Oncogenic Regulator Research Articles

KRAS modulates immune infiltration levels and survival outcomes in patients with lung adenocarcinoma

The murine sarcoma virus oncogene (KRAS) is a key gene associated with tumorigenesis and chemotherapy resistance. However, little is known about the molecular mechanisms and immune infiltration of RASs in lung adenocarcinoma. Gene Expression Profiling Interaction Analysis was used for RASs expression analysis, and Kaplan–Meier analysis was used to analyze the potential of RASs in clinical prognosis. The effect of KRAS on immune infiltration was analyzed by TIMER. In addition, the correlation between KRAS expression and molecular mechanisms was investigated by TIMER and Cancer Single-cell State Atlas (Cancer SEA). KRAS expression levels were associated with good prognosis and tumor progression. Furthermore, KRAS expression correlates with several immune cell markers and regulates tumorigenesis. KRAS expression is involved in the regulation of multiple oncogenes and tumorigenesis, especially in the prognosis and immune infiltration of lung adenocarcinoma.

Phospholipase PLCE1 Promotes Transcription and Phosphorylation of MCM7 to Drive Tumor Progression in Esophageal Cancer.

PLCE1 promotes tumor progression in ESCC by activating PKCα-mediated phosphorylation of E2F1 to upregulate MCM7 and miR-106b-5p expression and by potentiating MCM7 phosphorylation by RIOK2.

CRISPR/Cas9 in the treatment of -thalassemia

Based on clinical evidence, medication resistance poses a significant challenge to the treatment of cancer. It causes the disease to become uncontrollable and raises death rates. Drug resistance arises from a variety of causes, but a change in the inherited makeup of tumor cells is typically the root reason. The ability to modify the genome is growing with the recent discovery of clustered regularly interspaced short palindromic repeats (CRISPR)/associated (Cas)9 technology, which may be helpful in reducing drug resistance. Owing to its exceptional accuracy and efficiency, the CRISPR/Cas 9 system has been used to investigate the relevant roles of cancer-causing genes, create animal models of tumors, and identify potential therapeutic targets. As a result, it has emerged as the go-to technique for therapeutic gene editing. Utilizing CRISPR/Cas 9 technologies in the treatment of different diseases is growing. Because oncogene regulation differs from normal gene regulation, the CRISPR/Cas 9 system offers efficient methods for oncogene elimination, interference with expression, and modification of activity, all of which can effectively impede the growth of tumors. This article discusses the potential of the CRISPR/Cas9 system to identify resistance targets in drug-resistant breast cancer and reverse resistance gene alterations. Furthermore, the difficulties that prevent this technology from being clinically applicable and emphasize the CRISPR/Cas9 systems are discussed. The CRISPR/Cas9 system will be a crucial component of personalized medicine and is anticipated to have a significant impact on reducing drug resistance in cancer therapy.

Palmitoylation landscapes across human cancers reveal a role of palmitoylation in tumorigenesis

BackgroundProtein palmitoylation, which is catalyzed by palmitoyl-transferase and de-palmitoyl-transferase, plays a crucial role in various biological processes. However, the landscape and dynamics of protein palmitoylation in human cancers are not well understood.MethodsWe utilized 23 palmitoyl-acyltransferases and seven de-palmitoyl-acyltransferases as palmitoylation-related genes for protein palmitoylation analysis. Multiple publicly available datasets were employed to conduct pan-cancer analysis, examining the transcriptome, genomic alterations, clinical outcomes, and correlation with c-Myc (Myc) for palmitoylation-related genes. Real-time quantitative PCR and immunoblotting were performed to assess the expression of palmitoylation-related genes and global protein palmitoylation levels in cancer cells treated with Myc depletion or small molecule inhibitors. Protein docking and drug sensitivity analyses were employed to predict small molecules that target palmitoylation-related genes.ResultsWe identified associations between palmitoylation and cancer subtype, stage, and patient survival. We discovered that abnormal DNA methylation and oncogenic Myc-driven transcriptional regulation synergistically contribute to the dysregulation of palmitoylation-related genes. This dysregulation of palmitoylation was closely correlated with immune infiltration in the tumor microenvironment and the response to immunotherapy. Importantly, dysregulated palmitoylation was found to modulate canonical cancer-related pathways, thus influencing tumorigenesis. To support our findings, we performed a proof-of-concept experiment showing that depletion of Myc led to reduced expression of most palmitoylation-related genes, resulting in decreased global protein palmitoylation levels. Through mass spectrometry and enrichment analyses, we also identified palmitoyl-acyltransferases ZDHHC7 and ZDHHC23 as significant contributors to mTOR signaling, DNA repair, and immune pathways, highlighting their potential roles in tumorigenesis. Additionally, our study explored the potential of three small molecular (BI-2531, etoposide, and piperlongumine) to modulate palmitoylation by targeting the expression or activity of palmitoylation-related genes or enzymes.ConclusionsOverall, our findings underscore the critical role of dysregulated palmitoylation in tumorigenesis and the response to immunotherapy, mediated through classical cancer-related pathways and immune cell infiltration. Additionally, we propose that the aforementioned three small molecule hold promise as potential therapeutics for modulating palmitoylation, thereby offering novel avenues for cancer therapy.

STAT5-Feedback Controls Distinct Metabolic States for Dynamic Transitions between Cellular Activation and Quiescence in Acute Lymphoblastic Leukemia

Background and significance: B-cell acute lymphoblastic leukemia (B-ALL) is characterized by dynamic shifts between activation and quiescence. These cycles are predicated by fluctuations in oncogenic signaling, which mimic pre-BCR and cytokine receptor signaling, e.g. IL7 receptor signaling and phosphorylation of STAT5. These fluctuations in cytokine receptor and STAT5 signaling are mitigated by powerful feedback regulators, including CISH and SOCS (suppressors of cytokine signaling) family members. While B-ALL cells depend on oncogenic STAT5 signaling, CISH and SOCS2 negative feedback regulators of STAT5 are highly expressed in aggressive B-ALL and high expression levels are strongly linked to poor clinical outcome, positive MRD and increased likelihood of bone marrow relapse in children (COG P9906) and adults (ECOG E2993). To determine whether high levels of CISH and SOCS2 are biomarkers of high oncogenic STAT5 signaling or mechanistically contribute to clonal fitness and adaptability of B-ALL, we performed genetic experiments in mouse models for B-ALL. Here we examined the mechanisms and consequences of active and inactive states of STAT5 by studying constitutively active (CA) and non-phosphorylatable Y694F (YF) mutations of STAT5. Results: Consistent with a central role of STAT5-feedback control in B-ALL survival, inducible ablation of Cishfl/fl resulted in rapid depletion of B-ALL cells. Socs2-/- B-ALL cells rapidly underwent cellular senescence, lacked colony forming and leukemia-initiating capacity in serial transplantation experiments. Likewise direct interference with STAT5-function, by mutations resulting in constitutive activation (STAT5-CA) or an inactive state (STAT5-YF). Consistent with a requirement of adaptive STAT5-feedback control in B-ALL, both Stat5-CA and Stat5-YF resulted in rapid cell death. Induction of Stat5-CA caused accumulation of biomass indicated by their increased cell size, whereas Stat5-YF caused rapid cell shrinkage ( Figure A). To determine whether the mTOR cell growth pathway was responsible for cell death induced by Stat5-CA, we tested whether the genetic deletion of Mtor or pharmacological inhibition of protein synthesis were sufficient to rescue B-ALL cell death. As expected, B-ALL cells retaining intact Mtor rapidly underwent energy crisis and cell death, while genetic deletion of Mtor reversed the toxic effects of Stat5-CA, suggesting that Stat5-CA is associated with excessive protein synthesis and defective ER turnover. Indeed, Stat5-CA increased protein synthesis rate and ER content compared to EV control, and these effects were opposed by Stat5-YF. To compare the metabolic outcomes of Stat5-CA and Stat5-YF, we performed mass spectrometry-based metabolomic analyses ( Figure B). Consistent with the role of mTOR in promoting glycolysis, Stat5-CA increased the content of glycolytic intermediates in B-ALL cells. In contrast, Stat5-YF increased phospholipid intermediates and phosphatidylethanolamine (PtdEtn). Opposed by Myc, Stat5-YF increased the expression levels of Bcl6 and autophagic genes, suggesting that Bcl6-dependent programs promote PtdEtn-LC3B conjugation, thereby autophagosome formation. As expected, microscopic validation with LC3B-GFP reporter revealed that Stat5-YF increased the number of LC3B-GFP puncta, upon pharmacological inhibition of autophagosome-lysosome fusion ( Figure A). Consistent with STAT5-CA promoting Myc- as opposed to STAT5-YF driving Bcl6-dependent programs, a flow cytometry analysis of Myc-eGFP/Bcl6-mCherry dual reporter expression in murine B-ALL cells demonstrated that changes between glycolytic Myc+ and autophagic Bcl6+ states were the direct consequence of Stat5-CA and Stat5-YF induction, respectively. Conclusions: Our results demonstrate feedback regulators of STAT5, including SOCS2 and CISH are not only biomarkers of increased oncogenic STAT5 activity and a more aggressive course of disease linked to poor overall outcomes. Importantly, negative STAT5 feedback control mechanisms are essential to enable nimble adaptations of B-ALL cells in response to fluctuations of oncogenic signaling strength and availability of nutrients during distinct metabolic states of cellular activation (MYC) and quiescence (BCL6).

Comprehensive analysis of HOXC8 associated with tumor microenvironment characteristics in colorectal cancer

BackgroundAccumulating evidence have highlighted the essential roles of HOX genes in embryonic development and carcinogenesis. As a member of the HOX gene family, the abnormal expression of HOXC8 gene is associated with the progression and metastasis of various tumors. However, potential roles of HOXC8 in colorectal cancer (CRC) prognosis and tumor microenvironment (TME) remodeling remain unclear. MethodsWe conducted an integrated analysis of clinical and molecular characteristics, relevant oncogenic and immune regulation roles and drug sensitivity features of HOXC8 in CRC. ResultsHOXC8 expression was markedly high expressed in CRC samples compared to normal samples, and the upregulated expression of HOXC8 was associated with poor prognosis. High HOXC8 expression was significantly associated with invasion-related pathways especially epithelial-mesenchymal transition (EMT). In vitro experiments showed significantly up-regulated HOXC8 expression in some CRC cell lines and its promoting effect on EMT and cell proliferation. TME categorization through transcriptomic analysis of CRC patients with high HOXC8 expression identified two different TME subtypes known as immune-enriched with fibrotic subtype and immune-depleted subtype. Patients with immune-enriched, fibrotic subtype exhibited significantly longer progression-free survival (PFS), upregulated PD-L1 and CTLA4 expression and higher TMB than those with the immune-depleted subtype. ConclusionsHOXC8 overexpression was associated with poor prognosis and specific TME subtypes in CRC. This study provided valuable resource for further exploring the potential mechanisms and therapeutic targets of HOX genes in CRC.

Transfer RNAs as dynamic and critical regulators of cancer progression.

Transfer RNAs (tRNAs) have been historically viewed as non-dynamic adaptors that decode the genetic code into proteins. Recent work has uncovered dynamic regulatory roles for these fascinating molecules. Advances in tRNA detection methods have revealed that specific tRNAs can become modulated upon DNA copy number and chromatin alterations and can also be perturbed by oncogenic signalling and transcriptional regulators in cancer cells or the tumour microenvironment. Such alterations in the levels of specific tRNAs have been shown to causally impact cancer progression, including metastasis. Moreover, sequencing methods have identified tRNA-derived small RNAs that influence various aspects of cancer progression, such as cell proliferation and invasion, and could serve as diagnostic and prognostic biomarkers or putative therapeutic targets in various cancers. Finally, there is accumulating evidence, including from genetic models, that specific tRNA synthetases - the enzymes responsible for charging tRNAs with amino acids - can either promote or suppress tumour formation. In this Review, we provide an overview of how deregulation of tRNAs influences cancer formation andprogression.

MAPK13 stabilization via m6A mRNA modification limits anticancer efficacy of rapamycin

N6-adenosine methylation (m6A) is the most abundant mRNA modification that controls gene expression through diverse mechanisms. Accordingly, m6A-dependent regulation of oncogenes and tumor suppressors contributes to tumor development. However, the role of m6A-mediated gene regulation upon drug treatment or resistance is poorly understood. Here, we report that m6A modification of mitogen-activated protein kinase 13 (MAPK13) mRNA determines the sensitivity of cancer cells to the mechanistic target of rapamycin complex 1 (mTORC1)-targeting agent rapamycin. mTORC1 induces m6A modification of MAPK13 mRNA at its 3' untranslated region through the methyltransferase-like 3 (METTL3)-METTL14-Wilms' tumor 1-associating protein(WTAP) methyltransferase complex, facilitating its mRNA degradation via an m6A reader protein YTH domain family protein 2. Rapamycin blunts this process and stabilizes MAPK13. On the other hand, genetic or pharmacological inhibition of MAPK13 enhances rapamycin's anticancer effects, which suggests that MAPK13 confers a progrowth signal upon rapamycin treatment, thereby limiting rapamycin efficacy. Together, our data indicate that rapamycin-mediated MAPK13 mRNA stabilization underlies drug resistance, and it should be considered as a promising therapeutic target to sensitize cancer cells to rapamycin.

Functional Variants in MicroRNAs (rs895819, rs11614913 and rs2910164) Are Associated with Susceptibility and Clinicopathological Features in Mexican Patients with Colorectal Cancer.

miRNAs are non-coding RNAs participating actively in the post-translational regulation of oncogenes, tumor suppressor, and DNA repair genes implicated in colorectal cancer (CRC). This study aims to examine the association of the variants miR-27a (rs895819 A>G), miR-196a2 (rs11614913 T>G) and miR-146a (rs2910164 C>G) in Mexican CRC patients. DNA samples from 183 patients and 186 healthy Mexican subjects were analyzed. Variants were identified by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) methodology. Association was calculated by the odds ratio (OR) and adjusted by the Bonferroni test. Patients carrying the G/G genotype of the rs895819 variant in the miR-27a gene showed an increased risk of CRC (19% vs 12%, P=0.013). A similar tendency was noticed for patients younger than 50 years carrying A/G (48% vs 41%, P=0.014). The A/G genotype in TNM stages I+II (55.7% vs 40.8%, P=0.011) and tumor location in the colon (69.5 vs 40.8%, P=0.001) were also increased. For the variant rs11614913 of the miR-196a2 gene, carriers of the C/C genotype showed an increased risk of CRC (32% vs 22%, P=0.009). This genotype was more frequent in TNM stage III+IV (36.8% vs 22.5%, P=0.007) and the tumor had a more recurrent location in the rectum (31.6% vs 22.5%, P=0.013). The rs2910164 variant of the miR-146a gene was found to have no significant risk associations. Our results reveal that the rs895819 variant in miR-27a and rs11614913 in miR-196a2 have a substantial impact on the development of CRC.

Knockdown of PTK7 Reduces the Oncogenic Potential of Breast Cancer Cells by Impeding Receptor Tyrosine Kinase Signaling.

Protein tyrosine kinase 7 (PTK7), a catalytically defective receptor tyrosine kinase (RTK), is often upregulated in various cancers. This study aimed to validate PTK7 as a target for breast cancer (BC) and investigate its oncogenic signaling mechanism. BC tissue analysis showed significantly elevated PTK7 mRNA levels, especially in refractory triple-negative breast cancer (TNBC) tissues, compared with normal controls. Similarly, BC cell lines exhibited increased PTK7 expression. Knockdown of PTK7 inhibited the proliferation of T-47D and MCF-7 hormone-receptor-positive BC cell-lines and of HCC1187, MDA-MB-231, MDA-MB-436, and MDA-MB-453 TNBC cells. PTK7 knockdown also inhibited the adhesion, migration, and invasion of MDA-MB-231, MDA-MB-436, and MDA-MB-453 cells, and reduced the phosphorylation levels of crucial oncogenic regulators including extracellular signal-regulated kinase (ERK), Akt, and focal adhesion kinase (FAK). Furthermore, PTK7 interacts with fibroblast growth factor receptor 1 (FGFR1) and epidermal growth factor receptor (EGFR) expressed in MDA-MB-231 cells. Knockdown of PTK7 decreased the growth-factor-induced phosphorylation of FGFR1 and EGFR in MDA-MB-231 cells, indicating its association with RTK activation. In conclusion, PTK7 plays a significant role in oncogenic signal transduction by enhancing FGFR1 and EGFR activation, influencing BC tumorigenesis and metastasis. Hence, PTK7 represents a potential candidate for targeted BC therapy, including TNBC.

The pioneer factor SOX9 competes for epigenetic factors to switch stem cell fates

During development, progenitors simultaneously activate one lineage while silencing another, a feature highly regulated in adult stem cells but derailed in cancers. Equipped to bind cognate motifs in closed chromatin, pioneer factors operate at these crossroads, but how they perform fate switching remains elusive. Here we tackle this question with SOX9, a master regulator that diverts embryonic epidermal stem cells (EpdSCs) into becoming hair follicle stem cells. By engineering mice to re-activate SOX9 in adult EpdSCs, we trigger fate switching. Combining epigenetic, proteomic and functional analyses, we interrogate the ensuing chromatin and transcriptional dynamics, slowed temporally by the mature EpdSC niche microenvironment. We show that as SOX9 binds and opens key hair follicle enhancers de novo in EpdSCs, it simultaneously recruits co-factors away from epidermal enhancers, which are silenced. Unhinged from its normal regulation, sustained SOX9 subsequently activates oncogenic transcriptional regulators that chart the path to cancers typified by constitutive SOX9 expression.

GOLPH3 promotes endotoxemia-induced liver and kidney injury through Golgi stress-mediated apoptosis and inflammatory response

Sepsis is a serious clinical condition characterized by a systemic inflammatory response, a leading cause of acute liver and kidney injury, and is associated with a high morbidity and mortality. Understanding the molecular mechanisms underlying the acute liver and kidney injury is crucial for developing an effective therapy. Golgi apparatus plays important roles and has various substrates mediating cellular stress responses. Golgi phosphoprotein 3 (GOLPH3), linking Golgi membranes to the cytoskeleton, has been identified as an important oncogenic regulator; however, its role in endotoxemia-induced acute liver and kidney injury remains elusive. Here, we found that upregulation of GOLPH3 was associated with endotoxemia-induced acute liver and kidney injury. Lipopolysaccharide (LPS) treatment increased Golgi stress and fragmentation, and associated pro-inflammatory mediator (Tnfα, IL-6, and IL-1β) production in vivo and in vitro. Interestingly, the downregulation of GOLPH3 significantly decreased LPS-induced Golgi stress and pro-inflammatory mediators (Tnfα, IL-6, Mcp1, and Nos2), and reversed apoptotic cell deaths in LPS-treated hepatocytes and renal tubular cells. GOLPH3 knockdown also reduced inflammatory response in LPS-treated macrophages. The AKT/NF-kB signaling pathway was suppressed in GOLPH3 knockdown, which may be associated with a reduction of inflammatory response and apoptosis and the recovery of Golgi morphology and function. Taken together, GOLPH3 plays a crucial role in the development and progression of acute liver and kidney injury by promoting Golgi stress and increasing inflammatory response and apoptosis, suggesting GOLPH3 as a potential therapeutic target for endotoxemia-induced tissue injury.

KRAS regulation of miRNA: Stepping on the brake to go faster

In this issue of Molecular Cell, Shui etal.1 use a systems biology approach to unravel a paradoxical role of microRNA in oncogenic KrasG12D regulation of gene and protein expression.

Cryo‐EM structure of the chain‐elongating E3 ubiquitin ligase UBR5

UBR5 is a nuclear E3 ligase that ubiquitinates a vast range of substrates for proteasomal degradation. This HECT domain‐containing ubiquitin ligase has recently been identified as an important regulator of oncogenes, e.g., MYC, but little is known about its structure or mechanisms of substrate engagement and ubiquitination. Here, we present the cryo‐EM structure of human UBR5, revealing an α‐solenoid scaffold with numerous protein–protein interacting motifs, assembled into an antiparallel dimer that adopts further oligomeric states. Using cryo‐EM processing tools, we observe the dynamic nature of the UBR5 catalytic domain, which we postulate is important for its enzymatic activity. We characterise the proteasomal nuclear import factor AKIRIN2 as an interacting protein and propose UBR5 as an efficient ubiquitin chain elongator. This preference for ubiquitinated substrates and several distinct domains for protein–protein interactions may explain how UBR5 is linked to several different signalling pathways and cancers. Together, our data expand on the limited knowledge of the structure and function of HECT E3 ligases.

Abstract A082: The epigenetic impact and therapeutic opportunity of AR-directed therapy for desmoplastic small round cell tumor

Abstract Desmoplastic small round cell tumor (DSRCT) is a rare, usually incurable, aggressive sarcoma subtype that occurs predominantly in adolescent and young adult (AYA) males. At diagnosis, most present with hundreds of intraabdominal nodules composed of malignant cells that harbor a EWSR1-WT1 chromosomal translocation and resultant fusion protein (FP). It was shown that a subset of DSRCT cells (mostly of epithelial histotype) highly express the androgen receptor (AR), a key epigenetic driver of prostate cancer (PC). Given the male predilection and the high expression of AR, we sought to assess the role of AR more comprehensively in DSRCT and ask if this tumor shared AR resistance mechanism to PC. We tested if AR antagonists curb cell proliferation and tumor growth, where both enzalutamide and AR-antisense therapy blocked DHT-induced cell proliferation and reduced xenograft tumor burden. Next, to mechanistically interrogate AR’s oncogenic effects, we performed single-nuclei RNA-seq (snRNA-eq) and chromatin immunoprecipitation sequencing (ChIP-seq) on frozen patient specimens. Those studies revealed a surprising epigenetic similarity between DSRCT to PC. Though overlap exists in the DNA binding MOTIFs of AR in DSRCT and PC, our ChIP-seq resultsrevealed DSRCT-specific AR DNA binding sites adjacent to key oncogenic regulators, including FOXF1 and WT1 (the C-terminal partner of the pathognomonic FP). To our surprise, we identified a subset of DSRCT samples that underwent partial neuroendocrine (NE) epigenetic reprogramming, akin to what occurs in ~1/3 of castrate-resistant PC (CRPC). Since androgen deprivation therapy (ADT) isn’t yet a standard treatment for DSRCT, it remains an enigma why DSRCT would undergo NE reprogramming or how this may affect ADT sensitivity. To address this, nine DSRCT patient samples were profiled using snRNA-seq. Sub-clustering revealed epithelial, mesenchymal, or NE signatures and marked inter-patient and intra-tumoral heterogeneity. Notably, five of nine patients exhibited NE markers (SYP, ENO2, CHGA, FOXA2, ASCL1, and SOX2), while three expressed epithelial markers (MUC1, MUC6, KRT18, KRT23, CDH1). One patient exhibited a hybrid AR indifferent phenotype. While strikingly different from PC morphologically and phenotypically, our data suggest that DSRCT is a second androgen-stimulated malignancy (third if we consider breast cancers that rely on shared nuclear receptor family signaling). Shared dependence upon AR for tumor growth and survival provides an exciting opportunity to prospectively study AR signaling in a different cancer type and younger DSRCT-stricken patient population. Ongoing work will determine if DSRCT undergoes dedifferentiation towards a more stem-like cell as an intermediary step before undergoing neural lineage commitment or transdifferentiation directly from an epithelial cell type towards a neuroendocrine cell fate. We are also exploring if the FP acts as a Pioneer factor to direct AR towards DSRCT-specific androgen response elements that explain this sarcoma subtype’s unique clinical presentation. Citation Format: Danh D. Truong, Salah-Eddine Lamhamedi-Cherradi, Mayinuer Maitituoheti, Hannah C. Beird, Chia-Chin Wu, Sandhya Krishnan, Davis Ingram, P. Andrew Futreal, Mark Titus, Alexander Lazar, Kunal Rai, A. Robert MacLeod, Najat C. Daw, Andrea Hayes, Joseph Ludwig. The epigenetic impact and therapeutic opportunity of AR-directed therapy for desmoplastic small round cell tumor [abstract]. In: Proceedings of the AACR Special Conference: Advances in Prostate Cancer Research; 2023 Mar 15-18; Denver, Colorado. Philadelphia (PA): AACR; Cancer Res 2023;83(11 Suppl):Abstract nr A082.

TRNA-derived fragments (tRFs) as regulators of oncogenes and tumor suppressor genes in head and neck squamous cell carcinoma.

e18082 Background: Roughly 50,000 individuals are diagnosed with head and neck cancers in the United States yearly. Though risk factors and common therapeutic strategies are well-established, early detection of head and neck cancers remains challenging. One strategy for early detection is high-throughput analysis of both coding and noncoding RNA transcripts, which has become increasing implicated in cancer pathogenesis. One such noncoding transcript is tRNA-derived fragments (tRFs), which are the products of enzymatic cleavage of precursor tRNAs. Though tRFs have been suggested to play important roles in the regulation of mRNA translation (similar to other noncoding RNAs), their utility as cancer biomarkers is not well-known. Methods: In this study, we investigate tRFs for correlation to cancer prevalence with specific consideration of translational regulation of oncogenes (OG) and tumor suppressor genes (TSG). tRF read counts were obtained for 499 head and neck squamous cell carcinoma tumor tissue samples and 44 adjacent normal samples. Results: The read counts between both groups were compared to identify tRFs dysregulated in tumor samples, which may be pertinent biomarkers for diagnosis. Ten tRFs were found to be significantly dysregulated in cancer samples. These tRFs were further assessed for correlation to expression of OGs and TSGs using the COSMIC database. Due to the mRNA-degrading nature of tRFs, we analyzed tRF abundance for inverse correlation to gene expression. Four tRFs upregulated in tumor samples showed significant anticorrelation to select TSG expression (ATP2B3, CSMD3, LZTR1, NTHL1, PTPRC), and three tRFs downregulated in tumor samples showed anticorrelation to OG expression (A1CF, MPL, SALL4, TNC). Notably, LeuCAG 5’ tRF was associate with high binding affinity for the TSGs CSMD3 and LZTR1, supporting the likelihood of tRF-mediated degradation. Interestingly, this tRF was inversely correlated with patient survival length. LeuCAG 5’ was also of significantly lesser abundance in patients who experienced complete or partial remission following chemotherapy treatment, further indicating this tRFs’ clinical relevance in HNSCC, potentially as an oncogenic-related agent. Conclusions: Investigation into these tRFs may reveal their potential for use in early diagnosis. High abundance of this tRF may be indicative of oncogenesis. In exploring tRFs’ for their potential as biomarkers of cancer, they may prove useful in allowing earlier diagnosis. Moreover, studying tRFs may provide additional considerations for patient care and treatment.

Liquidambaric lactone is a potent inhibitor of TRAF2 for cancer therapy

BackgroundTumor necrosis factor (TNF) receptor-associated factor 2 (TRAF2) is an oncogenic regulator of Wnt/β-catenin signaling in colon cancer. Previously we have reported a pentacyclic triterpenoid compound liquidambaric acid (LDA) inhibiting Wnt/β-catenin signaling via targeting TRAF2, however, LDA inhibition of cancer cells was observed only at high doses. It is important to identify small molecules targeting TRAF2 in colon cancer with higher potency . MethodsMicroscale thermophoresis (MST) assay was used to screen a panel of pentacyclic triterpenoids. Cellular thermal shift assay (CETSA) was used to confirm target engagment in living cells. Drug affinity responsive target stability (DARTS) coupled with mass spectrometry (MS) was used to identify the potential targets of candidate TRAF2 binder. Wnt signaling inhibition was evaluated by 7TGC reporter assay, TOPFlash assay, reverse transcription and real-time quantitative PCR, as well as zebrafish eyeless assay. Cancer inhibition was assessed by cell viability assay, colony formation assay and xenograft studies. CRISPR/Cas9 knockout HCT116 cells was used to assess the requirement of TRAF2 for liquidambaric lactone (LDL) inhibition of cancer. ResultsA LDA analogue LDL selectively targeted TRAF2 with higher binding affinity. Both LDL and LDA targeted the TRAF-C domain of TRAF2 with slightly different binding sites. Of note, LDL showed much stronger inhibition of colon cancer cells than LDA in colony formation assay. LDL inhibition of cancer was also comfirmed in xenograft mice. Depletion of TRAF2 totally blocked LDL inhibition of Wnt signaling, TNF signaling and growth of cancer cells. ConclusionsA natural product LDL is a potent inhibitor of TRAF2 for cancer therapy, and TRAF2 is required for LDL inhibition of cancer.

Advances in Immunocompetent Mouse and Rat Models.

Rodent models of breast cancer have played critical roles in our understanding of breast cancer development and progression as well as preclinical testing of cancer prevention and therapeutics. In this article, we first review the values and challenges of conventional genetically engineered mouse (GEM) models and newer iterations of these models, especially those with inducible or conditional regulation of oncogenes and tumor suppressors. Then, we discuss nongermline (somatic) GEM models of breast cancer with temporospatial control, made possible by intraductal injection of viral vectors to deliver oncogenes or to manipulate the genome of mammary epithelial cells. Next, we introduce the latest development in precision editing of endogenous genes using in vivo CRISPR-Cas9 technology. We conclude with the recent development in generating somatic rat models for modeling estrogen receptor-positive breast cancer, something that has been difficult to accomplish in mice.

Comprehensive transcriptomic analyses identify KDM genes-related subtypes with different TME infiltrates in gastric cancer

Histone lysine demethylases (KDMs) have been reported in various malignances, which affect transcriptional regulation of tumor suppressor or oncogenes. However, the relationship between KDMs and formation of tumor microenvironment (TME) in gastric cancer (GC) remain unclear and need to be comprehensively analyzed.In the present study, 24 KDMs were obtained and consensus molecular subtyping was performed using the "NMF" method to stratify TCGA-STAD into three clusters. The ssGSEA and CIBERSORT algorithms were employed to assess the relative infiltration levels of various cell types in the TME. The KDM_score was devised to predict patient survival outcomes and responses to both immunotherapy and chemotherapy.Three KDM genes-related molecular subtypes were Figured out in GC with distinctive clinicopathological and prognostic features. Based on the robust KDM genes-related risk_score and nomogram, established in our work, GC patients’ clinical outcome can be well predicted. Furthermore, low KDM genes-related risk_score exhibited the more effective response to immunotherapy and chemotherapy.This study characterized three KDM genes-related TME pattern with unique immune infiltration and prognosis by comprehensively analyses of transcriptomic profiling. Risk_score was also built to help clinicians decide personalized anticancer treatment for GC patients, including in prediction of immunotherapy and chemotherapy response for patients.

TAF1D promotes proliferation by transcriptionally activating G2/M phase-related genes in MYCN-amplified neuroblastoma.

High-risk neuroblastoma (HR-NB) is an aggressive childhood cancer that responds poorly to currently available therapies and is associated with only about a 50% 5-year survival rate. MYCN amplification is a critical driver of these aggressive tumors, but so far there have not been any approved treatments to effectively treat HR-NB by targeting MYCN or its downstream effectors. Thus, the identification of novel molecular targets and therapeutic strategies to treat children diagnosed with HR-NB represents an urgent unmet medical need. Here, we conducted a targeted siRNA screening and identified TATA box-binding protein-associated factor RNA polymerase I subunit D, TAF1D, as a critical regulator of the cell cycle and proliferation in HR-NB cells. Analysis of three independent primary NB cohorts determined that high TAF1D expression correlated with MYCN-amplified, high-risk disease and poor clinical outcomes. TAF1D knockdown more robustly inhibited cell proliferation in MYCN-amplified NB cells compared with MYCN-non-amplified NB cells, as well as suppressed colony formation and inhibited tumor growth in a xenograft mouse model of MYCN-amplified NB. RNA-seq analysis revealed that TAF1D knockdown downregulates the expression of genes associated with the G2/M transition, including the master cell-cycle regulator, cell-cycle-dependent kinase 1 (CDK1), resulting in cell-cycle arrest at G2/M. Our findings demonstrate that TAF1D is a key oncogenic regulator of MYCN-amplified HR-NB and suggest that therapeutic targeting of TAF1D may be a viable strategy to treat HR-NB patients by blocking cell-cycle progression and the proliferation of tumor cells.