Common Pathogenetic Mechanisms Underlying Aging and Tumor and Means of Interventions

Effect of RNA Demethylase FTO Overexpression on Biomass and Bioactive Substances in Diatom Phaeodactylum tricornutum

Phaeodactylum tricornutum is rich in bioactive substances, rendering it valuable in nutrition and medicine. Epigenetic editing mediated by human RNA demethylase FTO can significantly increase the yields of rice and potato and offers significant potential for the genetic breeding of microalgae. This study aimed to enhance the production of certain metabolites in P. tricornutum via FTO-mediated epigenetic editing. Phenotypic analysis revealed that transgenic P. tricornutum exhibits significantly reduced RNA m6A modification levels and faster growth, producing markedly higher levels of lipids, proteins, and carotenoids than the wild type. Transcriptome analysis revealed 1009 upregulated genes and 378 downregulated genes. KEGG analysis demonstrated the upregulated expression of multiple key enzymes involved in long-chain fatty acid synthesis (e.g., ACSL, fabF, and fabG), carotenoid synthesis (e.g., crtQ, PDS, and PSY1), and amino acid synthesis (e.g., dapF, glyA, and aroK) in transgenic P. tricornutum, consistent with our phenotypic results. These results indicate that FTO can promote growth and increase the bioactive compound content in P. tricornutum by regulating the m6A modification of RNA, and further suggest that FTO has the potential to serve as a new tool for the epigenetic editing of microalgae.

Prognostic factors of survival in patients with lung cancer after low-dose computed tomography screening: a multivariate analysis of a lung cancer screening cohort in China

OBJECTIVE

This study aimed to evaluate the prognostic factors influencing the survival of patients with lung cancer identified from a lung cancer screening cohort in the community.

METHODS

A total of 25,310 eligible participants were enrolled in this population-based prospective cohort study, derived from a community lung cancer screening program started from 2013 to 2017. Survival analyses were conducted using the Kaplan-Meier method and the log-rank test. Cox proportional hazards regression models were utilized to identify prognostic factors, including demographic characteristics, risk factors, low-dose CT (LDCT) screening, and treatment information.

RESULTS

The screening cohort identified a total of 429 patients with lung cancer (276 men, 153 women) during the study period. The 1-year, 3-year, and 5-year survival rates were 74.4%, 59.4% and 54.5%, respectively. The prognostic factors discovered by the multivariate analysis include gender (male vs. female, HR: 2.96, 95% CI: 1.88-4.64), age (HR: 1.02, 95% CI: 1.00-1.05), personal monthly income (2000-3999 CNY vs. < 2000 CNY, HR: 0.70, 95% CI: 0.52-0.95), pathological type (small cell carcinoma vs. adenocarcinoma, HR: 2.55, 95% CI: 1.39-4.66), stage (IV vs. 0-I, HR: 5.21, 95% CI: 2.78-9.75; III vs. 0-I, HR: 3.81, 95% CI: 1.88-7.74), surgery (yes vs. no, HR: 0.36, 95% CI: 0.23-0.57), and KPS (HR: 0.98, 95% CI: 0.98-0.99) among lung cancer patients identified by the basic model. Furthermore, solid nodule (non-solid nodule vs. solid nodule, HR: 0.47, 95% CI: 0.23-0.96) and larger-sized nodule (HR: 1.02, 95% CI: 1.00-1.03) were associated with a worse prognosis for lung cancer in the LDCT screening model.

CONCLUSION

Prognostic factors of patients with lung cancer detected by LDCT screening were identified, which could potentially guide clinicians in the decision-making process for lung cancer management and treatment. Further studies with larger sample sizes and more detailed follow-up data are warranted for prognostic prediction.

The telomere connection between aging and cancer: The burden of replication stress and dysfunction

Aging is a complex process that affects individuals at the molecular, cellular, tissue, and systemic levels, arising from the cumulative effects of damage and reduced repair mechanisms. This process leads to the onset of age-related diseases, including cancer, which exhibits increased incidence with age. Telomeres, the protective caps at chromosome ends, play a crucial role in genome stability and are closely connected with aging and age-related disorders. Both excessively short and long telomere lengths may contribute to cancer development when their balance is disrupted. Fragile telomeres, characterized by abnormalities and replication stress, may provide novel insights into the connection between aging and cancer. The accumulation of fragile telomeres, possibly due to intense replicative stress, may represent a key factor. Given the dynamic nature of telomeres, large longitudinal studies are essential for understanding their role in aging and cancer susceptibility, which is crucial for developing effective strategies to promote healthy aging and mitigate cancer risk.

Basic helix-loop-helix ARNT like 1 regulates the function of immune cells and participates in the development of immune-related diseases

The circadian clock is an internal timekeeper system that regulates biological processes through a central circadian clock and peripheral clocks controlling various genes. Basic helix-loop-helix ARNT-like 1 (BMAL1), also known as aryl hydrocarbon receptor nuclear translocator-like protein 1 (ARNTL1), is a key component of the circadian clock. The deletion of BMAL1 alone can abolish the circadian rhythms of the human body. BMAL1 plays a critical role in immune cell function. Dysregulation of BMAL1 is linked to immune-related diseases such as autoimmune diseases, infectious diseases, and cancer, and vice versa. This review highlights the significant role of BMAL1 in governing immune cells, including their development, differentiation, migration, homing, metabolism, and effector functions. This study also explores how dysregulation of BMAL1 can have far-reaching implications and potentially contribute to the onset of immune-related diseases such as autoimmune diseases, infectious diseases, cancer, sepsis, and trauma. Furthermore, this review discusses treatments for immune-related diseases that target BMAL1 disorders. Understanding the impact of BMAL1 on immune function can provide insights into the pathogenesis of immune-related diseases and help in the development of more effective treatment strategies. Targeting BMAL1 has been demonstrated to achieve good efficacy in immune-related diseases, indicating its promising potential as a targetable therapeutic target in these diseases.

Immunometabolism in the Aging Heart

Structural, functional, and molecular-level changes in the aging heart are influenced by a dynamic interplay between immune signaling and cellular metabolism that is referred to as immunometabolism. This review explores the crosstalk between cellular metabolic pathways including glycolysis, oxidative phosphorylation, fatty acid metabolism, and the immune processes that govern cardiac aging. With a rapidly aging population that coincides with increased cardiovascular risk and cancer incidence rates, understanding the immunometabolic underpinnings of cardiac aging provides a foundation for identifying therapeutic targets to mitigate cardiac dysfunction. Aging alters the immune environment of the heart by concomitantly driving the changes in immune cell metabolism, mitochondrial dysfunction, and redox signaling. Shifts in these metabolic pathways exacerbate inflammation and impair tissue repair, creating a vicious cycle that accelerates cardiac functional decline. Treatment with cancer therapy further complicates this landscape, as aging-associated immunometabolic disruptions augment the susceptibility to cardiotoxicity. The current review highlights therapeutic strategies that target the immunometabolic axis to alleviate cardiac aging pathologies. Interventions include modulating metabolic intermediates, improving mitochondrial function, and leveraging immune signaling pathways to restore cardiac health. Advances in immunometabolism thus hold significant potential for translating preclinical findings into therapies that improve the quality of life for the aging population and underscore the need for approaches that address the immunometabolic mechanisms of cardiac aging, providing a framework for future research.

A pan-cancer analysis of the oncogenic role of N-acetyltransferase 8 like in human cancer

BACKGROUND

N-Acetyltransferase 8 Like (NAT8L) inhibits natural killer (NK)/T-cell cytotoxicity by impairing the formation of the immunological synapse via N-acetylaspartate (NAA). Existing research has predominantly focused on the metabolic functions of NAT8L, particularly in adipose tissues and myelination in the brain. However, in contrast to other N-acetyltransferases such as NAT1 and NAT2, the role of NAT8L in cancer has been less extensively studied. In this study, we conducted a comprehensive pan-cancer analysis to investigate the carcinogenic role of NAT8L in human cancers.

METHODS

We utilized the standardized TCGA pan-cancer dataset to analyze differential expression, clinical prognosis, gene mutation, immune infiltration, epigenetic modification, tumor stemness, and heterogeneity. Additionally, we evaluated the sensitivity of NAT8L to small molecule drugs using the GDSC and CTRP databases.

RESULTS

In this study, we identified that NAT8L expression was upregulated in 6 cancers and downregulated in 12 compared to normal tissues. We analyzed its prognostic value in 5 tumor types (KIRP, COAD, COADREAD, GBMLGG, LUSC) and found correlations with overall survival (OS), disease-specific survival (DSS), and progression-free interval (PFI). Furthermore, NAT8L expression was significantly correlated with levels of most immune checkpoints, immunomodulators, and immune cell infiltration. The mutation frequencies for bladder cancer (BLCA), glioblastoma multiforme and glioma (GBMLGG), lower-grade glioma (LGG), and KIRP were 1.2%, 0.9%, 0.8%, and 0.4%, respectively.

CONCLUSION

Our findings suggest that NAT8L may serve as a potential prognostic marker and therapeutic target across a variety of cancers, particularly in KIRP, COAD, COADREAD, GBMLGG, and lung squamous cell carcinoma (LUSC).

Chen's peiyuan tang and premature ovarian failure: unveiling the mechanisms through network pharmacology

Background

Chen's Peiyuan Tang (CSPYT) is a compound herbal formula that has shown the potential to enhance ovarian function and reduce autophagy in ovarian granulosa cells, which plays a crucial role in follicular development and maturation. The application of Chinese herbal medicine offers a promising alternative to traditional hormone replacement therapy (HRT).

Methods

This study explores CSPYT's therapeutic mechanisms in treating POF, focusing on its modulation of autophagy through network pharmacology and transcriptomics-based analysis, predicting potential interactions and pathways. KGN cell line and rat ovarian granulosa cells were used for in vitro experiment. 4-Hydroperoxy cyclophosphamide(4-HC) stimulation was carried out for establishing the POF cell model. Q-PCR, Western Blot, Transmission electron microscopy to detect the results.

Results

According to the drug and disease database, the common targets of Chen's Peiyuan Tang and premature ovarian failure were screened, combined with autophagy gene targets and transcriptome analysis, and finally 8 intersection targets were obtained, namely CDKN1B, MAPK3, PRKCD, CDKN1A, MAPK1, RAF1, BIRC5, CTSB. Enrichment analysis of 8 genes found that they were closely related to the animal autophagy pathway. Construct PPI network diagram. CytoScape 3.9.1 builds CSPYT Drug Target-POF Disease Target-Autophagy Gene Network Diagram. Based on the PPI network diagram and CytoScape 3.9.1 analysis results, it is estimated that MAPK1 and MAPK3 are the key targets of CSPYT in the treatment of POF. The eight final intersection targets were docked with the corresponding active pharmaceutical ingredients. The one that docked most closely with the MAPK family was naringenin. In cell experiment verification, it was confirmed that Chen's Peiyuan Tang can inhibit the MAPK signaling pathway, significantly reduce the number of autophagosomes, and reduce autophagy damage in ovarian granulosa cells.

Discussion

CSPYT can inhibit the MAPK signaling pathway, prevent autophagy overexpression and restore ovarian granulosa cell function, effectively alleviating the disease pressure of POF.

Application of 3D printing in the treatment of diabetic foot ulcers: current status and new insights

Background and Aims

Diabetic foot ulcers (DFUs) are a serious complication of diabetes mellitus (DM), affecting around 25% of individuals with DM. Primary treatment of a DFU involves wound off-loading, surgical debridement, dressings to provide a moist wound environment, vascular assessment, and appropriate antibiotics through a multidisciplinary approach. Three-dimensional (3D) printing technology is considered an innovative tool for the management of DFUs. The utilization of 3D printing technology in the treatment of DFU involves the modernization of traditional methods and the exploration of new techniques. This review discusses recent advancements in 3D printing technology for the application of DFU care, and the development of personalized interventions for the treatment of DFUs.

Methods

We searched the electronic database for the years 2019-2024. Studies related to the use of 3D printing technology in Diabetic foot were included.

Results

A total of 25 identified articles based on database search and citation network analysis. After removing duplicates, 18 articles remained, and three articles that did not meet the inclusion criteria were removed after reading the title/abstract. A total of 97 relevant articles were included during the reading of references. In total, 112 articles were included.

Conclusion

3D printing technology offers unparalleled advantages, particularly in the realm of personalized treatment. The amalgamation of traditional treatment methods with 3D printing has yielded favorable outcomes in decelerating the progression of DFUs and facilitating wound healing. However, there is a limited body of research regarding the utilization of 3D printing technology in the domain of DFUs.

Harnessing Artificial Intelligence for the Detection and Management of Colorectal Cancer Treatment

Currently, eight million people in the United States suffer from cancer and it is a major global health concern. Early detection and interventions are urgently needed for all cancers, including colorectal cancer. Colorectal cancer is the third most common type of cancer worldwide. Based on the diagnostic efforts to general awareness and lifestyle choices, it is understandable why colorectal cancer is so prevalent today. There is a notable lack of awareness concerning the impact of this cancer and its connection to lifestyle elements, as well as people sometimes mistaking symptoms for a different gastrointestinal condition. Artificial intelligence (AI) may assist in the early detection of all cancers, including colorectal cancer. The usage of AI has exponentially grown in healthcare through extensive research, and since clinical implementation, it has succeeded in improving patient lifestyles, modernizing diagnostic processes, and innovating current treatment strategies. Numerous challenges arise for patients with colorectal cancer and oncologists alike during treatment. For initial screening phases, conventional methods often result in misdiagnosis. Moreover, after detection, determining the course of which colorectal cancer can sometimes contribute to treatment delays. This article touches on recent advancements in AI and its clinical application while shedding light on why this disease is so common today.

Network pharmacology-based approach to investigate the molecular targets and molecular mechanisms of Rosmarinus officinalis L. for treating aging-related disorders

Aging, a natural biological process, presents challenges in maintaining physiological well-being and is associated with increased vulnerability to diseases. Addressing aging mechanisms is crucial for developing effective preventive and therapeutic strategies against age-related ailments. Rosmarinus officinalis L. is a medicinal herb widely used in traditional medicine, containing diverse bioactive compounds that have been studied for their antioxidant and anti-inflammatory properties, which are associated with potential health benefits. Using network pharmacology, this study investigates the anti-aging function and underlying mechanisms of R. officinalis. Through network pharmacology analysis, the top 10 hub genes were identified, including TNF, CTNNB1, JUN, MTOR, SIRT1, and others associated with the anti-aging effects. This analysis revealed a comprehensive network of interactions, providing a holistic perspective on the multi-target mechanism underlying Rosemary's anti-aging properties. GO and KEGG pathway enrichment analysis revealed the relevant biological processes, molecular functions, and cellular components involved in treating aging-related conditions. KEGG pathway analysis shows that anti-aging targets of R. officinalis involved endocrine resistance, pathways in cancer, and relaxin signaling pathways, among others, indicating multifaceted mechanisms. Genes like MAPK1, MMP9, and JUN emerged as significant players. These findings enhance our understanding of R. officinalis's potential in mitigating aging-related disorders through multi-target effects on various biological processes and pathways. Such approaches may reduce the risk of failure in single-target and symptom-based drug discovery and therapy.

Comprehensive analysis of stearoyl-coenzyme A desaturase in prostate adenocarcinoma: insights into gene expression, immune microenvironment and tumor progression

Prostate adenocarcinoma (PRAD) is a prevalent global malignancy which depends more on lipid metabolism for tumor progression compared to other cancer types. Although Stearoyl-coenzyme A desaturase (SCD) is documented to regulate lipid metabolism in multiple cancers, landscape analysis of its implications in PRAD are still missing at present. Here, we conducted an analysis of diverse cancer datasets revealing elevated SCD expression in the PRAD cohort at both mRNA and protein levels. Interestingly, the elevated expression was associated with SCD promoter hypermethylation and genetic alterations, notably the L134V mutation. Integration of comprehensive tumor immunological and genomic data revealed a robust positive correlation between SCD expression levels and the abundance of CD8+ T cells and macrophages. Further analyses identified significant associations between SCD expression and various immune markers in tumor microenvironment. Single-cell transcriptomic profiling unveiled differential SCD expression patterns across distinct cell types within the prostate tumor microenvironment. The Gene Ontology and Kyoto Encyclopedia of Genes and Genome analyses showed that SCD enriched pathways were primarily related to lipid biosynthesis, cholesterol biosynthesis, endoplasmic reticulum membrane functions, and various metabolic pathways. Gene Set Enrichment Analysis highlighted the involvement of elevated SCD expression in crucial cellular processes, including the cell cycle and biosynthesis of cofactors pathways. In functional studies, SCD overexpression promoted the proliferation, metastasis and invasion of prostate cancer cells, whereas downregulation inhibits these processes. This study provides comprehensive insights into the multifaceted roles of SCD in PRAD pathogenesis, underscoring its potential as both a therapeutic target and prognostic biomarker.

The Role of Natural Products from Herbal Medicine in TLR4 Signaling for Colorectal Cancer Treatment

The toll-like receptor 4 (TLR4) signaling pathway constitutes an intricate network of protein interactions primarily involved in inflammation and cancer. This pathway triggers intracellular signaling cascades, modulating transcription factors that regulate gene expression related to immunity and malignancy. Previous studies showed that colon cancer patients with low TLR4 expression exhibit extended survival times and the TLR4 signaling pathway holds a significant role in CRC pathogenesis. In recent years, traditional Chinese medicines (TCMs) have garnered substantial attention as an alternative therapeutic modality for CRC, primarily due to their multifaceted composition and ability to target multiple pathways. Emerging evidence indicates that specific TCM products, such as andrographolide, rosmarinic acid, baicalin, etc., have the potential to impede CRC development through the TLR4 signaling pathway. Here, we review the role and biochemical processes of the TLR4 signaling pathway in CRC, and natural products from TCMs affecting the TLR4 pathway. This review sheds light on potential treatment strategies utilizing natural TLR4 inhibitors for CRC, which contributes to the advancement of research and accelerates their clinical integration into CRC treatment.

Biological clock regulation by the PER gene family: a new perspective on tumor development

The Period (PER) gene family is one of the core components of the circadian clock, with substantial correlations between the PER genes and cancers identified in extensive researches. Abnormal mutations in PER genes can influence cell function, metabolic activity, immunity, and therapy responses, thereby promoting the initiation and development of cancers. This ultimately results in unequal cancers progression and prognosis in patients. This leads to variable cancer progression and prognosis among patients. In-depth studies on the interactions between the PER genes and cancers can reveal novel strategies for cancer detection and treatment. In this review, we aim to provide a comprehensive overview of the latest research on the role of the PER gene family in cancer.

A new perspective on prostate cancer treatment: the interplay between cellular senescence and treatment resistance

The emergence of resistance to prostate cancer (PCa) treatment, particularly to androgen deprivation therapy (ADT), has posed a significant challenge in the field of PCa management. Among the therapeutic options for PCa, radiotherapy, chemotherapy, and hormone therapy are commonly used modalities. However, these therapeutic approaches, while inducing apoptosis in tumor cells, may also trigger stress-induced premature senescence (SIPS). Cellular senescence, an entropy-driven transition from an ordered to a disordered state, ultimately leading to cell growth arrest, exhibits a dual role in PCa treatment. On one hand, senescent tumor cells may withdraw from the cell cycle, thereby reducing tumor growth rate and exerting a positive effect on treatment. On the other hand, senescent tumor cells may secrete a plethora of cytokines, growth factors and proteases that can affect neighboring tumor cells, thereby exerting a negative impact on treatment. This review explores how radiotherapy, chemotherapy, and hormone therapy trigger SIPS and the nuanced impact of senescent tumor cells on PCa treatment. Additionally, we aim to identify novel therapeutic strategies to overcome resistance in PCa treatment, thereby enhancing patient outcomes.

Symptom networks in older adults with cancer: A network analysis

INTRODUCTION

Due to aging, older adults with cancer (OAC) may be confronted with a complex interplay of multiple age-related issues; coupled with receiving cancer treatment, OAC may experience multiple concurrent symptoms that require the identification of the core symptom for effective management. Constructing symptom networks will help in the identification of core symptoms and help achieve personalized and precise interventions. Currently, few studies have used symptom networks to identify core symptoms in OAC. Our objectives were to construct symptom networks of OAC, explore the core symptoms, and compare the differences in symptom networks among various subgroups.

MATERIALS AND METHODS

Secondary analysis was performed using data from 485 OAC collected in 2021 from a cross-sectional survey named the Shanghai CANcer Survivor (SCANS) Report. The MD Anderson Symptom Inventory (MDASI) was used to assess the incidence and severity of cancer-related symptoms. We used the R package to construct symptom networks and identify the centrality indices. The network comparison test was used to compare network differences among the subgroups.

RESULTS

The most common and severe symptoms reported were fatigue, disturbed sleep, and difficulty remembering. The network density was 0.718. Vomiting (rs = 1.81, rb = 2.13), fatigue (rs = 1.54, rb = 1.93), and sadness (rs = 0.81, rb = 0.69) showed the highest strength values, which suggested that these symptoms were more likely to co-occur with other symptoms. The network comparison tests showed significant differences in symptom network density between the subgroups categorized as survival "< 5 years" and survival "≥ 5 years" (p = 0.002), as well as between the those with comorbidities and those without comorbidities (p = 0.037).

DISCUSSION

Our study identified symptom networks in 485 OAC. Vomiting, fatigue, and sadness were important symptoms in the symptom networks of OAC. The symptom networks differed among populations with different survival durations and comorbidities. Our network analysis provides a reference for future targeted symptom management and interventions in OAC. In the future, conducting dynamic research on symptom networks will be crucial to explore interaction mechanisms and change trends between symptoms.

SKA3 targeted therapies in cancer precision surgery: bridging bench discoveries to clinical applications - review article

Spindle and kinetochore-associated complex subunit 3 (SKA3) is a microtubule-binding subcomplex of the outer kinetochore, which plays a vital role in proper chromosomal segregation and cell division. Recently, SKA3 have been demonstrated its oncogenic role of tumorigenesis and development in cancers. In this review, the authors comprehensively deciphered SKA3 in human cancer from various aspects, including bibliometrics, pan-cancer analysis, and narrative summary. The authors also provided the top 10 predicted drugs targeting SKA3. The authors proposed that SKA3 was a potential target and brought new therapeutic opportunities for cancer patients.

Pan-cancer analysis of RNA 5-methylcytosine reader (ALYREF)

The increasing interest in RNA modifications has significantly advanced epigenomic and epitranscriptomic technologies. This study focuses on the immuno-oncological impact of ALYREF in human cancer through a pan-cancer analysis, enhancing understanding of this gene's role in cancer. We observed differential ALYREF expression between tumor and normal samples, correlating strongly with prognosis in various cancers, particularly kidney renal papillary cell carcinoma (KIRP) and liver hepatocellular carcinoma (LIHC). ALYREF showed a negative correlation with most tumor-infiltrating cells in lung squamous cell carcinoma (LUSC) and lymphoid neoplasm diffuse large B-cell lymphoma (DLBC), while positive correlations were noted in LIHC, kidney chromophobe (KICH), mesothelioma (MESO), KIRP, pheochromocytoma and paraganglioma (PARD), and glioma (GBMLGG). Additionally, ALYREF expression was closely associated with tumor heterogeneity, stemness indices, and a high mutation rate in TP53 across these cancers. In conclusion, ALYREF may serve as an oncogenic biomarker in numerous cancers, meriting further research attention.

Establishment of novel ferroptosis-related prognostic subtypes correlating with immune dysfunction in prostate cancer patients

Background

We aimed to identify two new prognostic subtypes and create a predictive index for prostate cancer (PCa) patients based on ferroptosis database.

Methods

The nonnegative matrix factorization approach was used to identify molecular subtypes. We investigate the differences between cluster 1 and cluster 2 in terms of clinical features, functional pathways, tumour stemness, tumour heterogeneity, gene mutation and tumour immune microenvironment score after identifying the two molecular subtypes. Colony formation assay and flow cytometry assay were performed.

Results

The stratification of two clusters was closely connected to BCR-free survival using the nonnegative matrix factorization method, which was validated in the other three datasets. Furthermore, multivariate Cox regression analysis revealed that this classification was an independent risk factor for patients with PCa. Ribosome, aminoacyl tRNA production, oxidative phosphorylation, and Parkinson's disease-related pathways were shown to be highly enriched in cluster 1. In comparison to cluster 2, patients in cluster 1 exhibited significantly reduced CD4+ T cells, CD8+ T cells, neutrophils, dendritic cells and tumor immune microenvironment scores. Only HHLA2 was more abundant in cluster 1. Moreover, we found that P4HB downregulation could significantly inhibit the colony formation ability and contributed to cell apoptosis of C4-2B and DU145 cell lines.

Conclusions

We discovered two new prognostic subtypes associated with immunological dysfunction in PCa patients based on ferroptosis-related genes and found that P4HB downregulation could significantly inhibit the colony formation ability and contributed to cell apoptosis of PCa cell lines.

Targeting Prolyl 4-Hydroxylase Subunit Beta (P4HB) in Cancer: New Roads to Travel

Prolyl 4-hydroxylase subunit beta (P4HB) can catalyze the formation, breakage and rearrangement of disulfide bonds through two thioredoxin domains, which is important for the maintenance of oxidizing environment in endoplasmic reticulum. Recently, P4HB has been demonstrated its oncogenic role of tumorigenesis and development in cancers. Therefore, we comprehensively deciphered P4HB in human cancer from various aspects, including pan-cancer analysis and narrative summary. We also provided some possible interacted molecules and the top 10 predicted drugs targeting P4HB to contribute to future research. We proposed that P4HB was a potential target and brought new therapeutic opportunities for cancer patients.

Prognostic factors and survival prediction of resected non-small cell lung cancer with ipsilateral pulmonary metastases: a study based on the Surveillance, Epidemiology, and End Results (SEER) database

BACKGROUND

Prognostic factors and survival outcomes of non-small cell lung cancer (NSCLC) with Ipsilateral pulmonary metastasis (IPM) are not well-defined. Thus, this study intended to identify the prognostic factors for these patients and construct a predictive nomogram model.

METHODS

One thousand, seven hundred thirty-two patients with IPM identified between 2000 to 2019 were from the Surveillance, Epidemiology, and End Results (SEER) database. Independent prognostic factors were identified using multivariate Cox regression analyses. Nomograms were constructed to predict the overall survival (OS), C-index, the area under the curve (AUC), and the calibration curve to determine the predictive accuracy and discrimination; the decision curve analysis was used to confirm the clinical utility.

RESULTS

Patients were randomly divided into training (n = 1213) and validation (n = 519) cohorts. In the training cohort, the multivariable analysis demonstrated that age, sex, primary tumor size, N status, number of regional lymph nodes removed, tumor grade, and chemotherapy were independent prognostic factors for IPM. We constructed a 1-year, 3-year, and 5-year OS prediction nomogram model using independent prognostic factors. The C-index of this model for OS prediction was 0.714 (95% confidence interval [CI], 0.692 to 0.773) in the training cohort and 0.695 (95% CI, 0.660 to 0.730) in the validation cohort. Based on the AUC of the receiver operating characteristic analysis, calibration plots, and decision curve analysis, we concluded that the prognosis model of IPM exhibited excellent performance. Patients with total nomogram points greater than 96 were considered high-risk.

CONCLUSION

We constructed and internally validated a nomogram to predict 1-year, 3-year, and 5-year OS for NSCLC patients with IPM according to independent prognostic factors. This nomogram demonstrated good calibration, discrimination, clinical utility, and practical decision-making effects for the prognosis of NSCLC patients with IPM.

Identification of senescence-related lncRNA prognostic index correlating with prognosis and radiosensitivity in prostate cancer patients

BACKGROUND

An increasing number of studies are shown how crucial a role cellular senescence plays in tumor development. In this study, we developed a senescence-related lncRNA prognostic index (SRLPI) to forecast radiosensitivity and the probability of biochemical recurrence (BCR) in patients with prostate cancer (PCa).

METHODS

PCa cohorts in TCGA and GEO databases were downloaded. Senescence-and prognosis-related lncRNA with differential expression in tumor and normal samples were identified and used to establish the SRLPI score. Mutation landscape, function pathway, tumor stemness and heterogeneity and tumor immune microenvironment were also analyzed. We performed the analysis using R 3.6.3 and the appropriate tools.

RESULTS

A SRLPI score was constructed based on SNHG1 and MIAT in the TCGA cohort. Our classification of PCa patients into high- and low-risk groups was based on the median SRLPI score. When compared to the low-SRLPI group, the high-SRLPI group was more vulnerable to BCR (HR: 3.33). In terms of BCR-free survival and metastasis-free survival, the GSE116918 showed similar findings. Surprisingly, the SRLPI score demonstrated a high level of radiosensitivity for diagnosis (AUC: 0.98). Age, Gleason score, T stage, N stage, positive lymph nodes, and residual tumor were all significantly greater in patients with high SRLPI scores. Furthermore, this score was significantly related to markers of senescence. Protein secretion and androgen response were found to be substantially enriched in the low-SRLPI group, whereas E2F targets were found to be strongly enriched in the high-SRLPI group for pathway analysis. For the tumor microenvironment assessment, B cells, CD8+ T cells, immune score and TIDE score were positively related to SRLPI score while endothelial level was negatively associated with SRLPI score with statistical significance.

CONCLUSIONS

We developed a SRLPI score that was related to prognosis and radiosensitivity and might be helpful in clinical practice.

Relationship between plasma circulating cell-free DNA concentration and treatment outcomes including prognosis in patients with advanced non-small cell lung cancer

BACKGROUND

Some research found that elevated plasma cell-free DNA (cfDNA) concentrations and poor prognosis are associated in non-small cell lung cancer (NSCLC). However, more studies need to be carried out to verify this conclusion. Therefore, this study investigated the relationship between cfDNA concentration and treatment outcomes including prognosis in patients with advanced NSCLC.

METHODS

We retrospectively collected medical records and cfDNA data from 160 patients with advanced NSCLC. Progression-free survival (PFS) were calculated using the Kaplan-Meier method and were compared between groups using the log rank test. Cox regression analysis was used for estimating the independent predictors of PFS. And we used logistic regression to evaluate the relationship between baseline biomarkers and efficacy. In our study, BT1 cfDNA, BT2 cfDNA, and BT3 cfDNA were defined as cfDNA concentration before the first treatment (baseline cfDNA concentration), cfDNA concentration before the second treatment, and cfDNA concentration before the third treatment, respectively.

RESULTS

Patients with low cfDNA (BT1 cfDNA < 15 (ng/mL)) were reported a significantly prolonged median progression-free survival (mPFS) compared with patients with patients with high cfDNA (BT1 cfDNA ≥ 15(ng/mL)) (mPFS: 14.6 vs. 8.3 months, P = 0.002), as well as patients with neutrophil/lymphocyte ratio (NLR)<2.98 (mPFS: 13.1 vs. 7.9 months, P = 0.023). In addition, Cox proportional hazards regression analysis identified independent indicators associated with PFS including BT1 cfDNA ≥ 15 (ng/mL), NLR ≥ 2.98 and extrapulmonary metastasis. The best cut-off value for BT3 cfDNA for predicting disease progression is 41.46 (ng/mL) (Area Under the Curve (AUC): 0.652, 95%CI: 0.516-0.788), achieving 90.7% sensitivity and 37.5% specificity for the prediction of disease progression. BT3 cfDNA (OR = 6.08, 95% CI: 1.94-19.57, P = 0.002) was an independent factor for disease progression in patients with advanced NSCLC.

CONCLUSIONS

BT1 cfDNA may be a biomarker to assess the prognosis of advanced NSCLC. Patients with advanced NSCLC with lower cfDNA and NLR before treatment had a better prognosis. Increased BT3 cfDNA concentration was an independent factor of disease progression in advanced NSCLC patients. These findings may assist in identifying high-risk patients and guiding treatment strategies.

Senescence-associated secretory phenotype constructed detrimental and beneficial subtypes and prognostic index for prostate cancer patients undergoing radical prostatectomy

BACKGROUND

Cellular senescence is growing in popularity in cancer. A dual function is played by the senescence-associated secretory phenotype (SASP) that senescent cells produce in the development of pro-inflammatory niches, tissue regeneration or destruction, senescence propagation, and malignant transformation. In this study, we conducted thorough bioinformatic analysis and meta-analysis to discover detrimental and beneficial subtypes and prognostic index for prostate cancer (PCa) patients using the experimentally confirmed SASP genes.

METHODS

We identified differentially expressed and prognosis-related SASP genes and used them to construct two molecular subtypes and risk score. Another two external cohorts were used to confirm the prognostic effect of the above subtypes and risk score and meta-analysis was further conducted. Additionally, functional analysis, tumor stemness and heterogeneity and tumor microenvironment were also evaluated. We completed analyses using software R 3.6.3 and its suitable packages. Meta-analysis was performed by software Stata 14.0.

RESULTS

Through multivariate Cox regression analysis and consensus clustering analysis, we used VGF, IGFBP3 and ANG to establish detrimental and beneficial subtypes in the TCGA cohort, which was validated through other two independent cohorts. Meta-analysis showed that detrimental SASP group had significantly higher risk of biochemical recurrence (BCR) than beneficial SASP group (HR: 2.48). Moreover, we also constructed and validated risk score based on these genes to better guide clinical practice. DNA repair, MYC target, oxidative phosphorylation, proteasome and ribosome were highly enriched in detrimental SASP group. Detrimental SASP group had significantly higher levels of B cells, CD8+ T cells, homologous recombination deficiency, loss of heterozygosity, microsatellite instability, purity, tumor mutation burden, mRNAsi, differentially methylated probes and epigenetically regulated RNA expression than beneficial SASP group. The top mutation genes between detrimental and beneficial SASP groups were SPOP, FOXA1, KMT2C, APC, BSN, DNAH17, MYH6, EPPK1, ZNF536 and ZC3H13 with statistical significance.

CONCLUSIONS

From perspective of SASP, we found detrimental and beneficial tumor subtypes which were closely associated with BCR-free survival for PCa patients, which might be important for the furture research in the field of PCa.

Prolyl 4-hydroxylase subunit beta (P4HB) could serve as a prognostic and radiosensitivity biomarker for prostate cancer patients

BACKGROUND

Prolyl 4-hydroxylase subunit beta (P4HB) has been reported as a suppressor in ferroptosis. However, no known empirical research has focused on exploring relationships between P4HB and prostate cancer (PCa). In this research, we initially examine the function of P4HB in PCa by thorough analysis of numerous databases and proliferation experiment.

METHODS

We analyzed the correlations of P4HB expression with prognosis, clinical features, mutation genes, tumor heterogeneity, stemness, tumor immune microenvironment and PCa cells using multiple databases and in vitro experiment with R 3.6.3 software and its suitable packages.

RESULTS

P4HB was significantly upregulated in tumor tissues compared to normal tissues and was closely related to biochemical recurrence-free survival. In terms of clinical correlations, we found that higher P4HB expression was significantly related to older age, higher Gleason score, advanced T stage and residual tumor. Surprisingly, P4HB had highly diagnostic accuracy of radiotherapy resistance (AUC 0.938). TGF beta signaling pathway and dorso ventral axis formation were upregulated in the group of low-expression P4HB. For tumor stemness, P4HB expression was positively related to EREG.EXPss and RNAss, but was negatively associated with ENHss and DNAss with statistical significance. For tumor heterogeneity, P4HB expression was positively related to MATH, but was negatively associated with tumor ploidy and microsatellite instability. For the overall assessment of TME, we observed that P4HB expression was negatively associated with all parameters, including B cells, CD4+ T cells, CD8+ T cells, neutrophils, macrophages, dendritic cells, stromal score, immune score and ESTIMATE score. Spearman analysis showed that P4HB expression was negatively related to TIDE score with statistical significance. In vitro experiment, RT-qPCR and western blot showed that three siRNAs of P4HB were effective on the knockdown of P4HB expression. Furthermore, we observed that the downregulation of P4HB had significant influence on the cell proliferation of six PCa cell lines, including LNCap, C4-2, C4-2B, PC3, DU145 and 22RV1 cells.

CONCLUSIONS

In this study, we found that P4HB might serve as a prognostic biomarker and predict radiotherapy resistance for PCa patients. Downregulation of P4HB expression could inhibit the cell proliferation of PCa cells.

A pan-cancer analysis of the oncogenic and immunological roles of apolipoprotein F (APOF) in human cancer

BACKGROUND

Apolipoprotein F (APOF) has been less studied in cancers. Thus, we aimed to perform a pan-cancer analysis of the oncogenic and immunological effects of APOF on human cancer.

METHODS

A standardized TCGA pan-cancer dataset was downloaded. Differential expression, clinical prognosis, genetic mutations, immune infiltration, epigenetic modifications, tumor stemness and heterogeneity were analyzed. We conducted all analyses through software R (version 3.6.3) and its suitable packages.

RESULTS

Overall, we found that the common cancers differentially expressed between tumor and normal samples and prognostic-associated were BRCA, PRAD, KIRP, and LIHC in terms of overall survival (OS), disease-free survival (DFS) and progression-free survival (PFS). The pan-cancer Spearman analysis showed that the mRNA expression of APOF was negatively correlated with four tumor stemness indexes (DMPss, DNAss, ENHss, and EREG-METHss) with statistical significance for PRAD and was positively correlated for LIHC. In terms of BRCA and PRAD patients, we found negative correlation of APOF with TMB, MSI, neo, HRD and LOH. The mutation frequencies of BRCA and LIHC were 0.3%. APOF expression was negatively correlated with immune infiltration and positively correlated with tumor purity for PRAD patients. The mRNA expression of APOF was negatively associated with most TILs for LIHC, B cells, CD4+ T cells, neutrophils, macrophages and dendritic cells, but was positively associated with CD8+ T cells.

CONCLUSIONS

Our pan-cancer study offered a relatively comprehensive understanding of the roles of APOF on BRCA, PRAD, KIRP, and LIHC.

A bibliometric and visual analysis of low carbohydrate diet

Introduction

Numerous studies have confirmed the effects of low carbohydrate diet (LChD) on metabolism and chronic diseases. However, there were no bibliometric studies on LChD. This study was conducted through a bibliometric analysis to investigate the current status, hotspots and frontiers trends.

Methods

We searched all research publications related to LChD from 2002 to 2021 on the Web of Scientific Core Collection (WoSCC). CiteSpace and VOSviewer software was used to analyze countries/regions, institutions, journals, authors, references, and keywords.

Results

A total of 6938 papers were included, with an increasing trend of annual publication. LChD categories mainly included nutrition, endocrinology, and neurosciences which reflected the interdisciplinary characteristics. USA was with the largest number and the world science center in LChD field. Universities were main research institutions and five of the top 10 institutions were from USA. Eric Heath Kossoff had 101 publications and ranked first. Nutrients was the leading journal. "A randomized trial of a low-carbohydrate diet for obesity" and "Obesity" were considered to be the most co-cited and cited reference respectively. The hotspots of LChD are four aspects, "ketogenic diet", "metabolism disease", "cardiovascular disease" and "cancer". We summarized that "oxidative stress", "gut microbiota", and "inflammation factors" are becoming frontiers trends of LChD research in the future and deserve further study.

Discussion

Over the past 20 years research on LChD has gained great attention. To better explore LChD field, multilevel mechanism studies will be required in the future.