bluuebunny/crossref_metadata_2025 huggingface dataset:
Figure S6 from CD38 x ICAM-1 Bispecific Antibody Is a Novel Approach for Treating Multiple Myeloma and Lymphoma
Authors: Chen Xiaocheng , Wong Oi Kwan , Reiman Lauren , Sherbenou Daniel W. , Post Leonard
Published: February 2024

Low toxicity on non-plasma cells
Figure S4 from CD38 x ICAM-1 Bispecific Antibody Is a Novel Approach for Treating Multiple Myeloma and Lymphoma
Authors: Chen Xiaocheng , Wong Oi Kwan , Reiman Lauren , Sherbenou Daniel W. , Post Leonard
Published: February 2024

FACS analysis of NK92 cells
Figure S12 from CD38 x ICAM-1 Bispecific Antibody Is a Novel Approach for Treating Multiple Myeloma and Lymphoma
Authors: Chen Xiaocheng , Wong Oi Kwan , Reiman Lauren , Sherbenou Daniel W. , Post Leonard
Published: February 2024

ICAM-1 and CD38 expression after TNFa treatment
Supplementary Fig. S8 from Amelioration of Tumor-promoting Microenvironment via Vascular Remodeling and CAF Suppression Using E7130: Biomarker Analysis by Multimodal Imaging Modalities
Authors: Ito Ken , Yamaguchi Masayuki , Semba Taro , Tabata Kimiyo , Tamura Moe , Aoyama Muneo , Abe Takanori , Asano Osamu , Terada Yasuhiko , Funahashi Yasuhiro , Fujii Hirofumi
Published: February 2024

ktrans and apparent diffusion coefficient (ADC) values in xenografted tumors
Supplementary Fig. S7 from Amelioration of Tumor-promoting Microenvironment via Vascular Remodeling and CAF Suppression Using E7130: Biomarker Analysis by Multimodal Imaging Modalities
Authors: Ito Ken , Yamaguchi Masayuki , Semba Taro , Tabata Kimiyo , Tamura Moe , Aoyama Muneo , Abe Takanori , Asano Osamu , Terada Yasuhiko , Funahashi Yasuhiro , Fujii Hirofumi
Published: February 2024

E7130 reduced CA-9, a hypoxia marker, expression level in the MCF-7 xenografted tumors
Supplementary Fig. S6 from Amelioration of Tumor-promoting Microenvironment via Vascular Remodeling and CAF Suppression Using E7130: Biomarker Analysis by Multimodal Imaging Modalities
Authors: Ito Ken , Yamaguchi Masayuki , Semba Taro , Tabata Kimiyo , Tamura Moe , Aoyama Muneo , Abe Takanori , Asano Osamu , Terada Yasuhiko , Funahashi Yasuhiro , Fujii Hirofumi
Published: February 2024

Representative IHC image for CD31 and Collagen IV (Col IV) expression levels in various xenografted tumors
Supplementary Table 1 from An Antibody–Drug Conjugate Directed to Tissue Factor Shows Preclinical Antitumor Activity in Head and Neck Cancer as a Single Agent and in Combination with Chemoradiotherapy
Authors: Bakema Jantine E. , Stigter-van Walsum Marijke , Harris Jeffrey R. , Ganzevles Sonja H. , Muthuswamy Anantharaman , Houtkamp Mischa , Plantinga Theo S. , Bloemena Elisabeth , Brakenhoff Ruud H. , Breij Esther C.W. , van de Ven Rieneke
Published: February 2024

HNSCC cell lines characteristics
Supplementary Fig. S10 from Amelioration of Tumor-promoting Microenvironment via Vascular Remodeling and CAF Suppression Using E7130: Biomarker Analysis by Multimodal Imaging Modalities
Authors: Ito Ken , Yamaguchi Masayuki , Semba Taro , Tabata Kimiyo , Tamura Moe , Aoyama Muneo , Abe Takanori , Asano Osamu , Terada Yasuhiko , Funahashi Yasuhiro , Fujii Hirofumi
Published: February 2024

Plasma TGF-β1 levels in human breast and SCCHN cancer patients
Supplemental Table S3 from Amelioration of Tumor-promoting Microenvironment via Vascular Remodeling and CAF Suppression Using E7130: Biomarker Analysis by Multimodal Imaging Modalities
Authors: Ito Ken , Yamaguchi Masayuki , Semba Taro , Tabata Kimiyo , Tamura Moe , Aoyama Muneo , Abe Takanori , Asano Osamu , Terada Yasuhiko , Funahashi Yasuhiro , Fujii Hirofumi
Published: February 2024

List of ELISA kits for vasculature markers
Table S3 from SKP2 Knockout in Rb1/p53–Deficient Mouse Models of Osteosarcoma Induces Immune Infiltration and Drives a Transcriptional Program with a Favorable Prognosis
Authors: Ferrena Alexander , Wang Jichuan , Zhang Ranxin , Karadal-Ferrena Burcu , Al-Hardan Waleed , Singh Swapnil , Borjihan Hasibagan , Schwartz Edward L. , Zhao Hongling , Oktay Maja H. , Yang Rui , Geller David S. , Hoang Bang H. , Zheng Deyou
Published: February 2024

SKP2 gene correlation results from NCI TARGET OS cohort
Table S2 from SKP2 Knockout in Rb1/p53–Deficient Mouse Models of Osteosarcoma Induces Immune Infiltration and Drives a Transcriptional Program with a Favorable Prognosis
Authors: Ferrena Alexander , Wang Jichuan , Zhang Ranxin , Karadal-Ferrena Burcu , Al-Hardan Waleed , Singh Swapnil , Borjihan Hasibagan , Schwartz Edward L. , Zhao Hongling , Oktay Maja H. , Yang Rui , Geller David S. , Hoang Bang H. , Zheng Deyou
Published: February 2024

DESeq2 results and DESEq2 size-factor normalize counts for TKO vs DKO bulk RNAseq samples
Figure S8 from SKP2 Knockout in Rb1/p53–Deficient Mouse Models of Osteosarcoma Induces Immune Infiltration and Drives a Transcriptional Program with a Favorable Prognosis
Authors: Ferrena Alexander , Wang Jichuan , Zhang Ranxin , Karadal-Ferrena Burcu , Al-Hardan Waleed , Singh Swapnil , Borjihan Hasibagan , Schwartz Edward L. , Zhao Hongling , Oktay Maja H. , Yang Rui , Geller David S. , Hoang Bang H. , Zheng Deyou
Published: February 2024

Gene set overrepresentation analysis of genes significantly correlated with SKP2 in the NCI TARGET OS cohort
Figure S7 from SKP2 Knockout in Rb1/p53–Deficient Mouse Models of Osteosarcoma Induces Immune Infiltration and Drives a Transcriptional Program with a Favorable Prognosis
Authors: Ferrena Alexander , Wang Jichuan , Zhang Ranxin , Karadal-Ferrena Burcu , Al-Hardan Waleed , Singh Swapnil , Borjihan Hasibagan , Schwartz Edward L. , Zhao Hongling , Oktay Maja H. , Yang Rui , Geller David S. , Hoang Bang H. , Zheng Deyou
Published: February 2024

SKP2 KO signature is associated with macrophages and improved survival in Kuijjer 2012 OS cohort
Figure S5 from SKP2 Knockout in Rb1/p53–Deficient Mouse Models of Osteosarcoma Induces Immune Infiltration and Drives a Transcriptional Program with a Favorable Prognosis
Authors: Ferrena Alexander , Wang Jichuan , Zhang Ranxin , Karadal-Ferrena Burcu , Al-Hardan Waleed , Singh Swapnil , Borjihan Hasibagan , Schwartz Edward L. , Zhao Hongling , Oktay Maja H. , Yang Rui , Geller David S. , Hoang Bang H. , Zheng Deyou
Published: February 2024

Immunohistochemistry for macrophage markers
Data from CD38 x ICAM-1 Bispecific Antibody Is a Novel Approach for Treating Multiple Myeloma and Lymphoma
Authors: Chen Xiaocheng , Wong Oi Kwan , Reiman Lauren , Sherbenou Daniel W. , Post Leonard
Published: February 2024

Abstract
The cluster of differentiation 38 (CD38) is a well-validated target for treating multiple myeloma. Although anti-CD38 mAbs have demonstrated outstanding initial responses in patients with multiple myeloma, nearly all patients eventually develop resistance and relapse. In addition, currently approved CD38 targeting therapies have failed to show monotherapy efficacy in lymphomas, where CD38 expression is present but at lower levels. To effectively target CD38 on tumor cells, we generated an antibody-dependent cellular cytotoxicity (ADCC) enhanced bispecific CD38 x intercellular cell adhesion molecule 1 (ICAM-1) antibody, VP301. This bispecific antibody targets unique epitopes on CD38 and ICAM-1 on tumor cells with reduced red blood cell binding compared with the benchmark CD38 antibody daratumumab. VP301 demonstrated potent ADCC and antibody-dependent cellular phagocytosis activities on a selected set of myeloma and lymphoma cell lines even those with low CD38 expression. In an ex vivo drug sensitivity assay, we observed responses to VP301 in multiple myeloma primary samples from relapsed/refractory patients. Moreover, VP301 demonstrated potent tumor inhibition activities in in vivo myeloma and lymphoma models. Interestingly, combination of VP301 with the immunomodulatory drug, lenalidomide, led to synergistic antitumor growth activity in an in vivo efficacy study. In conclusion, the CD38 x ICAM-1 bispecific antibody VP301 demonstrated promising efficacy and specificity toward CD38+ and ICAM-1+ tumor cells and represents a novel approach for treating multiple myeloma and lymphoma.
Data from Amelioration of Tumor-promoting Microenvironment via Vascular Remodeling and CAF Suppression Using E7130: Biomarker Analysis by Multimodal Imaging Modalities
Authors: Ito Ken , Yamaguchi Masayuki , Semba Taro , Tabata Kimiyo , Tamura Moe , Aoyama Muneo , Abe Takanori , Asano Osamu , Terada Yasuhiko , Funahashi Yasuhiro , Fujii Hirofumi
Published: February 2024

Abstract
E7130 is a novel anticancer agent created from total synthetic study of the natural compound norhalichondrin B. In addition to inhibiting microtubule dynamics, E7130 also ameliorates tumor-promoting aspects of the tumor microenvironment (TME) by suppressing cancer-associated fibroblasts (CAF) and promoting remodeling of tumor vasculature. Here, we demonstrate TME amelioration by E7130 using multi-imaging modalities, including multiplexed mass cytometry [cytometry by time-of-flight (CyTOF)] analysis, multiplex IHC analysis, and MRI. Experimental solid tumors characterized by large numbers of CAFs in TME were treated with E7130. E7130 suppressed LAP-TGFβ1 production, a precursor of TGFβ1, in CAFs but not in cancer cells; an effect that was accompanied by a reduction of circulating TGFβ1 in plasma. To our best knowledge, this is the first report to show a reduction of TGFβ1 production in TME. Furthermore, multiplex IHC analysis revealed reduced cellularity and increased TUNEL-positive apoptotic cells in E7130-treated xenografts. Increased microvessel density (MVD) and collagen IV (Col IV), an extracellular matrix (ECM) component associated with endothelial cells, were also observed in the TME, and plasma Col IV levels were also increased by E7130 treatment. MRI revealed increased accumulation of a contrast agent in xenografts. Moreover, diffusion-weighted MRI after E7130 treatment indicated reduction of tumor cellularity and interstitial fluid pressure. Overall, our findings strongly support the mechanism of action that E7130 alters the TME in therapeutically beneficial ways. Importantly, from a translational perspective, our data demonstrated MRI as a noninvasive biomarker to detect TME amelioration by E7130, supported by consistent changes in plasma biomarkers.
Data from Targeting Dysregulated Ion Channels in Liver Tumors with Venom Peptides
Authors: Achimba Favour , Faezov Bulat , Cohen Brandon , Dunbrack Roland , Holford Mandë
Published: February 2024

Abstract
The regulation of cellular processes by ion channels has become central to the study of cancer mechanisms. Designing molecules that can modify ion channels specific to tumor cells is a promising area of targeted drug delivery and therapy. Despite their potential in drug discovery, venom peptides—a group of natural products—have largely remained understudied and under-characterized. In general, venom peptides display high specificity and selectivity for their target ion channels. Therefore, they may represent an effective strategy for selectively targeting the dysregulation of ion channels in tumor cells. This review examines existing venom peptide therapies for different cancer types and focuses on the application of snail venom peptides in hepatocellular carcinoma (HCC), the most common form of primary liver cancer worldwide. We provide insights into the mode of action of venom peptides that have been shown to target tumors. We also explore the benefit of using new computational methods like de novo protein structure prediction to screen venom peptides and identify potential druggable candidates. Finally, we summarize the role of cell culture, animal, and organoid models in developing effective therapies against HCC and highlight the need for creating models that represent the most disproportionately affected ethnicities in HCC.
Abstract A027: Targeting MYC-induced reprogramming of mitochondrial metabolism in breast cancer
Authors: Anttila Johanna M. , Savelius Mariel , Nicorici Daniel , Awadhpersad Ryan , Munne Pauliina M. , Id Linda , Tervonen Topi A. , Jackson Christopher , Nieminen Anni I. , Klefström Juha
Published: February 2024

Oncogenic MYC is frequently overexpressed in breast cancer, and its overexpression is associated with aggressiveness and unfavorable prognosis of breast cancer. MYC overexpression promotes tumor growth by stimulating cell cycle progression and rewiring metabolism – creating cancer vulnerabilities that can be therapeutically targeted via synthetic lethal strategies. A large part of our current understanding of the MYC overexpression biology and related synthetic lethal pathways is based on findings in various inducible MYC overexpression systems, which demonstrate the acute effects of MYC activation but may poorly represent long-term MYC overexpression status in real cancers. Here we classified 15 triple-negative breast cancer (TNBC) cell lines according to both MYC target gene set expression and MYC protein expression into MYC-high and MYC-low categories and explored the MYC-high status-coupled therapeutic responses and cancer-relevant metabolic changes. We show that mitochondrial respiration inhibiting biguanide drug metformin inhibits cell proliferation and generates senescence-like features in MYC-high TNBC cells. Furthermore, high-resolution respirometry experiments show that MYC-high TNBC cells have higher mitochondrial respiration rates than MYC-low TNBC cells, a phenotype not explained by a higher number of mitochondria. Also, targeting mitochondrial respiration with small molecule inhibitors specifically reduces proliferation in MYC-high TNBC cells and sensitizes them to apoptosis – indicating that MYC-high TNBC cells have higher dependency on mitochondrial respiration than the MYC-low cells. Targeted metabolomic flux experiments demonstrate that small molecule inhibitors of mitochondrial respiration rewire TCA cycle, resulting in suppression of MYC-driven glutamine anaplerosis, which offers a possible explanation for the apoptotic sensitization. In conclusion, our findings provide new insight into the long-term MYC overexpression-associated metabolic changes – highlighting mitochondrial respiration as a potential target for the development of MYC-dependent synthetic lethal strategies against breast cancer.

Citation Format: Johanna M. Anttila, Mariel Savelius, Daniel Nicorici, Ryan Awadhpersad, Pauliina M. Munne, Linda Id, Topi A. Tervonen, Christopher Jackson, Anni I. Nieminen, Juha Klefström. Targeting MYC-induced reprogramming of mitochondrial metabolism in 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 A027.
Abstract A082: Stretching towards relief: The Kent-Collins protocol for radiation-induced eustachian tube dysfunction
Authors: Kent Matthew E , Colllins Patrick J , Aizer Ayal A
Published: February 2024

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 A089: Role of Vardhamana Pippali Rasayana (VPR) in human breast cancer cells
Authors: Tripathi Dr.Richa , Singh Shivam , Gupta Subhash , Huddar VG , Nesari Tanuja M , Sharma Ashok
Published: February 2024

Serious concerns include delayed diagnosis and adverse side-effects of conventional treatment leading to residual morbidity in Breast cancer (BC) globally. Traditional Indian medicines/herbs via combination of conventional cancer are gaining increasing acceptance worldwide, playing a pivotal role as proven by their efficacy evaluation studies. Many plants are known to reduce the cell proliferation and tumor development after their treatment. Vardhamana Pippali Rasayana (VPR), an Ayurvedic herbal preparation of pippali (Piper longum) in gradually increasing and tapering dose is used to treat many cancers without any adverse side-effects. However, its anti-cancer role in breast cancer is not known yet. The present study has explored the cytotoxic and apoptotic effects of VPR in triplicates on human breast cancer (MCF7) and normal breast epithelial (MCF10A) cell lines at different concentrations after extracting piperine in aqueous and hydro-alcoholic soxhlet extract (0.25 to 50 μg/μl). The cytotoxic activity was carried out by MTT assay and results showed that a low IC50 was observed at 3.75 μg/μl of VPR against MCF-7 as compared with normal breast epithelial cells. Detection of apoptotic cells using suitable Annexin V was done and there was a time-dependent increase in percentage of annexin V positive cells upon treatment. The above results indicate that VPR may have a strong anti-cancerous potential. But other functional assays are warranted to validate the efficacy of the drug against breast cancer which are under progress in our laboratory.

Citation Format: Dr.Richa Tripathi, Shivam Singh, Subhash Gupta, VG Huddar, Tanuja M Nesari, Ashok Sharma. Role of Vardhamana Pippali Rasayana (VPR) in human breast cancer cells [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 A089.
Abstract B029: Combinations of metformin and BH3-mimetic drugs synergistically induce immunogenic cell death in breast cancer cells
Authors: Savelius Mariel , Id Linda , Anttila Johanna , Liu Ruixian , Suleymanova Ilida , Saarela Jani , Klefström Juha
Published: February 2024

There is a compelling medical need for novel and safe treatment options for patients with advanced and difficult to treat breast cancer. Our previous findings have demonstrated that a combination of metformin and navitoclax (BCL-2/BCL-XL inhibitor) successfully prevents tumor growth in patient derived xenograft and syngrafted mouse models of aggressive MYC-driven breast cancer. This outcome is due to the synthetic lethal action of these drugs in tumors with elevated MYC expression. Here, we explored the combinations of metformin with all clinically applicable anti-apoptotic BCL-2 family protein inhibitors (BH3-mimetics) in a panel of 15 triple-negative breast cancer cell lines with distinct endogenous MYC levels, as well as inducible MYC models. We used cytotoxicity assays and analyzed the data with SynergyFinder, an interactive analysis and visualization tool, to calculate the degree of combination synergy utilizing Zero interaction potency reference model. Through these cytotoxicity assays, we defined which metformin and BH3-mimetic drug combination induces most synergistic cell death in a MYC-synthetic lethal manner. Additionally, we used DAMP reporter cell lines and peripheral blood mononuclear cell-based dendritic cell activation assays to evaluate the immunogenic potential of combination-induced cell death. We show that targeting MCL-1 or BCL-2/XL with BH3-mimetics MIK-665 and navitoclax, respectively, and combining them with metformin, induces synergistic cell death in MYC-high cancer cells. We also show that cell death caused by these drug combinations promotes maturation of dendritic cells. In conclusion, targeting MYC-high tumors with synthetic lethal strategies, including BH3-mimetics and metformin, may offer new opportunities to combine with immunotherapies for the treatment of breast cancer.

Citation Format: Mariel Savelius, Linda Id, Johanna Anttila, Ruixian Liu, Ilida Suleymanova, Jani Saarela, Juha Klefström. Combinations of metformin and BH3-mimetic drugs synergistically induce immunogenic cell death in breast cancer cells [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 B029.
Abstract B033: Targeting CaMKK2 inhibits actin cytoskeletal assembly to suppress cancer metastasis
Authors: Mukherjee Debarati , Previs Rebecca A , Haines Corinne N , Abo Muthana Al , Juras Patrick K , Strickland Kyle C , Chakraborty Binita , Whitaker Regina , Patierno Steven R , Freedman Jennifer A , Chang Ching-Yi , McDonnell Donald P
Published: February 2024

Triple-negative breast cancers (TNBCs) tend to become invasive and metastatic at early stages in their development. Despite some treatment successes in early stage localized TNBC, the rate of distant recurrence remains high, and long-term survival outcomes remain poor. In a search for new therapeutic targets for this disease, we observed that elevated expression of the serine/threonine kinase calcium/calmodulin (CaM)-dependent protein kinase kinase 2 (CaMKK2) is highly correlated with tumor invasiveness. In validation studies, genetic disruption of CaMKK2 expression or inhibition of its activity with small molecule inhibitors disrupted spontaneous metastatic outgrowth from primary tumors in murine xenograft models of TNBC. High-grade serous ovarian cancer (HGSOC), a high-risk, poor prognosis ovarian cancer subtype, shares many features with TNBC, and CaMKK2 inhibition effectively blocked metastatic progression in a validated xenograft model of this disease. Mechanistically, CaMKK2 increased the expression of the phosphodiesterase PDE1A which hydrolyzed cyclic guanosine monophosphate (cGMP) to decrease the cGMP-dependent activity of protein kinase G1 (PKG1). Inhibition of PKG1 resulted in decreased phosphorylation of vasodilator stimulated phosphoprotein (VASP), which in its hypophosphorylated state binds to and regulates F-actin assembly to facilitate cell movement. Together, these findings establish a targetable CaMKK2-PDE1A-PKG1-VASP signaling pathway that controls cancer cell motility and metastasis by impacting the actin cytoskeleton. Further, it identifies CaMKK2 as a potential therapeutic target that can be exploited to restrict tumor invasiveness in patients diagnosed with early-stage TNBC or localized HGSOC.

Citation Format: Debarati Mukherjee, Rebecca A Previs, Corinne N Haines, Muthana Al Abo, Patrick K Juras, Kyle C Strickland, Binita Chakraborty, Regina Whitaker, Steven R Patierno, Jennifer A Freedman, Ching-Yi Chang, Donald P McDonnell. Targeting CaMKK2 inhibits actin cytoskeletal assembly to suppress cancer metastasis [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 B033.
Abstract IA23: "NO Target for Cancer Stem Cells"
Authors: Chang Jenny C.
Published: February 2024

Developing novel therapies that target cancer metastasis, chemoresistant cancer stem cells, and augment the efficacy of systemic chemo/radiotherapies is crucial to reducing cancer-associated mortality. A protein within the tumor microenvironment that has gained interest as a promising therapeutic target is nitric oxide synthase (NOS). Our previous findings have shown that increased inducible nitric oxide synthase (iNOS) expression is a poor prognostic indicator and associated with worse overall survival in triple negative breast cancer (TNBC) patients. Nitric oxide (NO) is a unique molecule in its ability to target multiple oncogenic pathways in a spatial and temporal manner, such as PI3K, extracellular signal-regulated kinase (ERK), β-catenin pathway, transforming growth factor beta (TGFβ) signaling, and hypoxia-inducible factor (HIF). Growing evidence has also suggested that hyperactivation of the phosphoinositide-3-kinase (PI3K) survival signaling pathway may be one of the most common oncogenic aberrations in certain TNBC subsets, in particular metaplastic breast cancer (MpBC). We will summarize the role of NO in PI3K-Akt pathway activation in human TNBC, as well as data from The Cancer Genome Atlas of the role of iNOS and PI3K-Akt interaction. This review discusses the current knowledge of the roles of nitric oxide (NO) in tumor progression and cancer metastasis, and promising preclinical studies that evaluated NOS inhibitors as an anti-cancer therapy. Lastly, we will offer a perspective on utilizing NOS inhibitors in the clinical setting, highlighting the prospects and outstanding challenges.

Citation Format: Jenny C. Chang. "NO Target for Cancer Stem Cells" [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 IA23.
Abstract PR02: Modeling breast cancer through somatic precision gene editing with high flexibility and efficiency
Authors: Bu Wen , Li Yi , Creighton Chad J , Heavener Kelsey S , Gutierrez Carolina , Dou Yongchao , Jiang Weiyu , Zhang Bing , Ku Amy T , Huang Shixia
Published: February 2024

CRISPR/Cas9 has been used successfully to introduce indels in somatic cells of rodents; however, precise editing of single nucleotides has been hampered by limitations of flexibility and efficiency. Here, we report technological modifications to the CRISPR/Cas9 vector system that now allows homology-directed repair-mediated precise editing of any proto-oncogene in murine somatic tissues to generate tumor models with high flexibility and efficiency. Somatic editing of either Kras or Pik3ca in both normal and hyperplastic mammary glands led to swift tumorigenesis. The resulting tumors shared some histological, transcriptome, and proteome features with tumors induced by lentivirus-mediated expression of the respective oncogenes, but they also exhibited some distinct characteristics, particularly showing less inter-tumor variation, thus potentially offering more consistent models for cancer studies and therapeutic development. Therefore, this technological advance fills a critical gap between the power of CRISPR technology and high-fidelity mouse models for studying human tumor evolution and preclinical drug testing.

Citation Format: Wen Bu, Yi Li, Chad J Creighton, Kelsey S Heavener, Carolina Gutierrez, Yongchao Dou, Weiyu Jiang, Bing Zhang, Amy T Ku, Shixia Huang. Modeling breast cancer through somatic precision gene editing with high flexibility and efficiency [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 PR02.
Abstract PR09: Functional and clinical characterization of hypomorphic missense variants in the BRCA2 cancer predisposition gene
Authors: Huang Huaizhi (Gilbert) , Hu Chunling , Na Jie , Abozaid Mohamed , Munankarmy Amik , Rao Tara , Lumby Carolyn A. Dunn , Lyra Paulo Cilas Morais , Couch Ronan E. , Persons Benjamin R. , Polley Eric C. , Karam Rachid , Pesaran Tina , Yadav Siddhartha , Monteiro Alvaro N.A. , Boddicker Nicholas J. , Domchek Susan M. , Richardson Marcy E. , Couch Fergus J.
Published: February 2024

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 A001: Genomic signatures of past and present chromosomal instability in Barrett’s esophagus and early esophageal adenocarcinoma
Authors: Bao Chunyang
Published: February 2024

Abstract: The progression of precancerous lesions to malignancy is often accompanied by increasing complexity of chromosomal alterations but how these alterations arise is poorly understood. Here we perform haplotype-specific analysis of chromosomal copy-number evolution in the progression of Barrett’s esophagus (BE) to esophageal adenocarcinoma (EAC) on multiregional whole-genome sequencing data of BE with dysplasia and microscopic EAC foci. We identify distinct patterns of copy-number evolution indicating multigenerational chromosomal instability that is initiated by cell division errors but propagated only after p53 loss. While abnormal mitosis, including whole-genome duplication, underlies chromosomal copy-number changes, segmental alterations display signatures of successive breakage-fusion-bridge cycles and chromothripsis of unstable dicentric chromosomes. Our analysis elucidates how multigenerational chromosomal instability generates copy-number variation in BE cells, precipitates complex alterations including DNA amplifications, and promotes their independent clonal expansion and transformation. In particular, we suggest sloping copy-number variation as a signature of ongoing chromosomal instability that precedes copy-number complexity. These findings suggest copy-number heterogeneity in advanced cancers originates from chromosomal instability in precancerous cells and such instability may be identified from the presence of sloping copy-number variation in bulk sequencing data.

Citation Format: Chunyang Bao. Genomic signatures of past and present chromosomal instability in Barrett’s esophagus and early esophageal adenocarcinoma [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 A001.
Abstract A017: Computational and mouse models of adaptive therapy with multiple drugs in breast cancer
Authors: Maley Carlo C. , Seyedi Sareh , Saha Daniel , Anderson Alexander
Published: February 2024

Adaptive therapy is an evolutionary approach to cancer therapy designed to maintain control of therapeutically resistant cells and thereby extend both time to progression and patient survival. Most of the previous work in adaptive therapy has used a single cytotoxic drug, and yet there are still many variations of adaptive therapy protocols. Although multidrug therapy is standard for most cancers, there is a combinatorial explosion of possible protocols with an increase in the number of drugs used. We set out to explore which protocols are likely to work best, under which conditions, using computational models. We explored 2 drug therapies but allowed the drugs to be cytotoxic or cytostatic. We tested the effects of varying the fitness cost of resistance, the amount of turnover in the tumors, and the ability of cells to replace their neighbors under crowded conditions. Adaptive therapy tends to work best when there is more competition between cells in the cancers. We also explored different dosing schedules with both fixed doses and with varying the doses as a function of tumor burden dynamics. We also selected ER+ breast cancer (MCF7) cells to be resistant to both fulvestrant (an anti-estrogen therapy) and palbociclib (a CDK4/6 targeted therapy). These endocrine-resistant ER+ breast cancer cells represent the target population for a clinical trial in endocrine-resistant ER+ metastatic breast cancer that we are seeking to open at the Mayo Clinic. We tested a few of the adaptive therapy protocols with those cells in immune-compromised mice, using either gemcitabine, capecitabine or both drugs. In general, our computational models suggest that the less drug that a protocol uses, the longer we are able to keep control over the cancers. This was corroborated in our mouse experiments. However, if too little drug is used it can’t even control the sensitive cells in the tumors, leading to a sort of Goldilocks effect for the dosing. Capping the maximum dose at a relatively low level, and modulating the dose below that level, led to long-term control for many of the protocols. Many of the tumors in the mice remained dormant for many weeks after we stopped adaptive therapy, for unknown reasons. Our results support adaptive therapy as a promising approach for both extending time to progression and improving quality of life by reducing toxicity. We are using these results to design our clinical trial.

Citation Format: Carlo C. Maley, Sareh Seyedi, Daniel Saha, Alexander Anderson. Computational and mouse models of adaptive therapy with multiple drugs in breast 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 A017.
Abstract B036: Mutational landscape and genetic feature of gastric adenocarcinoma in multiple Chinese ethnicities
Authors: Zong Liang
Published: February 2024

Gastric cancer is a heterogeneous malignancy and the fifth most common cancer worldwide, with 44% of cases occurring in China. Elucidation of genetic subtypes may improve gastric cancer treatment planning. Matched tumour and peritumoural (non-malignant gastric mucosa) tissue samples were collected from 306 Chinese patients and subjected to whole-exome sequencing (WES). The results were used to produce a Chinese Gastric Cancer Genome Atlas (CGCGA). Patients from nine Chinese ethnic groups (Han, Zhuang, Hui, Uygur, Yi, Tibetan, Mongolian, Bai, and Kazakh), representing 95% of the Chinese population were included. Systematic comparison of CGCGA data with TCGA (The Cancer Genome Atlas) data, in which 437 gastric cancer cases are represented, showed that genomic alteration signatures in the present cohort differed markedly from those reported for Western cohorts. TP53 and FAT1 deletions were more frequent (35% vs. 0%) while ARID1A deletions (13% vs. 25%), MYC oncogene amplifications (53% vs. 70%), and SMAD4 deletions (34% vs. 46%) were less frequent in our CGCGA data than in the TCGA data. TRIM49B mutation was associated with worse survival. Thus, TRIM49B was identified as a novel oncogene. The Zhuang ethnic group had a much higher tumour mutation burden (TMB) than the other ethnic groups. Typically, tumours from Han group had microsatellite stability, whereas those from the other groups had microsatellite instability (MSI). We further propose a molecular classification of four gastric cancer subtypes that are associated with distinct survival outcomes: TP53 mutation positive (TP53+)/TTN_missense+; TP53+/TTN_missense–; TP53–/TTN_missense+, and TP53–/TTN_missense–. Our study established a comprehensive gastric cancer genome atlas in China and underscored the importance of considering population context in genomic mapping and rational treatment options for the disease.

Citation Format: Liang Zong. Mutational landscape and genetic feature of gastric adenocarcinoma in multiple Chinese ethnicities [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 B036.
Abstract B043: Quantifying selection intensity and epistatic interactions among gene variants within angiosarcoma
Authors: Hampson Caralynn E. , Cannataro Vincent L.
Published: February 2024

Evolutionary processes underlie cancer development. Mutations occur and accumulate in somatic tissues, and some mutations result in increases in cell division or survival and fix in cell populations more often than expected by chance. Computational techniques that account for differences in mutation rate across the genome and between tissues have helped pinpoint which genes are contributing to tumor growth within a wide array of cancer types. However, rare cancers are often understudied due to lack of funding, availability of data, and applicable tools that are capable of incorporating data from different sources. Recent initiatives, such as the Angiosarcoma Project, have increased data availability for the study of angiosarcoma, a rare cancer with approximately 300 new cases a year. In this study, we incorporate whole-genome, whole-exome, and targeted sequencing data from different sources—accounting for study-specific differences in genome coverage—into an evolutionary analysis of angiosarcoma tumorigenesis. Prior to our study, potential genes with oncogenic activity for angiosarcoma have been primarily evaluated based on genetic variant prevalence among tumor samples, but substitution prevalence is dependent on intrinsic mutation rate and thus relative prevalence of variants may not correspond with relative tumorigenic potential. We calculate the intensity of selection, a measure of the magnitude of increase of cell division and survival, of individual variants driving angiosarcoma, and complement existing studies that have previously determined KDR and TP53 mutations to be a driver of angiosarcoma, and we also implicate novel putative drivers that have high calculated selection intensity, including BRAF V600E, IGDCC4 S1020A, and SETD2 Q1152E. Additionally, we evaluated epistatic interactions among genes and found that selection for TP53 is increased after mutation of other genes such as MUC16, FAT1, and NOTCH2. This study demonstrates the feasibility of applying computational models informed by evolutionary approaches to a rare disease as well as identifies gene variants that likely have a large impact on angiosarcoma tumorigenesis.

Citation Format: Caralynn E. Hampson, Vincent L. Cannataro. Quantifying selection intensity and epistatic interactions among gene variants within angiosarcoma [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 B043.
Abstract IA003: Composing each patient's equation: Deciphering brain tumor dynamics and evolution by integrating multi-regional image-localized biopsies
Authors: Swanson Kristin R.
Published: February 2024

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. We use 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. Specifically, we build mathematical models that fuse locoregional changes on MRI to underlying changes in tumor biology. We apply the resultant spatio-temporal models to serial imaging of patients receiving a variety of standard of care and novel therapeutics to track tumor dynamics under said therapies. This allows us unprecedent insight into the dynamics of each patients tumor under therapy. This includes detecting clonal loss through targeted therapies as well as shifts in the tumor ecosystem under immunotherapies. In this presentation, I will demonstrate how these methods can be brought together to help us detect, decipher and predict tumor dynamics and evolution in patients. Specifically, I 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 evolutionary- and ecologically-adaptive precision oncology for glioblastoma patients.

Citation Format: Kristin R. Swanson. Composing each patient's equation: Deciphering brain tumor dynamics and evolution by integrating multi-regional image-localized biopsies [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 IA003.
Abstract IA017: Extrachromosomal DNA (ecDNA): Cancer’s dynamic circular genome
Authors: Mischel Paul
Published: February 2024

Human genes are arranged on 23 pairs of chromosomes, but in cancer, tumor-promoting genes and regulatory elements can free themselves from chromosomes and relocate to circular, extrachromosomal pieces of DNA (ecDNA). ecDNA poses one of the greatest challenges for cancer patients, affecting children and adults and women and men, with a wide variety of cancer types. Although ecDNA was first observed more than 50 years ago, its critical importance has only recently come to light. ecDNA, because of its non-chromosomal inheritance, drives high-copy number oncogene amplification and enables tumors to evolve their genomes rapidly, contributing to treatment resistance and shorter survival for patients. Furthermore, the circular ecDNA architecture fundamentally alters gene regulation and transcription. In this talk, I will discuss recent collaborative discoveries that highlight how the higher order, spatial organization of ecDNA, and its mechanism of inheritance, contributes to aggressive tumorigenesis, accelerated evolution, and treatment resistance.

Citation Format: Paul Mischel. Extrachromosomal DNA (ecDNA): Cancer’s dynamic circular genome [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 IA017.
Abstract PR014: Multiregion biopsies and corresponding neurosphere cultures reveal spatial divergence in glioblastoma evolution
Authors: Salatino Roberto , Onubogu Ugoma , Oakes Benjamin , Szentirmai Oszkar , Janiszewska Michalina
Published: February 2024

Spatial organization of normal tissues is key for their function, yet the role of distribution of distinct clones of cancer cells in tumor in not usually studied as a potential vulnerability in cancer. This is of particular interest in glioblastoma (GBM), most aggressive brain tumor, in which extensive intratumor heterogeneity hampers effectiveness of treatment. Multiregion sampling has been used in multiple studies to uncover evolutionary trajectories of the tumor. To better understand tumor evolution and the complexity of cancer ecosystem in GBM, we performed profiling of biopsies collected from MRI-defined regions of the tumors, spanning the surface, tumor core and deep tumor margins, which drive local recurrence after surgery. To test how spatially distinct biopsies differ in their cancer cell composition and how heterogeneous the tumor microenvironment is in these samples, we took advantage of 5-ALA metabolite fluorescence, which accumulates in GBM cells. 5-ALA administration prior to the surgery allows the surgeon to visualize cancer under blue light. We used it to separate cancer cells (predominantly 5-ALAhigh) from tumor microenvironment (5-ALAlow) and subjected the fractions to bulk and single cell transcriptomics, respectively. We found a gradient of cellular states associated with location in the tumor, with the deep margin samples having more 5-ALAlow cancer cells and generally less defined phenotype. We have also developed neurosphere cultures from our collection of spatially distant biopsies. Despite the selection pressure of the in vitro culture conditions, cells from different regions of the tumor adopted different morphologies, suggesting retention of some of their differential features. The differences between cultures were reflected in metabolism, proliferation, and differential sensitivity to a drug panel. Whole exome sequencing and transcriptomic analysis were also performed to identify the selection bottleneck of culture conditions, establish evolutionary trajectory of the distinct regions and neurosphere cultures, and test how strongly our cultures represent both the 5-ALAhigh and 5-ALAlow subpopulations of GBM cells. Our study identified properties associated with different spatial locations within GBM tumors, which will help uncover the cellular and microenvironmental dependencies that could lead to novel therapeutic targets for this highly heterogeneous tumor.

Citation Format: Roberto Salatino, Ugoma Onubogu, Benjamin Oakes, Oszkar Szentirmai, Michalina Janiszewska. Multiregion biopsies and corresponding neurosphere cultures reveal spatial divergence in glioblastoma evolution [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 PR014.
Supplementary Table 2 from PKCδ Regulates Chromatin Remodeling and DNA Repair through SIRT6
Authors: Affandi Trisiani , Haas Ami , Ohm Angela M. , Wright Gregory M. , Black Joshua C. , Reyland Mary E.
Published: February 2024

Supplementary Table 2. List of primers used for qRT-PCR.
Supplementary Figure 1 from Exosomal lncRNA NEAT1 Inhibits NK-Cell Activity to Promote Multiple Myeloma Cell Immune Escape via an EZH2/PBX1 Axis
Authors: Wang Qing-Ming , Lian Guang-Yu , Sheng Su-Mei , Xu Jing , Ye Long-Long , Min Chao , Guo Shu-Fang
Published: February 2024

Supplementary Figure 1 shows that MM exosomes derived from U266 cells inhibit the proliferation and activity of NK cells but enhance the NK cells’ apoptosis, while the MM exosomes derived from U266 cells that NEAT1 knockdown have lost this function.