bluuebunny/crossref_metadata_2025 huggingface dataset:
Data from PMP22 Regulates Self-Renewal and Chemoresistance of Gastric Cancer Cells
Authors: Cai Wangyu , Chen Gang , Luo Qicong , Liu Jun , Guo Xiaofeng , Zhang Tian , Ma Fei , Yuan Liang , Li Boan , Cai Jianchun
Published: April 2023

Abstract
Cancer stem cells possess self-renewal and chemoresistance activities. However, the manner in which these features are maintained remains obscure. We sought to identify cell surface protein(s) that mark self-renewing and chemoresistant gastric cancer cells using the explorer antibody microarray. We identified PMP22, a target gene of the Wnt/β-catenin pathway, as the most upregulated cell surface protein in gastric cancer xenografts exposed to cisplatin (DDP). PMP22 expression was markedly upregulated in tumorspheric cells and declined with differentiation. Infecting gastric cancer cells with lentivirus expressing PMP22 shRNAs reduced proliferation, tumorsphere formation, and chemoresistance to cisplatin in vitro and in NOD/SCID mice. When combined with bortezomib, a PMP22 inhibitor, the chemotherapeutic sensitivity to cisplatin treatment was dramatically increased by inducing cell apoptosis in cultured cells and xenograft mouse models. Finally, mRNA expression levels of PMP22 were detected in 38 tumor specimens from patients who received six cycles of perioperative chemotherapy. A strong correlation between PMP22 level and tumor recurrence was revealed, thus showing a pivotal role of PMP22 in the clinical chemoresistance of gastric cancer. Our study is the first to show the role of PMP22 in gastric cancer stemness and chemoresistance and reveals a potential new target for the diagnosis and treatment of recurrent gastric cancer. Mol Cancer Ther; 16(6); 1187–98. ©2017 AACR.
Data from Inhibition of the Receptor Tyrosine Kinase AXL Restores Paclitaxel Chemosensitivity in Uterine Serous Cancer
Authors: Palisoul Marguerite L. , Quinn Jeanne M. , Schepers Emily , Hagemann Ian S. , Guo Lei , Reger Kelsey , Hagemann Andrea R. , McCourt Carolyn K. , Thaker Premal H. , Powell Matthew A. , Mutch David G. , Fuh Katherine C.
Published: April 2023

Abstract
Uterine serous cancer (USC) is aggressive, and the majority of recurrent cases are chemoresistant. Because the receptor tyrosine kinase AXL promotes invasion and metastasis of USC and is implicated in chemoresistance in other cancers, we assessed the role of AXL in paclitaxel resistance in USC, determined the mechanism of action, and sought to restore chemosensitivity by inhibiting AXL in vitro and in vivo. We used short hairpin RNAs and BGB324 to knock down and inhibit AXL. We assessed sensitivity of USC cell lines to paclitaxel and measured paclitaxel intracellular accumulation in vitro in the presence or absence of AXL. We also examined the role of the epithelial–mesenchymal transition (EMT) in AXL-mediated paclitaxel resistance. Finally, we treated USC xenografts with paclitaxel, BGB324, or paclitaxel plus BGB324 and monitored tumor burden. AXL expression was higher in chemoresistant USC patient tumors and cell lines than in chemosensitive tumors and cell lines. Knockdown or inhibition of AXL increased sensitivity of USC cell lines to paclitaxel in vitro and increased cellular accumulation of paclitaxel. AXL promoted chemoresistance even in cells that underwent the EMT in vitro. Finally, in vivo studies of combination treatment with BGB324 and paclitaxel showed a greater than 51% decrease in tumor volume after 2 weeks of treatment when compared with no treatment or single-agent treatments (P < 0.001). Our results show that AXL expression mediates chemoresistance independent of EMT and prevents accumulation of paclitaxel. This study supports the continued investigation of AXL as a clinical target, particularly in chemoresistant USC. Mol Cancer Ther; 16(12); 2881–91. ©2017 AACR.
Data from Augmentation of the Enhanced Permeability and Retention Effect with Nitric Oxide–Generating Agents Improves the Therapeutic Effects of Nanomedicines
Authors: Islam Waliul , Fang Jun , Imamura Takahisa , Etrych Tomas , Subr Vladimir , Ulbrich Karel , Maeda Hiroshi
Published: April 2023

Abstract
Enhanced permeability and retention (EPR) effect–based nanomedicine is a promising strategy for successful anticancer therapy. The EPR effect is based on tumor blood flow. Because advanced large tumors, as frequently seen in clinical settings, are heterogeneous, with regions of defective vasculature and blood flow, achieving the desired tumor drug delivery is difficult. Here, we utilized the EPR effect to increase drug delivery. To augment the EPR effect for improved therapeutic effects of nanomedicine, we exploited vascular mediators—the nitric oxide (NO) generators nitroglycerin (NG), hydroxyurea, and l-arginine. These compounds generate NO in tumors with relatively high selectivity. Using different nanosized drugs in our protocol significantly increased (1.5–2 times) delivery of nanomedicines to different solid tumor models, along with markedly improving (2–3-fold) the antitumor effects of these drugs. Also, in 7,12-dimethylbenz[a]anthracene–induced advanced end-stage breast cancer, often seen in clinical settings, 2 mg/kg polymer-conjugated pirarubicin (P-THP) with NG (0.2 mg/mouse) showed better effects than did 5 mg/kg P-THP, and 5 mg/kg P-THP used with NG resulted in cures or stable tumors (no tumor growth) for up to 120 days. Moreover, in a murine autochthonous azoxymethane/dextran sulfate sodium-induced colon cancer model, NO donors markedly improved the therapeutic effects of P-THP even after just one injection, results that were comparable with those achieved with three weekly P-THP treatments. These findings strongly suggest the potential usefulness of NO donors as EPR effect enhancers to improve the therapeutic efficacy of nanomedicines.
Data from Covalent Targeting of Fibroblast Growth Factor Receptor Inhibits Metastatic Breast Cancer
Authors: Brown Wells S. , Tan Li , Smith Andrew , Gray Nathanael S. , Wendt Michael K.
Published: April 2023

Abstract
Therapeutic targeting of late-stage breast cancer is limited by an inadequate understanding of how tumor cell signaling evolves during metastatic progression and by the currently available small molecule inhibitors capable of targeting these processes. Herein, we demonstrate that both β3 integrin and fibroblast growth factor receptor-1 (FGFR1) are part of an epithelial–mesenchymal transition (EMT) program that is required to facilitate metastatic outgrowth in response to fibroblast growth factor-2 (FGF2). Mechanistically, β3 integrin physically disrupts an interaction between FGFR1 and E-cadherin, leading to a dramatic redistribution of FGFR1 subcellular localization, enhanced FGF2 signaling and increased three-dimensional (3D) outgrowth of metastatic breast cancer cells. This ability of β3 integrin to drive FGFR signaling requires the enzymatic activity of focal adhesion kinase (FAK). Consistent with these mechanistic data, we demonstrate that FGFR, β3 integrin, and FAK constitute a molecular signature capable of predicting decreased survival of patients with the basal-like subtype of breast cancer. Importantly, covalent targeting of a conserved cysteine in the P-loop of FGFR1–4 with our newly developed small molecule, FIIN-4, more effectively blocks 3D metastatic outgrowth as compared with currently available FGFR inhibitors. In vivo application of FIIN-4 potently inhibited the growth of metastatic, patient-derived breast cancer xenografts and murine-derived metastases growing within the pulmonary microenvironment. Overall, the current studies demonstrate that FGFR1 works in concert with other EMT effector molecules to drive aberrant downstream signaling, and that these events can be effectively targeted using our novel therapeutics for the treatment of the most aggressive forms of breast cancer. Mol Cancer Ther; 15(9); 2096–106. ©2016 AACR.
Data from Oxaliplatin–DNA Adducts as Predictive Biomarkers of FOLFOX Response in Colorectal Cancer: A Potential Treatment Optimization Strategy
Authors: Zimmermann Maike , Li Tao , Semrad Thomas J. , Wu Chun-Yi , Yu Aiming , Cimino George , Malfatti Michael , Haack Kurt , Turteltaub Kenneth W. , Pan Chong-xian , Cho May , Kim Edward J. , Henderson Paul T.
Published: April 2023

Abstract
FOLFOX is one of the most effective treatments for advanced colorectal cancer. However, cumulative oxaliplatin neurotoxicity often results in halting the therapy. Oxaliplatin functions predominantly via the formation of toxic covalent drug–DNA adducts. We hypothesize that oxaliplatin–DNA adduct levels formed in vivo in peripheral blood mononuclear cells (PBMC) are proportional to tumor shrinkage caused by FOLFOX therapy. We further hypothesize that adducts induced by subtherapeutic “diagnostic microdoses” are proportional to those induced by therapeutic doses and are also predictive of response to FOLFOX therapy. These hypotheses were tested in colorectal cancer cell lines and a pilot clinical study. Four colorectal cancer cell lines were cultured with therapeutically relevant (100 μmol/L) or diagnostic microdose (1 μmol/L) concentrations of [14C]oxaliplatin. The C-14 label enabled quantification of oxaliplatin–DNA adduct level with accelerator mass spectrometry (AMS). Oxaliplatin–DNA adduct formation was correlated with oxaliplatin cytotoxicity for each cell line as measured by the MTT viability assay. Six colorectal cancer patients received by intravenous route a diagnostic microdose containing [14C]oxaliplatin prior to treatment, as well as a second [14C]oxaliplatin dose during FOLFOX chemotherapy, termed a “therapeutic dose.” Oxaliplatin–DNA adduct levels from PBMC correlated significantly to mean tumor volume change of evaluable target lesions (5 of the 6 patients had measurable disease). Oxaliplatin–DNA adduct levels were linearly proportional between microdose and therapeutically relevant concentrations in cell culture experiments and patient samples, as was plasma pharmacokinetics, indicating potential utility of diagnostic microdosing.
Data from Cooperative Targets of Combined mTOR/HDAC Inhibition Promote MYC Degradation
Authors: Simmons John K. , Michalowski Aleksandra M. , Gamache Benjamin J. , DuBois Wendy , Patel Jyoti , Zhang Ke , Gary Joy , Zhang Shuling , Gaikwad Snehal , Connors Daniel , Watson Nicholas , Leon Elena , Chen Jin-Qiu , Kuehl W. Michael , Lee Maxwell P. , Zingone Adriana , Landgren Ola , Ordentlich Peter , Huang Jing , Mock Beverly A.
Published: April 2023

Abstract
Cancer treatments often require combinations of molecularly targeted agents to be effective. mTORi (rapamycin) and HDACi (MS-275/entinostat) inhibitors have been shown to be effective in limiting tumor growth, and here we define part of the cooperative action of this drug combination. More than 60 human cancer cell lines responded synergistically (CI<1) when treated with this drug combination compared with single agents. In addition, a breast cancer patient–derived xenograft, and a BCL-XL plasmacytoma mouse model both showed enhanced responses to the combination compared with single agents. Mice bearing plasma cell tumors lived an average of 70 days longer on combination treatment compared with single agents. A set of 37 genes cooperatively affected (34 downregulated; 3 upregulated) by the combination responded pharmacodynamically in human myeloma cell lines, xenografts, and a P493 model, and were both enriched in tumors, and correlated with prognostic markers in myeloma patient datasets. Genes downregulated by the combination were overexpressed in several untreated cancers (breast, lung, colon, sarcoma, head and neck, myeloma) compared with normal tissues. The MYC/E2F axis, identified by upstream regulator analyses and validated by immunoblots, was significantly inhibited by the drug combination in several myeloma cell lines. Furthermore, 88% of the 34 genes downregulated have MYC-binding sites in their promoters, and the drug combination cooperatively reduced MYC half-life by 55% and increased degradation. Cells with MYC mutations were refractory to the combination. Thus, integrative approaches to understand drug synergy identified a clinically actionable strategy to inhibit MYC/E2F activity and tumor cell growth in vivo. Mol Cancer Ther; 16(9); 2008–21. ©2017 AACR.
Data from Improved Therapeutic Window in BRCA-mutant Tumors with Antibody-linked Pyrrolobenzodiazepine Dimers with and without PARP Inhibition
Authors: Zhong Haihong , Chen Cui , Tammali Ravinder , Breen Shannon , Zhang Jing , Fazenbaker Christine , Kennedy Maureen , Conway James , Higgs Brandon W. , Holoweckyj Nicholas , Raja Rajiv , Harper Jay , Pierce Andrew J. , Herbst Ronald , Tice David A.
Published: April 2023

Abstract
Pyrrolobenzodiazepine dimers (PBD) form cross-links within the minor groove of DNA causing double-strand breaks (DSB). DNA repair genes such as BRCA1 and BRCA2 play important roles in homologous recombination repair of DSB. We hypothesized that PBD-based antibody–drug conjugates (ADC) will have enhanced killing of cells in which homologous recombination processes are defective by inactivation of BRCA1 or BRCA2 genes. To support this hypothesis, we found 5T4–PBD, a PBD-dimer conjugated to anti-5T4 antibody, elicited more potent antitumor activity in tumor xenografts that carry defects in DNA repair due to BRCA mutations compared with BRCA wild-type xenografts. To delineate the role of BRCA1/2 mutations in determining sensitivity to PBD, we used siRNA knockdown and isogenic BRCA1/2 knockout models to demonstrate that BRCA deficiency markedly increased cell sensitivity to PBD-based ADCs. To understand the translational potential of treating patients with BRCA deficiency using PBD-based ADCs, we conducted a “mouse clinical trial” on 23 patient-derived xenograft (PDX) models bearing mutations in BRCA1 or BRCA2. Of these PDX models, 61% to 74% had tumor stasis or regression when treated with a single dose of 0.3 mg/kg or three fractionated doses of 0.1 mg/kg of a PBD-based ADC. Furthermore, a suboptimal dose of PBD-based ADC in combination with olaparib resulted in significantly improved antitumor effects, was not associated with myelotoxicity, and was well tolerated. In conclusion, PBD-based ADC alone or in combination with a PARP inhibitor may have improved therapeutic window in patients with cancer carrying BRCA mutations.
Abstract 1017: A novel blood diagnostic method for fibrolamellar hepatocellular carcinoma
Authors: Wang Ruisi , Hurley Arlene M. , Simon Sanford M.
Published: April 2023

Fibrolamellar hepatocellular carcinoma (FLC) is an often-lethal liver cancer affecting primarily children and young adults. The disease presents with vague symptoms, and, as a result, it is usually diagnosed at an advanced stage. Thus, there is a high recurrence rate among those who undergo surgical resection. Diagnostic tests based on scans are differentially interpreted by pathologists and radiological, and scans often miss small tumors. We are developing tests for FLC based on metabolites and nucleic acids in the blood and in the urine. We used samples from 29 FLC patients and 9 age/gender-matched healthy donors. A clinical testing lab was used to quantify the plasma for Vitamin B12, alpha-fetoprotein (AFP), estrogen (E2), and liver panel (albumin, alkaline phosphatase, alanine transaminase, aspartate transferase, creatine kinase, direct bilirubin, total bilirubin, total protein, globulin). We found no difference between FLC vs. non-FLC subjects in the liver panel tests. In addition, there is no difference between the AFP and E2 tests. Vitamin B12 levels were about 8.5 times higher (p<0.05) in FLC patients compared to healthy donors. We are currently validating other protein and metabolite markers in the blood and urine, and C-reactive protein in blood and orotic acid in urine.

In nucleic acid assays, we found specific miRNAs increased in the circulation. These included: miR-122-5p, miR-514a-5p, miR-192-5p, miR-615-5p, miR-4532, miR-4322, miR-214-3p, and miR-122-3p. They were upregulated 8- to 21-fold in FLC (n= 24) vs. non-FLC patients (n=16). These results identified biomarkers and microRNAs associated with FLC tumors. The tests are currently being evaluated as part of a larger study to determine whether they can detect recurrence of disease and help assess therapeutic responses in FLC patients.

Citation Format: Ruisi Wang, Arlene M. Hurley, Sanford M. Simon. A novel blood diagnostic method for fibrolamellar hepatocellular carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1017.
Abstract 1079: Combination of tipifarnib with KRAS G12C inhibitors to prevent adaptive resistance
Authors: Patel Hetika Vora , Smith Alison , Chan Stacia , Kessler Linda , Burrows Francis , Malik Shivani
Published: April 2023

Selective KRAS G12C inhibitors, including AMG510 (sotorasib) and MRTX849 (adagrasib), have exhibited clinical activity in patients with non-small cell lung cancer (NSCLC); however, drug resistance and relapse inevitably occur through various mechanisms, which limits the ability of these therapeutic agents to achieve durable responses. Resistance mechanisms include feedback reactivation of compensatory, oncogenic signaling pathways and the attainment of a drug-tolerant state, each of which allows cancer cells to survive the anti-tumor effects of these highly active drugs. Compensatory mechanisms ameliorating KRAS blockade include HRAS/NRAS and the PI3K-AKT-mTOR pathway. Tipifarnib is a clinical stage farnesyltransferase inhibitor known to inhibit multiple farnesylation-dependent proteins in tumor cells. We have recently shown that tipifarnib can prevent feedback-mediated adaptive resistance to the PI3Kα inhibitor, alpelisib, through inhibition of both HRAS and RHEB, allowing simultaneous blockade of two key nodes of the oncogenic MAPK- and PI3K-signaling pathways. In another example, tipifarnib has been demonstrated by others to inhibit the ability of tumor cells to enter a drug-tolerant state induced by the EGFR inhibitor, osimertinib, in EGFR-mutant NSCLC models. In these models, inhibition of farnesylation of certain RHO proteins appear to contribute to the death of drug-tolerant cells prior to the emergence of acquired resistance mutations. Building on these two mechanisms of how tipifarnib may prevent adaptive resistance, we propose that tipifarnib can be used as an effective partner drug to delay or prevent the onset of adaptive resistance to KRAS G12C inhibitors. We have conducted in vitro 2D and 3D viability and regrowth experiments using combinations of tipifarnib with KRAS G12C inhibitors and have observed synergistic, anti-proliferative effects in KRAS G12C NSCLC cell lines as well as enhanced activity of combination in a KRAS G12C NSCLC PDX model. We are currently expanding the scope of in vitro and in vivo combination studies to further evaluate the molecular mechanism(s) of resistance that tipifarnib targets when combined with KRAS G12C inhibitors.

Citation Format: Hetika Vora Patel, Alison Smith, Stacia Chan, Linda Kessler, Francis Burrows, Shivani Malik. Combination of tipifarnib with KRAS G12C inhibitors to prevent adaptive resistance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1079.
Abstract 2191: Detection of actionable lung cancer fusion genes with known and novel partners from highly degraded FFPE material
Authors: Lee Bongyong , Babu Alisha , Zhang Aiguo , Sha Michael Y.
Published: April 2023

Chromosomal rearrangements resulting in expression of oncogenic chimeric proteins drive tumor progression. Gene fusions are promising targets for cancer therapy in various types of cancers. Therefore, faithful detection of gene fusions is essential in precision medicine. Previously, fusions have been detected using FISH, RT-PCR and RNA-seq. Targeted sequencing provides better sensitivity as only the regions associated with the driver genes are sequenced, increasing possible coverage depth, and reducing cost. We developed a targeted RNA-based lung cancer fusion panel utilizing 5’ RACE technology to construct a NGS library for detection of fusion transcripts present in total RNA from highly degraded samples, such as blood or FFPE samples. The panel is deliberately designed to cover 64 known actionable fusion genes as well as novel gene fusions. Using an in-house fusion RNA mix comprising of 52 fusion transcripts, the panel was optimized and balanced. A total of 40 lung cancer patient FFPE samples, one 6-fusion FFPE reference sample and three fusion positive cell line samples were used for validating the panel. Limit of detection (LoD) was determined using the in-house RNA mix and normal lung tissue RNA. The minimum RNA input to detect all 52 fusion transcripts was 10-4 ng (0.1 pg) of mixture of RNAs in background of 10 ng of normal lung tissue RNA. The panel successfully detected all six fusion transcripts with 10 ng of RNA from a 6-fusion reference FFPE sample. With this confirmation, we tested clinically relevant sample types which are damaged RNAs from FFPE material. This study demonstrates the performance of our newly developed NGS fusion gene panel with clinical samples. It accommodates highly degraded RNA samples with low amounts of input. The next step would be to expand the testing to include more samples and cell-free RNAs.

Citation Format: Bongyong Lee, Alisha Babu, Aiguo Zhang, Michael Y. Sha. Detection of actionable lung cancer fusion genes with known and novel partners from highly degraded FFPE material [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2191.
Abstract 2771: KSQ-4279 mediated USP1 inhibition induces replication associated DNA gaps that contribute to cell death
Authors: Nayak Sumeet , Sullivan Pamela , Mishina Yuji , Dodson Anne , Kao Pei-Lun , Gannon Hugh , Middleton Chris , Shenker Sol , Murray Morgan , Schlabach Michael , Stegmeier Frank , Tobin Erica , Cadzow Louise , Wylie Andrew
Published: April 2023

Tumors with defects in DNA double strand break (DSB) repair pathways, including those with mutations in BRCA1/2, are often treated with either poly (ADP-ribose) polymerase-1 (PARP1) inhibitors or platinum-based chemotherapy. Despite their clinical benefits, many patients develop resistance leading to the need for novel therapeutic approaches. To address this unmet clinical need, we applied our CRISPRomics® platform to identify novel therapeutic targets for DNA damage and repair deficient cancers. One of the top ranked targets was the deubiquitinating enzyme, USP1, with known functions in DNA damage repair pathways of translesion synthesis (TLS) and fanconi anemia (FA). We developed a novel small molecule inhibitor, KSQ-4279, that selectively inhibits USP1 and leads to accumulation of mono-ubiquitinated USP1 substrates such as proliferating nuclear antigen (PCNA). In addition to KSQ-4279’s activity in BRCA mutant tumors with known homologous recombination deficiencies (HRD), KSQ-4279 also exhibits synergistic activity in combination with PARP inhibitors and re-sensitizes PARP refractory tumors. Mechanistically, we show that in sensitive cell lines, treatment with KSQ-4279 alters the replication fork dynamics resulting in replication stress via induction of replication associated single stranded DNA gaps and subsequent fork degradation. Additionally, KSQ-4279 leads to loss of the essential DNA replication and repair protein, PCNA, which can be rescued by blocking PCNA ubiquitination either through Rad18 knockout or by ectopic expression of a PCNA K164R mutant. This loss of PCNA and sensitizing ssDNA lesions eventually lead to DNA double strand breaks (DSBs) and wide-spread DNA damage accumulation that contributes to cell death. This mechanistic insight supports the ongoing clinical trial of KSQ-4279 in patients with tumors harboring BRCA1/2 or other HRD mutations, both as a single agent and in combination with PARP inhibitors.

Citation Format: Sumeet Nayak, Pamela Sullivan, Yuji Mishina, Anne Dodson, Pei-Lun Kao, Hugh Gannon, Chris Middleton, Sol Shenker, Morgan Murray, Michael Schlabach, Frank Stegmeier, Erica Tobin, Louise Cadzow, Andrew Wylie. KSQ-4279 mediated USP1 inhibition induces replication associated DNA gaps that contribute to cell death [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2771.
Abstract 3035: Phase I trial of alpha-lactalbumin vaccine in high-risk operable triple-negative breast cancer
Authors: Budd George Thomas , Johnson Justin M. , Rhoades Emily , Moore Halle , Levengood Holly , Kruse Megan , Roesch Erin , Abraham Jame , Elliott Brenna , Haury Elena , Swartz Rachel , Pederson Holly , Hilli Zahraa Al , Tuohy Vincent
Published: April 2023

Background: Triple-negative breast cancer (TNBC) has a poor prognosis and may be associated with germline mutations. α-lactalbumin (aLA) is expressed in lactating breasts but not at other times or in other tissues. Expression of aLA is found in 70% of TNBC (PMID: 27322324) so could be an immunologic target for TNBC based on the “retired protein hypothesis” (PMID: 31926646). In pre-clinical studies vaccination with aLA inhibited growth of established breast tumors and provided protection from development of autochthonous tumors in transgenic murine models of breast cancer and against 4T1 transplantable breast cancer in BALB/c mice (PMID: 20512124).

Methods: To determine the safety and immunogenicity of aLA, patients with early stage TNBC are being entered in a Phase I trial of aLA with GMP-grade zymosan adjuvant in Montanide ISA 51 VG vehicle. Subjects receive 3 vaccinations given once every 2 weeks. Events of Common Terminology Criteria for Adverse Events (CTCAE) grade ≥2 are considered dose-limiting toxicities (DLTs).

Results: CTCAE toxicity by dose level is summarized below. All DLTs were injection site reactions, with ulceration and need for incisional drainage representing the grade 3 events. ELISpot assays to determine frequencies of T-cells producing IFN-γ and IL-17 in response to recombinant aLA and ELISA assays of antibody response to aLA will be available in December 2022.

Conclusion: Dose level 2 appears to be the maximum tolerated dose. Accrual to dose levels 1 and 2 will be expanded to further define toxicity and immunologic effects. Accrual of patients with BRCA1 or PALB2 mutations planning to undergo prophylactic mastectomy is beginning in order to define the toxicity and immunologic effects in this group and to determine whether inflammatory changes from occult lactational foci will be produced.

Funding Source: Department of Defense (W81XWH-17-1-0592 and W81XWH-17-1-0593)

Worst Toxicity by Dose Level Dose Level aLAC (mcg) dose Zymosan (mcg) dose n Patients n Grade 0 n Grade 1 n Grade 2 n Grade 3 1 10 10 3 3 2 100 10 3 3 3 500 10 3 2 1 Original 2 100 100 1 1

Citation Format: George Thomas Budd, Justin M. Johnson, Emily Rhoades, Halle Moore, Holly Levengood, Megan Kruse, Erin Roesch, Jame Abraham, Brenna Elliott, Elena Haury, Rachel Swartz, Holly Pederson, Zahraa Al Hilli, Vincent Tuohy. Phase I trial of alpha-lactalbumin vaccine in high-risk operable triple-negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3035.
Abstract 4195: Spatially resolved single cell transcriptomic profiling in formalin-fixed paraffin-embedded (FFPE) tissues
Authors: He Jiang , He Justin , Wiggin Timothy , Foreman Rob , Chen Renchao , Fernandez Nicolas , Emanuel George
Published: April 2023

Formalin-fixed paraffin-embedded (FFPE) tissues are the most widely used clinical sample types in histology and molecular diagnosis, but these samples are often challenging for single-cell transcriptomic analysis due to RNA degradation and protein crosslinking. A spatial transcriptomics technique with high detection efficiency and single molecule resolution is required in order to accurately profile the gene expression in FFPE samples in situ. Vizgen’s MERSCOPE platform, built on multiplexed error robust in situ hybridization MERFISH technology, directly profiles intact tissue’s transcriptome with subcellular spatial resolution. Here, we demonstrate the FFPE MERSCOPE workflow in tissues from 10 mouse and human samples, including archival clinical samples. In each sample, hundreds of thousands of cells were captured with >100 million transcript counts, generating detailed spatial transcriptomic data for the profiled genes in each sample. A comparison of FFPE and matched fresh frozen samples indicated that the FFPE workflow performs similarly in detection efficiency as compared to the fresh frozen protocol. We further demonstrated the MERSCOPE FFPE workflow is compatible with protein imaging by performing simultaneous protein-based cell boundary staining with MERFISH to accurately profile gene expression and map cell types in archival clinical human samples. Finally, we constructed a spatially resolved single cell atlas across eight major tumor types, mapped and cataloged different cell types within the tumor microenvironment and systematically characterized the gene expression among cells. This study demonstrates the potential for spatially resolved transcriptomic profiling of FFPE samples at single cell level to contribute to a wide range of biomedical research areas, including many applications to study human diseases.

Citation Format: Jiang He, Justin He, Timothy Wiggin, Rob Foreman, Renchao Chen, Nicolas Fernandez, George Emanuel. Spatially resolved single cell transcriptomic profiling in formalin-fixed paraffin-embedded (FFPE) tissues. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4195.
Abstract 4482: Discovery of GH2616, a potent and selective KIF18A inhibitor with robust in vivo efficacy in p53 mutant cancer
Authors: Li Jie Jack , Zhang Guiping , Li Jiapeng
Published: April 2023

Chromosomal instability (CIN) is one of the hallmarks of cancer. Cancer cells often undergo whole-genome doubling (WGD) and P53 represents a major barrier to the proliferation of WGD+ cells. Therefore, cancer cells with either CIN or WGD often harbor the p53 mutation. Recently, KIF18A has emerged as a potential therapeutic target in CIN or WGD cancer cells. We have identified a potent and selective KIF18A inhibitor, GH2616. In vitro, GH2616 inhibited the kinesin motor activity with an IC50 less than 50 nM, and with an EC50 less than 50 nM in the mitotic index assay using HT29 cells (WGD). In vivo, GH2616 inhibited the growth of WGD CDX models with a dose dependent manner. GH2616 has good oral bioavailability in different species and metabolic stability for QD dosing. This compound also showed low potential of DDI thus suitable for drug combinations. In a cell panel with more than 200 cell lines, GH2616 selectively inhibit the growth of cells with p53 mutant and some other specific biomarkers in multiple tumor types. In conclusion, we discovered GH2616 as a novel KIF18A inhibitor with potent in vivo efficacy. It is currently under evaluation in IND-enabling studies and IND filing is expected in Q4, 2023.

Citation Format: Jie Jack Li, Guiping Zhang, Jiapeng Li. Discovery of GH2616, a potent and selective KIF18A inhibitor with robust in vivo efficacy in p53 mutant cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4482.
Abstract 4989: Discovery and evaluation of ISM6466A, a novel covalent CDK12 inhibitor for the treatment of cancer
Authors: Min Lihua , Lu Hongfu , Zhang Yihong , Wu Jianping , Cai Xin , Zheng Min , Cui Hui , Qiao Junwen , Ding Xiao , Rao Sujata , Ren Feng , Zhavoronkov Alex
Published: April 2023

Cyclin-dependent kinase 12 (CDK12) belongs to the cyclin-dependent kinase (CDK) family of serine/threonine protein kinases. The CDK12/cyclin K complex regulates the elongation step of RNA transcription by phosphorylating Ser2 on the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II, and selectively affects the expression of genes, such as BRCA1 and BRCA2, involved in DNA Damage Response (DDR). CDK12 mutations as well as overexpression have been reported in different types of malignancies, making it an attractive cancer target. In this study, a series of covalent CDK12 inhibitors were designed and profiled in biochemical and cellular assays. ISM6466A was identified as a lead compound, demonstrating good in vitro efficacy, ADME properties, safety pharmacology profile (e.g., CYP, hERG), and a reasonable in vivo PK profile. Biochemically, ISM6466A exhibited reasonable selectivity over other CDKs, and inhibited cell proliferation in a panel of tumor cell lines with IC50 values in the nanomolar range (e.g., IC50 of ~100nM in the TNBC and AML cell lines, SUM149PT and MV4-11, respectively). Cell-based assays showed that ISM6466A has a selective inhibitory action for the phosphorylation of Ser2 on the CTD, but not for that of Ser5 or Ser7. Notably, ISM6466A demonstrated excellent in vivo anti-tumor efficacy in the SUM149PT breast cancer CDX model (Tumor Growth Inhibition, TGI, of 114% at 60 mg/kg QD) and in the MV4-11 AML CDX model (TGI of 95% at 30 mg/kg QD), without body weight loss. Data from an endpoint PKPD study in the MV4-11 CDX model revealed that ISM6466A inhibited phosphorylation of Ser2 on the CTD, and also inhibited DDR genes such as BRCA1 and ATR. Results from a 28-day rat DRF study revealed that the compound did not show evident signs of toxicity at the tested doses, suggesting a reasonable safety window for ISM6466A.In summary, the novel, covalent, small-molecule CDK12 inhibitor, ISM6466A, demonstrated excellent preclinical efficacy along with favorable drug-like properties. Our results underscore the therapeutic potential of ISM6466A for the treatment of cancer.

Citation Format: Lihua Min, Hongfu Lu, Yihong Zhang, Jianping Wu, Xin Cai, Min Zheng, Hui Cui, Junwen Qiao, Xiao Ding, Sujata Rao, Feng Ren, Alex Zhavoronkov. Discovery and evaluation of ISM6466A, a novel covalent CDK12 inhibitor for the treatment of cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4989.
Abstract 5009: Inhibition of TGFBR2 signaling re-sensitizes TMZ-resistant glioblastoma cells to therapy
Authors: Johnson Maya K. , Korleski Jack , Johnson Amanda , Sall Sophie , Laterra John , Lopez-Bertoni Hernando
Published: April 2023

Glioblastoma (GBM), the most aggressive and lethal form of brain tumors, recurs in 90% of cases and the standard protocol of care—temozolomide (TMZ)—is an ineffective method to combat chemo-resistant GBM. It is therefore imperative that we identify, develop, and design novel therapeutics to effectively combat recurrent GBM (rGBM). Multi-potent stem-like cell subpopulations within GBM (also referred to as glioma stem cells or GSCs) play important roles in tumor propagation, therapeutic resistance, and recurrence following treatment. Understanding the molecular mechanisms that drive resistance in GSCs can lead to novel therapeutic approaches for rGBM. Bioinformatics analyses of transcriptome data sets from rGBM clinical specimens identified transforming growth factor-beta receptor type 2 (TGFBR2) as a putative driver of resistance and recurrence in GBM. We show that TMZ-resistant cells become more stem-like concurrent with higher expression of TGFBR2 protein and mRNA. Importantly, shRNA-mediated inhibition of TGFBR2 decreases proliferation of TMZ-resistant cells and enhances the effects of TMZ. We hypothesize that by developing targeted therapeutics to reduce TGFBR2 expression we will inhibit the growth capacity and/or re-sensitize rGBM cells to ionizing radiation (IR) or TMZ treatment by simultaneously targeting multiple putative oncogenes implicated in the induction of stem-like resistant GBM cell subsets. Future directions include inhibiting TGFBR2 signaling in clinical specimens derived from rGBM patients using two translatable approaches: (1) ITD1, a small molecule TGFBR2 inhibitor predicted to cross the blood-brain-barrier and (2) microRNAs to target multiple TGFBR2 target genes up-regulated in rGBM.

Citation Format: Maya K. Johnson, Jack Korleski, Amanda Johnson, Sophie Sall, John Laterra, Hernando Lopez-Bertoni. Inhibition of TGFBR2 signaling re-sensitizes TMZ-resistant glioblastoma cells to therapy. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5009.
Abstract 822: Target-specific nanoparticle-based strategy for improved therapeutic efficacy to treat pancreatic cancer
Authors: Vivero-Escoto Juan Luis , Tarannum Mubin , Mukherjee Pinku
Published: April 2023

Pancreatic ductal adenocarcinoma (PDAC) accounts for over 90% of the pancreatic cancer cases and is the fourth-leading cause of cancer-related mortality. Unfortunately, despite the tremendous scientific efforts, it is shocking to note that PDAC has the worst prognosis with 5-year survival rate of 10% which has not significantly improved from the past 40 years. The high mortality and awful prognosis of PDAC can be attributed to multifactorial reasons like its intrinsic and acquired resistant behavior, early micrometastatic dissemination, desmoplastic effect and heterogeneities in tumors, rendering the current treatments rather ineffective. Developing reliable methods for the effective treatment of PDAC will have a major impact on the clinical outcome for this deadly disease. Nanoparticle-based drug delivery using mesoporous silica nanoparticles (MSNs) can be a potential alternative for the treatment of PDAC owing to their outstanding properties such as high surface area, tunable pore diameters, external and internal surface, which make this platform suitable for high drug loading and functionalization. We have designed, synthesized and characterized a target-specific, stimuli-responsive MSN platform for the controlled delivery of cisplatin (cisPt) and gemcitabine (Gem) (TAB004-Gem-cisPt-MSNs) with an optimal drug ratio. Our results demonstrate that this delivery system effectively targets tumor associated MUC1 (tMUC1), increases therapeutic efficiency with reduced toxicity in both a syngeneic and a spontaneous mouse model that overexpressed tMUC1. Moreover, the same MSN platform has been used in a sequential treatment where MSNs containing a Sonic Hedgehog (SHh) inhibitor, cyclopamine (CyP), and the Gem-cisPt-MSNs as the main delivery system led to reduction in the tumor stroma along with an improvement in the treatment of PDAC. Taken together, our findings support the potential of drug delivery using MSN nanoparticles for stroma modulation and to prevent pancreatic cancer progression.

Citation Format: Juan Luis Vivero-Escoto, Mubin Tarannum, Pinku Mukherjee. Target-specific nanoparticle-based strategy for improved therapeutic efficacy to treat pancreatic cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 822.
Supplemental Figures S1-S7 from Role of Rac1 Pathway in Epithelial-to-Mesenchymal Transition and Cancer Stem-like Cell Phenotypes in Gastric Adenocarcinoma
Authors: Yoon Changhwan , Cho Soo-Jeong , Chang Kevin K. , Park Do Joong , Ryeom Sandra W. , Yoon Sam S.
Published: April 2023

Supplemental Figure S1. A. Western blot for putative CSC markers in AGS, MKN-45, and NCI-N87 cells grown as monolayers or as spheroids. Supplemental Figure S2. A. Western blot of CD44(-) and CD44(+) AGS, MKN-45 and NCI-N87 spheroid cells for CD44, Sox2, Oct-4, Nanog, and c-Myc. Supplemental Figure S3. A. Western blot of AGS and NCI-N87 monolayer and spheroid cells for total and phosphorylated MAPK proteins. Supplemental Figure S4. A. Migration and invasion assays of GA monolayer and spheroid cells. Supplemental Figure S5. A. Western blot of AGS and NCI-N87 spheroid cells for total and phosphorylated JNK, active Rac1, N-cadherin, Slug, Snail, and Zeb1. Supplemental Figure S6. Proliferation assays for GA monolayer cells (A) and spheroid cells (B) following treatment with the Rac1 inhibitor NSC23766, 5-fluorouracil (5-FU), cisplatin, and/or carrier (DMSO). Supplemental Figure S7. A. Western blot of MKN-45 cells for total Rac1 following transduction with Rac1 shRNA (sh.Rac1) or scrambled control shRNA (sh.Scr).
Supplementary Figure Legends from RETRACTED: KRAS Activation in Gastric Adenocarcinoma Stimulates Epithelial-to-Mesenchymal Transition to Cancer Stem–Like Cells and Promotes Metastasis
Authors: Yoon Changhwan , Till Jacob , Cho Soo-Jeong , Chang Kevin K. , Lin Jian-xian , Huang Chang-ming , Ryeom Sandra , Yoon Sam S.
Published: April 2023

Supplementary Figure Legends 1-7
Data from miR-155–Deficient Bone Marrow Promotes Tumor Metastasis
Authors: Yu Fang , Jia Xuemei , Du Fen , Wang Junfeng , Wang Yuzhen , Ai Walden , Fan Daping
Published: April 2023

Abstract
Infiltration of immune cells in primary tumors and metastatic sites is known to influence tumor progression and metastasis. Macrophages represent the most abundant immune cells in the tumor microenvironment, and evidence has shown that macrophages promote seeding, extravasation, and persistent growth of tumor cells at metastatic sites. miR-155 plays an essential role in immune cell development/function, and its aberrant expression is associated with lymphomas and several solid tumor types. However, it is unknown how miR-155 expression in immune cells affects solid tumor growth and metastasis. To this end, bone marrow transplantation was performed using miR-155–deficient mice as bone marrow donors and wild-type (WT) mice as recipients, and the chimeric mice were inoculated with tumor cells. We demonstrate that bone marrow lacking miR-155 significantly enhanced lung metastasis without a substantial effect on primary tumor growth. Relative to mice with WT bone marrow, miR-155–deficient bone marrow accumulated more macrophages in the spleen and lungs. Further analysis revealed that miR-155–deficient macrophages in metastatic sites exhibited a tumor-promoting M2 phenotype. In vitro study suggested that miR-155–null macrophages were prone to M2 polarization upon incubation with tumor cell–conditioned medium, due to elevated expression of C/EBPβ, an identified miR-155 target. These data, for the first time, demonstrate that miR-155 in host immune cells plays a vital role in modulating solid tumor metastasis by affecting the recruitment and polarization of bone marrow–derived macrophages.

Implications: Targeted inhibition of miR-155 delays tumor development but inhibition in host immune cells may encourage metastasis. Mol Cancer Res; 11(8); 923–36. ©2013 AACR.
Data from Tpl2 Kinase Impacts Tumor Growth and Metastasis of Clear Cell Renal Cell Carcinoma
Authors: Lee Hye Won , Joo Kyeung Min , Lim Joung Eun , Cho Hyun Jung , Cho Hee Jin , Park Min Chul , Seol Ho Jun , Seo Seong Il , Lee Jung-Il , Kim Sunghoon , Jeong Byong Chang , Nam Do-Hyun
Published: April 2023

Abstract
Due to the innate high metastatic ability of renal cell carcinoma (RCC), many patients with RCC experience local or systemic relapses after surgical resection. A deeper understanding of the molecular pathogenesis underlying advanced RCC is essential for novel innovative therapeutics. Tumor progression locus 2 (Tpl2), upregulated in various tumor types, has been reported to be associated with oncogenesis and metastatic progression via activation of the MAPK signaling pathway. Herein, the relevance of Tpl2 in tumor growth and metastasis of RCC is explored. Inspection of The Cancer Genome Atlas (TCGA) indicated that Tpl2 overexpression was significantly related to the presence of metastases and poor outcome in clear cell RCC (ccRCC), which is the most aggressive subtype of RCC. Moreover, expression of Tpl2 and CXCR4 showed a positive correlation in ccRCC patients. Depletion of Tpl2 by RNAi or activity by a Tpl2 kinase inhibitor in human ccRCC cells remarkably suppressed MAPK pathways and impaired in vitro cell proliferation, clonogenicity, anoikis resistance, migration, and invasion capabilities. Similarly, orthotopic xenograft growth and lung metastasis were significantly inhibited by Tpl2 silencing. Furthermore, Tpl2 knockdown reduced CXCL12-directed chemotaxis and chemoinvasion accompanied with impaired downstream signaling, indicating potential involvement of Tpl2 in CXCR4-mediated metastasis. Taken together, these data indicate that Tpl2 kinase is associated with and contributes to disease progression of ccRCC.

Implications:Tpl2 kinase activity has prognostic and therapeutic targeting potential in aggressive clear cell renal cell carcinoma. Mol Cancer Res; 11(11); 1375–86. ©2013 AACR.
Data from Integrin α3β1 Can Function to Promote Spontaneous Metastasis and Lung Colonization of Invasive Breast Carcinoma
Authors: Zhou Bo , Gibson-Corley Katherine N. , Herndon Mary E. , Sun Yihan , Gustafson-Wagner Elisabeth , Teoh-Fitzgerald Melissa , Domann Frederick E. , Henry Michael D. , Stipp Christopher S.
Published: April 2023

Abstract
Significant evidence implicates α3β1 integrin in promoting breast cancer tumorigenesis and metastasis-associated cell behaviors in vitro and in vivo. However, the extent to which α3β1 is actually required for breast cancer metastasis remains to be determined. We used RNA interference to silence α3 integrin expression by approximately 70% in 4T1 murine mammary carcinoma cells, a model of aggressive, metastatic breast cancer. Loss of α3 integrin reduced adhesion, spreading, and proliferation on laminin isoforms, and modestly reduced the growth of orthotopically implanted cells. However, spontaneous metastasis to lung was strikingly curtailed. Experimental lung colonization after tail vein injection revealed a similar loss of metastatic capacity for the α3-silenced (α3si) cells, suggesting that critical, α3-dependent events at the metastatic site could account for much of α3β1′s contribution to metastasis in this model. Reexpressing α3 in the α3si cells reversed the loss of metastatic capacity, and silencing another target, the small GTPase RhoC, had no effect, supporting the specificity of the effect of silencing α3. Parental, α3si, and α3-rescued cells, all secreted abundant laminin α5 (LAMA5), an α3β1 integrin ligand, suggesting that loss of α3 integrin might disrupt an autocrine loop that could function to sustain metastatic growth. Analysis of human breast cancer cases revealed reduced survival in cases where α3 integrin and LAMA5 are both overexpressed.

Implications: α3 integrin or downstream effectors may be potential therapeutic targets in disseminated breast cancers, especially when laminin α5 or other α3 integrin ligands are also over-expressed. Mol Cancer Res; 12(1); 143–54. ©2013 AACR.