Reprogramming tumor-associated macrophages: The role of MEK-STAT3 inhibition in lung cancer

Tumor-associated macrophages (TAMs) crucially contribute to lung cancer's advancement and escape from the immune system. TAMs, particularly the M2 phenotype, promote an immunosuppressive microenvironment, facilitating tumor growth and metastasis. The MEK-STAT3 signalling pathway is a critical mediator in this process, driving TAM reprogramming and contributing to lung cancer's resistance to treatment. Inhibiting the MEK and STAT3 pathways disrupts key cancer-promoting mechanisms, including immune evasion, angiogenesis, and metastasis. Preclinical studies have demonstrated the effectiveness of MEK inhibitors, such as trametinib and selumetinib, in synergistic therapies for NSCLC, particularly in modulating the tumor microenvironment. We analyse the present understanding of approaches that can transform TAMs via the inhibition of MEK-STAT3 with either solo or combined treatments in lung cancer therapy.

IGF2BP2 orchestrates global expression and alternative splicing profiles associated with glioblastoma development in U251 cells

Glioblastoma (GBM) is a highly invasive and malignant central nervous system tumor with a median survival duration of 15 months despite multimodal therapy. The insulin-like growth factor 2 mRNA binding protein 2 (IGF2BP2) has been implicated in various cancers and is known to regulate RNA metabolism and alternative splicing (AS). However, its role in GBM remains unclear. Overexpression of IGF2BP2 led to significant alterations in gene expression, with 472 genes upregulated and 99 downregulated. Gene ontology (GO) analysis indicated enrichment in immune-related biological processes. Notably, IGF2BP2 was found to regulate AS events, with 1372 regulated AS genes (RASGs) and 2096 significantly distinct ASEs identified. Furthermore, IGF2BP2 selectively bound to 3' and 5' untranslated regions (UTRs) via GG[AU]C motifs, and IFIH1 was identified as a direct binding partner and upregulated gene upon IGF2BP2 overexpression. Functional enrichment analysis suggested that IGF2BP2 influences pathways related to RNA splicing and immune responses. Our findings demonstrate that IGF2BP2 plays a crucial role in GBM by modulating the transcriptome and AS events. The upregulation of immune-related genes and the regulation of AS by IGF2BP2 highlight its potential as a therapeutic target in GBM, particularly for immunotherapy. The study provides a foundation for further investigation into the molecular mechanisms of IGF2BP2 in GBM and its implications for cancer treatment.

Evaluation of the Chetomin effect on histopathological features in a murine acute spinal cord injury model

Background

Several research studies have been focused on improving the treatment and prognosis of acute spinal cord injury, as part of this initiative we investigated the use of Chetomin to reduce the inflammatory response in this pathology.

Methods

An experimental, prospective, cross-sectional study was performed using 42 Wistar rats where we analyzed the effect of Chetomin compared to methylprednisolone administered 1 and 8 h after the spinal cord injury in a murine model.

Results

Chetomin administration 8h post-injury decreased IL-6 and VEGF expression; and, and its administration 1h post-injury decreased NF-kB expression.

Conclusions

Chetomin has anti-inflammatory effects in acute spinal cord injury, whether these effects are observable with other proinflammatory markers should be investigated.

Overexpression of FBP1 enhances dendritic cell activation and maturation by inhibiting glycolysis and promoting the secretion of IL33 in lung adenocarcinoma

Fructose 1,6-diphosphatase 1 (FBP1) is an enzyme involved in gluconeogenesis and glycolysis inhibition. Dendritic cells (DCs) are antigen-presenting cells, and antigens presented to T cells activate the immune response. FBP1 inhibits the development of several tumors, and high FBP1 expression inhibits the proliferation, migration, and invasion of lung cancer cells. However, the mechanism through which FBP1 mediates the tumor immune microenvironment is unclear. This study mainly analyzed the role of FBP1 in regulating the function of DCs through metabolic reprogramming and immune microenvironment using in vitro and in vivo experiments. The positive association of FBP1 with DCs was found by bioinformatic analysis. The in vitro experiments revealed that the extracellular acidification rate and lactate level were lower in the FBP1 overexpression cells than in the control cells and that the lower lactate level reduced the inhibition of DC function. In addition, high FBP1 expression promoted the secretion of IL33 by activating the cGAS/STING/NF-κB/IL33 pathway, which was identified and verified via high-throughput sequencing and in vitro experiments. FBP1 activated the cGAS/STING pathway by increasing the degree of DNA damage, as revealed by the level of γH2AX and comet assay. IL33 enhanced the expression of the DC costimulatory molecules CD86 and HLA-DR as well as that of the functional factor IL-1β. The results demonstrated that FBP1 promoted the activation and maturation of DCs by inhibiting glycolysis and promoting the secretion of IL33 as well as by further activating the function of CD8+T cells. Finally, the humanized immune system mouse models confirmed the above role of FBP1. Thus, FBP1 may serve as a new target to cure lung adenocarcinoma, and IL33 may improve the efficiency of immune therapy in lung adenocarcinoma.

Post-translational modifications in drug resistance

Resistance to antitumor drugs, antimicrobial drugs, and antiviral drugs severely limits treatment effectiveness and cure rate of diseases. Protein post-translational modifications (PTMs) represented by glycosylation, ubiquitination, SUMOylation, acetylation, phosphorylation, palmitoylation, and lactylation are closely related to drug resistance. PTMs are typically achieved by adding sugar chains (glycosylation), small proteins (ubiquitination), lipids (palmitoylation), or functional groups (lactylation) to amino acid residues. These covalent additions are usually the results of signaling cascades and could be reversible, with the triggering mechanisms depending on the type of modifications. PTMs are involved in antitumor drug resistance, not only as inducers of drug resistance but also as targets for reversing drug resistance. Bacteria exhibit multiple PTMs-mediated antimicrobial drug resistance. PTMs allow viral proteins and host cell proteins to form complex interaction networks, inducing complex antiviral drug resistance. This review summarizes the important roles of PTMs in drug resistance, providing new ideas for exploring drug resistance mechanisms, developing new drug targets, and guiding treatment plans.

Chromosomal instability as a driver of cancer progression

Chromosomal instability (CIN) refers to an increased propensity of cells to acquire structural and numerical chromosomal abnormalities during cell division, which contributes to tumour genetic heterogeneity. CIN has long been recognized as a hallmark of cancer, and evidence over the past decade has strongly linked CIN to tumour evolution, metastasis, immune evasion and treatment resistance. Until recently, the mechanisms by which CIN propels cancer progression have remained elusive. Beyond the generation of genomic copy number heterogeneity, recent work has unveiled additional tumour-promoting consequences of abnormal chromosome segregation. These mechanisms include complex chromosomal rearrangements, epigenetic reprogramming and the induction of cancer cell-intrinsic inflammation, emphasizing the multifaceted role of CIN in cancer.

MYBBP1A‑mediated IGFBP4 promoter methylation promotes epithelial‑mesenchymal transition and metastasis through activation of NOTCH pathway in liver cancer

Metastatic hepatocellular carcinoma (HCC) seriously threatens patients' prognosis. It was previously suggested that the insulin growth factor binding protein (IGFBP) family could serve as cancer suppressors in the development and metastasis of HCC. However, the role of IGFBP4 and its underlying molecular mechanism in HCC metastasis is elusive. In the present study, it was found that IGFBP4 is significantly downregulated in HCC, whose expression is positively correlated with the prognosis of patients with HCC. Overexpression of IGFBP4 restrained migration abilities and cancer metastasis of HCC cells both in vitro and in vivo. Furthermore, it was found that IGFBP4 represses HCC metastasis by inhibiting epithelial‑mesenchymal transition. Molecular mechanism studies showed that overexpression of IGFBP4 obviously suppresses NOTCH1 signaling in HCC. As for the upstream regulatory mechanism, it was revealed that downregulation of IGFBP4 in HCC was caused by CpG islands' hyper‑methylation‑dependent degradation mediated by MYBBP1A. Inhibition of MYBBP1A limited HCC metastatic ability and silence of IGFBP4 at the same time restored HCC metastatic potentials. Clinical data demonstrated that low expression of IGFBP4 was found in patients with HCC, especially with lymphatic metastasis. High MYBBP1A expression and low IGFBP4 expression in HCC were correlated with poor survival of patients with HCC. Summarily, in the present study, it was revealed that MYBBP1A/IGFBP4/NOTCH1 pathway could play a crucial role in the progression and metastasis of HCC, which stimulates novel therapeutic and diagnostic strategies against metastatic HCC.

Vaccinia virus-mediated oncolytic immunotherapy: Emerging strategies for gastrointestinal cancer treatment at dawn

Oncolytic vaccinia virus (VVs) based immunotherapy is a rapidly developing treatment for gastrointestinal (GI) cancers. Conventional treatments, such as chemotherapy, radiotherapy and surgery achieve good effects in early-stage GI cancers, but effects are limited in advanced disease. Immunotherapy has limited efficacy in GI cancers due to tumor heterogeneity and complex immunosuppressive mechanisms. Oncolytic VV immunotherapy is a novel treatment approach showing promising results in preclinical and clinical trials. Oncolytic VV's intracytoplasmic replication and assembly mechanism, diverse mature forms, and use methods make it extremely safe and versatile for drug delivery. Combining oncolytic VV with conventional therapies and immunotherapy (e.g., ICIs, CAR-T) enhances tumor regression and survival compared to monotherapies. Researchers are establishing response protocols and improvement strategies, rapidly developing VV tumor oncolytic immunotherapy. This article focuses on oncolytic vaccinia development and outlook in gastrointestinal cancer therapy, advantages when combined with other drugs to improve clinical survival, safety, and risk reduction for patients.

High-fat/high-sucrose diet results in a high rate of MASH with HCC in a mouse model of human-like bile acid composition

BACKGROUND

Wild-type (WT) mice fed a conventional high-fat/high-sucrose diet (HFHSD) rarely develop metabolic dysfunction-associated steatohepatitis (MASH) with HCC. Because mouse bile acid (BA) is highly hydrophilic, we hypothesized that making it hydrophobic would lead to MASH with HCC.

METHODS

Eleven-week-old WT and Cyp2a12/Cyp2c70 double knockout (DKO) mice were divided into two groups, including one which was fed a normal chow diet, and one which was fed an HFHSD. Samples were collected after 15, 30, 47, and 58 weeks for histological, biochemical, and immunological analyses.

RESULTS

In the HFHSD group, body weight gain did not differ in WT versus DKO mice, although HFHSD-fed DKO mice exhibited markedly accelerated liver inflammation, fibrosis, and carcinogenesis. HFHSD upregulated lipogenesis and downregulated fatty acid oxidation in both WT and DKO mice, which increased liver lipid accumulation and lipotoxicity. However, the increase in reactive oxygen species production and carcinogenesis observed in DKO mice could not be explained by abnormal lipid metabolism alone. Regarding BA metabolism, DKO mice had a higher hydrophobicity index. They exhibited an age-associated increase in chenodeoxycholic acid (CDCA) levels because of CYP8B1 activity inhibition due to the farnesoid X receptor activation. HFHSD further downregulated CYP8B1, presumably by activating the Liver X receptor. Liver CDCA accumulation was associated with increased inflammation, reactive oxygen species production, and hepatocyte FGF15 induction. Moreover, in noncancerous liver tissues, HFHSD appeared to activate STAT3, an oncogenic transcription factor, which was enhanced by a CDCA-rich environment.

CONCLUSIONS

Here, we developed a new model of MASH with HCC using mice with human-like BA composition and found that HFHSD and elevated hepatic CDCA synergistically increased the risk of MASH with HCC.

Diverse functions of DEAD-box proteins in oligodendrocyte development, differentiation, and homeostasis

Oligodendrocytes, a type of glial cell in the central nervous system, have a critical role in the formation of myelin around axons, facilitating saltatory conduction, and maintaining the integrity of nerve axons. The dysregulation of oligodendrocyte differentiation and homeostasis have been implicated in a wide range of neurological diseases, including dysmyelinating disorders (e.g., Pelizaeus-Merzbacher disease), demyelinating diseases (e.g., multiple sclerosis), Alzheimer's disease, and psychiatric disorders. Therefore, unraveling the mechanisms of oligodendrocyte development, differentiation, and homeostasis is essential for understanding the pathogenesis of these diseases and the development of therapeutic interventions. Numerous studies have identified and analyzed the functions of transcription factors, RNA metabolic factors, translation control factors, and intracellular and extracellular signals involved in the series of processes from oligodendrocyte fate determination to terminal differentiation. DEAD-box proteins, multifunctional RNA helicases that regulate various intracellular processes, including transcription, RNA processing, and translation, are increasingly recognized for their diverse roles in various aspects of oligodendrocyte development, differentiation, and maintenance of homeostasis. This review introduces the latest insights into the regulatory networks of oligodendrocyte biology mediated by DEAD-box proteins.

Early separation and parallel clonal selection of dedifferentiated and well-differentiated components in dedifferentiated liposarcoma

Dedifferentiated liposarcoma (DDLPS) comprises a high-grade dedifferentiated (DD) component and a juxtaposed well-differentiated (WD) component. The DD component is believed to originate from the WD component by acquiring additional genomic alterations. In this study, we performed multiregion genome, epigenome, and transcriptome analyses of three patients with DDLPS. In two patients, there were few common genomic alterations across all samples, but many common alterations within DD or WD component samples. Phylogenetic trees predicted from the genomic alterations were consistent with those predicted from DNA methylation patterns. The expression patterns of adipogenesis-related genes differed between DD and WD components and also among patients in connection with their CpG island methylation status. These results indicate that in some patients, WD and DD components are evolutionarily separated at very early stages of tumorigenesis, and are formed through relatively long clonal selection with acquisition of different driver genomic alterations and DNA methylation changes.

Depletion of β1,6-N-acetylglucosaminyltransferase reduces E-selectin binding capacity and migratory potential of human gastrointestinal adenocarcinoma cells

The commonly altered glycosylation of tumor cells is a hallmark of tumor progression and metastasis formation. One prominent example is the interaction of sialylated glycans at the tumor cell surface with endothelial (E)-selectin as an early event of an adhesion cascade that enables extravasation of circulating tumor cells (CTCs) into distant tissues. In a previous study, we identified GCNT3 (mucin-type core2/ core4 β1,6-N-acetylglucosaminyltransferase) highly over-expressed in gastrointestinal adenocarcinoma cells that facilitate the canonical E-selectin ligands sialyl-Lewis A and X (sLeA/X) for E-selectin binding and endothelial adhesion. Here we show that shRNA-mediated, stable depletion of GCNT3 reduced sLeA (tumor marker CA19-9) presentation on two out of three tested human gastrointestinal adenocarcinoma cell lines, concurrently showing reduced static E-selectin binding. Significant effects of GCNT3 depletion on dynamic, shear-resistant tumor cell adhesion on immobilized E-selectin as well as endothelial cells were only partially and inconsistently observable as were effects on tumor cell proliferation (2D) or 3D colony formation. Nevertheless, tumor cell migration was consistently reduced upon GCNT3 depletion in all tested cell lines. Detailed glycome analyses revealed that GCNT3 depletion caused cell line-specific alterations in N- and O-glycans as well as glycosphingolipids, collectively mainly associating with decreased Core-2 structures resulting in varied abundance of sialylation and Lewis antigen with consistent phenotypic changes. Distinctive N- and O-glycosylation features were found to be inherent to specific cell types. These findings suggest GCNT3 products as possible carriers of sLeA and static E-selectin binding sites as well as common pro-migratory glycans in human gastrointestinal cancer.

The role of oligodendrocyte progenitor cells in the spatiotemporal vascularization of the human and mouse neocortex

Brain vasculature formation begins with vessel invasion from the perineural vascular plexus, which expands through vessel sprouting and growth. Recent studies have indicated the existence of oligodendrocyte-vascular crosstalk during development. However, the relationship between oligodendrocyte progenitor cells (OPCs) and the ordered spatiotemporal vascularization of the neocortex has not been elucidated. Our findings suggest that OPCs play a complex role in the vessel density of the embryonic and postnatal neocortex. Analyses of normal human and mouse embryonic cerebral cortex show that vascularization and OPC distribution are tightly controlled in a spatially and temporally restricted manner, exhibiting a positive correlation. Loss of OPCs at both embryonic and postnatal stages led to a reduction in vascular density, suggesting that OPC populations play a role in vascular density. Nonetheless, dynamic observation on cultured brain slices and staining of tissue sections indicate that OPC migration is unassociated with the proximity to blood vessels, primarily occurring along radial glial cell processes. Additionally, in vitro experiments demonstrate that OPC secretions promote vascular endothelial cell (VEC) growth. Together, these observations suggest that vessel density is influenced by OPC secretions.

Inducing Cellular Senescence in Mouse Embryonic Fibroblasts (MEFs)

Inducing cellular senescence in mouse embryonic fibroblasts (MEFs) is a robust tool to study the molecular mechanisms underlying senescence establishment and their heterogeneity. This protocol provides a detailed guide to generate MEFs and routinely induce senescence in MEFs using several DNA damage-dependent and DNA damage-independent induction methods.

Direct visualization of emergent metastatic features within an ex vivo model of the tumor microenvironment

Ischemic conditions such as hypoxia and nutrient starvation, together with interactions with stromal cells, are critical drivers of metastasis. These conditions arise deep within tumor tissues, and thus, observing nascent metastases is exceedingly challenging. We thus developed the 3MIC-an ex vivo model of the tumor microenvironment-to study the emergence of metastatic features in tumor cells in a 3-dimensional (3D) context. Here, tumor cells spontaneously create ischemic-like conditions, allowing us to study how tumor spheroids migrate, invade, and interact with stromal cells under different metabolic conditions. Consistent with previous data, we show that ischemia increases cell migration and invasion, but the 3MIC allowed us to directly observe and perturb cells while they acquire these pro-metastatic features. Interestingly, our results indicate that medium acidification is one of the strongest pro-metastatic cues and also illustrate using the 3MIC to test anti-metastatic drugs on cells experiencing different metabolic conditions. Overall, the 3MIC can help dissecting the complexity of the tumor microenvironment for the direct observation and perturbation of tumor cells during the early metastatic process.

NUAKs promote mTOR/c-Myc-induced glucose and glutamine reprogramming for cell growth and metastasis in breast cancer cells

Breast cancer progression and metastasis are closely connected to changes in glucose and glutamine metabolism. While Novel (nua) kinase family 1 (NUAK1) and Novel (nua) kinase family 2 (NUAK2), which are two members of the AMPK-related kinases, have been associated with breast tumorigenesis, their role in the metabolic reprogramming that occurs during breast cancer progression remains unclear. Our research uncovers that NUAKs expression is significantly higher in breast cancer tissues and cell lines, and it is positively related to glycolysis, the pentose phosphate pathway (PPP), glutamine metabolism, and a poor prognosis for breast cancer patients. We show that NUAKs significantly increase metabolic reprogramming, including aerobic glycolysis, PPP, and glutamine metabolism in triple negative breast cancer subtypes but only induce aerobic glycolysis and PPP in luminal breast cancer subtypes to meet the anabolic demands of rapidly dividing breast cancer cells. In contrast, the depletion of NUAKs has the opposite effect. Mechanistic insights reveal that NUAKs activate mammalian target of rapamycin (mTOR) signaling, which in turn upregulates the c-Myc transcription factor, a crucial regulator of glucose and glutamine metabolic gene expression. Moreover, we demonstrate that NUAKs enhance mTOR/c-Myc signaling pathways, leading to increased glucose and glutamine reprogramming, which supports rapid cell proliferation and metastatic potential in breast cancer cells. Importantly, pretreating breast cancer cells with mTOR inhibitors blocked the metabolic reprogramming and tumor-promoting effect of NUAK1/2. Therefore, targeting NUAKs may represent a novel therapeutic strategy for the treatment of breast cancer.

GPR68 supports AML cells through the calcium/calcineurin pro-survival pathway and confers chemoresistance by mediating glucose metabolic symbiosis

Accumulating evidence demonstrates that the "Warburg effect" that glycolysis is enhanced even in the presence of oxygen existed in hematopoietic malignancies, contributing to extracellular acidosis. G-protein coupled receptor 68 (GPR68), as a proton sensing GPCR responding to extracellular acidosis, is expected to play a critical role in hematopoietic malignancies. In the present study, we found that GPR68 was overexpressed in acute myeloid leukemia (AML) cells, and GPR68 deficiency impaired AML cell survival in vitro and cell engraftment in vivo. Mechanistic studies revealed that unlike GPR68 regulates Calpain1 in myelodysplastic syndromes (MDS) cells, GPR68 deficiency reduced cytosolic Ca2+ levels and calcineurin (CaN) activity in AML cells through an NFAT-independent mechanism. Moreover, the decreased Ca2+ levels disturbed cellular respiration (i.e., oxidative phosphorylation, OxPhos) by inhibiting isocitrate dehydrogenase (IDH) activity; this was more pronounced when BCL2 was inhibited simultaneously. Interestingly, GPR68 inhibition also decreased aerobic glycolysis in AML cells in a Ca2+-independent manner, suggesting that GPR68 mediated glucose metabolic symbiosis. As glucose metabolic symbiosis and the heterogeneous dependencies on aerobic glycolysis and cellular respiration tremendously impact chemosensitivity, the inhibition of GPR68 potentiated the tumoricidal effect of first-line chemotherapeutic agents, including BCL-2 inhibitors targeting OxPhos and cytarabine (Ara-C) targeting glycolysis. Consistent with these in vitro observations, higher levels of GPR68 were associated with inferior clinical outcomes in AML patients who received chemotherapies. In short, GPR68 drives the Ca2+/CaN pro-survival pathway and mediates glucose metabolic pathways in AML cells. Targeting GPR68 eradicates AML cells and alleviates chemoresistance, which could be exploited as a therapeutic target.

Metabolomics and proteomics reveal the inhibitory effect of Lactobacillus crispatus on cervical cancer

Cervical cancer remains a significant global health issue due to its high morbidity and mortality rates. Recently, Lactobacillus crispatus has been recognized for its crucial role in maintaining cervical health. While some studies have explored the use of L. crispatus to mitigate cervical cancer, the underlying mechanisms remain largely unknown. In this study, we employed non-targeted proteomics and metabolomics to investigate how L. crispatus affects the growth of cervical cancer cells (SiHa) and normal cervical cells (Ect1/E6E7). Our findings indicated that the inhibitory effect of L. crispatus on SiHa cells was associated with various biological processes, notably the ferroptosis pathway. Specifically, L. crispatus was found to regulate the expression of proteins such as HMOX1, SLC39A14, VDAC2, ACSL4, and LPCAT3 by SiHa cells, which are closely related to ferroptosis. Additionally, it activated the tricarboxylic acid (TCA) cycle in SiHa cells, leading to increased levels of reactive oxygen species (ROS) and lipid peroxides (LPO). These results revealed the therapeutic potential of L. crispatus in targeting the ferroptosis pathway for cervical cancer treatment, opening new avenues for research and therapy in cervical cancer.

Expression, molecular mechanisms and therapeutic potentials of ATF1 in cancers

Activating transcription factor 1 (ATF1) is a crucial cellular regulator, with its misregulation implicated in numerous cancers. As a key player in the ATF/CREB family, ATF1 modulates gene expression in response to extracellular signals, significantly impacting cancer progression. This review examines ATF1's structural features, its role in tumorigenesis, and its potential therapeutic applications. Data from various databases consistently show ATF1 overexpression in diverse cancers, associated with poor prognosis and aggressive phenotypes. The review explores ATF1's complex regulatory mechanisms, influencing cell proliferation, apoptosis, migration, invasion, and therapeutic resistance, and its interactions with regulatory networks. Emerging strategies targeting ATF1, such as engineered antibodies, natural compounds, and small molecule inhibitors, show efficacy in preclinical models. ATF1 may also act as a biomarker for personalized therapeutic response and resistance. Future research should focus on ATF1's role in the tumor microenvironment and its interaction with the immune system, potentially leading to new immunotherapeutic strategies. A deeper understanding of ATF1 could enhance cancer treatment and patient outcomes.

Histone-acetyl epigenome regulates TGF-β pathway-associated chemoresistance in colorectal cancer

TGF-β signaling pathway has been demonstrated to be closely related to chemoresistance, which is the major cause of recurrence and poor outcome in colorectal cancer (CRC), however, the comprehensive epigenetic landscape that functionally implicates in the regulation of TGF-β pathway-associated chemoresistance has not yet well established in CRC. In our study, chromatin immunoprecipitation sequencing (ChIP-seq) and Western blot were employed to investigate epigenetic modifications for histones in response to TGF-β1 intervene. We found that the activation of the TGF-β pathway was characterized by genome-wide high levels of H3K9ac and H3K18ac. Mechanistically, the activation of the TGF-β signaling pathway leads to the downregulation of the deacetylase HDAC4, resulting in the upregulation of H3K9ac and H3K18ac. Consequently, this cascade induces oxaliplatin chemoresistance in CRC by triggering the anti-apoptotic PI3K/AKT signaling pathway. Our in vivo experiment results confirmed that overexpression of HDAC4 significantly enhances the sensitivity of CRC to oxaliplatin chemotherapy. Moreover, the expression level of HDAC4 was positively correlated with patients' prognosis in CRC. Our data suggest that histone-acetyl modification demonstrates a crucial role in modulating TGF-β pathway-associated chemoresistance in CRC, and HDAC4 would be a biomarker for prognostic prediction and potential therapeutic target for treatment in CRC.

Beyond ATP: Metabolite Networks as Regulators of Physiological and Pathological Erythroid Differentiation

Hematopoietic stem cells (HSCs) possess the capacity for self-renewal and the sustained production of all mature blood cell lineages. It has been well established that a metabolic rewiring controls the switch of HSCs from a self-renewal state to a more differentiated state, but it is only recently that we have appreciated the importance of metabolic pathways in regulating the commitment of progenitors to distinct hematopoietic lineages. In the context of erythroid differentiation, an extensive network of metabolites, including amino acids, sugars, nucleotides, fatty acids, vitamins, and iron, is required for red blood cell (RBC) maturation. In this review, we highlight the multifaceted roles via which metabolites regulate physiological erythropoiesis as well as the effects of metabolic perturbations on erythroid lineage commitment and differentiation. Of note, the erythroid differentiation process is associated with an exceptional breadth of solute carrier (SLC) metabolite transporter upregulation. Finally, we discuss how recent research, revealing the critical impact of metabolic reprogramming in diseases of disordered and ineffective erythropoiesis, has created opportunities for the development of novel metabolic-centered therapeutic strategies.

Identification of cancer-associated fibrolast subtypes and distinctive role of MFAP5 in CT-detected extramural venous invasion in gastric cancer

Extramural venous invasion (EMVI) detected by computed tomography has been identified as an independent risk factor for distant metastasis in patients with advanced gastric cancer (GC). Cancer-associated fibroblasts (CAFs) are critical for remodeling the tumor microenvironment in GCs. Here, we report that MFAP5+ CAFs promote the formation of EMVI imaging in GC. We detected gene expression in pathological samples from 13 advanced GC patients with EMVI. Radiogenomics results showed the degree of CAFs infiltration was directly proportional to the EMVI score and EMT pathway in GC patients. Single-cell sequencing data analysis results showed that MFAP5+CAFs subtypes in GC were negatively correlated with patient prognosis and were enriched in tumor lactylation modification and EMT pathways. Immunohistochemistry results showed that the expression of MFAP5, L-lactyl and EMT markers in GC tissues was proportional to the EMVI score. CAF from gastric cancer tissue was extracted using collagenase method and co-cultured with GC cell line in vitro. After lentivirus knockdown of MFAP5 in CAFs, the levels of L-lactoyl and histone lactylation modifications were significantly reduced, and the sphere-forming and vascularization abilities of CAFs were significantly inhibited. Cell function experiments showed that MFAP5+ CAFs can affect the EMT, metastasis and invasion capabilities of GC cells. In vivo experimental results of the nude mouse in situ EMVI model suggest that MFAP5+ CAF may promote the formation of EMVI imaging features in GC by regulating lactylation modification. This innovative work may provide important new references for the diagnosis and treatment of GC.

Methionine restriction promotes the polarization of macrophages towards M1 and the immunotherapy effect of PD-L1/PD-1 blockades by inhibiting the secretion of MIF by gastric carcinoma cells

BACKGROUND

The limited curative effect of PD-L1/PD-1 blockades presents challenges to immunotherapy for advanced gastric cancer. We have found that methionine restriction (MR) enhances the drug resistance of gastric carcinoma cells. We aimed to explore whether MR can enhance the efficacy of PD-L1/PD-1 blockades in gastric cancer.

METHODS

To conduct MR, gastric carcinoma cells were transfected with LV-METase in vitro, and 615 mice were injected with MFC cells with stable METase expression in vivo. Flow cytometry was conducted to measure the proportions of M1/M2 macrophages and CD8+ GZMB+/IFN-γ+ T cells. Additionally, the levels of M1/M2 macrophage markers and MIF were also detected.

RESULTS

MR increased M1 and down-regulated M2 macrophages. MR suppressed MIF levels in gastric carcinoma cells, while the addition of anti-MIF neutralizing antibody inhibited the effect of MR on macrophage M1/M2 polarization. MR enhanced the increase of the proportion of CD8+ GZMB+ T cells and CD8+ IFN-γ+ T cells induced by PD-L1/PD-1 blockades. In vivo detection verified the efficacy of the combination of MR and PD-L1/PD-1 blockades on gastric cancer.

CONCLUSIONS

MR inhibits the secretion of MIF by gastric carcinoma cells, promotes macrophage M1 polarization, and enhances the therapeutic effect of PD-L1/PD-1 blockades in gastric cancer.

Expression of MYD88 L265P Mutation in Subtypes of Diffuse Large B-Cell Lymphoma in the Pakistani Population

MYD88 L265P mutation is a gain-of-function driver mutation. It is observed in a significant proportion of Waldenstrom macroglobulinemia and activated B-cell subtype of diffuse large B-cell lymphoma (DLBCL; non-germinal center subtype). The incidence of this mutation in the subtypes of DLBCL has not yet been documented in the Pakistani population. This study aimed to ascertain the frequency and association of MYD88 L265P mutation within 2 subtypes of DLBCL, germinal center B-cell-like (GCB) and non-GCB B-cell lymphoma (non-GCB), in the local population. This cross-sectional study was conducted at the Armed Forces Institute of Pathology, Punjab, Pakistan. All newly diagnosed cases of DLBCL were included in the study. We analyzed 82 biopsy-proven cases of DLBCL (28 cases of GCB subtype and 54 cases of non-GCB subtype). DNA was extracted from formalin-fixed paraffin-embedded tissue blocks, and a conventional polymerase chain reaction was used to detect the MYD88 L265P mutation. The MYD88 L265P mutation was detected in 01 of 28 (3.6%) cases of the GCB subtype (95% CI: 0%-10%) and in 12 of 54 (22.2%) cases of the non-GCB subtype (95% CI: 11%-33%). Pearsos χ2 test revealed a statistically significant association of MYD88 L265P mutation with non-GCB subtype of DLBCL (P = 0.024). This association will assist in identifying a target population that may benefit from MYD88-specific treatment regimens. This may exponentially improve the outcome of patients with DLBCL harboring this mutation.

Biohybrid nano-platforms manifesting effective cancer therapy: Fabrication, characterization, challenges and clinical perspective

Nanotechnology-based delivery systems have brought a paradigm shift in the management of cancer. However, the main obstacles to nanocarrier-based delivery are their limited circulation duration, excessive immune clearance, inefficiency in interacting effectively in a biological context and overcoming biological barriers. This demands effective engineering of nanocarriers to achieve maximum efficacy. Nanocarriers can be maneuvered with biological components to acquire biological identity for further regulating their biodistribution and cell-to-cell cross-talk. Thus, the integration of synthetic and biological components to deliver therapeutic cargo is called a biohybrid delivery system. These delivery systems possess the advantage of synthetic nanocarriers, such as high drug loading, engineerable surface, reproducibility, adequate communication and immune evasion ability of biological constituents. The biohybrid delivery vectors offer an excellent opportunity to harness the synergistic properties of the best entities of the two worlds for improved therapeutic outputs. The major spotlights of this review are different biological components, synthetic counterparts of biohybrid nanocarriers, recent advances in hybridization techniques, and the design of biohybrid delivery systems for cancer therapy. Moreover, this review provides an overview of biohybrid systems with therapeutic and diagnostic applications. In a nutshell, this article summarizes the advantages and limitations of various biohybrid nano-platforms, their clinical potential and future directions for successful translation in cancer management.

Knockdown of CENPF induces cell cycle arrest and inhibits epithelial‑mesenchymal transition progression in glioma

Gliomas are among the most common malignant tumors of the central nervous system. Despite surgical resection followed by postoperative radiotherapy and chemotherapy, their prognosis remains unfavorable. The present study aimed to assess new mechanisms and explore promising prognostic biomarkers for patients with glioma using comprehensive bioinformatics analysis and in vitro and in vivo assays. Overlapping differentially expressed genes were screened from The Cancer Genome Atlas, GSE111260 and GSE16011 samples for protein-protein interaction networks, a risk score model, gene mutation analysis and a nomogram to identify the prognostic hub genes. Subsequently, an immunoassay was performed to determine key genes. Functional and animal assays were then performed to assess the tumorigenesis of the key genes in glioma. Using bioinformatics analysis, centromere protein F (CENPF), kinesin superfamily member 20A, kinesin superfamily protein 4A and marker of proliferation Ki-67 were identified as potential prognostic biomarkers for patients with glioma. Furthermore, CENPF knockdown was demonstrated to suppress the proliferation and metastasis of glioma cells, and induce G2 arrest in the cell cycle. Moreover, CENPF knockdown was revealed to decrease Vimentin and increase E-cadherin levels in glioma cells, and significantly reduce the size and mass of tumors in vivo. Overall, the present study identified new clinical biomarkers and revealed that CENPF may promote glioma progression by regulating the epithelial-mesenchymal transition pathway. By elucidating the complexities of glioma and identifying prognostic biomarkers, the present research enables further improvement of patient outcomes and the advancement of precision medicine for this disease.

Immunogenic clearance combined with PD-1 blockade elicits antitumor effect by promoting the recruitment and expansion of the effector memory-like CD8+T cell

Immune checkpoint inhibition shows promise for cancer treatment, but only a minority of patients respond. Combination strategies have been explored to overcome this resistance. Combining immunogenic clearance using immunogenic cell death inducers with a rho kinase inhibitor enhances phagocytosis of immunogenically dying cancer cells by antigen-presenting cells, stimulating tumor-specific immune responses by activating CD8+T cells via dendritic cell-mediated priming. This approach increases the responsiveness of immune checkpoint blockade (ICB)-resistant cancer to ICB. However, the precise mechanisms remain unclear. This study elucidates cellular mechanisms of immunogenic clearance enhancing ICB response. Using single-cell RNA sequencing, we observed an increase in effector memory-like CD8+T cells within the tumor microenvironment with combined treatment. We propose this cell cluster may originate from proliferating CD8+T cells elevated by immunogenic clearance. Notably, abundant effector memory-like CD8+T cells in ICB-responsive patients suggest their antitumor effect. Thus, increasing this cell population through enhanced T cell priming may improve the response of ICB-resistant tumors.

Machine learning-derived prognostic signature for progression-free survival in non-metastatic nasopharyngeal carcinoma

BACKGROUND

Early detection of high-risk nasopharyngeal carcinoma (NPC) recurrence is essential. We created a machine learning-derived prognostic signature (MLDPS) by combining three machine learning (ML) models to predict progression-free survival (PFS) in patients with non-metastatic NPC.

METHODS

A cohort of 653 patients with non-metastatic NPC was divided into a training (n = 457) and validation (n = 196) dataset (7:3 ratio). The study included clinicopathological characteristics, hematologic markers, and MRI findings in three machine learning models-random forest (RF), extreme gradient boosting (XGBoost), and least absolute shrinkage and selection operator (LASSO)-to predict progression-free survival (PFS). A Venn diagram identified the overlapping signatures from the three ML algorithms. Cox proportional hazard analysis determined the MLDPS for PFS.

RESULTS

The RF, XGBoost, and LASSO algorithms identified six consensus factors from the 33 signatures. Cox proportional hazards analysis showed that the MLDPS includes age, lymphocyte count, number of positive lymph nodes, and regional lymph node density. Additionally, MLDPS effectively stratified prognosis, with low-risk individuals showing better PFS than high-risk individuals (p < 0.001).

CONCLUSION

MLDPS, based on clinicopathological characteristics, hematologic markers, and MRI findings, is crucial for guiding clinical management and personalizing treatments for patients with non-metastatic NPC.

Mechanisms of RNA Polymerase II Termination at the 3'-End of Genes

RNA polymerase II (RNAPII) is responsible for the synthesis of a diverse set of RNA molecules, including protein-coding messenger RNAs (mRNAs) and many short non-coding RNAs (ncRNAs). For this purpose, RNAPII relies on a multitude of factors that regulate the transcription cycle, from initiation and promoter-proximal pausing, through elongation and finally termination. RNAPII transcription termination at the end of genes ensures the release of RNAPII from the DNA template and its efficient recycling for further rounds of transcription. Termination of RNAPII is tightly coupled to 3'-end mRNA processing, which constitutes an important trigger for the subsequent transcription termination event. In this review, we discuss the current understanding of RNAPII termination mechanisms, focusing on 'canonical' termination at the 3'-end of genes. We also integrate the allosteric and 'torpedo' models into a unified model of termination, and describe the different termination factors that have been identified to date, paying special attention to the human factors and their mechanism of action at the molecular level. Indeed, in recent years the development of novel approaches in structural biology, biochemistry and cell biology have together led to a more detailed comprehension of the different mechanisms of RNAPII termination, and a better understanding of their importance in regulating gene expression, especially under cellular stress and pathological situations.

EML4-ALK G1202R and EML4-ALK L1196M mutations induce crizotinib resistance in non-small cell lung cancer cells through activating epithelial-mesenchymal transition mediated by MDM2/MEK/ERK signal axis

Crizotinib, as the first-generation of anaplastic lymphoma kinase (ALK) inhibitor, effectively improves the survival time of ALK-positive non-small cell lung cancer (NSCLC) patients. However, its efficacy is severely limited by drug resistance caused by secondary mutations. G1202R and L1196M are classical mutation sites located in ALK kinase domain. They may hinder the binding of ALK inhibitors to the target kinase domain, resulting in drug resistance in patients. However, the exact mechanism of drug resistance mediated by these mutations remains unclear. In this study, we aimed to evaluate how G1202R and L1196M mutations mediate crizotinib resistance. To explore the resistance mechanism, we constructed EML4-ALK G1202R and L1196M mutant cell lines with A549 cells. The results showed that the mutant cells exhibited significant epithelial-mesenchymal transition (EMT) and metastasis compared to control (A549-vector) or wild type (A549-EML4-ALK) cells. Subsequently, it was found that the occurrence of EMT was correlated to the high expression of murine double minute 2 (MDM2) protein and the activation of mitogen-activated protein kinase (MEK)/extracellular signal-regulated kinase (ERK) pathway in mutant cells. Down-regulation of MDM2 inhibited the activation of MEK/ERK pathway, thus reversed the EMT process and markedly increased the inhibitory effect of crizotinib on the growth of mutant cells. Collectively, resistance of ALK-positive NSCLC cells to crizotinib is induced by G1202R and L1196M mutations through activation of the MDM2/MEK/ERK signalling axis, promoting EMT process and metastasis. These findings suggest that the combination of MDM2 inhibitors and crizotinib could be a potential therapeutic strategy.

Oncointerpreter.ai enables interactive, personalized summarization of cancer diagnostics data

OBJECTIVES

Cancer diagnosis comes as a shock to many patients, and many of them feel unprepared to handle the complexity of the life-changing event, understand technicalities of the diagnostic reports, and fully engage with the clinical team regarding the personalized clinical decision-making.

MATERIALS AND METHODS

We develop Oncointerpreter.ai an interactive resource to offer personalized summarization of clinical cancer genomic and pathological data, and frame questions or address queries about therapeutic opportunities in near-real time via a graphical interface. It is built on the Mistral-7B and Llama-2 7B large language models trained on a local database trained using a large, curated corpus.

RESULTS

We showcase its utility with case studies, where Oncointerpreter.ai extracted key clinical and molecular attributes from deidentified pathology and clinical genomics reports, summarized their contextual significance and answered queries on pertinent treatment options. Oncointerpreter also provided personalized summary of currently active clinical trials that match the patients' disease status, their selection criteria, and geographic locations. Benchmarking and comparative assessment indicated that the model responses were generally consistent, and hallucination, ie, factually incorrect or nonsensical response was rare; treatment- and outcome related queries led to context-aware responses, and response time correlated with verbosity.

DISCUSSION

The choice of model and domain-specific training also affected the response quality.

CONCLUSION

Oncointerpreter.ai can aid the existing clinical care with interactive, individualized summarization of diagnostics data to promote informed dialogs with the patients with new cancer diagnoses.

AVAILABILITY

https://github.com/Siris2314/Oncointerpreter.

Novel design of potent anti-tumour activity of IL-2 prodrug by FAPα-mediated activation

Interleukin-2 (IL-2) is a T cell growth factor that is essential for the proliferation of T cells and the generation of effector and memory cells. The antitumor activity of high-dose IL-2 therapy requires maintaining the affinity between IL-2 and IL2-Rα, which can also bring serious toxic side effects. To address this issue, we designed ZGP-Cysteamine-IL-2-K64C and (ZGP-Cysteamine)2-IL-2-(K43C, K64C) based on the strategy of FAPα enzyme-activated prodrugs, and investigated their anti-tumour activity and side effects. In vitro FAPα enzyme cleavage results indicated that the side-chain modified ZGP-Cysteamine moiety could be precisely recognized and cleaved by FAPα, thereby restoring the activity of native IL-2 capable of binding to IL-2Rα in the tumour microenvironment, where it promotes the expansion of CD8+ T cells. Meanwhile, surface plasmon resonance analysis revealed that, compared to wt-IL-2, both ZGP-Cysteamine-IL-2-K64C and (ZGP-Cysteamine)2-IL-2-(K43C, K64C) exhibited significantly reduced affinity for IL-2Rα, while their affinity for IL-2Rβγ remained unchanged. Remarkably, ZGP-Cysteamine-IL-2-K64C and (ZGP-Cysteamine)2-IL-2-(K43C, K64C) almost completely eliminated the pulmonary edema and vascular permeability. Furthermore, the combination of ZGP-Cysteamine-IL-2-K64C and PD-1 blockade showed robust anti-tumour activity in mice tumour models. Our study provides new insights into the structural design of IL-2 prodrug with low side effect and robust anti-tumour efficacy.

Nature killer cell for solid tumors: Current obstacles and prospective remedies in NK cell therapy and beyond

In recent years, cell therapy has emerged as an innovative treatment method for the management of clinical tumors following immunotherapy. Among them, Natural killer (NK) cell therapy has achieved a significant breakthrough in the treatment of hematological tumors. However, the therapeutic effectiveness of NK cells in the treatment of solid tumors remains challenging. With the progress of gene editing and culture techniques and their application to NK cell engineering, it is expected that NK cell therapy will revolutionize the treatment of solid tumors. In this review, we explore the discovery and biological properties of NK cells, their role in the tumor microenvironment, and the therapeutic strategies, clinical trials, challenges, and prospects of NK cells in the treatment of solid tumors.

SS18-SSX Expression and Clinicopathologic Profiles in a Contemporary Cohort of Primary Paratesticular Synovial Sarcoma: A Series of Fourteen Patients

Synovial sarcoma (SS) is a rare genitourinary malignancy with a specific SS18::SSX 1/2 gene fusion in majority of the instances. The paratesticular location of this neoplasm is extremely rare and only 4 cases are reported in the literature. Herein, we describe the clinicopathologic features and molecular profile of paratesticular SS in the largest case series to date and to the best of our knowledge, and the only series to use novel SS18-SSX antibody for immunohistochemistry. Clinicopathologic, immunohistochemical (IHC), molecular, treatment, and follow-up data of the patients were analyzed. There were 14 patients, ranging from 15 to 47 years (mean: 30 y). The tumor size ranged from 4​​​​​​ to 15 cm. The tumors were unilateral, solid, and homogeneous tan-white with monomorphic spindle cell histology. All 14 tumors expressed SS18-SSX and TLE1 IHC and harbored SS18 rearrangement. In addition, the tumor with multifocal SS18-SSX expression had lower break-apart signals in the FISH assay (38% of the tumor cells; range: 29% to 85%). Radical orchiectomy was performed in all 14 patients and adjuvant chemotherapy was administered in 9 patients. Follow-up was available in 9 patients. The follow-up duration ranged from 5 to 24 months (median=10 mo). Four patients died of metastatic disease (range: 5 to 16 mo) and 2 patients who are alive had metastatic disease at the last follow-up. Based on our experience with the largest series to date and aggregate of the published data, paratesticular SS has a poor prognosis despite aggressive therapy. Owing to its rarity, the differential diagnosis is wide and requires a systematic approach for ruling out key morphologic mimics aided with SS18-SSX IHC and molecular confirmation because this distinction carries important therapeutic and prognostic implications. Due to the excellent concordance of SS18-SSX IHC results with FISH results as observed in our study, we would like to suggest inclusion of SS18-SSX in the diagnostic immunohistochemistry panel of all spindle cell sarcomas where synovial sarcoma is considered as a morphologic differential. SS18-SSX-positive staining may be used as a surrogate for FISH assay in a resource-limited setting where molecular assay is not available. Furthermore, IHC has a fairly shorter turn-around-time, is less complex, and of low cost.

Lympho-myeloid aggregate-infiltrating CD20+ B cells display a double-negative phenotype and correlate with poor prognosis in esophageal squamous cell carcinoma

According to morphological features, tumor-infiltrating B cells (TIL-Bs) can be classified as lympho-myeloid aggregates (LMAs) and tertiary lymphoid structures (TLSs). As a disease with high incidence and mortality, research on esophageal squamous cell carcinoma (ESCC) TIL-Bs is still unclear. Thus, we aimed to investigate the prognostic value and functional involvement of TIL-Bs in ESCC. Based on CD20 immunohistochemical staining of 147 ESCC samples, the TIL-Bs at different anatomic subregions (intra-tumor (T), invasive margin (IM) and peri-tumor (P)) were quantified and correlated with survival by Kaplan-Meier analyses. We found that LMAs were widely distributed throughout the whole section and were associated with poor prognosis, especially those located in the T subregion, which was contrary to the positive clinical significance of TLSs. Based on the number of LMAs and TLSs, a four-level immune type was constructed as an independent predictor for survival. Using multiplexed immunofluorescence (mIF) staining, we found that the main phenotype of infiltrating B cells in LMAs was CD20+IgD-CD27- double-negative (DN) B cells. DN B cells were abundant in ESCC tumor tissue, and their high expression was related to shortened overall survival time. Subsequently, we demonstrate a close relationship between DN B cells and regulatory T cells (Tregs) using single cell RNA-seq data, bulk RNA-seq data and flow cytometry, and verified the spatial proximity of DN B cells and Tregs by mIF staining. Trajectory analysis and flow cytometry revealed that DN B cells highly expressed genes involved in the antigen processing and presentation pathway, such as HLA-DR. The abundance of DN B cells and LMAs in ESCC provides novel potential targets for optimal immunotherapy against ESCC.

Potential of epithelial membrane protein 3 as a novel therapeutic target for human breast cancer

Amplification of human epidermal growth factor 2 receptor (HER2) and overexpression of estrogen receptor (ER) and/or progesterone receptor (PR) are key determinants in the treatment planning for human breast cancer (BC). Currently, targeted therapies for BC are focused mainly on these biomarkers. However, development of resistance to targeted drugs is almost unavoidable, emphasizing the importance of biochemical and pharmaceutical advances to improve treatment outcomes. To the best of our knowledge, the present study is the first to show functional crosstalk in vitro between HER2 and epithelial membrane protein 3 (EMP3), a tetraspan membrane protein, in human BC. EMP3 overexpression significantly promoted BC cell proliferation, invasion and migration by Transwell assays via epithelial-mesenchymal transition and transactivated the HER family, resulting in increased ER and PR expression in vitro. Knocking down EMP3 notably suppressed cell proliferation and migration and was accompanied by decreased expression of HER1‑HER3 and p‑SRC proteins. Suppression of EMP3 expression enhanced sensitivity of BC cells to trastuzumab in vitro. Xenograft experiments revealed decreased expression of HER1 and HER2 in stable EMP3‑knockdown cells, resulting in decreased tumor weight and size. In patients with BC, EMP3 overexpression was detected in 72 of 166 cases (43.4%), with 18 of 43 (41.9%) HER2‑amplified BC samples co‑expressing EMP3. Co‑expression of EMP3 and HER2 was positively associated with ER expression (P=0.028) and tended to be associated with nodal metastasis (P=0.085), however this was not significant. Taken together, the present results supported the potential of targeting EMP3 as a novel therapeutic strategy for human BC via co‑expression of HER2 and EMP3.

Dephosphorylation of branched-chain α-keto acid dehydrogenase E1α (BCKDHA) promotes branched-chain amino acid catabolism and renders cancer cells resistant to X-rays by mitigating DNA damage

Branched-chain amino acids (BCAAs) facilitate cancer cell proliferation and survival. Stresses, including X-irradiation, increase BCAA uptake. However, the role of BCAA metabolism in cancer cell survival remains unclear. Therefore, this study aimed to elucidate the role of the BCAA catabolic pathway in cancer cell survival following X-irradiation. X-irradiation dose-dependently dephosphorylated branched-chain α-keto acid dehydrogenaseE1α (BCKDHA) suggesting the activation of the BCKDH complex, which catalyzes the rate-determining step of BCAA catabolism. We considered that activation of BCKDH promoted the BCAA catabolism, which resulted in cancer cell resistance to X-irradiation. Consistent with this notion, cells with BCKDHA knockdown exhibited increased radiosensitivity, which was associated with the increase in mitotic catastrophe and residual double-strand breaks by decreasing cellular ATP levels after X-irradiation. Our results suggest that BCKDHA dephosphorylation promotes BCAA catabolism, leading to cell survival by mitigating DNA damage after X-irradiation. Thus, BCAA catabolic pathway may be a target for radiation therapy.

Phosphoproteomic Analysis of Signaling Pathways in Lymphomas

Cellular fate is regulated by intricate signal transduction mediated by posttranslational protein modifications like phosphorylation to transmit information. As other cancer types, lymphomas frequently show dysregulation of signaling pathways that contribute to malignant transformation and tumor progression. For example, in diffuse large B-cell lymphoma the B-cell antigen receptor was identified as an oncogenic driver mediating cellular growth and survival signals. Thus, the elucidation of these complex signaling networks is crucial to gain insight into the mechanisms underlying tumorigenesis and to identify target proteins for innovative therapeutic approaches.Here, we describe a mass spectrometry-based phosphoproteomic approach for the global analysis of intracellular signaling events and their dynamics. The workflow combines phosphopeptide enrichment and fractionation with liquid chromatography-coupled mass spectrometry for the amino acid site-specific identification and quantification of thousands of phosphorylation events. Such global signaling analyses have great potential for the elucidation of oncogenic pathomechanisms, diagnostic biomarkers, and drug targets.

Genotype from Phenotype: Using CRISPR Screens to Dissect Lymphoma Biology

Genome-wide screens are a powerful technique to dissect the complex network of genes regulating diverse cellular phenotypes. The recent adaptation of the CRISPR-Cas9 system for genome engineering has revolutionized functional genomic screening. Here, we present protocols used to introduce Cas9 into human lymphoma cell lines, produce high-titer lentivirus of a genome-wide sgRNA library, transduce and culture cells during the screen, select cells with a specified phenotype, isolate genomic DNA, and prepare a custom library for next-generation sequencing. These protocols were tailored for loss-of-function CRISPR screens in human B-cell lymphoma cell lines but are highly amenable for other experimental purposes.

Detection, significance and potential utility of circulating tumor cells in clinical practice in breast cancer (Review)

Although advances in diagnostic techniques, new therapeutic strategies and personalization of breast cancer (BC) care have improved the survival for a number of patients, BC remains a major cause of morbidity and mortality for women. The study of circulating tumor cells (CTCs) has significant potential in translational oncology since these cells represent promising biomarkers throughout the entire course of BC in patients. CTCs also have notable prognostic value in early BC as well as metastatic BC. Based on current knowledge, it seems that the dynamics of CTCs that change during therapy reflect therapy response, and CTCs could serve as a tool for risk stratification and real-time monitoring of treatment in patients with BC. The question of how to use this information in everyday clinical practice and how this information can guide or change therapy to affect the clinical outcome of patients with BC remains unanswered. The present review aims to discuss current completed and ongoing trials that have been designed to demonstrate the clinical significance of CTCs, offer insights into treatment efficacy and assess CTC utility, facilitating their implementation in the routine management of patients with BC.

Research progress and the prospect of using single-cell sequencing technology to explore the characteristics of the tumor microenvironment

In precision cancer therapy, addressing intra-tumor heterogeneity poses a significant obstacle. Due to the heterogeneity of each cell subtype and between cells within the tumor, the sensitivity and resistance of different patients to targeted drugs, chemotherapy, etc., are inconsistent. Concerning a specific tumor type, many feasible treatments or combinations can be used by specifically targeting the tumor microenvironment. To solve this problem, it is necessary to further study the tumor microenvironment. Single-cell sequencing techniques can dissect distinct tumor cell populations by isolating cells and using statistical computational methods. This technology may assist in the selection of targeted combination therapy, and the obtained cell subset information is crucial for the rational application of targeted therapy. In this review, we summarized the research and application advances of single-cell sequencing technology in the tumor microenvironment, including the most commonly used single-cell genomic and transcriptomic sequencing, and their future development direction was proposed. The application of single-cell sequencing technology has been expanded to include epigenomics, proteomics, metabolomics, and microbiome analysis. The integration of these different omics approaches has significantly advanced the development of single-cell multiomics sequencing technology. This innovative approach holds immense potential for various fields, such as biological research and medical investigations. Finally, we discussed the advantages and disadvantages of using single-cell sequencing to explore the tumor microenvironment.

TP53 mutations in cancer: Molecular features and therapeutic opportunities (Review)

The tumour suppressor factor p53 plays an essential role in regulating numerous cellular processes, including the cell cycle, DNA repair, apoptosis, autophagy, cell metabolism and immune response. TP53 is the most commonly mutated gene in human cancers. These mutations are primarily non‑synonymous changes that produce mutant p53 proteins characterized by loss of function, a dominant negative effect on p53 tetramerisation and gain of function (GOF). GOF mutations not only disrupt the tumour‑suppressive activities of p53 but also endow the mutant proteins with new oncogenic properties. Recent studies analysing different pathogenic features of mutant p53 in cancer‑derived cell lines have demonstrated that restoring wild‑type p53, rather than removing GOF mutations, reduces cancer cell growth. These findings suggest that therapeutic strategies for reactivating wild‑type p53 function in cancer cells may bring a greater benefit than approaches halting mutant p53. This approach could involve the use of small molecules, gene therapy and other methods to re‑establish wild‑type p53 activity. This review describes the complexity of the biological activities of different p53 mutants and summarizes the current therapeutic approaches to restore p53 function.

Tertiary Lymphoid Structures in Central Nervous System Disorders

The central nervous system (CNS) constitutes a tightly regulated milieu, where immune responses are strictly controlled to prevent neurological damage. This poses considerable challenges to the therapeutic management of CNS pathologies, such as autoimmune disorders and cancer. Tertiary lymphoid structures (TLS) are ectopic, lymph node-like structures containing B- and T-cells, often associated with chronic inflammation or cancer, which have been shown to be detrimental in autoimmunity but beneficial in cancer. In-depth studies of TLS induction in CNS disorders, as well as their precise role in regulating adaptive immune responses in this context, will be paramount to the development of novel TLS-targeting therapies. In the present chapter, we review the anatomical and physiological peculiarities shaping TLS formation in the CNS, their relevance in autoimmunity and cancer, as well as their implications for the development of novel therapeutic modalities for these patients.

Advancement of Techniques for Precise Visualization and Quantification of Tertiary Lymphoid Structure-Associated Immune Cells in Tissue Samples

Tertiary Lymphoid Structures (TLS) are considered as genuine markers of inflammation. Their presence within inflamed tissues or the tumor microenvironment has been associated with the local development of an active immune response. While high densities of TLS are correlated with disease severity in autoimmune diseases or during graft rejection, it has been associated with longer patient survival in many cancer types and more recently with positive responses to anti-PD-1 immunotherapy. Their efficient visualization and quantification within human tissues may represent new tools for helping clinicians in adjusting their therapeutic strategy. In clinical settings, the use of single-marker immunohistochemistry (IHC) protocols prevails in immune cell infiltration in formalin-fixed, paraffin-embedded (FFPE) tissues. In contrast, the development of automated multiplex immunofluorescence markings, i.e., 40-plex, requires very costly investments in equipment and analysis stations. Yet, employing two or more markers can enhance the characterization of immune infiltrates, particularly in the context of TLS. Besides the growing development of multiplex labeling approaches, imaging can also be used to overcome some technical difficulties encountered during the immunolabeling of tissues with several markers.This chapter describes IHC methods to visualize in human tissue (tumoral or not) the presence of TLS. These methods are based on the immunostaining of four TLS-associated immune cell populations, namely, follicular B cells, follicular dendritic Cells (FDCs), mature Dendritic Cells (mDCs), and Follicular Helper T cells (TFH), together with non-TFH T cells. Methodologies for subsequent quantification of TLS density are also proposed, as well as a virtual multiplexing method based on image registration using the open-source software ImageJ (IJ), aiming at co-localizing several immune cell populations from different IHC stainings performed on serial tissue sections.

Cancer-Associated Lymphoid Aggregates in Histology Images: Manual and Deep Learning-Based Quantification Approaches

Quantification of lymphoid aggregates including tertiary lymphoid structures (TLS) with germinal centers in histology images of cancer is a promising approach for developing prognostic and predictive tissue biomarkers. In this article, we provide recommendations for identifying lymphoid aggregates in tissue sections from routine pathology workflows such as hematoxylin and eosin staining. To overcome the intrinsic variability associated with manual image analysis (such as subjective decision-making, attention span), we recently developed a deep learning-based algorithm called HookNet-TLS to detect lymphoid aggregates and germinal centers in various tissues. Here, we additionally provide a guideline for using manually annotated images for training and implementing HookNet-TLS for automated and objective quantification of lymphoid aggregates in various cancer types.

Detection and Characterization of Clonal Hematopoiesis

Clonal hematopoiesis (CH) is the age-related expansion of hematopoietic stem cell clones resulting from the acquisition of somatic point mutations or mosaic chromosomal alterations (mCAs). It is linked to adverse systemic effects, including hematologic malignancies, cardiovascular diseases, metabolic disorders, as well as liver and kidney ailments, ultimately contributing to elevated overall mortality.Given its diverse biological and clinical implications, the identification of clonal hematopoiesis holds significance in various contexts. While traditionally centered on mutations associated with myeloid malignancies, stem/progenitor cell involvement has been documented for various lymphoid malignancies, including T-cell lymphoma, chronic lymphocytic leukemia (CLL), and follicular lymphoma (FL). Lymphoid CH (L-CH) involves a broader spectrum of genes and occurs at a lower prevalence, resulting in reduced mutation prevalences per gene. This characteristic poses challenges for efficient CH detection.The major strategies to identify CH are whole exome sequencing (WES), whole genome sequencing (WGS), or targeted sequencing. Targeted sequencing allows for much higher sequencing depth compared to WES and WGS because of the focus on genes known to be associated with CH and therefore allows detecting potential variants at low frequencies with high precision. Here, we describe an error-corrected targeted sequencing approach for detection of CH in bone marrow (BM) or peripheral blood (PB) samples, which we have successfully established and used in various cohorts. This protocol includes the process of DNA isolation from PB and BM samples, library preparation with molecular tags including quality control steps and computational analysis including variant filtering.

Unveiling the therapeutic potential and mechanisms of stanniocalcin-1 in retinal degeneration

Retinal degeneration (RD) is a group of ocular diseases characterized by progressive photoreceptor apoptosis and visual impairment. Mitochondrial malfunction, excessive oxidative stress, and chronic activation of neuroglia collectively contribute to the development of RD. Currently, there is a lack of efficacious therapeutic interventions for RD. Stanniocalcin-1 (STC-1) is a promising candidate molecule to decelerate photoreceptor cell death. STC-1 is a secreted calcium/phosphorus regulatory protein that exerts diverse protective effects. Accumulating evidence suggests that STC-1 protects retinal cells from ischemic injury, oxidative stress, and excessive apoptosis through enhancing the expression of uncoupling protein-2 (UCP-2). Furthermore, STC-1 exerts its antiinflammatory effects by inhibiting the activation of microglia and macrophages, as well as the synthesis and secretion of proinflammatory cytokines, such as TNF-α, IL-1, and IL-6. By employing these mechanisms, STC-1 effectively shields the retinal photoreceptors and optic nerve, thereby slowing down the progression of RD. We summarize the STC-1-mediated therapeutic effects on the degenerating retina, with a particular focus on its underlying mechanisms. These findings highlight that STC-1 may act as a versatile molecule to treat degenerative retinopathy. Further research on STC-1 is imperative to establish optimal protocols for its clinical use.

Acute exercise boosts NAD+ metabolism of human peripheral blood mononuclear cells

Nicotinamide adenine dinucleotide (NAD+) coenzymes are the central electron carriers in biological energy metabolism. Low NAD+ levels are proposed as a hallmark of ageing and several diseases, which has given rise to therapeutic strategies that aim to tackle these conditions by boosting NAD+ levels. As a lifestyle factor with preventive and therapeutic effects, exercise increases NAD+ levels across various tissues, but so far human trials are mostly focused on skeletal muscle. Given that immune cells are mobilized and redistributed in response to acute exercise, we conducted two complementary trials to test the hypothesis that a single exercise session alters NAD+ metabolism of peripheral blood mononuclear cells (PBMCs). In a randomized crossover trial (DRKS00017686) with 24 young adults (12 female) we show that acute exercise increases gene expression and protein abundance of several key NAD+ metabolism enzymes with high conformity between high-intensity interval training (HIIT) and moderate-intensity continuous training (MICT). In a longitudinal exercise trial (DRKS00029105) with 12 young adults (6 female) we confirm these results and reveal that - similar to skeletal muscle - NAD+ salvage is pivotal for PBMCs in response to exercise. Nicotinamide phosphoribosyltransferase (NAMPT), the rate-limiting enzyme of NAD+ salvage pathway, displayed a pronounced increase in gene expression during exercise, which was accompanied by elevated intracellular NAD+ levels and reduced serum levels of the NAD+ precursor nicotinamide. These results demonstrate that acute exercise triggers NAD+ biosynthesis of human PBMCs with potential implications for immunometabolism, immune effector function, and immunological exercise adaptions.

Focused Ultrasound in Cancer Immunotherapy: A Review of Mechanisms and Applications

Ultrasound is well-perceived for its diagnostic application. Meanwhile, ultrasound, especially focused ultrasound (FUS), has also demonstrated therapeutic capabilities, such as thermal tissue ablation, hyperthermia, and mechanical tissue ablation, making it a viable therapeutic approach for cancer treatment. Cancer immunotherapy is an emerging cancer treatment approach that boosts the immune system to fight cancer, and it has also exhibited enhanced effectiveness in treating previously considered untreatable conditions. Currently, cancer immunotherapy is regarded as one of the four pillars of cancer treatment because it has fewer adverse effects than radiation and chemotherapy. In recent years, the unique capabilities of FUS in ablating tumors, regulating the immune system, and enhancing anti-tumor responses have resulted in a new field of research known as FUS-induced/assisted cancer immunotherapy. In this work, we provide a comprehensive overview of this new research field by introducing the basics of focused ultrasound and cancer immunotherapy and providing the state-of-the-art applications of FUS in cancer immunotherapy: the mechanisms and preclinical and clinical studies. This review aims to offer the scientific community a reliable reference to the exciting field of FUS-induced/assisted cancer immunotherapy, hoping to foster the further development of related technology and expand its medical applications.

Repurposing Phytochemicals against Breast Cancer (MCF-7) using Classical Structure-Based Drug Design

BACKGROUND

The significant public health effect of breast cancer is demonstrated by its high global prevalence and the potential for severe health consequences. The suppression of the proliferative effects facilitated by the estrogen receptor alpha (ERα) in the MCF-7 cell line is significant for breast cancer therapy.

OBJECTIVE

The current work involves in-silico techniques for identifying potential inhibitors of ERα.

METHODS

The method combines QSAR models based on machine learning with molecular docking to identify potential binders for the ERα. Further, molecular dynamics simulation studied the stability of the complexes, and ADMET analysis validated the compound's properties.

RESULTS

Two compounds (162412 and 443440) showed significant binding affinities with ERα, with binding energies comparable to the established binder RL4. The ADMET qualities showed advantageous characteristics resembling pharmaceutical drugs. The stable binding of these ligands in the active region of ERα during dynamic conditions was confirmed by molecular dynamics simulations. RMSD plots and conformational stability supported the ligands' persistent occupancy in the protein's binding site. After simulation, two hydrogen bonds were found within the protein-ligand complexes of 162412 and 443440, with binding free energy values of -27.32 kcal/mol and -25.00 kcal/mol.

CONCLUSION

The study suggests that compounds 162412 and 443440 could be useful for developing innovative anti-ERα medicines. However, more research is needed to prove the compounds' breast cancer treatment efficacy. This will help develop new treatments for ERα-associated breast cancer.