Clinical significance of HRAS and KRAS genes expression in patients with non-small-cell lung cancer - preliminary findings

Anti-carcinogenic effects and mechanisms of actions of Citrus limon fruit peel hydroethanolic extract and limonene in diethylnitrosmine/2-acetylaminofluorene-induced hepatocellular carcinoma in Wistar rats

Hepatocellular carcinoma (HCC) is the third most common cause of cancer death and disability in the world. Citrus species and their constituents have many biological activities including antioxidant, anti-inflammatory and anti-carcinogenic properties. This study aimed to assess the anti-carcinogenic effects and postulate the possible mechanisms of action for Citrus limon fruit peel hydroethanolic extract (CLFPHE) and limonene in diethylnitrosamine (DEN)/2-acetylaminofluorene (2AAF)-induced HCC in male Wistar rats. For analysis and characterization of CLFPHE, gas chromatography-mass spectrum (GC-MS) and high performance liquid chromatography (HPLC) methods were applied. A HCC was elaborated by DEN intraperitoneal injection (150 mg/kg/week) for two weeks followed by oral delivery of 2AAF (20 mg/kg) four times a week for three weeks. The DEN/2AAF-administered rats were treated with CLFPHE (50 mg/kg) and limonene (20 mg/kg) by oral gavage every other day for 24 weeks. CLFPHE and limonene significantly attenuated the harmful effects of DEN on liver function. Histopathological analysis confirmed that both treatments inhibited DEN/2AAF-induced tumorigenesis in association with the suppression of serum tumor markers including AFP, CEA, and CA19.9 and liver proliferator indicator (Ki-67). Moreover, CLFPHE and limonene prevented the oxidative stress and enhanced the antioxidant defenses in DEN/2AAF-administered rats. These ameliorations were manifested by decreases in liver lipid peroxidation, increases in GSH, SOD and GPx levels and upregulation of Nrf2. The treatments also abated inflammation by suppressing TNF-α and IL-1β levels and IL-8 and NF-κB expression. CLFPHE and limonene substantially decreased hepatic BCL-2, IQGAP1, IQGAP3, HRAS, KRAS and Ki-67 while they elevated BAX, P53, PDCD5 and IQGAP2 expressions. Our findings suggest that CLFPHE and limonene may abate HCC development via enhancement of apoptotic, antioxidant, cell anti-proliferatory and anti-inflammatory effects.

Atypical Exon 2/3 Mutants G48C, Q43K, and E37K Present Oncogenic Phenotypes Distinct from Characterized NRAS Variants

NRAS belongs to the RAS family of GTPases. In colorectal cancer (CRC), NRAS mutations are rare compared to KRAS, but may lead to worse outcomes. We report the functional characterization of the novel NRAS mutants-G48C, Q43K, and E37K-identified in Filipino young-onset CRC patients. Unlike previously characterized NRAS mutants with no apparent effects on cell proliferation, these mutants enhanced proliferation of both HCT116 and NIH3T3 cells. This was confirmed in 3D spheroid assays to mimic the spatial organization of cells. G48C and E37K showed apoptosis resistance in both cell lines, and Q43K showed resistance in HCT116 cells. All three showed no effect on cellular migration in NIH3T3, but G48C enhanced the migration rate of HCT116 cells. Actin staining of NIH3T3 cells expressing the mutants showed a shrunken cytoplasm and transient structures associated with motility and invasiveness. Docking simulations show that GDP is only able to bind fully within the binding pocket of wild-type NRAS, but not in the mutants. Further, G48C, Q43K, and E37K all have less negative ΔG values, indicating a weaker GDP-binding affinity compared to wild-type NRAS. Taken together, the results suggest that oncogenic readouts of NRAS mutants are codon- and mutation-specific, with potential repercussions on the aggressiveness, resistance, and therapeutic response.

Molecular landscape of borderline ovarian tumours: A systematic review

Borderline ovarian tumours (BOTs) show intriguing characteristics distinguishing them from other ovarian tumours. The aim of the systematic review was to analyse the spectrum of molecular changes found in BOTs and discuss their significance in the context of the overall therapeutic approach. The systematic review included articles published between 2000 and 2023 in the databases: PubMed, EMBASE, and Cochrane. After a detailed analysis of the available publications, we qualified for the systematic review: 28 publications on proto-oncogenes: BRAF, KRAS, NRAS, ERBB2, and PIK3CA, 20 publications on tumour suppressor genes: BRCA1/2, ARID1A, CHEK2, PTEN, 4 on adhesion molecules: CADM1, 8 on proteins: B-catenin, claudin-1, and 5 on glycoproteins: E-Cadherin. In addition, in the further part of the systematic review, we included eight publications on microsatellite instability and three describing loss of heterozygosity in BOT. Molecular changes found in BOTs can vary on a case-by-case basis, identifying carcinogenic mutations through molecular analysis and developing targeted therapies represent significant advancements in the diagnosis and treatment of ovarian malignancies. Molecular studies have contributed significantly to our understanding of BOT pathogenesis, but substantial research is still required to elucidate the relationship between ovarian neoplasms and extraneous disease, identify accurate prognostic indicators, and develop targeted therapeutic approaches.

Overexpression of wild-type HRAS drives non-alcoholic steatohepatitis to hepatocellular carcinoma in mice

Hepatocellular carcinoma (HCC), a prevalent solid carcinoma of significant concern, is an aggressive and often fatal disease with increasing global incidence rates and poor therapeutic outcomes. The etiology and pathological progression of non-alcoholic steatohepatitis (NASH)-related HCC is multifactorial and multistage. However, no single animal model can accurately mimic the full NASH-related HCC pathological progression, posing considerable challenges to transition and mechanistic studies. Herein, a novel conditional inducible wild-type human HRAS overexpressed mouse model (HRAS-HCC) was established, demonstrating 100% morbidity and mortality within approximately one month under normal dietary and lifestyle conditions. Advanced symptoms of HCC such as ascites, thrombus, internal hemorrhage, jaundice, and lung metastasis were successfully replicated in mice. In-depth pathological features of NASH- related HCC were demonstrated by pathological staining, biochemical analyses, and typical marker gene detections. Combined murine anti-PD-1 and sorafenib treatment effectively prolonged mouse survival, further confirming the accuracy and reliability of the model. Based on protein-protein interaction (PPI) network and RNA sequencing analyses, we speculated that overexpression of HRAS may initiate the THBS1-COL4A3 axis to induce NASH with severe fibrosis, with subsequent progression to HCC. Collectively, our study successfully duplicated natural sequential progression in a single murine model over a very short period, providing an accurate and reliable preclinical tool for therapeutic evaluations targeting the NASH to HCC continuum.

The Genomic, Transcriptomic, and Immunologic Landscape of HRAS Mutations in Solid Tumors

Tipifarnib is the only targeted therapy breakthrough for HRAS-mutant (HRASmt) recurrent or metastatic head and neck squamous cell carcinoma (HNSCC). The molecular profiles of HRASmt cancers are difficult to explore given the low frequency of HRASmt. This study aims to understand the molecular co-alterations, immune profiles, and clinical outcomes of 524 HRASmt solid tumors including urothelial carcinoma (UC), breast cancer (BC), non-small-cell lung cancer (NSCLC), melanoma, and HNSCC. HRASmt was most common in UC (3.0%), followed by HNSCC (2.82%), melanoma (1.05%), BC (0.45%), and NSCLC (0.44%). HRASmt was absent in Her2+ BC regardless of hormone receptor status. HRASmt was more frequently associated with squamous compared to non-squamous NSCLC (60% vs. 40% in HRASwt, p = 0.002). The tumor microenvironment (TME) of HRASmt demonstrated increased M1 macrophages in triple-negative BC (TNBC), HNSCC, squamous NSCLC, and UC; increased M2 macrophages in TNBC; and increased CD8+ T-cells in HNSCC (all p < 0.05). Finally, HRASmt was associated with shorter overall survival in HNSCC (HR: 1.564, CI: 1.16-2.11, p = 0.003) but not in the other cancer types examined. In conclusion, this study provides new insights into the unique molecular profiles of HRASmt tumors that may help to identify new targets and guide future clinical trial design.

Polystyrene microplastics induce anxiety via HRAS derived PERK-NF-κB pathway

Exposure to environmentally hazardous substances is recognized as a significant risk factor for neurological associated disorders. Among these substances, polystyrene microplastics (PS-MPs), widely utilized in various consumer products, have been reported to exhibit neurotoxicity. However, the potential association of PS-MPs with abnormal anxiety behaviors, along with the underlying molecular mechanisms and key proteins involved, remains insufficiently explored. Here, we delineated the potential mechanisms of PS-MPs-induced anxiety through proteomics and molecular investigations. We characterized the PS-MPs, observed their accumulation in the brain, leading to anxiety-like behavior in mice, which is correlated with microglia activation and pro-inflammatory response. Consistent with these findings, our studies on BV2 microglia cells showed that PS-MPs activated NF-κB-mediated inflammation resulting in the upregulation of pro-inflammatory cytokines such as TNFα and IL-1β. Of particular significance, HRAS was identified as a key factor in the PS-MPs induced pro-inflammatory response through whole proteomics analysis, and knockdown of H-ras effectively inhibited PS-MPs induced PERK-NF-κB activation and associated pro-inflammatory response in microglia cells. Collectively, our findings highlight that PS-MPs induce anxiety of mice via the activation of the HRAS-derived PERK-NF-κB pathway in microlglia. Our results contribute valuable insights into the molecular mechanisms of PS-MPs-induced anxiety, and may offer implications for addressing neurotoxicity and prevention the adverse effects of environmentally hazardous substances, including microplastics.

Genomic features of lung cancer patients in Indonesia's national cancer center

INTRODUCTION

Advances in molecular biology bring advantages to lung cancer management. Moreover, high-throughput molecular tests are currently useful for revealing genetic variations among lung cancer patients. We investigated the genomics profile of the lung cancer patients at the National Cancer Centre of Indonesia.

METHODS

A retrospective study enrolled 627 tissue biopsy samples using real time polymerase chain reaction (RT-PCR) and 80 circulating tumour DNA (ctDNA) liquid biopsy samples using next-generation sequencing (NGS) from lung cancer patients admitted to the Dharmais Cancer Hospital from January 2018 to December 2022. Data were obtained from medical records. Data statistically analysed with p < 0.05 is considered significant.

RESULT

The EGFR test results revealed by RT-PCR were wild type (51.5%), single variant (38.8%), double variant (8.3%), and triple variant (1.4%), with 18.66% L85R, 18.22% Ex19del, and 11.08% L861Q variant. Liquid biopsy ctDNA using NGS showed only 2.5% EGFR wild type, 62.5% single variant and 35% co-variant, with EGFR/TP53 and EGFR/PIK3CA as the highest.

CONCLUSION

EGFR variants are the most found in our centre. Liquid biopsy with ctDNA using NGS examination could detect broad variants and co-variants that will influence the treatment planning.

Characterization of exosomal microRNAs in preterm infants fed with breast milk and infant formula

Breastfeeding not only reduces infection-related morbidity, but also increases growth of preterm infants. Advantages of breast milk (BM) for preterm infants are significant. They continue to be studied. However, because not all preterm infants can receive breastfeeding, bovine-based infant formula (IF) is used as an alternative, which may increase the risk of several preterm complications. Exosomes isolated from biofluids are emerging as biomarkers in research of various diseases. Here, we characterized miRNA contents of exosomes in urine and serum samples of preterm infants who were BM and IF fed and performed transcriptomic analysis of small RNA libraries. We identified significantly up-regulated 6 miRNAs and 10 miRNAs, respectively. Gene Ontology (GO) analysis revealed that target genes of these miRNAs might participate in neuronal development, immunity modulation, detoxification of reactive oxygen species, and transmembrane exchange. Our data suggest that exosome-based systemic screening for preterm infants with breastfeeding might be a screening tool for identifying target molecules involved in therapy for preterm infants in neonatal intensive care unit (NICU) and for future application as nutraceutical formulations or pharmaceuticals.

The Anticancer Effects of Marine Carotenoid Fucoxanthin through Phosphatidylinositol 3-Kinase (PI3K)-AKT Signaling on Triple-Negative Breast Cancer Cells

Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer that lacks specific targets such as estrogen, progesterone, and HER2 receptors. TNBC affects one in eight women in the United States, making up 15-20% of breast cancer cases. Patients with TNBC can develop resistance to chemotherapy over time, leading to treatment failure. Therefore, finding other options like natural products is necessary for treatment. The advantages of using natural products sourced from plants as anticancer agents are that they are less toxic, more affordable, and have fewer side effects. These products can modulate several cellular processes of the tumor microenvironment, such as proliferation, migration, angiogenesis, cell cycle arrest, and apoptosis. The phosphatidyl inositol 3-kinase (PI3K)-AKT signaling pathway is an important pathway that contributes to the survival and growth of the tumor microenvironment and is associated with these cellular processes. This current study examined the anticancer effects of fucoxanthin, a marine carotenoid isolated from brown seaweed, in the MDA-MB-231 and MDA-MB-468 TNBC cell lines. The methods used in this study include a cytotoxic assay, PI3K-AKT signaling pathway PCR arrays, and Wes analysis. Fucoxanthin (6.25 µM) + TNF-α (50 ng/mL) and TNF-α (50 ng/mL) showed no significant effect on cell viability compared to the control in both MDA-MB-231 and MDA-MB-468 cells after a 24 h treatment period. PI3K-AKT signaling pathway PCR array studies showed that in TNF-α-stimulated (50 ng/mL) MDA-MB-231 and MDA-MB-468 cells, fucoxanthin (6.25 µM) modulated the mRNA expression of 12 genes, including FOXO1, RASA1, HRAS, MAPK3, PDK2, IRS1, EIF4EBP1, EIF4B, PTK2, TIRAP, RHOA, and ELK1. Additionally, fucoxanthin significantly downregulated the protein expression of IRS1, EIF4B, and ELK1 in MDA-MB-231 cells, and no change in the protein expression of EIF4B and ELK1 was shown in MDA-MB-468 cells. Fucoxanthin upregulated the protein expression of RHOA in both cell lines. The modulation of the expression of genes and proteins of the PI3K-AKT signaling pathway may elucidate fucoxanthin's effects in cell cycle progression, apoptotic processes, migration, and proliferation, which shows that PI3K-AKT may be the possible molecular mechanism for fucoxanthin's effects. In conclusion, the results obtained in this study elucidate fucoxanthin's molecular mechanisms and indicate that fucoxanthin may be considered a promising candidate for breast cancer-targeted therapy.

Proteomic analysis of STEAP1 knockdown in human LNCaP prostate cancer cells

Prostate cancer (PCa) continues to be one of the most common cancers in men worldwide. The six transmembrane epithelial antigen of the prostate 1 (STEAP1) protein is overexpressed in several types of human tumors, particularly in PCa. Our research group has demonstrated that STEAP1 overexpression is associated with PCa progression and aggressiveness. Therefore, understanding the cellular and molecular mechanisms triggered by STEAP1 overexpression will provide important insights to delineate new strategies for PCa treatment. In the present work, a proteomic strategy was used to characterize the intracellular signaling pathways and the molecular targets downstream of STEAP1 in PCa cells. A label-free approach was applied using an Orbitrap LC-MS/MS system to characterize the proteome of STEAP1-knockdown PCa cells. More than 6700 proteins were identified, of which a total of 526 proteins were found differentially expressed in scramble siRNA versus STEAP1 siRNA (234 proteins up-regulated and 292 proteins down-regulated). Bioinformatics analysis allowed us to explore the mechanism through which STEAP1 exerts influence on PCa, revealing that endocytosis, RNA transport, apoptosis, aminoacyl-tRNA biosynthesis, and metabolic pathways are the main biological processes where STEAP1 is involved. By immunoblotting, it was confirmed that STEAP1 silencing induced the up-regulation of cathepsin B, intersectin-1, and syntaxin 4, and the down-regulation of HRas, PIK3C2A, and DIS3. These findings suggested that blocking STEAP1 might be a suitable strategy to activate apoptosis and endocytosis, and diminish cellular metabolism and intercellular communication, leading to inhibition of PCa progression.

Proactive and reactive roles of TGF-β in cancer

Cancer cells adapt to varying stress conditions to survive through plasticity. Stem cells exhibit a high degree of plasticity, allowing them to generate more stem cells or differentiate them into specialized cell types to contribute to tissue development, growth, and repair. Cancer cells can also exhibit plasticity and acquire properties that enhance their survival. TGF-β is an unrivaled growth factor exploited by cancer cells to gain plasticity. TGF-β-mediated signaling enables carcinoma cells to alter their epithelial and mesenchymal properties through epithelial-mesenchymal plasticity (EMP). However, TGF-β is a multifunctional cytokine; thus, the signaling by TGF-β can be detrimental or beneficial to cancer cells depending on the cellular context. Those cells that overcome the anti-tumor effect of TGF-β can induce epithelial-mesenchymal transition (EMT) to gain EMP benefits. EMP allows cancer cells to alter their cell properties and the tumor immune microenvironment (TIME), facilitating their survival. Due to the significant roles of TGF-β and EMP in carcinoma progression, it is essential to understand how TGF-β enables EMP and how cancer cells exploit this plasticity. This understanding will guide the development of effective TGF-β-targeting therapies that eliminate cancer cell plasticity.

Biosensors for the detection of lung cancer biomarkers: A review on biomarkers, transducing techniques and recent graphene-based implementations

Lung cancer remains the leading cause of cancer-related death. In addition to chest X-rays and computerised tomography, the detection of cancer biomarkers serves as an emerging diagnostic tool for lung cancer. This review explores biomarkers including the rat sarcoma gene, the tumour protein 53 gene, the epidermal growth factor receptor, the neuron-specific enolase, the cytokeratin-19 fragment 21-1 and carcinoembryonic antigen as potential indicators of lung cancer. Biosensors, which utilise various transduction techniques, present a promising solution for the detection of lung cancer biomarkers. Therefore, this review also explores the working principles and recent implementations of transducers in the detection of lung cancer biomarkers. The transducing techniques explored include optical techniques, electrochemical techniques and mass-based techniques for detecting biomarkers and cancer-related volatile organic compounds. Graphene has outstanding properties in terms of charge transfer, surface area, thermal conductivity and optical characteristics, on top of allowing easy incorporation of other nanomaterials. Exploiting the collective merits of both graphene and biosensor is an emerging trend, as evidenced by the growing number of studies on graphene-based biosensors for the detection of lung cancer biomarkers. This work provides a comprehensive review of these studies, including information on modification schemes, nanomaterials, amplification strategies, real sample applications, and sensor performance. The paper concludes with a discussion of the challenges and future outlook of lung cancer biosensors, including scalable graphene synthesis, multi-biomarker detection, portability, miniaturisation, financial support, and commercialisation.

New insights into the functional role of protein phosphatase 4 regulatory subunit PP4R3A/SMEK1 in the regulation of leukemic cell fate

The serine/threonine protein phosphatase 4 holoenzyme consists of a PP4 catalytic subunit (PP4c), which interacts with four different regulatory subunits. Previous studies have shown that PP4c acts as a tumour suppressor. Emerging evidence suggests that the protein phosphatase 4 regulatory subunits might regulate cell fate independently of PP4c. To this end, we investigated the role of PP4R3A (SMEK1) in Jurkat and CEM-C7 leukemic cell lines. SMEK1 overexpression decreased cell growth, increased spontaneous apoptosis, and reduced the colony forming ability of leukemic cells. Conversely, siRNA-mediated silencing of SMEK1 led to increased short and long-term survival in these cells. Phospho-protein arrays revealed that increased expression of SMEK1 affected the phosphorylation of key proteins involved in MAPK3, AKT, JAK/STAT, NFκB and TGFβ signalling pathways. These proteins include transcription factors such as NFκB, STAT3, c-JUN, SMAD1, and SMAD5, suggesting a role for SMEK1 in the regulation of gene expression. RNA sequencing confirmed the role of SMEK1 in the regulation of gene expression. RNA sequencing also confirmed the tumour suppressor role of SMEK1. Taken together, this study shows that SMEK1 regulates leukemic T cell survival, indicating that SMEK1 dysfunction may be important in the development and progression of leukemia.

Differential proteome and functional analysis of NSCLC cell lines in response to Tualang honey treatment

ETHNOPHARMACOLOGICAL RELEVANCE

Honey's therapeutic and nutrition effects have been discovered for centuries. Traditionally, it is applied as a health supplement as well as an alternative treatment for a variety of medical issues ranging from wound healing to anticancer therapy. Tualang honey (TH) is a natural sweet substance produced by Apis dorsata, naturally has a dark brown appearance from its high polyphenolic compounds. TH has been reported to show anticancer effects on various types of cancers including breast, oral, leukemia, cervical and lung cancer through several pathways. The detailed molecular mechanism of anticancer activity of TH as a chemopreventive and therapeutic agent is an interesting endeavor to understand.

AIM OF THE STUDY

Despite the anticancer effects of Tualang honey (TH) on various types of cancer have been widely reported, the exact molecular mechanism underlying its' anticancer action remains unpublished. Thus, this study aimed to investigate changes that occur on the proteome profile and the functional analysis of proteins with differential abundances within non-small cell lung cancer (NSCLC) cells that were treated with TH and discover the plausible molecular mechanism governing its' anticancer action.

MATERIALS AND METHODS

NSCLC cell lines (H23 and A549) were treated with 3.6% and 3.1% v/v of TH for 24 h, respectively. Protein extracts were obtained from control NSCLC cells and TH-treated NSCLC cells. Label-free quantitative proteomic analysis was subsequently performed in nanoACQUITY UPLC with quadrupole-time of flight (Q-TOF) Synapt G2 HDMS mass spectrometer system to identify and quantify proteins of TH-treated NSCLC cells. The gene ontology (GO) PANTHER classification system was performed to categorize the identified proteins based on their protein class, biological processes, and pathway. Meanwhile, the STRING functional protein association network database was used to analyze the functional protein-protein interaction and associated pathways of significantly different proteins of NSCLC cells.

RESULTS

A total of 634 and 554 proteins were identified from H23 and A549 cell lines where 88 differential proteins were upregulated and 103 were downregulated in TH-treated H23 cells, whilst 66 differential proteins were upregulated and 61 were downregulated in TH-treated A549 cells. Differently expressed proteins of NSCLC were observed to be associated with the cell cycle, apoptosis, and VEGFA-VEGFR signaling pathway. TH modulated these signaling pathways through downregulation of ELAVL1, H3F3A and PCNA proteins. Three potential protein markers were significantly downregulated in NSCLC cells such as HRAS, HSPB1, and TUBA1C when treated with TH.

CONCLUSIONS

Our findings suggested the anticancer activity of TH on NSCLC cells through modulation of pertinent cancer-related proteins that are associated with cell proliferation, apoptosis inhibition, and induction of angiogenesis.

PATTERN OF KRAS GENE EXPRESSION IN IRAQI WOMEN OVARIAN CARCINOMA

OBJECTIVE

The aim: The goal of this study was to detect if KRAS gene and levels of had any clinical significance in the ovarian cancer by measuring levels of KRAS mRNA.

PATIENTS AND METHODS

Materials and methods: The investigation was conducted on 84 tissue samples from newly diagnosed patients with ovarian cancer. Twenty-eight tissue sections with benign ovarian tumors were used as a control group. The qRT- PCR technique was used for measuring and analyzing levels of KRAS mRNA.

RESULTS

Results: Relative increasing of KRAS mRNA level in cancer samples was statistically significant (P<0.01) when compared to benign tumors. Statistically no significant differences were found between KRAS mRNA levels and menopausal status or family history. Gene expression has been substantially connected with age groups as the highest levels of KRAS mRNA was recorded in patients with age 50-74 years (P<0.01). Endometrium tumors exhibited significant correlations (P<0.01) across histopathological tumor types. In correlation with tumor stages, stage I was substantially linked compared to stage I (P<0.01).

CONCLUSION

Conclusions: It was concluded that over expression of the KRAS gene is linked to early stages of ovarian cancer, which implying that mRNA levels could be used as a diagnostic and predictive factor for ovarian cancer. More research with larger groups of ovarian cancer specimens in both primary and advanced stages is needed.

Unfolding the role of autophagy in the cancer metabolism

Autophagy is considered an indispensable process that scavenges toxins, recycles complex macromolecules, and sustains the essential cellular functions. In addition to its housekeeping role, autophagy plays a substantial role in many pathophysiological processes such as cancer. Certainly, it adapts cancer cells to thrive in the stress conditions such as hypoxia and starvation. Cancer cells indeed have also evolved by exploiting the autophagy process to fulfill energy requirements through the production of metabolic fuel sources and fundamentally altered metabolic pathways. Occasionally autophagy as a foe impedes tumorigenesis and promotes cell death. The complex role of autophagy in cancer makes it a potent therapeutic target and has been actively tested in clinical trials. Moreover, the versatility of autophagy has opened new avenues of effective combinatorial therapeutic strategies. Thereby, it is imperative to comprehend the specificity of autophagy in cancer-metabolism. This review summarizes the recent research and conceptual framework on the regulation of autophagy by various metabolic pathways, enzymes, and their cross-talk in the cancer milieu, including the implementation of altered metabolism and autophagy in clinically approved and experimental therapeutics.

Comprehensive Profiling of Genomic and Transcriptomic Differences between Risk Groups of Lung Adenocarcinoma and Lung Squamous Cell Carcinoma

Lung cancer is the second most frequently diagnosed cancer type and responsible for the highest number of cancer deaths worldwide. Lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) are subtypes of non-small-cell lung cancer which has the highest frequency of lung cancer cases. We aimed to analyze genomic and transcriptomic variations including simple nucleotide variations (SNVs), copy number variations (CNVs) and differential expressed genes (DEGs) in order to find key genes and pathways for diagnostic and prognostic prediction for lung adenocarcinoma and lung squamous cell carcinoma. We performed a univariate Cox model and then lasso-regularized Cox model with leave-one-out cross-validation using The Cancer Genome Atlas (TCGA) gene expression data in tumor samples. We generated 35- and 33-gene signatures for prognostic risk prediction based on the overall survival time of the patients with LUAD and LUSC, respectively. When we clustered patients into high- and low-risk groups, the survival analysis showed highly significant results with high prediction power for both training and test datasets. Then, we characterized the differences including significant SNVs, CNVs, DEGs, active subnetworks, and the pathways. We described the results for the risk groups and cancer subtypes separately to identify specific genomic alterations between both high-risk groups and cancer subtypes. Both LUAD and LUSC high-risk groups have more downregulated immune pathways and upregulated metabolic pathways. On the other hand, low-risk groups have both up- and downregulated genes on cancer-related pathways. Both LUAD and LUSC have important gene alterations such as CDKN2A and CDKN2B deletions with different frequencies. SOX2 amplification occurs in LUSC and PSMD4 amplification in LUAD. EGFR and KRAS mutations are mutually exclusive in LUAD samples. EGFR, MGA, SMARCA4, ATM, RBM10, and KDM5C genes are mutated only in LUAD but not in LUSC. CDKN2A, PTEN, and HRAS genes are mutated only in LUSC samples. The low-risk groups of both LUAD and LUSC tend to have a higher number of SNVs, CNVs, and DEGs. The signature genes and altered genes have the potential to be used as diagnostic and prognostic biomarkers for personalized oncology.