bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 237: Coincidence of InDels with missense mutations: 0, 1 or 2 artifacts
Authors: Craven Kelly E. , Fischer Catherine G. , Jiang LiQun , Pallavajjala Aparna , Lin Ming-Tseh , Eshleman James R. 
Published: April 2023

Abstract
The purpose of this study was to explain a serendipitously discovered next generation sequencing (NGS) artifact. While reviewing clinical cases, we found a case of a large deletion that also contained multiple missense mutations. This phenotype was unknown to several molecular pathologists in our group. We reviewed 46 clinical cases with short insertions or deletions (InDels) (1-30 bases) or FLT3 internal tandem duplications (ITDs) (6-183 bases) of solid or hematologic malignancy processed with a clinical NGS assay and identified misaligned reads, ranging from 3 to 100% of reads showing mismapped bases. Reads that straddled the InDel with sufficient numbers of bases on both sides were correctly anchored both upstream and downstream of the InDel, and were called correctly. However, reads that ended in the middle of the InDel were incorrectly mapped onto the deletion, thereby producing artifactual missense mutations. The frequency of mismapped bases increased with InDel size, and the VAF of the InDel can be markedly underestimated. The ratio of forward to reverse reads was commonly skewed for the mismapped base compared to the ratio for the wildtype base at that position. ABRA2 was able to correct 41 to 100% of the reads with mismapped bases and led to absolute increases in the VAF from 1 to 61% along with correction of all of the SBSs except for two cases. Knowledge of the various artifacts commonly seen in next generation sequencing is essential to safely sign out molecular pathology cases.
Citation Format: Kelly E. Craven, Catherine G. Fischer, LiQun Jiang, Aparna Pallavajjala, Ming-Tseh Lin, James R. Eshleman. Coincidence of InDels with missense mutations: 0, 1 or 2 artifacts [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 237.
Abstract 2414: Early biological impacts of radiotherapy-activated NBTXR3 nanoparticles
Authors: Silva Jordan Da , Bienassis Célia , Paris Sebastien 
Published: April 2023

Abstract
Since many decades, radiotherapy (RT) is worldwide used and crucial therapeutic approach for the treatment of cancers. Nowadays, about 50% of cancer patients will receive radiotherapy during their treatment. Nevertheless, the use of RT is limited by the damage induced by ionizing radiation on healthy tissues. To overcome this constraint, we have developed high electron density of functionalized hafnium oxide nanoparticles (NBTXR3), allowing a high probability of interaction with incoming ionizing radiation, increasing energy dose deposit within cells. Many preclinical data have shown that RT-activated NBTXR3 (NBTXR3+RT) increase cancer cell destruction as well as better control treated tumor growth, compared to RT alone. In clinic, the benefit of NBTXR3+RT compared to RT alone has been demonstrated for patients with locally advanced Soft Tissue Sarcoma, in the randomized controlled phase II/III Act.in.Sarc study (NCT02379845). We also demonstrated in preclinical settings that, beyond the destruction of tumor cells, NBTXR3+RT was also able to induce an antitumor immune response capable to produce a significant abscopal effect, linked to the increase of CD8 infiltrates in tumors. It has been recently reported that NBTXR3+RT can also restore anti-PD1 efficacy in an anti-PD1 resistant mouse model. At the cancer cell level, we reported that NBTXR3+RT could modulate the immunopeptidome of cancer cells, induce the activation of the cGAS-STING pathway and increase the expression of ICD biomarkers. All these data indicate that NBTXR3+RT has the ability to transform the tumor into an in situ vaccine more efficiently than RT alone and could have important implications for the use of NBTXR3+RT in combination with immunotherapy. Nevertheless, we currently have relatively few elements on the early cellular events that could trigger or explain the above reported performances of NBTXR3+RT, compared to RT alone. To address this question, we have carried out a series of in vitro studies (cytometry, microscopy) on different cancer models (human and murine). We have thus identified that the vast majority of NBTXR3 nanoparticles are located in lysosomes after endocytosis by tumor cells. Once activated by RT, we detected lysosomal membrane permeabilization (LMP) only in cells treated with NBTXR3+RT, but not in cells only treated by RT. Following LMP, we measured a significant increase of in lipid peroxidation. These first elements allow a better understanding of the early biological consequences induced by NBTXR3+RT, compared to RT alone.
Citation Format: Jordan Da Silva, Célia Bienassis, Sebastien Paris. Early biological impacts of radiotherapy-activated NBTXR3 nanoparticles [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 2414.
Abstract 2417: Liver regeneration after radiation therapy: clinical observations and a new rat model
Authors: Su Tingshi , Zhao Weidong , Li qing , Wu Qiaoyuan 
Published: April 2023

Abstract
Background and Purpose: Radiation-induced liver damage, a dose-limiting complication of radiotherapy for liver tumors, has been focused mainly on prevention and treatment but has largely ignored the molecular mechanisms underlying the liver’s regenerative capacity after irradiation. Whether liver regeneration compensates for radiation-induced liver damage is of great clinical significance. This study aims to observe clinical liver regeneration and the potential molecular mechanism in rat models after irradiation.
Methods: To stimulate the liver regeneration response, we delineated a liver protection area in the patient’s normal liver to protect it from excessive irradiation, and designed a rat model in which large single fractions of 25 Gy or 15 Gy of radiation were delivered to 1/2 or 2/3 of the total liver volume to investigate liver regeneration after irradiation. We used proteomics analysis and western blotting assays to investigate liver regeneration signaling and molecular mechanisms.
Results: Four patients’ pairs of liver specimens from areas of high irradiation and regeneration (protected liver) were collected. Proteomics analysis showed enrichment in several pathways, with some of the greatest changes observed in PI3K-Akt signaling, further confirmed in liver-irradiated rat models. After irradiation, the liver injury index was significantly elevated on day-1 and gradually recovered to normal levels by day-8 in rat models. The model of a single 25-Gy fraction delivered to half of the liver volume best represented the clinically similar phenomenon of liver regeneration in the protected liver. We tested the effects of an Akt/mTOR activator (carbamazepine), which enhanced regeneration, and an Akt/mTOR inhibitor (temsirolimus), which inhibited regeneration. Finally, liver regeneration was enhanced in rats treated with temsirolimus followed by carbamazepine.
Conclusions: Our results suggest that protecting the normal liver outside the irradiated area enhances the probability of successful regeneration to compensate for radiation-induced liver injury. PI3K/AKT/mTOR is essential in liver regeneration after irradiation, and carbamazepine may enhance liver regeneration after irradiation in rats.
Citation Format: Tingshi Su, Weidong Zhao, qing Li, Qiaoyuan Wu. Liver regeneration after radiation therapy: clinical observations and a new rat model [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 2417.
Abstract 2439: RPL27 augments growth and stemness properties in colorectal cancer through PLK1 signaling
Authors: Park Keon Uk , Hwang Ilseon , Ryoo Hun Mo , Lee Yun-Han , Park So-Young 
Published: April 2023

Abstract
Background: In 2020, colorectal cancer (CRC) had the second highest mortality rate worldwide and was the third most common cancer type among various carcinomas, accounting for 10.0% and 9.4% of all carcinomas, respectively. Although the expression of ribosomal protein L27 (RPL27) is upregulated during CRC development, oncogenic roles of RPL27 have not yet been elucidated. We aimed in this study to investigate the effect of RPL27 targeting on CRC growth and whether RPL27 gained an extra-ribosomal function during CRC development.
Methods: Human CRC cell lines, HCT116 and HT29, were transfected with RPL27-specific siRNA and tested for growth inhibition and apoptotic induction using MTS, FACS and Western blotting. To obtain insights into the molecular changes in response to RPL27 knockdown, global changes in gene expression were examined using RNA sequencing.
Results: We observed that inhibition of RPL27 expression suppresses CRC cell growth and long-term colony formation through an induction of apoptotic cell death. Targeting RPL27 also significantly inhibited the growth of human CRC xenografts in nude mice. Noticeably, polo-like kinase 1 (PLK1), which is known to play an important role in mitotic cell cycle progression and stemness, was commonly down-regulated in both HCT116 and HT29 cells with RPL27 depletion. Western blot analysis confirmed that RPL27 silencing reduces the levels of PLK1 protein and G2/M-associated regulators, such as p-CDC25C, CDK1, and cyclin B1. Reflecting these molecular responses, knockdown of RPL27 reduced the migration and invasion abilities of CRC cells. In terms of CSC phenotypic changes, RPL27 knockdown suppressed sphere forming capacity of isolated CD133+ CSC population accompanying with the reduction in CD133 and PLK1 levels.
Conclusion: Taken together, these findings indicate that RPL27 contributes to promotion of CRC growth and stemness through PLK1 signaling and that targeting RPL27 could be a next-line therapeutic strategy for both primary CRC treatment and prevention of metastasis and/or recurrence.
Citation Format: Keon Uk Park, Ilseon Hwang, Hun Mo Ryoo, Yun-Han Lee, So-Young Park. RPL27 augments growth and stemness properties in colorectal cancer through PLK1 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 2439.
Abstract 2452: A study of AXIN2-regulatory mechanisms and their role in the stem cell origin of human CRC
Authors: Zhang Chi , Facey Caroline , Opdenaker Lynn , Boman Bruce 
Published: April 2023

Abstract
Colorectal cancer (CRC) originates from stem cell (SC) overpopulation, which is driven by constitutively activated WNT-signaling due to mutations in genes that encode components of the WNT-signaling pathway, particularly APC. WNT-signaling is regulated by the ꞵ-catenin destruction complex, which contains APC, AXIN1, AXIN2 and other proteins. Availability of AXIN1/2 proteins is the rate-limiting factor of destruction complex function.
The Gap in Our Knowledge is how to target AXIN in order to restore destruction complex function in APC-mutant colon tissues. A growing body of scientific evidence shows both AXIN1 & AXIN2 promote ꞵ-catenin degradation and AXINs are hub proteins involved in regulation of multiple cellular pathways that play a role in tumor phenotype. While AXIN2 expression is up-regulated in CRC, the increased level of AXIN2 is incapable of deterring CRC progression. This evidence indicates that AXIN2 is in a key pivotal position to therapeutically target WNT signaling whereby the availability of AXIN2 can be used to fine-tune ꞵ-catenin levels.
We HYPOTHESIZE that the intracellular level of AXIN2 and AXIN1 determines the degree of WNT-signaling activity in APC-mutant CRC cells and affects tumor cell phenotypic properties relevant to CRC progression. Accordingly, we have created siRNA-mediated AXIN2 knockdown and lentiviral-based AXIN2 overexpressing HT29 and SW480 cells to study the effect of modulating AXIN2 levels.
The RESULTS show that decreasing AXIN2 leads to increased WNT-signaling and increasing AXIN2 leads to increased expression of WNT-target genes. Moreover, increasing AXIN2 leads to diminished tumor cell phenotype as shown by: 1) lower cell proliferation rate; 2) up-regulated expression of SC markers (ALDH & LGR5) and increased SC population size (ALDEFLUOR+ or LGR5+); 3) down-regulated cell cycle rate; 4) down-regulated apoptosis. Moreover, our bioinformatics analyses of the effect of tankyrase inhibitors (TIs), which prevent AXIN degradation, indicate that efficacy of TIs against CRC cells depends on the APC genotype. Thus, our findings indicate that AXIN2, by down-regulating WNT-signaling, reduces cancer stem cell phenotype including decreased SC population size.
SIGNIFICANCE: discovering ways to target AXIN2-based mechanisms has vast clinical importance for developing new treatment against CRC.
Citation Format: Chi Zhang, Caroline Facey, Lynn Opdenaker, Bruce Boman. A study of AXIN2-regulatory mechanisms and their role in the stem cell origin of human CRC [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 2452.
Abstract 2461: The cell migration inhibitor dihydromotuporamine C regulates actin-myosin contractility and actin polymerization
Authors: von Kalm Laurence , Seavey Corey 
Published: April 2023

Abstract
The motuporamines are a promising class of anti-metastatic compounds. Dihydromotuporamine C (Motu33) has been shown to activate the small GTPase RhoA, however, little is known about subsequent downstream events leading to cell migration inhibition. In the present study, we investigated the mechanism of action of Motu33 and a synthetic derivative, Motu-(CH2)-33, in Drosophila by manipulating the gene dose of positive and negative regulators of actin dynamics. Consistent with previous findings, reduced gene dose of Rho1 (the Drosophila RhoA ortholog) attenuates motuporamine activity, confirming that RhoA/Rho1 is targeted by these compounds. Actin-myosin contraction is controlled by the RhoA-ROCK-myosin regulatory light chain (MRLC) pathway. Reduced gene dose of the myosin binding subunit of myosin phosphatase, a negative regulator of the RhoA-ROCK-MRLC pathway, enhances motuporamine activity indicating that the motuporamines stimulate actin-myosin contraction through activation of the myosin regulatory light chain. RhoA also activates diaphanous (dia) to control actin polymerization. Surprisingly, reduced gene dose of dia enhances motuporamine activity, suggesting that the motuporamines act on dia in a RhoA-independent manner. Reduction in gene dose of the Drosophila Rac orthologs also enhances motuporamine activity. In contrast, motuporamine activity is unaltered by reduced gene dose of slingshot (ssh) which acts to trigger actin severing and depolymerization. Since ssh is directly regulated by Rac, the enhanced activity of motuporamines observed when Rac gene dose is reduced may reflect an indirect mode of action on the Rac GTPases leading to increased RhoA activity. In summary, these findings demonstrate that motuporamines act through RhoA and diaphanous to regulate actin-myosin contractility and actin polymerization.
Citation Format: Laurence von Kalm, Corey Seavey. The cell migration inhibitor dihydromotuporamine C regulates actin-myosin contractility and actin polymerization [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 2461.
Abstract 2464: Novel models of breast cancer metastasis with different metastatic competence
Authors: Bhatt Akshita B. , Wang Ruishan , Jia Hong , Labelle Myriam 
Published: April 2023

Abstract
Metastasis is responsible for poor overall survival of cancer patients and a better understanding of the molecular mechanisms that drive metastasis is crucial for improving disease outcome. In mouse models, gene expression profiling of cancer cells isolated from metastases and from their matched primary tumors is an approach that has been successfully employed to identify biomarkers and drivers of metastasis. However, only few such tumor pairs have been derived from immunocompetent mouse models, limiting our ability to compare the metastatic potentials of these pairs in the context of an intact immune system. Moreover, most of the metastatic cancer cell lines currently available on the C57BL/6 background have a relatively low metastatic potential, complicating the evaluation of therapeutic interventions that may inhibit metastasis.
To address these critical limitations, we developed novel cell lines from distinct spontaneous lung metastases and corresponding primary breast tumors from C57BL/6 mice. Specifically, C57BL/6 mice were orthotopically injected with copGFP-expressing E0771 breast cancer cells and the tumors were allowed to grow for 28 days. Tumor cells at different stages of the metastatic cascade - primary tumor evolution, transit through the blood circulation (circulating tumor cells), survival at secondary site, dormancy, and metastatic outgrowth, were captured by collecting and culturing copGFP-positive cancer cell lines from the primary tumor, blood circulation, and metastatic lungs at the experimental endpoint. These cells were reintroduced orthotopically (mammary fat pad injection) and intravenously (tail-vein injection) to evaluate tumor growth and metastasis in vivo. Interestingly, cell lines derived from overt metastases displayed a wide array of metastatic competences, indicating that some metastases retain that ability to further metastasize while others do not. RNA sequencing of these cell lines identified genes and pathways that are significantly upregulated in highly metastatic vs. poorly metastatic cancer cell lines. Future studies will investigate whether modulation of these pathways in the primary tumor and CTCs can be used to predict metastatic recurrence and serve as a basis for developing novel biomarker-based therapeutic approaches for the treatment of metastatic disease. We also envision that the cell lines we generated will be useful for studies of the influence of host-tumor cells interactions on metastasis on the immunocompetent C57BL/6 background.
Citation Format: Akshita B. Bhatt, Ruishan Wang, Hong Jia, Myriam Labelle. Novel models of breast cancer metastasis with different metastatic competence [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 2464.
Abstract 2469: Investigating the effects of in vivo silencing of RBBP6 gene on tumor growth in the FVBN-Tg(MMTV PyVT)634MulJ breast cancer mouse model
Authors: Moela Pontsho , Govender Mayur , Ambele Melvin 
Published: April 2023

Abstract
Breast cancer is one of the most common causes of cancer mortality, with close to two million new cases and just over 600 000 cancer deaths projected in 2022 in the United States of America alone. Identifying prognostic markers for breast cancer is critical to reducing these numbers. Retinoblastoma binding protein 6 (RBBP6) is considered a potential cancer biomarker due to its association with cell proliferation and the fact that it is overexpressed at breast cancer sites where there is marked apoptosis and elevated p53. More information is emerging regarding the role of RBBP6 in cancer treatment, specifically its potential to sensitize cancer cells to radiation and certain chemotherapeutic agents. In vivo studies on RBBP6 in breast cancer mouse models are limited. Our study aims to investigate the molecular function and the prognostic potential of RBBP6 in breast cancer using MCF-7 cell line and the FVB/N-Tg(MMTV PyVT)634Mul/J breast cancer mouse model. The expressional effects of RBBP6 on cancer cell proliferation and metastatic tumour growth in cancer mice were examined in vitro and in vivo using RT-PCR, western blotting, and tumour size monitoring. The results demonstrate that RBBP6 mRNA expression was significantly higher in both local and distal tumours with a corresponding overexpression of angiogenic and metastatic key markers, VEGF164 and CD31, respectively. In addition, tumour growth reduced gradually over a period of two weeks in response to RBB6 gene knockdown. Our study indicated that RBBP6 may be a potential metastatic marker in breast tumours.
Citation Format: Pontsho Moela, Mayur Govender, Melvin Ambele. Investigating the effects of in vivo silencing of RBBP6 gene on tumor growth in the FVBN-Tg(MMTV PyVT)634MulJ breast cancer mouse model [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 2469.