bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 6933: Decoding the archetypes and eco-hubs of triple-negative breast cancer in responses to chemotherapy
Authors: Yan Yun , Lin Yiyun , Kumar Tapsi , Bai Shanshan , Li Jianzhuo , Tran Tuan , Hu Min , Ravenberg Elizabeth , Rauch Maia , Clayborn Alyson , Thompson Alastair , Lim Bora , Huo Lei , Moulder Stacy , Yam Clinton , Navin Nicholas 
Published: March 2024

Abstract
Triple-negative breast cancer (TNBC) is a highly aggressive type of breast cancer commonly treated with neoadjuvant chemotherapy (NAC). While about 50% of patients achieve a pathological complete response (pCR), the remainder often develop resistance and metastasis, leading poor survivals. Currently, the factors linking pre-treatment cancer cells and the tumor microenvironment (TME) to NAC response are unclear. To investigate this question, we conducted single-cell RNA sequencing on fresh pre-treatment core biopsy samples collected from patients in the ARTEMIS clinical trial. We identified 13 gene expression meta-programs of cancer cells and about 50 cell states of immune and stromal cell types. Based on the cancer cells alone, we identified four TNBC archetypes at patient-level: luminal secretory-associated (LSA), basal-associated (BA), immunoreactive (IR), and luminal androgen receptor (LAR). Notably, the archetype BA and IR were associated with non-pCR and pCR, respectively. Additionally, we found the TNBC ecosystem was composed of eight eco-hubs, reflecting the co-occurrence patterns of cancer and TME cell states. These eco-hubs revealed different cell community across archetypes and NAC outcomes. For example, an eco-hub with a co-occurrence of interferon response-related cancer cells and immune cells was prevalent in the archetype IR and pCR patients. To facilitate a clinical application, we further developed a 13-gene-based machine learning model to predict NAC response. In summary, these results provide new insights into the cellular determinants of TNBC biology and chemotherapeutic response.
Citation Format: Yun Yan, Yiyun Lin, Tapsi Kumar, Shanshan Bai, Jianzhuo Li, Tuan Tran, Min Hu, Elizabeth Ravenberg, Maia Rauch, Alyson Clayborn, Alastair Thompson, Bora Lim, Lei Huo, Stacy Moulder, Clinton Yam, Nicholas Navin. Decoding the archetypes and eco-hubs of triple-negative breast cancer in responses to chemotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6933.
Abstract 6937: High throughput single cell simultaneous DNA and RNA sequencing identified cell-of-origin of breast cancer
Authors: Wang Kaile , Ye Rui , Bai Shanshan , Xiao Zhenna , Yano Lei , Li Jianzhuo , Lin Yiyun , Sei Emi , Lin Steven , Thompson Alastair , Krishnamurthy Savitri , Navin Nicholas 
Published: March 2024

Abstract
Understanding the relationship between genotype and phenotype in breast cancer cells has been challenging at single cell resolution, mainly because existing high-throughput methods are limited to measuring a single modality and data must be integrated indirectly via computational methods. To address this challenge, we developed wellDR-seq, a high-throughput single cell method that can simultaneously measure the single cell whole genome and transcriptome directly from thousands of single cells in parallel. Using this method, we profiled 17,427 single cells in 6 different ER+ breast cancer patients with either premalignant disease (Ductal-carcinoma-in-situ) or invasive ductal carcinoma (IDC). From these data we identified the epithelial cell-of-origin in 3 cases, showing that ER+ breast cancer cells originated from Luminal Hormone Responsive (LumHR) in the normal breast tissues. We also found that autosomal somatic copy number aberrations were exclusively present in LumSec (&lt; 2%) and LumHR epithelial cells, while chrX gain or loss also occurred in stromal cells (eg fibroblast and endothelial) but a low frequency (&lt;2%) in our datasets. Additionally, our data show the impact of subclonal copy number profiles on gene expression programs, which reflects both gene dosage effects in CNA regions and more complex deregulation in copy-neutral regions. wellDR-seq offers a powerful tool for large-scale single cell genome and transcriptome simultaneous sequencing across different clinical samples, opens new avenue to investigate genotype and phenotypes interactions, identify tumor cells origins, reveal somatic copy number and mutation events, quantify the gene dosage effect and discerning differential genes expression between tumor subclones.
Citation Format: Kaile Wang, Rui Ye, Shanshan Bai, Zhenna Xiao, Lei Yano, Jianzhuo Li, Yiyun Lin, Emi Sei, Steven Lin, Alastair Thompson, Savitri Krishnamurthy, Nicholas Navin. High throughput single cell simultaneous DNA and RNA sequencing identified cell-of-origin of breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6937.
Abstract 6952: The role of interleukin-11 (IL11) in cancer-associated cachexia (CAC)
Authors: Drinkwater Kimberly , Meyers Ashlyn , Kargari Samin , Crisan Natalie , Mody Aaron , Shim Minsub 
Published: March 2024

Abstract
Cancer-associated cachexia (CAC), characterized by loss of skeletal muscle and involuntary body weight loss, is responsible for increased chemotherapy toxicity, reduced quality of life, and impaired survival in cancer patients. While interleukin-11 (IL11), one of the IL6 family cytokines, was originally thought to be involved in hematopoiesis, studies increasingly suggest its involvement in tumorigenesis including chemoresistance, metastasis, and survival of cancer cells. However, the precise role of IL11 in CAC has not been determined. Our lab has previously shown that IL11 treatment suppressed the myogenic differentiation of C2C12 myoblasts, suggesting that IL11 may interfere with differentiation and subsequent regeneration of muscle. In this study, we investigated the role of IL11 in cancer-induced muscle wasting using cell culture and mouse models. The mRNA expression of IL11 was highly up-regulated in C26 and Lewis lung carcinoma (LLC) cells, two well-known cachectic mouse cancer cell lines, while its expression was low in a non-cachectic MC38 mouse colon cancer cell line. Knockdown of IL11 in C26 cells using two independent lentiviral shRNAs significantly reduced the mRNA levels of the cytokines involved in CAC including GDF15, LIF, and VEGFA, while the mRNA level of IL6 was not significantly altered. Additionally, IL11 knockdown significantly reduced the mRNA and protein levels of ATF4, CHOP, and TRIB3, suggesting that IL11 may be responsible for the activation of unfolded protein response, an adaptive mechanism for growth, survival, and angiogenesis of cancer. Knockdown of IL11 in C26 and LLC cell lines also significantly reduced the volume of tumors in syngeneic mouse models, while over-expression of IL11 in MC38 cells increased tumor size. Moreover, the knockdown of IL11 in cachectic cancer cells partially prevented the loss of muscle and body weight in tumor-bearing mice, although the amelioration of muscle loss by IL11 knockdown may be associated with the decreased tumor burden. Together, these results indicate that IL11 may contribute to muscle wasting and provide novel insight into the previously unestablished role of IL11 in CAC.
Citation Format: Kimberly Drinkwater, Ashlyn Meyers, Samin Kargari, Natalie Crisan, Aaron Mody, Minsub Shim. The role of interleukin-11 (IL11) in cancer-associated cachexia (CAC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6952.
Abstract 6955: Activation of ERK pathway by mutant Ras oncoproteins derived from THP-1 cell exosomes
Authors: Hwang Joseph B. , Marquardt Laura , Sait Osama , Gilliam Brooke , Xiao Qiang 
Published: March 2024

Abstract
The study of exosomes has attracted worldwide research due to its ability to modulate cellular activities, especially in the progression of cancer. Exosomes are membrane vesicles that can deliver lipids, proteins, and nucleic acids from one cell to another through membrane fusion, providing a unique form of cell-to-cell communication. It has been shown that KRAS G12V oncoprotein has been detected inside various pancreatic cancer cell derived exosomes. Our goal for this study was to examine the effect of KRAS G12V oncoprotein, detected inside exosomes isolated from THP-1 cell line supernatant, to activate MAPK pathway in MCF-7 breast cancer and AsPC-1 pancreatic cancer cells. To this end, we developed MILLIPLEX® immunoassays to detect cell signaling proteins as well as the exosome markers (CD9, CD63 and CD81), using Luminex® xMAP® technology which allows multiplex detection of proteins in a small volume of sample. Exosomes were isolated from THP-1 derived cell supernatant, using Qiagen exoEasy Maxi kit according to the kit protocol. KRAS G12V oncoprotein was detected in isolated THP-1 exosomes. As a control, THP-1 exosomes were enriched with exosome markers such as CD9, CD63 and CD81. After 48-hour incubation of AsPC-1 cells with KRAS G12V containing THP-1 exosomes, significant increase in KRAS G12V levels were detected in AsPC-1 cells. More importantly, this increase in KRAS G12V levels corresponded with an increase in phosphorylated ERK signaling, but not JNK, p38, NFκB, Akt, STAT3 and STAT3 pathways. In contrast, 48-hour incubation of MCF-7 cells with KRAS G12V containing THP-1 exosomes had no effect on any signaling pathways. Using MILLIPLEX® multiplex immunoassays, our data supports research findings that exosomes contain mitogenic signaling components that may enhance progression of cancer.
Citation Format: Joseph B. Hwang, Laura Marquardt, Osama Sait, Brooke Gilliam, Qiang Xiao. Activation of ERK pathway by mutant Ras oncoproteins derived from THP-1 cell exosomes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6955.
Abstract 6961: The cell adhesion molecule ninjurin 2 modulates tumorigenesis, inflammatory response and metabolism via modulating and pyroptosis
Authors: Zhang Jin , Zhang Weici , Chen Xinbin 
Published: March 2024

Abstract
The nerve injury induced protein 2 (NINJ2) belongs to a family of homophilic adhesion molecules and was initially found to be involved in nerve regeneration. However, the role of NINJ2 in other cellular process are not well studied. Here, by generating a Ninj2-deficient mouse model, we showed that mice deficient in Ninj2 have a short lifespan and are prone to spontaneous tumors, systemic inflammation and metabolic defects. To better understand the metabolic traits that contributes to these phenotypes, we performed comprehensive carbohydrate and lipid metabolic analyses. Indeed, carbohydrate metabolic analyses indicated that NINJ2-deficiency led to defects in monosaccharide metabolism along with accumulation of multiple disaccharides and sugar alcohols. Similarly, lipidomic analyses indicated that Ninj2 deficiency altered patterns of several lipids including triglycerides, phospholipids and ceramides. To identify a cellular process that associate with these metabolic defects, we examined the role of Ninj2 in pyroptosis, a programmed cell death that links cancer, inflammation and metabolic disorders. Indeed, we found that loss of NINJ2 promotes pyroptosis by activating the NLRP3 inflammasome. Taken together, these data reveal a critical role of NINJ2 in tumorigenesis, inflammatory response, and metabolism via modulating pyroptosis.
Citation Format: Jin Zhang, Weici Zhang, Xinbin Chen. The cell adhesion molecule ninjurin 2 modulates tumorigenesis, inflammatory response and metabolism via modulating and pyroptosis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6961.
Abstract 6968: Extracellular vesicles as carriers of signaling factors in cancer
Authors: Schubert Antonia , Winkler Nadine , Mongkolsittisilp Ajaree , Schulz Matthias , Voloshanenko Oksana , Schaffrinski Meike , Kranz Dominique , Nienhaus Karin , Jäger Dirk , Trümper Lorenz , Büntzel Judith , Binder Claudia , Nienhaus Gerd Ulrich , Boutros Michael 
Published: March 2024

Abstract
Extracellular vesicles (EVs) are small, membrane-bound structures released by cells. They contain various biomolecules and have emerged as mediators of cellular signaling. EVs of various origins can be isolated from body fluids and hold potential as novel biomarkers. However, their clinical implementation as biomarkers is hampered by complex isolation procedures, limited expertise in routine labs, and a lack of mechanistic understanding of signal transfer, particularly in vivo.
To better understand how EVs carry oncogenic signaling factors, we performed mechanistic investigations into the role of EVs in WNT signaling as a representative cancer-associated signaling pathway, as well as ex vivo validation experiments analyzing patient-derived EVs.
Hydrophobic WNT ligands can use EVs to travel the extracellular space. However, little is known about the quantities of WNT secretion onto different EV fractions and potentially other vehicles. To explore WNT secretory routes and potential functional differences, we generated fluorescently tagged marker constructs of the non-canonical ligand WNT5a, which has context-dependent tumor-suppressing or -promoting functions in cancer. In additional in vitro experiments, we tested how the WNT signaling activation state and cancer-specific WNT mutations, such as CRISPR/Cas9-induced APC truncations, quantitatively and qualitatively affect EV shedding in colorectal cancer cell lines. Further functional testing of EV-bound vs. non-EV WNT ligands is ongoing.
For proof-of-concept analyses and to test EVs as biomarkers, we set up the liquid biopsy study EValuate. The project aims for cross-entity analysis of EV profiles and correlation of results to cancer presence, stage, and survival. For quality control and before pipeline implementation, we tested various EV isolation methods and compared different sample pre-processing steps.
By combining multidisciplinary expertise in biophysics, molecular biology, and basic and clinical cancer research, we aim to gain a better mechanistic understanding of EV-mediated signal transfer and facilitate the integration of EVs as diagnostic and prognostic biomarkers into clinical studies.
Citation Format: Antonia Schubert, Nadine Winkler, Ajaree Mongkolsittisilp, Matthias Schulz, Oksana Voloshanenko, Meike Schaffrinski, Dominique Kranz, Karin Nienhaus, Dirk Jäger, Lorenz Trümper, Judith Büntzel, Claudia Binder, Gerd Ulrich Nienhaus, Michael Boutros. Extracellular vesicles as carriers of signaling factors in cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6968.
Abstract 6973: Investigates the role of exosomes in dasatinib treated HT29 colon cancer cells
Authors: Koo Hui Min , Lu Yi-Wen , Hou Xiang-Ling , Chao Wei-Ting 
Published: March 2024

Abstract
The mortality rate due to metastasis in cancer is as high as 90%. The underlying mechanisms have been studied, however, the process of metastasis is complicated, current therapies still cannot inhibit metastasis efficiently. In recent years, studies have mentioned that extracellular vesicles play an important role in cancer cell metastasis and tumor microenvironment. Extracellular vesicles can be divided into microvesicles, apoptotic bodies and exosomes, which can carry different substances into the tumor microenvironment. Especially exosomes, whose diameter is around 30-160nm, can carry DNA, RNA, miRNA, membrane proteins, lipids and other intracellular molecules into the cell through endocytosis for regulation. The process of metastasis and the drug resistance were also been demonstrated can be regulated by exosomes. At present, the physiological functions of exosomes are not clear. HT29 colon cancer cells previously discovered in our laboratory can have different responses to dasatinib treatment, and cells can be isolated to dasatinib selected cells(DSTS) and resistant cells(DSTR). In this study, the role of exosome upon dasatinib treatment in HT29 cell is investigated. In the experiment, exosomes from HT29, DSTS, and DSTR were isolated by ExoQuick-TC. Transmission electron microscope was used to observe the difference in exosome size. Exosomes from different cells were treated in HT29 cells, and differences at the protein and mRNA levels were observed using western blot and reverse transcription-polymerase chain reaction(RT-PCR). In my results, the diameter of exosomes in DSTS cells was smaller than that in DSTR and HT29 cells. The protein expression levels of Cavoelin-1 and Clathrin in HT29 were also increased in the treatment of exosome that from three types of cells. In addition, the DSTR derived-exosomes can induce the expression of pFAK and Clathrin mRNA in HT29 cells. The preliminary results suggest that DSTR derived-exosomes may affect cell migration. This study provides the clues that through understanding exosomes that secreted from different cells, cancer diagnosis and treatment can be conducted according to their characteristics, so as to reduce the possibility of cell metastasis precisely.
Citation Format: Hui Min Koo, Yi-Wen Lu, Xiang-Ling Hou, Wei-Ting Chao. Investigates the role of exosomes in dasatinib treated HT29 colon cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6973.
Abstract 6979: Uncovering the BRAF interactome to identify novel therapeutic targets for BRAF driven melanoma and lung cancer
Authors: OToole Kayla T. 
Published: March 2024

Abstract
BRAF protein kinases act downstream of RAS-GTP and upstream of MEK&gt;ERK MAP Kinase signaling. Notably, mutational activation of BRAF is a driver of approximately 8% of all cancers, with a particular prevalence in lung cancer, thyroid cancer, and melanoma. Importantly, melanoma is responsible for the largest number of skin cancer deaths per year. Patients whose melanoma is driven by mutationally-activated BRAF account for ~50% of cutaneous melanoma cases. The most common mutational alteration is BRAFT1799A, which encodes the BRAFV600E oncoprotein kinase. Combined inhibition of BRAFV600E plus MEK1/2 has been approved for the treatment of BRAFV600E-driven melanoma and lung cancer. Although patients with mutationally-activated BRAF often have a significant response to BRAFV600E-targeted therapeutics, many patients develop lethal drug-resistant disease. The BRAFV600E oncoprotein kinase is proposed to be a monomer, yet many questions remain regarding the biochemistry of these signaling interactions. Thus, we aim to better understand the molecular mechanisms driving BRAFV600E-mediated melanoma and lung cancer cell growth. Preliminary data using gel filtration chromatography and immunoblotting analysis indicates that BRAFV600E is detected in a large multiprotein complex. Interestingly, the addition of a BRAFV600E inhibitor, vemurafenib, shifted the elution of complexes with BRAFV600E into lower molecular weight fractions. Based on these preliminary results, we characterized the components of these complexes to advance our understanding of how mutationally activated BRAF exists in melanoma cells; and thus, provide future insight into how we can better therapeutically target BRAFV600E. Moreover, in order to further elucidate BRAF interactions, we employed a novel form of proximity labeling, TurboID, to unbiasedly identify novel BRAF interactors and better understand how drug treatments change the BRAF interactome. The top ten statistically significant interactors are being investigated to understand how BRAF complexes are formed within the cell, how the complexes are influenced by drug treatments, and how important the individual components are in the formation of complexes with BRAF. Here, we investigate an interaction between BRAFV600E and the tumor suppressor, TP53. Moreover, elucidating the molecular architecture of BRAFV600E signaling complexes could highlight new therapeutic options for patients who display either primary or acquired resistance to inhibitors of BRAFV600E signaling.
Citation Format: Kayla T. OToole. Uncovering the BRAF interactome to identify novel therapeutic targets for BRAF driven melanoma and lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6979.