T-cell leukemia/lymphoma

Super-enhancers (SEs) play an important role in regulating tumor-specific gene expression. JQ1, a Bromodomain-containing protein 4 (BRD4) inhibitor, exerts antitumor effects by disrupting SE-mediated regulation of gene expression. We investigated the anti-adult T-cell leukemia/lymphoma (ATL) effects of JQ1. JQ1 induced apoptosis and inhibited ATL cell proliferation. JQ1 suppressed RUNX1expression through the disruption of SE-mediated gene regulation. In the previous reports, it was shown that IC50s of AI-10-104 and Ro5-3335, RUNX1 inhibitors were 1-10 µM for lymphoblastic leukemia cell lines carrying RUNX1 mutations. In the present study, we demonstrated that IC50s of AI-10-104 and Ro5-3335 were also 1-10 µM or lower for ATL cell lines. Simultaneously, AI-10-104 suppressed MYC proto-oncogene (c-MYC) expression. RUNX1 is a potential therapeutic target for ATL that promotes c-MYC expression. We showed that RUNX1 expression is regulated via SEs in ATL and that RUNX1 may be a novel therapeutic target for ATL.

Recent advances in targeted drug delivery systems for multiple myeloma

Despite significant therapeutic advances, multiple myeloma (MM) remains a challenging, incurable, hematological malignancy. The efficacy of traditional chemotherapy and currently available anti-MM agents is in part limited by their adverse effects, which restrict their therapeutic potential. Nanotherapeutics is an emerging field of cancer therapy that can overcome the biological and chemical barriers of existing anticancer drugs. This review presents an overview of recent advancements in nanoparticle- and immunotherapy-based drug delivery systems for MM treatment. It further delves into the targeting strategies, mechanism of controlled drug release, and challenges associated with the development of drug delivery systems for the treatment of MM.

ICAT-Mediated Crosstalk Between Cervical Cancer Cells and Macrophages Promotes M2-Like Macrophage Polarization to Reinforce Tumor Malignant Behaviors

Inhibitor of β-catenin and T-cell factor (ICAT) is a classical inhibitor of the Wnt signaling pathway. Nonetheless, our previous work found that ICAT is overexpressed in cervical cancer (CC), resulting in the augmentation of migration and invasion capabilities of CC cells. It remains unclear what molecular mechanism underlies this phenomenon. The interaction between cancer cells and the tumor microenvironment (TME) promotes the outgrowth and metastasis of tumors. Tumor-associated macrophages (TAMs) are a major constituent of the TME and have a significant impact on the advancement of CC. Consequently, our inquiry pertains to the potential of ICAT to facilitate tumor development through its modulation of the cervical TME. In this study, we first verified that ICAT regulated the secretion of cytokines interleukin-10 (IL-10) and transforming growth factor-β (TGF-β) in CC cells, leading to M2-like macrophage polarization and enhancement of the migration and invasion of CC cells. Furthermore, the system of co-culturing human umbilical vein endothelial cells (HUVECs) with macrophages revealed that depending on the CC cells' overexpression or inhibition of ICAT, the vascular tube formation by HUVECs can be either increased or decreased. Overall, our study indicates that ICAT stimulates M2-like polarization of TAMs via upregulating IL-10 and TGF-β, which results in increased neovascularization, tumor metastasis, and immunosuppression in CC. In upcoming times, inhibiting crosstalk between CC cells and TAMs may be a possible strategy for CC therapy.

Advancing the next generation of cancer treatment with circular RNAs in CAR-T cell therapy

Chimeric Antigen Receptor T-cell (CAR-T) therapy has revolutionized the treatment of hematological malignancies. However, its effectiveness against solid tumors remains constrained by challenges such as T-cell exhaustion, limited persistence, and off-target effects. These challenges highlight critical gaps in current CAR-T cell therapeutic strategies, particularly for solid tumor applications. Circular RNAs (circRNAs) represent a transformative class of non-coding RNAs, known for their exceptional stability and precise regulatory functions, positioning them as promising candidates for enhancing next-generation CAR-T cell therapies. Notably, circRNAs can bridge the gap between preclinical research and clinical application by offering innovative solutions to overcome technical hurdles and improve therapeutic outcomes. Despite their potential, circRNAs remain underexplored in clinical application of CAR-T cell therapies for solid tumors, presenting a significant opportunity for innovation. The mechanisms through which circRNAs modulate CAR-T cell exhaustion, persistence, and tumor specificity are not yet fully understood, and technical challenges, such as achieving efficient and targeted circRNA delivery, which still need to be addressed. This review highlights the importance of integrating circRNAs into CAR-T cell therapy to enhance specificity, minimize off-target effects, and improve therapeutic durability. By emphasizing the innovative potential of circRNAs and identifying key research gaps, this review provides a roadmap for advancing CAR-T cell therapy and setting the stage for the next generation of personalized cancer treatments.

Circulating nucleosomes as a potential cancer biomarker in dogs with splenic nodular lesions

Splenic nodular lesions in dogs can be either benign or malignant. They might be discovered incidentally or, in case of rupture, they may lead to hemoabdomen. Nevertheless, splenectomy followed by histopathology is essential for diagnosis and to prevent rupture. Yet, this invasive procedure might be postponed for dogs with benign splenic nodular lesions. Conversely, owners may opt for euthanasia over surgery for malignancies with poor prognosis like hemangiosarcoma. Thus, anticipating diagnosis with non-invasive biomarkers is crucial for proper patient management. In this prospective study, plasma samples were collected from 66 dogs with histologically confirmed splenic nodular lesions. A canine-specific ELISA kit was applied to assess nucleosome concentration, with histopathology of the spleen serving as the gold standard. Nucleosome concentration was found to be significantly higher in dogs with malignant splenic nodular lesions, particularly in those with hemangiosarcoma and other malignancies. The presence of hemoabdomen, more prevalent in dogs with splenic malignancy, also resulted in increased plasmatic nucleosome concentrations. Plasma nucleosomes could serve as a biomarker for detecting malignant splenic nodular lesions in dogs. More research is needed to understand how nucleosome concentration relate to disease stage and prognosis in dogs with hemangiosarcoma.

REMR: Identification of RNA Editing-mediated MiRNA Regulation in Cancers

Dysregulation of adenosine-to-inosine (A-to-I) RNA editing has been implicated in cancer progression. However, a comprehensive understanding of how A-to-I RNA editing is incorporated into miRNA regulation to modulate gene expression in cancer remains unclear, given the lack of effective identification methods. To this end, we introduced an information theory-based algorithm named REMR to systematically identify 12,006 A-to-I RNA editing-mediated miRNA regulatory triplets (RNA editing sites, miRNAs, and genes) across ten major cancer types based on multi-omics profiling data from The Cancer Genome Atlas (TCGA). Through analyses of functional enrichment, transcriptional regulatory networks, and protein-protein interaction (PPI) networks, we showed that RNA editing-mediated miRNA regulation potentially affects critical cancer-related functions, such as apoptosis, cell cycle, drug resistance, and immunity. Furthermore, triplets can serve as biomarkers for classifying cancer subtypes with distinct prognoses or drug responses, highlighting the clinical relevance of such regulation. In addition, an online resource (http://www.jianglab.cn/REMR/) was constructed to support the convenient retrieval of our findings. In summary, our study systematically dissected the RNA editing-mediated miRNA regulations, thereby providing a valuable resource for understanding the mechanism of RNA editing as an epitranscriptomic regulator in cancer.

The Prognostic Significance of CD47, CD68, and CD163 Expression Levels and Their Relationship with MLR and MAR in Locally Advanced and Oligometastatic Nasopharyngeal Carcinoma

BACKGROUND

This study aimed to assess the prognostic and predictive implications of CD47, CD68, and CD163, biomarkers of tumor-associated macrophages (TAMs), on the treatment efficacy and clinical outcomes of nasopharyngeal carcinoma (NPC). Additionally, the prognostic value of TAM-related indices, such as the monocyte-to-lymphocyte ratio (MLR) and monocyte-to-albumin ratio (MAR), was evaluated.

METHODS

A retrospective cohort of 54 patients with locally advanced or oligometastatic NPC treated with concurrent chemoradiotherapy (CCRT), with or without induction chemotherapy, was analyzed. Patients were categorized based on the cumulative expression scores for CD47, CD68, and CD163: negative/low (0-3 points) and high (4-6 points). MLR and MAR were also stratified as low MLR (<0.545) vs. high MLR (≥0.545) and low MAR (<16.145) vs. high MAR (≥16.145). The primary endpoint was overall survival (OS).

RESULTS

High CD47, CD68, and CD163 expression levels were correlated with advanced clinical stage, reduced CCRT response, and elevated MLR and MAR. These TAM biomarkers were linearly correlated with each other and with established risk factors such as advanced age and elevated EBV-DNA levels. Kaplan-Meier analysis revealed that patients with low TAM expression had significantly longer OS and progression-free survival (PFS) than those with high TAM expression. Multivariate analysis identified high CD163, MLR, and MAR levels as independent adverse prognostic factors for OS. Elevated MLR is an independent risk factor for both OS and PFS in patients with NPC.

CONCLUSIONS

CD47, CD68, and CD163 are significant prognostic markers in NPC, with higher levels being associated with poorer OS and PFS. Elevated MLR and MAR values also predict worse outcomes, underscoring their value as prognostic tools. CD163 and MLR are particularly strong predictors, highlighting the crucial role of TAMs in NPC management and suggesting that CD163 is a potential therapeutic target within the immune checkpoint pathway.

Generation of tumor neoantigens by RNA splicing perturbation

Immunotherapy has revolutionized cancer treatment, but the limited availability of tumor-specific neoantigens still remains a challenge. The potential of alternative mRNA splicing-derived neoantigens as a source of new immunotherapy targets has gained significant attention. Tumors exhibit unique splicing changes and splicing factor mutations which are prevalent in various cancers and play a crucial role in neoantigen production. We present advances in splicing modulation approaches, including small-molecule drugs, decoy and splice-switching antisense oligonucleotides (SSOs), CRISPR, small interfering RNAs (siRNAs), and nonsense-mediated RNA decay (NMD) inhibition, that can be adapted to enhance antitumor immune responses. Finally, we explore the clinical implications of these approaches, highlighting their potential to transform cancer immunotherapy and broaden its efficacy.

ADAR1 enhances tumor proliferation and radioresistance in non-small cell lung cancer by interacting with Rad18

PURPOSE

Posttranslational modification significantly contributes to the transcriptional diversity of tumors. Adenosine deaminase acting on RNA 1 (ADAR1) and its mediated adenosine-to-inosine (A-to-I) editing have been reported to influence tumorigenesis across various cancer types. Nevertheless, the relationship between ADAR1 and radioresistence remains to be elucidated.

METHODS

The protein expression was detected by immunohistochemistry and Western Blot, while the mRNA expression was measured by RT-qPCR. The tumor growth was evaluated by CCK8, colony formation assays, EdU assay, and in-vivo mouse model. γ-H2AX foci formation, neutral comet tailing assay, and clonogenic cell survival assay were performed to determine the DNA damage and radiosensitivity. RNA-seq was conducted to identify the main downstream effector. The interaction between ADAR1 and Rad18 was examined by immunofluorescence and co-immunoprecipitation.

RESULTS

We reported that ADAR1 was upregulated and correlated with poor prognosis in non-small cell lung cancer (NSCLC). In addition, we demonstrated that silencing ADAR1 significantly impaired tumor growth and improved tumor sensitivity to radiotherapy in vitro and in vivo. Mechanistically, we found that Rad18, which has been established as a versatile modulator of DNA repair, was the major downstream effector of ADAR1. ADAR1 not only regulated Rad18 mRNA expression by E2F3 but also colocalized and interacted with Rad18. Finally, our rescue experiments demonstrated that ADAR1's protumorigenic functions were partially dependent on Rad18.

CONCLUSION

Our results revealed the role of ADAR1 in cooperation with Rad18 in modulating oncogenesis and radioresistance in NSCLC for the first time, and suggested the therapeutic potential of targeting ADAR1 in overcoming radioresistance.

Therapeutic advances in the targeting of ROR1 in hematological cancers

Receptor tyrosine kinases (RTKs) are key cell surface receptors involved in cell communication and signal transduction, with great importance in cell growth, differentiation, survival, and metabolism. Dysregulation of RTKs, such as EGFR, VEGFR, HER2 or ROR, could lead to various diseases, particularly cancers. ROR1 has emerged as a promising target in hematological malignancies. The development of ROR1 targeted therapies is continuously growing leading to remarkable novel therapeutical approaches using mAbs, antibody-drug conjugates, several small molecules or CAR T cells which have shown encouraging preclinical results. In the hematological field, mAbs, small molecules, BiTEs or CAR T cell therapies displayed promising outcomes with the clinical trials data encouraging the use of anti-ROR1 therapies. This paper aims to offer a comprehensive analysis of the current landscape of ROR1-targeted therapies in hematological malignancies marking the innovative approaches with promising preclinical and clinical. Offering a better understanding of structural and functional aspects of ROR1 could lead to new perspectives in targeting a wide spectrum of malignancies.

Deciphering the Language of Protein-DNA Interactions: A Deep Learning Approach Combining Contextual Embeddings and Multi-Scale Sequence Modeling

Deciphering the mechanisms governing protein-DNA interactions is crucial for understanding key cellular processes and disease pathways. In this work, we present a powerful deep learning approach that significantly advances the computational prediction of DNA-interacting residues from protein sequences. Our method leverages the rich contextual representations learned by pre-trained protein language models, such as ProtTrans, to capture intrinsic biochemical properties and sequence motifs indicative of DNA binding sites. We then integrate these contextual embeddings with a multi-window convolutional neural network architecture, which scans across the sequence at varying window sizes to effectively identify both local and global binding patterns. Comprehensive evaluation on curated benchmark datasets demonstrates the remarkable performance of our approach, achieving an area under the ROC curve (AUC) of 0.89 - a substantial improvement over previous state-of-the-art sequence-based predictors. This showcases the immense potential of pairing advanced representation learning and deep neural network designs for uncovering the complex syntax governing protein-DNA interactions directly from primary sequences. Our work not only provides a robust computational tool for characterizing DNA-binding mechanisms, but also highlights the transformative opportunities at the intersection of language modeling, deep learning, and protein sequence analysis. The publicly available code and data further facilitate broader adoption and continued development of these techniques for accelerating mechanistic insights into vital biological processes and disease pathways. In addition, the code and data for this work are available at https://github.com/B1607/DIRP.

Innovative anti-proliferative effect of the antiviral favipiravir against MCF-7 breast cancer cells using green nanoemulsion and eco-friendly assessment tools

Telomerase enzyme prevents telomere shortening during division, having human telomerase reverse transcriptase (hTERT) as its catalytic subunit. Favipiravir (FAV), an RNA-dependent RNA polymerases inhibitor, shared structural similarity with hTERT and thus assumed to have cytotoxic effect on cancer cells, in addition to its prophylactic effect to immunocompromised cancer patients. Nanoemulsion (NE) is a potential tumor cells targeting delivery system, thereby enhancing therapeutic efficacy at the intended site, mitigating systemic toxicity, and overcoming multidrug resistance. The objective of this study is to develop a green FAV nanoemulsion (FNE) that is environmentally friendly and safe for patients, while aiming to enhance its cytotoxic effects. The study also highlights the environmental sustainability of the developed RP-HPLC method and assesses its greenness impact. The FNE formulation underwent thermodynamic stability testing and invitro characterization. Greenness was assessed using advanced selected tools like the Analytical Eco-Scale (AES), Analytical Greenness Metric for Sample Preparation (AGREEprep), and green analytical procedure index (GAPI). The cytotoxic potential of FNE was screened against MCF-7 breast cancer and Vero normal cell lines using SRB assay. Stable and ecofriendly FNE was formulated having a particle size (PS) of 25.29 ± 0.57 nm and a zeta potential of -6.79 ± 5.52 mV. The cytotoxic effect of FNE on MCF-7 cells was more potent than FAV with lower IC50 while FNE showed non-toxic effect on VERO normal cell line. Therefore, the FAV nanoemulsion formulation showed targeted cytotoxicity on MCF-7 cells while being non-toxic on normal Vero cells.

Exploring the therapeutic potential of precision T-Cell Receptors (TCRs) in targeting KRAS G12D cancer through in vitro development

Objectives

The Kirsten rat sarcoma virus (KRAS) G12D oncogenic mutation poses a significant challenge in treating solid tumors due to the lack of specific and effective therapeutic interventions. This study aims to explore innovative approaches in T cell receptor (TCR) engineering and characterization to target the KRAS G12D7-16 mutation, providing potential strategies for overcoming this therapeutic challenge.

Methods

In this innovative study, we engineered and characterized two T cell receptors (TCRs), KDA11-01 and KDA11-02 with high affinity for the KRAS G12D7-16 mutation. These TCRs were isolated from tumor-infiltrating lymphocytes (TILs) derived from tumor tissues of patients with the KRAS G12D mutation. We assessed their specificity and anti-tumor activity in vitro using various cancer cell lines.

Results

KDA11-01 and KDA11-02 demonstrated exceptional specificity for the HLA-A*11:01-restricted KRAS G12D7-16 epitope, significantly inducing IFN-γ release and eliminating tumor cells without cross-reactivity or alloreactivity.

Conclusions

The successful development of KDA11-01 and KDA11-02 introduces a novel and precise TCR-based therapeutic strategy against KRAS G12D mutation, showing potential for significant advancements in cancer immunotherapy.

Bulk and single-cell RNA-seq analyses reveal canonical RNA editing associated with microglia homeostasis and its role in sepsis-associated encephalopathy

Previous studies have demonstrated the roles of both microglia homeostasis and RNA editing in sepsis-associated encephalopathy (SAE), yet their relationship remains to be elucidated. In this study, we analyzed bulk and single-cell RNA-seq (scRNA) datasets containing 107 brain tissue and microglia samples from mice with microglial depletion and repopulation to explore canonical RNA editing associated with microglia homeostasis and evaluate its role in SAE. Analysis of mouse brain RNA-Seq revealed hallmarks of microglial repopulation, including peak expressions of Apobec1 and Apobec3 at Day 5 of repopulation and dramatically altered B2m RNA editing. Significant time-dependent changes in brain RNA editing during microglial depletion and repopulation were primarily observed in synapse-related genes, such as Tbc1d24 and Slc1a2. ScRNA-Seq revealed heterogeneous RNA editing among microglia subpopulations and their distinct changes associated with microglia homeostasis. Moreover, repopulated microglia from lipopolysaccharide (LPS)-induced sepsis mice exhibited intensified up-regulation of Apobec1 and Apobec3, with distinct RNA editing responses to LPS, mainly involved in immune-related pathways. The hippocampus from sepsis mice induced by peritoneal contamination and infection showed upregulated Apobec1 and Apobec3 expression, and altered RNA editing in immune-related genes, such as B2m and Mier1, and nervous-related lncRNA Meg3 and Snhg11, both of which were repressed by microglial depletion. Furthermore, the expression of complement-related genes, such as C4b and Cd47, was substantially correlated with RNA editing activity in microglia homeostasis and SAE. Our study demonstrates canonical RNA editing associated with microglia homeostasis and provides new insights into its potential role in SAE.

Emerging Ocular Side Effects of Immune Checkpoint Inhibitors: A Comprehensive Review

Immune checkpoint inhibitors (ICIs) have revolutionized cancer treatment, offering significant improvements in patient survival across various malignancies. However, their use is associated with a broad spectrum of immune-related adverse events (irAEs), including those affecting the eye and its surrounding structures, collectively termed ocular irAEs (OirAEs). Although rare, OirAEs (e.g., keratitis, uveitis, retinal vasculitis, etc.) can significantly impact a patient's quality of life, leading to ocular complications if left untreated. This review provides a comprehensive overview of OirAEs associated with ICIs, including their clinical manifestations, underlying mechanisms, and current management strategies. We delve into the anterior and posterior segment adverse events, highlighting conditions such as dry eye, uveitis, and retinal disorders, as well as neuro-ophthalmic and orbital complications. Furthermore, we discuss the challenges in diagnosing and treating these conditions, particularly given the overlap with other autoimmune and paraneoplastic syndromes. Finally, we identify key knowledge gaps and suggest future research directions aimed at optimizing the management of OirAEs while maintaining the efficacy of cancer therapy. This review underscores the need for increased awareness among clinicians to prevent irreversible ocular damage and enhance patient outcomes.

Emerging strategies to overcome ovarian cancer: advances in immunotherapy

Ovarian cancer is the second most common malignant neoplasm of gynecological origin and the leading cause of death from cancer in the female reproductive system worldwide. This scenario is largely due to late diagnoses, often in advanced stages, and the development of chemoresistance by cancer cells. These challenges highlight the need for alternative treatments, with immunotherapy being a promising option. Cancer immunotherapy involves triggering an anti-tumor immune response and developing immunological memory to eliminate malignant cells, prevent recurrence, and inhibit metastasis. Some ongoing research investigate potentially immunological advancements in the field of cancer vaccines, immune checkpoint blockade, CAR-T cell, and other strategies.

Advances in mRNA LNP-Based Cancer Vaccines: Mechanisms, Formulation Aspects, Challenges, and Future Directions

After the COVID-19 pandemic, mRNA-based vaccines have emerged as a revolutionary technology in immunization and vaccination. These vaccines have shown remarkable efficacy against the virus and opened up avenues for their possible application in other diseases. This has renewed interest and investment in mRNA vaccine research and development, attracting the scientific community to explore all its other applications beyond infectious diseases. Recently, researchers have focused on the possibility of adapting this vaccination approach to cancer immunotherapy. While there is a huge potential, challenges still remain in the design and optimization of the synthetic mRNA molecules and the lipid nanoparticle delivery system required to ensure the adequate elicitation of the immune response and the successful eradication of tumors. This review points out the basic mechanisms of mRNA-LNP vaccines in cancer immunotherapy and recent approaches in mRNA vaccine design. This review displays the current mRNA modifications and lipid nanoparticle components and how these factors affect vaccine efficacy. Furthermore, this review discusses the future directions and clinical applications of mRNA-LNP vaccines in cancer treatment.

Advances in Trop-2 targeted antibody-drug conjugates for breast cancer: mechanisms, clinical applications, and future directions

Breast cancer remains a leading cause of cancer-related deaths among women worldwide, highlighting the need for novel therapeutic strategies. Trophoblast cell surface antigen 2 (Trop-2), a type I transmembrane glycoprotein highly expressed in various solid tumors including all subtypes of breast cancer, has emerged as a promising target for cancer therapy. This review focuses on recent advancements in Trop-2-targeted antibody-drug conjugates (ADCs) for breast cancer treatment. We comprehensively analyzed the structure and mechanism of action of ADCs, as well as the role of Trop-2 in breast cancer progression and prognosis. Several Trop-2-targeted ADCs, such as Sacituzumab Govitecan (SG) and Datopotamab Deruxtecan (Dato-DXd), have demonstrated significant antitumor activity in clinical trials for both triple-negative breast cancer (TNBC) and hormone receptor-positive/HER2-negative (HR+/HER2-) breast cancer. We systematically reviewed the ongoing clinical studies of these ADCs, highlighting their efficacy and safety profiles. Furthermore, we explored the potential of combining Trop-2-targeted ADCs with other therapeutic modalities, including immunotherapy, targeted therapies, and small molecule inhibitors. Notably, Trop-2-targeted ADCs have shown promise in reprogramming the tumor microenvironment through multiple signaling pathways, potentially enhancing antitumor immunity. This review aims to provide new insights and research directions for the development of innovative breast cancer therapies, offering potential solutions to improve treatment outcomes and quality of life for breast cancer patients.

Revolutionizing microorganism inactivation: Magnetic nanomaterials in sustainable photocatalytic disinfection

The rapid emergence of antibiotic-resistant microorganisms and the demand for sustainable water purification methods have spurred research into advanced disinfection, with photocatalysis as a promising approach. This study explores magnetic nanomaterials as catalysts in photocatalytic processes for microorganism inactivation. Magnetic nanoparticles and composites, due to their unique properties, are promising for enhancing photocatalytic disinfection. Their inherent magnetic traits enable easy separation and recyclability, reducing operational costs and environmental impact. These materials also act as efficient electron transfer mediators, enhancing overall photocatalytic efficiency. The review covers the synthesis and characterization of magnetic nanomaterials for photocatalytic applications, focusing on their structural, magnetic, and surface properties. Photocatalytic mechanisms, including reactive oxygen species (ROS) generation vital for microorganism inactivation, are discussed. The study examines combining common photocatalysts like TiO2, ZnO, and semiconductors with magnetic nanomaterials, highlighting synergistic effects. Recent advances and challenges, such as optimal nanomaterials selection and scalability for large-scale applications, are addressed. Case studies and experimental setups for microorganism inactivation underscore the potential of magnetic nanomaterials in water treatment, air purification, and medical disinfection. Finally, further research directions and research highlights the substantial potential of magnetic nanomaterials as catalysts in photocatalytic processes, offering an efficient and sustainable solution for microorganism inactivation and contributing valuable insights to environmental and public health advancement.

Unraveling the complex role of neutrophils in lymphoma: From pathogenesis to therapeutic approaches (Review)

Lymphoma, a malignancy of the lymphatic system, which is critical for maintaining the body's immune defenses, has become a focal point in recent research due to its intricate interplay with neutrophils-white blood cells essential for combating infections and inflammation. Unlike prior perceptions associating neutrophils only with tumor support, contemporary studies underscore their intricate and multifaceted involvement in the immune response to lymphoma. Recognizing the nuanced participation of neutrophils in lymphoma is crucial for developing innovative treatments to improve patient outcomes.

Advancements of engineered live oncolytic biotherapeutics (microbe/virus/cells): Preclinical research and clinical progress

The proven efficacy of immunotherapy in fighting tumors has been firmly established, heralding a new era in harnessing both the innate and adaptive immune systems for cancer treatment. Despite its promise, challenges such as inefficient delivery, insufficient tumor penetration, and considerable potential toxicity of immunomodulatory agents have impeded the advancement of immunotherapies. Recent endeavors in the realm of tumor prophylaxis and management have highlighted the use of living biological entities, including bacteria, oncolytic viruses, and immune cells, as a vanguard for an innovative class of live biotherapeutic products (LBPs). These LBPs are gaining recognition for their inherent ability to target tumors. However, these LBPs must contend with significant barriers, including robust immune clearance mechanisms, cytotoxicity and other in vivo adverse effects. Priority must be placed on enhancing their safety and therapeutic indices. This review consolidates the latest preclinical research and clinical progress pertaining to the exploitation of engineered biologics, spanning bacteria, oncolytic viruses, immune cells, and summarizes their integration with combination therapies aimed at circumventing current clinical impasses. Additionally, the prospective utilities and inherent challenges of the biotherapeutics are deliberated, with the objective of accelerating their clinical application in the foreseeable future.

RNA Modifications Shape Hematopoietic Stem Cell Aging: Beyond the Code

Hematopoietic system aging is characterized by both hematopoietic stem cell (HSC) and niche degeneration resulting in myeloid lineage-biased differentiation, reduced B cell and T cell lymphopoiesis, increased HSC mobilization, and fat deposition in the bone marrow. Both alterations in RNA splicing and editing during HSC aging contribute to increased myeloid lineage skewing and inflammation-responsive transcription factors, underscoring the importance of epitranscriptomic mechanisms in the acquisition of an age-related phenotype.

Deoxyarbutin targets mitochondria to trigger p53-dependent senescence of glioblastoma cells

Cellular senescence is a natural barrier of the transition from premalignant cells to invasive cancer. Pharmacological induction of senescence has been proposed as a possible anticancer strategy. In this study, we found that deoxyarbutin inhibited the growth of glioblastoma (GBM) cells by inducing cellular senescence, independent of tyrosinase expression. Instead, deoxyarbutin induced mitochondrial oxidative stress and damage. These aberrant mitochondria were key to the p53-dependent senescence of GBM cells. Facilitating autophagy or mitigating mitochondrial oxidative stress both suppressed p53 expression and alleviated cellular senescence induced by deoxyarbutin. Thus, our study reveals that deoxyarbutin induces mitochondrial oxidative stress to trigger the p53-dependent senescence of GBM cells. Importantly, deoxyarbutin treatment resulted in accumulation of p53, induction of cellular senescence, and inhibition of tumor growth in a subcutaneous tumor model of mouse. In conclusion, our study reveals that deoxyarbutin has therapeutic potential for GBM by inducing mitochondrial oxidative stress for p53-dependent senescence of GBM cells.

Identification and characterization of ADAR1 mutations and changes in gene expression in human cancers

ADAR1 (Adenosine deaminase action on RNA1) is involved in post-transcriptional RNA editing. ADAR1 mutations have been identified in many cancers but its role in tumor formation is still not well understood. Here we used available cancer genomes deposited on CSOMIC and cBioPortal to identify and characterize mutations and changes in ADAR1 expression in cancer cells. We identify several high frequency substitutions including one at R767 which is located in one of the dsRNA interacting domains. In silico protein structure analysis suggest the R767 mutations affect the protein stability and are likely to destabilize interaction with dsRNA. Gene expression analysis shows that in samples with under-expressed ADAR1, there is a statistically significant increase in expression of BLCAP (Bladder Cancer Associated Protein). Although BLCAP was initially identified in bladder cancers, more recent evidence shows that it is a tumor suppressor and BLCAP mutations have been detected in many cancer cells. Epistatic analysis using the cBioPortal mutual exclusivity calculator for the TCGA pan-cancer data shows that co-mutations between ADAR1 and other genes regulated by it are likely in cancer cells except for PTEN, AKT1 and BLCAP. This suggests that when ADAR1 function is impaired, PTEN, AKT1 and BLCAP become essential for survival of cancer cells. We also identified several samples with high mutation burden between ADAR1 and other genes regulated primarily in endometrial cancers. Finally, we show that the deaminase domain is highly conserved in metazoans and mutations within conserved residues do occur in human cancers suggesting that destabilization of the enzyme function is contributing to cancer development.

Liquid biopsy: Comprehensive overview of circulating tumor DNA (Review)

Traditional tumor diagnosis methods rely on tissue biopsy, which can be invasive and unsuitable for long-term monitoring of tumor dynamics. The advent of liquid biopsy has notably improved the overall management of patients with cancer. Liquid biopsy techniques primarily involve detection of circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA). The present review focuses on ctDNA because of its significance in tumor diagnosis, monitoring and treatment. The use of ctDNA-based liquid biopsy offers several advantages, including non-invasive or minimally invasive collection methods, the ability to conduct repeated assessment and comprehensive insights into tumor biology. It serves crucial roles in disease management by facilitating screening of high-risk patients, dynamically monitoring therapeutic responses and diagnosis. Furthermore, ctDNA can be used to demonstrate pseudo-progression, monitor postoperative tumor status and guide adaptive treatment plans. The present study provides a comprehensive review of ctDNA, exploring its origins, metabolism, detection methods, clinical role and the current challenges associated with its application.

Recent advancements in nanomedicine as a revolutionary approach to treating multiple myeloma

Multiple myeloma, the second most common hematological malignancy, remains incurable with a 5-year survival rate of approximately 50 % and recurrence rates near 100 %, despite significant attempts to develop effective medicines. Therefore, there is a pressing demand in the medical field for innovative and more efficient treatments for MM. Currently, the standard approach for treating MM involves administering high-dose chemotherapy, which frequently correlates with improved results; however, one major limiting factor is the significant side effects of these medications. Furthermore, the strategies used to deliver medications to tumors limit their efficacy, whether by rapid clearance from circulation or an insufficient concentration in cancer cells. Cancer treatment has shifted from cytotoxic, nonspecific chemotherapy regimens to molecularly targeted, rationally developed drugs with improved efficacy and fewer side effects. Nanomedicines may provide an effective alternative way to avoid these limits by delivering drugs into the complicated bone marrow microenvironment and efficiently reaching myeloma cells. Putting drugs into nanoparticles can make their pharmacokinetic and pharmacodynamic profiles much better. This can increase the drug's effectiveness in tumors, extend its time in circulation in the blood, and lower its off-target toxicity. In this review, we introduce several criteria for the rational design of nanomedicine to achieve the best anti-tumoral therapeutic results. Next, we discuss recent advances in nanomedicine for MM therapy.

A tumorigenicity evaluation platform for cell therapies based on brain organoids

BACKGROUND

Tumorigenicity represents a critical challenge in stem cell-based therapies requiring rigorous monitoring. Conventional approaches for tumorigenicity evaluation are based on animal models and have numerous limitations. Brain organoids, which recapitulate the structural and functional complexity of the human brain, have been widely used in neuroscience research. However, the capacity of brain organoids for tumorigenicity evaluation needs to be further elucidated.

METHODS

A cerebral organoid model produced from human pluripotent stem cells (hPSCs) was employed. Meanwhile, to enhance the detection sensitivity for potential tumorigenic cells, we created a glioblastoma-like organoid (GBM organoid) model from TP53-/-/PTEN-/- hPSCs to provide a tumor microenvironment for injected cells. Midbrain dopamine (mDA) cells from human embryonic stem cells were utilized as a cell therapy product. mDA cells, hPSCs, mDA cells spiked with hPSCs, and immature mDA cells were then injected into the brain organoids and NOD SCID mice. The injected cells within the brain organoids were characterized, and compared with those injected in vivo to evaluate the capability of the brain organoids for tumorigenicity evaluation. Single-cell RNA sequencing was performed to identify the differential gene expression between the cerebral organoids and the GBM organoids.

RESULTS

Both cerebral organoids and GBM organoids supported maturation of the injected mDA cells. The hPSCs and immature mDA cells injected in the GBM organoids showed a significantly higher proliferative capacity than those injected in the cerebral organoids and in NOD SCID mice. Furthermore, the spiked hPSCs were detectable in both the cerebral organoids and the GBM organoids. Notably, the GBM organoids demonstrated a superior capacity to enhance proliferation and pluripotency of spiked hPSCs compared to the cerebral organoids and the mouse model. Kyoto Encyclopedia of Genes and Genomes analysis revealed upregulation of tumor-related metabolic pathways and cytokines in the GBM organoids, suggesting that these factors underlie the high detection sensitivity for tumorigenicity evaluation.

CONCLUSIONS

Our findings suggest that brain organoids could represent a novel and effective platform for evaluating the tumorigenic risk in stem cell-based therapies. Notably, the GBM organoids offer a superior platform that could complement or potentially replace traditional animal-based models for tumorigenicity evaluation.

Optogenetically engineered Septin-7 enhances immune cell infiltration of tumor spheroids

Chimeric antigen receptor T cell therapies have achieved great success in eradicating some liquid tumors, whereas the preclinical results in treating solid tumors have proven less decisive. One of the principal challenges in solid tumor treatment is the physical barrier composed of a dense extracellular matrix, which prevents immune cells from penetrating the tissue to attack intratumoral cancer cells. Here, we improve immune cell infiltration into solid tumors by manipulating septin-7 functions in cells. Using protein allosteric design, we reprogram the three-dimensional structure of septin-7 and insert a blue light-responsive light-oxygen-voltage-sensing domain 2 (LOV2), creating a light-controllable septin-7-LOV2 hybrid protein. Blue light inhibits septin-7 function in live cells, inducing extended cell protrusions and cell polarization, enhancing cell transmigration efficiency through confining spaces. We genetically edited human natural killer cell line (NK92) and mouse primary CD8+ T-cells expressing the engineered protein, and we demonstrated improved penetration and cytotoxicity against various tumor spheroid models. Our proposed strategy to enhance immune cell infiltration is compatible with other methodologies and therefore, could be used in combination to further improve cell-based immunotherapies against solid tumors.

Super-Enhancer-Driven IRF2BP2 is Activated by Master Transcription Factors and Sustains T-ALL Cell Growth and Survival

Super enhancers (SEs) are large clusters of transcriptional enhancers driving the expression of genes crucial for defining cell identity. In cancer, tumor-specific SEs activate key oncogenes, leading to tumorigenesis. Identifying SE-driven oncogenes in tumors and understanding their functional mechanisms is of significant importance. In this study, a previously unreported SE region is identified in T-cell acute lymphoblastic leukemia (T-ALL) patient samples and cell lines. This SE activates the expression of interferon regulatory factor 2 binding protein 2 (IRF2BP2) and is regulated by T-ALL master transcription factors (TFs) such as ETS transcription factor ERG (ERG), E74 like ETS transcription factor 1 (ELF1), and ETS proto-oncogene 1, transcription factor (ETS1). Hematopoietic system-specific IRF2BP2 conditional knockout mice is generated and showed that IRF2BP2 has minimal impact on normal T cell development. However, in vitro and in vivo experiments demonstrated that IRF2BP2 is crucial for T-ALL cell growth and survival. Loss of IRF2BP2 affects the MYC and E2F pathways in T-ALL cells. Cleavage under targets and tagmentation (CUT&Tag) assays and immunoprecipitation revealed that IRF2BP2 cooperates with the master TFs of T-ALL cells, targeting the enhancer of the T-ALL susceptibility gene recombination activating 1 (RAG1) and modulating its expression. These findings provide new insights into the regulatory network within T-ALL cells, identifying potential new targets for therapeutic intervention.

Cancer stem cells: Masters of all traits

Cancer is a heterogeneous disease, which contributes to its rapid progression and therapeutic failure. Besides interpatient tumor heterogeneity, tumors within a single patient can present with a heterogeneous mix of genetically and phenotypically distinct subclones. These unique subclones can significantly impact the traits of cancer. With the plasticity that intratumoral heterogeneity provides, cancers can easily adapt to changes in their microenvironment and therapeutic exposure. Indeed, tumor cells dynamically shift between a more differentiated, rapidly proliferating state with limited tumorigenic potential and a cancer stem cell (CSC)-like state that resembles undifferentiated cellular precursors and is associated with high tumorigenicity. In this context, CSCs are functionally located at the apex of the tumor hierarchy, contributing to the initiation, maintenance, and progression of tumors, as they also represent the subpopulation of tumor cells most resistant to conventional anti-cancer therapies. Although the CSC model is well established, it is constantly evolving and being reshaped by advancing knowledge on the roles of CSCs in different cancer types. Here, we review the current evidence of how CSCs play a pivotal role in providing the many traits of aggressive tumors while simultaneously evading immunosurveillance and anti-cancer therapy in several cancer types. We discuss the key traits and characteristics of CSCs to provide updated insights into CSC biology and highlight its implications for therapeutic development and improved treatment of aggressive cancers.

Immunological facets of prostate cancer and the potential of immune checkpoint inhibition in disease management

Prostate cancer (PCa) is the most common non-cutaneous cancer in men and a major cause of cancer-related deaths. Whereas localized PCa can be cured by surgery and radiotherapy, metastatic disease can be treated, but is not curable. Inhibition of androgen signaling remains the main therapeutic intervention for treatment of metastatic PCa, in addition to chemotherapy, radionuclide therapy and emerging targeted therapies. Although initial responses are favorable, resistance to these therapies invariably arise with development of castration resistant PCa (CRPC) and lethal phenotypes. Recent findings have implicated the crosstalk between PCa cells and the tumor microenvironment (TME) as a key factor for disease progression and metastasis, and the immune system is becoming an increasingly attractive target for therapy. Given the striking success of immune checkpoint inhibitors (ICIs) in various cancer types, preclinical and clinical studies have begun to explore their potential in PCa. It has become clear that the PCa TME is largely immunosuppressive, and ICI therapy does not have efficacy for PCa. Intense effort is therefore being made in the field to understand the mechanisms of suppression and to turn the immunosuppressive TME into an immune active one that would enable ICI efficacy. Herein we examine this recent body of knowledge and how the mutational landscape of PCa integrates with an immunosuppressive TME to circumvent ICI-mediated T-cell activity and tumor killing. We then review the emerging potential success of combinatorial ICI approaches, utility of careful patient selection, and potential novel strategies to improve the efficacy of ICI for PCa therapy.

RABV antigenic peptide loaded polymeric nanoparticle production, characterization, and preliminary investigation of its biological activity

Nanoparticle-based antigen carrier systems have become a significant area of research with the advancement of nanotechnology. Biodegradable polymers have emerged as particularly promising carrier vehicles due to their ability to address the limitations of existing vaccine systems. In this study, we successfully encapsulated the G5-24 linear peptide, located between amino acids 253 and 275 in the primary sequence of the rabies virus G protein, into biodegradable and biocompatible PLGA copolymer using the double emulsion solvent evaporation method. The resulting nanoparticles had a size of approximately 230.9 ± 0.9074 nm, with a PDI value of 0.168 ± 0.017 and a zeta potential value of -9.86 ± 0.132 mV. SEM images confirmed that the synthesized nanoparticles were uniform in size and distribution. Additionally, FTIR spectra indicated successful peptide loading into the nanoparticles. The encapsulation efficiency of the peptide-loaded nanoparticles was 73.3%, with a peptide loading capacity of 48.2% and a reaction yield of 30.4%. Peptide release studies demonstrated that 65.55% of the peptide was released in a controlled manner over 28 d, following a 'biphasic burst release' profile consistent with the degradation profile of PLGA. This controlled release is particularly beneficial for vaccine studies. Cytotoxicity tests revealed that the R-NP formulation did not induce cytotoxicity in fibroblast cells and enhanced NO production in macrophages, indicating its potential for vaccine development.

Redefining the tumor microenvironment with emerging therapeutic strategies

The environment surrounding a tumor, known as the tumor microenvironment (TME), plays a role in how cancer progresses and responds to treatment. It poses both challenges and opportunities for improving cancer therapy. Recent progress in understanding the TME complexity and diversity has led to approaches for treating cancer. This perspective discusses the strategies for targeting the TME, such as adjusting networks using extracellular vesicles to deliver drugs and enhancing immune checkpoint inhibitors (ICIS) through combined treatments. Furthermore, it highlights adoptive cell transfer (ACT) therapies as an option for tumors. By studying how components of the TME interact and utilizing technologies like single-cell RNA sequencing and spatial transcriptomics, we can develop more precise and efficient treatments for cancer. This article emphasizes the need to reshape the TME to boost antitumor immunity and overcome resistance to therapy, providing guidance for research and clinical practices in precision oncology.

Multimodal ultrasound plus tumor markers demonstrates a high value in enhanced diagnosis of breast cancer

OBJECTIVE

To determine the diagnostic value of multimodal ultrasound combined with tumor markers in breast cancer (BC).

METHODS

A retrospective analysis was conducted on 198 patients with breast lesions treated at the Affiliated Wuxi People's Hospital of Nanjing Medical University between May 2020 and May 2023. All patients underwent multimodal ultrasound and tumor marker testing. Among the 198 patients, 88 patients were pathologically diagnosed with benign disease (benign group) and 110 patients were pathologically diagnosed with malignant disease (malignant group). With the pathological results as the gold standard, the benign and malignant results from different diagnostic methods were compared, focusing on specificity, sensitivity and accuracy.

RESULTS

The areas under the curves (AUCs) of carbohydrate antigen 153 (CA153), CA125, and carcinoembryonic antigen (CEA) for diagnosing BC were 0.810, 0.812, and 0.790, respectively. When these tumor markers were used in combination for diagnosing BC, the AUC increased to 0.928. The AUC of multimodal ultrasound alone in diagnosing BC was 0.845. Additionally, the AUC of multimodal ultrasound combined with tumor markers in diagnosing BC reached 0.971, with the corresponding specificity, sensitivity and accuracy of 90.00%, 94.43% and 91.92%, respectively.

CONCLUSION

In patients with early BC, the combination of multimodal ultrasound and tumor marker detection significantly improves the accuracy of diagnosing benign and malignant breast lesions compared to using either modality alone.

Unleashing nanotechnology to redefine tumor-associated macrophage dynamics and non-coding RNA crosstalk in breast cancer

Breast cancer is a significant global health issue. Tumor-associated macrophages (TAMs) are crucial in influencing the tumor microenvironment and the progression of the disease. TAMs exhibit remarkable plasticity in adopting distinct phenotypes ranging from pro-inflammatory and anti-tumorigenic (M1-like) to immunosuppressive and tumor-promoting (M2-like). This review elucidates the multifaceted roles of TAMs in driving breast tumor growth, angiogenesis, invasion, and metastatic dissemination. Significantly, it highlights the intricate crosstalk between TAMs and non-coding RNAs (ncRNAs), including microRNAs, long noncoding RNAs, and circular RNAs, as a crucial regulatory mechanism modulating TAM polarization and functional dynamics that present potential therapeutic targets. Nanotechnology-based strategies are explored as a promising approach to reprogramming TAMs toward an anti-tumor phenotype. Various nanoparticle delivery systems have shown potential for modulating TAM polarization and inhibiting tumor-promoting effects. Notably, nanoparticles can deliver ncRNA therapeutics to TAMs, offering unique opportunities to modulate their polarization and activity.

A circularly permuted CasRx platform for efficient, site-specific RNA editing

Inactive Cas13 orthologs have been fused to a mutant human ADAR2 deaminase domain at the C terminus to enable programmable adenosine-to-inosine (A-to-I) RNA editing in selected transcripts. Although promising, existing RNA-editing tools generally suffer from a trade-off between efficacy and specificity, and off-target editing remains an unsolved problem. Here we describe the development of an optimized RNA-editing platform by rational protein engineering, CasRx-based Programmable Editing of RNA Technology (xPERT). We demonstrate that the topological rearrangement of a CasRx K940L mutant by circular permutation results in a robust scaffold for the tethering of a deaminase domain. We benchmark our tool against the REPAIR system and show that xPERT exhibits strong on-target activity like REPAIRv1 but low off-target editing like REPAIRv2. Our xPERT platform can be used to alter RNA sequence information without risking genome damage, effect temporary cellular changes and customize protein function.