GEM Model Research Articles

Research on the Competitiveness Evaluation of Rural B&B Cluster Based on GEMS Model——Taking Pengzhou Longmen Mountain Jianjiang River Valley Eco-tourism Area as an Example

In the context of rural revitalization, the rural B&B industry demonstrates notable dynamism and exhibits a tendency towards clustering. Using the GEMS model, the competitiveness of the local rural B&B industry cluster is evaluated at four levels: foundation, enterprise, market and environment. The findings indicate that the rural B&B industry cluster in the Pengzhou Longmen Shan Jinjiang Valley Eco-tourism Area exhibits certain competitive advantages. However, there is potential for enhancement at the market and enterprise levels. Consequently, recommendations for promoting the sustainable development of the cluster are proposed.

Abstract B019: Sensitivity and specificity of detecting premalignant pancreatic lesions by hyperpolarized magnetic resonance

Abstract Introduction: The high mortality rate of pancreatic cancer (PC) results from a lack of methods for early detection. The progression of PC occurs primarily via two precursor pathways, either through microscopic pancreatic intraepithelial neoplasias (PanINs) or macroscopic cystic lesions, of which intraductal papillary mucinous neoplasms (IPMNs) are the most common. The progression from either PanIns or IPMN to PC, provides an opportunity for early detection of this lethal disease. PC cells have extensively reprogrammed metabolism and we have successfully employed hyperpolarized 1-13C pyruvate metabolic imaging (HP MR) to measure non-invasively the metabolic plasticity as the disease initiates and evolves. Concurrently, the specificity of HP MR of detecting premalignant lesions will be determined by imaging pancreatitis induced mice at different timepoints and compare them to the premalignant models. Methods: HP 1-13C Pyruvate MRS was employed to study the metabolic processes in tamoxifen inducible GEM models (P48CreERT2;LSL-KrasG12D (iKC)) with pre-invasive PanIN precursor lesions, invasive PC model (P48CreERT2;LSL-KrasG12D;LSL-p53R172H (iKPC)) and control animals (P48CreERT2 (iC)). These mice were imaged at different time points, before tamoxifen induction, 10-, 20-, and 30-weeks post induction. HP MR was also employed on IPMN mouse model (p48Cre;LSL- KrasG12D;Rosa26R-LSL-rtTA-TetO-GnasR201C) that develop premalignant cystic lesions, that progresses to PC on doxycycline diet (Dox+) for 15 weeks and control mice on normal diet (Dox-). These mice were imaged after 15 weeks of (Dox±) treatment. Simultaneously, wildtype, iC and iKC mice were treated with caerulein for three weeks for the development of pancreatitis and imaged 24 hours after treatment. Results: In the PanIN model, the lactate-to-pyruvate (lac/pyr) ratio increased in the PC models compared to the control model. For the aggressive iKPC mouse model, at the 20-week post induction imaging there was a significant increase of the lac/pyr ratio (0.28±0.04) compared to the 10-week time point (0.22±0.03). At the 20-week time point, the iKPC ratio was higher than the iKC and control ratios, (0.28±0.04 compared to 0.23±0.03 and 0.22±0.02 respectively) indicating the invasive nature of the cancer. Even in the iKC model there is a slight increase of the lac/pyr ratio at 20-weeks (0.23±0.03) compared to control (0.22±0.02). Mice treated with caerulein developed pancreatitis as demonstrated by tissue histology. Surprisingly, the lac/pyr ratio remained constant in both iC and iKC mice that developed pancreatitis, around 0.15±0.03 for both groups. In the IPMN model, IPMN mice feed with doxycycline showed increase pancreatic lesions and an increased lac/pyr ratio (0.43±0.05) compared to mice on normal diet (0.24±0.05). Conclusion: HP MR can detect metabolic shift to lactate in two different models of PC premalignancy representing two different pathways of PC progression. This finding can be potentially translated to the clinic for detection of premalignant pancreatic lesions in high-risk populations. Citation Format: José S Enriquez, Rian M Howell, Olivereen Le Roux, Shivanand Pudakalakatti, Prasanta Dutta, Florencia McAllister, Pratip K Bhattacharya. Sensitivity and specificity of detecting premalignant pancreatic lesions by hyperpolarized magnetic resonance [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 B019.

Adding metabolic tasks to human GEM models to improve the study of gene targets and their associated toxicities

Genetic minimal cut sets (gMCS) are genes that must be deactivated simultaneously to avoid unwanted states in a metabolic model. The concept of gMCS can be applied to two different scenarios. First, it can be used to identify potential gene toxicities in generic or healthy cell models. Second, it can be used to develop genetic strategies to target cancer cells and prevent their proliferation. Up to now, gMCS have been evaluated using the traditional procedure of preventing biomass production. This paper proposes an additional way: using essential metabolic tasks, which any human cell should perform, to enlarge the set of unwanted states. Including this addition can significantly improve the study of toxicities and reveal targets that can be used to treat unhealthy cells. Excluding metabolic tasks can cause important information to be overlooked, which could impact the study’s success. Regarding toxicities, using the generic Human model, the number of detected generic toxicities with metabolic tasks increases from 106 to 281 (136 gMCSs of length 1 and 49 of length 2). We have used the following context-specific models to evaluate specific toxicities in different healthy tissues: blood, pancreas, liver, heart, and kidney. Again, considering metabolic tasks, we have found new toxicities (lengths 1 and 2) whose inactivation could damage these healthy tissues.Our research strategy has been applied to identify new cancer drug targets in two myeloma cell lines. We obtained new therapeutic targets of lengths 1 and 2 for each cell line. After analyzing the data, we conclude that incorporating metabolic tasks into cancer models can reveal important therapeutic targets previously disregarded by the conventional method of inhibiting biomass production. This approach also improves the evaluation of potential drug toxicities.

Abstract B019: Stearoyl-CoA desaturase is a synthetic lethal target in SMAD4-deficient cancers

Abstract Mothers against decapentaplegic homolog 4, or SMAD4, is a member of the SMAD family of transcription factors that mediate TGF-β signal transduction. SMAD4 loss of function mutation or deletion is found in about 30% of PDAC and 15% of COAD and EAC patients, and it is associated with their poor prognosis. Over the past two decades, its tumor suppressor role has been elucidated, and the loss of SMAD4 is sufficient to promote tumorigenesis in multiple GEM models. To identify novel therapeutic vulnerabilities for SMAD4-deficient cancers, a CRISPR dropout screening approach was employed in SMAD4 isogenic PDAC models. We identified stearoyl-CoA desaturase, SCD, as a synthetic lethal target in SMAD4-deficient context. SCD is critical for de novo lipid biogenesis and catalyzes the rate-limiting step in the production of monounsaturated fatty acid. Genetic and pharmacologic studies in vitro confirmed this synthetic lethal relationship. Additionally, drug-anchored CRISPR dropout screening and RNA expression profiling demonstrated that accumulation of saturated fatty acid in response to SCD inhibition drives cytotoxicity in SMAD4-deficient cells. Mouse studies with CRISPR-based knockout of SCD and a well-characterized SCD inhibitor (A939572) demonstrated anti-tumor efficacy in SMAD4-mutant xenograft models. However, compared to genetic KO of SCD the pharmacological inhibitor was less effective at inhibiting tumor proliferation in vivo. Together, these data identify SCD as a selective vulnerability in SMAD4-mutant cancers. Citation Format: Alvin Z. Lu, Silvia Fenoglio, Hsin-Jung Wu, Yingnan P. Chen. Stearoyl-CoA desaturase is a synthetic lethal target in SMAD4-deficient cancers [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Expanding and Translating Cancer Synthetic Vulnerabilities; 2024 Jun 10-13; Montreal, Quebec, Canada. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(6 Suppl):Abstract nr B019.

Abstract 2686: Glycolysis-stimulated lactate production by tumor-associated macrophages promotes their M2-like phenotype

Abstract Tumor-associated macrophages (TAMs) are the predominant immune cells within the tumor microenvironment (TME), and their phenotypic modulation is influenced by environmental cues in the TME. In early tumors, TAMs adopt a pro-inflammatory M1-like phenotype, characterized by the secretion of immunogenic cytokines and the ability to kill cancer cells, thus opposing tumorigenesis. However, as tumors progress, TAMs mainly transition to an anti-inflammatory M2-like phenotype, promoting angiogenesis, suppressing anti-tumor immunity, and supporting metastasis. Importantly, a high M2-like/M1-like TAM ratio correlates with poor survival and decreased treatment responses.Despite the significance of TAMs, the molecular mechanisms driving their pro-tumorigenic M2-like phenotype remain unclear. One potential mechanism is metabolic reprogramming, where, traditionally, M1 macrophages favor glycolysis, and M2 macrophages rely on oxidative phosphorylation. However, this paradigm is primarily derived from in vitro experiments using well-defined polarization cocktails, which may not accurately replicate the complex TME. For instance, while in in vitro experiments IL4 and IL13 can induce oxidative phosphorylation and an M2-like phenotype, these cytokines do not seem essential for M2-like TAM polarization in vivo.Our studies reveal that, relative to M1-like TAMs, M2-like TAMs exhibit heightened glycolysis, intracellular lactate accumulation, and increased histone lysine lactylation - an epigenetic mark directly stimulated by lactate. Importantly, we demonstrate that TAM glycolysis and the M2-like phenotype are positively associated with hypoxia within a single tumor (GEM model and human tumors) and across various tumor types (syngeneic models). Inhibition of glycolysis-stimulated lactate production in TAMs through myeloid cell-specific deletion of lactate dehydrogenase A (mLdha-/-) reduces the M2-like:M1-like TAM ratio. This intervention increases tumor-infiltrating CD8+ T cells and reduces tumor growth in pre-clinical models, particularly in highly hypoxic environments. Moreover, to exclude the role of cancer cell-derived lactate on TAMs’ phenotypic changes, we reduced glycolysis in cancer cells by deleting pyruvate kinase muscle isozyme M2 (PKM2). This resulted in decreased lactate production and suppressed tumor growth. However, the M2/M1 ratio remained unaffected, suggesting that the intrinsic lactate production by TAMs is crucial for their phenotype modulation.Our findings underscore the pivotal role of hypoxia-induced glycolysis and lactate production in TAMs, shaping their M2-like phenotype and impacting tumor progression. This understanding not only advances our knowledge of macrophage metabolism and phenotype dynamics in the context of cancer but also in other diseases. Citation Format: Katarzyna Kurylowicz, Kasturi Chakraborty, Chang Cui, Gustavo Gastão Davanzo, Guolin Zhou, Xu Anna Tang, Kelly Q. Schoenfelt, Natalie Pulliam, Catherine A. Reardon, Swati Kulkarni, Tomas Vaisar, Pedro M. Moraes-Vieira, Yingming Zhao, Lev Becker. Glycolysis-stimulated lactate production by tumor-associated macrophages promotes their M2-like phenotype [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 2686.

Abstract 4460: Investigating a non-canonical role for SHP2 in pancreatic ductal adenocarcinoma metabolism and response to dietary modifications

Abstract Pancreatic ductal adenocarcinoma (PDAC) is predicted to be the second leading cause of cancer death in the US by 2025, with rising incidence. Mutant KRAS in >90% of PDAC cases promotes activation of the MAPK pathway, yet targeting the MAPK pathway clinically has failed to improve patient outcomes. SHP2 canonically promotes KRAS activation and is essential for PDAC development in mouse models. Because targeting MAPK is insufficient, yet SHP2 loss blocks PDAC development, we hypothesized SHP2 has both MAPK dependent and independent functions. Initial studies revealed that SHP2 inhibition with SHP099 in murine KPC [K8484: KRASG12D/+, p53R172H/+, Pdx1Cre/+] cells required concentrations exceeding 50 μM to elicit a minimal ERK inhibition. This led us to predict that there may be a tumor suppressive mechanism of SHP2 inhibition that is KRAS/MAPK independent. We utilized available RNAseq data (NCBI GEO: PRJNA558508) of PDAC MiaPaCa2 cells treated with the MEK inhibitor, Trametinib, or SHP099 to compare the direct effects of inhibition on transcriptional outcomes. We identified inositol phosphate signaling as a candidate target, whose downstream consequence is Ca2+ flux. We measured IL-1β induced Ca2+ flux in a panel of human PDAC cells exposed to MEK or SHP2 inhibition. Trametinib treated cells showed no effect on Ca2+ flux, however, SHP099 led to a drastic depletion of free Ca2+ and response to stimulus. We then validated the Ca2+ response to IL-1β stimulus in Crispr-Cas9 SHP2-knockout K8484 cells. While we did not observe a difference in basal free calcium, we still found a reduction in response to IL-1β stimulus. Because Ca2+ is an important co-factor for mitochondrial metabolism, we then interrogated metabolic effects. We tested mitochondrial function using a Seahorse Mito-Stress test and found that while MEK inhibition failed to affect mitochondrial metabolism, SHP2 inhibition ablated it. A Glycolysis-Stress Test revealed that SHP2 inhibition led to glucose consumption primarily through anaerobic respiration. TMT-labeled phospho-proteomic analysis comparing SHP2KO and MEK inhibited K8484s revealed SHP2 dependent deficiencies in mitochondrial proteins, among others, involved in mitochondrial fission and lipid metabolism. Western diets have been shown to promote tumor progression in GEM models of PDAC, so we used KRASG12D/+, SHP2fl/fl or wt./wt, Ptf1aCre/+ (SKC and KC) mice to demonstrate that while diet-induced obesity affects KC tumor burden, the lack of SHP2 in SKCs prevents the diet associated discrepancy in tumor progression. Collectively, these data led us to conclude that while SHP2 has been studied as a contributor to KRAS signaling in PDAC, the outcomes of its role specifically on mitochondrial metabolism have yet to be appreciated or thoroughly investigated, opening the path for a new approach to its contribution to tumor progression. Citation Format: R. McKinnon Walsh, Jarrid L. Jack, Austin E. Eades, Bailey A. Bye, Mariana T. Ruckert, Joseph Ambrose, Michael N. VanSaun. Investigating a non-canonical role for SHP2 in pancreatic ductal adenocarcinoma metabolism and response to dietary modifications [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 4460.

Abstract 558: Stearoyl-CoA desaturase is a synthetic lethal target in SMAD4-deficient cancers

Abstract Mothers against decapentaplegic homolog 4, or SMAD4, is a member of the SMAD family of transcription factors that mediate TGF-β signal transduction. SMAD4 loss of function mutation or deletion is found in about 30% of PDAC and 15% of COAD and EAC patients, and it is associated with their poor prognosis. Over the past two decades, its tumor suppressor role has been elucidated, and the loss of SMAD4 is sufficient to promote tumorigenesis in multiple GEM models. To identify novel therapeutic vulnerabilities for SMAD4-deficient cancers, a CRISPR dropout screening approach was employed in SMAD4 isogenic PDAC models. We identified stearoyl-CoA desaturase, SCD, as a synthetic lethal target in SMAD4-deficient context. SCD is critical for de novo lipid biogenesis and catalyzes the rate-limiting step in the production of monounsaturated fatty acid. Genetic and pharmacologic studies in vitro confirmed this synthetic lethal relationship. Additionally, drug-anchored CRISPR dropout screening and RNA expression profiling demonstrated that accumulation of saturated fatty acid in response to SCD inhibition drives cytotoxicity in SMAD4-deficient cells. Mouse studies with CRISPR-based knockout of SCD and a well-characterized SCD inhibitor (A939572) demonstrated anti-tumor efficacy in SMAD4-mutant xenograft models. However, compared to genetic KO of SCD the pharmacological inhibitor was less effective at inhibiting tumor proliferation in vivo. Together, these data identify SCD as a selective vulnerability in SMAD4-mutant cancers. Citation Format: Alvin Lu, Silvia Fenoglio, Hsin-Jung Wu, Minjie Zhang, Alice Tsai, Maria L. Ferdinez, Lauren Grove, Shangtao Liu, Edward Wu, Ashley Choi, Scott Throner, Samuel Meier, Yi Yu, Wenhai Zhang, John Maxwell, Jannik N. Andersen, Teng Teng, Brian B. Haines, Yingnan P. Chen. Stearoyl-CoA desaturase is a synthetic lethal target in SMAD4-deficient cancers [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 558.

Analysis of Competitiveness in the Domestic Semiconductor Cluster Using Entropy Technique: Based on the GEM-ESG Model

Purpose - The study aims to conduct an empirical analysis of semiconductor cluster integrated competitiveness with a focus on the GEM-ESG model. Specifically, the study seeks to compare and analyze the development factors of semiconductor clusters in different regions. The results of the empirical study will reveal a clear concentration phenomenon in the semiconductor industry clusters of some regions.
 Design/Methodology/Approach - Previous research has established the factors influencing the competitive advantage of industrial clusters. The study collected competitive indicators from major South Korean cities and regions, incorporating these into the GEM model, and exploring ESG indicators relevant to the semiconductor industry. The study utilized Entropy Technique analysis to empirically assess the competitiveness of the South Korean semiconductor cluster and conduct comparative testing of the research findings.
 Findings - The results revealed a concentration phenomenon in the semiconductor industry clusters of Yongin and Chungbuk Province. Additionally, the study highlighted the importance of factors such as “groundings (G)”, “enterprise management (E)”, “market conditions (M)”, and ESG practices in determining competitiveness.
 Research Implications - Through empirical analyses, the study emphasizes the significance of GEM and ESG factors in the analysis of industrial clusters, particularly in contributing to long-term sustainability and competitive advantage focusing on the collaboration and alignment of ESG values.

A study on the evaluation of competitiveness in the aviation logistics industry cluster in Zhengzhou

As the global economy continues to evolve, air transportation is increasingly seen as a crucial factor in enhancing regional competitiveness. In particular, aviation logistics industry clusters have emerged as a new driving force for regional economic development. In this context, the current study aims to evaluate the competitiveness of the aviation logistics industry cluster in Zhengzhou, China. To achieve this goal, the study employs the “GEM model” and constructs a GKA evaluation model using evaluation index data from 21 logistics node cities across China in 2021. The entropy-weighted TOPSIS method is used for empirical analysis of the data. The results of the study reveal that the competitiveness of Zhengzhou’s aviation logistics industry cluster is moderately low. This is primarily due to the weak competitiveness of its foundational and regulatory subsystems. Specifically, the study finds that Zhengzhou’s resources, facilities, markets, government, and industry aspects are all less competitive when compared to other cities in China. In order to enhance the competitiveness of Zhengzhou’s aviation logistics industry cluster, the study recommends that efforts be made to improve the competitiveness of key elements such as resources, facilities, markets, and government. In particular, the focus should be on elevating industry competitiveness, followed by the development of appropriate regulatory strategies. By doing so, the aviation logistics industry cluster in Zhengzhou would be better positioned to compete with other clusters within China and globally.

Abstract A089: Quantitative MRI metrics and single cell transcriptome reveal effects of stroma-directed drug and chemotherapy in a GEM model of pancreatic cancer

Abstract Hypothesis: The dense stroma present in pancreatic ductal adenocarcinoma (PDA) harbors a unique tumor microenvironment (TME) that is immune suppressive and underlies the chemo-resistance of PDA. We have evaluated synthetic vitamin D combined with chemoimmunotherapy in a pilot clinical study (NCT03519308). To elucidate the underlying mechanisms of this treatment, we designed a matched study in a genetically engineered mouse model of PDA (KPC mice) to test the hypothesis that synthetic vitamin D enhances the effect of chemotherapy with or without immune checkpoint inhibition. To detect changes in TME, we have integrated diffusion weighted (DW) and dynamic contrast enhanced (DCE) MRI with immunohistochemistry (IHC) and single cell RNA sequencing (scRNAseq). Methods: KPC mice were randomly assigned to one of four groups: 1) Control (untreated); 2) Nab-paclitaxel + gemcitabine + cisplatin (Chemo); 3) Chemo + synthetic vitamin D (calcipotriol, Cal); 4) Chemo + Cal + PD-L1. The treatment lasted for 14 days followed by euthanasia and tumor collection for IHC and scRNAseq. Respiratory motion-robust DW- and DCE-MRI were performed on treatment days 0, 7 and 14. Results: Compared to consistent tumor growth (measured by MRI) in the Control group, both progression and regression were observed in groups 2) - 4), suggesting that the KPC model captured the varied treatment responses observed in the clinic. Capillary perfusion/permeability of the tumor measured by Ktrans (a DCE-MRI metric) was reduced at day 7 in the Chemo group (P<0.05), whereas Chemo+Cal reversed the reduction of Ktrans. Chemo-induced Ktrans reduction was corroborated with a significant reduction of microvascular density by IHC of CD31 compared to the Control. Addition of PD-L1 did not appear to enhance the tumor growth delay by Chemo+Cal. scRNAseq analysis revealed that while Chemo significantly delayed the tumor growth compared to the Control, it increased the portion of mesenchymal cells in the tumor and upregulated epithelial-to-mesenchymal transition (EMT) genes known to resist chemotherapy. In contrast, Chemo+Cal increased the fraction of epithelial cells and downregulated EMT genes compared to Chemo. Trasncriptome analysis of the tumor cells demonstrated that Chemo treatment increased the expression of Fibronectin 1 (FN1), a gene associated with tumor invasiveness, EMT, and metastasis, while lowering the expression of Trefoil Factor Family1 (Tff1), which is related to tumor-suppression and chemosensitivity. Chemo+Cal treatment reversed the expression of both FN1 and Tff1 gene compared to Chemo treatment. Conclusion: Single cell transcriptome analysis provided valuable insights into treatment-induced molecular subtype changes, which may predict future resistance and invasiveness. Our study revealed important mechanisms of calcipotriol that enhance the efficacy of chemotherapy by improving microvascular perfusion and permeability and by reducing chemo-resistance by enriching epithelial cells in PDA tumors. Citation Format: Hoon Choi, Mamta Gupta, Thomas Karasic, Miguel Joaquim, Emma Furth, Stephen Pickup, Cynthia Clendenin, Hee Kwon Song, Yong Fan, Jeffrey Duda, James Gee, Mark Rosen, Peter O’Dwyer, Rong Zhou. Quantitative MRI metrics and single cell transcriptome reveal effects of stroma-directed drug and chemotherapy in a GEM model of pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr A089.

Xpo-1 Antagonism Impairs CSF-1R Expression and Depletes Lymphoma-Associated Macrophages in T-Cell Lymphomas

Background: Lymphoma-associated macrophages (LAM) provide ligands for antigen, costimulatory, and cytokine receptors expressed by malignant T cells and directly promote T-cell lymphomagenesis. LAM also play an important role in suppressing host anti-tumor immunity and indirectly promote T-cell lymphomagenesis. Therefore, LAM are a therapeutic vulnerability in T-cell lymphomas (TCL), and their depletion from the tumor microenvironment (TME) is a rational therapeutic goal. Methods: XPO1 and CD163 expression were examined by immunohistochemical staining. In order to determine the extent to which XPO1 antagonism depletes LAM, a pharmacologic strategy was adopted using selinexor. Viability of human monocyte-derived and TCL conditioned macrophages upon selinexor treatment was examined in vitro using standard methods. RNA binding to eIF4e was determined by RNA immunoprecipitation (RIP) using eIF4e and IgG antibodies and quantification performed by qPCR. Nuclear export of eIF4e client mRNA upon XPO1 antagonism with selinexor was examined by qRT-PCR in nuclear and cytoplasmic pools of RNA. LAM depletion upon selinexor treatment was examined in vivo using a previously described GEM ( Smarcb1-deficient) model and CD68-GFP reporter mice. Results: As we had previously demonstrated that CD163 identifies LAM that are alternatively polarized and proliferative, co-staining was performed with CD163 and XPO1, and CD163+XPO-1+ LAM identified in 69% of PTCL cases (n=26) examined. We previously demonstrated that LAM within a PTCL context are resistant to inhibition by selective CSF-1R antagonists. Therefore, we performed an unbiased, high-throughput screen using monocytes cultured in the presence of cell-free conditioned media (CFCM) obtained from T-cell lymphoma cell lines and primary specimens. This screen identified selinexor as a potential therapeutic vulnerability. Therefore, we cultured normal-donor monocytes in RPMI media alone, or in media supplemented with cell free conditioned media (CFCM) obtained from PTCL/CTCL cell lines (n=2) or primary specimens (n=5) and determined cell viability. Consistent with our prior findings, CFCM from PTCL/CTCL cells promoted the growth and survival of monocyte-derived macrophages (MDM), but this effect was abrogated upon selinexor treatment. These findings converged with the observation that CSF-1R transcripts are eIF4e clients in ALCL cells. Therefore, the extent to which transcripts required for macrophage survival (i.e. CSF-1R), proliferation (i.e. PU.1), and polarization (i.e. STAT3) are eIF4e clients was examined by eIF4e-RIP in MDM. These experiments demonstrated that CSF-1R, PU.1 and STAT3 are eIF4e clients, and selinexor treatment significantly decreased their nuclear export in MDM. Given the obvious clinical relevance of CSF-1R as a therapeutic target, CSF-1R expression in MDM following selinexor treatment was examined, and compatible with these results, a significant decrease in CSF-1R expression observed upon selinexor treatment. We previously employed CD68-GFP reporter mice in a Smarcb1-deficient GEM model, demonstrating that GFP+ macrophages in this TCL model are transcriptionally reprogrammed and proliferative. Selective CSF-1R antagonists minimally impair LAM survival in this model. In contrast, selinexor significantly depleted LAM ex vivo in this model and impaired the viability of bone marrow derived macrophages. In order to extend these findings, lymphoma-bearing GEM mice were treated with selinexor and the abundance of CD11b+Ly6G- LAM determined by flow cytometry, whereby a significant reduction in LAM abundance and TCL progression were observed, compatible with our in vitro/ex vivo findings. Conclusions: Therefore, we concluded that XPO1 inhibition indirectly impairs T-cell lymphoma growth and survival by depleting LAM, which are a dependency in these lymphomas.

Pre-Clinical Activity of Navitoclax in TCR-Driven and Non-ALCL Mature T-Cell Lymphomas

Background: In contrast to many B-cell lymphomas that highly express BCL-2, BCL-2 expression is observed in <50% of most mature T-cell lymphoma (MTCL) subtypes, although a clinical trial investigating venetoclax in BCL-2 positive relapsed/refractory PTCL is ongoing (NCT03552692). In contrast, BCL-xL and/or MCL-1 are expressed in the majority of MTCL. Consistent with these findings, MCL-1 expressing anaplastic large cell lymphomas (ALCL) and typical (non-ETP) T-ALL, which highly express BCL-xL, have been shown by BH3 profiling to be dependent upon MCL-1 or BCL-xL, respectively. Among the more common MTCL subtypes, including cutaneous T-cell lymphomas (CTCL), the extent to which BCL-2 family members are a therapeutic vulnerability is uncertain. However, we have previously demonstrated that antigen- and costimulatory receptor signaling promote the growth and survival of these lymphomas and confers resistance to chemotherapy, and in conventional (non-malignant) T cells, these same signals upregulate BCL-xL, which is required for their clonal expansion and escape from cell death following T-cell activation. Therefore, given the increasing availability of selective BH3 mimetics and the need for improved therapeutic strategies, we were motivated to examine BCL-2 family member dependencies in these lymphomas. Methods: Peptides generated from BH3-only proteins and selective BH3 mimetics were utilized to perform “BH3 profilng” in MTCL. Cell viability upon exposure to BH3 mimetics was determined using standard approaches. Results: To pre-clinically assess BCL-2 family member dependencies and the mitochondrial apoptotic pathway in T-cell lymphoproliferative neoplasms, we performed BH3 profiling in 17 cell lines. Peptides derived from BIM and PUMA, which are promiscuous, were utilized to assess the extent to which cells are “primed” for apoptosis. Differences in apoptotic priming were not observed across subtypes, and most cell lines examined were highly primed. We next examined the dependence on specific antiapoptotic proteins by BH3 profiling using BAD (antagonizes BCL-2, BCL-xL, and BCL-w), HRK (antagonizes BCL-xL), MS1 (antagonizes MCL-1), and FS1 (antagonizes A1/BFL-1) peptides. BCL-2 dependence was not observed in the T-cell lymphoma cell lines we examined. However, and in stark contrast, most non-ALCL cell lines were BCL-xL dependent, whereas ALCL cell lines were largely MCL-1 dependent. In an effort to further confirm these results, and examine the extent to which peptide-based BH3 profiling predicts sensitivity to selective BH3 mimetics in MTCL, cell lines were treated with venetoclax, A1155463 (a BCL-xL selective antagonist), navitoclax (a BCL-2/BCL-xL antagonist), or S63845 (MCL-1 antagonist), and cell viability determined. Consistent with peptide-based BH3 profiling, all cell lines examined were resistant to venetoclax. ALCL cell lines were largely MCL-1 dependent, whereas the non-ALCL cell lines examined were largely BCL-xL dependent. Therefore, we examined BCL-xL and MCL-1 expression in these cells and observed a strong association between BCL-xL expression and both cytochrome c release in response to HRK peptide and cell viability in the presence of A1155463. A similar association was observed between MCL-1 expression and sensitivity to MS1 and S63845. Transcriptionally profiled MTCL specimens were stratified by MTCL classification (ALCL vs. non-ALCL) and in keeping with the data obtained using cell lines increased BCL-xL expression was observed in non-ALCL MTCL subtypes. Given the observed association between BCL-xL expression and vulnerability to BCL-xL antagonists, we sought to examined mechanisms that promote its expression. Both TCR signaling and CD28 costimulation are exploited by non-ALCL subtypes. We examined the extent to which TCR/CD28 stimulation regulates BCL-xL transcription. In MTCL specimens, a significant increase in BCL-xL transcription and sensitization to Bcl-xL antagonism were observed upon TCR/CD28 stimulation. A TCR-dependent GEM model was utilized, demonstrating that these MTCL are Bcl-xL dependent and sensitive to navitoclax. Conclusions: These findings suggest that BCL-xL is a therapeutic vulnerability for MTCL subsets, particularly non-ALCL subtypes that are TCR dependent, and provide a robust pre-clinical rationale for future studies investigating navitoclax in these lymphomas.

Simultaneous application of enzyme and thermodynamic constraints to metabolic models using an updated Python implementation of GECKO.

The metabolism of biological cells is an intricate network of reactions that interconvert chemical compounds, gathering energy, and using that energy to grow. The static analysis of these metabolic networks can be turned into a computational model that can efficiently output the distribution of fluxes in the network. With the inclusion of enzymes in the network, we can also interpret the role and concentrations of the metabolic proteins. However, the models and the experimental data often clash, resulting in a network that cannot grow. Here, we tackle this situation with a suite of relaxation algorithms in a package called geckopy. Geckopy also integrates with other software to allow for adding thermodynamic and metabolomic constraints. In addition, to ensure that enzyme-constrained models follow the community standards, a format for the proteins is postulated. We hope that the package and algorithms presented here will be useful for the constraint-based modeling community.

Estimating of gases emission from waste sites to generate electrical energy as a case study at Al-Hillah City in Iraq

Methane (CH4) is a greenhouse gas resulting from human activities, especially landfills, and it has many potential environmental issues, such as its major role in global warming. On the other hand, methane can be converted to liquid fuel or electricity using chemical conversion or gas turbine generators. Therefore, reusing such gases could be of great environmental and economic benefit. In this context, this study aims to estimate the emissions of methane gas from the landfills in Al-Hillah City, Iraq, from 2023 to 2070 and the producible electric energy from this amount. The estimating process was carried out using the Land GEM model and compared with traditional models. The obtained results demonstrated that the total estimated landfill methane emissions for 48 years are 875,217 tons, and the average annual methane emission is 18,234 tons based on a yearly waste accumulation rate of 1,046,413 tons and a total waste amount of 50,227,808 tons. The anticipated loads of methane gas can be utilized to generate about 287,442 MW/year of electricity from 2023 to 2070. In conclusion, the results obtained from this study could be evidence of the potential environmental and economic benefits of harvesting and reusing methane gas from landfills.

Theoretical Prediction of Electrical Conductivity Percolation of Poly(lactic acid)-Carbon Nanotube Composites in DC and RF Regime.

Polymer composites based on polylactic acid (PLA) reinforced with 0.25-5 wt.% of carbon nanotubes (CNTs) were synthesized by melt blending. The static (DC) and microwave (RF) electrical conductivity have been investigated on the PLA-CNT composites. The electrical percolation threshold has been theoretically determined using classical models of percolation in order to predict the conductivity of the different nanocomposites. Through the fitting process, it has been found that the percolation threshold is obtained at 1 wt.% of CNTs in the DC regime and reached below 0.25 wt.% of CNTs in the microwave regime. Among the Mamunya, McLachlan, or GEM models, the McCullough model remarkably fits the experimental DC and RF electrical conductivities. The obtained results are correlated to the electrical properties of a range of CNT-based composites, corresponding to the percolation threshold required for a three-dimensional network of CNTs into the polymer matrix.

On Strategic Emerging Industry Cluster Development in Anhui based on the Perspective of Global Value Chain

With the development of economic globalization, the role of strategic emerging industries embedded in global value chains (GVCs) as clusters to actively participate in the global industrial division of labor has become increasingly significant. The present situation and problems of strategic emerging industry clusters in Anhui are analyzed qualitatively from three aspects: dynamic mechanism, development mode and governance mode, and their status in GVC is inferred quantitatively by using GVC index. Secondly, Bengbu silicon-based new materials industry is used as an example for empirical research, and the GEM model and multiple linear regression model are used to build a data evaluation system and analyze the factors affecting the competitiveness of industrial clusters. Finally, we propose a scientific and reasonable upgrading path and policy suggestions based on GVC perspective, which can provide guidance and reference significance for promoting regional industrial economic development.

Abstract 10: Orthotopic nGEM glioma growth rates in allogenic hosts associate with hypoxia and proximity to host cells

Abstract Genomic profiling of glioblastoma uncovers fundamental differences in the driver events of malignant transformation and progression, yet the nuances driving the particular growth rate of glioblastoma in individual patients remain poorly defined. We exploited the availability of fourteen histocompatibility-matched mouse hosts from the collaborative cross (CC) [PMID: 15514660] as hosts for a non-germline, engineered model of murine glioblastoma [PMCID: PMC4210043] to interrogate cell types, functional states and proximity in situ in tumors with varying growth rates. Specifically, Kaplan-Meier survival data was used to determine the rates of Nf1:TP53 null tumor growth in different cc host groups. Spatial transcriptomics and single nucleus RNA seq (sn-seq) analyses were conducted in tumor-bearing brain tissue from C57Bl/6 (syngeneic) and 2 CC histocompatible allogeneic mouse strains with differential survival outcomes. Spatial analysis was conducted using a disease-focused multiplexed mRNA probe set assembled from annotations of GBM/glioma specific genes reported in the literature. Cell segmentation of the data was performed to investigate the spatial pattern of single-cell level expression. The spatial transcriptomic dataset was also analyzed with a segmentation-free pipeline. In addition, to detect cell clusters, the probability of genes detected in close proximity (genes within a cell 5px radius [0.5 um]) was determined using Pdgfra as the tumor marker (anchor). We identified differential levels of spatially correlated expression of cell clusters expressing hypoxia markers such as HIF-1a and PDK1 between hosts with fast and slow growing tumors. Tumors from the 3 hosts were also processed for sn-seq. Integrated analysis of cell clustering was used to determine differences in clusters between the fast growing and slow growing groups. Enrichment of expression of Top2a, a gene associated with proliferation and poor prognosis in glioma, was detected in a unique cluster of cells in the slow-growing tumor when compared to the fast-growing group. This suggests that the host microenvironment may play a role in influencing the decelerated growth of this tumor. These results support the utility of spatial transcriptomics and sn-seq in understanding how differences in tumor:host cell interactions contribute to tumor growth. Future opportunities enabled by histocompatible allogeneic hosts for GEM and nGEM glioma models include unraveling host effects on drug sensitivity, tumor heterogeneity, molecular plasticity, angiogenesis, invasion, and lymphoid and myeloid microenvironmental dependencies, each with profound opportunities for clinical translation. Citation Format: Angela S. Baker. Orthotopic nGEM glioma growth rates in allogenic hosts associate with hypoxia and proximity to host cells [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 10.

Abstract 1712: Targeting asparagine dependency as a therapy for TP53-mutated castration-resistant prostate cancer

Abstract Background: The TP53 tumor suppressor is frequently altered in lethal, castration-resistant prostate cancer (CRPC). However, to date there are no effective treatments that specifically target TP53 gain-of-function (GOF) mutants. Thus, there is an urgent need to identify and target vulnerabilities that perpetuate disease progression and treatment resistance resulting from TP53 GOF mutants. Methods: We performed RNA sequencing (RNA-seq) and liquid chromatography-mass spectrometry (LC-MS)-based metabolomics on GEM and PDX CRPC models with or without TP53 GOF mutations. Our findings were validated using genetic and pharmacologic approaches in relevant in vitro and in vivo models. We assessed the effect of L-asparaginase (ASNase) or/and glutaminase (GLS) inhibitor CB-839 in cell lines, organoids and PDX models. Tumors were characterized by histology and immunohistochemistry for relevant markers. Results: Using transcriptomic and metabolomic analyses, we show here that TP53-mutated prostate cancer (PCa) exhibits an increased dependency on asparagine and overexpresses asparagine synthetase (ASNS, the enzyme catalyzing the synthesis of asparagine). Mechanistically, TP53 GOF mutations transcriptionally activate ASNS expression, directly as well as via ATF4, driving de novo asparagine biosynthesis to support CRPC growth. TP53-mutated CRPC cells are sensitive to asparagine restriction by knockdown of ASNS and L-asparaginase treatment to deplete the intracellular and extracellular sources of asparagine respectively. This effect was rescued by asparagine addition. Notably, pharmacological inhibition of intracellular asparagine biosynthesis using a glutaminase (GLS) inhibitor and depletion of extracellular asparagine with L-asparaginase significantly reduced asparagine production and effectively impaired CRPC growth. Conclusions: This study highlights the significance of ASNS-mediated metabolic adaptation as a synthetic vulnerability in CRPC with TP53 GOF mutations, providing a rationale for co-targeting intracellular and extracellular asparagine production to treat these lethal prostate cancers. Citation Format: Young A Yoo. Targeting asparagine dependency as a therapy for TP53-mutated castration-resistant prostate cancer [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 1712.

Abstract IA013: Preclinical testing of CD73 inhibitors for pancreatic cancer immunoprevention

Abstract Introduction: The all stages combined five-year survival rate for pancreatic adenocarcinoma (PDA) is 11%; however, the five-year survival rate for localized PDA is 42%. These statistics highlight the importance of early prevention strategies to prevent disease progression and metastatic dissemination. Through the NCI PREVENT program, this research program explores immunoprevention strategies for PDA by targeting CD73, a gatekeeper ectoenzyme responsible for production of extracellular adenosine. We have recently shown aggressive subtypes of pancreatic intraepithelial neoplasia (PanIN) and PDA arising in ductal pancreatic epithelium have elevated CD73 and intrapancreatic adenosine indicating adenosine generation may be an early trigger of immunosuppression. We hypothesize inhibition of CD73 and adenosine generation will promote a more robust anti-tumor immune response and prevent PanIN and PDA progression. Methods: We tested three small molecule CD73 inhibitors (APCP, OP-5244, and AB680) in a syngeneic PDA mouse model by injecting 100-200k murine PDA cells derived from KrasG12D;Trp53R172H/+;Pdx:Cre (KPC) mice in the flanks of C57BL/6 female mice. Tumor sizes were measured weekly and tumor volume and mass were recorded at time of death. Dosage: APCP oral gavage (3x/week at 20mg/kg) and intraperitoneal (IP) (3x/week at 20 mg/kg). OP-5244 oral (3x/week at 25mg/kg and 10mg/kg). AB680 oral gavage (3x/week at 10mg/kg). HPLC analysis was performed for each inhibitor to quantify adenosine levels. Results: IP delivery of APCP significantly reduced tumor growth and intratumoral adenosine levels; however oral gavage delivery did not reduce tumor growth. Similarly, oral gavage delivery of OP-5244 did not reduce tumor growth. AB680 significantly reduced tumor volume and intratumoral adenosine levels and CyTOF immunoprofiling showed activated CD8+ T cells, dendritic cells, and macrophages were significantly increased in the tumors from AB680 treated mice. Conclusion: APCP IP delivery is more effective than oral gavage delivery and OP-5244 oral gavage delivery does not significantly decrease tumor growth. AB680 oral gavage delivery significantly decreases tumor growth and tumor adenosine concentrations. We observed a significant increase in infiltration of activated CD8+ T cells. AB680 shows high translational potential for preclinical testing in spontaneous GEM models. Citation Format: Lincoln Ballew, Kanchan Singh, Vidhi Chandra, Tingting Mills, Erika Y. Faraoni, Victoria Mota, Trent Clark, Lana Vornik, Michelle I. Savage, Shizuko Sei, Altaf Mohammed, Holger K. Eltzschig, Powel H. Brown, Florencia McAllister, Jennifer M. Bailey-Lundberg. Preclinical testing of CD73 inhibitors for pancreatic cancer immunoprevention [abstract]. In: Proceedings of the Second Biennial NCI Meeting: Translational Advances in Cancer Prevention Agent Development (TACPAD); 2022 Sep 7-9. Philadelphia (PA): AACR; Can Prev Res 2022;15(12 Suppl_2): Abstract nr IA013.

Avalanche Modeling in Mextram 505 and Implications on Circuit Simulations

This paper presents several recent advances in compact modeling of avalanche multiplication in Mextram 505, an industry standard transistor model, including both new model features and improved model implementations. Implications of these improvements on circuit simulation are illustrated using RF SiGe HBTs.Feature wise, Mextram 505 adds a new physics-based model of the avalanche multiplication factor that accounts for the complex evolution of the epi-layer electric field at high current density, which can be activated with swavl=3. At a given collector-base bias VCB, the avalanche factor Gem is constant at low collector current density JC, starts to decrease when mobile electron density becomes comparable to epi-layer doping density due to charge compensation, and ultimately increases again when the base pushes out, and the electrical CB junction shifts to the epi-layer/buried layer interface. A parameter exavl can be used to turn on/off the rise of Gem at very high JC. An example of fitting IB versus IE for a common-base RF SiGe HBT at a fixed VCB=3V is given in Fig. 1. The measured base current is calculated from the difference of measured IE and IC, and hence shows some measurement noise. At low IE, Gem is constant, IB is linearly proportional to IE, with exavl=0, only the decrease of Gem with increasing JC is modeled, the IB bends upward at 0.05 A. With exavl=1, the rise of Gem at high JC is modeled, allowing the fitting of the downward bending of IB above 0.1 A. We will also discuss implications of such complex Gem behavior for RF linearity, particularly on the modeling of linearity sweet spots, i.e. biasing currents and voltages at which linearity peaks.Implementation wise, Mextram 505 uses the main current In as the initiating current in calculating the avalanche current Iavl, i.e. Iavl = In*Gem, as opposed to using the epi-layer current Ic1c2, i.e. Iavl = Ic1c2*Gem in Mextram 504. While for DC I-V, one can always use slightly different Gem model parameters to achieve the same degree of fitting, we found that the Mextram 504 approach can lead to unphysically high avalanche noise in voltage-controlled oscillator (VCO) circuits in some cases. Users should inspect the waveforms of Iavl as well as In to determine if this problem exists. The root problem is that the epi-layer current Ic1c2 also includes the CB junction capacitive charge current, which should not experience avalanche as the corresponding electron motion occurs outside the space charge region. While the Iavl error introduced has a small absolute value, the noise it introduces is often significant, and significantly increases oscillator phase noise.At the device level, this unphysical avalanche of capacitive charge current comes into play during modeling of the CB depletion capacitance, CCB, which is often extracted from off state y-parameter. Fig. 2 compares the CCB vs VCB simulated using In (505) and Ic1c2 (504) as avalanche initiating current, together with the CCB from measurement. The Gem value is shown on the right y-axis. When Gem approaches 1, the simulated CCB using Iavl = Ic1c2*Gem increases sharply, and becomes negative when Gem>1, a unphysical result users of Mextram 504 need to be aware of for high Gem biases. Using Iavl = In*Gem, as is in Mextram 505, the simulated CCB remains physical when Gem is high. An analytical model of such discrepancy has been developed using small signal frequency domain analysis and will be presented.In Mextram 504 and earlier versions of Mextram 505, Gem is limited to be less than 1 and then further limited through elegant considerations that ensure the collector current increases monotonically with the external VBE. Such limiting, however, cannot possibly work for the dynamic charge current which is the issue in the off-state CCB example as well as the VCO example above, due to how model equations are implemented in circuit simulators. One side effect of this Gem limiting is that avalanche induced runaway cannot be modeled for investigating safe operating area (SOA). A switch swgemlim is introduced in Mextram 505.3 to allow the users to turn off Gem limiting for such modeling, as shown in Fig. 3. The new avalanche model in Mextram 505 also enhances its ability to accurately predict the SOA boundary due to electrothermal runaway from the combined effects of avalanche and self-heating. Figure 1