bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 6886: Orion™: 17-plex single-step stain and imaging of normal lung section adjacent to non-small cell lung carcinoma
Authors: Larkin Selena , George Tad , Kaldjian Eric
Published: March 2024

Background: The ability to image tissue microenvironments (TME) at high-plex over a whole slide without requiring multiple staining steps allows for unprecedented ability to study tissue architecture and molecular mechanisms of immune and disease processes. Here we investigate a sample of normal lung section adjacent to non-small cell lung carcinoma using whole slide, single-step stain and imaging at single-cell resolution.

Methods: These images profiled a whole slide tissue section of normal lung section adjacent to non-small cell lung carcinoma, stained with a 17-plex immuno-oncology biomarker panel. In this profile, we designed a high-plex panel of 17 biomarkers where the tissue autofluorescence was imaged and isolated as an additional fluorescence channel. All markers were stained in a single staining procedure and imaged in a single scan. Whole slide spatial staining and imaging was conducted on the Orion spatial biology platform. The full protocol is quick and simple, using standard histology tools: •Mount sections on glass slides•De-paraffinize and perform antigen retrieval•Quench autofluorescence•Stain slides with a panel of ArgoFluor™ conjugated antibodies•Coverslip with ArgoFluor Mounting Medium and cure overnight•Image whole slides at 20X magnification using the Orion instrument•Process to ome.TIFF and analyze.

Results: Data revealed intact normal lung alveolar architecture, with scattered immune cell infiltrates. Multiplexed imaging revealed epithelial cells, which make up alveoli, and endothelial vasculature as well as immune cells infiltrates in the alveolar space. Various immune cell populations were observed to be present (T cells, B cells, macrophages) and immune cell activation could be distinguished using PCNA and/or Ki-67 markers. Various T cell subsets could also be identified among the infiltrate using markers for CD4, CD8 and T-regulatory marker FOXP3. Through the use of multiplex staining, immune cell activity could also be characterized with respect to bronchiolar, artery, and capillary tissue architecture.

Conclusions: High-quality subcellular imaging of TME can lead to greater spatial investigation and more in-depth understanding of immune function in normal and diseased tissue. Here, multiplexed imaging identified distinct immune cell collections among cancer-adjacent normal lung tissue, providing validation of instrumentation and methods to obtain benchmarks for spatial quantitation of immune cells in control regions adjacent to cancer tissue.

Citation Format: Selena Larkin, Tad George, Eric Kaldjian. Orion™: 17-plex single-step stain and imaging of normal lung section adjacent to non-small cell lung carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6886.
Abstract 6963: Cysteinyl leukotriene receptors promote melanoma progression and metastasis
Authors: Sabu Kattuman Emma Elizabeth , Teegala Lakshminarayan Reddy , Darzi Somayeh , Paruchuri Sailaja
Published: March 2024

Background: Cysteinyl leukotrienes (cys-LTs; LTC4, LTD4, LTE4) are pro-inflammatory mediators mainly produced by hematopoietic cells, which enhance inflammation through their receptors, CysLT1R and CysLT2R. They play a pivotal role in the development of chronic asthma in humans. Recent association of inflammation with cancer has led to immense interest on the role of cysteinyl leukotrienes in cancer progression and metastasis. However, the exact molecular mechanisms regarding how these inflammatory mediators regulate the tumor proliferation and metastasis remain unexplored. A thorough investigation of these precise molecular mechanisms and identification of the specific receptor/s responsible can aid in understanding the therapeutic potential of these receptors in various cancers like melanoma. Since the inhibitors of these receptors are already FDA approved for the treatment of asthma, our goal is to repurpose these drugs to treat melanoma progression.

Objective: To determine the mechanistic aspects of how CysLTRs regulate melanoma tumor initiation, progression, and metastasis.

Methods: Protein expression by western blotting and ELISA, transcript expression by qPCR, viability, and proliferation by XTT and BrDU, migration using trans-well assay, tumor growth and metastasis were confirmed through in vivo experiments.

Results & Conclusion: B16F10 melanoma cells express high CysLT1R compared to CysLT2R and produce endogenous cys-LTs that function in an autocrine signaling pattern. Further, cys-LTs mediated the activation of several signaling proteins such as ERK, p38, AKT, and CREB that are important for melanoma survival and proliferation. Moreover, treatment with CysLTR antagonists significantly reduced melanoma cell proliferation, survival, and migration. Accordingly, we observed a significant reduction in the melanoma tumor volume in vivo in both Cysltr1−/- and Cysltr2−/− mice compared to the WT mice. Interestingly, angiogenesis was significantly reduced in Cysltr2−/- mice but not in Cysltr1−/−.Therefore, we speculate that while both receptors play a crucial role in tumor proliferation in vivo, CysLT2R is the main driver of angiogenesis and metastasis. Therefore, targeting both these receptors using their specific antagonists can offer potential therapy for melanoma progression and metastasis.

Citation Format: Emma Elizabeth Sabu Kattuman, Lakshminarayan Reddy Teegala, Somayeh Darzi, Sailaja Paruchuri. Cysteinyl leukotriene receptors promote melanoma progression and metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6963.
Abstract 7025: Advancing methylation analysis: TAPS v1.0: A fast, scalable, and non-destructive sequencing method
Authors: Haimes Josh , Marshall Craig , Sanders Travis , Vogel Sam , Ranik Martin , Casas Eduard , Wendel Doug , Karamanof Leo , Faurholme Bjarne , de Beer Abre , French Lee , Wadsworth Ross , Giordia Kristina , van der Walt Eric , Kudlow Brian
Published: March 2024

In the pursuit of advancing multi-cancer early detection, the exploration of cell-free DNA (cfDNA) through methylation profiling has emerged as a promising avenue. However, the realization of its full potential is impeded by limitations inherent in conventional methodologies, notably the 'gold standard' bisulfite conversion methods. These approaches pose challenges such as DNA destruction and the generation of low-complexity sequences resulting from the conversion of unmethylated cytosines to thymine. TET Assisted Pyridine-Borane Sequencing (TAPS) holds the potential as a non-destructive, rapid, and scalable alternative for base-level methylation analysis.

In this context, we introduce TET Assisted Pyridine-Borane Sequencing version 1.0 (TAPS v1.0), showcasing advancements to the technology originally introduced by Schuster-Böckler, Song, and their collaborators. TAPS v1.0 transforms 5mC into dihydrouracil (DHU) through a series of oxidation and reduction reactions. Ultimately, DHU is recognized as dU during PCR resulting in C-to-T conversions at 5mC sites, leaving unmethylated cytosines, the majority of cytosines, unchanged. The nondestructive nature of 5mC conversion yields significantly higher library yield and complexity compared to BS-seq. By leveraging Watchmaker's proprietary polymerase evolution platform, a DNA polymerase tolerant to DHU was selected for library amplification post DHU conversion, enabling unimpeded detection of 5mC, particularly in densely packed CpG repeats. Coupled with an optimized End Repair and A-tailing chemistry preceding TAPS v1.0, clinically relevant cfDNA samples of low quality and/or quantity can be analyzed in methylation detection pipelines.

To evaluate the performance of TAPS v1.0, human genomic DNA with control spike-ins featuring varying methylation statuses were employed. TAPS v1.0 exhibited significantly higher final library yield and greater complexity compared to BS-seq. Similar outcomes were observed in clinically relevant cfDNA samples.

Citation Format: Josh Haimes, Craig Marshall, Travis Sanders, Sam Vogel, Martin Ranik, Eduard Casas, Doug Wendel, Leo Karamanof, Bjarne Faurholme, Abre de Beer, Lee French, Ross Wadsworth, Kristina Giordia, Eric van der Walt, Brian Kudlow. Advancing methylation analysis: TAPS v1.0: A fast, scalable, and non-destructive sequencing method [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7025.
Abstract 7042: Enhancing TCR T cell function in solid tumors through in vivo combinatorial screens and single-cell analysis
Authors: Polyak Dina , Fuhriman Jessica , Susanto Josephine , Merrell Allyson , Simon Mandi , Oh Catherine , Cordazo Andrew , DeTomasso David , Tocchini Carla , Sail Vibhavari , Cui Eric , Milush Jeff , Gray-Rupp Levi , Galvin Brendan , Murriel Christopher , Zheng Grace , Boroughs Angela C. , Thakore Pratiksha , Oh Soyoung , Freimer Jake , Chen Bob , Eidenschenk Celine , Wheeler Emily , Levine Jacob , Huetter Jan-Christian , Schartner Jill , Geiger-Schuller Katie , Rozenblatt-Rosen Orit , Rutz Sascha , Mellman Ira , Haining W. Nicholas
Published: March 2024

The therapeutic potential of T cell therapies for treating solid tumors can be limited by intrinsic T cell exhaustion mechanisms and the suppressive tumor microenvironment. To better understand these challenges and identify genetic perturbations to enhance T cell functions, we developed in vivo exhaustion models and performed pooled CRISPR/Cas9-based screens with detailed characterization of T cell states through single cell RNA-sequencing (scRNA-seq). In vivo Xenograft exhaustion models were developed in the format of T cell receptor (TCR) T cells, with tumor cell lines expressing TCR-specific antigen (NY-ESO-1) respectively. Individual perturbations were introduced into T cells via non-viral editing and pooled before transferred into mice with established tumors of various sizes that provided continuous antigen exposure to drive exhaustion, while providing sufficient number of T cells from tumor and spleen tissues for scRNA-seq. The pooled CRISPR in vivo screens in human TCR T cells enabled us to evaluate T cell phenotypes resulting from gain-of-function, loss-of-function, or combinations of these modifications across a wide array of target genes. We identified known and previously uncharacterized combinatorial perturbations that were enriched or depleted and were associated with distinct transcriptional phenotypes over the course of chronic stimulation. This approach allows us to bridge the gaps in our understanding of how T cells can be reprogrammed to overcome exhaustion and function more effectively in the challenging environment of solid tumors.

Citation Format: Dina Polyak, Jessica Fuhriman, Josephine Susanto, Allyson Merrell, Mandi Simon, Catherine Oh, Andrew Cordazo, David DeTomasso, Carla Tocchini, Vibhavari Sail, Eric Cui, Jeff Milush, Levi Gray-Rupp, Brendan Galvin, Christopher Murriel, Grace Zheng, Angela C. Boroughs, Pratiksha Thakore, Soyoung Oh, Jake Freimer, Bob Chen, Celine Eidenschenk, Emily Wheeler, Jacob Levine, Jan-Christian Huetter, Jill Schartner, Katie Geiger-Schuller, Orit Rozenblatt-Rosen, Sascha Rutz, Ira Mellman, W. Nicholas Haining. Enhancing TCR T cell function in solid tumors through in vivo combinatorial screens and single-cell analysis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7042.
Abstract 7110: Characterizing pY240-PTEN:Ki-67 interactions and development of a PPI disrupting peptide
Authors: Jones Brandon , Patel Sejal , Furnari Frank
Published: March 2024

Glioblastoma (GBM) is the most aggressive and common malignant primary brain tumor. Standard of care for GBM patients involves chemotherapy and ionizing radiation which induce DNA damage to kill tumor cells; however resistance to these treatment modalities commonly develop through various mechanisms. One novel mechanism of radioresistance is through enhanced homologous recombination (HR) DNA damage response (DDR) mediated by nuclear-localized tyrosine-phosphorylated PTEN (pY240-PTEN) recruited to chromatin through interaction with the PP1 Binding Domain (PP1BD) of Ki-67. PTEN is known to play an important tumor-suppressive role and is found to be mutated in approximately 40% of GBMs. A Y240F-PTEN knock-in mouse model has shown that loss of Y240 phosphorylation results in IR sensitivity. Ki-67 dependent, pY240-PTEN facilitated DDR may be regulated by currently uncharacterized interactions within the Ki-67 PP1BD and determination of these interactions may enable development of complex-disrupting peptides capable of radiosensitizing glioma cells. To this end, I have identified residues in the Ki-67 PP1BD that are essential for pY240-PTEN interaction via streptavidin pulldown of N-terminal biotinylated peptides synthesized with alanine mutations at all residues spanning the Ki-67 PP1BD. Orthogonally, glioma cell lines have been engineered that stably express Ki-67 minigene constructs harboring mutation of the identified PP1BD residues. The effects of these mutations on PTEN:Ki-67 interaction, as well as DDR, HR, chromatin accessibility, and colony formation efficiency are currently being interrogated. Competitor peptides have been designed based on candidate Ki-67 residues and evaluated for their ability to bind PTEN. Further optimization of these peptides has led to candidates that are being assessed for stability and potential to radiosensitize glioma cells. In addition, regulation of pY240-PTEN:Ki-67 interaction by posttranslational modification of the Ki-67 PP1BD by aurora B kinase and cyclin dependent kinase 1 has been investigated through pulldown of biotinylated peptides harboring phosphorylated candidate residues. Lastly, Ki-67 has been knocked out in U87 glioma cells, as well as TS528 glioma stem like cells, and the resulting effect on IR sensitivity and DDR is being investigated in the absence, or presence of PTEN. Overall, this project has begun to characterize the regulation and critical molecular interactions between pY240-PTEN and Ki-67, elucidating potential strategies that could disrupt these interactions to enhance the efficacy of radiotherapy.

Citation Format: Brandon Jones, Sejal Patel, Frank Furnari. Characterizing pY240-PTEN:Ki-67 interactions and development of a PPI disrupting peptide [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7110.
Abstract 7132: Preclinical characterization of LAE119, a novel PARP1 selective inhibitor and trapper
Authors: Li Ming , Chen Yan , Chen Junyan , Jiang Ling , Lin Xiaofen , Gu Justin
Published: March 2024

Current PARP inhibitors primarily target PARP1/2 and demonstrate high efficacy against tumors with deficiencies in homologous recombination repair, such as those with BRCA mutations. However, these inhibitors are also associated with significant hematological toxicities. Studies have indicated that the synthetic lethality observed with BRCA mutations is mainly driven by PARP1, while PARP2 is not essential in this context. PARP2 has been shown to be crucial for the survival of hematopoietic stem/progenitor cells in animal models. Therefore, selective inhibition of PARP1 could potentially reduce toxicity and improve therapeutic outcomes. Here we introduce LAE119, a potent and selective PARP1 inhibitor and PARP1-DNA trapper. It demonstrates more than a 1000-fold selectivity for PARP1 DNA trapping compared to PARP2. In comparison to most PARP inhibitors including AZD5305, LAE119 exhibits extremely long residence time on PARP1 in both biochemical and cellular assays. It demonstrates robust anti-proliferation activity against BRCA2−/− DLD-1 cells and MDA-MB-436 cells, with IC50 value of 0.6 nM in both cell lines. In CAL51 cells, which has a BRCA2 mutation but with low PARP1 expression level and are much less sensitive to AZD5305, LAE119 demonstrates much better activity than AZD5305, particularly when PARP1 level is increased with transgene expression. LAE119 demonstrated substantial tumor inhibition in MDA-MB-436 and Capan-1 xenograft models. LAE119 also displays favorable ADME properties and PK profiles. It has high tumor/plasma ratio which is beneficial for sustainable anti-tumor effect and reduction of off-target effects. In rat hematologic toxicity study, LAE119 at 10 mpk QD dose was well tolerated and had minimal effects on hematologic parameters. Both in vitro and in vivo data strongly support the further clinical investigation of LAE119.

Citation Format: Ming Li, Yan Chen, Junyan Chen, Ling Jiang, Xiaofen Lin, Justin Gu. Preclinical characterization of LAE119, a novel PARP1 selective inhibitor and trapper [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7132.
Abstract 7134: Treatment of pancreatic cancer cells with tumor treating fields (TTFields) and PARP inhibitors
Authors: Ene Hila , Meir Kerem Ben , Martinez-Conde Antonia , Frechtel-Gerzi Roni , Gabay Hila , Gerasimova Daria , Engelman Rotem , Dor-On Eyal , Haber Adi , Giladi Moshe , Palti Yoram
Published: March 2024

Background: Therapeutic options for advanced stage pancreatic cancer are limited. Patients harboring germline BRCA mutations benefit from PARP inhibitors (PARPi); unfortunately, such mutations are rare in pancreatic cancer. Tumor Treating Fields (TTFields), electric fields that disrupt cellular processes crucial for cancer cell viability, have shown effectiveness against pancreatic cancer cells, and are currently under clinical investigation for the treatment of patients with pancreatic cancer. The mechanism of action of TTFields in various cancer types has suggested involvement of BRCA downregulation. The current study examined the potential sensitization of BRCA wild-type pancreatic cancer cell lines to PARPi with TTFields application.

Methods: BxPC3 and AsPC1 human pancreatic BRCA wild-type cancer cells were treated for 72 h with TTFields (frequency of 150 kHz; intensity of 1 and 0.5 V/cm RMS, respectively), using the inovitro device. The PARPi niraparib and olaparib were each administered to the cells at various concentrations, with or without co-application of TTFields. At treatment cessation, cell count, colony formation, and apoptosis were measured.

Results: Applying PARPi to pancreatic cell lines yielded a dose-dependent cytotoxic and anti-clonogenic effects, and induced apoptosis. TTFields application also induced such effects when applied alone, while delivery of TTFields together with PARPi amplified the effects demonstrated by PARPi alone.

Conclusions: Concomitant application of TTFields and PARPi in BRCA wild type pancreatic cancer cells exhibits a potential improvement relative to the mono-therapies. This could be rationalized based on the previously demonstrated ability of TTFields to induce a state of BRCAness in cancer cells, and suggests benefit for TTFields and PARPi co-treatment in the absence of background BRCA mutations.

Citation Format: Hila Ene, Kerem Ben Meir, Antonia Martinez-Conde, Roni Frechtel-Gerzi, Hila Gabay, Daria Gerasimova, Rotem Engelman, Eyal Dor-On, Adi Haber, Moshe Giladi, Yoram Palti. Treatment of pancreatic cancer cells with tumor treating fields (TTFields) and PARP inhibitors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7134.
Abstract 7147: ASN-3186 is a potent and selective inhibitor of USP1 for the treatment of BRCA1/2 mut and HRD+ cancers
Authors: Sun Qiaoling , Chen Yunfei , Wu Maojiang , Lv Jing , Jin Hongyue , Zeng Peng , Song Xia , Hou Wenfeng , Huang Qi , Niu Wei , Zhang Mengyao , Wang Tie-Lin , Chen Alice
Published: March 2024

Ubiquitin-specific protease 1 (USP1), a well-characterized member of the deubiquitinating enzyme family, selectively cleaves ubiquitin from various target proteins, including DNA repair protein PCNA. USP1 contributes to oncogenesis by playing critical roles in DNA damage repair processes including translesion synthesis and the Fanconi anemia pathway. Despite the clinical benefit achieved with PARP inhibitors (PARPi) in BRCA-mutated (BRCAm) or homologous recombination deficient (HRD+) populations, some patients either do not respond to therapy or develop resistance. USP1 inhibitors may have the potential to address this unmet clinical need as USP1 functions in distinct DNA damage repair pathway as compared to PARP. ASN-3186 is a novel, potent, and selective USP1 inhibitor with enzyme IC50 value of single digit nanomolar and selectivity >1000-fold against other family members. ASN-3186 demonstrated potent anti-proliferative activity in the BRCA1m triple negative breast cancer (TNBC) cell line, MDA-MB-436 (IC50 <30 nM). MDA-MB-436 CDX mouse model confirmed dose-dependent, single-agent inhibitory activity of ASN-3186 in vivo with higher potency than KSQ4279, possibly due to ASN-3186’s higher oral bioavailability. Efficacy is consistent with increase of pharmacodynamic biomarker ub-PCNA. The combination of ASN-3186 and PARPi Olaparib yielded a more robust and durable anti-tumor response, with near-complete tumor regression demonstrated at higher combination dose. Moreover, addition of ASN-3186 significantly sensitized Olaparib’s minimal anti-tumor activity in CAOV3 (ovarian, HRD high) and MX-1 (TNBC, BCRA1/2 mut) models, which are resistant to PAPRi, indicating that it has the potential to overcome PARPi resistance. Synthetic lethal activity was also observed when ASN-3186 was combined with DNA damage drug Gemcitabine. Furthermore, ASN-3186 displayed desirable ADME and PK profiles with high oral bioavailabilities (>75%) across species. These data support further clinical development of ASN-3186 as a potential best-in-class USP1 inhibitor, both as a single agent as well as in combination with PARPi, for treatment of BRCA1/2 mut and HRD+ cancers.

Citation Format: Qiaoling Sun, Yunfei Chen, Maojiang Wu, Jing Lv, Hongyue Jin, Peng Zeng, Xia Song, Wenfeng Hou, Qi Huang, Wei Niu, Mengyao Zhang, Tie-Lin Wang, Alice Chen. ASN-3186 is a potent and selective inhibitor of USP1 for the treatment of BRCA1/2 mut and HRD+ cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7147.
Abstract 7184: Simulating extended dosing intervals for atezolizumab: A comparative analysis between NONMEM and Pumas
Authors: Bateman Francis , Arisa Oluwatobi , Cabanas Natalia Corvalan , Zeng Yi , Peer Cody , Schmidt Keith , Figg William Douglas
Published: March 2024

The initially approved dosage regimens of 840 mg every 2 weeks, 1200 mg every 3 weeks, and 1680 mg every 4 weeks are considered excessive concerning the specified minimum effective concentration of 6 ug/mL and the significant exposure-response relationship with Adverse Events of Special Interest (AESI). Our previous research, demonstrated through simulation, indicated that an extended-interval dosing regimen (840 mg every 6 weeks) after two standard loading doses maintained efficacy with a nonsignificant exposure-response relationship with AESI.In alignment with the FDA's initiative "Project Optimus," which aims to optimize drug dosing for improved therapeutic outcomes, we explore alternative dosage regimens for atezolizumab. Through a comparison of the traditional 30-year-old industry standard NONMEM software and the recently developed PumasAI software, we simulate these regimens, utilizing our previously published article as a benchmark. Given the rapid evolution of artificial intelligence (AI) and machine learning, it is crucial for pharmacokinetic modeling to adapt and leverage these advancements. We anticipate that this paper will contribute to the integration of AI and machine learning software in pharmacokinetic analysis, aligning with the goals of "Project Optimus" to ensure that drug concentrations are optimized for efficacy and safety.

Table 1: Comparative Summary of Simulated Pharmacokinetic Parameters: Pumas vs. NONMEM Pumas NONMEM Regimen Cycle Week Cmax (ug/mL) Cmax (ug/mL) Cmax (ug/mL) Cmax (ug/mL) Cmin (ug/mL) Weekly AUC (ug*day/mL) 1200 mg q3w 1st 3 384(278-533) 64.1(31.4-112) 919(640-1290) 394 (278-559) 75.6 (44.5-121) 1003 (755-1342) 7th 21 541(371-795) 146(53.8-349) 1750(977-3210) 583 (414-847) 180 (75.9-396) 2014 (1169-3535) 840 mg q2w x2, 840 mg q6w 1st 2 270(195-379) 61.6(35.5-100) 775(570-1085) 275 (184-397) 71.2 (46.4-108) 834 (620-1131) 7th 38 314(221-448) 33.6(8.8-127) 650(357-1375) 336 (235-487) 46.9 (13.5-150) 774 (441-1562) 1200 mg q3w x2, 840 mg q6w 1st 3 384(278-533) 64.1(31.4-112) 919(640-1290) 394 (278-559) 75.6 (44.5-121) 1003(755-1342) 7th 39 316(224-459) 36.0(8.4-129) 670(340-1406) 327 (217-492) 46.6 (13.4-157) 763 (411-1594) 1680 mg q4w x2, 840 mg q6w 1st 4 545(380-779) 63.1(26.9-122) 1096(735-1555) 552 (375-793) 78.1 (40.7-135) 1203(869-1651) 7th 40 318(222-469) 33.9(7.7-126) 657(343-1385) 332 (227-491) 46.5 (13.6-140) 771 (436-1464)

Citation Format: Francis Bateman, Oluwatobi Arisa, Natalia Corvalan Cabanas, Yi Zeng, Cody Peer, Keith Schmidt, William Douglas Figg. Simulating extended dosing intervals for atezolizumab: A comparative analysis between NONMEM and Pumas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7184.
Abstract 7193: ABCB1-mediated chemotherapeutic drug resistance is reversed by a potent p53-MDM2 inhibitor NVP-HDM201
Authors: Patel Harsh , Cai Chaoyun , Wu Zhuoxun , Teng Qiuxu , Li Hanli , Chen Zhe-Sheng
Published: March 2024

The failure of chemotherapy in cancer persists as a result of overexpression of various ATP-binding cassette (ABC) transporters. ABCB1 is one such transporter that actively pumps out chemotherapeutic drugs and it is one of the reasons for multidrug resistance (MDR). In the last few years, activation of p53 has been targeted as a therapeutic strategy in the treatment of cancers. Siremadlin (NVP-HDM201) is a potent and selective inhibitor of p53-MDM2 interaction. The objective of this study was to explore the ability of HDM201 to reverse tumor MDR attributable to overexpression of ABC transporters. According to our findings, HDM201 significantly increased the sensitivity of ABCB1-overexpressing cells to ABCB1 substrates, such as colchicine and doxorubicin. We found that HDM201 reverses ABCB1-mediated MDR by interacting with ABCB1 and blocking its function without affecting the expression and cellular localization of ABCB1. Moreover, HDM201 promoted the accumulation of paclitaxel in cell lines that overexpress ABCB1. At both high and low doses, HDM201 increased the ATPase activity of ABCB1. The computational support for the cross-reactivity of this p53 inhibitor with human ABCB1 comes from docking simulation results that align with the binding conformation of HDM201 within the vast cavity of the transmembrane region of ABCB1. In conclusion, by blocking the transport function of ABCB1, HDM201 can reverse ABCB1-mediated MDR in vitro.

Citation Format: Harsh Patel, Chaoyun Cai, Zhuoxun Wu, Qiuxu Teng, Hanli Li, Zhe-Sheng Chen. ABCB1-mediated chemotherapeutic drug resistance is reversed by a potent p53-MDM2 inhibitor NVP-HDM201 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7193.
Abstract 720: Combining zelasudil, a small molecule ROCK2 inhibitor, with chemotherapy or immunotherapy improves response in preclinical models of pancreatic cancer
Authors: Pajic Marina , McLean Benjamin , Fajardo Diego Chacon , Porazinski Sean , Upton Dannielle H. , Schuhmacher Diana , Istadi Aji , Cox Thomas , Timpson Paul , Wilcock Daniel J. , Anderson Katie J. , Mason Helen , Guisot Nicolas E. , Jones Clifford D. , Phillips Caroline , Armer Richard
Published: March 2024

Zelasudil (RXC007) is an orally available, highly selective small molecule inhibitor of Rho-associated coiled-coil containing protein kinase 2 (ROCK2), which has demonstrated pre-clinical anti-fibrotic efficacy and is currently being tested in a Phase 2a clinical trial for the treatment of idiopathic pulmonary fibrosis (IPF) (NCT05570058). Pancreatic ductal adenocarcinoma (PDAC) is an aggressive and therapeutically challenging disease with a dense and highly fibrotic tumor microenvironment which may limit efficacy of conventional therapies. Here, we investigate the benefit of combining an anti-fibrotic, RXC007, with either standard of care chemotherapy or immunotherapy in mouse models of PDAC.In a fibrotic patient-derived metastatic PDAC orthotopic model, RXC007 (10mg/kg, 50mg/kg and 100mg/kg BID 5d on/2d off PO) in combination with SoC chemotherapy Gemcitabine (100mg/kg IP QW)/Abraxane (30 mg/kg IP QW) improved survival in a dose-dependent manner (all P<0.0001) compared to Gemcitabine/Abraxane alone.In the immunocompetent orthotopic LSL-KrasG12D/+; LSL-Trp53R172H/+; Pdx1-Cre (KPC) model of metastatic PDAC, survival was significantly increased (P<0.0001) upon treatment with a combination of RXC007 (50 mg/kg BID 5d on/2d off PO) and anti-PD1 (200 ug BIW) compared to anti-PD1 alone. ROCK2 inhibition elicited positive immunomodulatory effects in KPC pancreatic tumors, with increase of CD8+ (P=0.0031) and CD4+ (P=0.008) T cell infiltrate into the tumor cortex and reduction in immunosuppressive FOXP3+ regulatory T cells at the tumor border. Furthermore, RXC007 monotherapy exhibited anti-fibrotic effects, via a decrease in collagen content and organization, effects associated with CAF reprogramming and reduced intra-tumoral aSMA+ PDPN+ myofibroblast-like CAFs (myCAFs; P=0.0406).This data highlights the potential for treating highly fibrotic tumours with RXC007 in combination with SoC chemotherapy or immunotherapy in order to improve patient outcomes in this aggressive and treatment-refractory cancer.

Citation Format: Marina Pajic, Benjamin McLean, Diego Chacon Fajardo, Sean Porazinski, Dannielle H. Upton, Diana Schuhmacher, Aji Istadi, Thomas Cox, Paul Timpson, Daniel J. Wilcock, Katie J. Anderson, Helen Mason, Nicolas E. Guisot, Clifford D. Jones, Caroline Phillips, Richard Armer. Combining zelasudil, a small molecule ROCK2 inhibitor, with chemotherapy or immunotherapy improves response in preclinical models of pancreatic cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 720.
Abstract 7254: Evaluation of scFv and diabody pseudotyped Sindbis engineered retrovectors for targeted cancer therapy
Authors: Sato Makoto , Cunha Alexander , Collins Sara , Kasahara Noriyuki , Roh Cecilia , Johnson Robert G.
Published: March 2024

Engineering viral vectors to target specific cells and organs after intravenous delivery remains a challenge. Transcriptional targeting with cell-specific promoters is a commonly used approach but does not change vector biodistribution. We have developed a novel gene delivery system targeted to tumor cells by pseudotyping the vector with Sindbis Virus (SB) envelope bearing an antigen-binding domain. Prototype vectors were generated by inserting a universal IgG binding domain from Protein A into the SB envelope (SB-ZZ). Antibodies (Abs) against various cell-surface targets (HLA, HER2, CD47, EGFR, Nectin-4), were conjugated to SB-ZZ vectors delivering a luciferase (Luc) reporter gene. Targeted transduction was confirmed on cells expressing the corresponding antigens by significantly higher Luc activity compared to SB-ZZ vectors without Abs. SB envelopes were further engineered by adding or removing furin cleavage sites and linkers, transduction-enhancing point mutations, and direct incorporation of single-chain variable fragment (scFv) in different VH and VL orientations, or diabody (DB) sequences, against the same targets. The specificity of optimized HER2-targeting vectors delivering the Luc reporter was evaluated in SKBR3 (HER2 over-expressing) and MDA-MB-468 (HER2-null) cells. Robust Luc activity was observed in SKBR3 cells, but only negligible activity in MDA-MB-468 cells. In MDA-MB-468 cells overexpressing HER2, significantly higher transduction was observed compared to the wild-type cells. When comparing HER2-targeting vectors with scFv vs. DB sequences based on the same antibody, transduction capability was higher with the DB motif in HER2-positive cell lines. Targeting vectors delivering HSV-eTK were also constructed, and ganciclovir (GCV)-mediated cell killing was evaluated in vitro. SKBR3 cells transduced with HER2-targeting vectors showed significantly more cell killing after GCV treatment than after transduction with an amphotropic reference vector. Our results indicate a method for directing gene therapy vectors to specific populations of tumor cells, and provide a framework for highly modular targeted gene therapy and immunotherapeutics. Experiments are underway to examine in vivo delivery of targeted vs amphotropic vectors.

Citation Format: Makoto Sato, Alexander Cunha, Sara Collins, Noriyuki Kasahara, Cecilia Roh, Robert G. Johnson. Evaluation of scFv and diabody pseudotyped Sindbis engineered retrovectors for targeted cancer therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7254.
Abstract 728: Oral TGF-beta receptor1 inhibitor vactosertib promotes osteosarcoma regression by targeting tumor proliferation and enhancing anti-tumor immunity
Authors: Choi Sung Hee , Myers Jay , Tomchuck Suzanne , Bonner Melissa , Eid Saada , Kingsley Daniel , VanHeyst Kristen , Kim Seong-Jin , Kim Byung-Gyu , Huang Alex Y.
Published: March 2024

Osteosarcoma (OS) is an aggressive malignant bone cancer, with the lung as the most frequent site of metastasis. Unresectable pulmonary metastasis remains a significant challenge with a survival rate of less than 20%. Identification of novel therapeutic strategies are desperately needed. Transforming growth factor-β1 (TGF-β) is a potent immune suppressive cytokine in OS tumor microenvironment (TME). TGF-β1 expression is increased in the sera and tumor tissues of OS patients and this increase is associated with high-grade OS and lung metastases. Therefore, blocking TGF-β1 signaling may be a novel therapy for OS treatment. In this study, we show that blocking TGF-β1 signaling using the orally bioavailable small molecule TGF-βR1 inhibitor, Vactosertib, significantly inhibited OS proliferation in vitro and in vivo. Notably, Vactosertib inhibits c-Myc expression in the OS cells and oral administration of Vactosertib significantly reduces OS growth in vivo. Vactosertib increased immune effectors (e.g., IFNγ+CD8+ cells and NK cells) and inhibited immune suppressors (e.g., M2-like TAM, MDSC) in the OS TME. Our results suggest that inhibition of TGF-β1 signaling is an effective therapeutic strategy against OS through a multi-pronged approach that targets tumor intrinsic and extrinsic factors to achieve optimal immune-effector functions and maximal clinical response.

Citation Format: Sung Hee Choi, Jay Myers, Suzanne Tomchuck, Melissa Bonner, Saada Eid, Daniel Kingsley, Kristen VanHeyst, Seong-Jin Kim, Byung-Gyu Kim, Alex Y. Huang. Oral TGF-beta receptor1 inhibitor vactosertib promotes osteosarcoma regression by targeting tumor proliferation and enhancing anti-tumor immunity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 728.
Abstract 7326: TP53 p.Pro47Ser polymorphism in breast cancer susceptibility in Mali
Authors: Diakite Brehima , Kassogue Yaya , Maiga Mamoudou , Kassogue Oumar , Cisse Kadidiatou , Diarra Fousseyni , Traore Cheick Traore B. , Kamate Bakarou , Holl Jane L. , Hou Lifang
Published: March 2024

Background: The aim of this study was to assess the potential association of p.Pro47Ser polymorphisms of TP53 with the risk of developing breast cancer in the Malian population.

Methods: We analyzed DNA samples from 72 breast cancer patients and 121 unrelated healthy, age-matched individuals to examine the presence of the polymorphisms. The genotyping of TP53 polymorphism was performed using PCR-RFLP and HRM (high-resolution melting) methods.

Results: The genotypic frequencies of PP, PS, and SS were found to be 63.9% PP, 30.6% PS, and 5.6% SS in breast cancer patients, compared to 70.2% PP, 22.3% PS, and 7.4% SS in the control group. The frequencies of P and S alleles of TP53 p.P47S polymorphism were 79.2% vs 81.4%, 20.8% vs 18.6%, and 5% vs 4.5% in patients and controls, respectively. In this study, no significant correlation was observed between TP53 p.Pro47Ser polymorphism and breast cancer in the Malian population (Pro/Ser vs Pro/Pro: OR = 1.55, 95% CI = 0.80-3.05, P = 0.19; Ser/Ser vs Pro/Pro: OR = 1.27, 95% CI = 0.34-4.74, P = 0.71; and Ser vs Pro allele: OR = 1.39, 95% CI = 0.80-2.32, P = 0.24).

Conclusion: Despite the absence of a genetic association between TP53 p.Pro47Ser and the risk of breast cancer in Malian patients, our findings suggest that individuals carrying at least one minor Ser allele are not protected against the disease.

Citation Format: Brehima Diakite, Yaya Kassogue, Mamoudou Maiga, Oumar Kassogue, Kadidiatou Cisse, Fousseyni Diarra, Cheick Traore B. Traore, Bakarou Kamate, Jane L. Holl, Lifang Hou. TP53 p.Pro47Ser polymorphism in breast cancer susceptibility in Mali [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7326.
Abstract 7345: Double-strand break inference from mosaic chromosomal alterations
Authors: Dutch Abraham , Bumgardner Cody , Jakubek Yasminka
Published: March 2024

Double-strand breaks (DSBs) can cause alterations and rearrangements in chromosomes leading to large structural mutations. There have been previous efforts to identify DSBs in tumors and utilize these as a measure of homologous repair deficiency and response to therapy. In contrast, DSBs have not been well characterized in non-tumor human tissues. To address this void, we explore the distribution of DSBs in hematopoietic stem cells (HSCs) through the analyses of mosaic chromosomal alteration (mCA) breakpoints. Specifically, this work explores the relationship between the likelihood of DSB occurrences and the chromosomes on which they occur. Using data from the UK Biobank, mCA breakpoints were labeled as either DSBs or nonDSBs by proximity to telomeres and centromeres. mCA calls from the UK Biobank were obtained from Loh et al 2020. The START_MB_RANGE and END_MB_RANGE fields were treated as two separate breakpoint events for each entry in the data. Each of these breakpoint ranges was checked to see if it was close to either of the telomeres or to the centromere. Those falling within one Mb were categorized as mCA breakpoints that were likely not a result of DSBs, but rather missegregation of chromosomes or chromosome arms. Ranges that met either of these conditions were labeled “nonDSB” while ranges that did not were labeled “DSB.” These labeled data were processed in R using the Hmisc package. The 1-alpha binomial probability was calculated for the total number of DSBs versus the total number of breakpoint events. The point estimate for each chromosome was plotted along with the upper and lower confidence intervals. This work investigates the properties of DSBs. It is important to note that the observed putative DSBs are not representative of the frequency of DSBs in HSCs, since the resulting mutations can have different impacts on cellular fitness. This point is highlighted by our finding of increased putative DSBs on chromosome 13, as copy number changes involving the 13q14 locus are well documented drivers of chronic lymphocytic leukemia. In this investigation we observe that the proportion of putative DSBs is not correlated with chromosome length (p = 0.2). This result is likely due to the differential fitness effect of mCAs. However, it may also reflect differences in the likelihood of DSBs across the genome. We are currently working on methods from Machine Learning to further understand if there are genetic features which can predict DSBs which give rise to mCAs in HSCs.

Citation Format: Abraham Dutch, Cody Bumgardner, Yasminka Jakubek. Double-strand break inference from mosaic chromosomal alterations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7345.
Abstract 7357: Comparative transcriptomic analysis reveals novel insights into targetable B-cell lymphoma mechanisms
Authors: Kim Sehi , Rapier-Sharman Naomi , Told Michael T. , O’Neill Kim L. , Pickett Brett E.
Published: March 2024

B-cell lymphoma is a severe type of lymphatic cancer that is often misdiagnosed in adolescents. While some cases of B-cell lymphoma respond well to chemo- and radiation therapy, there are severe side effects, and many cases are refractory and fail to achieve remission. On the other hand, though CD19 CAR T-cell therapy is highly effective at treating B-cell lymphoma, its association with long-term immunocompromisation justifies the exploration of alternative treatments. Comparing B-cell lymphomas to an autoimmune disease that affects the same tissue type may grant us additional insights into immuno-oncology related treatments for B-cell lymphoma. We have developed a novel tool to compare cancer and autoimmune disease by analyzing bulk RNA-sequencing (RNA-seq) data. This algorithmic approach uses the transcriptional profile to improve our understanding of B-cell specific mechanisms that can be targeted in B-cell lymphoma. Using this tool, we compared the transcriptional signatures of primary B-cell lymphomas with primary B-cells from patients with systemic lupus erythematosus, an autoimmune disease. We identified specific genes and enriched functions associated with B-cell lymphoma’s immune signature. We expect that the results of our B-cell lymphoma analysis could be used to develop beneficial treatments alternative to current therapies, potentially mitigating side effects for B-cell lymphoma patients and increasing their quality of life.

Citation Format: Sehi Kim, Naomi Rapier-Sharman, Michael T. Told, Kim L. O’Neill, Brett E. Pickett. Comparative transcriptomic analysis reveals novel insights into targetable B-cell lymphoma mechanisms [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7357.
Abstract 7373: Generative Bayesian networks for augmentation of molecular data from commercial genetics panels
Authors: Tracy Dillon H. , Sherman Jeff , Baron Maayan
Published: March 2024

Background: Computational models in medical research which use molecular features to predict patient sensitivities or outcomes are traditionally limited to producing a scalar output for a given disease phenotype, e.g. progression-free survival or drug response. Even for relatively intelligible models, it is generally difficult to place confidence limits on the prediction or develop an intuition for how a prediction varies with respect to “what-if” changes in those features or how sensitive a prediction is to changes in input variables. Moreover, while essential for understanding and modeling tumor behavior, molecular features from patient tumors in real-world settings are typically limited to profiles of hundreds of genes, while the biologically relevant inputs to the patient’s condition can be much larger.

Approach: To generate data required to enhance the interpretation of predictive models and extend the utility of real-world patient oncology datasets, a distribution of conditions consistent with the observed features and their incidence across cancer patient cohorts is required. We hypothesized we could synthesize patient samples drawn from the joint probability distribution of a broader universe of features when a subset of them is held fixed at the observed values. We model this joint distribution by learning a Bayesian network over a broad feature set for which some training data is available and generate feature profiles by applying Gibbs sampling to the learned network.

Results: We assessed the potential clinical utility of using these generated feature profiles in predicting drug response and enhancing biological interpretation of different model outputs. We found generative somatic mutations were useful for predicting cancer patient outcomes, including drug response predictions in breast cancer tumors from AACR Project GENIE. Synthesized patient feature profiles enhanced biological interpretability of nominal panel data (100-200 genes), providing a means to assign probabilities to outcomes and uncovering previously described mechanisms of drug response in real-world patient data.

Conclusion: We introduce an approach that leverages Bayesian networks to synthesize richly annotated patient feature profiles from limited molecular data routinely collected in real-world settings. This approach addresses challenges associated with limited molecular data, biological interpretability and evaluation of predictive models and enhances the utility of real-world datasets for cancer research.

Citation Format: Dillon H. Tracy, Jeff Sherman, Maayan Baron. Generative Bayesian networks for augmentation of molecular data from commercial genetics panels [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7373.