bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 833: Exosomes isolation via lyophilization for Philadelphia-positive leukemia therapy
Authors: Rehman Fawad Ur , Qazi Rida e Maria , Sajid Zahra , Mian Afsar Ali
Published: April 2023

Background: Exosomes are extracellular vesicles having less than 200 nm size, secreted extracellularly by almost all types of cells. They regulate intercellular communication by delivering RNAi, proteins, viruses, and soluble factors as inherited payloads. In recent years, the application of exosomes to deliver small molecules have been widely investigated in tissue regeneration, therapeutics, as well as diagnostics. However, the isolation of exosomes has remained challenging mainly due to limitations of specialized instruments and the least cost-effective reagents. In this study, we developed a novel method to isolate exosomes from cultured cells.

Experimental: The supernatant from cultured cells was collected and subjected to lyophilization after low-speed centrifugation. The characterization and quantification of exosomes were performed using Bradford assay. Scanning Electron Microscopy (SEM) and Nanoparticles Tracking Analysis (NTA) were carried out for shape and size distribution. Western blot was performed for the evaluation of the exosome specific surface markers (CD63, CD9, CD81, calnexin, HSP70, and TSG101). The as-isolated exosomes were loaded with commercial dyes (Cy5, Eosin) for the evaluation of their drug delivery properties. Furthermore, their drug loading and release were confirmed by loading tyrosine kinase inhibitors (TKIs) as a payload. Finally, the anti-leukemic drugs (dasatinib and ponatinib) were loaded on the isolated exosomes for targeting leukemia cell line i.e., K562 and BCR-ABL expressing Ba/F3 cells in in vitro model, using MTT assay for cell proliferation and Annexin-V/PI for apoptosis detection.

Results: Here we found that the isolated exosomes have round shape with an average size of ~130 nm. They expressed known exosome markers including CD63, CD9, CD81, calnexin, HSP70, and TSG101. These exosomes could efficiently target and deliver dyes (Eosin and Cy5) and TKIs (dasatinib and ponatinib) to K562 and Ba/F3-cells expressing BCR-ABL. The TKIs-loaded exosomes inhibited the growth of leukemic cells and induced apoptosis in a dose dependent manner.

Conclusion: We claim the development of a new method for active exosome isolation from cell culture. These exosomes could qualify for all the essential characterization, drug loading, and release ability by harnessing proliferation and inducing apoptosis in Ph+ leukemia cells.

Citation Format: Fawad Ur Rehman, Rida e Maria Qazi, Zahra Sajid, Afsar Ali Mian. Exosomes isolation via lyophilization for Philadelphia-positive leukemia therapy [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 833.
Abstract 837: Preclinical development of ELU001: A folate receptor alpha (FRα)-targeted C’Dot drug conjugate (CDC) for the treatment of brain metastases
Authors: Adams Gregory P. , Khor Tin , Chen Feng , Ma Kai , Scocca Marion , Venkatesan Aranapakam , Reddick Cathy , Hilgart Mary , Gardinier Thomas , Wu Fei , Turker Melik , Chen Peiming , Patel Vaibhav , Bayever Eliel
Published: April 2023

Antibody-drug conjugates (ADCs) exhibit limited efficacy against brain malignancies due to their inability to cross the blood-brain barrier (BBB) and penetrate into solid tumors. In clinical imaging studies C’Dots readily crossed tumor-disrupted BBB and penetrated across/localized in tumors in the brain avoiding healthy brain. CDCs are ultra-small (6-7 nm) nanoparticles with a silica core coated by short polyethylene glycol chains conjugated to up to 80 small payload and targeting moieties, creating highly potent and avid agents. CDCs’ small size mediates rapid renal clearance leading to limited exposure to healthy tissues.

ELU001 is a potent anti-FRα CDC with an average of 21 exatecan topoisomerase-1 inhibitor payload molecules and 13 folic acid targeting molecules on its surface. ELU001 is currently in a dose escalation trial in patients with systemic solid tumor indications that have the potential to overexpress FRα. Early signs of activity with a manageable safety profile have been seen across antigen expression levels.

ELU001 exhibits in vitro potency in the sub/low nanomolar range against cancer cell lines that express 3+, 2+ or 1+ levels of FRα. In studies performed in immunodeficient mice bearing intracranial NCI-H2228-luc bioluminescent non-small cell lung cancer tumors, ELU001 was observed to penetrate across disrupted BBB and localize in tumors. Microscopic analysis revealed that ELU001 distributed throughout the tumors but not into the healthy brain. Treatment with a single cycle of ELU001 Q3Dx3 in mice bearing either early (Day 7) or late (Day 14) brain tumors was well tolerated and resulted in significant reduction in tumor burden measured by bioluminescence as well as a prolonged survival benefit. Retreatment of these animals resulted in an additional decrease in tumor burden. These results suggest that ELU001 may have promise for the treatment of metastatic brain tumors that are difficult to treat with currently available agents.

Citation Format: Gregory P. Adams, Tin Khor, Feng Chen, Kai Ma, Marion Scocca, Aranapakam Venkatesan, Cathy Reddick, Mary Hilgart, Thomas Gardinier, Fei Wu, Melik Turker, Peiming Chen, Vaibhav Patel, Eliel Bayever. Preclinical development of ELU001: A folate receptor alpha (FRα)-targeted C’Dot drug conjugate (CDC) for the treatment of brain metastases [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 837.
Abstract 860: The dynamics of LINE-1 retrotransposition in cellular populations
Authors: Martis Stephen , Solovyov Alexander , Lihm Jayon , Li Hao , Greenbaum Benjamin
Published: April 2023

Retrotransposons are genetic elements that have the ability to copy and paste themselves in the genome via the proteins they encode. Since the rapid growth of a retrotransposon can be highly deleterious at the organismal level, many of these genetic parasites are suppressed or have been inactivated over evolutionary time. However, the human genome still hosts the active retrotransposon LINE-1, whose aberrant expression is associated with various diseases, especially epithelial cancers. Despite these associations, a quantitative understanding of the dynamics and diversity of LINE-1 insertions in somatic tissue is lacking. In order to address this gap, we present a population dynamic model of LINE-1 retrotransposition in individual cells. Using the model, we show that at demographic equilibrium, the LINE-1 copy number distribution is broader than would be expected from classical population genetic models. We demonstrate how this broadening distorts the frequency spectrum of insertions. We compare the model's predictions to data from whole genome sequencing of individual tumor cells.

Citation Format: Stephen Martis, Alexander Solovyov, Jayon Lihm, Hao Li, Benjamin Greenbaum. The dynamics of LINE-1 retrotransposition in cellular 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 860.
Abstract 882: Functional enrichment analysis of somatic mutations identifies novel risk factors for pediatric neuroblastoma
Authors: Middleton Nolan D. , Shelden Eric
Published: April 2023

Pediatric neuroblastoma is among the most common solid tumors in children and accounts for approximately 15% of childhood cancer mortalities. Neuroblastomas are highly heterogeneous cancers, and few common genetic alterations are currently associated with neuroblastoma tumorigenesis. Additionally, few genetic variations have been established as predictive factors for clinical outcomes in neuroblastoma cases. Here, a biological systems-level approach utilizing publicly-accessible data from the Genomic Data Commons was taken to identify genetic variations associated with altered survival times in neuroblastoma cases. Two survival analyses of clinical neuroblastoma cases were conducted: one associated with genetic variations in individual somatic genes and the other associated with groups of mutations identified using functional enrichment analysis. Mutations in only two individual genes displayed significant associations with altered survival: ALK (ALK receptor tyrosine kinase), a known hallmark of neuroblastoma, and DNAH17 (dynein axonemal heavy chain 17). In contrast, patient cohorts established by functional enrichment analysis of mutated genes identified 148 biological systems where somatic gene variations were significantly associated with altered survival. Gene sets defined by the function of their products in ALK signaling, as well as alteration in cells treated with Crizotinib, an inhibitor of receptor tyrosine kinases including ALK, both displayed highly significant association with altered survival. Of the 148 systems identified, 128 others lacked any association with ALK. Of these, eight showed a more significant association with altered survival than the ALK signaling pathway itself. These results identify novel risk factors associated with reduced survival in pediatric neuroblastoma patients

and illustrate the potential of systems-level analysis to generate insight into the biology of heterogeneous cancers.

Citation Format: Nolan D. Middleton, Eric Shelden. Functional enrichment analysis of somatic mutations identifies novel risk factors for pediatric neuroblastoma [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 882.
Abstract 91: Multi-omic single-cell approach reveals transcriptional and epigenetic plasticity in breast cancer
Authors: Mohammed Hisham
Published: April 2023

Breast cancer is known to be highly heterogenous at the transcriptional and genetic level. In order to study functional consequences of this heterogeneity, we applied single-cell RNA-seq and single-cell Multi-ome (RNA+ATAC) on hormone responsive cell line and organoid models after multiple timepoint hormone treatments. We also developed TITAN, an LDA based machine learning tool to identify ‘cell states’ in single-cell datasets. Our results suggest that response to hormone signalling is highly heterogenous at the single-cell level, resulting in multiple divergent epigenetic and transcriptional cell states. We identified driver transcription factors for these states and defined epigenetic mechanisms regulating state change. Subsequently, we also investigated epigenetic and transcriptional states in primary breast tumors. We analysed 20 breast tumor samples using the single-cell Multi-ome (ATAC+RNA) approach and compared them to matched adjacent normal tissues. Our results identified epigenetic reprogramming events in breast cancer and novel transcription factors in the process. Using bulk DNA-sequencing as a reference, we inferred sub-clonal populations from both the RNA and ATAC modalities, allowing us to define heterogenous chromatin accessibility events that align with genetic sub-clones as well as those that are independent of it. Our dataset provides a comprehensive view of epigenetic and transcriptional events in breast tumorigenesis.

Citation Format: Hisham Mohammed. Multi-omic single-cell approach reveals transcriptional and epigenetic plasticity 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 91.
Abstract 946: A silver jubilee for synthetic lethality in cancer treatment: where do we stand
Authors: Lee Joo Sang , Chung Youngmin , Kammula Ashwin V. , Schaffer Alejandro A. , Ruppin Eytan
Published: April 2023

Background: Synthetic lethality (SL) denotes a genetic interaction between two genes whose co-inactivation is detrimental to cells. Since the seminal paper of Hartwell and colleagues has raised the possibility that SL can be used to devise highly selective cancer treatments, it has been one of the promising approaches for precision oncology and drug discovery. Many different avenues have so far been explored to bring this idea to the clinic. As 25 years have passed by now, we take stock and systematically and comprehensively chart the landscape of SL-based preclinical research and clinical trials.

Approach and Key Findings: We systematically mined both public and commercial databases to curate the preclinical and clinical landscape of the SL-based oncology studies. Our analysis shows that the number of SL oncology studies is rapidly growing since the first identification of the well-known BRCA-PARP synthetic lethality axis. Importantly, we find that the success rate of SL oncology trials is significantly higher than non-SL-based trials. While more than 70% of SL-oncology trials involve genes in the most-studied DNA damage response (DDR) pathways, the fraction of SL trials involving non-DDR pathways keeps growing since 2009. We further charted the landscape of SL triplets, which is a promising future higher-order extension of the conventional pairwise SL interactions. We find that only about 8% of preclinically validated SL triplets were clinically tested in trials, providing new opportunities for more refined clinical trial design. Our analysis suggests that emerging opportunities in SL oncology may arise from metabolic and paralogous interactions, disease-agnostic biomarkers, context-specific combinations against treatment resistance, artificial intelligence and data science approaches, and multi-omics patient stratification signatures.

Significance: Taken together, our findings testify that a considerable potential benefits of SL based approaches are yet untapped, reinforcing the belief that the synthetic lethality approach may serve as a key driver of precision oncology going forward.

Citation Format: Joo Sang Lee, Youngmin Chung, Ashwin V. Kammula, Alejandro A. Schaffer, Eytan Ruppin. A silver jubilee for synthetic lethality in cancer treatment: where do we stand [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 946.
Abstract 956: FBXW7 regulates imatinib chemoresistance through targeting MCL1 for apoptotic regulation in gastrointestinal stromal tumors
Authors: Wu Xiyu , Iwatsuki Masaaki , Lou Meiyue , Ishimoto Takatsugu , Baba Yoshifumi , Miyamoto Yuji , Baba Hideo
Published: April 2023

Introduction: Imatinib definitively contribute to improve prognosis for high-risk or unresectable GISTs. Due to therapeutic efficacy is limited by imatinib chemoresistance and toxicity, the exploration of predictive markers of imatinib therapeutic efficacy that early enable patients to utilize more effective therapeutic strategies remains urgent. Here, we evaluate that the ability of FBXW7 acts as a predictor of imatinib therapeutic effect in preclinical models, and the potential of FBXW7-MCL1 axis promote imatinib-induced apoptosis response.

Methods: The cellular and in vivo correlation between FBXW7 and imatinib chemoresistance via FBXW7-MCL1 axis were evaluated by detecting IC50 value, apoptosis assay, and GIST xenograft studies. The clinical significance of FBXW7 as a predictor of imatinib treatment efficacy was examined in 140 high-risk patients with GISTs by immunohistochemical staining and multivariate analyses.

Results: FBXW7 affects imatinib chemoresistance through regulating cellular apoptosis in GIST-T1 cells. FBXW7 targets MCL1 to regulate cellular apoptosis. MCL1 involves in the regulation of imatinib chemoresistance through inhibiting apoptosis of GIST-T1 cells. FBXW7 regulates imatinib chemoresistance via down-regulating MCL1 for enhancing imatinib-induced apoptosis in vitro. FBXW7 regulates imatinib sensitivity of GIST cells via targeting MCL1 to predict therapeutic efficacy of imatinib treatment in vivo. Through 5-year RFS rates analysis and multivariate analysis, the ability of FBXW7 predicting therapeutic efficacy of high-risk GIST patients with adjuvant imatinib was proved.

Conclusions: FBXW7 regulates imatinib chemoresistance through inhibiting MCL1 for enhancing imatinib-induced apoptosis in GIST and acted as a reliable predictor of imatinib treatment efficacy in high-risk GIST patients treated imatinib.

Citation Format: Xiyu Wu, Masaaki Iwatsuki, Meiyue Lou, Takatsugu Ishimoto, Yoshifumi Baba, Yuji Miyamoto, Hideo Baba. FBXW7 regulates imatinib chemoresistance through targeting MCL1 for apoptotic regulation in gastrointestinal stromal 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 956.
Abstract 96: Integrated molecular analysis of human dedifferentiated liposarcoma identifies a population of liposarcoma progenitors vulnerable to TGF beta inhibition
Authors: Gruel Nadège , Quignot Chloé , Vibert Julien , Bonvalot Sylvie , Zein Sophie El , Tzanis Dimitri , Baulande Sylvain , Mariani Odette , Waterfall Joshua , Delattre Olivier , Watson Sarah
Published: April 2023

Introduction: Dedifferentiated liposarcomas (DDLPS) are the most frequent high-grade soft tissue sarcoma in adults. From a pathological point of view, these tumors are composed of high-grade undifferentiated tumor cells (DD), often showing an abrupt transition from a compartment of well-differentiated adipocytic tumor cells (WD). Tumor cells from both WD and DD compartments are characterized by recurrent MDM2 amplification, but their cellular origin and the molecular mechanisms associated with dedifferentiation are poorly understood.

Methods: We performed an integrated molecular analysis of tumors collected from 11 patients undergoing surgery for primary untreated DDLPS. DDLPS tumors were analyzed by single-cell RNA sequencing (scRNAseq) and bulk RNA sequencing on paired WD and DD samples from the same tumors. Results were validated in vitro and in vivo in an additional cohort of human tumors, patient-derived xenografts and DDLPS cell lines.

Results: Through RNA-sequencing of 102,753 individual cells from 11 primary DDLPS lesions, major cell clusters were identified based on unsupervised clustering of gene expression profiles and canonical markers. They include 31 tumor microenvironment clusters and 11 tumor cell clusters. A cluster of tumor cells from the WD compartment is characterized by signatures of early adipocytic progenitors, previously identified as TGFβ-dependent, DPP4-positive stromal progenitors. We show that these cells harbor specifically the truncal genomic alterations of the cancer, with further subclonal mutations identifiable in both WD and DD compartments of DDLPS. Furthermore, these cells have multipotent properties and their differentiation towards the adipocytic lineage is inhibited by TGFβ. Treatment of DD tumor cells with TGFβ inhibitors restores their adipocytic phenotype in vitro and in vivo.

Conclusion: We provide the first single-cell atlas of human DDLPS tumor and microenvironment and identify a population of adipocytic tumor progenitors at the origin of both WD and DD compartments. This study provides rationale for the development of therapeutic strategies based on TGFβ inhibition in advanced DDLPS.

Citation Format: Nadège Gruel, Chloé Quignot, Julien Vibert, Sylvie Bonvalot, Sophie El Zein, Dimitri Tzanis, Sylvain Baulande, Odette Mariani, Joshua Waterfall, Olivier Delattre, Sarah Watson. Integrated molecular analysis of human dedifferentiated liposarcoma identifies a population of liposarcoma progenitors vulnerable to TGF beta inhibition [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 96.
Abstract 967: Real-world transcriptomic biomarkers as replacement for immunohistochemistry and FISH studies in breast cancer
Authors: Albitar Maher , Goy Andre , Pecora Andrew , Graham Deena , McNamara Donna Donna , Charifa Ahmad Ahmad , IP Andrew , Ma Wanlong , Waintraub Stanley
Published: April 2023

Background: Human epidermal growth factor receptor-2 (HER2) and hormone receptors are typically used as binary biomarkers for selecting breast cancer therapy. There is a need to explore the clinical relevance of these biomarkers as continuous variables. This is particularly relevant for the new class of antibody-drug conjugates (ADC), in which a relatively low HER2 expression level is adequate for targeting tumor cells. We explored the potential of RNA profiling, determined by next generation sequencing (NGS), to provide more flexible clinical biomarkers as compared with immunohistochemistry (IHC) or fluorescent in situ hybridization (FISH).

Methods: Clinical and laboratory data from 57 breast cancers collected by the COTA real-world data company were used to study biomarker levels as detected by routine clinical transcriptomic tests. HER2 (ERBB2), estrogen receptor alpha (ESR1), and androgen receptor (AR) mRNA levels were compared with reported HER2 and estrogen receptor (ER) IHC and FISH results.

Results: RNA levels accurately reflected and predicted HER2 amplification (see table below). Importantly, RNA data showed significant variation and overlap in the levels of ERBB2 mRNA between cases scored by IHC as zero, 1+, and 2+. This variation correlated with progression-free survival (PFS). Similarly, the ESR1 RNA levels accurately reflected ER status and demonstrated significant variation between positive cases. RNA data also showed significant variations in the AR levels. Patients wssith high AR mRNA levels had significantly better PFS (P=0.05). Patients expressing high ER and AR levels had significantly better PFS than those expressing low ESR1 and AR levels (P=0.03).

Conclusions: These findings suggest that RNA analysis using NGS is an alternative to IHC and FISH. RNA provides continuous data that can determine cut-off points predicting response to therapy and should be explored in predicting ADC response.

ERBB2 mRNA levels (FPKM) in various HER2 IHC groupss IHC Score Valid N Mean Median Minimum Maximum Quartile Range Std.Dev. Zero 19 231 243 63 537 170 110 Zero vs one 3 151 155 45 253 208 104 Zero to one vs one 18 397 302 172 845 365 222 One Vs two 13 495 423 159 1094 273 284 Two vs three 4 7523 7649 937 13859 7183 5310

Citation Format: Maher Albitar, Andre Goy, Andrew Pecora, Deena Graham, Donna Donna McNamara, Ahmad Ahmad Charifa, Andrew IP, Wanlong Ma, Stanley Waintraub. Real-world transcriptomic biomarkers as replacement for immunohistochemistry and FISH studies 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 967.
Abstract SY30-03: Composing each patient’s equation: Unraveling brain tumor complexity by integrating multi-regional image-localized biopsies
Authors: Swanson Kristin R.
Published: April 2023

Glioblastoma is a uniquely challenging and aggressive cancer that is practically considered uniformly fatal. This aggressiveness is driven by heterogeneity between and within patients and the diffuse invasion of tumor cells deep into the normal appearing brain tissue surrounding the frank tumor abnormality. Mathematical neuro-oncology (MNO) is a burgeoning field that seeks to bring together individual patient data (like patient imaging, tissue biopsies etc) to tune mathematical models that accurately predict and quantify response to treatments for each patient. These mathematical models use both mechanistic “weather forecasting” methods and artificial intelligence pattern recognition methods. Ultimately, these models form the basis of modern "precision medicine" approaches to tailor therapy in a patient-specific manner. These models can be used to overcome the limited ability of imaging to accurately detect tumor cells, improve prognostic predictions, stratify patients, and assess treatment response in silico in the construction of effective clinical trials and treatment protocols, thus accelerating the pace of clinical research.

This presentation will focus on the growing translation of MNO to clinical neuro-oncology highlighting burgeoning insights into sex differences in tumor incidence, outcomes, and response to therapy. Specifically, I will discuss 1) use of our 4,500+ patient cohorts of 100,000+ annotated serial MR imaging data to develop digital twins accurately predict response and outcomes in patients and 2) our unique collection of 1000+ image-localized biopsies across nearly 200 patients to detect sex-distinct patterns of mapping between regional imaging features and underlying regional tumor biology. We will demonstrate the value of these novel combined resources in predicting response to treatment for EGFR-targeted therapies in 3 clinical trials and differentiating response to novel dendritic cells vaccines and CAR T-cell therapies in 2 additional clinical trials.

Taken together, these complimentary approaches provide a platform to incorporate inter- and intra- tumoral heterogeneity into accurate predictive models that advance precision oncology for glioblastoma patients.

Citation Format: Kristin R. Swanson. Composing each patient’s equation: Unraveling brain tumor complexity by integrating multi-regional image-localized biopsies. [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 SY30-03.
Abstract SY33-02: Novel molecular mechanisms of lung cancer plasticity and targeting lung squamous cell carcinoma
Authors: Han Cecil
Published: April 2023

Lung cancer is marked by a high degree of genetic and histopathological heterogeneity. Lineage plasticity, the ability of cells to transform from one cell type to another, has been associated with intratumoral heterogeneity and therapeutic resistance. The molecular drivers and mechanisms of cancer cell plasticity and histological transdifferentiation of lung cancer are largely unknown. A deubiquitinating enzyme, Ubiquitin-Specific Peptidase 13 (USP13), is frequently amplified at chromosome 3q.26 amplicon in lung squamous cell carcinoma. USP13 knock-in overexpressing mouse model was crossed with KrasLSL-G12D; Trp53fl/fl (KP) mouse to generate KrasLSL-G12D; Trp53fl/fl; Usp13LSL (KPU) mouse model. Intratracheal administration of adenovirus expressing Cre recombinase to the lung of the KPU mouse developed aggressive lung tumors and a shortened survival compared to the KP mouse model. Importantly, while the KP mice developed lung adenocarcinoma, 100% of KPU mice developed lung squamous cell carcinoma. The squamous cell carcinoma of the KPU mice faithfully mimicked the molecular signatures, cellular pathways, and tumor microenvironments of human lung squamous cell carcinoma. Delivery of cell type-restricted viruses to the lungs further identified bronchiolar secretory club cells as the predominant cell-of-origin of KPU-induced lung squamous cell carcinoma. USP13 altered the levels of TTF-1 and c-Myc in club cells of the airway and reinforced the fate of CC10+ club cells to squamous carcinoma development instead of adenocarcinoma. USP13 directly acted on the K48-linked ubiquitination of c-Myc and increased the protein stability of c-Myc in human lung cancer cells. Overexpression of USP13 increased the half-life of c-Myc while inhibiting USP13 deubiquitinase activity decreased the c-Myc protein level. USP13 upregulated the expression of squamous lineage markers (Sox2, CK5, P40) in the primary mouse and advanced human lung cancer cells. Our findings revealed that USP13 promotes the lineage plasticity of origin-of-cells of the lung and drives transdifferentiation to squamous cell carcinoma. Finally, our study suggests the critical role of USP13 in unlocking the phenotypic plasticity of lung cancer, which may lead to novel therapeutics targeting lung cancer.

Citation Format: Cecil Han. Novel molecular mechanisms of lung cancer plasticity and targeting lung squamous cell carcinoma. [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 SY33-02.
Supplementary Fig. 2 from Transcription Factor Interactions Mediate EGF-Dependent COX-2 Expression
Authors: Xu Kaiming , Shu Hui-Kuo G.
Published: April 2023

Supplementary Fig. 2 - PDF file 101K, Src and p38-MAPK induces FOXM1 and COX-2 expression and COX-2 regulation requires FOXM1
Supplementary Table 1 from HSPC111 Governs Breast Cancer Growth by Regulating Ribosomal Biogenesis
Authors: Zhang Changwen , Yin Chunyang , Wang Lei , Zhang Shuping , Qian Yi , Ma Juan , Zhang Zhihong , Xu Yong , Liu Sijin
Published: April 2023

PDF file - 35K, Supplementary Table 1. Primer sequences used in the study.
Supplementary Figure Legends from HSPC111 Governs Breast Cancer Growth by Regulating Ribosomal Biogenesis
Authors: Zhang Changwen , Yin Chunyang , Wang Lei , Zhang Shuping , Qian Yi , Ma Juan , Zhang Zhihong , Xu Yong , Liu Sijin
Published: April 2023

PDF file - 42K
Supplementary Figure 1 from HSPC111 Governs Breast Cancer Growth by Regulating Ribosomal Biogenesis
Authors: Zhang Changwen , Yin Chunyang , Wang Lei , Zhang Shuping , Qian Yi , Ma Juan , Zhang Zhihong , Xu Yong , Liu Sijin
Published: April 2023

PDF file - 52K, Supplemental Fig. 1. Representative results of c-Myc and HSPC111 expression. The mRNA levels of c-Myc and HSPC111 were evaluated by end-point PCR in MCF-7 cells upon induction of tamoxifen (at 1microM) for 24 hrs.
Supplementary Figure 1 from Tpl2 Kinase Impacts Tumor Growth and Metastasis of Clear Cell Renal Cell Carcinoma
Authors: Lee Hye Won , Joo Kyeung Min , Lim Joung Eun , Cho Hyun Jung , Cho Hee Jin , Park Min Chul , Seol Ho Jun , Seo Seong Il , Lee Jung-Il , Kim Sunghoon , Jeong Byong Chang , Nam Do-Hyun
Published: April 2023

PDF file - 53K, Kaplan-Meier graphs representing the probability of cumulative overall survival (OS) in patients with papRCCs stratified according to Tpl2 level in their primary tumors. For TCGA data, high, moderate and low expression were designated as >mean+SD, mean-SD~mean+SD and
Supplementary Figure Legend from Oncogenic MUC1-C Promotes Tamoxifen Resistance in Human Breast Cancer
Authors: Kharbanda Akriti , Rajabi Hasan , Jin Caining , Raina Deepak , Kufe Donald
Published: April 2023

PDF file - 29K
Supplementary Figure 4 from Resveratrol and P-glycoprotein Inhibitors Enhance the Anti-Skin Cancer Effects of Ursolic Acid
Authors: Junco Jacob J. , Mancha Anna , Malik Gunjan , Wei Sung-Jen , Kim Dae Joon , Liang Huiyun , Slaga Thomas J.
Published: April 2023

PDF file - 860K, Figure S4: UA and RES synergistically reduced viability of metastatic mouse melanoma B16F10 cells (average of 3 independent experiments, n=3/exp, * p<0.05, ** p<0.01, *** p<0.005, and **** p<0.001).
Supplementary Figure 1 from Resveratrol and P-glycoprotein Inhibitors Enhance the Anti-Skin Cancer Effects of Ursolic Acid
Authors: Junco Jacob J. , Mancha Anna , Malik Gunjan , Wei Sung-Jen , Kim Dae Joon , Liang Huiyun , Slaga Thomas J.
Published: April 2023

PDF file - 75K, , Figure S1: Representative experiments for data in tables 1 and 2, showing the enhancing effect of 50 or 100 microM VRP, CsA, or RES on UA-mediated cytotoxicity in MT1/2 or Ca3/7 cells (n=3/exp, * indicates p<0.05 between UA+veh and UA+50microM, # indicates p<0.05 between UA+veh and UA+100microM).
Supplementary Figure 6 from Autophagy-Dependent Metabolic Reprogramming Sensitizes TSC2-Deficient Cells to the Antimetabolite 6-Aminonicotinamide
Authors: Parkhitko Andrey A. , Priolo Carmen , Coloff Jonathan L. , Yun Jihye , Wu Julia J. , Mizumura Kenji , Xu Wenping , Malinowska Izabela A. , Yu Jane , Kwiatkowski David J. , Locasale Jason W. , Asara John M. , Choi Augustine M.K. , Finkel Toren , Henske Elizabeth P.
Published: April 2023

PDF file - 98K, Autophagy and pentose phosphate pathway inhibition suppresses proliferation of Tsc2-null cystadenoma 105K cells.
Supplementary Figure 5 from Dysregulating IRES-Dependent Translation Contributes to Overexpression of Oncogenic Aurora A Kinase
Authors: Dobson Tara , Chen Juan , Krushel Les A.
Published: April 2023

PDF file - 68K, IRES activity from various IRESes does not correlate with Aurora A protein expression.
Supplementary Figure 4 from Dysregulating IRES-Dependent Translation Contributes to Overexpression of Oncogenic Aurora A Kinase
Authors: Dobson Tara , Chen Juan , Krushel Les A.
Published: April 2023

PDF file - 114K, Changes in cap-dependent translation initiation do not correlate with Aurora A protein expression levels.
Supplementary Figure 3 from Dysregulating IRES-Dependent Translation Contributes to Overexpression of Oncogenic Aurora A Kinase
Authors: Dobson Tara , Chen Juan , Krushel Les A.
Published: April 2023

PDF file - 64K, Aurora A protein degradation after cycloheximide treatment.
Supplementary Figure Legend from Balanced Tiam1-Rac1 and RhoA Drives Proliferation and Invasion of Pancreatic Cancer Cells
Authors: Guo Xingjun , Wang Min , Jiang Jianxin , Xie Chengchen , Peng Feng , Li Xu , Tian Rui , Qin Renyi
Published: April 2023

PDF file - 69K
Supplementary Figure 1 - 8, Table 1 from PTP1B Contributes to Calreticulin-Induced Metastatic Phenotypes in Esophageal Squamous Cell Carcinoma
Authors: Wang Xiao-Min , Shang Li , Zhang Yu , Hao Jia-Jie , Shi Feng , Luo Wei , Zhang Tong-Tong , Wang Bo-Shi , Yang Yang , Liu Zhi-Hua , Zhan Qi-Min , Wang Ming-Rong
Published: April 2023

PDF file - 1061K, S Figure 1. Down-regulation of CRT expression reduces PTP1B mRNA and protein expression in KYSE510 cells. S2. PTP1B promotes ESCC cell invasion and migration in KYSE510 cells. KYSE510 cells were transfected with PTP1B-specific siRNA (siRNA PTP1B) or non-targeting siRNA control (siRNA cont). S3. CRT regulates cell motility through PTP1B in ESCC cells. (A-C) 1x105 KYSE150 cells were seeded on 24-well plates with three replicates. S4. Cancer-inflammatory response was minimal in mouse model. S5. CRT regulates PTP1B transcription through Stat5a. S6. The expression of CRT and PTP1B in 176 ESCC tissues was evaluated by immunohistochemistry. S7. Correlation of PTP1B expression with overall survival in patients with CRT high-expressing tumors. S8. Model of CRT-dependent signaling pathway in ESCC cell metastasis. Supplementary Table 1. The candidate genes altered in CRT-siRNA KYSE150 cells as compared with non-targeting siRNA cells detected by cDNA array
Supplementary Table 1 from NEDD9 Depletion Leads to MMP14 Inactivation by TIMP2 and Prevents Invasion and Metastasis
Authors: McLaughlin Sarah L. , Ice Ryan J. , Rajulapati Anuradha , Kozyulina Polina Y. , Livengood Ryan H. , Kozyreva Varvara K. , Loskutov Yuriy V. , Culp Mark V. , Weed Scott A. , Ivanov Alexey V. , Pugacheva Elena N.
Published: April 2023

PDF file - 30K
Supplementary Figure 3 from NEDD9 Depletion Leads to MMP14 Inactivation by TIMP2 and Prevents Invasion and Metastasis
Authors: McLaughlin Sarah L. , Ice Ryan J. , Rajulapati Anuradha , Kozyulina Polina Y. , Livengood Ryan H. , Kozyreva Varvara K. , Loskutov Yuriy V. , Culp Mark V. , Weed Scott A. , Ivanov Alexey V. , Pugacheva Elena N.
Published: April 2023

PDF file - 159K, Supplementary Figure 3. (A). Representative images of bioluminescence (BLI) of mice orthotopically injected with BT-549 cells expressing doxycycline inducible shCon or shNEDD9 (shN1) RNAs. shRNA-Day0 represents 2 weeks post injection, before addition of doxycycline chow; shRNA-Day14 is 2 weeks post addition of doxycycline-containing diet. 6 mice/each shRNA (12 mice total). (B). WB (right panel) analysis of primary tumor tissue dissected at shRNA-Day14 with anti-NEDD9, and -GAPDH antibodies. Quantification of sRNA depletion 2 (left panel) from tumors from 3 mice/per shRNA, t-test *p=0.0019. (C). Quantification of tumor growth based on BLI (shRNA-Day0, -Day14) in 3 independent experiments, n=6/group, mean photon flux, +/-S.E.M, two-way ANOVA, p values are non-significant (ns) for shRNA-Day0 (shCon/shN1); *p=0.0007 for shRNA-Day14 (shCon/shN1). (D). Quantification of RFP/luc2/DNA positive tumor cells in peripheral blood of shCon and shNEDD9 (N1) mice at indicated time points, n=6/group. Results are plotted as number of cells per 200μl of blood, +/- S.E.M, two-way ANOVA, ns (shRNA-Day0: shCon/shN1); p<0.001 (shRNA-Day14: shCon/shN1).
Supplementary Figure from Combinatorial Treatment with PARP-1 Inhibitors and Cisplatin Attenuates Cervical Cancer Growth through Fos-Driven Changes in Gene Expression
Authors: Gupte Rebecca , Lin Ken Y. , Nandu Tulip , Lea Jayanthi S. , Kraus W. Lee
Published: April 2023

Supplementary Figure from Combinatorial Treatment with PARP-1 Inhibitors and Cisplatin Attenuates Cervical Cancer Growth through Fos-Driven Changes in Gene Expression
Supplementary Table from Small-Molecule NSC59984 Induces Mutant p53 Degradation through a ROS-ERK2-MDM2 Axis in Cancer Cells
Authors: Zhang Shengliang , Zhou Lanlan , El-Deiry Wafik S.
Published: April 2023

Supplementary Table from Small-Molecule NSC59984 Induces Mutant p53 Degradation through a ROS-ERK2-MDM2 Axis in Cancer Cells
Supplementary Figure from Pan-Cancer HLA Gene-Mediated Tumor Immunogenicity and Immune Evasion
Authors: Gong Xutong , Karchin Rachel
Published: April 2023

Supplementary Figure from Pan-Cancer HLA Gene-Mediated Tumor Immunogenicity and Immune Evasion
Supplementary Data from Integrated Proteomics-Based Physical and Functional Mapping of AXL Kinase Signaling Pathways and Inhibitors Define Its Role in Cell Migration
Authors: Majumder Anurima , Hosseinian Sina , Stroud Mia , Adhikari Emma , Saller James J. , Smith Matthew A. , Zhang Guolin , Agarwal Shruti , Creixell Marc , Meyer Benjamin S. , Kinose Fumi , Bowers Kiah , Fang Bin , Stewart Paul A. , Welsh Eric A. , Boyle Theresa A. , Meyer Aaron S. , Koomen John M. , Haura Eric B.
Published: April 2023

Supplementary Data from Integrated Proteomics-Based Physical and Functional Mapping of AXL Kinase Signaling Pathways and Inhibitors Define Its Role in Cell Migration
Supplementary Figure 2 from XIAP and PHB1 Regulate Anoikis through Competitive Binding to TRAF6
Authors: Yang Bo , Lou Chao , Chen Shengkai , Zhang Zhiyuan , Xu Qin
Published: April 2023

S2. Effects of CAPE on NF-kappaB signaling activation.
Supplementary Figure S3 from Sox2 Is an Oncogenic Driver of Small-Cell Lung Cancer and Promotes the Classic Neuroendocrine Subtype
Authors: Voigt Ellen , Wallenburg Madeline , Wollenzien Hannah , Thompson Ethan , Kumar Kirtana , Feiner Joshua , McNally Moira , Friesen Hunter , Mukherjee Malini , Afeworki Yohannes , Kareta Michael S.
Published: April 2023

SOX2 CUT & RUN mapping
Data from Calcium Sensor, NCS-1, Promotes Tumor Aggressiveness and Predicts Patient Survival
Authors: Moore Lauren M. , England Allison , Ehrlich Barbara E. , Rimm David L.
Published: April 2023

Abstract
Neuronal Calcium Sensor 1 (NCS-1) is a multi-functional Ca2+-binding protein that affects a range of cellular processes beyond those related to neurons. Functional characterization of NCS-1 in neuronal model systems suggests that NCS-1 may influence oncogenic processes. To this end, the biological role of NCS-1 was investigated by altering its endogenous expression in MCF-7 and MB-231 breast cancer cells. Overexpression of NCS-1 resulted in a more aggressive tumor phenotype demonstrated by a marked increase in invasion and motility, and a decrease in cell-matrix adhesion to collagen IV. Overexpression of NCS-1 was also shown to increase the efficacy of paclitaxel-induced cell death in a manner that was independent of cellular proliferation. To determine the association between NCS-1 and clinical outcome, NCS-1 expression was measured in two independent breast cancer cohorts by the Automated Quantitative Analysis method of quantitative immunofluorescence. Elevated levels of NCS-1 were significantly correlated with shorter survival rates. Furthermore, multivariate analysis demonstrated that NCS-1 status was prognostic, independent of estrogen receptor, progesterone receptor, HER2, and lymph node status. These findings indicate that NCS-1 plays a role in the aggressive behavior of a subset of breast cancers and has therapeutic or biomarker potential.

Implications: NCS-1, a calcium-binding protein, is associated with clinicopathologic features of aggressiveness in breast cancer cells and worse outcome in two breast cancer patient cohorts. Mol Cancer Res; 15(7); 942–52. ©2017 AACR.
Data from Integration of Distinct ShcA Signaling Complexes Promotes Breast Tumor Growth and Tyrosine Kinase Inhibitor Resistance
Authors: Ha Jacqueline R. , Ahn Ryuhjin , Smith Harvey W. , Sabourin Valerie , Hébert Steven , Cepeda Cañedo Eduardo , Im Young Kyuen , Kleinman Claudia L. , Muller William J. , Ursini-Siegel Josie
Published: April 2023

Abstract
The commonality between most phospho-tyrosine signaling networks is their shared use of adaptor proteins to transduce mitogenic signals. ShcA (SHC1) is one such adaptor protein that employs two phospho-tyrosine binding domains (PTB and SH2) and key phospho-tyrosine residues to promote mammary tumorigenesis. Receptor tyrosine kinases (RTK), such as ErbB2, bind the ShcA PTB domain to promote breast tumorigenesis by engaging Grb2 downstream of the ShcA tyrosine phosphorylation sites to activate AKT/mTOR signaling. However, breast tumors also rely on the ShcA PTB domain to bind numerous negative regulators that limit activation of secondary mitogenic signaling networks. This study examines the role of PTB-independent ShcA pools in controlling breast tumor growth and resistance to tyrosine kinase inhibitors. We demonstrate that PTB-independent ShcA complexes predominately rely on the ShcA SH2 domain to activate multiple Src family kinases (SFK), including Src and Fyn, in ErbB2-positive breast cancers. Using genetic and pharmacologic approaches, we show that PTB-independent ShcA complexes augment mammary tumorigenesis by increasing the activity of the Src and Fyn tyrosine kinases in an SH2-dependent manner. This bifurcation of signaling complexes from distinct ShcA pools transduces non-redundant signals that integrate the AKT/mTOR and SFK pathways to cooperatively increase breast tumor growth and resistance to tyrosine kinase inhibitors, including lapatinib and PP2. This study mechanistically dissects how the interplay between diverse intracellular ShcA complexes impacts the tyrosine kinome to affect breast tumorigenesis.

Implications: The ShcA adaptor, within distinct signaling complexes, impacts tyrosine kinase signaling, breast tumor growth, and resistance to tyrosine kinase inhibitors. Mol Cancer Res; 16(5); 894–908. ©2018 AACR.
Data from FOXD3 Regulates CSC Marker, DCLK1-S, and Invasive Potential: Prognostic Implications in Colon Cancer
Authors: Sarkar Shubhashish , O'Connell Malaney R. , Okugawa Yoshinaga , Lee Brian S. , Toiyama Yuji , Kusunoki Masato , Daboval Robert D. , Goel Ajay , Singh Pomila
Published: April 2023

Abstract
The 5′ (α)-promoter of the human doublecortin-like kinase 1 (DCLK1) gene becomes epigenetically silenced during colon carcinogenesis, resulting in loss of expression of the canonical long(L)-isoform1 (DCLK1-L) in human colon adenocarcinomas (hCRCs). Instead, hCRCs express a short(S)-isoform2 (DCLK1-S) from an alternate (β)-promoter of DCLK1. The current study, examined if the transcriptional activity of the (β)-promoter is suppressed in normal versus cancerous cells. On the basis of in silico and molecular approaches, it was discovered that FOXD3 potently inhibits the transcriptional activity of the (β)-promoter. FOXD3 becomes methylated in human colon cancer cells (hCCC), with loss of FOXD3 expression, allowing expression of the DCLK1(S) variant in hCCCs/hCRCs. Relative levels of FOXD3/DCLK1(S/L) were measured in a cohort of CRC patient specimens (n = 92), in relation to overall survival (OS). Patients expressing high DCLK1(S), with or without low FOXD3, had significantly worse OS compared with patients expressing low DCLK1(S). The relative levels of DCLK1-L did not correlate with OS. In a pilot retrospective study, colon adenomas from high-risk patients (who developed CRCs in <15 years) demonstrated significantly higher staining for DCLK1(S) + significantly lower staining for FOXD3, compared with adenomas from low-risk patients (who remained free of CRCs). Latter results strongly suggest a prognostic value of measuring DCLK1(S)/FOXD3 in adenomas. Overexpression of DCLK1(S), but not DCLK1(L), caused a significant increase in the invasive potential of hCCCs, which may explain worse outcomes for patients with high DCLK1-S–expressing tumors. On the basis of these data, FOXD3 is a potent repressor of DCLK1-S expression in normal cells; loss of FOXD3 in hCCCs/hCRCs allows upregulation of DCLK1-S, imparting a potent invasive potential to the cells. Mol Cancer Res; 15(12); 1678–91. ©2017 AACR.
Data from Characterization of HCC Mouse Models: Towards an Etiology-Oriented Subtyping Approach
Authors: Friemel Juliane , Frick Lukas , Unger Kristian , Egger Michele , Parrotta Rossella , Böge Yannick T. , Adili Arlind , Karin Michael , Luedde Tom , Heikenwalder Mathias , Weber Achim
Published: April 2023

Abstract
Murine liver tumors often fail to recapitulate the complexity of human hepatocellular carcinoma (HCC), which might explain the difficulty to translate preclinical mouse studies into clinical science. The aim of this study was to evaluate a subtyping approach for murine liver cancer models with regard to etiology-defined categories of human HCC, comparing genomic changes, histomorphology, and IHC profiles. Sequencing and analysis of gene copy-number changes [by comparative genomic hybridization (CGH)] in comparison with etiology-dependent subsets of HCC patients of The Cancer Genome Atlas (TCGA) database were conducted using specimens (75 tumors) of five different HCC mouse models: diethylnitrosamine (DEN) treated wild-type C57BL/6 mice, c-Myc and AlbLTαβ transgenic mice as well as TAK1LPC-KO and Mcl-1Δhep mice. Digital microscopy was used for the assessment of morphology and IHC of liver cell markers (A6-CK7/19, glutamine synthetase) in mouse and n = 61 human liver tumors. Tumor CGH profiles of DEN-treated mice and c-Myc transgenic mice matched alcohol-induced HCC, including morphologic findings (abundant inclusion bodies, fatty change) in the DEN model. Tumors from AlbLTαβ transgenic mice and TAK1LPC-KO models revealed the highest overlap with NASH-HCC CGH profiles. Concordant morphology (steatosis, lymphocyte infiltration, intratumor heterogeneity) was found in AlbLTαβ murine livers. CGH profiles from the Mcl-1Δhep model displayed similarities with hepatitis-induced HCC and characteristic human-like phenotypes (fatty change, intertumor and intratumor heterogeneity).
Implications:
Our findings demonstrate that stratifying preclinical mouse models along etiology-oriented genotypes and human-like phenotypes is feasible. This closer resemblance of preclinical models is expected to better recapitulate HCC subgroups and thus increase their informative value.