tbuckley/cabot-search huggingface dataset:
Abstract 770: The innate immune system response to malignancy- under the radar
Authors: Martin Tobi, Harvinder Talwar, Benita McVicker
Journal: Cancer Research (2024)

Abstract It has become clear that many cancers evade detection by, for example, silencing of immune checkpoints. Re-activation of the immune armamentarium by checkpoint inhibitors has improved survival in many types of cancer. However, we still are unable to gauge the response of the innate immune system (InImS) to incipient malignancy. The InImS is likely both a sentient early warning system and an immediately deployed cancer combatant. We describe a potential marker that quantifies the innate immune system response to multiple deadly tumors. Methods: We obtained a database of patients at high risk of colorectal neoplasia and prospectively noted those who contracted cancer on follow up. We contrasted the historic, premorbid biomarker response from the time of enrolment, primarily using the FERAD ratio. This was obtained by dividing the ferritin blood concentration by the denominator of fecal shedding of a Paneth cell marker, p87. We also compared the FERAD response to the absolute neutrophil:lymphocyte ratio (NLR), a known prognostic biomarker, and also the available, known PDL-1 response for each group of cancers. Results: We found that certain groups of cancers historically had very low FERAD ratios while others were high. Using FERAD ratios for lung, gastric, non-Hodgkin’s lymphoma, melanoma, thyroid, renal, and head and neck cancers, there is a significant inverse correlation between survival and FERAD (r=-0.8;p&amp;lt;0.025) which is similar to that of NLR (r=-0.7;p&amp;lt;0.035). For prostate cancer, breast, colorectal cancer (CRC), leukemia/MDS, there is a direct correlation between survival and FERAD (r=0.99;p&amp;lt;0.002). There is also an inverse relationship between NLR and PDL-1 response rates (r=-0.8;p&amp;lt;0.04). An observed mild positive trend for FERAD PDL-1 response rates may bode well for melanoma, lung, head and neck and renal cancers. Conclusions: Since p87 could be manipulated by dietary means to affect the FERAD ratio favorably, this could be incorporated into more effective chemotherapy regimens and result in better cancer treatment outcomes. Hepatocellular cancer (HCC) and CRC-liver metastasis appear to be immunological outliers. This will need an additional unique approach such as TIGIT intervention therapy (Zheng et al.. Immune checkpoint targeting TIGIT in HCC. Am J Transl Res. 2020). This may allow modulation of the immune response based on FERAD, NLR ratios, and other considerations of mutational burden and genetic mutations, in patients with selected cancers. Citation Format: Martin Tobi, Harvinder Talwar, Benita McVicker. The innate immune system response to malignancy- under the radar [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 770.
Abstract 774: Genetic architecture, evolutionary genomics, and genomic risk of prostate cancer in sub-Saharan Africa
Authors: Timothy R. Rebbeck, Rohini Janivara, Wenlong C. Chen, Ujani Hazra, Joseph Lachance
Journal: Cancer Research (2024)

Abstract Men of African descent have the highest prostate cancer (CaP) incidence and mortality rates, yet the genetic basis of CaP in African men has been understudied. We performed the first large-scale genomic analysis of CaP across sub-Saharan Africa (SSA). We evaluated the evolutionary history of CaP-associated loci, generated a novel genomic risk score, inferred ancestry-specific genetic architectures, and fine-mapped disease associations using in 3,963 CaP cases and 3,509 controls recruited in Ghana, Nigeria, Senegal, South Africa, and Uganda through the Men of African Descent and Carcinoma of the Prostate (MADCaP) Network. Fifteen independent associations at 8q24.21, 6q22.1, and 11q13.3 reached genome-wide significance, including four novel associations. Multiple lead SNPs were private alleles in SSA, a pattern arising from recent mutations and the out-of-Africa bottleneck. These SSA-specific alleles contribute to haplotypes with odds ratios for CaP above 2.4. The genetic architecture of CaP differs across SSA, with effect size differences contributing more to this heterogeneity than allele frequency differences. Population genetic analyses reveal that SSA CaP associations are largely governed by neutral evolution, as opposed to natural selection. This finding is consistent with the late onset of this disease. Focusing on 2,502 age-matched cases and 2,222 non-cancer controls, we generated a novel genomic predictor of CaP. We then assessed the extent to which this polygenic risk score was correlated with age of onset, PSA levels, genetic ancestry, and family history of study participants. The performance of this novel polygenic risk score was tested on other populations of African descent, as well as populations with non-African ancestry. Our findings emphasize the utility of conducting genetic studies in diverse populations. Citation Format: Timothy R. Rebbeck, Rohini Janivara, Wenlong C. Chen, Ujani Hazra, MADCaP Network, Joseph Lachance. Genetic architecture, evolutionary genomics, and genomic risk of prostate cancer in sub-Saharan Africa [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 774.
Abstract 777: Notch signaling dependent chemoresistance in racial disparity in ER+ breast cancer
Authors: Shailesh Singh, Megha Das, Rumela Chakrabarti
Journal: Cancer Research (2024)

Abstract Breast cancer (BCa) is the leading cause of cancer related death in women worldwide. The most common BCa subtype is the Estrogen/Progesterone receptor (ER+/PR+) luminal subtype, comprising up to 75% of all newly diagnosed BCa. Although these patients show initial benefit with chemotherapy and endocrine therapy, however, 40-50% of them eventually don’t respond to treatment due to resistance. Thus, the need for additional targeted therapies for this large subset of ER+ BCa patients is critical. Based on recent studies, it is observed that Afro-American (AA) patients experience substantially higher BCa mortality (40% more) than White American (WA) women in ER+ breast cancer. Unfortunately, the cause behind this difference in mortality in AA patients is not well understood. Notch signaling is a highly conserved intercellular communication mechanism critical for many cellular processes and is composed of several receptors and ligands. Recent data show that Notch receptors are overexpressed in hormone treatment refractory ER− patients of (Afro-American) AA origin, hinting connection of Notch signaling to racial disparity in breast cancer. Notch signaling is also identified in several metabolic disorders involving fatty acids and other lipids. However, function of Notch signaling in context of chemoresistance in AA ER+ breast cancer is still unknown. Using single cell sequencing, we found that chemo-resistant AA ER+ breast cancer patient samples have a distinct Notch signature enriched subpopulations in tumor cells, which was missing in WA patients. Notch signaling happens through juxtacrine signaling of ligand/receptor signaling. Further analysis in tumor microenvironment shows lipid enriched tumor associated macrophages, which are Notch dependent, suggesting potential crosstalk between lipid heavy tumor-macrophages and tumor cells, which may drive the chemoresistance in AA patients. Further analysis using patient derived explants, an attractive new tool for drug efficacy testing in ex vivo, we found that chemotherapy itself increases Notch signaling in the tumors. Ongoing studies involving scRNAseq, untargeted lipidomics and chemo-resistant PDE will delineate the precise mechanism of action between tumor cells and tumor associated lipid heavy macrophages in context of Notch signaling in chemo-resistant AA ER+ breast cancer. Citation Format: Shailesh Singh, Megha Das, Rumela Chakrabarti. Notch signaling dependent chemoresistance in racial disparity in ER+ breast 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 777.
Abstract 781: Impact of vitamin D and pyruvate carboxylase on hypoxia inducible lipid droplet associated (HILPDA) protein in metastatic breast cancer cells
Authors: Yazhen Song, Chaylen Andolino, Dorothy Teegarden
Journal: Cancer Research (2024)

Abstract Metastatic breast cancer, a critical health issue for women globally, is closely linked to aberrant lipid metabolism. One feature of this dysregulated metabolism is the increase in lipid storage in the form of cytoplasmic lipid droplets (CLDs), although what drives their accumulation or their role in metastasis is not clear. In prior studies, we demonstrated that the active form of vitamin D (1,25-dihydroxyvitamin D, 1,25(OH)2D) downregulates pyruvate carboxylase (PC), a key metabolic enzyme, thereby reducing lipid accumulation in metastatic breast cancer cells (MCF10CA1a). Additionally, we have demonstrated that both 1,25(OH)2D treatment and PC-inhibition reduce breast cancer cell migration. Therefore, the goal of the current research is to identify the proteins associated with CLDs in metastatic MCF10CA1a breast cancer cells following 1,25(OH)2D treatment or reduction in PC expression (shPC). Proteins from CLDs and whole cell lysates (WCL) were processed for untargeted proteomic analysis. In the CLD fractions, 1562 identified enriched proteins were common to both MCF10CA1a and 1,25(OH)2D treated cells, while 160 proteins were higher in the MCF10CA1a cells, and 550 proteins were higher in the 1,25(OH)2D-treated cells compared to MCF10CA1a CLD fraction. In the CLD fractions, MCF10CA1a and shPC cells had a similar level of 380 enriched proteins, although 65 were higher in the shPC compared with MCF10CA1a, whereas 1268 were more enriched in the MCF10CA1a CLD fraction. Hypoxia Inducible Lipid Droplet Associated (HILPDA, known to inhibit triacylglycerol lipolysis) was only enriched in the CLD fraction of the metastatic MCF10CA1a cells. HILPDA was not identified in the CLDs of the 1,25(OH)2D treated or the shPC cells, nor in any WCL fraction. Further investigation of HILPDA is important to determine if HILPDA plays a role in dysregulated cellular metabolism, including CLD accumulation, or migration, and may potentially be a target for future therapies to prevent breast cancer progression. Citation Format: Yazhen Song, Chaylen Andolino, Dorothy Teegarden. Impact of vitamin D and pyruvate carboxylase on hypoxia inducible lipid droplet associated (HILPDA) protein in metastatic breast cancer 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 781.
Abstract 780: Normal breast tissues harbor rare populations of aneuploid epithelial cells
Authors: Yiyun Lin, Junke Wang, Kaile Wang, Shanshan Bai, Aatish Thennavan, Runmin Wei, Yun Yan, Jianzhuo Li, Heba Elgamal, Emi Sei, Anna Casasent, Mitchell Rao, Chenling Tang, Jessica Montalvan, Chandandeep Nagi, Sebastrian Winocour, Bora Lim, Alastair Thompson, Nicholas Navin
Journal: Cancer Research (2024)

Abstract Although aneuploidy is a hallmark of invasive breast cancers, the presence of aneuploid cells in breast tissues of disease-free women is poorly understood. Furthermore, the expansion of aneuploid cells and the specific copy number events that they harbor, as well as their relationship to invasive breast cancers has not been characterized in large cohorts of women. In this study, we obtained viable cell suspensions from 31 disease-free women that underwent reduction mammoplasty surgeries and fresh tissue collection in the HBCA project along with the collection of clinical metadata. The viable cell suspensions from 31 women were enriched for epithelial cells and used to perform high-thoughput nanowell scDNA-seq. In total, 55,321 cells were analyzed. The normal breast tissue samples were also embedded into OCT and frozen to perform Spatial Transcriptomics (Visium 10X Genomics) profiling and embedded into FFPE to perform histopathological analysis. Our data shows that all women harbored rare populations of aneuploid epithelial cells (mean 4.3%) that increased in frequency and their number of copy number aberrations with age. Many aneuploid epithelial cells (mean 79%) in normal breast tissues underwent clonal expansions of their genomes and harbored chromosomal aberrations detected in invasive breast cancers (gain of 1q and loss of 7q, 10q, 16q). Spatial mapping showed that aneuploid cells are localized in focal regions of ductal and lobular epithelial structures with normal histopathological features. Collectively, these data show that aneuploid epithelial cells exist in the normal breast tissues of disease-free women and increase with age. In many women, the aneuploid cells expand and harbor CNA events associated with invasive breast cancer. Citation Format: Yiyun Lin, Junke Wang, Kaile Wang, Shanshan Bai, Aatish Thennavan, Runmin Wei, Yun Yan, Jianzhuo Li, Heba Elgamal, Emi Sei, Anna Casasent, Mitchell Rao, Chenling Tang, Jessica Montalvan, Chandandeep Nagi, Sebastrian Winocour, Bora Lim, Alastair Thompson, Nicholas Navin. Normal breast tissues harbor rare populations of aneuploid epithelial 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 780.
Abstract 771: A TGF-β superfamily member, myostatin contributes to MASH and HCC via muscle atrophy by disrupting TGF-β signaling, and is a potential marker with PKM2 for human HCC
Authors: Kazufumi Ohshiro, Krishanu Bhowmick, Xiyan Xiang, Shivani Kapoor, Richard Amdur, Srinivasan Dasarathy, Adrian R. Krainer, Lopa Mishra
Journal: Cancer Research (2024)

Abstract Background: In patients with cirrhosis and hepatocellular carcinoma (HCC), sarcopenia or skeletal muscle loss, as well as metabolic alterations are frequent and progressive comorbidities. Myostatin, a TGF-β superfamily member is expressed primarily in skeletal muscle, inhibits muscle growth, and causes sarcopenia in cirrhosis. Previously, we had observed liver-specific knockout of the SMAD3 adaptor, βII-spectrin -Sptbn1 (βS-LSKO) or siRNA targeting βII-spectrin blocks sarcopenia, fatty liver disease-MASH and HCC (Sci TM 2021), suggesting that βII-spectrin may be a viable strategy to identify mechanisms, as well as new biomarkers of MASH and HCC. Methods: 1. SPTBN1Flox (control) and liver-specific βII-spectrin knockout (SPTBN1LSKO) mice were fed Western diet (WD) and treated with Diethylnitrosamine (DEN) for obesity-associated HCC. Muscle mass, body weight and multiple enzymes involved in glycolysis as well as sarcopenia were measured in mutant mice. 2. In tumors, a rate-limiting enzyme in glycolysis, pyruvate kinase isozyme M2 (PKM2) that mediates inflammation and aerobic glycolysis in Warburg effect. Therefore, we further examined TGF-β pathway-enriched biomarkers such as Myostatin and PKM2 for markers of HCC and whether these could stratify risk in patients with cirrhosis for HCC, in a four-institution cohort, (n=157) compared to cirrhosis patients (n=380). Results: 1. Like human fatty liver disease, obese mutant mice show marked sarcopenia with increased PKM2 and Myostatin levels with decreased p-RPS6/total-RPS6 ratio (indicating mTOR signaling inhibition) in striated muscle tissue. In contrast, levels are restored to normal in the liver specific knockout of SPTBN1. 2. Using the 108 markers as well as PKM2 and myostatin (MSTN), we found 31 markers with false discovery rate (FDR) p values &amp;lt; 0.10 from univariable Kruskal-Wallis tests for the associations of markers with HCC vs. cirrhosis. Conclusions: Our results reveal that SMAD3 adaptor, βII-spectrin liver-specific knockout decreases Myostatin and PKM2 expression, providing new insight into molecular mechanisms in MASH and HCC. These studies reflect that these are biologically functional circuits that could provide new serum markers, such as Myostatin and PKM2 for risk stratification of HCC. Citation Format: Kazufumi Ohshiro, Krishanu Bhowmick, Xiyan Xiang, Shivani Kapoor, Richard Amdur, Srinivasan Dasarathy, Adrian R. Krainer, Lopa Mishra. A TGF-β superfamily member, myostatin contributes to MASH and HCC via muscle atrophy by disrupting TGF-β signaling, and is a potential marker with PKM2 for human HCC [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 771.
Abstract 6426: Identification of potential immune biomarkers for GSK-3 inhibitor elraglusib (9-ING-41) in patients with relapsed/refractory metastatic cancer
Authors: Taylor Weiskittel, Kelsey Huntington, Leiqing Zhang, Austin Koukol, Benedito A. Carneiro, Hu Li, Andrey Ugolkov, Wafik El-Deiry, Andrew Mazar
Journal: Cancer Research (2024)

Abstract Cytokines mediate strong immunomodulatory effects in cancer. Elraglusib (9-ING-41), an inhibitor of GSK-3, is a potent antitumor and immune-modulatory agent in phase 2 clinical trials for the treatment of various cancers. Here, we examined the immune environment of elraglusib-treated cancer patients by measuring peripheral blood protein levels to explore whether the expression level of cytokines/chemokines/soluble cell receptors/growth factors (CCSG) is correlated with clinical outcome. Using a customized Luminex platform, the expression of forty CCSG hypothesized to be linked to GSK-3 activity was assessed in pre-dose plasma samples obtained from 45 cancer patients with relapsed/refractory metastatic disease (NCT03678883; the 1801 trial). All patients in the 1801 trial were treated with elraglusib (dose range: 1-15 mg/kg) either as a single agent (Part 1; n=21) or in combination with chemotherapy (Part 2; n=24). Pre-dose peripheral blood protein levels were examined as binary predictors of clinical outcome using optimal cutoff points determined by maximally selected rank statistics. In the aggregate Part 1 and 2 populations (n=45), we identified 13 CCSG that significantly stratified the cohort by overall survival (OS). High pre-dose levels of CD95 and TNFRSF10C were associated with better OS. CD95 was a better prognostic of OS than TNFRSF10C (HR: 2.27, 95% CI: 1.10-4.67, p-value: 0.023). Low pre-dose levels of 11 CCSG were also significantly associated with favorable OS, with IL-8 being the most predictive (HR: 0.137, 95% CI: 0.0545-0.346, p-value: &amp;lt;0.0001). Part 1 and 2 predose samples were also analyzed separately, and many of the biomarkers identified in the aggregate analysis retained significance in the separated analysis. In Part 1, CXCL5, IFN-alpha, and IL-18 emerged as unique markers, and in Part 2, CCL22 was the single unique marker.The results of our exploratory study identified several putative biomarkers of elraglusib clinical benefit and demonstrated potential immunomodulatory mechanisms of elraglusib that will be used to inform the further clinical development of elraglusib for the treatment of metastatic cancer. Citation Format: Taylor Weiskittel, Kelsey Huntington, Leiqing Zhang, Austin Koukol, Benedito A. Carneiro, Hu Li, Andrey Ugolkov, Wafik El-Deiry, Andrew Mazar. Identification of potential immune biomarkers for GSK-3 inhibitor elraglusib (9-ING-41) in patients with relapsed/refractory metastatic 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 6426.
Abstract 6539: RNAi mediated silencing of <i>STAT3</i> in tumor-associated immune cells induces robust anti-tumor effects in immunotherapy resistant tumors
Authors: Shanthi Ganesh, Minju Kim, Jenny Lee, Xudong Feng, Harini Sivagurunatha Krishnan, Rene Rijnbrand, Amber Beaudry, Jennifer A. Lockridge, Vinita Uttamsingh, John Hanrahan
Journal: Cancer Research (2024)

Abstract Malignant tumors are often associated with an immunosuppressive tumor microenvironment (TME), rendering most of them resistant to standard-of-care immune checkpoint inhibitors (CPIs). Signal transducer and activator of transcription 3 (STAT3), a ubiquitously expressed transcription factor, has well-defined immunosuppressive functions in several leukocyte populations within the TME. Since the STAT3 protein has been challenging to target using conventional pharmaceutical modalities, we investigated the feasibility of applying systemically delivered RNA interference (RNAi) agents to silence its mRNA directly in tumor-associated immune cells. In preclinical murine tumor models, chemically stabilized acetylated small-interfering RNAs (siRNAs) selectively silenced Stat3 mRNA in multiple relevant cell types in TME and tumor-draining lymph nodes (TDLN), reduced STAT3 protein levels, and increased cytotoxic T-cell infiltration. In murine models of CPI-resistant tumors, RNAi-mediated Stat3 silencing resulted in tumor growth inhibition, which was further enhanced and resulted in tumor regressions in combination with CPIs. Our findings suggest that targeting STAT3 directly and reducing STAT3 protein in the suppressive immune cell populations in the TME and TDLN may overcome some of the current limitations of immunotherapy and be of therapeutic benefit especially for cancer patients who failed to respond to standard immunotherapy treatments alone. A human active STAT3 conjugate is currently in Phase 1 clinical trial for treatment of immunotherapy refractory cancer types (NCT06098651). Citation Format: Shanthi Ganesh, Minju Kim, Jenny Lee, Xudong Feng, Harini Sivagurunatha Krishnan, Rene Rijnbrand, Amber Beaudry, Jennifer A. Lockridge, Vinita Uttamsingh, John Hanrahan. RNAi mediated silencing of STAT3 in tumor-associated immune cells induces robust anti-tumor effects in immunotherapy resistant tumors [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 6539.