bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 1742: Cediranib reverses taxane resistance in CLIP-170S expressing gastric cancer
Authors: Stone William G. , Castillo Urko del , Thakkar Prashant V. , Shah Manish A. , Giannakakou Paraskevi
Published: April 2023

Taxane-based chemotherapy is a first-line treatment for patients with Gastric Cancer (GC), however, many will not respond due to mechanisms of resistance. Recently, we reported the discovery of a novel truncated variant of the microtubule plus-end binding protein CLIP-170, hereafter CLIP-170S, whose expression is enriched in taxane-resistant cell lines and in 65% of patients with GC, non-responsive to Cabazitaxel monotherapy. CLIP-170S knockdown reversed taxane resistance and its ectopic expression led to resistance, suggesting causation. Computational analysis of RNA-seq data in conjunction with the connectivity map from taxane-sensitive and -resistant GC cell lines, predicted imatinib as the top candidate drug to overcome drug resistance. Imatinib treatment completely reversed taxane resistance, experimentally confirming the prediction, and did so unexpectedly by selective depletion of CLIP-170S. Other RTK inhibitors, such as Sunitinib, Ponatinib, Axitinib, and Cediranib also depleted CLIP-170S, suggesting a class effect, however, the mechanism is unknown. To investigate the mechanism of RTKi induced depletion of CLIP-170S, we sought to investigate the involvement of proteasomal and lysosomal cellular compartments. Preliminary results indicated that treatment of CLIP-170S expressing cells with Imatinib or Cediranib led to an increase in lysosome size, suggesting increased lysosomal activity. In parallel, we are testing in-vivo the synergistic activity of the RTKi, Cediranib, in combination with docetaxel in GC tumors expressing CLIP-170S. Together, these results will allow us to implement a novel clinical trial for patients with GC by using Cediranib as a treatment to increase taxane efficacy through CLIP-170S depletion.

Citation Format: William G. Stone, Urko del Castillo, Prashant V. Thakkar, Manish A. Shah, Paraskevi Giannakakou. Cediranib reverses taxane resistance in CLIP-170S expressing gastric 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 1742.
Abstract 1754: Targeting the mitochondrial protein MAGMAS increases sensitivity to docetaxel in neuroendocrine prostate cancer cells
Authors: Durán Alfonso M. , Yoo Christian H. , Tran Jennifer D. , Santiago Krystal , Mohammed Adil S. , Casiano Carlos A. , Almaguel Frankis A.
Published: April 2023

Metastatic prostate cancer (PCa) is the leading cause of PCa-associated deaths and one of the leading causes of cancer mortality in men. Novel therapeutics, such as Prostate Specific Membrane Antigen (PSMA) ligand therapy, are emerging as effective treatment strategies for metastatic prostate cancer. However, neuroendocrine differentiated (NED) metastatic PCa, which lacks the PSMA antigen, is deprived of effective biomarkers for disease treatment. Magmas, a 13.8 kDa mitochondrial protein, imports nuclear-encoded mitochondrial proteins into the mitochondrial matrix. Magmas is overexpressed in several aggressive tumors, such as breast cancer, glioblastoma, and prostate cancer. When overexpressed, Magmas plays a role as a cytoprotective protein by acting as a reactive oxygen species (ROS) scavenger that maintains sufficient ROS levels to promote cell proliferation, but below the threshold levels that could lead to apoptosis. This study was designed to investigate the pro-survival and therapy-resistance functions of Magmas in PCa cells expressing NED markers. Predictively, we observed that the docetaxel (DTX)-resistant PC3-DR and DU145-DR PCa cell lines expressed significantly higher levels of Magmas compared to their drug-sensitive parental cell lines. We hypothesized that inhibiting Magmas reduces the aggressive properties of highly proliferative DTX- resistant metastatic PCa cell lines and re-sensitize them to DTX. Magmas knockdown in DTX-sensitive and DTX-resistant PC3 and DU145 cells in the presence of increasing DTX treatments enhanced sensitivity to DTX. Consistent with these results, pharmacological inhibition of Magmas with the novel BT#9 inhibitor in combination with increasing DTX concentrations also enhanced sensitivity to DTX in these cell lines. Additional studies using clonogenic assays, cell migration/invasion assays, and tumorsphere formation assays are currently underway to further establish Magmas as a potential therapeutic target to attenuate the aggressive properties of chemoresistant PCa cells. Lastly, we will investigate the diagnostic potential of Magmas as a biomarker for NED and BT#9 as an imaging/therapeutic-specific agent for NED.

Citation Format: Alfonso M. Durán, Christian H. Yoo, Jennifer D. Tran, Krystal Santiago, Adil S. Mohammed, Carlos A. Casiano, Frankis A. Almaguel. Targeting the mitochondrial protein MAGMAS increases sensitivity to docetaxel in neuroendocrine prostate cancer 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 1754.
Abstract 1805: Identification of a small molecule that induces targeted protein degradation of ADAR1
Authors: Liu Yuan , Larsen Mads B. , Lin Bo , Kennerdell Jason R. , Alfaras Irene , Camarco Daniel P. , Tuncer Ferhan , Finkel Toren , Chen Bill B.
Published: April 2023

Adenosine deaminase acting on RNA (ADAR) are a family of enzymes that catalyzes the posttranscriptional conversion of adenosine to inosine in double-stranded RNA (dsRNA). Recent evidence suggests that genetic deletion of ADAR1 render tumors cells substantially more vulnerable to immunotherapy. In cells, ADAR1 is expressed as two different isoforms, the constitutively expressed ADAR1p110 and the inducible ADAR1p150. Evidence suggests that ADAR1p150 is the isoform that confers oncogenic and immune modulating effects in most tumors. Of note, many of the effects of ADAR1p150 appear to be independent of the protein’s RNA editing function suggesting that a small molecule which induces ADAR1p150 targeted protein degradation might be preferable to agents that simply block deaminase activity. We have recently developed a high throughput platform that allows for the identification of ligands that can bind to wide variety of protein targets. Using this approach, we screened a diverse chemical library of 100,000 small molecules to identify compounds that bind to the unique N-terminal region of ADAR1p150. One such molecule, CL-AD-100, directly bound to ADAR1p150 but not ADAR1p110. Moreover, sub-micromolar concentrations of CL-AD-100, induced proteasomal mediated degradation of ADAR1p150, without effecting ADAR1p110 expression. Cells treated with CL-AD-100 exhibited a signature consistent with what has been observed with ADAR1p150 genetic deletion, namely accumulation of dsRNA, an inflammatory gene expression profile and interferon-dependent cell death. These results therefore demonstrate the feasibility of generating a small molecule that induces the specific targeted protein degradation of ADAR1p150. Such a molecule should have wide applicability in ADAR1-addicted tumors, as well as more broadly, in immuno-oncology.

Citation Format: Yuan Liu, Mads B. Larsen, Bo Lin, Jason R. Kennerdell, Irene Alfaras, Daniel P. Camarco, Ferhan Tuncer, Toren Finkel, Bill B. Chen. Identification of a small molecule that induces targeted protein degradation of ADAR1 [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 1805.
Abstract 1819: Integrin inhibitor GLPG-0187 promotes T-cell killing of mismatch repair-deficient colorectal cancer cells by suppression of SMAD/TGF-β signaling
Authors: Verschleiser Brooke , MacDonald William , Carlsen Lindsey , Huntington Kelsey E. , Zhou Lanlan , El-Deiry Wafik
Published: April 2023

Colorectal cancer is the third leading cause of cancer-related death and the third most common cause of cancer. As the five-year survival with advanced metastatic colorectal cancer (mCRC) is 14%, new treatment strategies are needed. Immune checkpoint blockade which takes advantage of an individual's immune system in order to fight cancer, is a promising future direction of research, although it is only effective and approved for the treatment of mismatch repair (MMR)-deficient CRCs. Long-term outcomes even in MMR-deficient mCRC suggest that most patients are not cured but eventually develop therapy resistance. We hypothesized that targeting TGF- β signaling may enhance immune-mediated T-cell killing by MMR-deficient CRC cells. Using GLPG-0187, an inhibitor of multiple integrin receptors and TGF- β, we demonstrate minimal cytotoxicity against MMR-deficient HCT116 or p53-null HCT116 human CRC cells. However, GLPG-0187 promoted significant immune cell killing of the CRC cells by TALL-104 T lymphoblast cells. GLPG-0187 reduced pSMAD2 in HCT116 p53-null cells either in the absence or presence of exogenous TGF- β. We observed a reduction in CCL20, CXCL5, prolactin, and TRAIL-R3 while GDF-15 was increased in TALL-104 cells treated with a T-cell activating dose of GLPG-0187 (4 μM). Our results suggest that TGF- signaling inhibition by a general integrin receptor inhibitor may boost T-cell killing of MMR-deficient colorectal cancer cells, and suggest that a combination of anti-GDF-15 in combination with TGF- β blockade should be further investigated in the treatment of MMR-deficient mCRC. Our results support the development of a novel immune-based therapeutic strategy to treat colorectal cancer by targeting the TGF-β signaling pathway through integrin receptor blockade.

Citation Format: Brooke Verschleiser, William MacDonald, Lindsey Carlsen, Kelsey E. Huntington, Lanlan Zhou, Wafik El-Deiry. Integrin inhibitor GLPG-0187 promotes T-cell killing of mismatch repair-deficient colorectal cancer cells by suppression of SMAD/TGF-β signaling [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 1819.
Abstract 1824: Discovery and evaluation of an anti-IL18BP antibody to enhance anti-tumor immunity
Authors: Jun H. Toni , Witherden Deborah A. , Elliot Eric K. , Chidester Christine M. , Willen Maggie , Peguero Bryan R. , Chai Merrick , Horlick Robert A. , King David J.
Published: April 2023

Interleukin-18 (IL18) is a proinflammatory cytokine that modulates both innate and adaptive immune responses. Although recombinant mIL18 has demonstrated efficacy in mouse tumor models, recombinant human IL18 has not been efficacious in clinical studies, likely due to upregulation of IL18 binding protein (IL18BP), a negative regulator of the IL18 signaling axis. IL18BP is induced 10 - 100 fold after IL18 administration, binds to IL18 with high affinity, and prevents IL18 binding to the IL18 receptor. Analysis of expression data from the TCGA database as well as archived patient samples from select indications revealed that both IL18 and IL18BP are co-expressed in a number of tumor types, suggesting there may be a preexisting pool of IL18/IL18BP complex at the site of the tumor in some patients. Inhibition of IL18/IL18BP binding using a monoclonal antibody may therefore allow release of IL18 in situ, leading to IL18-mediated proinflammatory effects and enhanced anti-tumor immunity. Although the interaction of IL18 with IL18BP is a high affinity interaction, we have been able to identify very high affinity antibodies which can both inhibit complex formation and disrupt existing mouse IL18/IL18BP complexes. These antibodies are active in a number of cell-based functional assays, resulting in potent stimulation of interferon gamma production from cell lines or splenocytes. In vivo, we observed efficacy in a mouse syngeneic tumor model using an anti-mIL18BP antibody. RNA and protein analysis demonstrated expression of both IL18BP and IL18 within the tumors. Combined, these data suggest that inhibition of IL18/IL18BP binding may prove efficacious in the treatment of cancers where existing pools of IL18/IL18BP complexes prevent an IL18-mediated proinflammatory response. Experiments exploring anti-IL18BP therapy in combination with other checkpoint inhibitors such as anti-PD-1 are under current investigation.

Citation Format: H. Toni Jun, Deborah A. Witherden, Eric K. Elliot, Christine M. Chidester, Maggie Willen, Bryan R. Peguero, Merrick Chai, Robert A. Horlick, David J. King. Discovery and evaluation of an anti-IL18BP antibody to enhance anti-tumor immunity [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 1824.
Abstract 1831: A long-acting and CD122-enhanced IL-2 analog, HM16390, synergizes with immune checkpoint inhibitor by remodeling an immune cell profile in tumor microenvironment
Authors: Choi Jaehyuk , Kim Jinyoung , Kim Yu Yon , Jeong Seongju , Bae Sungmin , Kim Daejin , Choi In Young
Published: April 2023

Immune checkpoint inhibitors (CPI) are widely used for cancer immunotherapy. However, the response to CPIs is dependent on phenotype of tumor microenvironment (TME). A cold tumor known as immune-excluded or -desert has shown poor response to CPIs due to an absence of effector T cells in TME. IL-2 analog, which is immune stimulator and able to recruit cancer-fighting cells into TME, may be promising therapeutic partner for overcoming a limitation of CPIs. Previously, HM16390, a long-acting CD-122-enhanced IL-2 analog, exerted dose-dependent anti-tumor activity in low immunogenic B16F10 melanoma mice. Here, we further investigated the immune cells composition in TME following HM16390 treatment and synergistic anti-tumor effect after combination with CPI. B16F10 mice were sacrificed at days 1, 3, and 8 following single subcutaneous administration of HM16390 or 5 consecutive daily administrations of aldesleukin. According to the result, HM16390 transiently increased peripheral cytokines (IFNγ and TNFα) more than aldesleukin. In line with this, we observed that the tumor-infiltrating NK/Treg ratio was significantly increased approximately 19 by treatment of HM16390 while showing 4.2 in aldesleukin treated group at Day 3. Furthermore, tumor-infiltrating CD8+/Treg ratio was also upregulated approximately 74 by treatment of HM16390 while only showing 6.1 in aldesleukin treated group at Day 8. Significantly increased pro-inflammatory molecules such as GrzB and IFNγ were also observed in HM16390 treated group compared to aldesleukin (p<0.01 and p<0.001, respectively). Next, we investigated synergistic anti-tumor effects in combination with CPI. B16F10 mice were repeatedly given HM16390 once a week or aldesleukin 5 consecutive days per week with or without mouse anti-PD1. After four weeks treatment, 25% of B16F10 mice showed complete response by treatment of HM16390, and significantly increased up to 88% by combination with anti-PD1. However, none of the mice showed complete response by treatment of aldesleukin/anti-PD1 combo. In conclusion, HM16390 effectively induced tumor growth inhibition through the activation and tumor infiltration of cytotoxic lymphocytes. This favorable immune alteration in tumor elicited a TME remodeling in which CPI could sufficiently respond.

Citation Format: Jaehyuk Choi, Jinyoung Kim, Yu Yon Kim, Seongju Jeong, Sungmin Bae, Daejin Kim, In Young Choi. A long-acting and CD122-enhanced IL-2 analog, HM16390, synergizes with immune checkpoint inhibitor by remodeling an immune cell profile in tumor microenvironment [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 1831.
Abstract 1906: MSH3: An underestimated DNA MMR gene in colorectal carcinogenesis and its potential role in disparity
Authors: Rashid Mudasir , Rashid Rumaisa , Koi Minoru , Carethers John M. , Brim Hassan , Ashktorab Hassan
Published: April 2023

Background: Unique mutations in cancer genes have been found in different races including African Americans (AA) population. Maintenance of proficient mismatch repair genes is important in colorectal cancer. Among them, MSH3 is found to be more important in colorectal cancer in AA particularly as its alterations associate with EMAST phenotype that has poor prognosis. However, there are regional variations in the classification and criteria used to determine the pathogenicity of these mutations particularly in AA due to their high genomic diversity. Aim: To analyze unique and novel MSH3 mutations using specific in-silico prediction tools and to validate their biological significances in AA-CRC. Results: In this study, we validated our targeted exome sequencing data of MSH3 mutations in AA and Caucasians (CA) CRC samples. A cost effective in-silico approach was employed to narrow down most significant MSH3 mutations. Interestingly, we and found six non-synonymous novel, pathogenic mutations in MSH3 gene (c.G1237A, c.C2759T, c.G1397A, c.G2926A, c.C3028T, c.G3241A) correspond to MSH3 protein (E413K; S466N; S920F; E976K; H1010Y; E1081K), in AA than CA samples. Also, we observed loss or gain of different chemical bonding patterns (hydrogen, ionic, hydrophobic, and di-sulfide bonding) between wild type and mutant MSH3 protein. Interestingly, some of these mutations were within the ATPase site while others are in MSH3-MSH2 interacting domains. Furthermore, Molecular Dynamics Simulation (MDS) of these six mutants of MSH3 proteins showed an overall effect on MSH3 protein stability especially in MSH3-MSH2 interaction compared to wild type MSH3 protein.Conclusion: Our data showed that, six MSH3 non-synonymous mutations are deleterious as they affect important sites within MSH3-MSH2 interactive and ATPase domain. Assessing the real frequency of these mutations in large cohort and their specific effect on function may shed light on EMAST phenotype, high prevalence, and overall poor prognosis in the AA population. In vitro functional assays using CRISPR-Cas9 knock-in and in vivo studies are underway to mimic these mutations.

Citation Format: Mudasir Rashid, Rumaisa Rashid, Minoru Koi, John M. Carethers, Hassan Brim, Hassan Ashktorab. MSH3: An underestimated DNA MMR gene in colorectal carcinogenesis and its potential role in disparity [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 1906.
Abstract 1953: Association between genetic ancestry and all-cause mortality among Black and White ever-smokers in the PLCO cohort
Authors: Dill Courtney D. , Crump Dontray , Landy Rebecca , Cheung Li C. , Huang Wen-Yi , Berndt Sonja , Freedman Neal , Katki Hormuzd
Published: April 2023

Introduction: It is unknown how much of the increased all-cause mortality risk in Black individuals who ever-smoked is due to race as a social construct versus biological factors such as genetic ancestry. We examined the association of genetic ancestry with all-cause mortality, controlling for risk factors and self-reported race/ethnicity, in the PLCO cohort.

Methods: We used PLCO data from 52,708 White individuals who ever-smoked (18281 deaths) and 2,585 Black individuals who ever-smoked (1108 deaths). Genetic ancestry was determined by GRAF (https://github.com/ncbi/graf) on a set of 10,000 pre-selected fingerprinting variants. Percent ancestry for each of Europe, Africa, and East-Asia was determined for each person. We fit Cox models for time to death, controlling for smoking history and other risk factors.

Results: Self-reported Black individuals who ever-smoked had increased all-cause mortality versus self-reported White individuals who ever-smoked (HR=1.14, 95%CI: 1.07-1.22, p=0.00007). For White individuals, increases in European ancestry were associated with increased death risk, (HR=1.009 per 1% increase in European ancestry, 95%CI:1.003-1.015, p=0.002). HRs for European ancestry, by quartile, were 1.040, 1.061 and 1.063, with the last two HRs demonstrating statistical significance (95%CI:1.0018-1.106, p = 0.005, and 95%CI:1.020-1.108, p=0.004), respectively. For Black individuals, increases in African ancestry were associated with increased death risk, (HR=1.003 per 1% increase in African ancestry, 95%CI: 0.998-1.008, p=0.214), although not statistically significant. HRs for African ancestry, by quartile, were 1, 1.16, 1.14, and 1.21, with the last HR demonstrating statistical significance (95%CI:1.010-1.450, p = 0.03).

Conclusions: For self-reported White individuals who ever-smoked, increasing European ancestry was associated with an increased all-cause mortality risk. For self-reported Black individuals who ever-smoked, there was suggestive evidence that increasing African ancestry may increase all-cause mortality risk. However, associations with ancestry were small and may be vulnerable to residual confounding.

Impact/Significance: A mechanistic explanation for this finding is unclear, but it could be related to population genetic “fitness” with reduced genetic admixture leading to decreased fitness for survival.

Citation Format: Courtney D. Dill, Dontray Crump, Rebecca Landy, Li C. Cheung, Wen-Yi Huang, Sonja Berndt, Neal Freedman, Hormuzd Katki. Association between genetic ancestry and all-cause mortality among Black and White ever-smokers in the PLCO cohort [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 1953.
Abstract 1965: Racially divergent mitochondrial ND5 gene mutation promotes prostate cancer progression and confers therapeutic resistance
Authors: Vikramdeo Kunwar Somesh , Keel Christopher E. , Heslin Martin J. , Singh Seema , Singh Ajay Pratap , Dasgupta Santanu
Published: April 2023

Compared to European American (EA), African American (AA) men often develop lethal forms of prostate cancer (PCa) and experience high mortality despite having a primary diagnosis of low-risk indolent disease. Understanding the molecular basis of this disparity is thus a dire need for better prevention, accurate monitoring, and guided therapeutics. Aggressive cancer growth is intimately associated with the reprogramming of metabolism and apoptosis, where mitochondrial DNA (mtDNA) alterations play a critical role. In the mitochondrial energy generation cascade, respiratory complex I (RCI) serves as the entry gate to initiate electron transfer through the oxidative phosphorylation system (OXPHOS). Alteration in RCI function could alter metabolism and attenuate apoptosis, hallmarks of malignant progression. Through next-generation sequencing of the entire mitochondrial genome, we identified a prevalence of RCI gene mutations in the AAPCa compared to the EAPCa patients. Among the RCI mutations, a homoplasmic 13709C>G mutation in NADH dehydrogenase 5 (ND5) was identified as the most frequently occurring mtDNA mutation among AA men. Forced expression of the 13709C>G mutation in the mitochondria of the AA-PCa patient-derived MDA PCa 2b and EA-PCa patient-derived LNCaP cells, remarkably enhanced their growth and malignant potential. The increased tumorigenicity was associated with a significant increase in the production of mitochondrial reactive oxygen species (ROS), O2 consumption, overall respiration, and ATP production. The ND5-mutant PCa cells exhibited remarkable resistance to androgen deprivation and docetaxel treatment. Induction of CXCR4, HIF-1α, and NF-kB was also noted in these ND5-mutant PCa cells. In clinical tissue samples, an abundance of CXCR4 protein expression was evident in AA-PCa patients harboring ND5 gene mutation but not in the AA or EA-PCa patients with wild-type ND5. Blockade of CXCR4 expression in the ND5-mutant PCa cells diminished NF-kB activity, thereby suggesting a potential role of the CXCR4/HIF-1α/NF-kB signaling axis in ND5 mutation-driven PCa tumorigenesis. The RCI-ND5 could be an attractive target for therapeutic and biomarker development for the better management of PCa in racially disparate populations.

Citation Format: Kunwar Somesh Vikramdeo, Christopher E. Keel, Martin J. Heslin, Seema Singh, Ajay Pratap Singh, Santanu Dasgupta. Racially divergent mitochondrial ND5 gene mutation promotes prostate cancer progression and confers therapeutic resistance [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 1965.
Abstract 1977: Body mass index genetic risk score and obesity related cancer risk in Black and White adults
Authors: Katzmarzyk Peter T. , Yang Shengping , Brown Justin C. , Mire Emily F. , Zabaleta Jovanny
Published: April 2023

A total of 13 cancers are known to be strongly associated with obesity. The purpose of this study was to examine the association between a composite genotype risk score (GRS) for high body mass index (BMI) and the odds of obesity-related cancer. A nested case-control study was created within the Pennington Center Longitudinal Study, an ongoing prospective cohort study of the effects of obesity and lifestyle factors on the development of chronic diseases and premature mortality in Black and White Americans. A total of 459 participants developed an obesity-related cancer, and after stratification by sex and race, incidence density sampling was applied to select matched control participants (2:1) of the same age as cases (± 2 y). After deletion of participants with missing data, the analytic sample included 1242 participants (435 cases;136 Black, 299 White). A BMI GRS was derived using 21 single nucleotide polymorphisms (SNPs) with consistent evidence of association from the literature and which showed concordant associations in effect size and direction in our cohort. The GRS score was computed by summing the number of BMI risk alleles. In a model including age, race, sex, exam year and smoking as covariates, the BMI GRS was significantly associated with obesity-related cancer [odds ratio (OR): 1.18; 95% confidence interval: 1.04, 1.34; p=0.01]. Further adjustment for BMI did not change the association [1.20; 1,06-1.36; p=0.004]. In conclusion, the BMI GRS appears to provide added value in identifying obesity-related cancer risk, even after adjustment for BMI. Future studies are required to validate these results and better delineate the phenotypic and genetic contributions of BMI to obesity-related cancer risk.

Citation Format: Peter T. Katzmarzyk, Shengping Yang, Justin C. Brown, Emily F. Mire, Jovanny Zabaleta. Body mass index genetic risk score and obesity related cancer risk in Black and White adults [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 1977.
Abstract 1987: Delivery of potent cytotoxic camptothecin derivatives to tumors by OncoFAP-based small molecule-drug conjugates
Authors: Bocci Matilde , Cazzamalli Samuele , Neri Dario , Galbiati Andrea
Published: April 2023

Small Molecule-Drug Conjugates (SMDCs) are anti-cancer pro-drugs composed by a tumor-targeting small organic ligand, a linker structure and a potent cytotoxic payload. OncoFAP is an ultra-high affinity ligand of Fibroblast Activation Protein (FAP), a stromal protein overexpressed in multiple types of solid human malignancies. Nuclear medicine studies validated the applicability of the OncoFAP technology for tumor-targeting applications in a wide variety of tumor types. We have recently reported the development of SMDC products in which OncoFAP is used to deliver Monomethyl Auristatin E (MMAE) to tumors, exploiting linkers that are selectively cleaved by FAP. Here we describe the generation and in vivo characterization of novel OncoFAP-based SMDC products bearing potent camptothecin derivatives acting as topoisomerase I inhibitors. Those drug payloads have been already included in approved ADC products (EnhertuTM and TrodelvyTM). The FAP-cleavable linker technology was directly compared against linker strategies used for approved ADCs. Therapy results in preclinical xenograft models of solid tumors revealed that SMDC products activated by FAP show superior anti-cancer activity and deserve industrial development for the treatment of various human solid tumors.

Citation Format: Matilde Bocci, Samuele Cazzamalli, Dario Neri, Andrea Galbiati. Delivery of potent cytotoxic camptothecin derivatives to tumors by OncoFAP-based small molecule-drug conjugates [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 1987.
Abstract 1989: DNA-encoded affinity maturation libraries enable the discovery of low picomolar fibroblast activation protein inhibitors suitable for radioligand therapy of solid tumors
Authors: Puglioli Sara , Prati Luca , Oehler Sebastian , Galbiati Andrea , Neri Dario , Cazzamalli Samuele , Bassi Gabriele , Favalli Nicholas
Published: April 2023

The discovery of potent ligands highly specific to accessible cancer-associated antigens is essential for the development of small molecule therapeutics with broad therapeutic index. DNA-encoded chemical libraries (DELs) can be used to discover novel binders and to improve binding affinity of existing small organic ligands by affinity maturation procedures. OncoFAP is a 680 pM inhibitor of the stromal pan-tumoral antigen Fibroblast Activation Protein (FAP). OncoFAP displays best-in-class tumor targeting performance in patients, although its relatively short half-life limits the applicability as radioligand therapeutic against solid malignancies. We designed three focused affinity maturation DELs, containing 50,730 compounds bearing two sets of building blocks coupled to a propargylglycine central scaffold. Library selections against FAP from multiple species enabled the discovery of novel FAP inhibitors with potencies in the low picomolar range. 177Lu-DOTAGA conjugates of the most potent novel ligands (named “OncoFAP-11” and “BiOncoFAP-11”) localized to tumors implanted in mice, with excellent tumor-to-blood and tumor-to-kidney ratios at late time-points after systemic administration. The high affinity FAP ligands described here enable the efficient delivery of therapeutic radionuclides to tumors with long residence time and with low uptake in normal tissues. The results presented here show that DEL-based affinity maturation procedures can lead to the improvement of the targeting performance of FAP binders, without compromising their tumor selectivity.

Citation Format: Sara Puglioli, Luca Prati, Sebastian Oehler, Andrea Galbiati, Dario Neri, Samuele Cazzamalli, Gabriele Bassi, Nicholas Favalli. DNA-encoded affinity maturation libraries enable the discovery of low picomolar fibroblast activation protein inhibitors suitable for radioligand therapy of solid tumors [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 1989.
Abstract 2033: Assessment of human reference genomes on cancer somatic mutation detection in tumor-normal paired reference samples using whole genome short-read sequencing data
Authors: Xiao Chunlin , Schneider Valerie
Published: April 2023

A typical cancer somatic mutation identification workflow involves using a standard human reference genome for aligning the sequencing reads and annotating the uncovered somatic variants. The completeness and the correctness of the reference genome, and the haplotype representations may all impact the sequencing read alignments and subsequent somatic variant identifications. However, the exact impacts of the underlying references being used on somatic mutation analysis has not been investigated. In this study, we selected 3 human reference genomes, including GRCh38, T2TCHM13, and a personalized genome (PG) that was derived from a normal cell line, and 12 tumor normal paired replicates of Illumina short read sequencing data for the HCC1395 breast cancer cell line and a matched normal cell line, and aim to illustrate and quantify the effects of the reference genomes on the accuracy of somatic SNV/SV mutation detection using various somatic variant callers. Our analysis shows that the use of a personalized haplotype-specific genome assembly, rather than an unrelated genome such as GRCh38 or T2TCHM13 as a reference, not only improves read alignments for short-read sequencing data but also ameliorates the detection accuracy of somatic SNVs and SVs. While most somatic mutation calls are identical or equivalent, we identify GRCh38 and T2TCHM13 specific somatic mutations that may need to be avoided for further pursuit of incorrect treatment options. We uncover novel somatic mutations only when personalized genome assembly is used as a reference, some of which overlap with genes involving with pathways related to cancer invasion and metastasis (e.g., CDH23, ST14 etc.). The predicted somatic SVs are found more precise. Such results may provide additional interventional target choices for patients, researchers or clinicians, and physicians to look into further for personalized patient care.

Citation Format: Chunlin Xiao, Valerie Schneider. Assessment of human reference genomes on cancer somatic mutation detection in tumor-normal paired reference samples using whole genome short-read sequencing data [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 2033.
Abstract 2052: High-plex spatial multiomics of pediatric and adult diffuse midline glioma, H3 K27-altered
Authors: Damodharan Sudarshawn , Rosenbloom Alyssa , Dey Mahua
Published: April 2023

Background: Diffuse midline glioma (DMG), H3 K27-altered are highly aggressive malignancies of the central nervous system that affect both pediatric and adult populations. The immune layout and genetic changes within the tumor microenvironment associated with these high-grade malignancies are thought to play an integral role in the phenotypic differences in tumor presentation and clinical course between both populations. Comparative landscapes between pediatric and adult DMGs is not known.

Methods: The NanoString GeoMxTM Digital Spatial Profiler platform was used to determine the immune marker and genetic layout in a cohort of both pediatric and adult DMG, H3 K27-altered tissue samples. Three fluorescently labeled antibodies targeting immune cells (CD45), epithelial cells (PanCK), tumor cells (H3 K27M) and a nucleic acid stain (SYTO-13) were used to identify and separate out the various components within the tumor tissues from selected regions of interest. The resultant information was then pooled into libraries that were run through the Illumina sequencing platform to assess transcriptomic and proteomic data for both cohorts of samples.

Results: Our data revealed the immune and genetic expression seen within both populations across multiple regions of interest within the samples. Differences were seen specific to each population that may have clinical significance and warrant further exploration including a significant increase in genes associated with RTK pathways in the pediatric samples.

Conclusion: The digital spatial analysis of pediatric and adult DMG, H3 K27-altered shows differences within the molecular landscape which may contribute to the clinical differences between both populations. These observed differences may play a role in future treatments and further research is needed to explore this.

Citation Format: Sudarshawn Damodharan, Alyssa Rosenbloom, Mahua Dey. High-plex spatial multiomics of pediatric and adult diffuse midline glioma, H3 K27-altered [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 2052.
Abstract 2058: Identifications of novel variants using system biology-based approaches in NT5C2, its association to relapse acute lymphoblastic leukaemia
Authors: V Sugunakar , Bandapalli Obul Reddy , Sharma Ramita
Published: April 2023

Acute Lymphoblastic Leukaemia (ALL) patients experience relapse despite having a good prognosis; approximately 90% of children and 75% to 85% of adolescents and young adults survive for five years. Chemotherapy resistance and a poor prognosis are linked to relapsed acute lymphoblastic Leukaemia (R-ALL). Evidence suggests that the cytosolic 5 nucleotidase II (NT5C2) gene mutations play a crucial role in the emergence of recurrent ALL; The early R-ALL is usually accompanied by 6-MP resistance, which is typically brought on by gain-of-function mutations impacting NT5C2-driven mutation in relapse mutations by different mechanisms is still unknown. The study aims to identify novel top missense variants of NT5C2 that play a crucial role in the resistance of chemotherapy drugs, altered biological pathways and their impact on the treatment of relapse leukaemia. NT5C2 (5'-Nucleotidase, Cytosolic II) is a Protein Coding gene. This gene induces resistance to chemotherapeutic drug 6 mercaptopurine Which causes leukaemia cell growth and leukaemia-initiating cell activity. The NT5C2 gene variants are extracted from Genome Aggregation Database (gnomAD) and ExAC. The extracted data contained 2280 variants with chromosome number, position reference allele, and altered allele and these were functionally annotated using the ANNOVAR tool. The variants are screened through various computational tools to narrow down based on non-synonymous and stopgain mutations in the exonic region. The predicted 519 variants narrow down by scoring GERP (>2.0) and CADD PHRED (cut-off score >10), ClinVar, SIFT score, Polyphen, PhyloP, PhastCons, LRT score predictions and which indicates the top 10% deleterious variants including reported and unknown variants. The SNPs, insertions, deletions, CNVs or structural variants of top missense variants on genes, transcripts, and protein sequence determined on Variants Effect Predictor on the ensemble. These variants were verified on dbSNP and Clinvar through their variant IDs. The functional prediction of these variants was made to detect their significant role in R-ALL. These findings examine the future role of NT5C2 mutations in the chemoresistance of relapse ALL. This may help to find a new therapeutic combination of drugs to treat relapse acute lymphoblastic leukaemia to improve overall survival.

Citation Format: Sugunakar V, Obul Reddy Bandapalli, Ramita Sharma. Identifications of novel variants using system biology-based approaches in NT5C2, its association to relapse acute lymphoblastic leukaemia [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 2058.
Abstract 2086: ISCVAM, an Interactive Single Cell Visual Analytics for Multiomics, accelerates the identification of novel rare cell populations
Authors: Nguyen Thanh N. M.
Published: April 2023

BACKGROUND Emergent single cell technologies have accelerated the discovery of rare cell populations and characterization of complex tumor microenvironment (TME). We developed an Interactive Single Cell Visual Analytics for Multiomics, ISCVAM, a bioinformatics infrastructure to integrate and visualize high-dimensional sparse multiome single cell data.

METHODS We built an interactive tool, ISCVAM with react.js for the web frontend, and node.js in the backend, with a data bridge to portable HDF5 storage. Commonly used R packages including Seurat, Signac, SingleR, and scType, were used offline for data processing and analyses. We investigated cell populations using two Multiome datasets for proof of principle:1) ~22K cells from the matched pairs of sorted CD8+Tissue resident memory (TRM) and recirculating (ReCir) T cells from 4 ovarian cancer patients in (Anadon, Yu et al. 2022) and 2) ~11K cells from a PBMC sample (from 10X Genomics).

RESULTS ISCVAM enables users to investigate both user-defined markers in multiple modalities (RNA and ATAC) individually and jointly (through weighted nearest neighbor), in different dimension reduction projections and on multiple panels. It also allows discovery of novel signatures of unidentified cell populations using unsupervised clustering algorithms in multiple resolutions. Using the paired TRM and ReCir samples from a single patient as the discovery set, ISCVAM identified a small cluster of mucosal-associated invariant T (MAIT) cells with unique gene and open chromatin peak profiles in both samples (2.18% of the ReCir T cells and 1.50% of the TRM T cells), which was not reported in the original study. Using the identified signature (with SLC4A10, TLE1 and their linked peaks), the MAIT cells were observed in remaining 6 ovarian samples (5.39 ±4.05% cells in 3 ReCir samples and 1.05 ± 1.02% cells in 3 TRM samples) from the same study. The markers are robust and also validated in an independent PBMC 10X Genomics dataset.

CONCLUSION The tool ISCVAM enables the discovery of rare immune cell populations by integrating transcriptional and epigenic profiles simultaneously at multiple resolutions. This information rich tool with multiple panels and modalities with high interactivity enables rapid identification of rare cell populations. This will accelerate the understanding of complex TME in cancer research.

Citation Format: Thanh N. M. Nguyen. ISCVAM, an Interactive Single Cell Visual Analytics for Multiomics, accelerates the identification of novel rare cell populations [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 2086.
Abstract 2179: The role of ATP-binding cassette transporter A5 in colorectal cancer progression
Authors: Bajbouj Khuloud , Alketbi Latifah , Hamid Qutayba , Talaat Iman
Published: April 2023

Background: Colorectal cancer (CRC) is one of the most common malignancies worldwide; it is the fourth leading cause of cancer-related deaths. The lack of novel diagnostic and therapeutic targets and the development of chemoresistance are major issues when dealing with CRC. The overexpression of ATP-binding cassette (ABC) transporters is considered one facilitating mechanism for chemoresistance. Furthermore, several ABCA superfamily transporters have been shown to mediate cancer development and multidrug resistance. However, the role of ABCA5 in CRC development and progression is elusive. The current study aimed at profiling the expression of ABCA5 at the different grades of CRC.

Experimental Methods: Forty-nine (9 Well differentiated, 26 moderately differentiated and 14 poorly differentiated) primarily diagnosed CRC cases, and 15 normal colonic tissues were included in the study. Formalin-fixed paraffin-embedded samples were interpreted for the differential expression of ABCA5 by immunohistochemistry. The immunoreactivity of ABCA5 was assessed in the cells based on the staining intensity and the percentage of the positively stained cells to create the immunoreactive score.

Results: In total, 49 CRC cases were recruited, with a mean age of 63.77 years (range 33-86); 21 female and 28 male patients. All specimens were diagnosed as adenocarcinoma (NOS). Immunohistochemical analysis of the 49 CRC samples revealed diffuse ABCA5 immunoreactivity in the majority of cases. Seven cases showed mild expression, 25 showed moderate expression, whereas 17 cases revealed intense ABCA5 expression. Intriguingly, negative to a mild expression of ABCA5 was noted in the normal colonic tissues. ABCA5 intensity was higher in poorly differentiated CRC compared to the other grades.

Conclusion: Higher expression of ABCA5 is associated with CRC differentiation, indicating that it might contribute to CRC development and progression. Thus, it may be a novel diagnostic biomarker.

Citation Format: Khuloud Bajbouj, Latifah Alketbi, Qutayba Hamid, Iman Talaat. The role of ATP-binding cassette transporter A5 in colorectal cancer progression [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 2179.
Abstract 2185: Septin isoform expression as a potential biomarker for differential response to microtubule targeted chemotherapy in breast cancer
Authors: Essif Jacob N. , Yee Samantha S. , Risinger April
Published: April 2023

The primary cause of cancer-associated death is due to the development of metastatic disease. Metastasis is a multistage process requiring displacement of cells from the primary tumor, survival in circulation, and adhesion and growth in a secondary location. Reorganization of both the actin and microtubule cytoskeleton is critical for metastasis of solid tumors. Drugs that inhibit microtubule dynamics, including microtubule stabilizers and destabilizers, are used to treat metastatic breast cancer, however there is no rationale to guide the choice among these drugs. Septins, a class of small GTPases, interact with both microtubules and actin to functionally link these cytoskeletal components. Expression of a specific isoform, septin9_i1, is associated with breast cancer development, migration, and drug resistance. This isoform is unique among septins in that it contains a specific microtubule binding domain required for association of septins with microtubules. We found that microtubule stabilizing or destabilizing chemotherapeutics currently used to treat metastatic breast cancer promoted respective microtubule or actin localization of oncogenic septins, particularly when septin9_i1 was expressed. This differential cellular distribution correlated with our finding that microtubule destabilizers were more effective than stabilizers at inhibiting the migration of septin9_i1 expressing breast cancer cells in vitro whereas the drugs were equally effective in isogenic cells depleted of septin9_i1. We are currently testing the hypothesis that septin9_i1 promotes in vivo metastasis of breast tumors and that microtubule destabilizers will be more effective than stabilizers at inhibiting this metastasis. This supports our ongoing clinical investigations to determine whether septin9_i1 expression could be used as a predictive biomarker to guide the selection among microtubule-targeted chemotherapeutics, which is significant as there is currently no molecular guidance to inform on this choice. Our findings will promote the more targeted and rational use of this highly used but mechanistically underappreciated class of chemotherapy.

Citation Format: Jacob N. Essif, Samantha S. Yee, April Risinger. Septin isoform expression as a potential biomarker for differential response to microtubule targeted chemotherapy in breast 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 2185.