tbuckley/cabot-search huggingface dataset:
Abstract A018: Dihydroceramide desaturase 1 (DES1) promotes anchorage-independent survival and metastasis of HER2-positive and basal breast cancer through regulation of caspase 14
Authors: Deanna M Peperno, Danielle Lambadis, Victoria Alvarado, Andrew E Resnick, Christopher J Clarke
Journal: Cancer Research (2024)

Abstract Despite improvements in therapies, metastasis still leads to high mortality rates in breast cancer (BC). Consequently, discovering new therapies that are effective at targeting metastatic disease remains a critical need, particularly for the aggressive HER2+ and basal BC subtypes. The ability of cancer cells to survive in the absence of an extracellular matrix – termed anchorage-independent survival (AIS) – is central to the metastatic cascade and has emerged as a target biology of interest for reducing metastatic burden. Previously, we identified the SL enzyme dihydroceramide desaturase 1 (DES1) as a critical node for AIS of HER2+ BC cells. Here, we have extended these data to show that targeting DES1 through pharmacological inhibitors (4HPR), siRNA, or CRISPR-cas9 knockout was able to overcome AIS in basal BC cells as well as HER2+ BC cells that, functionally, led to a reduction of in vitro colony formation in soft agar. Extending these findings in vivo, we found that DES1 knockout led to a significant reduction in lung metastasis of both HER2+ and basal BC cells in murine models of experimental metastasis. Moreover, treatment of PyMT mice with the DES1 inhibitor 4HPR was able to reduce metastatic burden. To define downstream effectors of DES1 required for AIS, we performed a microarray analysis of control and DES1 knockout cells in suspension, leading us to identify caspase 14 as a downstream effector of DES1 in HER2+ and basal BC. Consistent with these findings, siRNA knockdown of caspase 14 led to a striking decrease in cell viability in colony formation assays. Finally, analysis of publicly available data found that high levels of DES1 and Caspase 14 were associated with poor clinical outcomes in both HER2+ and basal BC. Taken together, these data establish DES1 as a mediator of BC metastasis, likely through promoting AIS, and define caspase 14 as a target of DES1-driven signaling. Furthermore, results suggest that both DES1 and caspase 14 expression may be useful as biomarkers of metastasis-prone tumors. Citation Format: Deanna M Peperno, Danielle Lambadis, Victoria Alvarado, Andrew E Resnick, Christopher J Clarke. Dihydroceramide desaturase 1 (DES1) promotes anchorage-independent survival and metastasis of HER2-positive and basal breast cancer through regulation of caspase 14 [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Breast Cancer Research; 2023 Oct 19-22; San Diego, California. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_1):Abstract nr A018.
Abstract A026: EGF/EGFR signaling in priming for resistance to BRAF/MEK inhibitors in melanoma
Authors: Robert J. Vander Velde, Sydney M. Shaffer
Journal: Cancer Research (2024)

Abstract Targeted therapies kill cancer cells very efficiently. However, the effectiveness of targeted therapies is limited by the eventual emergence of resistance, arising from a small subset of cells capable of surviving therapy. Our work has shown genetically homogeneous cells, in distinct transcriptomic states, are capable of surviving combination BRAF and MEK inhibition. In the presence of targeted therapies these rare cells transform into resistant cells, we therefore call these cells ‘primed’ for resistance. Our research has focused on characterizing these primed cells, however, the mechanisms of survival remain unknown. Since primed cells overexpress receptor tyrosine kinases (RTKs), which are associated with growth and survival, we tested if overexpression of the RTK EGFR could explain priming and subsequent resistance. While melanoma cells in which we artificially overexpressed EGFR had no significant increase in resistance, EGFR overexpressing cells in the presence of exogenous EGF are highly resistant to combination BRAF/MEK inhibition. While EGF is not overexpressed in primed cells, preliminary data suggests that while most cells reduce EGF expression in the presence of BRAF/MEK inhibition, primed cells maintain their baseline expression, potentially maintaining EGF/EGFR signaling in these colonies. We are therefore testing if EGF/EGFR signaling is necessary in vitro by knocking out EGF or EGFR. Furthermore, to test if EGF/EGFR signaling can create a primed state, we used flow cytometry to determine expression of the prime cell marker NT5E. In cells with confirmed EGFR overexpression we observed an increased fraction of NT5E overexpressing cells, suggesting that EGF/EGFR signaling could initiate aspects of primeness beyond simple survival. Further research will determine if EGF/EGFR signaling can initiate an overall primed transcriptional state. The heritability of any primeness as a consequence of EGF/EGFR signaling will inform us if this signaling is a potential cause of priming or a mechanism by which paracrine signaling and/or stromal protection can eventually result in independent resistance. Citation Format: Robert J. Vander Velde, Sydney M. Shaffer. EGF/EGFR signaling in priming for resistance to BRAF/MEK inhibitors in melanoma [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Translating Cancer Evolution and Data Science: The Next Frontier; 2023 Dec 3-6; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_2):Abstract nr A026.
Abstract B071: A genetic approach to selectively inhibit macropinocytosis while sparing autophagy
Authors: Rebecca M Lim, Brandon Chu, Aimee Lara Edinger
Journal: Cancer Research (2024)

Abstract Macropinocytosis is a bulk endocytic process that can fuel tumor growth and drug resistance by providing access to extracellular protein and necrotic cell debris. This process is primarily studied by utilizing the chemical inhibitor, 5-(N-ethyl-N-isopropyl)-Amiloride (EIPA), but this inhibitor is nonselective can hinder proliferation even in non-macropinocytic breast cancer cells. Hence, a more selective, genetic approach is needed. Formation of macropinosomes is dependent on the actin cytoskeleton, which in turn is regulated by CARMIL1, a large multimeric protein that regulates the actin capping protein. CARMIL1 is essential for macropinocytosis, and mutation of two residues in the Capping-Protein Interaction (CPI) region of CARMIL1 to alanine (CARMIL1-AA) limits the CARMIL1-capping protein interaction and more importantly, inhibits macropinocytosis upon introduction of exogenous CARMIL1-AA in tumor cells. Therefore, CARMIL1-AA is a genetic tool to study the effects of macropinocytosis on other cellular processes. However, autophagy, a lysosome-dependent recycling system that enables cell survival, additionally utilizes actin to form autophagosomes. The overall goal of this project is to determine whether CARMIL1-AA specifically inhibits macropinocytosis while still supporting autophagy. CARMIL1-WT and -AA mutant cells were generated using the MMTV-PyMT tumor model and HeLa cell lines and validated for CARMIL1 expression by western blot and quantitative PCR and for macropinocytosis by dextran analysis. These cells were evaluated for autophagic flux by western blot for LC3 I/II and by utilizing a GFP-LC3-RFP-LC3ΔG reporter. Our observation that CARMIL1-AA does not impact autophagy enables further investigation of the importance of macropinocytosis in therapeutic resistance and in shaping the tumor microenvironment. Citation Format: Rebecca M Lim, Brandon Chu, Aimee Lara Edinger. A genetic approach to selectively inhibit macropinocytosis while sparing autophagy [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Breast Cancer Research; 2023 Oct 19-22; San Diego, California. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_1):Abstract nr B071.
Abstract B011: BRCA2 haploinsufficiency induces P53 degradation in primary mammary epithelial cells – a crucial early event in breast tumor promotion
Authors: Haohui Duan, Margaret Gillis, Deboral Dillon, Judy Garber, Shailja Pathania
Journal: Cancer Research (2024)

Abstract The presence of heterozygous germline BRCA2 mutations is associated with an increased risk of breast and ovarian cancer. In order to design effective preventative strategies, it is critical to understand early tumor promoting events that the mammary epithelial cells undergo on their way to tumorigenesis. To investigate the impact of BRCA2 heterozygosity on tumor formation, we utilized primary BRCA2mut/+ mammary epithelial cells obtained from prophylactic breast tissue of women with BRCA2 mutations. Our findings indicate that BRCA2mut/+ cells display haploinsufficiency for repairing stalled replication forks and resolving RPA32 from these sites, indicative of impaired stalled fork repair. Moreover, they exhibit defects in RAD51 recruitment to double strand break sites indicating a defective homologous recombination dependent double strand break repair efficiency. BRCA2mut/+ cells also show increased sensitivity to both replication stress and double strand break-inducing agents. Interestingly, we find that BRCA2 heterozygous cells downregulate P53 protein levels when compared to BRCA2 wild type cells, and that this downregulation is MDM2-dependent. The decreased P53 levels appear to promote the survival of BRCA2 heterozygous cells under endogenous replication stress conditions. Notably, treatment with nutlin, a P53 protein stabilizer, leads to cell death in BRCA2 heterozygous cells but not in BRCA2 wildtype cells, highlighting the sensitivity of BRCA2 heterozygous cells to endogenous P53 protein levels. Moreover, complete loss of P53 in BRCA2 heterozygous cells results in rescue of sensitivity of these cells to both replication stress and double strand break inducing agents. Furthermore, whole genome sequencing analysis of BRCA2 heterozygous cells deleted for P53 reveal DNA mutational signatures similar to those observed in BRCA2 mutant tumors, implying that loss or downregulation of P53 is an early event driving tumorigenesis in the context of BRCA2 heterozygosity. In summary, our study uncovers the significance of BRCA2 haploinsufficiency in replication stress suppression and highlights the role of P53 loss in promoting BRCA2 heterozygosity-driven cancer. These findings contribute to a better understanding of the molecular mechanisms underlying BRCA2-associated tumorigenesis and may have implications for targeted preventative therapies in the future. Citation Format: Haohui Duan, Margaret Gillis, Deboral Dillon, Judy Garber, Shailja Pathania. BRCA2 haploinsufficiency induces P53 degradation in primary mammary epithelial cells – a crucial early event in breast tumor promotion [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Breast Cancer Research; 2023 Oct 19-22; San Diego, California. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_1):Abstract nr B011.
Abstract A031: The role of nuclear epidermal growth factor receptor in cell migration and wound healing
Authors: Danielle M DiFranco, Joyce Schroeder
Journal: Cancer Research (2024)

Abstract In breast cancer cells, epidermal growth factor receptor (EGFR) can retrotranslocate to the nucleus where it acts as a transcription cofactor and activates pro-oncogenic pathways such as stemness and migration. This retrotranslocation can occur through interaction with the BAR domain-containing protein Sorting Nexin 1 (SNX1). Upon retrotranslocation, EGFR is removed from the membrane via the Sec61 translocon, where the now soluble EGFR can interact with heat shock proteins and nuclear importins via its conserved nuclear localization sequence (NLS). Presence of the NLS in all wildtype EGFR indicates nuclear EGFR (nEGFR) also plays a role in non-cancerous tissue. EGFR is a known contributor to wound-healing, migration, and mammary gland development but the role of nEGFR in these processes has yet to be elucidated. Our lab has created cSNX1.3, a peptide-based therapeutic that recapitulates the BAR domain of Sorting Nexin 1. CSNX1.3 competitively binds to EGFR to prevent nuclear trafficking, and this treatment is effective at killing cancer cells that express EGFR, while leaving non-cancerous cells alive. In addition, cSNX1.3 is a potent inhibitor of EGF-dependent cell migration in Triple Negative Breast Cancer cell lines. Based on this data, we hypothesize that, in response to a wound, nEGFR activates cell migration pathways to promote wound healing. To better understand the role of nEGFR in wound healing and migration of non-cancer cell types, we have utilized CRISPR/Cas9 to insert mScarlet or mVenus, improved fluorescent proteins, onto the C-terminus of endogenous EGFR in immortalized MCF10A cells. Using a live cell imaging platform, we discovered that cells on the leading edge of a wound have increased levels of nEGFR. Furthermore, treatment with cSNX1.3 inhibits the migration of MCF10As and reduces levels of nEGFR. This data implies a role for nEGFR in the migration of MCF10As during wound healing. Future studies will delve deeper into the triggers of EGFR retrotranslocation to the nucleus and investigate the specific proteins nEGFR interacts with to affect cell migration. By elucidating the intrinsic role of nuclear EGFR in non-cancerous tissue types, we can better understand how cancer takes advantage of these molecular pathways and possibly its role in the cell migration essential to metastatic progression. Citation Format: Danielle M DiFranco, Joyce Schroeder. The role of nuclear epidermal growth factor receptor in cell migration and wound healing [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Breast Cancer Research; 2023 Oct 19-22; San Diego, California. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_1):Abstract nr A031.
Abstract B002: The impact of mir-4728 on translation and pathway regulation in HER2-amplified breast cancer
Authors: Völundur Hafstad, Euisuk Han, Helena Persson
Journal: Cancer Research (2024)

Abstract MicroRNAs (miRNAs) are a class of small non-coding RNAs that have been implicated in cancer. Our research focuses on the miRNA mir-4728, which is located in an intron in the HER2 locus. The HER2 locus is amplified in approximately 15% of all breast tumors and is associated with a poor prognosis. Current therapeutic strategies for HER2-positive tumors involve targeted inhibition of the HER2 protein with monoclonal antibodies such as trastuzumab in combination with chemotherapy and surgery. However, if mir-4728 has a function independent of its host gene, targeting the HER2 protein alone may be insufficient. To investigate the role of mir-4728, we utilized antisense oligonucleotides to specifically block mir-4728 in a HER2-amplified breast cancer cell line, while leaving the protein receptor in tact. Polysome fractionation and ribosome profiling revealed that blocking the miRNA resulted in a substantial change in protein translation. We hypothesize that this effect may come as a result of mir-4728 being an indirect regulator of EIF4A, a key factor in the initiation of translation. In addition, we have observed changes in the synthesis of aromatase, a crucial enzyme in estrogen synthesis. These findings suggest that mir-4728 may play a role in the regulation of multiple pathways that contribute to cancer progression. Further investigation into this mechanism may provide valuable insight into the development of new therapeutic strategies for cancer treatment. Citation Format: Völundur Hafstad, Euisuk Han, Helena Persson. The impact of mir-4728 on translation and pathway regulation in HER2-amplified breast cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Breast Cancer Research; 2023 Oct 19-22; San Diego, California. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_1):Abstract nr B002.
Abstract A082: Stretching towards relief: The Kent-Collins protocol for radiation-induced eustachian tube dysfunction
Authors: Matthew E Kent, Patrick J Colllins, Ayal A Aizer
Journal: Cancer Research (2024)

Abstract Background: Eustachian tube dysfunction is a common side effect of radiotherapy for head and neck cancers or brain tumors, although few effective treatments exist. The Kent-Collins Protocol represents a novel therapeutic option for post-radiotherapy Eustachian tube dysfunction. Case Presentation: The Kent-Collins Protocol was employed in one patient with Eustachian tube dysfunction following fractionated stereotactic radiotherapy for HER-2 positive breast cancer with cerebral metastases. The Kent-Collins Protocol provided relief of symptoms (conductive hearing loss, aural fullness, and otalgia) for a range of 5 to 45 minutes. The protocol could be repeated when symptoms returned to provide additional relief. The patient also reported psychological benefit from this protocol, knowing the hearing loss was reversible and not likely to be permanent. Conclusions: This case demonstrates the potential of The Kent-Collins Protocol for the treatment of post-radiotherapy Eustachian tube dysfunction. The protocol is effective, inexpensive, easy to teach, and safe, offering an alternative to invasive therapies currently in existence. Citation Format: Matthew E Kent, Patrick J Colllins, Ayal A Aizer. Stretching towards relief: The Kent-Collins protocol for radiation-induced eustachian tube dysfunction [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Breast Cancer Research; 2023 Oct 19-22; San Diego, California. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_1):Abstract nr A082.
Abstract A087: Morphometric analysis of the terminal ductal lobular unit architecture in human breast
Authors: Markus Peurla, Oona Paavolainen, Ella Tammelin, Suvi-Riitta Sulander, Larissa Mourao, Pia Boström, Nina Brück, Colinda LGJ Scheele, Pauliina Hartiala, Emilia Peuhu
Journal: Cancer Research (2024)

Abstract The major lactiferous ducts of the human breast branch out and ultimately end at terminal ductal lobular units (TDLUs). These glandular structures are the source of milk upon lactation, and also the most common origin of breast cancer. Despite their functional and clinical importance, the three dimensional (3D) architecture of TDLUs has remained undetermined, largely due to their absence in rodent animal models. By utilizing recent technological advances in optical tissue clearing and microscopy, we imaged the 3D structure of healthy human breast tissue to determine whether general branching patterns or cell type specific niches exist in the TDLU. Our data demonstrate that TDLUs have a consistent shape and their branch parameters are largely comparable between different TDLUs and individuals irrespective of age or parity. Simulation of TDLU branching morphogenesis in 3D by mathematical modelling suggests that evolutionarily conserved mechanisms regulate mammary gland branching in humans and mice, despite their anatomical differences. The data also demonstrate a new level of organization within the TDLU structure identifying a main branch that dominates in bifurcation events and exhibits a more duct-like keratin expression pattern. In all, our data provide the first structural insights into 3D human breast anatomy and branching, and exemplify the power of volumetric imaging in deeper understanding of human breast biology. Citation Format: Markus Peurla, Oona Paavolainen, Ella Tammelin, Suvi-Riitta Sulander, Larissa Mourao, Pia Boström, Nina Brück, Colinda LGJ Scheele, Pauliina Hartiala, Emilia Peuhu. Morphometric analysis of the terminal ductal lobular unit architecture in human breast [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Breast Cancer Research; 2023 Oct 19-22; San Diego, California. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_1):Abstract nr A087.
Abstract B017: Elucidating the role of CPPED1 in triple-negative breast cancer
Authors: Talieh Zomorrodinia
Journal: Cancer Research (2024)

Abstract Triple-negative breast cancer (TNBC) represents a daunting challenge in clinical oncology due to its aggressive nature and limited treatment options. In light of this unmet need, our research efforts are to gain comprehensive insights into the mechanisms underlying TNBC and explore novel therapeutic strategies. We have identified an enzyme, calcineurin-like phosphoesterase domain-containing protein 1 (CPPED1), that functions as a phosphatase targeting phospho-serine/threonine residues and is amplified in breast cancer. While previous studies on bladder cancer linked CPPED1 to promoting cell death, our preliminary findings in TNBC cell lines, MDA-MB-231 and HS578T, present a contrasting role. Knockdown of CPPED1 in TNBC cell lines leads to reduced cell colony formation and increased apoptosis, indicating its role in promoting cell proliferation in TNBC. Analysis of human patient data from TCGA also shows that expression of CPPED1 is associated with poor survival in both ER+ and ER- breast cancer. These observations hint at CPPED1's potential to exhibit diverse molecular characteristics depending on the cancer type. By thoroughly elucidating the molecular mechanisms and functional role of CPPED1 in breast cancer, our research holds promise in guiding the development of targeted and more effective treatments tailored to address the challenges posed by TNBC. Citation Format: Talieh Zomorrodinia. Elucidating the role of CPPED1 in triple-negative breast cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Breast Cancer Research; 2023 Oct 19-22; San Diego, California. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_1):Abstract nr B017.
Abstract IA001: Molecular archeology of cancer
Authors: Peter Van Loo
Journal: Cancer Research (2024)

Abstract Tumor development is driven by changes to the genome and epigenome leading to fitness advantages underlying successive clonal expansions. As somatic genetic and epigenetic changes occur across most or all cell cycles, the cancer (epi)genome carries an archeological record of its past. Over the past years, we have developed several approaches to mine that archeological record from the cancer genome, which we collectively call 'molecular archeology of cancer'. Using these approaches, we are able to infer the subclonal architecture of tumors, and gain key insights into the order and timing of the genomic changes that occurred over their evolutionary history. We have applied these approaches in a large-scale pan-cancer setting, showing that intra-tumor heterogeneity is pervasive across cancers and that the timelines of tumor evolution span multiple years to decades. Key driver events in tumor evolution typically occur early, and copy number gains often accumulate as punctuated bursts, commonly after genome doubling. Late genome doubling is frequent in cancer evolution and is typically followed by an increase in the rate of copy number gains. Genome duplications affect the selection landscape of copy number losses, while only minimally impacting copy number gains. We have recently also started to develop methods that leverage the cancer epigenome to reconstruct the subclonal architecture of cancer, which will open up new avenues to study tumor evolution. Citation Format: Peter Van Loo. Molecular archeology of cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Translating Cancer Evolution and Data Science: The Next Frontier; 2023 Dec 3-6; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_2):Abstract nr IA001.