tbuckley/cabot-search huggingface dataset:
Abstract 7602: Discovery of GH1581, a potent and selective WRN inhibitor as a cancer therapy
Authors: Jiapeng Li, Guiping Zhang, Jie Jack Li
Journal: Cancer Research (2024)

Abstract Defects in DNA mismatch repair (MMR) proteins could induce damage of genome, resulting microsatellite instability (MSI). MSI is highly correlated with the occurrence of several types of cancers, mainly in colon, gastric, endometrial, and ovarian cancers. Despite advances in the treatment of MSI-high cancers, tumor evolution and drug resistance remain the leading causes of treatment failure and death in cancer patients. About 50% MSI cancers have no response to immune checkpoint inhibitors. There is still unmet needs to be fulfilled for MSI-high patients. WRN is a RecQ family helicase involves in genome stability maintenance, DNA repair, replication, transcription, and telomere maintenance. Recent studies have identified WRN as a synthetic lethal target of MSI-high cancers. Employing structure-based drug design strategy, we have discovered a potent and selective WRN inhibitor, GH1581. In vitro, GH1581 displayed specific &amp;lt; 10 nM potency in ADP-Glo assay and &amp;lt; 10 nM potency in cell proliferation assay using MSI cancer cell lines. In vivo, GH1581 demonstrated favorable pharmacokinetic properties in different species. In SW48 xenograft model, it inhibited the tumor growth with 100% TGI at QD dosing of 10 mg/kg without severe adverse effect on body weight. In summary, we discovered GH1581 as a novel inhibitor of WRN with high in vitro and in vivo efficacy. Citation Format: Jiapeng Li, Guiping Zhang, Jie Jack Li. Discovery of GH1581, a potent and selective WRN inhibitor as a 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 7602.
Abstract 6896: Biomimetic hydrogels at physiological stiffness reprogram patient derived melanoma cells
Authors: Yi L. Liu, Justyna Gleba, Chantal Kopecky, Matthew Pawlush, John A. Copland, Kristopher A. Kilian
Journal: Cancer Research (2024)

Abstract Melanoma is a uniquely difficult cancer to treat due to complex tumor heterogeneity and resistance, where upon dissemination, survival drops to less than 17%. Drug resistance has arisen for the current standard of care and combinatorial therapies, expediting the need for new efficacious agents. The lack of physiologically relevant preclinical models has impeded the development of these therapeutics. Potential melanoma drugs are typically assayed using cell lines on tissue culture plastic, then tested for in vivo efficacy and side effects in animals. This paradigm is inherently unsuitable for the generation of effective therapies as typical cell culture platforms fail to replicate the complex microenvironments known to play critical roles in tumor pathology and rodent models are prohibitively expensive for optimizing novel and combination therapies. Thus, our goal is to synthesize tissue-engineered melanoma models using biomimetic polymers that recapitulate patient tumor characteristics to assess combination and novel therapies that attenuate resistance and disrupt metastatic processes. In this study, patient melanoma cells, which were unable to recapitulate drug responses on traditional cell culture platforms, were cultured in a controlled spatial and temporal manner on polyacrylamide hydrogels. The hydrogel scaffolds feature stiffnesses spanning that of physiological tissue, with microcontact printed human fibronectin for biomimetic protein presentation to create a microtumor array. Cells cultured on the hydrogel showed a 2.5-fold increase in expression of the cancer stem cell biomarkers, CD271 and ABCB5, which play a key role in melanoma survival and recurrence, compared to cells cultured on plastic or glass substrates. Further study identified BRAF mutant, drug resistant patient cells, regained resistance to standard of care targeted therapies, trametinib and dabrafenib. Through hydrogel microarrays featuring physiological similarities, the technology has enabled the exploration of heterogeneous cell populations with novel and combinatorial therapeutics. Citation Format: Yi L. Liu, Justyna Gleba, Chantal Kopecky, Matthew Pawlush, John A. Copland, Kristopher A. Kilian. Biomimetic hydrogels at physiological stiffness reprogram patient derived melanoma cells [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 6896.
Abstract 322: Ultraplex genome and exome sequencing of rare single cells
Authors: Ioanna Andreou, Samuel Rulli, Katja Heitz, Silke Huebner, Christin Meerschiff, Eric Lader
Journal: Cancer Research (2024)

Abstract Single-cell genome analysis enables researchers to gain novel insights into tumor heterogeneity. Conducting single-cell genomic analysis using next-generation sequencing (NGS) methods has traditionally been challenging since the amount of genomic DNA present in a single cell is limited. PCR-based amplification methods normally have high error rates, low coverage uniformity, and extensive allelic drop-outs making interpretation of SNVs and CNVs challenging.Here we introduce a new whole-genome amplification method which utilizes an optimized isothermal DNA amplification reaction with a Hi-fidelity, error correcting polymerase and downstream library preparation protocol to allow pooling of amplified DNA. The key DNA amplification steps use multiple displacement amplification (MDA) technology to amplify gDNA directly from single cells, nuclei or previously isolated genomic DNA. During the MDA reaction, sample-barcodes are incorporated into the newly synthetized DNA, allowing the amplified DNA to be pooled and processed in to one ultraplex library. This method saves library preparation time, reduces DNA library costs and limits plastic consumable usage.Our current workflow allows 24 samples to be multiplexed in one library and 24 libraries to be produced for a total of 576 samples per sequencing flow cell. This method can be used to investigate chromosomal instability with low pass sequencing or SNV and CNV analysis following whole genome, exome-capture workflows. Citation Format: Ioanna Andreou, Samuel Rulli, Katja Heitz, Silke Huebner, Christin Meerschiff, Eric Lader. Ultraplex genome and exome sequencing of rare single cells [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 322.
Abstract 6885: Investigating a novel role of DCLK1 isoforms in colitis and colitis associated colon cancer
Authors: Kafayat Aderonke Yusuf, Badal C. Roy, Shrikant Anant, Shahid Umar
Journal: Cancer Research (2024)

Abstract Chronic intestinal inflammation in patients diagnosed with inflammatory bowel disease (IBD) significantly increases their risk of colorectal cancer (CRC). Despite the rising global frequency of IBD, the precise mechanisms that regulate the transition from IBD to colon cancer are poorly understood. Doublecortin-like kinase 1 (DCLK1) is a protein with two major isoforms, DCLK1-L and DCLK1-S. Previous studies have shown that hypermethylation of the DCLK-1α promoter encoding DCLK1-L, particularly in colorectal cancer, allows switching to the DCLK1-S isoform that confers an invasive tumor phenotype. The DCLK1-L is a tuft cell marker that protects against colitis by sensing and eliminating gut pathogenic infection through various mechanisms. On the contrary, the role of DCLK1-S in colitis and colitis-associated cancer has not been thoroughly investigated. Studies from our lab have identified a marked elevation of DCLK1-S in tissue samples of IBD patients. We also recently discovered that DCLK1-S is predominantly expressed in Ly6G+; MHCII- neutrophils, which coincide with elevated levels of inflammation and tissue damage in the colon. To further understand the role of DCLK1 isoforms in driving the progression of colitis to colon cancer, we bred Dclk1fl/fl mice with MRP8-Cre-ires/GFP mice to generate Dclk1fl/fl;MRP8-Cre+/- that eliminates DCLK1-L upon tamoxifen injection resulting in sustained expression of DCLK1-S in the granulocytes especially neutrophils. When infected with Citrobacter rodentium (CR), MRP8;Dclk1−/− mice compared to MRP8;Dclk1+/− or WT mice developed more severe colitis. We have also discovered a novel interaction between DCLK1-S and MMP13 in an unbiased docking study that correlated with significant co-localization of DCLK1-S with MMP13 in the colons of CR-infected mice. Employing a knock-in mice over-expressing the DCLK1-S +19 under the CAG promoter, the DCLK1-MMP13 co-localization correlated with severe ulceration and colitis with loss of crypts and immune cell infiltration including Ly6G+ neutrophils. Studies are underway to see if the severity of colitis in MRP8;Dclk1−/− mice translates into enhanced tumorigenesis and to see if potential interaction between DCLK1-S and MMP13 could provide a plausible mechanism of colitis progression to colon cancer through ECM remodeling and tissue damage. Citation Format: Kafayat Aderonke Yusuf, Badal C. Roy, Shrikant Anant, Shahid Umar. Investigating a novel role of DCLK1 isoforms in colitis and colitis associated colon 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 6885.
Abstract 3249: Simple, rapid, and robust bioluminescent cell-based assay for detecting neutralizing antibodies against AAV in serum
Authors: Morten Seirup, Kirsten Wingate, Jeff Nelson, Kara Machleidt, Vanessa Ott, Trish Hoang, Marjeta Urh
Journal: Cancer Research (2024)

Abstract Adeno-associated viruses (AAV) are prevalent gene therapy vectors, delivering therapeutic transgenes to treat various diseases including cancer and rare monogenic diseases. Individuals with pre-existing immunity to AAVs are less likely to benefit from AAV-based therapies due to both, a reduction in cellular AAV uptake and activation of a cytotoxic T-cell response to transduced cells, decreasing efficacy or changing the safety profile. Measurement of serum neutralizing antibodies (NAbs) against AAV is essential to determine treatment eligibility and to identify clinical trial candidates. Here we introduce a cell-based assay using NanoLuc® luciferase to detect NAbs in serum samples. The superior brightness of NanoLuc® luciferase in our AAV reporter system results in the need of low concentrations of AAV and a short 24h assay time. The minimal AAV concentration in our assay aids in detecting low NAb titers in serum samples, reducing false negatives and enhancing decision-making accuracy. Testing 60 human serum samples against a range of AAV serotypes, we found that a large fraction of the population had pre-existing NAbs to at least one serotype, and of the pre-exposed individuals a majority displayed NAbs against multiple AAV serotypes. Interestingly, fewer samples were seropositive for AAV-DJ than for either parental serotype (AAV2, AAV8 or AAV9), highlighting the assays utility in the development of engineered capsids. Furthermore, the broad dynamic range of our assay facilitates serum sample categorization into four NAb tiers: negative, low, medium, and high using a single serum dilution. Neutralizing titers (ND50) which was determined by serial dilution of the serum samples strongly agreed with the assigned NAb tiers. Our study with 40 naïve mice further validated the assay's robustness, showing a clear correlation between NAb levels and injected AAV viral loads. Taken together, this rapid, highly sensitive, and reliable assay enabled by NanoLuc® AAV reporter technology precisely measures NAbs against AAVs in both human and animal serum. Further validation of the assay is required for future use in a clinical setting. Citation Format: Morten Seirup, Kirsten Wingate, Jeff Nelson, Kara Machleidt, Vanessa Ott, Trish Hoang, Marjeta Urh. Simple, rapid, and robust bioluminescent cell-based assay for detecting neutralizing antibodies against AAV in serum [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 3249.
Abstract 4425: Metabolic vulnerabilities of dedifferentiated liposarcoma
Authors: Jamie O. Brett, Ji Seul Han, Choah Kim, Liam P. Kelley, SeongJun Han, Dylan Boone, Joseph Crowley, Shakchhi Joshi, Chandrajit P. Raut, Anna Greka, Marcia C. Haigis
Journal: Cancer Research (2024)

Abstract Dedifferentiated liposarcoma (DDLPS) is a rare, life-threatening malignancy in the family of adipocytic sarcomas. DDLPS, which usually arises in the retroperitoneum of middle-aged adults, has a poor prognosis. This is due to the propensity of DDLPS to metastasize and recur locally, combined with a dearth of effective systemic therapies. A longstanding curiosity is that DDLPS has non-lipogenic morphology and no lipid droplets, while its less aggressive sister sarcoma, well-differentiated liposarcoma (WDLPS), resembles benign adipose tissue and contains large lipid droplets. How DDLPS metabolizes lipids and the metabolic vulnerabilities of DDLPS in patients, which may form new therapeutic targets, are unknown. In our project, we investigate the metabolism of DDLPS versus WDLPS using patient samples and cell lines. Snap-frozen tissues from patients were obtained from the Dana-Farber/Harvard Cancer Center specimen bank of DDLPS and WDLPS. We performed metabolomics and lipidomics on these samples. We complemented these results with publicly available transcriptional profiles of separate cohorts of DDLPS, WDLPS, and other cancers. In vitro, we made use of a panel of multiple DDLPS-derived cell lines, WDLPS-derived cells, benign preadipocytes, and benign adipocytes. We measured mitochondrial function and the cellular effects of perturbing various metabolites in screens in culture. Overall, our initial results indicate strong alterations in mitochondrial metabolism in DDLPS in patients. In culture, DDLPS is susceptible to multiple metabolic perturbations related to mitochondrial dysfunction. These metabolic vulnerabilities of DDLPS provide potential therapeutic opportunities. Work is ongoing to optimize the targeting of these vulnerabilities in vivo, elucidate the molecular roles of specific metabolites, and complete a blueprint of DDLPS metabolic weaknesses in patients. Citation Format: Jamie O. Brett, Ji Seul Han, Choah Kim, Liam P. Kelley, SeongJun Han, Dylan Boone, Joseph Crowley, Shakchhi Joshi, Chandrajit P. Raut, Anna Greka, Marcia C. Haigis. Metabolic vulnerabilities of dedifferentiated liposarcoma [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 4425.
Abstract 110: Adoptive transfer of tumor antigen-specific T cells alters the renal tumor microenvironment in the presence and absence of immunotherapy
Authors: Holly Stephens, Elizabeth Elkins, Francesca Dempsey, Zoey Swalley, Jing Li, Jianqing Zhang, Richard Kirkman, Bo-Ruei Chen, Zachary Roberts, Sunil Sudarshan, Barry Sleckman, Hubert Tse, Daniel L. Smith, Lyse A. Norian
Journal: Cancer Research (2024)

Abstract Immunotherapies are the standard of care for patients with renal cancer, yet their effects on renal tumor antigen-specific CD8 T cell responses and their subsequent ability to modulate the renal tumor microenvironment remain difficult to evaluate. In order to address this gap in the field, we developed a novel murine model to examine tumor-antigen specific CD8 T cell immune responses in orthotopic renal cancer utilizing a new cell line, Renca-tERK-LUC. Parental Renca cells were transduced with a lentivirus expressing the naturally-occurring, mutated tERK peptide found in CMS5 fibrosarcoma cells to create Renca-tERK-LUC tumor cells. The tERK mutation consists of a one base pair change that creates an Sfc1 site, so it can be detected by RT-PCR followed by restriction enzyme digestion. Our data show that Renca-tERK-LUC cells express tERK at high levels and grow progressively in control BALB/c mice, but are rejected in DUC Thy1.1 mice, which contain endogenous TCR transgenic CD8+ T cells specific for tERK peptide/MHC I complexes. We then performed adoptive transfers of 5 × 105 DUC Thy1.1 T cells into mice with established, orthotopic Renca-tERK-LUC tumors to evaluate: 1) the effects of immunotherapy on tumor-antigen-specific T cell responses; and 2) the effects of tumor-antigen-specific T cells on the broader renal tumor microenvironment. Our data indicate that the transfer of relatively low numbers of tumor antigen-specific CD8+ T cells induces transcriptomic and cellular changes in the tumor microenvironment in both the presence and absence of immunotherapy. Defining the parameters surrounding tumor-antigen-specific T cell responses and their ability to modulate the renal tumor microenvironment under the influence of clinically relevant immunotherapeutic intervention has the potential to increase the understanding of immunity to renal tumors, which could ultimately prove beneficial for renal cancer patients. Citation Format: Holly Stephens, Elizabeth Elkins, Francesca Dempsey, Zoey Swalley, Jing Li, Jianqing Zhang, Richard Kirkman, Bo-Ruei Chen, Zachary Roberts, Sunil Sudarshan, Barry Sleckman, Hubert Tse, Daniel L. Smith, Lyse A. Norian. Adoptive transfer of tumor antigen-specific T cells alters the renal tumor microenvironment in the presence and absence of immunotherapy [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 110.
Abstract 5243: CAR B cells to accelerate antigen presentation in cancer
Authors: Mary Ellen Molloy, Jessica Balero, Ana Contreras-Sandoval, Mark Selby, Hangil Park, Srinivas Kothakota, Kathleen Boyle, Rosa Romano, Smrithi Rajendiran, Moises Hernandez, Ariel Pios, Rusty Williams
Journal: Cancer Research (2024)

Abstract Engineered B cells hold promise for multiple therapeutic applications. Walking Fish Therapeutics is engineering B cells to produce replacement proteins for deficiency diseases, antibodies of defined specificity and effector function, and Chimeric Antigen Receptor (CAR) B cells with and without therapeutic payloads for use in the oncology setting. B cells are professional antigen presenting cells (APCs) with the ability to present antigen to CD4+ T cells. Recent studies have found the presence of tumor infiltrating B cells are associated with favorable outcomes across multiple cancer types. Adoptive transfer of B cells has demonstrated antitumor activity in a syngeneic mouse model. B cells from OVA-vaccinated transgenic luciferase mice were adoptively transferred to mice bearing EG7.OVA-tumors. We observed B cells migrating to the tumor and tumor draining lymph node (TDLN), locations where B cells can engage with antigen. Further, we observed a strong anti-tumor response in mice receiving B cells from OVA-vaccinated donors. Based on these results, we hypothesized that B cells engineered to target tumor specific antigens may engage and activate the immune system leading to an enhanced antitumor immune response. We generated CAR B cells expressing synthetic BCRs with tumor-antigen specific scFvs fused to designated B cell signaling motifs. Expression of different CAR constructs were confirmed in both human and mouse B cells. Upon antigen engagement CAR B cells release pro-inflammatory cytokines. Importantly, we demonstrate in vitro that antigen-specific CAR B cells can recognize cognate cell surface antigen, leading to uptake, processing, and presentation on MHCII as detected by activation of peptide-specific CD4+ T cells. When administered in vivo by IV administration, we observed a significant increase in mouse CAR B cells at the tumor site compared to unengineered B cells. We are currently investigating additional CAR formats that may lead to enhanced anti-tumor activity. Citation Format: Mary Ellen Molloy, Jessica Balero, Ana Contreras-Sandoval, Mark Selby, Hangil Park, Srinivas Kothakota, Kathleen Boyle, Rosa Romano, Smrithi Rajendiran, Moises Hernandez, Ariel Pios, Rusty Williams. CAR B cells to accelerate antigen presentation in 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 5243.
Abstract 4434: Cancer cell-derived adrenomedullin downregulates Zeb1 in adipocytes to induce adipolysis and promote breast cancer progression
Authors: Lixia Cao, Xiao Chen, Yi Shi, Shuang Yang
Journal: Cancer Research (2024)

Abstract Background: Once breast carcinoma in situ breaks through the basement membrane, it preferentially invades the lipid-rich microenvironment around the mammary gland, which indicates a poor prognosis. However, the detailed mechanisms of this interaction remain elusive. Here, we describe bidirectional communication between breast cancer cells and cancer-associated adipocytes (CAAs). Different from the common hormone-driven mechanism of lipolysis of adipocytes, we found that CAAs perform a unique lipolysis program, and Zeb1 plays an important role in this lipolysis process. Methods: Fabp4-cre;Zeb1-/- as adipose tissue-specific Zeb1 gene knockout homozygous mice and Fabp4-cre;Zeb1 tg as adipose tissue-specific Zeb1 gene overexpression mice were constructed to study mammary gland development and perform orthotopic tumor transplantation experiments. Tetracycline-induced Zeb1-overexpressing stable cells were constructed from mouse preadipocytes 3T3-L1 to study phenotypes of lipolysis. Single-cell sequencing, targeted lipidomics, and RNA sequencing analysis were used to investigate the interaction between cancer cells and adipocytes. Western blotting and immunohistochemical staining assays were used to detect the expression Zeb1 at the cellular level, in mouse models and in patient tissue samples. Results: Our results indicated that breast cancer cell-derived adrenomedullin (ADM) significantly down-regulates Zeb1 expression in adipocytes, which drives downstream gene expression of Pnpla2/HSL/SCD1 and induces adipocyte lipolysis into CAA, a process that results in the release of excess palmitoleic acid. Consequently, we proved that palmitoleic acid could replace arachidonic acid (ARA) in the phospholipid sn-2 position of breast cell membrane, which enhances the fluidity and invasiveness of cancer cells. In addition, overexpression of Zeb1 in adipocytes reduces the ability of cancer cells to induce adipolysis and inhibits the malignant progression of cancer cells. Conclusion: These results indicate that Zeb1 plays a pivotal role as core transcriptional factor in CAA lipolysis. The interaction between breast cancer cells and adipocytes leads to the reprogramming of metabolism within their tumor microenvironment, which may become a new target for breast cancer treatment. Citation Format: Lixia Cao, Xiao Chen, Yi Shi, Shuang Yang. Cancer cell-derived adrenomedullin downregulates Zeb1 in adipocytes to induce adipolysis and promote breast cancer progression [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 4434.