tbuckley/cabot-search huggingface dataset:
Abstract B072: Loss of the tumor and metastasis suppressor RasGAP DAB2IP mediates therapeutic resistance in HER2+ breast cancer
Authors: Naiara Perurena, Amy Schade, Natalie Pilla, Patrick Loi, Carrie Rodriguez, Alycia Gardner, Karen Cichowski
Journal: Cancer Research (2024)

Abstract Resistance to HER2 inhibitors remains a clinical challenge in HER2+ breast cancer. Therefore, there is an urgent need to 1) understand the mechanisms that underlie resistance to these current treatments and 2) develop improved, and more importantly, curative combination therapies. We previously showed that the RasGAP DAB2IP is a tumor and metastasis suppressor in breast cancer. Interestingly, we have now generated robust data demonstrating that the loss of DAB2IP also mediates therapeutic resistance in HER2+ breast cancer. First, we genetically ablated DAB2IP in multiple HER2+ breast cancer cell lines and performed manual counting experiments after 6 days of HER2 TKI treatment. In all cell lines, DAB2IP knockdown conferred resistance to HER2 inhibitors. Since HER2 inhibitors are known to induce both apoptosis and senescence, we next investigated how DAB2IP loss specifically affects these phenotypes. Interestingly, DAB2IP knockdown prevented TKI-induced caspase-3/7 activation, measured by Incucyte live cell imaging, and enabled the regrowth of cells in long-term 10-day treatment and drug washout experiments, monitored by Incucyte or crystal violet staining. Mechanistically, stable knockdown of DAB2IP reduced the suppression of the AKT and ERK pathways and the induction of the pro-apoptotic protein Bim upon HER2i treatment. In addition, cell cycle progression pathways were enriched in DAB2IP-deficient cells on lapatinib treatment and immunoblots revealed higher residual levels of pRb and low levels of p27 in these cells. Interestingly, the levels of these proteins were restored and regrowth in low density assays was inhibited with co-treatment with an NF-kB inhibitor. We next evaluated the relevance of DAB2IP loss in mediating HER2 inhibitor resistance in a SUM190 orthotopic xenograft model. Importantly, while control tumors regressed upon lapatinib treatment, DAB2IP-deficient tumors did not regress and grew with kinetics comparable to vehicle-treated tumors after few days on treatment. Further understanding the pathways deregulated by DAB2IP loss upon HER2i treatment will be essential for developing effective therapeutic strategies to combat resistance induced by DAB2IP loss. Citation Format: Naiara Perurena, Amy Schade, Natalie Pilla, Patrick Loi, Carrie Rodriguez, Alycia Gardner, Karen Cichowski. Loss of the tumor and metastasis suppressor RasGAP DAB2IP mediates therapeutic resistance in HER2+ 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 B072.
Abstract A074: Targeting dormant disseminated tumor cells and their permissive niche by pro-resolving mediators derived from resolution-phase macrophages
Authors: Odelya Gilon, Keren Weidenfeld, Hadell Samara, Yonatan Feuermann, Sagie Schif-Zuck, Sergei Butenko, Edmond Sabo, Amiram Ariel, Dalit Barkan
Journal: Cancer Research (2024)

Abstract Metastatic breast cancer can recur years after primary tumor resection and adjuvant therapy and appears to arise from quiescent disseminated tumor cells (QDTC) that persist at distant sites and resist conventional therapies. To date there are no treatments to target QDTCs. Previously, the fibrotic-like microenvironment enriched with Type I collagen (Col-I) was shown to be required for the switch of QDTC to metastatic outgrowth in lungs of mice. Here, we examined whether soluble mediators secreted by ex-vivo generated pro-resolving CD11blow macrophages (CM-Mres) will reinstate resolution of inflammation thus inhibiting the establishment of the fibrotic-like-niche and in turn prevent the emergence of QDTC to metastatic outgrowth. Our findings indicate that CM-Mres promoted immune silencing of alveolar macrophages at the metastatic site where dormant DTCs reside. Immune silencing is one of the hallmarks of resolution of inflammation. Furthermore, CM-Mres inhibited the establishment of a fibrotic-like niche resulting in the inhibition of the metastatic outgrowth in vitro and in vivo. This was due to inhibition of fibroblasts differentiation to myofibroblasts independent of TGFbeta1 canonical signaling and abolishment of Col-I expression. Furthermore, CM-Mres deactivated myofibroblasts as part of the resolution process by inducing an increase in reactive oxygen species (ROS) via activation of NADPH oxidase. This in turn induced DNA damage leading to Go/G1 arrest and intrinsic apoptosis. Similarly, apoptosis mediated by oxidative stress was induced by CM-Mres in dormant and outbreaking QDTCs. Taken together our results demonstrate for the first time that by reinstating resolution of inflammation via physiological mediators, secreted by pro-resolving macrophages, can prevent metastatic outgrowth of QDTCs at their permissive site. Since conventional therapies fail to eradicate dormant DTCs and their transition to clinical metastasis, our findings hold great promise in the quest to identify novel strategies to prevent or treat recurrent metastatic disease. Citation Format: Odelya Gilon, Keren Weidenfeld, Hadell Samara, Yonatan Feuermann, Sagie Schif-Zuck, Sergei Butenko, Edmond Sabo, Amiram Ariel, Dalit Barkan. Targeting dormant disseminated tumor cells and their permissive niche by pro-resolving mediators derived from resolution-phase macrophages [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 A074.
Abstract A015: Mutations in mismatch repair genes that alter subcellular localization of the protein predict resistance to standard therapy but response to cell cycle inhibitors
Authors: Aloran Mazumder, Svasti Haricharan
Journal: Cancer Research (2024)

Abstract Hormone positive breast cancer is one of the most common cancer types in U.S. Every year, over 150,000 patients are detected with this cancer type of which, &amp;gt;40,000 patients will go on to die of their disease. We recently identified defects in a principal mismatch repair (MMR) gene, MLH1, as a driver of resistance to standard-care treatment and poor patient outcomes. Moreover, we demonstrated increased sensitivity to palbociclib, a CDK4/6 inhibitor, in experimental model systems in vitro and in vivo and in clinical trial data. MLH1 is mutated in 5-10% of treatment-resistant tumors, i.e., 4,000 patient tumors every year. However, most of these mutations are missense and variants of unknown significance (VUS). The impact of these mutations on mismatch repair capability and on treatment resistance remains uncertain. Here, we use experimental model systems (ER+/HER2- breast cancer cells, organoid models, and patient tumors) to study how variants of MLH1 and its subcellular localization predicts resistance to standard endocrine therapy but sensitivity to cell cycle inhibitors. We also assessed the ability of nuclear MLH1 to induce activation of G1/S cell cycle checkpoints by activating Chk2. Currently, there are few tests available in the clinic to predict response to therapies early in the timeline of hormone positive breast cancer patients. Due to the nature of the disease, this can result in years of overtreatment. Overtreatment comes at great financial, physical, and emotional cost to patients and their families. We for the first time show that stalling nuclear translocation of MLH1 inhibits Chk2 activation which counterbalances CDK4/6 activity. Therefore, cytoplasmic Mlh1 may be first in-class biomarker for CDK4/6 response in cancer types. Citation Format: Aloran Mazumder, Svasti Haricharan. Mutations in mismatch repair genes that alter subcellular localization of the protein predict resistance to standard therapy but response to cell cycle inhibitors [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 A015.
Abstract A069: The molecular landscape of injury-induced mammary epithelial cell fate switching
Authors: Queralt Vallmajo-Martin, Nikki K. Lytle, Divya Murali, Sumana Srinivasan, Zhibo Ma, Kavitha Mukund, Christopher Dravis, Liliana Zamora, Ana Peterson, Galina Khramtsova, Funmi Olopade, Shankar Subramaniam, Geoffrey M. Wahl
Journal: Cancer Research (2024)

Abstract The most aggressive cancers, such as triple negative basal-like breast cancer (TNBC), have high intratumoral heterogeneity that is often attributed to cell state reprogramming and contributes to cancer progression, treatment resistance, and ultimately cancer death. Tissue injury and microenvironmental changes can cause adult differentiated cells to acquire a plastic “developmentally unstable hybrid cell state” (DUHCS) enabling transdifferentiation into other cell types to effect repair. Yet, the relevant mechanisms that enable cell state reprogramming to arise remain under-explored. Here, we used CRISPR mediated homologous recombination to generate mice in which the mammary basal and luminal cells could be distinguished by their expression of Krt14-mClover-NLS or Krt18-tdTomato-NLS, respectively. We used this novel system to identify mammary epithelial cells undergoing cell state transitions in real time. Using a transplantation paradigm, we found that transplanted basal cells rapidly exhibited a DUHCS resembling mammary embryonic progenitors expressing Sox11, a tightly regulated differentiation factor shut off before birth. We discovered that Sox11 is also expressed in many murine models of TNBC and in single cell transcriptomes from untreated human BRCA1 mutant TNBCs. This suggests that Sox11-expressing cells might be developmentally plastic intermediates in TNBC malignant progression. In a preliminary cohort of patient-derived xenografts from TNBC patients diagnosed at different stages, we detected SOX11-expressing cells in earlier but not in advanced stages. Re-expression of Sox11 in TNBC is consistent with TNBCs being transcriptomically related to fetal mammary stem cells and p53 dysfunction resulting in enhanced cellular plasticity. Taken together, these studies highlight a role for mammary epithelial cell state reprogramming in early breast tumorigenesis, and reveals actionable steps to mitigate tumor heterogeneity by halting tumor progression. Citation Format: Queralt Vallmajo-Martin, Nikki K. Lytle, Divya Murali, Sumana Srinivasan, Zhibo Ma, Kavitha Mukund, Christopher Dravis, Liliana Zamora, Ana Peterson, Galina Khramtsova, Funmi Olopade, Shankar Subramaniam, Geoffrey M. Wahl. The molecular landscape of injury-induced mammary epithelial cell fate switching [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 A069.
Abstract B051: Breast cancer stem cells tolerate chromosomal instability during tumor progression via c-Jun/AXL stress signaling
Authors: Shahnawaz A Baba, Qi Sun, Samson Mugisha, Shreyas Labhsetwar, Richard Klemke, Jay S Desgrosellier
Journal: Cancer Research (2024)

Abstract Chromosomal instability (CIN) is an important driver of tumor evolution and metastasis, yet its role in stemness remains unclear. Here, we describe CIN tolerance as a key attribute of stem-like cancer cells. We identified CIN as a critical stress induced during early tumor initiation that may pose a significant barrier limiting the growth of new tumors. While basal CIN levels were not sufficient to distinguish stem from non-stem cell types, CIN was upregulated in early-stage tumors from breast cancer stem cells in an activated signaling state, suggesting these cells could better tolerate this stress. Indeed, stem-like cell lines were more resistant to increased CIN compared to basal-like cells, despite similar baseline levels. Further, the CIN induced during early tumor initiation appears to be transient, as levels diminish in more established disease. Mechanistically, CIN resistance in stem-like cells is mediated by expression of the receptor tyrosine kinase AXL downstream of activated c-Jun stress signaling. Thus, CIN tolerance due to activation of c-Jun/AXL may be a defining feature of stemness, contributing to breast cancer progression. Citation Format: Shahnawaz A Baba, Qi Sun, Samson Mugisha, Shreyas Labhsetwar, Richard Klemke, Jay S Desgrosellier. Breast cancer stem cells tolerate chromosomal instability during tumor progression via c-Jun/AXL stress signaling [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 B051.
Abstract A039: Metabolic evolution in breast cancer predicts organ-specific metastasis
Authors: Deepti Mathur, Chen Liao, Wendy Lin, Alessandro La Ferlita, Salvatore Alaimo, Samuel Taylor, Yi Zhong, Christine Iacobuzio-Donahue, Alfredo Ferro, Joao Xavier
Journal: Cancer Research (2024)

Abstract The metastatic cascade is a critical component of cancer evolution. Understanding the rewired metabolism in organ-specific metastasis in breast cancer could help identify strategies to improve the treatment and prevention of metastatic disease. Here, we used a systems biology approach to assess the evolution of metabolic fluxes from parental breast cancer cells to their brain- and lung-homing metastatic derivatives. We found that divergent lineages had distinct, heritable metabolic fluxes. Lung-homing cells maintained adaptations for high glycolytic flux despite low levels of glycolytic intermediates, constitutively activating a pathway sink into lactate. This exacerbated Warburg effect –– stronger than the Warburg effect in the primary tumor –– was associated with a high ratio of lactate dehydrogenase (LDH) to pyruvate dehydrogenase (PDH) expression, a signature which correlated with lung metastasis in patients with breast cancer. While feature classification models trained on clinical characteristics alone were unable to predict tropism, the LDH/PDH ratio was a significant predictor of a patient's future metastasis to the lung but not to other organs, independent of other transcriptomic signatures. Lung- and brain-homing lineages had differential selection patterns in acidic metabolic microenvironments. High lactate efflux was also a trait in lung-homing metastatic pancreatic cancer cells, suggesting that lactate production may be a convergent phenotype in lung metastasis. Together, these analyses highlight the essential role that metabolic evolution plays in organ-specific cancer metastasis and identify a putative biomarker for predicting lung metastasis in breast cancer patients. Citation Format: Deepti Mathur, Chen Liao, Wendy Lin, Alessandro La Ferlita, Salvatore Alaimo, Samuel Taylor, Yi Zhong, Christine Iacobuzio-Donahue, Alfredo Ferro, Joao Xavier. Metabolic evolution in breast cancer predicts organ-specific metastasis [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 A039.
Abstract A079: Loss of BPTF restores estrogen-regulated programs and suppress metastatic development of mammary tumors
Authors: Chen Chen, Michael F. Ciccone, Marygrace c. Trousdell, Deeptiman Chatterjee, Yixin Zhao, Steven M. Lewis, Dhivya Anandan, John E. Wilkinson, William C. K. Pomerantz, Adam Siepel, Camila O. dos Santos
Journal: Cancer Research (2024)

Abstract Chromatin remodeling controls transcriptional programs that drive mammary epithelial lineage commitment and cellular differentiation. This process is also important for the regulation of highly dynamic cellular states during mammary tumorigenesis, and perturbing the chromatin landscape of cancer cells can halt cellular and molecular mechanisms of mammary cancer development and progression. However, this paradigm assumes that all cancer cells that develop in the mammary tissue bear the same chromatin dependencies, and rely on similar programs throughout cancer progression. Here, we show that molecular dependencies regulated by the epigenetic factor BPTF control tumor development and progression across distinct mammary cancer cell states. With the utilization of classical models of mammary tumorigenesis, single cell transcriptional profiling, and organoid cultures, we demonstrate that BPTF loss results in the development of mammary tumors with a longer latency of ER•+ expression and tamoxifen sensitivity and the inhibition of lung metastasis development. While gain of ER• expression was associated with gain of luminal markers in Krt5+ BPTF KO mammary epithelial cells (MECs), metastasis-like signatures were significantly perturbed in cells with defined luminal fate. In addition, we detected a partial rescue of metastatic features via the activation of transcriptional programs controlled by TGF-•, thus indicating that BPTF sits atop a canonical metastatic pathway. Collectively, our studies illustrate how BPTF-specific chromatin remodeling inhibition induces phenotypes that differentially affect tumor development and progression, while allowing for the development of a murine model of ER•+ mammary tumorigenesis. Citation Format: Chen Chen, Michael F. Ciccone, Marygrace c. Trousdell, Deeptiman Chatterjee, Yixin Zhao, Steven M. Lewis, Dhivya Anandan, John E. Wilkinson, William C. K. Pomerantz, Adam Siepel, Camila O. dos Santos. Loss of BPTF restores estrogen-regulated programs and suppress metastatic development of mammary tumors [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 A079.
Abstract PR09: Functional and clinical characterization of hypomorphic missense variants in the <i>BRCA2</i> cancer predisposition gene
Authors: Huaizhi (Gilbert) Huang, Chunling Hu, Jie Na, Mohamed Abozaid, Amik Munankarmy, Tara Rao, Carolyn A. Dunn Lumby, Paulo Cilas Morais Lyra, Ronan E. Couch, Benjamin R. Persons, Eric C. Polley, Rachid Karam, Tina Pesaran, Siddhartha Yadav, Alvaro N.A. Monteiro, Nicholas J. Boddicker, Susan M. Domchek, Marcy E. Richardson, Fergus J. Couch
Journal: Cancer Research (2024)

Abstract Many germline BRCA2 missense variants of uncertain significance (VUS) remain to be clinically classified as pathogenic or benign. Here we identify 70 missense VUS in the DNA binding domain (DBD) of BRCA2 that partially reduced homologous recombination DNA repair activity of the protein in a homology directed DNA repair cell-based assay. CRISPR/cas9-based knockin of these variants reduced cell survival of haploid cells and conferred increased sensitivity to the PARP inhibitor Olaparib. Sequence alignment analysis found that the variants were highly conserved across species from pufferfish to human. Structural analysis showed that these variants are located predominantly in unstructured regions of the DBD. Case-control association studies showed that the hypomorphic variants conferred moderate risks of breast (OR:2.85; 95%CI:1.43-5.88) and ovarian cancer (OR:3.37; 95%CI:1.30-8.54) that were significantly different from risks associated with known pathogenic and benign variants. Cumulative lifetime risks of breast and ovarian cancer among carriers were estimated at 25% and 4.7%, respectively. Age at diagnosis of breast cancer among hypomorphs carriers was 55 years of age as opposed to 48 years of age for carriers of pathogenic variants. In addition, the combination of functional and other genetic data in an ACMG/AMP-like variant classification model reclassified 39 variants as likely pathogenic. This novel group of low penetrance missense variants further calibrate BRCA2 variant classification methods and have significant implications for the management of variant carriers. Citation Format: Huaizhi (Gilbert) Huang, Chunling Hu, Jie Na, Mohamed Abozaid, Amik Munankarmy, Tara Rao, Carolyn A. Dunn Lumby, Paulo Cilas Morais Lyra, Ronan E. Couch, Benjamin R. Persons, Eric C. Polley, Rachid Karam, Tina Pesaran, Siddhartha Yadav, Alvaro N.A. Monteiro, Nicholas J. Boddicker, Susan M. Domchek, Marcy E. Richardson, Fergus J. Couch. Functional and clinical characterization of hypomorphic missense variants in the BRCA2 cancer predisposition gene [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 PR09.
Abstract A090: Gender Disparities in the National Institutes of Health Funding for Breast Oncology
Authors: Janta Ukrani, Aruba Sohail, Sarah Khan, Ibrahim Zahid, Muhammad Zain Farooq, Michael Vishal Jaglal
Journal: Cancer Research (2024)

Abstract Introduction As a matter of course, there has been an under-representation of women in academic medicine, resulting in discriminatory distribution of research grants. This study examines the trend of funding allocation of R01 grants in Breast oncology by the National Institutes of Health with specific focus on the distribution of funding between gender. Methods The data were retrieved from the NIH RePORTER (Research Portfolio Online Reporting Tools Expenditure) using breast oncology-related search terms from 2018-2021. The gender was categorized using Genderize. The number of citations, publications, H-index, and seniority were obtained from Scopus and Web of Science in December 2022. Consumer Price Index was used to adjust funding amount to 2021 equivalent U.S. dollars. Linear regression was used for analysis. Results A total of 885 NIH-funded R01 grants amounting to $444.6 million were awarded for breast oncology research. Women (n=390; 44.1% [95% CI: 40.8%-47.3%]) received relatively fewer grants than men (n=495; 55.9% [95% CI: 52.7%-59.2%]). From 2018-2021, there was a significant increase in the number of grants awarded among both men (90 to 155, p&amp;lt;0.01) and women (71 to 115, p=0.036). Similarly, there was a significant increase in the grant amount (in millions) awarded among men (43.4 to 76.5, p&amp;lt;0.01) but not in women (36.7 to 56.1, p=0.11). Of the 212 co-PIs, 133 (62.7% [95% CI: 56.2%-69.2%]) were men and 76 (37.3% [95% CI: 30.8%-43.8%]) were women. There was no significant difference in h-index (48 vs 44, p=0.12), number of publications (158 vs 138, p=0.08), and citations (13272 vs 8092, p=0.06) between the male and female PIs. Funding amount was significantly associated with number of publications (β=0.35, p&amp;lt;0.01), seniority (β=0.25, p&amp;lt;0.01) and institution (p&amp;lt;0.01). Conclusion Our analysis shows continued gender disparity as only 44% of total R01 grants were awarded towards females for breast oncology between the fiscal years 2018 to 2021. Though the proportion of discrepancy is lower as compared to other malignancies. A collaborative effort is still needed to bridge the gap and advance gender equality. Citation Format: Janta Ukrani, Aruba Sohail, Sarah Khan, Ibrahim Zahid, Muhammad Zain Farooq, Michael Vishal Jaglal. Gender Disparities in the National Institutes of Health Funding for Breast Oncology [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 A090.