Hypoxic Gene Expression Research Articles

ANGI-10. NETWORK ANALYSIS ESTABLISHES CSF2RA’S REGIONAL INFLUENCE ON HYPOXIA RESPONSE IN THE INVASIVE RIM OF HIGH GRADE GLIOMA

Abstract BACKGROUND High-grade glioma (HGG) is the most common and aggressive form of primary brain cancer. Standard of care surgery employs Magnetic Resonance Imaging to identify the contrast enhancing (CE) core for resection, leaving a non-enhancing (NE) invasive rim of tumor which contributes to recurrence. The hypoxic tumor microenvironment is thought to drive invasion into healthy brain, and understanding cellular responses to hypoxia may provide insight into combatting recurrence. Here, we apply a graph network to integrate regionally heterogeneous data from a unique dataset of spatially-localized CE and NE biopsies from a large cohort of patients with HGG to identify gene networks regulating hypoxia response and invasion. METHODS RNA-sequencing of 1159 differentially expressed genes across 159 IDH-wt biopsies (74 patients) from NE/CE regions were represented as nodes in a Neo4j graph network. Candidate genes for network random walks occurred exclusively within NE communities detected by modularity optimization and were localized by cell-type using single-cell RNA-sequencing (scRNAseq). CSF2RA was selected as source (walk length = 5; 10,000 walks/source node). Frequently occurring genes (one-tailed test) in walks were ranked by correlation with CSF2RA expression in NE samples and analyzed by gene set enrichment analysis for biological processes (clusterProfiler). CSF2RA and hypoxia gene expression were visualized with DoHeatmap in composite NE/CE scRNAseq profiles. RESULTS CSF2RA, an immune receptor, was upregulated (logFC = 0.789) in NE samples, scRNAseq myeloid populations, and Glycolytic/Plurimetabolic glioma subtype. CSF2RA random walk genes (n=46) enriched metabolic/proliferative signatures. CSF2RA expression correlated negatively with hypoxia genes globally and regionally (NE/CE), while NE/CE scRNAseq revealed distinct cellular expression patterns of CSF2RA and hypoxia response genes. CONCLUSION CSF2RA expression may prime NE glioma cells for invasion by altering hypoxia response. The genetic network bridging CSF2RA and hypoxia response may be a targetable mechanism of tumor recurrence.

Abstract B085: The HIF-2 transcription factor mediates resistance to ferroptosis in pancreatic adenocarcinoma

Abstract Ferroptosis is an iron-dependent form of cell death converging on lipid peroxidation, first identified by examining compounds with enhanced lethality to KRAS mutant cells. Two compounds widely used as ferroptosis inducers are erastin, which acts as an inhibitor of cystine import and thereby depletes cellular glutathione, and RSL-3, which inhibits glutathione peroxidase 4. Despite over 90% of pancreatic adenocarcinoma (PDAC) tumors harboring KRAS mutations, PDAC exhibits relative resistance to ferroptosis compared to other tumor types, and the mechanisms behind this resistance remain unclear. The pancreatic tumor environment is marked by severe hypoxia, due to poor vascularity and a dense fibrotic stroma, and so we hypothesized that hypoxia might mediate resistance to ferroptosis. Here we report that across a panel of human and murine PDAC cell lines, hypoxia induces resistance to both ferroptosis inducing agents, erastin and RSL-3. The effect of hypoxia was synergistic with exposure to pancreatic cancer tumor interstitial fluid, which induces a hypoxic-like gene expression profile even under normoxia and enhances hypoxic gene expression changes when combined with hypoxia. Our findings reveal that hypoxia-mediated resistance to ferroptosis is orchestrated by the hypoxia-inducible transcription factor HIF-2, as evidenced by its complete abolition in HIF-2 knockout cell lines, while the protective effect of hypoxia was maintained in HIF-1 knockout lines. RNA-seq analyses and chromatin immunoprecipitation studies (chIP) identified several HIF-2 target genes responsible for coordinating ferroptosis resistance mechanisms. Cysteine is a precursor for glutathione, and HIF-2 increased cystine import through upregulation of both components of the cystine-glutamate antiporter system Xc (SLC7A11 and SLC3A2) and increased cysteine biosynthesis via upregulation of transsulfuration pathway enzymes (CBS and CTH). In addition, HIF-2 upregulated Parkin, which we identify as a novel regulator of ferroptosis, thereby increasing mitophagy and decreasing reactive oxygen species. In vivo studies using human and murine PDAC xenograft models confirmed that HIF-2 knockout impaired tumor growth and increased susceptibility to the pro-ferroptotic agent sulfasalazine. Collectively, these data identify a mechanism by which PDAC evades ferroptosis and identifies a possible therapeutic strategy of combining HIF-2 inhibitors with pro-ferroptotic agents in pancreatic cancer. Citation Format: Maimon E Hubbi, Catherine Wang, Erin Hollander, Yasir Suhail, Kshitiz, Alexander Muir, Ben Z Stanger, Chi V Dang. The HIF-2 transcription factor mediates resistance to ferroptosis in pancreatic adenocarcinoma [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr B085.

Maternal obesity and offspring neurodevelopment are associated with hypoxic gene expression in term human placenta.

One third of women in the United States are affected by obesity during pregnancy. Maternal obesity (MO) is associated with an increased risk of neurodevelopmental and metabolic disorders in the offspring. The placenta, located at the maternal-fetal interface, is a key organ determining fetal development and likely contributes to programming of long-term offspring health. We profiled the term placental transcriptome in humans (pre-pregnancy BMI 35+ [MO condition] or 18.5-25 [lean condition]) using single-nucleus RNA-seq to compare expression profiles in MO versus lean conditions, and to reveal potential mechanisms underlying offspring disease risk. We recovered 62,864 nuclei of high quality from 10 samples each from the maternal-facing and fetal-facing sides of the placenta. On both sides in several cell types, MO was associated with upregulation of hypoxia response genes. On the maternal-facing side only, hypoxia gene expression was associated with offspring neurodevelopmental measures, in Gen3G, an independent pregnancy cohort with bulk placental tissue RNA-seq. We leveraged Gen3G to determine genes that correlated with impaired neurodevelopment and found these genes to be most highly expressed in extravillous trophoblasts (EVTs). EVTs further showed the strongest correlation between neurodevelopment impairment gene scores (NDIGSs) and the hypoxia gene score. We reanalyzed gene expression of cultured EVTs, and found increased NDIGSs associated with exposure to hypoxia. Among EVTs, accounting for the hypoxia gene score attenuated 44% of the association between BMI and NDIGSs. These data suggest that hypoxia in EVTs may be a key process in the neurodevelopmental programming of fetal exposure to MO.

The Tumor Microbiome Reacts to Hypoxia and Can Influence Response to Radiation Treatment in Colorectal Cancer.

Tumor hypoxia reduces radiotherapy efficacy. In this study, we explored whether some of the clinical effects of hypoxia could be due to interaction with the tumor microbiome. Hypoxic gene expression scores associated with certain microbes and elicited an adaptive transcriptional response in others that could contribute to poor clinical outcomes.

Elevated nutrient availability enhances chondrocyte metabolism and biosynthesis in tissue-engineered cartilage

ObjectiveChondrocytes, which typically rely on anaerobic metabolism, exhibit upregulated biosynthetic activity when subjected to conditions that elicit mixed aerobic-anaerobic metabolism. Previously, we observed that increasing media volume resulted in the transition from anaerobic to mixed aerobic-anaerobic metabolism. Maximal extracellular matrix (ECM) accumulation occurred at this transition as a result of changes in HIF-1α signaling and associated hypoxic gene expression. This study aimed to explore the effect of further increases in media availability on ECM synthesis and chondrocyte metabolism. MethodsPrimary bovine chondrocytes were grown in 3D high-density tissue culture under varying levels of media availability (4 – 16 mL/106 cells). Changes in ECM accumulation and metabolism were determined through biochemical assays and 13C-metabolic flux analysis (13C-MFA). ResultsIncreasing media volumes resulted in higher accumulation of cartilaginous extracellular matrix (collagen and proteoglycans) and cellularity. Extracellular metabolite measurements revealed that elevated media availability led to increased glucose and glutamine metabolism, along with increased anaerobic activity. 13C-MFA utilizing [U-13C] glucose demonstrated that increased media availability significantly impacted central carbon metabolism, upregulating all glucose-related metabolic pathways (glycolysis, lactate fermentation, the TCA cycle, hexosamine biosynthetic pathway, and the malate-aspartate shuttle). Furthermore, 13C-MFA indicated that glutamine was donating carbons to the TCA cycle, and additional studies involving [U-13C] glutamine tracing supported this notion. ConclusionsElevated media availability upregulates extracellular matrix synthesis and leads to significant changes in metabolic phenotype. Glutamine plays an important role in chondrocyte metabolism and increases in glutamine metabolism correlate with increases in extracellular matrix accumulation.

Prognostic PET [11C]-acetate uptake is associated with hypoxia gene expression in patients with late-stage hepatocellular carcinoma – a bench to bed study

BackgroundPositron Emission Tomography (PET) with combined [18F]-FDG and [11C]-acetate (dual-tracer) is used for the management of hepatocellular carcinoma (HCC) patients, although its prognostic value and underlying molecular mechanism remain poorly understood. We hypothesized that radiotracer uptake might be associated with tumor hypoxia and validated our findings in public and local human HCC cohorts.MethodsTwelve orthotopic HCC xenografts were established using MHCC97L cells in female nude mice, with 5 having undergone hepatic artery ligation (HAL) to create tumor hypoxia in vivo. Tumors in both Control and HAL-treated xenografts were imaged with [11C]-acetate and [18F]-FDG PET-MR and RNA sequencing was performed on the resected tumors. Semiquantitative analysis of PET findings was then performed, and the findings were then validated on the Cancer Genome Atlas Liver Hepatocellular Carcinoma (TCGA-LIHC) cohort and patients from our institution.ResultsHAL-treated mice showed lower [11C]-acetate (HAL-treated vs. Control, tumor-to-liver SUV ratio (SUVTLR): 2.14[2.05–2.21] vs 3.11[2.75–5.43], p = 0.02) but not [18F]-FDG (HAL-treated vs. Control, SUVTLR: 3.73[3.12–4.35] vs 3.86[3.7–5.29], p = 0.83) tumor uptakes. Gene expression analysis showed the PET phenotype is associated with upregulation of hallmark hypoxia signature. The prognostic value of the hypoxia gene signature was tested on the TCGA-LIHC cohort with upregulation of hypoxia gene signature associated with poorer overall survival (OS) in late-stage (stage III and IV) HCC patients (n = 66, OS 2.05 vs 1.67 years, p = 0.046). Using a local cohort of late-stage HCC patients who underwent dual-tracer PET-CT, tumors without [11C]-acetate uptake are associated with poorer prognosis (n = 51, OS 0.25 versus 1.21 years, p < 0.0001) and multivariable analyses showed [11C]-acetate tumor uptake as an independent predictor of OS (HR 0.17 95%C 0.06–0.42, p < 0.0001).Conclusions[11C]-acetate uptake is associated with alteration of tumor hypoxia gene expression and poorer prognosis in patients with advanced HCC.

Abstract 6941: Transcriptomic effects of retinoblastoma progression-related somatic copy number alteration (SCNA)

Abstract Retinoblastoma is a pediatric retinal cancer that initiates in response to biallelic RB1 loss or MYCN amplification in a cone precursor cell of origin. After initial emergence, RB1-/- retinoblastomas progress to more aggressive forms by accumulation of single nucleotide variants (SNVs) and highly recurrent somatic copy number alterations including 1q+, 2p+, 6p+ and 16q- (RB SCNAs), resulting in heterogeneous mixtures of subclonal cell populations. SCNAs are enriched in highly evolved and aggressive tumor subtypes and show prognostic value in retinoblastoma liquid biopsies. However, the transcriptomic effects of retinoblastoma SCNAs are poorly understood. Single cell methods may enable comparison of tumor subclones within emerging retinoblastoma tumors and thereby provide insight into tumor progression. We retrieved single cell RNA sequencing data for 25 retinoblastoma tumors and inferred SCNAs and subclone phylogenies from scRNAseq information using a recently published tool, Numbat. We identified tumors with clonal variation in RB SCNAs and excluded samples with poor transcriptome quality or excessive additional SCNAs. We proceeded with analysis of 11 tumors with subclonal heterogeneity for an SCNA of interest, including 10 with 1q+, eight with 2p+, four with 6p+, and six with 16q-. After removal of nontumor cells, we defined cell clusters, cluster marker genes, and cell cycle phase gene signatures, and we compared cell state distributions for subclones with an acquired SCNA relative to their immediate antecedents. These analyses revealed recurrently discriminated transcriptomic clusters corresponding to six discrete cell cycle states (post-mitotic G1, G1, G1/S, S, S/G2, G2/M) and variable cell stress states, including a cluster with hypoxia and heat shock related marker gene expression in all samples. In each tumor, SCNA-defined tumor subclones had a distinct cell state distribution. Tumor subclones with acquired 1q+ were enriched in G2 states and depleted in G1 states. Subclones with 2p+ were enriched in G2 states. Subclones with 6p+ were enriched in S phase states. Subclones with 16q- were diminished in post-mitotic cell states. Tumor clones with 1q+ and 16q- were most strongly enriched for G2 phase cells. Such 1q+/16q- tumor cells were significantly differentially distributed in three tumor replicates. Tumor clones with other RB SCNAs were enriched over diploid clones in proliferating G2 cells without SCNA specific effects. To identify candidate drivers of SCNA-specific transcriptomic effects we measured RB SCNA clonal variation in gene expression within and across transcriptomic states. We identified recurrently differentially expressed in-segment genes in 1q+, 2p+, 6p+, and 16q-, as well as out-of-segment genes. Finally, we propose molecular mechanisms underlying SCNA recurrence that may enable tumor evolution in retinoblastoma. Citation Format: Kevin Stachelek, David E. Cobrinik. Transcriptomic effects of retinoblastoma progression-related somatic copy number alteration (SCNA) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6941.

Metabolic priming by multiple enzyme systems supports glycolysis, HIF1α stabilisation, and human cancer cell survival in early hypoxia

Adaptation to chronic hypoxia occurs through changes in protein expression, which are controlled by hypoxia-inducible factor 1α (HIF1α) and are necessary for cancer cell survival. However, the mechanisms that enable cancer cells to adapt in early hypoxia, before the HIF1α-mediated transcription programme is fully established, remain poorly understood. Here we show in human breast cancer cells, that within 3 h of hypoxia exposure, glycolytic flux increases in a HIF1α-independent manner but is limited by NAD+ availability. Glycolytic ATP maintenance and cell survival in early hypoxia rely on reserve lactate dehydrogenase A capacity as well as the activity of glutamate-oxoglutarate transaminase 1 (GOT1), an enzyme that fuels malate dehydrogenase 1 (MDH1)-derived NAD+. In addition, GOT1 maintains low α-ketoglutarate levels, thereby limiting prolyl hydroxylase activity to promote HIF1α stabilisation in early hypoxia and enable robust HIF1α target gene expression in later hypoxia. Our findings reveal that, in normoxia, multiple enzyme systems maintain cells in a primed state ready to support increased glycolysis and HIF1α stabilisation upon oxygen limitation, until other adaptive processes that require more time are fully established.

Clinical relevance and therapeutic predictive ability of hypoxia biomarkers in head and neck cancer tumour models.

Tumour hypoxia promotes poor patient outcomes, with particularly strong evidence for head and neck squamous cell carcinoma (HNSCC). To effectively target hypoxia, therapies require selection biomarkers and preclinical models that can accurately model tumour hypoxia. We established 20 patient-derived xenograft (PDX) and cell line-derived xenograft (CDX) models of HNSCC that we characterised for their fidelity to represent clinical HNSCC in gene expression, hypoxia status and proliferation and that were evaluated for their sensitivity to hypoxia-activated prodrugs (HAPs). PDX models showed greater fidelity in gene expression to clinical HNSCC than cell lines, as did CDX models relative to their paired cell lines. PDX models were significantly more hypoxic than CDX models, as assessed by hypoxia gene signatures and pimonidazole immunohistochemistry, and showed similar hypoxia gene expression to clinical HNSCC tumours. Hypoxia or proliferation status alone could not determine HAP sensitivity across our 20 HNSCC and two non-HNSCC tumour models by either tumour growth inhibition or killing of hypoxia cells in an ex vivo clonogenic assay. In summary, our tumour models provide clinically relevant HNSCC models that are suitable for evaluating hypoxia-targeting therapies; however, additional biomarkers to hypoxia are required to accurately predict drug sensitivity.

Cell state dependent effects of Bmal1 on melanoma immunity and tumorigenicity.

The circadian clock regulator Bmal1 modulates tumorigenesis, but its reported effects are inconsistent. Here, we show that Bmal1 has a context-dependent role in mouse melanoma tumor growth. Loss of Bmal1 in YUMM2.1 or B16-F10 melanoma cells eliminates clock function and diminishes hypoxic gene expression and tumorigenesis, which could be rescued by ectopic expression of HIF1α in YUMM2.1 cells. By contrast, over-expressed wild-type or a transcriptionally inactive mutant Bmal1 non-canonically sequester myosin heavy chain 9 (Myh9) to increase MRTF-SRF activity and AP-1 transcriptional signature, and shift YUMM2.1 cells from a Sox10high to a Sox9high immune resistant, mesenchymal cell state that is found in human melanomas. Our work describes a link between Bmal1, Myh9, mouse melanoma cell plasticity, and tumor immunity. This connection may underlie cancer therapeutic resistance and underpin the link between the circadian clock, MRTF-SRF and the cytoskeleton.

HIF-1α: a potential biomarker in obstructive sleep apnea

Obstructive sleep apnea (OSA) is a common breathing disorder characterized by repeated obstruction of the upper airway during sleep. Although polysomnography (PSG) is the widely used method for the diagnosis of OSA, it is a time-consuming and expensive method. Because it requires at least 1 night stay in the hospital and technical personnel are needed. Therefore, it has been focused on biomarkers that can be easily detected in blood for the diagnosis of OSA. Some studies have highlighted the relationship between OSA and cancer in humans, and HIF-1 is an important regulator in this process. KDM3A is a histone demethylase that increases hypoxic gene expression. We aimed to evaluate whether the expression levels of HIF-1α and KDM3A genes could be useful predictors in patients with OSA. Our study included 50 patients with OSA and 50 healthy controls. qRT-PCR was used to detect mRNA levels of HIF-1α, KDM3A, and epithelial-mesenchymal transition (EMT) genes in the leukocyte samples. The expression level of the HIF-1α gene was found significantly higher in the OSA group compared to the controls, and no statistically significant difference was detected in the expression levels of the KDM3A and EMT genes.

TMIC-30. HYPOXIA-INDUCED COMPLEMENT COMPONENT 3 PROMOTES AGGRESSIVE TUMOR GROWTH IN THE GLIOBLASTOMA MICROENVIRONMENT

Abstract Glioblastoma is the most aggressive primary adult brain tumor. Treatment includes surgery, irradiation and chemotherapy. Still, virtually all patients suffer a treatment resistant recurrent tumor. In previous studies from our lab, we have investigated the tumor microenvironment contribution to tumor progression, showing that stromal astrocytes become reactive upon irradiation and hypoxia and generate tumor-supportive conditions for glioblastoma cells. Common features of astrocyte reactivity in several neurological diseases, include upregulation of complement proteins including complement component 3 (C3). However, it remains unexplored if these complement proteins are expressed in stromal astrocytes in glioblastoma. In a genetically engineered glioma mouse model, C3 was expressed in the invasive front, hypoxic, and perivascular tumor areas. TCGA data analysis revealed an overall strong correlation between hypoxia and complement gene expression signatures in glioblastoma patients. Astrocytes and glioma cells cultured in hypoxic conditions upregulated C3, as well as other genes associated with an infiltrative phenotype of GBM. In hypoxia, glioma cell lines, but not astrocytes, upregulated the C3a Receptor. GBM tumor single-cell sequencing data confirmed a subpopulation of highly C3-expressing astrocytes, enriched for cellular pathways comprising epithelial mesenchymal transition (EMT), TNF-alpha, hypoxia, and IFN-signaling. In vitro, C3 enhanced proliferation of glioma cells specifically under hypoxic conditions. Blocking C3a-C3aR signaling in vivo prolonged survival of glioma-bearing mice both alone and in combination with radiotherapy. Overall, our data indicate a strong link between hypoxia and complement expression in the brain tumor microenvironment of glioblastoma, where local expression of complement proteins lead to tumor promoting signaling. Inhibition of C3a-C3aR enhanced survival of glioma-bearing mice and could represent a promising avenue for further investigations.

HIF-1 regulates common bidirectional gene expression changes during hypoxia and iron deficiency in human induced pluripotent stem cell derived cardiomyocytes

Abstract Background Heart failure regardless of cause is characterised by extensive transcriptional reprogramming and a switch to foetal developmental programmes via unknown mechanisms (1-3). An additional factor that adversely impacts heart failure patients is iron deficiency (ID)(4). ID is also associated with worse prognosis in acute coronary syndromes (5). However, the mechanisms by which ID interferes with clinical outcomes in heart disease remain incompletely understood. Purpose The purpose of this study was to investigate gene expression changes in human cardiomyocytes during hypoxia and ID, two important stressors in the context of ischaemia and heart failure. Methods In this study, we use human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CM) derived through a protocol that promotes left ventricle cardiomyocyte differentiation (6). Cells were harvested at different stages of differentiation (day 6 and day 32) and mature (day 32) hiPSC-CMs were treated with 30 μM deferoxamine to induce ID either under normoxic or hypoxic conditions with 1% O2. hiPSC contraction was assessed using musclemotion software and metabolism through use of a Seahorse extracellular flux analyser. RNA was isolated using standard isolation kits and RNA-seq (n=5) was performed. Data was analysed for gene expression by alignment with the human hg19 reference genome using the software STAR. A log2 fold change of 1 and P value of &amp;lt;0.0001 were considered significant. Results We show that both hypoxic and ID hiPSC-CMs demonstrate impaired contractility and reduced oxygen consumption, features of cardiomyocytes from failing hearts. Importantly, hiPSC-CMs exposed to hypoxia, ID or the combination of the two exhibit bidirectional gene expression changes with significant overlap (Figure 1). Focusing on the commonly affected gene set, it becomes evident that hypoxia &amp; ID work via similar mechanisms involving activation of the HIF-1 pathway, that in turn orchestrates the metabolic switch to glycolysis and glutamine oxidation similar to foetal cells. Overall, hypoxia promotes a shift towards immature gene programmes, with 45% of dysregulated genes in hypoxia mimicking expression patterns of less mature cells. Interestingly changes in long non-coding RNA (lncRNA) profiles in hypoxia and ID mimic gene expression changes in these conditions (figure 2). Although restoring oxygen levels in hypoxic hiPSC-CMs rescues the hypoxic transcriptional signature, hiPSC-CMs previously exposed to hypoxia can use glycolytic pathways more efficiently upon further exposures to hypoxia. Conclusion These results shed light into the mechanisms ID impacts heart disease patients and are suggestive that HIF-1 is a key player in orchestrating the gene switch in ID and hypoxia.

FRI670 Osteoblast Rna Sequencing In T1d Mice Reveals Genetic Signature Of Maladaptation To Hypoxia And Compromised Collagen Synthesis

Abstract Disclosure: S. Kim: None. J. Hong: None. F. Sultana: None. E. Shelly: None. F. Korkmaz: None. J. Gimenez: None. T. Yuen: None. I. Daehn: None. J. Choi: None. M. Zaidi: None. The main feature of skeletal abnormality in type 1 diabetes (T1D) is low bone turnover with decreased osteoblastic bone formation [1, 2]. However, the mechanism of osteoblast dysfunction remains unclear. We generated T1D mice using low dose streptozotocin (STZ). T1D mice showed lower bone mass (g/cm2) at the femur (0.07 vs. 0.09*) and trends at lumbar spine (0.05 vs. 0.06, p=0.08) compared with control group at 8 weeks after inducing T1D. Osteoblasts were differentiated using bone marrow mesenchymal stem cells, and RNAseq was performed to analyze the transcriptome of osteoblasts. In gene set enrichment analysis, several pathways including immune, hypoxia, and glycolytic pathway were enriched. The osteogenic genes panel showed decreased Bglap and Col1a1 expression, together with lower expression of Bmp2 and Wnt5a, suggesting decreased bone formation might be related to the suppression of BMP and WNT signaling. Particularly, P4ha2, encoding prolyl 4-hydroxylase subunit alpha–2, which are responsible for posttranslational modification of collagen were downregulated in T1D osteoblasts (log2FC = – 1.7**). Among genes in hypoxia pathway, Egln3 encoding prolyl hydroxylase domain-containing protein 2 and Vhl encoding von Hippel-Lindau tumor suppressor, both of which stabilize HIF–α were downregulated (log2FC = – 2.8** and – 0.31*, respectively) likely for promoting HIF–α dependent gene expression in hypoxia. However, genes of the growth signaling pathway namely Pgf, Vegfa, and Igf1r were downregulated (log2FC = – 3.1**, – 0.4* and – 0.5**, respectively). Altogether, our findings suggest that maladaptation to hypoxic condition in T1D with compromised growth signaling pathway and impaired collagen synthesis might be related to osteoblasts dysfunction in T1D bone. (* p &amp;lt; 0.05 and ** p &amp;lt; 0.001) [1] Shanbhogue VV et al, JBMR. 2015[2] Rubin MR et al, JCEM. 2022 Presentation: Friday, June 16, 2023

Prognostic Value of Hypoxia Gene Expression Signature in Early-Stage Non-Small Cell Lung Cancer Patients Treated with Stereotactic Body Radiation Therapy

Stereotactic body radiation therapy (SBRT) is an effective alternative to surgery in the treatment of early-stage non-small cell lung cancer (NSCLC). However, disease recurrence occurs in approximately 20-30% of patients. Hypoxia is a well-known factor promoting solid tumor progression, radiation resistance, and immune evasion. In this study, we utilize a previously published hypoxia gene expression signature (Buffa) and measure its association with clinical outcomes in patients with NSCLC treated with SBRT. Our study focused on patients with localized, node-negative NSCLC treated with SBRT, and we identified 92 patients treated at our institution between 2008 and 2018 with available gene expression data. Total RNA from formalin-fixed paraffin-embedded archival biopsy specimens (pre-therapy) was isolated and mRNA expression was analyzed using an assay for human samples. For each gene in the Buffa signature, the top 50% of mRNA abundance values were given a score of +1, and the bottom 50% were given a score of -1 to generate a tumor hypoxia score. High scores suggest a hypoxic tumor and low scores imply normoxia. Kaplan-Meier curves were used to assess overall survival, disease-free survival, local recurrence, regional nodal recurrence, and distant recurrence. Cox proportional hazards were performed to account for confounding due to age, T stage, ECOG performance status, biologically effective dose, patient sex, and histology (squamous vs non-squamous). The patient's gene expression data were dichotomized based on their median hypoxia score (Table 1). Median follow-up was 23.9 months (95% CI 20.6 - 26.6). A high hypoxia score was associated with squamous histology (p = 0.003). On univariate analysis, a high hypoxia score was significantly associated with local recurrence (hazard ratio [HR] = 5.63; 95% CI 1.03 - 30.78; p = 0.046) and distant recurrence (HR = 1.85; 95% CI 1.14 - 3.02; p = 0.013). There was no significant difference in overall survival (HR = 1.93; 95% CI 0.98 - 3.82; p = 0.058), disease-free survival (HR = 2.13; 95% CI 0.93 - 4.89; p = 0.074), or regional nodal recurrence (HR = 1.45; 95% CI 0.41 - 5.14; p = 0.57). On multivariate analysis, a high hypoxia score was associated with worse overall survival (HR = 2.73; 95% CI 1.23 - 6.07; p = 0.014), local recurrence (HR = 12.85; 95% CI 1.08 - 152.49; p = 0.043) and distant recurrence (HR = 1.91; 95% CI 1.13 - 3.22; p = 0.016). Our findings demonstrate that a hypoxia gene signature is significantly associated with worse survival and increased local and distant recurrence after SBRT for localized NSCLC. This hypoxia signature may be useful in prognostication, selecting patients for surgery versus radiation, or selecting patients for treatment intensification with radiation or other systemic agents, and should be prospectively validated.

VHL L169P Variant Does Not Alter Cellular Hypoxia Tension in Clear Cell Renal Cell Carcinoma.

In the current era of tumor genome sequencing, single amino acid missense variants in the von Hippel-Lindau (VHL) tumor suppressor gene are frequently identified in clear cell renal carcinoma (ccRCC). Due to the incomplete knowledge of the structural architecture of VHL protein, the functional significance of many missense mutations cannot be assigned. L169P is one such missense mutation identified in the case of aggressive, metastatic ccRCC. Here, we characterized the biochemical activity, transcriptomic hypoxia signature and biological functions of the L169P variant. Lentiviral vector expressing either wildtype (WT) or L169P VHL were used to transduce two VHL-deficient human ccRCC cell lines, 786-O and RCC4. The stability of the VHL protein and the expression level of VHL, HIF1α and HIF2α were analyzed. The impact of restoring L169P or WT VHL on the hypoxia gene expression program in 786-O cells was assessed by mRNA sequencing (RNAseq) and computed hypoxic scores. The impact of restoring VHL expression on the growth of ccRCC models was assessed in cell cultures and in chorioallantoic membrane (CAM) xenografts. In the 786-O cells, the protein stability of L169P VHL was comparable to WT VHL. No obvious difference in the capability of degrading HIF1α and HIF2α was observed between WT and L169P VHL in the 786-O or RCC4 cells. The hypoxic scores were not significantly different in the 786-O cells expressing either wildtype or L169P VHL. From the cellular function perspective, both WT and L169P VHL slowed cell proliferation in vitro and in vivo. The L169P VHL variant is comparable to WT VHL in terms of protein stability, ability to degrade HIF1α factors and ability to regulate hypoxia gene expression, as well as in the suppression of ccRCC tumor cell growth. Taken together, our data indicate that the L169P VHL variant alone is unlikely to drive the oncogenesis of sporadic ccRCC.

ZmWRKY70 activates the expression of hypoxic responsive genes in maize and enhances tolerance to submergence in Arabidopsis

Hypoxic stress due to submergence is a serious threat to the growth and development of maize. WRKY transcription factors are significant regulators of plant responses to various abiotic and biotic stresses. Nevertheless, their function and regulatory mechanisms in the resistance of maize to submergence stress remain unclear. Here we report the cloning of a maize WRKY transcription factor gene, ZmWRKY70, transcripts of which accumulate under submergence stress in maize seedlings. Subcellular localization analysis and yeast transcriptional activation assay indicated that ZmWRKY70 was localized in the nucleus and had transcriptional activation activity. Heterologous overexpression of ZmWRKY70 in Arabidopsis increased the tolerance of seeds and seedlings to submergence stress by upregulating the transcripts of several key genes involved in anaerobic respiration, such as group VII ethylene-responsive factor (ERFVII) (AtRAP2.2), alcohol dehydrogenase (AtADH1), pyruvate decarboxylase (AtPDC1/2), and sucrose synthase (AtSUS4), under submergence conditions. Moreover, the overexpression of ZmWRKY70 in maize mesophyll protoplasts enhanced the expression of ZmERFVII members (ZmERF148, ZmERF179, and ZmERF193), ZmADH1, ZmPDC2/3, and ZmSUS1. Yeast one-hybrid and dual-luciferase activity assays further confirmed that ZmWRKY70 enhanced the expression of ZmERF148 by binding to the W box motif located in the promoter region of ZmERF148. Together, these results indicate that ZmWRKY70 plays a significant role in tolerance of submergence stress. This work provides a theoretical basis, and suggests excellent genes, for biotechnological breeding to improve the tolerance of maize to submergence through the regulation of ZmWRKY genes.

The Duration of Oxygen and Glucose Deprivation (OGD) Determines the Effects of Subsequent Reperfusion on Rat Pheochromocytoma (PC12) Cells and Primary Cortical Neurons.

Reperfusion is the fundamental treatment for ischaemic stroke; however, many ischaemic stroke patients cannot undergo reperfusion treatment. Furthermore, reperfusion can cause ischaemic reperfusion injuries. This study aimed to determine the effects of reperfusion in an in vitro ischaemic stroke model-oxygen and glucose deprivation (OGD) (0.3% O2)-with rat pheochromocytoma (PC12) cells and cortical neurons. In PC12 cells, OGD resulted in a time-dependent increase in cytotoxicity and apoptosis, and reduction in MTT activity from 2 h onwards. Reperfusion following shorter periods (4 and 6 h) of OGD recovered apoptotic PC12 cells, whereas after 12 h, OGD increased LDH release. In primary neurons, 6 h OGD led to significant increase in cytotoxicity, reduction in MTT activity and dendritic MAP2 staining. Reperfusion following 6 h OGD increased the cytotoxicity. HIF-1a was stabilised by 4 and 6 h OGD in PC12 cells and 2 h OGD onwards in primary neurons. A panel of hypoxic genes were upregulated by the OGD treatments depending on the duration. In conclusion, the duration of OGD determines the mitochondrial activity, cell viability, HIF-1a stabilization, and hypoxic gene expression in both cell types. Reperfusion following OGD of short duration is neuroprotective, whereas OGD of long duration is cytotoxic.

Abstract 271: MYC mediates enhanced lactate reutilization and resistance to anti-angiogenesis therapy in preclinical models of LKB1-deficient NSCLC

Abstract Deletion or loss of function mutations of the STK11/LKB1 tumor suppressor are associated with primary resistance to immunotherapy in KRAS-mutant lung adenocarcinoma (LUAD) and drive metabolic reprogramming of tumor cells. We observed that LKB1-deficient tumors were resistant to anti-angiogenic therapy in the hypoxic and nutrient-depleted or acidic tumor microenvironment (TME). We determined that MYC which is elevated in LKB1-deficient cells, regulated the expression of the lactate transporter, MCT4. Moreover, knockdown of MYC decreases glycolysis and cell proliferation. Therefore, we hypothesize that metabolic changes in LKB1-deficient tumor cells is at least partially driven by MYC upregulation, and that depletion of MYC or targeting of key enzymes or transporters downstream of MYC such as MCT4 may abrogate lactate reutilization and sensitize LKB1-deficient tumors to anti-angiogenic therapy. To explore the impact of MYC on lactate metabolism in LKB1-deficient NSCLC cells, we performed isotope tracing in KRAS mutant (K) and KRAS mutant LKB1 knockout (KL) syngeneic murine lung cancer cells. 13C3-lactate tracing revealed that isotopologues were significantly enriched in TCA components such as pyruvate, citrate and a-ketoglutarate in KL cells. Meanwhile, lactate-treated KL cells shows less reactive oxygen species (ROS), suggesting that LKB1-deficient tumor cells reutilize lactate as an energy source more efficiently than LKB1-intact cells. MCT4 KO significantly abrogated lactate incorporation into TCA cycle. Similarly, MYC knockdown or MCT4 KO decreased lactate-induced oxygen consumption, but increased ROS levels. In contrast, exhausted T cells were inefficient at lactate reutilization, and high levels of lactate increased ROS in T cells. Hence, LKB1-deficient tumors have a survival advantage over T cells in the lactate-rich TME. We queried scRNAseq data from K, KL and KL MCT4KO syngeneic models and similarly observed that KL tumor cells exhibited elevated hypoxia and angiogenesis gene expression signatures, which was reversed by MCT4 KO. However, ROS detoxification was decreased in T cells from KL tumors but increased in MCT4 KO tumors. Finally, we injected KL murine tumor cells into immunocompetent mice, and randomly treated them with vehicle or the VEGF blocking antibody, DC101. MYC knockdown or MCT4 KO sensitized KL tumors to VEGF inhibition, and significantly increased overall survival. Collectively, our data indicates that in LKB1-deficient tumors, upregulation of MYC promotes tumor cell metabolic reprogramming and that targeting MYC or MCT4 can inhibit lactate reutilization and enhance the efficacy of anti-angiogenic agents. These findings provide insight into the mechanisms driving the aggressive phenotype of KRAS-mutant LKB1-deficient tumors and identify a novel therapeutic strategy for targeting this patient population. Citation Format: Yu Qian, David Molkentine, Chendong Yang, Ana Galan Cobo, Irene Guijarro, Minghao Dang, Alissa Poteete, Peixin Jiang, Ferdinandos Skoulidis, Linghua Wang, Alexandre Reuben, John D. Minna, Ralph J. DeBerardinis, John V. Heymach. MYC mediates enhanced lactate reutilization and resistance to anti-angiogenesis therapy in preclinical models of LKB1-deficient NSCLC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 271.

Ellagic Acid Prevents Particulate Matter-Induced Pulmonary Inflammation and Hyperactivity in Mice: A Pilot Study

The inhalation of fine particulate matter (PM) is a significant health-related environmental issue. Previously, we demonstrated that repeated PM exposure causes hyperlocomotive activity in mice, as well as inflammatory and hypoxic responses in their lungs. In this study, we evaluated the potential efficacy of ellagic acid (EA), a natural polyphenolic compound, against PM-induced pulmonary and behavioral abnormalities in mice. Four treatment groups were assigned in this study (n = 8): control (CON), particulate-matter-instilled (PMI), low-dose EA with PMI (EL + PMI), and high-dose EA with PMI (EH + PMI). EA (20 and 100 mg/kg body weight for low dose and high dose, respectively) was orally administered for 14 days in C57BL/6 mice, and after the eighth day, PM (5 mg/kg) was intratracheally instilled for 7 consecutive days. PM exposure induced inflammatory cell infiltration in the lungs following EA pretreatment. Moreover, PM exposure induced inflammatory protein expression in the bronchoalveolar lavage fluid and the expression of inflammatory (tumor necrosis factor alpha (Tnfα), interleukin (Il)-1b, and Il-6) and hypoxic (vascular endothelial growth factor alpha (Vegfα), ankyrin repeat domain 37 (Ankrd37)) response genes. However, EA pretreatment markedly prevented the induction of expression of inflammatory and hypoxic response genes in the lungs. Furthermore, PM exposure significantly triggered hyperactivity by increasing the total moving distance with an increase in moving speed in the open field test. On the contrary, EA pretreatment significantly prevented PM-induced hyperactivity. In conclusion, dietary intervention with EA may be a potential strategy to prevent PM-induced pathology and activity.