Sensitive Cell Lines Research Articles

Abstract 1670: Mechanistic insight into mTOR signaling identifies RNA splicing machinery as a potential therapeutic target for cancer

Abstract Aberrant signal transduction regulating cell growth and proliferation is a hallmark of many cancers. Activation of mTOR signaling is common and is an attractive therapeutic target with mechanistically different mTOR inhibitors in clinical use. One consequence of exposure to the mTOR inhibitor rapamycin is an alteration of gene expression through a global increase in alternative exon inclusion (Cheng et al. 2022, doi.org/10.3390/ijms232012416). To examine the mechanisms underlying this effect, we utilized the TempO-Seq targeted sequencing platform to profile both the whole transcriptome and a selection of alternatively spliced RNA targets in the rapamycin sensitive and resistant breast cancer cell lines MCF-7 and MDA MB 231 following exposure to 13 mTOR inhibitors, some closely related and some from distinct chemical classes. Recent publications have demonstrated that high quality dose response data can be obtained using this sequencing platform (Harrill et al. 2021, doi: 10.1093/toxsci/kfab009; Ramaiahgari et al. 2019, doi: 10.1093/toxsci/kfz065) and TempO-Seq has been widely adopted in toxicology for deriving compound-specific expression signatures to identify mechanisms of action and long-term toxicity. Treated cells were also profiled using TempO-LINC, a novel high-throughput single-cell assay based on the same platform. We observed that certain mTOR inhibitors induced both common and cell-specific differential expression as well as widespread alternative exon inclusion, as expected. Intriguingly, transcripts with the most significant changes in splicing upon treatment were those encoding members of the SR family of splicing factors, often overexpressed or amplified in breast cancers (Park, et al. 2019, doi: 10.1016/j.celrep.2019.10.110). This is significant because SR protein expression is autoregulated by alternative inclusion of an exon containing a premature stop codon in a feedback loop leading to nonsense-mediated decay (NMD) and lowered protein levels. Indeed, NMD is known to be inhibited by rapamycin (Martinez-Nunez, et al. 2017, doi: 10.1093/nar/gkw1109), which would lead to the observed accumulation of these transcripts. Thus, monitoring a targeted selection of alternative splicing events and regulators revealed mTOR regulation of mRNA isoform abundance consistent with regulation of the NMD RNA turnover process and with overexpression of SR proteins in breast cancers. Importantly, targeted bulk and single-cell TempO-Seq assays enable efficient sequencing and simplified data analysis without the expense and bioinformatic burden of RNAseq, making them particularly well-suited for drug discovery. These results support the use of this approach for further characterization of cell-specific effects of mTOR inhibitors and their mechanisms of action. Citation Format: Gaelle Rondeau, Megan Opichka, Kevin White, Joanne M. Yeakley, Dennis J. Eastburn, Bruce Seligmann. Mechanistic insight into mTOR signaling identifies RNA splicing machinery as a potential therapeutic target for cancer [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 1670.

Abstract 5843: Exploring the implications of LPAR-1 expression in TKI-resistant NSCLC

Abstract Introduction: Non-small cell lung cancer (NSCLC) is the most common type of lung cancer in the United States with a 5-year survival rate hovering between 20-30%. Mutations in EGFR can initially cause the tumors to respond to tyrosine kinase inhibitors (TKI). Osimertinib, a third generation TKI, is the preferred first or second line of treatment and despite being effective, recent reports indicate that patients develop resistance within 10-18 months of treatment. TKI resistance limits therapeutic options for patients and therefore, alternative strategies are being explored. In this context, Lysophosphatidic acid receptors (LPARs), a family of G-protein coupled receptors consisting of LPARs 1-6 expressed differentially in prostate, breast, ovarian, pancreatic, and brain cancers are being explored as potential targets for drug resistant cancers. Specifically, LPAR-1 has been shown to play a role in tumor cell clonogenicity, migration, and response to therapy in EGFR mutant NSCLC cells. Pharmacological inhibition or CRIPSR based deletion of LPAR-1 in EGFR mutant NSCLC cell lines HCC827 and NCI-H3255, increased TKI sensitivity by reducing clonogenic potential. Further, detailed pathway analysis in TKI sensitive and resistant EGFR mutant cell lines suggests that LPAR-1 expression influences drug sensitivity. Surprisingly, the role of LPAR-1 in TKI sensitivity is not well understood. In the present study, we have performed detailed investigation on the implications of LPAR-1 expression in the development of Osimertinib resistance. Methods: Osimertinib resistant EGFR mutant cell lines (OR) were generated using dose-escalation method and drug-tolerant persisters (DTPs) were generated using a short-term high exposure method. Gene and protein expressions were examined using qPCR and western blotting. Subcutaneous tumor cell derived xenografts were generated for in vivo studies. Results: LPAR-1 is downregulated in Osimertinib resistant NSCLC cells. Further, we also observe that LPAR-1 levels are lower in DTP cells, confirming a progressive loss of LPAR-1 with Osimertinib treatment. In vivo studies in cell derived xenografts correlated with the in vitro studies. Conclusion: Our studies indicate LPAR-1 downregulation correlates to Osimertinib resistance in EGFR mutant NSCLC cell lines. LPAR-1 downregulation has a key role in development of Osimertinib resistance. Future studies will focus on delineating LPAR-1 signaling pathways related to TKI resistance and investigating the effect of LPAR-1 overexpression using CRISPR technology. Citation Format: Varsha Srinivasan, Zhaohui Li, Raghuraman Kannan, Anandhi Upendran. Exploring the implications of LPAR-1 expression in TKI-resistant NSCLC [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 5843.

Abstract 682: Development of novel eIF4E inhibitors to potently and selectively suppress tumor growth across multiple indications

Abstract Despite considerable progress in treating cancer, drug resistance remains the primary hurdle to achieving cures in patients. Tumors often develop resistance through reactivation of the drug-targeted pathway, or activation of alternative parallel pathways, thereby maintaining the original downstream signaling effects. One of the furthest downstream effectors and critical nodes for many oncogenic signaling pathways is eukaryotic translation initiation factor 4E (eIF4E); the main regulator and rate limiting factor for protein synthesis. eIF4E is reactivated by many resistance mechanisms to promote translation of multiple pro-oncogenic factors including Cyclin D1/3, making it an attractive target to potentiate the anti-cancer activity of targeted therapies and to overcome drug resistance. Here, we present the development of novel, potent, and selective eIF4E inhibitors for use in both treatment-naïve and resistance settings across multiple tumor indications. To capitalize on the potential of targeting eIF4E, we developed a series of compounds with unique properties that maintain anti-tumor efficacy while minimizing toxicity. Our novel, selective, and potent oral eIF4E inhibitors (RBX-eIF4Ei) elicit a reversible, dose-dependent cell cycle arrest. Unlike targeting eIF4A, eIF4E inhibition selectively regulates translation of cancer-dependent pathway proteins instead of global protein synthesis, thus reducing on-target toxicity and increasing tolerability. Cellular profiling demonstrates RBX-eIF4Ei are highly selective, nanomolar inhibitors across many tumor types including, NSCLC, CRC, breast, and melanoma. Additionally, RBX-eIF4Ei demonstrate consistent efficacy across both sensitive and resistant cell lines, including intrinsic and acquired resistance models. Combining RBX-eIF4Ei with standard of care targeted therapies produces additive responses in both settings, suggesting its potential anti-neoplastic benefits post progression. In vivo, daily oral monotherapy treatment with RBX-EIF4Ei causes significant tumor growth inhibition across a variety of indications including BRAFmut CRC, BRAFmut melanoma and ER+ breast cancer, with minimal signs of toxicity. Intratumoral concentration of RBX-eIF4Ei correlate with significant tumor cell growth inhibition, as well as reductions in eIF4E target proteins, ODC1 and Cyclin D1. Combination studies with standard of care in both the treatment naïve and resistant settings are ongoing. Collectively, these data support the addition of RBX-eIF4Ei to standard of care in both the naïve and treatment resistance settings across a variety of indications including NSCLC, breast, CRC, and melanoma. IND enabling studies are planned, marking a significant step toward advancing these promising eIF4E inhibitors into clinical development. Citation Format: Matthew B. Friedersdorf, Devon R. Blake, Sarah E. Thompson, Roheeth Pavana, Ramamurty V. Changalvala, Andrew S. Truong, Krista Marran, Abha Bias, Jessica A. Sorrentino. Development of novel eIF4E inhibitors to potently and selectively suppress tumor growth across multiple indications [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 682.

Abstract 1939: NT219, a dual inhibitor of IRS1/2 and STAT3, suppresses cancer stem cell mediated resistance to KRASG12C and KRASG12D inhibitors in solid tumors

Abstract Background NT219 is a novel small molecule, a dual inhibitor which uniquely triggers the degradation of Insulin Receptor Substrates 1/2 (IRS) and the dephosphorylation and suppression of STAT3, two major oncogenic targets that play a key role in drug resistance. Mutated KRAS (mKRAS) has long been referred to as undruggable until recently when KRASG12C inhibitors were approved. While KRASG12C is the most common oncogenic driver in NCSLC, KRASG12D is found in 42% of pancreatic tumors. We present NT219 suppressive effect on mKRASi resistant and sensitive cells of both PDAC and NSCLC, as well as on cancer stem cells (CSC) known to contribute to disease recurrence. Method The inhibitory effects of NT219 as a monotherapy or in combination with either KRASG12C inhibitors (sotorasib/adagrasib) or KRASG12D inhibitor (MTRX1133) were tested in 2D cell growth and colony formation assays using mKRAS inhibitor sensitive and resistant cancer cell lines. The effect of NT219 and mKRASi on cancer stem cells was assessed using 3D spheroid assay evaluating spheroid size (microscopic measurements), cell viability (CellTiterGlo) and stemness marker expression (FACS analysis). Results NT219 in combination with either sotorasib or MTRX1133 suppressed established spheroids of NSCLC(KRASG12C) and PDAC(KRASG12D) respectively, in terms of size, disintegration and viability. In NSCLC H358, spheroid satellites appeared following treatment with sotorasib, while the combination with NT219 suppressed it. CSC marker ALDH increased 7-fold in NSCLC spheroids as compared to 2D grown cells, while NT219 and sotorasib suppressed it. The expression of SOX2 stemness marker was reduced by NT219 alone (5 fold), unexpectedly induced by sotorasib (4 fold) and suppressed by NT219+sotorasib (15 fold vs sotorasib alone). In addition, significant induction of STAT3, was observed following sotorasib treatment and completely reversed by the addition of NT219. We also demonstrate that NT219 induces growth inhibition in both KRASiG12C resistant PDAC and NSCLC, and KRASiG12D resistant PDAC cells. NT219 exhibited synergistic effects with adagrasib and MTRX1133, in suppressing the proliferation of KRASG12C PDAC and NSCLC cells and KRASG12D PDAC cells, respectively. This combination showed a synergistic effect in xenograft model. Conclusion We first showed the effect of NT219 in suppressing cancer stem cells, known to promote resistance and tumor recurrence. Synergistic effect of NT219 and mKRAS inhibitors, G12Cand G12D, in NSCLC and PDAC respectively, was demonstrated. Initial results suggest involvement of NT219 target proteins in resistance to mKRASG12C/D inhibitors. Treatment with sotorasib induced enhancement in stemness potential of mKRASG12C NSCLC, which NT219 efficiently suppressed, suggesting a novel therapy for this unmet need and a novel mechanism to combat resistance to mKRAS inhibitors Citation Format: Hadas Reuveni, Mohammed Najeeb Al-Hallak, Sarah Motorwala, Eliza Beal, Steve Kim, Rafic Beydoun, Gergory Dyson, Bassel El-Rayes, Herbert Chen, Philip A. Philip, Anthony F. Shields, Boris Pasche, Katy Sigalov, Hava Ben-David, Daphna Miron, Asfar S. Azmi. NT219, a dual inhibitor of IRS1/2 and STAT3, suppresses cancer stem cell mediated resistance to KRASG12C and KRASG12D inhibitors in solid tumors [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 1939.

Abstract 614: Src family kinase inhibition demonstrates antitumor activity in vitro and in patient-derived xenograft models of human cholangiocarcinoma

Abstract Background: Cholangiocarcinoma (CCA) is a lethal and heterogenous malignancy of the biliary tree characterized by perineural invasion. About 85% of CCA show activation of YAP signaling, which promotes proliferation, anti-apoptosis, and therapeutic resistance. YAP signaling is mediated by Src family kinases (SFK) by phosphorylation of YAP (pYAPy357). NXP900 is a first-in-class, highly selective, SFK inhibitor with a novel mechanism of action which locks SFK in its closed and inhibited conformation, in contrast to other Src inhibitors such as dasatinib. A phase 1a study of NXP900 in patients with advanced solid tumors was recently initiated. Here, we examined treatment responses of CCA to NXP900 in vitro and in vivo. Methods: Cell viability was determined in seven CCA cell lines by CellTiter-Glo. Cell death and apoptosis were assayed by PI/Hoechst and Caspase-Glo 3/7 assay. CalcuSyn software was used to determine synergistic drug effects. Immunoblot analysis, RT-PCR, and IF staining of YAP localization were used to evaluate YAP knockdown. Clones of human CCA cell lines resistant to NXP900 were generated through escalating exposure to NXP900 over 6 months. Five patient-derived xenograft (PDX) tumors were expanded into flanks of NOD/SCID mice. Tumor bearing mice were randomized 1:1 with 5 mice per arm and treated with vehicle or NXP900 (40 mg/kg) once daily for up to 4 weeks. To determine drivers of sensitivity and resistance, predicted sensitivity scores based on tumor growth were linked to multi-omics (RNA seq and [phospho-]proteomics) of our PDX models. Results: All cell lines were sensitive to NXP900 with IC50 values between 7nM-15µM; IC50’s of resistant clones were 1000 times higher. NXP900 induced more cell death compared to vehicle, which appeared to be through apoptosis. NXP900 inhibited pSrc, decreased pYAPy357, and upregulated inactive pYAPs127. Correspondingly, decreased YAP target gene (Cyr61, NUAK, and CTGF) levels and a nuclear-to-cytoplasmic translocation were observed. NXP900/GemCis combination therapy increased cell death demonstrated a synergistic effect (Combination Indices <1) at all concentrations. In our PDX models, treatment was associated with a significant decrease in tumor growth in 3 models (mean fold change 3.1 vs. 14.2; 1.0 vs. 7.6; 1.4 vs. 2.6). The major resistant signature was the TRK signaling network, involved in nerve growth factor binding activity, while drivers of sensitivity included the SRC network. Conclusion: NXP900 demonstrated therapeutic activity in vitro and in human PDX models. We are currently performing multi-omic approaches in NXP900 sensitive and resistant cell lines to unravel determinants of activity and resistance. Additional in vivo studies will be performed to determine effects of NXP900/GemCis and NXP900/anti-PDL-1 combination therapy. Citation Format: Hendrien Kuipers, Jennifer L. Tomlinson, Danielle M. Carlson, Amro M. Abdelrahman, Erik Jessen, Jack W. Sample, Nathan W. Werneburg, Hannah E. Stumpf, Mark J. Truty, Sumera I. Ilyas, Gregory J. Gores, Rory L. Smoot. Src family kinase inhibition demonstrates antitumor activity in vitro and in patient-derived xenograft models of human cholangiocarcinoma [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 614.

Abstract 4675: Reduction in NSCLC tumorigenesis by targeting sphingosine kinase 2

Abstract Lung cancer will account for 21% of US cancer deaths in 2023 with 238,340 cases and 127,070 deaths. Treatment with EGFR-TKI (epidermal growth factor receptor tyrosine kinase) inhibitors initially decrease tumor growth, but often leads to TKI resistance. According to studies, non-small cell lung cancer (NSCLC) tumors express more SphK2 (Sphingosine kinase 2) than normal lung tissue and patients with overexpression have worse survival chances. However, SphK2's role in TKI resistance is unclear. We hypothesize that inhibiting/downregulating SphK2 could reduce tumorigenicity and overcome ER (Erlotinib) and OR (Osimertinib) resistance. We studied the expression of SphK2 in both drug-resistant (OR/ER) and drug sensitive (parental) H358, H2170, H3255, and PC9 NSCLC cell lines using Western blotting, qRT-PCR, and immunofluorescence. H3255OR cells were also bioprinted with GelMA hydrogel using an R-Gen 200 bioprinter to mimic the physiological tumor environment and treated with SphK2 siRNA or ABC294640 (SphK2i). Immunoblotting was done to analyze changes in the expression of SphK2 in H358 (WT-EGFR) and H3255 (mutant EGFR- L858R) parental and OR-resistant cell lines. Results indicated a 1.5-1.8-fold upregulation of SphK2. Increased SphK2 gene expression was observed using qPCR in TKI-resistant H3255OR (4.3-fold), PC9ER/OR with mutant EGFR (E746-A750del) (1.8-3.3-fold), and H2170ER/OR with WT EGFR (1.3-1.5-fold) compared to parental cells. Immunofluorescence studies showed increased fluorescence of SphK2 in H3255OR (2.6-fold), H358 ER (2.4-fold) and OR cells (2.3-fold) compared to parental cells. Spheroids formed from single cancer cells can "re-create" the growth of a tumor. The spheroid count of H3255OR was reduced by 73.98% and 56%, respectively, when SphK2i was added to the 3D-cell culture with Matrigel, compared to the diluent and OR alone (p≤0.01). We used 3D bioprinting to precisely stack cells on biological scaffolds to recreate lung tumors from patients and boost the therapeutic efficacy of these findings. When bioprinted spheroids of H3255OR were treated with SphK2i in combination with OR, the number of spheroids per microscopic field were reduced by 87.3% compared to OR alone. Bioprinted H3255OR spheroids treated with SphK2 siRNA and OR revealed a 75.8% and 84% reduction of spheroid count, respectively, compared to treatments with siRNA alone or OR alone (p≤0.05). This data supports the hypothesis that SphK2 suppression or downregulation can assist in mitigating oncogenesis. We also used H3255OR transwell migration assays to examine how SphK2 inhibition affects cell migration. Combining OR with SphK2i resulted in a 94.7% and 91.4% decrease in cell migration compared to diluent and OR alone (p≤0.01). In H358OR-resistant cells, combining OR with SphK2i resulted in a 94.97% inhibition compared to diluent (p≤0.01). These results suggest that targeting SphK2 could be a valuable approach for treating lung cancer. Citation Format: Ayesha Khan, Bamby Dieng, Namrata Dube, Mohammad Fazle Alam, Neelu Puri. Reduction in NSCLC tumorigenesis by targeting sphingosine kinase 2 [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 4675.

Abstract 514: Salt-inducible kinase inhibitor OMX-0407 drives cell-cycle arrest in vitro and in vivo: An in-depth MoA analysis by phospho-proteomics

Abstract Based on iOmx’ proprietary iOTargTM genetic screening platform, salt-inducible kinase (SIK) 3 was identified as a novel cell signaling modulator in cancer biology. OMX-0407, an orally available, spectrum-selective kinase inhibitor targets several members of the SIK family and is known to prevent tumor-promoting function of the SIK-family through repolarization of the tumor microenvironment by enhancing caspase-mediated apoptosis upon death-receptor signaling. In addition, OMX-0407 inhibits individual key members of the tyrosine and tyrosine-like kinase family that are involved in cancer cell proliferation and cell cycle regulation. Via this dual mode of action, OMX-0407 has the potential to effectively fight solid tumors as exemplified by its striking single-agent efficacy in multiple pre-clinical tumor models. A comprehensive anti-tumor viability screen of >200 human cancer cell lines revealed striking effects of OMX-0407 on cancer cell viability across various cancer indications, resulting in a distinct sensitivity profile across various tumor indications with particularly strong effects on renal cell carcinoma (RCC) and squamous non-small cell lung cancer (sqNSCLC). Phospho-proteomics screening demonstrated pharmacodynamic activity of OMX-0407 in sensitive tumor cell lines via inhibition of key cellular processes such as cell motility, proliferation, and cell cycle regulation across different indications. Orthogonal functional in vitro assays confirmed the association of the OMX-0407-mediated anti-tumor efficacy with the arrest of G1/S transition and corresponding downregulation of cell cycle associated proteins PAK1/2 and ARHGAP35. The profound impact of OMX-0407 on fundamental regulatory mechanisms of cell division and cancer cell apoptosis translates into dose-dependent single-agent, anti-tumor efficacy in various pre-clinical tumor models of selected indications. Combination with Axitinib, a selective orally available inhibitor of vascular endothelial growth factor receptor 2, significantly enhanced anti-tumor efficacy and pharmacodynamic inhibition of cell growth as well as angiogenesis. These data further strengthen the potential of OMX-0407 in the treatment of RCC as well as other indications. In summary, OMX-0407 is a novel spectrum selective kinase inhibitor, currently under evaluation in a clinical Phase I trial (NCT05826600). OMX-0407 demonstrates strong anti-tumor efficacy in monotherapy in selected sensitive indications through a dual-pronged MoA, by modulating the tumor microenvironment and exerting direct anti-tumor activity in solid tumor indications with high unmet medical need. Citation Format: Ilona-Petra Maser, Marisa Stebegg-Wagner, Bettina Bauer, Filippos Konstantinidis, Andreas Schirmer, Moritz Zulley, Sonja Lacher, Barbara Kracher, Parastou Kohvaei, Murray Yule, Hannes Loferer, Stefan Bissinger. Salt-inducible kinase inhibitor OMX-0407 drives cell-cycle arrest in vitro and in vivo: An in-depth MoA analysis by phospho-proteomics [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 514.

Abstract 7122: A novel USP1 inhibitor coupled with a novel proteomic response biomarker for precision oncology therapy

Abstract Ubiquitin-specific protease 1 (USP1) is a well-characterized deubiquitinating enzyme (DUB) that plays a critical role in DNA damage repair (DDR). It was shown to regulate various key repair processes, most notably proliferating cell nuclear antigen (PCNA) in the Translesion Repair (TLS) pathway and FANCD2/FANCI in the Fanconi Anemia (FA) repair pathway. Research indicates that USP1 deficiency leads to a decrease in cell survival and disruption of genomic stability, suggesting that USP1 inhibitors (USP1i) may hold promise in treating DDR deficient tumors. Through the integration of computational and medicinal chemistry approaches, we discovered a novel, potent inhibitor of USP1, showing anti-USP1 activity in both cell-free enzymatic assay and in measurement of PCNA-ubiquitination change upon USP1 inhibition in cells. We demonstrate anti tumor activity in DDR-related and other indications. By utilizing our platform to analyze the basal proteomics of resistant and sensitive cell lines treated with USP1i, we revealed a distinctive proteomic biomarker signature for USP1i response. This data demonstrates the potential of our novel USP1 inhibitor to serve as a potent therapeutic agent for DDR-deficient and other biomarker-positive cancer patients. Citation Format: Iris Alchanati, Andrew Morley, Avital Hay-Koren, Fabrizio Fierro, Galina Otonin, Shay Herman, Alon Shtrikman, Yonatan Katzenelenbogen, Gali Arad, Barr Tivon, Kirill Pevzner, Eran Seger. A novel USP1 inhibitor coupled with a novel proteomic response biomarker for precision oncology therapy [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 7122.

Abstract 955: Double-targeting of pancreatic ductal adenocarcinoma (PDAC): Unveiling the potent combination of NMS-873 and BAY-876

Abstract Pancreatic ductal adenocarcinoma (PDAC) stands out as one of the most aggressive and challenging-to-treat cancers known. Consequently, the development of effective therapeutic strategies holds significant importance in enhancing patient outcomes. In contrast to single-drug treatments, combination therapies offer the potential for improved results by addressing multiple pathways. This approach not only reduces the likelihood of drug resistance but also encourages synergistic effects, all while permitting the use of lower individual drug doses, thus minimizing potential side effects. In this study, we subjected a panel of PDAC cell lines with varying degrees of sensitivity to a high-throughput combinatorial drug screen. Mitochondrial complex 1/p97 inhibitor NMS-873 was tested in combination with 95 other compounds, revealing remarkable synergy when paired with Glut1 inhibitor BAY-876. In order to affirm the validity of these findings, we conducted further experiments involving multi-dose drug combinations within long-term clonogenic assays. These supplementary investigations also demonstrated significant synergistic effects between BAY-876 and NMS-873, as quantified through the calculation of Bliss and Zip scores. Notably, this combination exhibited superior efficacy when confronting PDAC cell lines that are more resistant to NMS-873, highlighting the potential of this combination to overcome therapy resistance. To gain insights into the underlying mechanisms behind these outcomes, we performed a gene enrichment analysis which revealed that the more sensitive cell lines exhibited elevated rates of cell division, while the more resistant ones demonstrated heightened cRNA processing and increased metabolic activity, particularly in protein, phospholipid, and lipid synthesis. The combination of BAY-876 and NMS-873 presents a promising avenue for the targeted treatment of PDAC. This study underscores the remarkable synergy observed in mouse PDAC cell lines with a particular emphasis on the heightened efficacy against cell populations that are more resistant to NMS-873. These results warrant further investigation to elucidate the underlying molecular mechanisms and validate these findings in clinical settings. Citation Format: Emily Rita Eppinger, Christian Schneeweis, Dieter Saur. Double-targeting of pancreatic ductal adenocarcinoma (PDAC): Unveiling the potent combination of NMS-873 and BAY-876 [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 955.

Abstract 5787: Structure-function mapping of DHODH shows deviations in protein structure

Abstract Dihydroorotate dehydrogenase (DHODH) is a CoQ-dependent enzyme that converts dihydroorotate to orotate in the de novo pyrimidine biosynthesis pathway. Multiple structures of DHODH in complex with various small molecule inhibitors have been solved that indicate that DHODH inhibitors bind in the CoQ binding tunnel of DHODH and act as competitive inhibitors of CoQ. We performed saturating mutagenesis screens to identify mutations in DHODH that confer resistance to brequinar and BAY2402234, two highly potent DHODH inhibitors. As expected, many of the resistance mutations localized to the drug/CoQ-binding tunnel of the enzyme. Among the top-scoring drug-binding-domain mutants in both the brequinar and BAY2402234 screens were substitutions A58H and A58T. In silico analysis predicted that A58H should impair DHODH binding to both brequinar and BAY2402234. However, A58T was predicted to only impair binding of DHODH to brequinar. We expressed the mutants in a DHODH inhibitor sensitive cell line and confirmed that they both confer resistance to brequinar and BAY2402234, and we then assessed the ability of the mutants to bind drug by cellular thermal shift assay (CETSA). We found that, as predicted, DHODH A58H did not bind brequinar or BAY2402234. However, to our surprise, we detected binding of both brequinar and BAY2402234 to DHODH A58T. We generated recombinant DHODH A58T and confirmed that the purified protein was enzymatically active and strongly drug-resistant by DCIP assay and then assessed binding of the mutant protein to brequinar and BAY2402234 by thermal shift assay (TSA). Consistent with our CETSA results, recombinant DHODH A58T bound both brequinar and BAY2402234 in vitro. These results suggested that DHODH A58T can simultaneously bind drug and CoQ. However, previously reported DHODH structures indicated that the drug/CoQ binding tunnel is quite narrow and rigid. To determine whether the structure of catalytically-active DHODH is more flexible than inhibitor-bound catalytically-inactive DHODH, we co-crystallized wild-type DHODH with decylubiquinone (DCU), a CoQ analog that can act as a DHODH co-substrate in vitro. We found that the structure of DCU-bound DHODH differs from previously published DHODH structures in two important ways: (1) there appears to be a second point of ingress into the active site of DHODH next to the CoQ tunnel that may be able to accommodate a highly non-polar molecule such as CoQ/DCU and (2) the ‘flap’ covering the DHO/orotate ingress/egress region of DHODH, which is ‘closed’ in inhibitor-bound DHODH, is ‘open’ in DCU-bound DHODH. We are currently working to solve the crystal structure of DHODH A58T bound to inhibitor and DCU to ask if DCU can access the active site of DHODH through an alternative hydrophobic tunnel and if DHODH A58T remains in the ‘open’ configuration when bound to drug. Citation Format: Ruchika Pokhriyal, Laura Evans, Hyuk-Soo Seo, Jillian K. O'Neil, Betty Rouaisnel, Atanas Kamburov, Judith Guenther, Stefan Gradl, Haribabu Arthanari, Sven Christian, Xiaoping Yang, Sirano Dhe-Paganon, Julie-Aurore Losman. Structure-function mapping of DHODH shows deviations in protein structure [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 5787.

Abstract 2837: Conservation of JAK-STAT signaling in canine lymphocytes responding to human IL-6, IL-7, and IL-1 alpha

Abstract Dogs share physiological similarities with humans, positioning them as valuable models for studying the efficacy and safety of drugs and their underlying mechanisms of action. The JAK-STAT pathway, a highly conserved signaling pathway across species, including humans and dogs, presents an opportunity to investigate the therapeutic potential of cytokines that utilize this pathway. In this study, we aimed to evaluate the functional activity of three canine cytokines on canine cells. To assess stimulation of the JAK/STAT pathway, we used a flow cytometry assay that measures phospho-STAT in activated canine or human lymphocytes in whole blood specimens. Testing of commercially available human and canine IL-6 proteins revealed that canine lymphocytes respond poorly to most canine IL-6 products, whereas all recombinant human IL-6 products stimulated STAT phosphorylation in canine lymphocytes, despite sharing low sequence similarity with canine IL-6. In human T cells, both canine IL-6 and human IL-6 stimulated STAT phosphorylation, demonstrating biological activity from the canine IL-6 products. Several JAK inhibitors inhibited cytokine-induced STAT phosphorylation in both canine and human CD4 T-cells, consistent with JAK inhibition, but targeting the IL-6 receptor with tocilizumab only blocked IL-6-induced STAT phosphorylation in human but not canine CD4 T-cells in whole blood. These findings demonstrate the potential of our assay system to assess cross-species cytokine reactivity, determine if JAK/STAT inhibitors used clinically might be useful in treating inflammatory conditions in dogs, and identify novel canine-specific inhibitors. Additionally, we explored the induction of IL-8 by human and canine IL-1 alpha in IL-1 alpha sensitive human cells. Human IL-1 alpha failed to stimulate a canine IL-1 alpha sensitive cell line, suggesting species-specific differences in IL-1 alpha activity. Furthermore, we discovered that canine IL-7 and human IL-7 are species-specific. In summary, this proof-of-concept study highlights the capability to assess the activation of STATs and pathway inhibition by JAK inhibitors in canine whole blood using flow cytometry. We confirmed that human IL-6 stimulates JAK/STAT signaling in canine CD4 T-cells. Our results also revealed significant differences in species cross-reactivity of human IL-6, IL-7, and IL-1 alpha, underscoring the importance of species-specific investigations. Leveraging the similarities and differences between canine and human cytokines targeting the JAK-STAT pathway can enhance drug development efforts and contribute to the advancement of safer and more effective therapies for both humans and pet dogs with similar diseases. This study was funded by NCI Contract No. 75N91019D00024. Citation Format: King Leung Fung, Melissa L. Breiner, James B. Mitchell, Ralph E. Parchment. Conservation of JAK-STAT signaling in canine lymphocytes responding to human IL-6, IL-7, and IL-1 alpha [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 2837.

Abstract 4723: Target engagement sheds light on difference in drug efficacy in breast cancer cell lines

Abstract Breast cancer is a serious disease that affects millions of women worldwide, and 700,000 people succumb to the disease annually. Breast cancers are divided into several functional subgroups based on molecular characteristics and growth pattern: Luminal A and B, HER2 positive (HER2+) and triple negative. The subgroups are important from a clinical perspective as they partially guide treatment strategies. In this study we wanted to investigate the difference in target engagement with four drugs indicated for treatment of different types of breast cancer: Alpelisib, Neratinib, Vinorelbine, and Docetaxel. Five different human breast cancer cell lines were included, representing Luminal A (MCF-7, T-47D), HER2+ (SK-BR-3, BT-474), and triple negative (BT-20). We used CETSA® (CEllular Thermal Shift Assay) coupled to mass spectrometry detection to assess proteome wide changes in protein thermal stability in intact breast cancer cell lines. CETSA is unique as a target engagement detection modality as it allows for target engagement assessment in intact cells with unaltered drug molecules. Also, as biology is intact in live cells it is possible to follow compound induced downstream signaling or phenotypic events that result in changed thermal stability of proteins. In addition to assessing protein thermal stability with CETSA, which is a short treatment of 1 h, we also subjected cells in culture to prolonged drug exposures, ≤72 h, in order to measure viability. This was done to correlate early changes in protein thermal stability to the viability phenotype that manifested later. In general, responses both in protein thermal stability and cell viability was heterogenous among the cell lines. The most homogenous response in viability was observed for the Phosphatidyl Inositol 3’ kinase inhibitor Alpelisib, which reduced viability to 20 - 40% in all cell lines. In contrast, partial resistance was shown to the other drugs by at least one of the cell lines. For Alpelisib, the amount and type of proteins that were thermally shifted correlated with the effect on viability. The covalent HER2 inhibitor Neratinib was most effective in inhibiting viability in HER2+ cells and proteins of the HER2 pathway were thermally shifted in these cells, which was not observed for the other cell lines. Viability of the other cell lines were also affected by Neratinib, but only at higher concentrations. Both microtubule inhibitors induced thermal stabilization of tubulins, but that did not always translate into efficacy in the viability assay. However, sensitive cell lines showed thermal shifts of tubulins at lower concentrations of compound. In oncology drug development it is important that effects on viability are driven by on-target efficacy and not by off-target effects. Here we show the benefit of connecting knowledge of target engagement and phenotypic readouts; what targets are engaged, at which concentrations, and what is the corresponding phenotype. Citation Format: Tomas Friman, Tuomas Tolvanen, Merve Kacal, Victoria Brehmer, Stina Lundgren, Laurence Arnold, Daniel Martinez Molina. Target engagement sheds light on difference in drug efficacy in breast cancer cell lines [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 4723.

Abstract 2638: Sensitizing immunotherapy-refractory prostate cancer to immune checkpoint blockade therapy with optimized ketogenic diet regimens

Abstract The purpose of this study is to investigate strategies for enhancing immune checkpoint blockade (ICB) therapy in prostate cancer (PCa). To achieve this, we established a series of ICB-resistant PCa cell lines derived from a previously sensitive cell line, which originated from a murine model of metastatic PCa. Notably, we observed a reduction in major histocompatibility complex (MHC) class I protein levels in the resistant sublines. Our study demonstrated synergistic efficacy through the combination of anti-PD1 and anti-CTLA4 antibodies with histone deacetylase inhibitor (HDACi) vorinostat, a cyclic ketogenic diet (CKD), or β-hydroxybutyrate (BHB) supplementation. Importantly, these interventions significantly delayed PCa tumor progression. Furthermore, our analysis revealed that the effects of these interventions were contingent on both BHB and adaptive immunity. In-depth single-cell transcriptomic and proteomic profiling unveiled mechanisms involving cancer-cell-intrinsic changes (upregulated MHC class I molecules) and extrinsic factors, including CD8+ T cell chemoattraction, M1/M2 macrophage rebalancing, monocyte differentiation toward antigen-presenting cells, and reduced neutrophil presence. In conclusion, our findings provide valuable insights into the potential clinical utility of combining HDACi and optimized ketogenic diet regimens to enhance ICB therapy for PCa. Citation Format: Sean Murphy, Sharif Rahmy, Dailin Gan, Jun Li, Xuemin Lu, Xin Lu. Sensitizing immunotherapy-refractory prostate cancer to immune checkpoint blockade therapy with optimized ketogenic diet regimens [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 2638.

Abstract 608: NEOS-223 is a small molecule kinase inhibitor which induces apoptosis in selected cancer models

Abstract Due to their critical role in cancer signaling pathways, members of the kinase family have emerged as one of the most comprehensively pursued targets in pharmacological cancer research. Deregulation of kinase activities leads to a variety of upstream and downstream signaling pathway changes in cancer cell. The Ras/Raf/MEK/ERK and PI3K/Akt/mTOR cascades are activated by genetic alterations in selected upstream signaling molecules such as receptor tyrosine kinases. Recently developed therapies which target such kinases (EGFR, BRAF, MEK) with kinase inhibitors have notably improved the prognosis within various cancer patient groups. However, patients with different mutations of EGFR, RAS, and BRAF do not respond completely. In this study the potential of NEOS-223 as a new kinase-targeted therapy in selected cancer models was investigated. Multiple cancer cell lines were assessed for cell growth as well as the direct inhibitory effects of NEOS-223 alone and in combination with other clinically approved kinase inhibitors. NEOS-223 treatment caused cell growth inhibition, blocked colony growth, and induced apoptosis in lung, pancreatic, melanoma, and colon cancer cell lines in vitro and demonstrated potent antitumor activity in in vivo xenograft models of colon and lung cancer. We were particularly interested in examining different components of the ERK and PI3K signaling pathways in selected sensitive cell lines, it was identified that NEOS-223 treatment led to downregulation of the expression of pERK and pAKT signaling. Blockage of the PI3K/mTOR pathways showed inhibitory synergy with NEOS-223 in lung cancer in vitro. Most importantly, in vivo data showed that while administration of NEOS-223 alone decreased tumor growth, the addition of PI3K/Akt/mTOR inhibitor onatasertib significantly enhanced anticancer effect in a lung cancer model. In lung and pancreatic cancer models, inhibition of EGFR by the small molecule drug gefitinib strongly showed synergistic effect with NEOS-223 both in vitro and in vivo. This may be because EGFR potentially activates both the mitogen activated protein kinase (MAPK/ERK) and the PI3K/mTOR signaling cascades in different mutant cancer models. These studies reveal that NEOS-223 inhibits cell proliferation and induces apoptosis via suppressing the PI3K/Akt/mTOR pathway and further suggest that the combination of PI3K/Akt/mTOR and EGFR inhibitors and that NEOS-223 would be a strong potential chemotherapeutic strategy against lung and pancreatic cancers. Citation Format: Harish Potu, Sara A. Little, Stephanie Fedorchak, Sumathi Chittamuru, Timothy M Murphy, Roseanne Wexler, Sarah Di Croce, Melanie George, Laxman S. Desai. NEOS-223 is a small molecule kinase inhibitor which induces apoptosis in selected cancer models [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 608.

Valproate modulates the activity of multidrug resistance efflux pumps, as a chemoresistance factor in gastric cancer cells.

Drug resistance is one of the most critical problems in gastric cancer therapy. This study was performed to investigate the valproic acid effects on the proliferation of sensitive and resistant cell lines of human gastric cancer, and to explore the mechanism of the agent on multi drug resistance and apoptosis genes. The cytotoxicity effect of valproic acid on the EPG85.257 and EPG85.257RDB cells was assessed by the MTT assay, and the IC50 concentration was evaluated. Apoptosis, genotoxicity, and drug resistance pump activity were evaluated using comet assay, Real-time PCR, and flow cytometry, respectively. Cell proliferation was assayed using a scratch test. Dose-dependent toxicity was recorded after treatment of cells with valproic acid. Valproic acid represented a significant growth inhibition on EPG85.257 cells with IC50 values of 5.84 µM and 4.78 µM after 48 h and 72 h treatment, respectively. In contrast, the drug-resistant counterpart represented 8.7 µM and 7.02 µM IC50 values after the same treatment time. Valproic acid induced PTEN, Bcl2, P53, Bax, P21, and caspase3 expression in EPG85.257 cells, whereas p21, p53, PTEN, and ABCB1 were overexpressed in EPG5.257RDB. Valproic acid hindered cell migration in both cell lines (P < 0.01). Valproate genotoxicity was significantly higher in the parent cells than in their resistant EPG85.257RDB counterparts. Valproate led to a 62% reduction in the daunorubicin efflux of the MDR1 pump activity. Valproate can affect drug resistance in gastric cancer via a unique mechanism independent of MDR1 expression.

Uncovering PROTAC Sensitivity and Efficacy by Multidimensional Proteome Profiling: A Case for STAT3.

Proteolysis-targeting chimera (PROTAC) is a powerful technology that can effectively trigger the degradation of target proteins. The intricate interplay among various factors leads to a heterogeneous drug response, bringing about significant challenges in comprehending drug mechanisms. Our study applied data-independent acquisition-based mass spectrometry to multidimensional proteome profiling of PROTAC (DIA-MPP) to uncover the efficacy and sensitivity of the PROTAC compound. We profiled the signal transducer and activator of transcription 3 (STAT3) PROTAC degrader in six leukemia and lymphoma cell lines under multiple conditions, demonstrating the pharmacodynamic properties and downstream biological responses. Through comparison between sensitive and insensitive cell lines, we revealed that STAT1 can be regarded as a biomarker for STAT3 PROTAC degrader, which was validated in cells, patient-derived organoids, and mouse models. These results set an example for a comprehensive description of the multidimensional PROTAC pharmacodynamic response and PROTAC drug sensitivity biomarker exploration.

Static magnetic field reduces cisplatin resistance via increasing apoptosis pathways and genotoxicity in cancer cell lines

Cisplatin is a chemotherapy drug widely used in cancer treatment. Alongside its clinical benefits, however, it may inflict intolerable toxicity and other adverse effects on healthy tissues. Due to the limitation of administering a high dose of cisplatin as well as cancer drug resistance, it is necessary to utilize new methods optimizing treatment modalities through both higher therapeutic efficacy and reduced administered doses of radiation and drugs. In this study, sensitive (A2780) and resistant (A2780CP) ovarian carcinoma cells underwent treatment with cisplatin + static magnetic field (SMF). First, the levels of genotoxicity after treatment were evaluated by Comet assay. Then, cell cycle analysis and apoptosis assay were conducted by a flow cytometer. Lastly, the expression levels of genes involved in apoptosis and cellular drug uptake were investigated by PCR. After treating different groups of cells for 24, 48, and 96 h, the co-treatment of SMF and cisplatin as a combination managed to increase the amount of DNA damage in both sensitive and resistant cell lines. A considerable increase in mortality of cells was also observed mostly in the form of apoptosis, which was caused by inhibition of the cell cycle. The combination also increased the expression levels of apoptotic genes, namely P53 and P21; however, it did not have much effect on the expression levels of BCL2. Besides, the levels of CTR1 gene expression increased significantly in the groups receiving the aforementioned combination. Our study suggests that the combination of cisplatin + SMF might have clinical potential which needs further investigations through future studies.

Exploring new quinazolin-4(3H)-one derivatives as CDK2 inhibitors: Design, synthesis, and anticancer evaluation.

In the present work, five series of new 2,3-disubstituted quinazolin-4(3H)-ones 4a-c, 5a-d, 6a-g, 7a,b, and 9a-c were designed, synthesized, and screened in vitro for their cytotoxic activity against 60 cancer cell lines by the National Cancer Institute, USA. Five candidates 4c, 6a, 6b, 6d, and 6g revealed promising cytotoxicity with significant percentage growth inhibition in the range of 81.98%-96.45% against the central nervous system (CNS) (SNB-19), melanoma (MDA-MB-435), and non-small cell lung cancer (HOP-62) cell lines. The in vitro cytotoxic half maximal inhibitory concentration (IC50 ) values for the most active compounds 4c, 6a, 6b, 6d, and 6g against the most sensitive cell lines were evaluated. Additionally, screening their cyclin-dependent kinase 2 (CDK2) inhibitory activity was performed. Ortho-chloro-benzylideneamino derivative 6b emerged as the most potent compound with IC50 = 0.67 µM compared to Roscovitine (IC50 = 0.64 µM). The most active candidates arrested the cell cycle at G1, S phases, or both, leading to cell death and inducing apoptosis against CNS (SNB-19), melanoma (MDA-MB-435), and non-small cell lung cancer (HOP-62) cell lines. The molecular docking study verified the resulting outcomes for the most active candidates in the CDK2-binding pocket. Finally, physicochemical, and pharmacokinetic properties deduced that compounds 4c, 6a, 6b, 6d, and 6g displayed significant drug-likeness properties. According to the obtained results, the newly targeted compounds are regarded as promising scaffolds for the continued development of novel CDK2 inhibitors.

A hypoxia-related genes prognostic risk model, and mechanisms of hypoxia contributing to poor prognosis through immune microenvironment and drug resistance in acute myeloid leukemia.

Objective: Acute myeloid leukemia (AML) is a malignant hematologic cancer with poor prognosis. Emerging evidence suggests a close association between AML progression and hypoxia. The purpose of this study was to establish a new risk prognostic model for AML based on hypoxia-related genes, and to explore the mechanisms by which hypoxia-related genes affect the prognosis of AML based on tumor immune microenvironment (TIME) and drug resistance. Methods: The AML patient samples obtained from Therapeutically Applicable Research to Generate Effective Treatments (TARGET) database were classified into C1 and C2 based on hypoxia-related genes, followed by analysis utilizing Gene Ontology (GO), Kyoto Encyclopaedia of Genes and Genomes (KEGG) and Gene Set Enrichment Analysis (GSEA). Through univariate and LASSO Cox regression analysis, the hypoxia-related hub genes 26S proteasome non-ATPase regulatory subunit 11 (PSMD11) and 26S proteasome non-ATPase regulatory subunit 14 (PSMD14) were identified to construct the model. AML patient samples were obtained from the TARGET and The Cancer Genome Atlas (TCGA) databases, serving as the training and the validation sets, and were stratified into high-risk and low-risk group according to the median risk score. The correlations between the model and TIME and anti-tumor drugs were analysed using CIBERSORT and Genomics of Drug Sensitivity in Cancer (GDSC) databases. The expressions of PSMD11/PSMD14 in clinical samples and AML sensitive and drug-resistant cell lines were detected by Western blot and real-time PCR. Results: The C1 group with high expression of hypoxia-related genes had lower overall survival (OS). Immune-related signaling pathways were different between C1/C2, and hypoxia was positively correlated with the activation of mammalian target of rapamycin (mTOR) signaling pathway. The model had good accuracy in both the training and the validation sets. The high-risk group exhibited lower OS and TIME activity, and was more sensitive to several anti-tumor drugs. PSMD11/PSMD14 were highly expressed in relapsed patients and AML drug-resistant cell lines. Conclusion: The established novel risk prognostic model and experiment results offer valuable insights for predicting AML prognosis and guiding drug selection. It also provides a fundamental framework for the mechanisms through which hypoxia impacts AML prognosis by modulating TIME and drug resistance.

Unveiling Gene Regulatory Networks That Characterize Difference of Molecular Interplays Between Gastric Cancer Drug Sensitive and Resistance Cell Lines.

Gastric cancer is a leading cause of cancer-related deaths globally and chemotherapy is widely accepted as the standard treatment for gastric cancer. However, drug resistance in cancer cells poses a significant obstacle to the success of chemotherapy, limiting its effectiveness in treating gastric cancer. Although many studies have been conducted to unravel the mechanisms of acquired drug resistance, the existing studies were based on abnormalities of a single gene, that is, differential gene expression (DGE) analysis. Single gene-based analysis alone is insufficient to comprehensively understand the mechanisms of drug resistance in cancer cells, because the underlying processes of the mechanism involve perturbations of the molecular interactions. To uncover the mechanism of acquired gastric cancer drug resistance, we perform for identification of differentially regulated gene networks between drug-sensitive and drug-resistant cell lines. We develop a computational strategy for identifying phenotype-specific gene networks by extending the existing method, CIdrgn, that quantifies the dissimilarity of gene networks based on comprehensive information of network structure, that is, regulatory effect between genes, structure of edge, and expression levels of genes. To enhance the efficiency of identifying differentially regulated gene networks and improve the biological relevance of our findings, we integrate additional information and incorporate knowledge of network biology, such as hubness of genes and weighted adjacency matrices. The outstanding capabilities of the developed strategy are validated through Monte Carlo simulations. By using our strategy, we uncover gene regulatory networks that specifically capture the molecular interplays distinguishing drug-sensitive and drug-resistant profiles in gastric cancer. The reliability and significance of the identified drug-sensitive and resistance-specific gene networks, as well as their related markers, are verified through literature. Our analysis for differentially regulated gene network identification has the capacity to characterize the drug-sensitive and resistance-specific molecular interplays related to mechanisms of acquired drug resistance that cannot be revealed by analysis based solely on abnormalities of a single gene, for example, DGE analysis. Through our analysis and comprehensive examination of relevant literature, we suggest that targeting the suppressors of the identified drug-resistant markers, such as the Melanoma Antigen (MAGE) family, Trefoil Factor (TFF) family, and Ras-Associated Binding 25 (RAB25), while enhancing the expression of inducers of the drug sensitivity markers [e.g., Serum Amyloid A (SAA) family], could potentially reduce drug resistance and enhance the effectiveness of chemotherapy for gastric cancer. We expect that the developed strategy will serve as a useful tool for uncovering cancer-related phenotype-specific gene regulatory networks that provide essential clues for uncovering not only drug resistance mechanisms but also complex biological systems of cancer.