RANK Pathway Research Articles

BatchFLEX: feature-level equalization of X-batch.

Integrative analysis of heterogeneous expression data remains challenging due to variations in platform, RNA quality, sample processing, and other unknown technical effects. Selecting the approach for removing unwanted batch effects can be a time-consuming and tedious process, especially for more biologically focused investigators. Here, we present BatchFLEX, a Shiny app that can facilitate visualization and correction of batch effects using several established methods. BatchFLEX can visualize the variance contribution of a factor before and after correction. As an example, we have analyzed ImmGen microarray data and enhanced its expression signals that distinguishes each immune cell type. Moreover, our analysis revealed the impact of the batch correction in altering the gene expression rank and single-sample GSEA pathway scores in immune cell types, highlighting the importance of real-time assessment of the batch correction for optimal downstream analysis. Our tool is available through Github https://github.com/shawlab-moffitt/BATCH-FLEX-ShinyApp with an online example on Shiny.io https://shawlab-moffitt.shinyapps.io/batch_flex/.

Multi-omics profiling of retinal pigment epithelium reveals enhancer-driven activation of RANK-NFATc1 signaling in traumatic proliferative vitreoretinopathy

During the progression of proliferative vitreoretinopathy (PVR) following ocular trauma, previously quiescent retinal pigment epithelial (RPE) cells transition into a state of rapid proliferation, migration, and secretion. The elusive molecular mechanisms behind these changes have hindered the development of effective pharmacological treatments, presenting a pressing clinical challenge. In this study, by monitoring the dynamic changes in chromatin accessibility and various histone modifications, we chart the comprehensive epigenetic landscape of RPE cells in male mice subjected to traumatic PVR. Coupled with transcriptomic analysis, we reveal a robust correlation between enhancer activation and the upregulation of the PVR-associated gene programs. Furthermore, by constructing transcription factor regulatory networks, we identify the aberrant activation of enhancer-driven RANK-NFATc1 pathway as PVR advanced. Importantly, we demonstrate that intraocular interventions, including nanomedicines inhibiting enhancer activity, gene therapies targeting NFATc1 and antibody therapeutics against RANK pathway, effectively mitigate PVR progression. Together, our findings elucidate the epigenetic basis underlying the activation of PVR-associated genes during RPE cell fate transitions and offer promising therapeutic avenues targeting epigenetic modulation and the RANK-NFATc1 axis for PVR management.

Tracing unknown tumor origins with a biological-pathway-based transformer model

Cancer of unknown primary (CUP) represents metastatic cancer where the primary site remains unidentified despite standard diagnostic procedures. To determine the tumor origin in such cases, we developed BPformer, a deep learning method integrating the transformer model with prior knowledge of biological pathways. Trained on transcriptomes from 10,410 primary tumors across 32 cancer types, BPformer achieved remarkable accuracy rates of 94%, 92%, and 89% in primary tumors and primary and metastatic sites of metastatic tumors, respectively, surpassing existing methods. Additionally, BPformer was validated in a retrospective study, demonstrating consistency with tumor sites diagnosed through immunohistochemistry and histopathology. Furthermore, BPformer was able to rank pathways based on their contribution to tumor origin identification, which helped to classify oncogenic signaling pathways into those that are highly conservative among different cancers versus those that are highly variable depending on their origins.

Abstract PO1-02-13: Germline mutation status of BRCA1/2 and other breast cancer predisposition genes as predictive and prognostic biomarker: Results of the GeparX study (GeparX-BRCA)

Abstract Germline mutation status of BRCA1/2 and other breast cancer predisposition genes as predictive and prognostic biomarker: Results of the GeparX study (GeparX-BRCA) Background: There is accumulating evidence that the RANK/RANKL signaling pathway plays a pivotal role in breast tumorigenesis, particularly in the development of BRCA1-mutated tumors. Targeting the RANK pathway has been shown to attenuate breast cancer (BC) proliferation in vitro and in vivo. Studies using bone modifying agents as adjuvant therapy showed reduced rates of bone metastases and improved BC survival, as well as prevention of treatment-induced skeletal events. The GeparX clinical trial assessed the use of denosumab in patients with primary BC as an adjunct to neoadjuvant chemotherapy for its ability to enhance pathological complete response (pCR) rate and improve outcome. The trial randomized 780 patients twice to a total of 4 treatment groups (to receive or not receive denosumab; to receive nab-paclitaxel 125 mg/m2 weekly for 12 weeks or days 1 and 8 every 3 weeks for 4 cycles, both followed by 4 cycles of epirubicin/cyclophosphamide, 90/600 mg/m2 every 2 weeks/every 3 weeks according to the investigator´s choice). Carboplatin was given in triple-negative breast cancer (TNBC), and trastuzumab biosimilar ABP980 plus pertuzumab was given in human epidermal growth factor-2-positive (HER2+) BC. Overall, the pCR (ypT0 ypN0) rate was 41% with denosumab vs 43% without; nab-paclitaxel at a dosage of 125 mg/m2 weekly resulted in a significantly higher pCR rate of 45% vs 39% with a dosage of 125 mg/m2 days 1 and 8 every 3 weeks. Research question: Does the germline mutation status of BRCA1/2 and other BC predisposition genes affect treatment outcome in the GeparX study? Methods: Genetic germline analyses assessing pathogenic variants in BRCA1/2 and 16 other BC predisposition genes were performed at the Center for Familial Breast and Ovarian Cancer, Cologne, Germany; 767 patients were included in this secondary investigation (308 TNBC, 306 HER2-/hormone receptor positive [HR+], 153 HER2+). Findings: Germline BRCA1/2 mutations were present in 91/767 patients (11.9%), with a higher mutation prevalence in TNBC (50/308, 16.2%) and HER2-/HR+ BC (37/306, 12.1%), and a low mutation prevalence in HER2+ BC (4/153, 2.6%). Overall, the pCR rate (ypT0 ypN0) was elevated in BRCA1/2 mutation carriers vs non-carriers (49.5% vs 41.1%, respectively; overall: OR 1.40, 95% CI 0.90-2.17; TNBC: OR 1.24, 95% CI 0.67-2.32; HER2-/HR+: OR 1.83, 95% CI 0.86-3.88). Highest pCR rates were observed in TNBC in BRCA1/2 mutation carriers vs non-carriers (60% vs. 54.7%, respectively). Highest pCR rate differences were observed HER2-/HR+ BC in BRCA1/2 mutation carriers vs non-carriers (32.4% vs. 20.8%, respectively). Regarding treatment arms, both BRCA1/2 mutation carriers and non-carriers benefitted most from nab-paclitaxel at a dosage of 125 mg/m2 weekly vs 125 mg/m2 days 1 and 8 every 3 weeks (BRCA1/2 mutation carriers: 55.3% vs 43.2%, respectively; OR 1.63, 95% CI 0.71-3.73; non-carriers: 43.7% vs 38.6%, respectively; OR 1.24, 95% CI 0.91-1.68). No beneficial effect was observed for denosumab vs no denosumab (51.1% vs 47.8% for BRCA1/2 mutation carriers, respectively; OR 1.14, 95% CI 0.50-2.60; 40.3% vs 41.9% for non-carriers, respectively; OR 0.94, 95% CI 0.69-1.27). Of the 617 BRCA1/2-negative patients, 59 patients carried mutations in other BC predisposition genes which did not predict therapy response compared to patients without any mutation. Conclusions: Irrespective of the treatment arm, higher pCR rates were observed in BRCA1/2 mutations carriers vs non-carriers. Both BRCA1/2 mutation carriers and non-carriers benefitted most from weekly nab-paclitaxel. No pronounced effect was observed for denosumab in either group. Key words: GeparX, denosumab, BRCA1/2 germline mutations, therapy response Funding: GeparX was financially supported by Amgen and BMS (Celgene). Citation Format: Rita K. Schmutzler, Theresa Link, Eric Hahnen, Mattea Reinisch, Jan Hauke, Marianne Just, Michael Untch, Corinna Ernst, Oliver Stötzer, Peter A. Fasching, Mohamad Kayali, Pauline Wimberger, Andreas Schneeweiss, Sandra Schmidt, Sabine Seiler, Christian Jackisch, Marc Thill, Kerstin Rhiem, Carsten Denkert, Valentina Nekljudova, Johannes Holtschmidt, Jens-Uwe Blohmer, Sibylle Loibl. Germline mutation status of BRCA1/2 and other breast cancer predisposition genes as predictive and prognostic biomarker: Results of the GeparX study (GeparX-BRCA) [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO1-02-13.

Abstract PS16-04: Denosumab as an enhancer of the immune infiltrate in hormone receptor-positive early breast cancer. Subgroup analysis from the D-Biomark window-of-opportunity clinical trial (NCT03691311)

Abstract Background: The receptor activator of nuclear factor κB (RANK) signaling pathway has emerged as a therapeutic target in breast cancer (BC). Recent studies indicate that inhibition of the RANK pathway induces tumor cell differentiation and may enhance the anti-tumor immune response. The D-Biomark clinical trial aims to evaluate the antitumor (antiproliferative and proapoptotic) and immunomodulatory effects of denosumab in HER2-negative early BC. Methods: Patients with early HER2-negative BC scheduled for primary surgery were randomized in a 2:1 ratio to receive two doses of 120 mg denosumab on days 1 and 8 vs no treatment before surgery. Immunohistochemistry (IHC) was used to assess Ki67 (proliferation), cleaved caspase-3 (cell survival), RANK and RANKL. Stromal tumor infiltrating lymphocytes (TILs) and serum markers including free RANKL (sRANKL), tartrate-resistant acid phosphatase 5b (TRACP5b), and osteoprotegerin (OPG) were also analyzed. Paired t-test was used to compare values between core biopsy (biopsy A) and surgical samples (biopsy B). Subgroup analysis by intrinsic subtype was performed on 47 matched cases using PAM50. Results: Between July 2019 and May 2021, we enrolled 60 patients, 58 evaluable, including 10 triple-negative breast cancer (TNBC). The clinicopathologic characteristics of the population at the time of enrollment were well balanced, but the TNBC recruited included 5 out of 10 tumors with a more indolent behavior than the typical tumors of this lineage (apocrine tumors, low cell proliferation). Due to this and the small number of cases, no conclusions can be drawn in this subgroup. RANK expression was detected in 19 tumor cases, while 17 cases expressed RANKL. The treated group showed a decrease in sRANKL (p < 0.000), indicating denosumab activity, while the control group showed no change (p1.0). OPG levels in the experimental group showed a non-significant increase (p0.07), while TRACP5b remained unchanged. Both groups showed a non-clinically relevant increase in cell proliferation (5 percentage points), control p0.04, experimental p0.01. Subgroup analysis of tumors with RANK+ or RANKL+ tumor cells also showed no reduction in Ki67. Cell survival did not decrease in the overall cohort (control p0.05, experimental p0.24), nor in subgroups or in tumors with RANK+ or RANKL+ tumor cells. Denosumab treatment increased TILs in the overall population (control p0.06, experimental p0.0006) and in the subgroups: RANK+ tumors, RANKL+ tumors, premenopausal and postmenopausal, less so in the TNBC group. The subgroup analysis is shown in Table 1. Analysis by intrinsic subtype showed that in the experimental group there was an increase in cases with a change to luminal A lineage (17%) compared to the control group (6%), suggesting a possible cellular differentiation towards less aggressive tumors. Although the number of patients is small, these changes warrant further investigation and highlight the role of denosumab as an immune activator in these luminal tumors known for their low inflammatory infiltrate. Conclusion: Two doses of denosumab prior to surgery did not reduce proliferation or increase apoptosis. However, this short course of denosumab increased TILs in early BC, particularly in luminal tumors, and may induce tumor cell differentiation into luminal A-like tumors. Table. Citation Format: Andrea Vethencourt, Eva Trinidad, Eduard Dorca, Anna Petit, Teresa Soler-Monsó, Agostina Stradella, Cristina Capo, Ander Urriticoechea, Marta Matas, Gema Pérez-Chacon, María Jimenez, Marina Ciscar, Emilia Brizzi, Gonzalo Soria Alcaide, Gonzalo Gomez, Elena Piñeiro, Elvira Purqueras, Amparo Garcia, Ariadna Iserte, M Jesus Pla, Miriam Campos, Miguel Gil-Gil, Sonia Pernas, Eva Gonzalez-Suarez, Catalina Falo. Denosumab as an enhancer of the immune infiltrate in hormone receptor-positive early breast cancer. Subgroup analysis from the D-Biomark window-of-opportunity clinical trial (NCT03691311) [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PS16-04.

Caffeine induces alveolar bone loss in rats submitted to orthodontic movement via activation of receptor activator of nuclear factor ҡB, receptor activator of nuclear factor ҡB ligand, and osteoprotegerin pathway

Caffeine is a widely consumed substance with several effects on bone metabolism. This study aimed to investigate the effect of caffeine on the bone tissue of rats submitted to orthodontic movement. Twenty-five male Wistar rats underwent orthodontic movement (21 days) of the first permanent maxillary molars on the left side. The experimental group (caffeine; n= 13) and control group (n= 12) received caffeine and water, respectively, by gavage. Microcomputed tomography was performed to analyze orthodontic movement. Histologic analysis of the inflammatory infiltrate and osteoclast count by tartrate-resistant acid phosphatase were conducted. Maxilla tissue was evaluated for receptor activator of nuclear factor ҡB (RANK), RANK ligand (RANKL), and osteoprotegerin by immunohistochemistry. Caffeine exhibited a lower bone volume/tissue volume ratio (78.09% ± 5.83%) than the control (86.84% ± 4.89%; P<0.05). Inflammatory infiltrate was increased in the caffeine group compared with the control group (P<0.05). A higher number of tartrate-resistant acid phosphatase-positive cells was observed in the caffeine (9.67 ± 1.73) than in the control group (2.66 ± 0.76; P<0.01). Immunoexpression of RANK and RANKL in the caffeine group was greater than the control (P<0.05). The use of caffeine thermogenic induces alveolar bone loss in rats submitted to orthodontic movement via activation of RANK, RANKL, and osteoprotegerin signaling pathways.

Treatment of gouty arthritis with traditional Chinese medicine decoction: Meta-analysis, network pharmacology analysis, and molecular docking.

Previous studies have shown that traditional Chinese medicine decoction (TCMD) could ameliorate the clinical symptoms and laboratory indicators of gouty arthritis (GA) patients. However, few investigations have been conducted on the efficacy and safety of TCMD for GA, the underlying mechanism of TCMD for GA, and the relationship between the TCMD active ingredients and GA targets. Randomized controlled trials of TCMD for GA were retrieved from Chinese and English databases. Meta-analysis was conducted by Stata 17 software. Potential sources of heterogeneity were identified through subgroup analysis, meta-regression, and heterogeneity test. Publication bias was assessed by Egger's test and funnel plots. The ingredients and targets related to TCMD and GA were obtained from multiple databases, such as TCMSP and DrugBank. The protein-protein interaction network, GO and KEGG analysis was constructed using STRING and DAVID. Molecular docking and visualization of the results were completed by AutoDock and PyMOL software. Eighty-four studies were included, involving 7151 patients and 10 outcome indicators. Meta-analysis showed that, compared to routine treatment, TCMD could better reduce the incidence of adverse events and the level of laboratory indicators including blood uric acid (BUA), C-reactive protein (CRP), erythrocyte sedimentation rate (ESR), interleukin 6 (IL-6), interleukin 8 (IL-8), interleukin 1β (IL-1β), and tumor necrosis factor-α (TNF-α). In the section of network pharmacology, we retrieved 150 active ingredients and 303 target genes from the top 10 herbs in 84 studies, as well as 3082 disease targets and 195 cross targets of the herbs and GA. The top ranked ingredients, intersection targets, and signaling pathways included quercetin, kaempferol, and wogonin; AKT1, TNF, and TP53; as well as IL-17, HIF-1, and PI3K-AKT, etc. Among the 81 molecular docking results, we visualized 10 results with low binding energy, including IL1B and beta-sitosterol, MYC and beta-sitosterol, etc. TCMD could be a satisfactory complementary and alternative therapy for GA. However, it should be verified by further studies. Future research could be conducted from the following active ingredients, targets, and signal pathways, such as wogonin, sitosterol, and sitosterol; AKT1, TNF, IL6, and TP53; and IL-17, HIF-1, and PI3K-AKT signaling pathway.

RANKL/RANK is required for cytokine-induced beta cell death; osteoprotegerin, a RANKL inhibitor, reverses rodent type 1 diabetes.

Treatment for type 1 diabetes (T1D) requires stimulation of functional β cell regeneration and survival under stress. Previously, we showed that inhibition of the RANKL/RANK [receptor activator of nuclear factor kappa Β (NF-κB) ligand] pathway, by osteoprotegerin and the anti-osteoporotic drug denosumab, induces rodent and human β cell proliferation. We demonstrate that the RANK pathway mediates cytokine-induced rodent and human β cell death through RANK-TRAF6 interaction and induction of NF-κB activation. Osteoprotegerin and denosumab protected β cells against this cytotoxicity. In human immune cells, osteoprotegerin and denosumab reduce proinflammatory cytokines in activated T-cells by inhibiting RANKL-induced activation of monocytes. In vivo, osteoprotegerin reversed recent-onset T1D in nonobese diabetic/Ltj mice, reduced insulitis, improved glucose homeostasis, and increased plasma insulin, β cell proliferation, and mass in these mice. Serum from T1D subjects induced human β cell death and dysfunction, but not α cell death. Osteoprotegerin and denosumab reduced T1D serum-induced β cell cytotoxicity and dysfunction. Inhibiting RANKL/RANK could have therapeutic potential.

Co-targeting RANK pathway treats and prevents acquired resistance to CDK4/6 inhibitors in luminal breast cancer

The combination of endocrine therapy (ET) and cyclin-dependent kinase 4/6 (CDK4/6) inhibitors (CDK4/6i) was a hallmark in metastatic luminal breast cancer (BC). However, intrinsic and acquired resistance affects long-term efficacy. Here, we study the role of the receptor activator of nuclear factor-κB (RANK) pathway in CDK4/6i resistance. We find that RANK overexpression in luminal BC is associated with intrinsic resistance to CDK4/6i, both invitro and in mouse xenografts, and decreased proliferation rate and chronic interferon (IFN) γ response are highlighted as resistance drivers. Gene expression data from the NeoPalAna CDK4/6i clinical trial, and studies with palbociclib-resistant cell lines, show that RANK is upregulated after treatment with CDK4/6i, supporting a role in acquired resistance. Our study shows that RANK ligand (RANKL) inhibitors can restore sensitivity to CDK4/6i and prevent acquired resistance. On the basis of these findings, we conclude that pharmacological inhibition of the RANK pathway through RANKL blocking could represent an add-on to ET+ CDK4/6i, warranting further clinical studies.

Asiaticoside promotes heart autonomic nerve repair through receptor activator of nuclear factor kappa-B ligand pathway in coronary heart disease

This experiment intends to observe the effects of Asiaticoside on angiotensin II (AngII)-induced coronary heart disease (CHD) by regulating nuclear factor κ-B ligand receptor activator and RANK pathway (RANKL/RANK). Cardiomyocytes of rats with CHD were divided into AngII group (2 μmol/L), blank control group, and asiaticoside group (2 μmol/L and 10 μmol/L). After 24 hours of intervention, proliferation and apoptosis was assessed. At the same time, the expressions of RANKL, RANK and α-smooth muscle actin (α-SMA) were measured. Compared with blank group, the proliferation ability of cardiomyocytes with CHD in AngII group was significantly decreased and it increased after asiaticoside treatment (P &lt;0.05). The apoptosis of cardiomyocytes in AngII group was higher than blank group and asiaticoside group. Cardiomyocytes proliferation in asiaticoside group was the most obvious (P &lt;0.05). α-SMA expression decreased in AngII group and increased after asiaticoside treatment (P &lt;0.05). RANKL and RANK mRNA in CHD were significantly upregulated after administration of asiaticoside (P &lt;0.05). RANKL/RANK expression was high in normal CHD cardiomyocytes and reduced after Ang II stimulation. Asiaticoside promotes cardiomyocyte proliferation in CHD by promoting RANKL/RANK signaling, thereby reducing the possibility of heart failure in CHD.

Redundancy-aware unsupervised ranking based on game theory: Ranking pathways in collections of gene sets.

In Genetics, gene sets are grouped in collections concerning their biological function. This often leads to high-dimensional, overlapping, and redundant families of sets, thus precluding a straightforward interpretation of their biological meaning. In Data Mining, it is often argued that techniques to reduce the dimensionality of data could increase the maneuverability and consequently the interpretability of large data. In the past years, moreover, we witnessed an increasing consciousness of the importance of understanding data and interpretable models in the machine learning and bioinformatics communities. On the one hand, there exist techniques aiming to aggregate overlapping gene sets to create larger pathways. While these methods could partly solve the large size of the collections' problem, modifying biological pathways is hardly justifiable in this biological context. On the other hand, the representation methods to increase interpretability of collections of gene sets that have been proposed so far have proved to be insufficient. Inspired by this Bioinformatics context, we propose a method to rank sets within a family of sets based on the distribution of the singletons and their size. We obtain sets' importance scores by computing Shapley values; Making use of microarray games, we do not incur the typical exponential computational complexity. Moreover, we address the challenge of constructing redundancy-aware rankings where, in our case, redundancy is a quantity proportional to the size of intersections among the sets in the collections. We use the obtained rankings to reduce the dimension of the families, therefore showing lower redundancy among sets while still preserving a high coverage of their elements. We finally evaluate our approach for collections of gene sets and apply Gene Sets Enrichment Analysis techniques to the now smaller collections: As expected, the unsupervised nature of the proposed rankings allows for unremarkable differences in the number of significant gene sets for specific phenotypic traits. In contrast, the number of performed statistical tests can be drastically reduced. The proposed rankings show a practical utility in bioinformatics to increase interpretability of the collections of gene sets and a step forward to include redundancy-awareness into Shapley values computations.

Abstract PD9-03: Breast Cancer Microenvironment Change After Neoadjuvant Endocrine Treatment Breast Cancer Microenvironment Change After Neoadjuvant Endocrine Treatment

Abstract Background: Estrogen receptor positive (ER+)/HER-2 negative breast cancer (BC) is considered to be an immunologically cold tumor compared to triple negative breast cancer. Therefore, the tumor microenvironment (TME) of ER+/HER-2 negative BC is understudied. The receptor activator of nuclear factor-kB ligand (RANKL)-RANK pathway was first identified, as mediator of T and dendritic cells interaction, but it is mostly known for its role as key regulator of bone remodeling and pathophysiology of bone metastases. RANK is a member of the tumor necrosis factor receptor (TNFR) superfamily that is activated upon RANKL binding, promoting cell proliferation, survival and differentiation. The RANKL-RANK pathway also emerged as a major mediator of hormone-driven breast carcinogenesis. The aim of this study is to investigate the TME and the immune response during neoadjuvant endocrine therapy (NET) and to correlate this with the treatment response in a real life setting. Methods: Expressions of immune checkpoint receptors and immune cells were examined immunohistochemically in pre- and post- NET on a cohort of 44 ER+/HER-2 negative BC patients. They were treated with tamoxifen (N=8), an aromatase inhibitor (N=36) or a combination of an aromatase inhibitor with a PI3K inhibitor (N= 7) for a median duration of 6 months (range 1-32) months. Monoclonal antibodies for PDL-1, PD-1, TIM-3, LAG-3, CTLA-4, CD4, CD68, FOXP3, RANK and RANKL were used. All staining were done according to validated protocols and scoring was done by a pathologist specialized in breast cancer. Positivity was defined as staining &amp;gt; 1% on TILs. Response to NET was evaluated according to tumor size change on imaging and Ki-67 change. Results: The median age was 62.5 (44–90.3) years. Diameter of tumor size decreased with a mean of 7.818 mm (p &amp;lt; 0.0001) during NET and the value of Ki-67 value decreased significantly after NET (value, p&amp;lt; 0.0004). An increase in PD-L1 expression after NET showed a trend towards significant (p= 0.088) and RANK expression on TILs significantly decreased with a median of 30% (range= -70 to 85) (p= 0.0007) after NET. A good response to NET defined as a decrease in tumor size and/or decrease of Ki-67 was found to be associated with a longer duration of NET, a change of CD4+ T-cells, a change of RANK expression on TILs and a higher number of CD68+ tumor-associated macrophages before the start of NET and also RANK expression on TILs before the start of NET. Conclusion: The immune micro-environment plays an important role in ER+/HER-2 negative BC. NET influences the composition and/or functional state of the infiltrating immune cells. Furthermore, changes in the immune micro-environment are also associated with treatment response. Breast Cancer Microenvironment Change After Neoadjuvant Endocrine Treatment Comparison of continuous and categorical parameters before and after NET. Comparison of the continuous parameters was done using Wilcoxon signed rank test. Comparison of the categorical parameters was done using a Chi-square test. sTIL: stromal tumour infiltrating lymphocytes and NET: neoadjuvant endocrine therapy. Bold values denote statistical significance at the p &amp;lt; 0.05 level. Citation Format: Gizem Oner, Glenn Broeckx, Christophe Van Berckelaer, Sevilay Altintas, Zafer Canturk, Wiebren Tjalma, Karen Zwaenepoel, Zwi Berneman, Marc Peeters, Patrick Pauwels, Peter A van Dam. Breast Cancer Microenvironment Change After Neoadjuvant Endocrine Treatment Breast Cancer Microenvironment Change After Neoadjuvant Endocrine Treatment [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr PD9-03.

Metabolomics profiling to characterize cerebral ischemia-reperfusion injury in mice.

Cerebral ischemia, resulting from compromised blood flow, is one of the leading causes of death worldwide with limited therapeutic options. Potential deleterious injuries resulting from reperfusion therapies remain a clinical challenge for physicians. This study aimed to explore the metabolomic alterations during ischemia-reperfusion injury by employing metabolomic analysis coupled with gas chromatography time-of-flight mass spectrometry (GC-TOF-MS) and ultraperformance liquid chromatography quadrupole (UPLC/Q)-TOF-MS. Metabolomic data from mice subjected to middle cerebral artery occlusion (MCAO) followed by reperfusion (MCAO/R) were compared to those of the sham and MCAO groups. A total of 82 simultaneously differentially expressed metabolites were identified among each group. The top three major classifications of these differentially expressed metabolites were organic acids, lipids, and organooxygen compounds. Metabolomics pathway analysis was conducted to identify the underlying pathways implicated in MCAO/R. Based on impactor scores, the most significant pathways involved in the response to the reperfusion after cerebral ischemia were glycerophospholipid metabolism, linoleic acid metabolism, pyrimidine metabolism, and galactose metabolism. 17 of those 82 metabolites were greatly elevated in the MCAO/Reperfusion group, when compared to those in the sham and MCAO groups. Among those metabolites, glucose-6-phosphate 1, fructose-6-phosphate, cellobiose 2, o-phosphonothreonine 1, and salicin were the top five elevated metabolites in MCAO/R group, compared with the MCAO group. Glycolysis, the pentose phosphate pathway, starch and sucrose metabolism, and fructose and mannose degradation were the top four ranked pathways according to metabolite set enrichment analysis (MSEA). The present study not only advances our understanding of metabolomic changes among animals in the sham and cerebral ischemia groups with or without reperfusion via metabolomic profiling, but also paves the way to explore potential molecular mechanisms underlying metabolic alteration induced by cerebral ischemia-reperfusion.

Abstract P036: Circulating osteoprotegerin levels and breast cancer risk among women with a BRCA1 mutation: A prospective study

Abstract Background: Upregulation of the receptor activator of nuclear factor κB (RANK) pathway has been implicated in the pathogenesis of BRCA1-associated breast cancer, and pharmacologic inhibition of the RANK pathway has been shown to suppress BRCA1-mammary tumorigenesis in animal studies. Osteoprotegerin (OPG) is the endogenous decoy receptor for RANK-ligand (RANKL) that inhibits RANK/RANKL-signaling. Lower levels of circulating OPG have been reported among women with a BRCA1 pathogenic variant (mutation). Thus, it is of interest to evaluate the association between circulating OPG and breast cancer as a potential novel biomarker of risk. Objective: To prospectively investigate the association between circulating OPG levels and breast cancer risk among women with a BRCA1 mutation. Methods: Eligible women from an on-going longitudinal study with a biobanked blood sample were included and had a confirmed BRCA1 mutation, no previous history of cancer, and no preventive bilateral mastectomy. Self-reported biennial questionnaires collected detailed information on key risk factors, screening, surgery, and cancer incidence. Serum OPG (pg/ml) was quantified using an enzyme-linked immunosorbent assay (ELISA). The exposure was dichotomized into high vs. low OPG level using the median OPG value in the entire cohort (low: ≤79.2 vs. high: &amp;gt;79.2 pg/ml) and continuously (per 10-unit increase). Cox proportional hazards models were used to estimate the hazard ratio (HR) and 95% confidence intervals (CI) of breast cancer by OPG level. The multivariable model adjusted for age, breastfeeding, smoking history, and coffee consumption. Results: There was a total of 662 BRCA1 mutation included in this prospective analysis with a mean age of 40.3 years (SD 12.1). Over a mean follow-up of 5.6 years (range 0.0-11.9), 49 incident breast cancers were diagnosed. Among women with low OPG, there were 31 incident cases compared to 18 incident cases among women with high OPG. Women with high OPG levels had a lower risk of developing breast cancer (HR 0.57; 95% CI 0.32-1.04; P value 0.07) compared to those with low OPG levels. Breast cancer risk decreased by a factor of 0.91 for every 10-unit increase in circulating OPG concentration (95% CI 0.84-1.00; P value 0.04). Conclusion: These findings suggest an inverse association between OPG levels and breast cancer risk among women with a BRCA1 mutation. Pending validation, circulating OPG levels may improve current risk prediction models and enhance the identification of women at the highest threshold of cancer risk. This may offer more personalized risk management strategies, and a potential for pharmacologic inhibition of the RANKL-signaling pathway as a novel approach to cancer prevention for high-risk women. Citation Format: Shana J. Kim, Tasnim Zaman, Aleksandra Uzelac, Ping Sun, Jan Lubinski, Steven A. Narod, Leonardo Salmena, Joanne Kotsopoulos. Circulating osteoprotegerin levels and breast cancer risk among women with a BRCA1 mutation: A prospective study. [abstract]. In: Proceedings of the AACR Special Conference: Precision Prevention, Early Detection, and Interception of Cancer; 2022 Nov 17-19; Austin, TX. Philadelphia (PA): AACR; Can Prev Res 2023;16(1 Suppl): Abstract nr P036.

Aggregated alpha-synuclein transcriptionally activates pro-inflammatory canonical and non-canonical NF-κB signaling pathways in peripheral monocytic cells

Parkinson’s disease (PD) is a neurodegenerative disorder characterized by chronic neuroinflammation, loss of dopaminergic neurons in the substantia nigra, and in several cases accumulation of alpha-synuclein fibril (α-syn) containing Lewy-bodies (LBs). Peripheral inflammation may play a causal role in inducing and perpetuating neuroinflammation in PD and accumulation of fibrillar α-syn has been reported at several peripheral sites including the gut and liver. Peripheral fibrillar α-syn may induce activation of monocytes via recognition by toll-like receptors (TLRs) and stimulation of downstream NF-κB signaling; however, the specific mechanism by which this occurs is not defined. In this study we utilized the THP-1 monocytic cell line to model the peripheral transcriptional response to preformed fibrillar (PFF) α-syn. Compared to monomeric α-syn, PFF α-syn displays overt inflammatory gene upregulation and pathway activation including broad pan-TLR signaling pathway activation and increases in TNF and IL1B gene expression. Notably, the non-canonical NF-κB signaling pathway gene and PD genome wide association study (GWAS) candidate NFKB2 was upregulated. Additionally, non-canonical NF-κB activation-associated RANK and CD40 pathways were also upregulated. Transcriptional-phenotype analysis suggests PFFs induce transcriptional programs associated with differentiation of monocytes towards macrophages and osteoclasts via non-canonical NF-κB signaling as a potential mechanism in which myeloid/monocyte cells may contribute to peripheral inflammation and pathogenesis in PD.

Pathway expression analysis

This paper introduces a pathway expression framework as an approach for constructing derived biomarkers. The pathway expression framework incorporates the biological connections of genes leading to a biologically relevant model. Using this framework, we distinguish between shedding subjects post-infection and all subjects pre-infection in human blood transcriptomic samples challenged with various respiratory viruses: H1N1, H3N2, HRV (Human Rhinoviruses), and RSV (Respiratory Syncytial Virus). Additionally, pathway expression data is used for selecting discriminatory pathways from these experiments. The classification results and selected pathways are benchmarked against standard gene expression based classification and pathway ranking methodologies. We find that using the pathway expression data along with selected pathways, which have minimal overlap with high ranking pathways found by traditional methods, improves classification rates across experiments.

A phase 3 study to determine the breast cancer risk reducing effect of denosumab in women carrying a germline BRCA1 mutation (BRCA-P Study).

TPS10616 Background: Women with BRCA1 mutations have a 50-70% lifetime risk of developing breast cancer. Currently, prophylactic mastectomy is the only strategy that significantly reduces breast cancer risk. Recent evidence suggests that the RANK/RANKL signaling pathway plays a pivotal role in the development of BRCA1-mutated tumors. Targeting the RANK pathway has been shown to attenuate breast epithelial proliferation in vitro and in vivo, and to profoundly reduce mammary tumor formation in mouse models. The RANKL inhibitor, denosumab, an FDA approved drug for the treatment of osteoporosis, is potentially an ideal chemopreventive agent for women with a germline BRCA1 mutation because it: (a) could potentially reduce breast cancer risk, and (b) concomitantly protect bone health in women who have already undergone bilateral salpingo-oophorectomy or in naturally postmenopausal women. The BRCA-P study will evaluate the reduction in the risk of any breast cancer (invasive or DCIS) in women with a germline BRCA1 mutation who are treated with denosumab compared to placebo. Sub-studies include measurement of bone turnover markers; epigenetic profiling of tumor tissues; measuring denosumab’s effect on bone and breast density; measurement of serum RANK, RANKL, OPG, progesterone, LH and FSH; and measurement of quality of life. Methods: This is a randomized, double-blind, placebo-controlled, multi-center international phase 3 study to determine the breast cancer risk reducing effect of denosumab in women carrying a germline BRCA1 mutation. Eligibility: Women with a confirmed BRCA1 germline mutation; ages ≥ 25 years and ≤ 55 years; no evidence of breast or ovarian cancer; no preventive breast surgery planned at randomization; ECOG performance status 0-1. Eligible participants will be randomized 1:1 to receive 120 mg of subcutaneous denosumab or placebo every 6 months for 5 years. Thereafter, all participants will be followed up for 5 years. Primary endpoints: Time to the occurrence of any breast cancer (invasive or DCIS). Secondary endpoints: Time to invasive triple negative breast cancer; time to other BRCA1 mutation associated malignancies, time to clinical fractures. Statistically, a 35% reduction in breast cancer risk would be detected with an 80% power and a two-sided significance level of 5% if 167 breast cancer cases are observed. We expect to observe the number of events needed if 1459 subjects per group (2918 in total) are randomized. The study is currently enrolling participants in Austria, Australia, Israel and Spain. The study will shortly begin accrual in Germany, United Kingdom, and at more than 30 sites across the United States. Globally, the trial is coordinated by the Austrian Breast &amp; Colorectal Cancer Study Group and by the Alliance for Clinical Trial in Oncology in the US. EudraCT: 2017-02505-35. Clinical trial information: NCT04711109.

RANKL Impairs the TLR4 Pathway by Increasing TRAF6 and RANK Interaction in Macrophages.

High serum levels of osteoprotegerin (OPG) are found in patients with obesity, type 2 diabetes, sepsis, or septic shock and are associated with a high mortality rate in stroke. The primary known function of OPG is to bind to the receptor activator of NF-κB ligand (RANKL), and by doing so, it inhibits the binding between RANKL and its receptor (RANK). TLR4 signaling in macrophages involves TRAF6 recruitment and contributes to low-grade chronic inflammation in adipose tissue. LPS is a classical activator of the TLR4 pathway and induces the expression of inflammatory cytokines in macrophages. We have previously observed that in the presence of RANKL, there is no LPS-induced activation of TLR4 in macrophages. In this study, we investigated the crosstalk between RANK and TLR4 pathways in macrophages stimulated with both RANKL and LPS to unveil the role of OPG in inflammatory processes. We found that RANKL inhibits TLR4 activation by binding to RANK, promoting the binding between TRAF6 and RANK, lowering TLR4 activation and the expression of proinflammatory mediators. Furthermore, high OPG levels aggravate inflammation by inhibiting RANKL. Our findings elect RANKL as a candidate for drug development as a way to mitigate the impact of obesity-induced inflammation in patients.

ARBRE: Computational resource to predict pathways towards industrially important aromatic compounds

Synthetic biology and metabolic engineering rely on computational search tools for predictions of novel biosynthetic pathways to industrially important compounds, many of which are derived from aromatic amino acids. Pathway search tools vary in their scope of covered reactions and compounds, as well as in metrics for ranking and evaluation. In this work, we present a new computational resource called ARBRE: Aromatic compounds RetroBiosynthesis Repository and Explorer. It consists of a comprehensive biochemical reaction network centered around aromatic amino acid biosynthesis and a computational toolbox for navigating this network. ARBRE encompasses over 33′000 known and 390′000 novel reactions predicted with generalized enzymatic reactions rules and over 74′000 compounds, of which 19′000 are known to biochemical databases and 55′000 only to PubChem. Over 1′000 molecules that were solely part of the PubChem database before and were previously impossible to integrate into a biochemical network are included into the ARBRE reaction network by assigning enzymatic reactions. ARBRE can be applied for pathway search, enzyme annotation, pathway ranking, visualization, and network expansion around known biochemical pathways and products of lignin degradation to predict valuable compound derivations. In line with the standards of open science, we have made the toolbox freely available to the scientific community on git (https://github.com/EPFL-LCSB/ARBRE) and we provide the web-version at http://lcsb-databases.epfl.ch/arbre/. We envision that ARBRE will provide the community with a new computational resource and comprehensive search tool to predict and rank pathways towards industrially important aromatic compounds.

Changes in adiposity over the life course and gene expression in postmenopausal women.

BackgroundEarly life adiposity and changes in adiposity over the life course are associated with mammographic breast density among postmenopausal women. However, the underlying mechanisms are unknown; therefore, we comprehensively examined the associations of early life body mass index (BMI) and changes in BMI from ages 10, 18 to age at mammogram with growth factor, RANK pathway, and sex hormone gene expression in 372 postmenopausal women.MethodsWe estimated early life BMI at age 10 using the validated 9‐level Stunkard pictogram. We calculated BMI at other ages (18, 30, and current age at mammogram) by dividing weight in kilograms at these ages with height in meters squared. Sequencing for gene expression was performed using the NanoString nCounter system. After adjusting for confounders, we estimated associations using multivariable linear regressions.ResultsA 10 kg/m2 increase in early life BMI at age 10 was associated with a 17.2% decrease in RANKL gene expression (95% confidence interval [CI] = −30.8, −0.9) but was not associated with changes in other markers. BMI changes from ages 10, 18 to age at mammogram were associated with an increase in BMP2 and decreases in RANK, RANKL, and TNFRSF13B gene expression but were not associated with gene expression of other markers. A 10 kg/m2 increase in early life BMI from age 10 to current age was associated with a 7.8% increase in BMP2 (95% CI = −1.4, 17.8), an 8.5% decrease in RANK (95% CI = −13.9, −2.8), a 10.4% decrease in RANKL (95% CI = −16.9, −3.3), and an 8.5% decrease in TNFRSF13B gene expression (95% CI = −13.8, −2.8).ConclusionThe results provide new insights into the biological mechanisms underlying the associations of adiposity changes from early life to adulthood and early life adiposity with mammographic breast density in postmenopausal women.