bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 492: Spatial overlap analysis of myeloid and T cell compartments identifies distinct subgroups in the cohort of selected colorectal primary tumors
Authors: Zwing Natalie , Canamero Marta , Gaire Fabien , Korski Konstanty
Published: August 2019

The immune contexture of colorectal cancer (CRC) tumors classifies clinically relevant immune subtypes that are extensively studied. Recent developments in digital computational pathology supporting spatial characterization of tumor immune infiltrate allow more comprehensive analysis of relevant cell to cell interactions. Leveraging that methodology in the current study, we tried to address the question how the distribution of myeloid cells in the tumor microenvironment (TME) of CRC affects the effector functions and distribution of cytotoxic T cells.

We applied multicolored immunohistochemistry to identify monocytic (CD11b/CD14) and granulocytic (CD11b/CD15) myeloid cell populations together with proliferating and non-proliferating cytotoxic T cells (Ki67/CD8). Through automated object detection and image registration using HALO software (IndicaLab), we measured the extent of overlap between the areas occupied by myeloid and T cells. Subsequently, we correlated it with other parameters such as CD8 T cell proliferation ratio, amount of necrosis, MMR status, tumor mutational burden and CMS classes. With this approach, we identified distinct categories of CRC based on the myeloid - T cell overlap irrespective of the MMR status. These categories reflect certain functional areas in the TME and correlate with specific gene signatures that mainly include T effector and memory together with myeloid inflammatory and immunosuppressive signatures.

Our results emphasize the importance of analyzing spatial organization of immune infiltrate in TME and shed a new light on myeloid and T cell interactions in CRC. The approach we used has a potential to be applied in immunotherapy related biomarker studies.

Citation Format: Natalie Zwing, Marta Canamero, Fabien Gaire, Konstanty Korski. Spatial overlap analysis of myeloid and T cell compartments identifies distinct subgroups in the cohort of selected colorectal primary tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 492.
Abstract 4921: TGF-beta signaling proteins and CYP24A1 may serve as surrogate markers for progesterone calcitriol treatment in ovarian and endometrial cancers of different histological types
Authors: Paucarmayta Ana , Taitz Hannah , Casablanca Yovanni , Rodriguez Gustavo C. , Maxwell G L. , Darcy Kathleen M. , Syed Viqar
Published: August 2019

Strategies are needed to coordinately block drivers and induce suppressors of cancer to reduce incidence and improve outcomes for individuals with inherited or acquired risk. We previously reported the chemopreventive and therapeutic efficacy of the combination of progestin and calcitriol in transformed and malignant endometrioid endometrial cancer and in ovarian cancer models involving attenuated expression of TGF-β signaling proteins and progestin-mediated inhibition of calcitriol-induced CYP24A1 expression. This study aims to expand the applications for this combination to other subtypes of endometrial and ovarian cancers including those with mutations in ARID1A or PIK3CA, DNA mismatch repair deficiency or BRCA1-null status. The end points for this in vitro investigation included assessments of cell growth and the expression of TGF-β ligands, receptors, SMAD proteins and CYP24A1. Treatment of ovarian clear cell carcinoma, endometrioid carcinoma, papillary serous adenocarcinoma, BRCA1 null, and DNA mismatch repair deficient endometrial cancer cell lines with progesterone alone or in combination with calcitriol inhibited cell growth and expression of TGF-β1, TGF-β2, TGF-Rβ1, TGF-βR2, pSMAD2/3 and CYP24A1. Expression of TGF-βR3, SMAD-4, PR and VDR was not altered in any cell line tested except, ES-2, where VDR expression was upregulated in response to treatment. These results suggest that progesterone alone and progesterone-calcitriol combination have broad application in both chemopreventive and therapeutic settings that merit further development in a wide variety of ovarian and endometrial cancers, including those derived from germline or somatic mechanisms. Moreover, our data suggest that TGF-β signaling proteins and CYP24A1 may be effective surrogate markers indicative of treatment response.

Citation Format: Ana Paucarmayta, Hannah Taitz, Yovanni Casablanca, Gustavo C. Rodriguez, G L. Maxwell, Kathleen M. Darcy, Viqar Syed. TGF-beta signaling proteins and CYP24A1 may serve as surrogate markers for progesterone calcitriol treatment in ovarian and endometrial cancers of different histological types [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4921.
Abstract 4923: Analysis of companion diagnostic potentials for multifaceted PD-L1 assays
Authors: Caldara Jeni , Krueger Joseph S. , Ergon Elliott , Kearney Staci , Vennapusa Bharathi
Published: August 2019

In vitro diagnostic (IVD) approvals of qualitative immunohistochemical (IHC) assays offer unique patient selection strategies by equipping pathologists with new tools to assess tumor status including tumor immune landscape. PD-L1/PD-1 checkpoint therapies require accurate diagnostic tools for optimal patient selections, however the interpretation of these tests may be very complicated upon manual assessment. As assessment criteria have increased in complexity, an accurate quantitative approach is needed to objectively and consistently interpret challenging paradigms. Recent IVD tests have multifaceted paradigms which assess both tumor and immune positivity. Although the Ventana PD-L1 SP263 and the Dako PD-L1 22C3 qualitative diagnostics are guiding immunotherapy decisions, interpretation of the results may be subjective and challenging in many cases. This creates a further level of complexity as tumor cell positivity, and immune cell presence and positivity must be assessed in combination.

In this study, we have used Flagship Biosciences’ image analysis platform (cTA®) to explore the use of artificial intelligence (AI) and machine learning in the context of complex PD-L1 assays to provide accurate and precise quantification that allows for objective interpretation of the IVD. Non-small cell lung cancer (NSCLC) and urothelial carcinoma (UC) samples were stained with the SP263 and 22C3 PD-L1 assays and image analysis was used to provide an interpretation status based upon the IVD scoring paradigms. A comparison of the cTA results across both tests and tissue indications was also performed to explore how we may further support cross-platform PD-L1 solutions that provide adaptable and objective quantification.

The use of Flagship’s cTA platform to identify per-cell biofeatures, using machine learning, may successfully quantify PD-L1 staining in various cell populations. The ability to independently assess these populations allows for a consistent and unbiased method for the assessment tumor status for PD-L1 immunotherapy treatment decisions.

Citation Format: Jeni Caldara, Joseph S. Krueger, Elliott Ergon, Staci Kearney, Bharathi Vennapusa. Analysis of companion diagnostic potentials for multifaceted PD-L1 assays [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4923.
Abstract 494: Immune cell screen of tumor micro environment of PD-L1 in positive/negative bladder cancer, melanoma, and lung cancer
Authors: Gonzalez Rachel , Fu Wei , Logis Evelin , Chen Casey , Cone Tiffany , Merritt Sonia , Wang Yiran , Wang Guanli , Ma Donghui
Published: August 2019

PD-L1/PD1 immune therapy has been very successful for some patients. Treatment is usually based on PD-L1 tumor expression levels in tumors; however some patients with positive tumors have shown no response to therapy. Recent, clinical trials have shown that treating patients with more than one immune therapy target results in better outcome suggesting the importance of understanding PD-L1 tumor micro environment. In this study, we look at a number of immune cell markers with PD-L1 expression to see if patterns of the immune cells infiltrating the tumor micro environment vary. PD-L1 expression in the tumors was assessed by multiple PD-L1 antibodies since no single PD-L1 antibody has been FDA approved for all tumor types. Immuno-histo chemistry (IHC) screen used 2 recombinant rabbit monoclonal antibodies (clone OR-5E3 and OR-5H8), one mouse anti PD-L1 clone UMAB229, and the FDA approved antibodies clones (SP142 and 28-8). Immune cell markers used in the IHC screen were CD3, CD8A, CD20, CD68, FOXP3, LAG3 and TIM3. The screen was done on sequential sections of bladder, melanoma, and lung tumors. Variation existed between five PD-L1 antibodies in their sensitivity and specificity to detect PD-L1 in the different tumor types; however, the differences were usually associated with the ability to detect low expressing tumors. Immune cell markers CD3, CD8A, CD20, CD68, FOXP3, LAG3, and TIM3 cell markers all produced strong staining if positive cells were present; however, they vary in number and distribution pattern throughout the three types of tumor. For example, when lung or bladder tumors presented strong PD-L1 staining at the edge of the tumor they often had a number of CD3E or CD8A immune positive cells present, this was not the case for CD20 which were foci clusters or scatter through the tumors. FOXP3 and CD68 staining were scarce event in all three tumor types. Although this study was limited to small sample size 10 tumors each it did show differences in the amount and distribution of immune cells in the 3 different types of tumor positive for PD-L1 expression.

Citation Format: Rachel Gonzalez, Wei Fu, Evelin Logis, Casey Chen, Tiffany Cone, Sonia Merritt, Yiran Wang, Guanli Wang, Donghui Ma. Immune cell screen of tumor micro environment of PD-L1 in positive/negative bladder cancer, melanoma, and lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 494.
Abstract 496: Block age effect on automated quantitative T cell count using multiplex immunfluorescence
Authors: Vidal Igor D. , Hicks Jessica , Davis Christine , Heaphy Christopher , Marzo Angelo Michael De
Published: August 2019

Introduction: Formalin fixation and paraffin embedding is the universal mechanism of tissue preservation. While the data showing detrimental effect on slide storage at room temperature1,2, the evidence supports that paraffin blocks archived at room temperature for as little as two years or as long as 25 years exhibited stable staining for the most of antigens evaluated. 3

Description of experimental procedures: In order to evaluate the effect of block age in inflammatory markers with immunofluorescence, two sets of antibodies were assembled and distributed in two distinct panels of five colors each, using the opal technology based on thyramide signal amplification. The first panel comprised foxp3, p63, CD3, CD4, CK8 and the second, p63, CD3, CD8 and CK8. Both panels were applied to a TMA with samples between sixteen to eighteen years old and compared to one with samples with less than one year old, fixed in FFPE. For each TMA construction, carcinoma prostatic tissue and matched normal prostate not inflamed tissue from forty patients were punched multiple times (between four to six) within regions of interest of each case. The slides were scanned and the image analysis performed. Statistic evaluation was performed using STATA13. The immunofluorescent count was validated using chromogenic CD3 stain controls using separate test TMAs.

Unpublished data: The analysis showed an increased number in CD3 positive T-cells in tumor areas, when compared to normal ones. For block age, there was no significant difference between old and new blocks.

Conclusion: The number of positive T cells for CD3 comparing new and old blocks of FFPE tissue shows no significant difference.

Citation Format: Igor D. Vidal, Jessica Hicks, Christine Davis, Christopher Heaphy, Angelo Michael De Marzo. Block age effect on automated quantitative T cell count using multiplex immunfluorescence [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 496.
Abstract 4960: Studying the impact of gut microbiome to hepatocellular cancer in an orthotopic murine model
Authors: Qi Xiaoqiang , Yang Ming , Stenberg Joseph , Li Guangfu , Staveley-O’Carroll Kevin
Published: August 2019

Background and Objective: As one of the most important components of human body, gut microbiota play a vital role in human health by participating in metabolomics and maintaining immunological homeostasis. Microbiota dysbiosis is significantly associated with initiation and progression of different diseases. Due to close anatomical and functional connection between gut and liver (gut-liver axis), gut microbiota are found to impact the development of liver diseases including hepatocellular cancer (HCC) without fully understanding mechanisms. The overall objective of present study is to investigate how microbiota modulate HCC growth by regulating intrahepatic immune response.

Methods: Administration of carbon tetrachloride in combination with transplant of oncogenic hepatocytes by intrasplenic injection was used to make an orthotopic mouse model of HCC. A specific antibiotics cocktail (ABX) was selected to inhibit some kinds of gut microbiota. 16s rRNA sequencing was used to characterize gut microbiota profile in mice with the different treatments. Magnetic resonance imaging (MRI) was used to monitor tumor growth. Adoptive transfer of tumor antigen-specific CD8+ T cells following the treatment was used to investigate how ABX administration impacted intrahepatic immune response. Flow cytometry and multiplex cytokine assay were used to detect the alteration of effector CD8+ T cell in phenotype, proliferation, and function. Immunohistochemistry (IHC) was used to investigate immune cell tumor-infiltration.

Results: The established murine model reflects the typical features of human HCC. ABX oral administration significantly changed gut microbiota composition, particularly in abundance of P. aeruginosa and Muribaculaceae. ABX-mediated alteration of gut microbiota significantly retarded HCC progression. Interestingly, ABX treatment was found to prevent adoptively transferred tumor antigen-specific CD8+ T cell from tumor-induced immune tolerance, as higher frequency of effector CD8+ T cell was detected in ABX-treated tumor-bearing mice compared to that in control tumor-bearing mice. Correspondingly, ABX treatment resulted in the increase in expression of CD69 and enhanced production of IFN-γ in tumor antigen-specific CD8+ T cells relevant to that in control mice.

Conclusion: Modulating microbiota with antibiotics is able to shape intrahepatic immune responses and therapeutically suppress tumor growth, providing a new option in HCC control.

Citation Format: Xiaoqiang Qi, Ming Yang, Joseph Stenberg, Guangfu Li, Kevin Staveley-O’Carroll. Studying the impact of gut microbiome to hepatocellular cancer in an orthotopic murine model [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4960.
Abstract 4993: The Kynurenine Pathway as a possible resistance mechanism to immunotherapy in sarcomas
Authors: Nafia Imane , Savina Ariel , Bessede Alban , ITALIANO Antoine
Published: August 2019

Background: Sarcomas are heterogenous malignant mesenchymal neoplasms known to be particularly resistant to immunotherapy, which thus calls the interest of the elucidation of related resistance mechanisms. We recently demonstrated an increase in Kynurenine Pathway (KP) activity in the plasma of patients undergoing Pembrolizumab and metronomic cyclophosphamide. The KP has already been described to favor tolerance and immune escape through the degradation of L-Tryptophan and production of a series of metabolites including L-Kynurenine. While Indoleamine 2,3 dioxygenase (IDO1), a first rate-limiting enzyme of the KP still represents an attractive therapeutic target, the exact functional role of the KP upon immunotherapy has not yet been clearly elucidated.

Methods: Using a preclinical syngeneic mouse model of sarcoma based on the inoculation of murine sarcoma MCA205 cell line, we investigated the modulation of the KP upon PDL1 blockade. Besides the evaluation of tumor growth and survival, intratumoral biopsy was performed and used for further gene expression analysis by RT-qPCR. More precisely, KP enzymes- and key cytokines-encoding genes were assessed. Using the same experimental setting on satellite mice, intratumoral microdialysis was performed on day 13 post-tumor inoculation and kynurenine contents were quantified within the tumoral microenvironment.

Results: PDL1 blockade, using a specific anti-PDL1 antibody (provided by Genentech), exhibited a clear anti-tumoral effect associated with an intratumoral inflammatory cytokines signature driven by Ifng, Tnfa and Il2. Interestingly, Ifng level was significantly and positively associated with response to anti-PDL1. As regards to KP enzymes, a slight upregulation of the tryptophan-degrading enzymes Ido1 and Ido2 was detected while no changes were observed for Tdo2. An increase of kynurenine-degrading enzymes, including Kmo (encoding for Kynurenine monoamine oxygenase) and Kynu (encoding for kynureninase), was also detected thereby suggesting that PDL1 blockade favors Kynurenine degradation as a possible compensatory mechanism. These results were confirmed by intratumoral microdialysis in the satellite study. Indeed, anti-PDL1 was able to decrease the Kynurenine to Tryptophan ratio(Kyn / Trp) while increasing intratumoral production of kynurenines catabolites.

In conclusion, this new set of data on a preclinical sarcoma model highlights for the first time that PDL1 blockade deeply modulates the Kynurenine Pathway with an effect not exclusively associated to the upper part of the pathway and thus warrants further investigation.

Citation Format: Imane Nafia, Ariel Savina, Alban Bessede, Antoine ITALIANO. The Kynurenine Pathway as a possible resistance mechanism to immunotherapy in sarcomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4993.
Abstract 4997: Responsiveness to immune checkpoint inhibitors in RET dependent cancers
Authors: Hegde Aparna , Huang Le , Liu Shuang , Hess Kenneth , Cabanillas Maria , Hu Mimi , Busaidy Naifa , Sherman Steven , Simon George , Blumenschein George , Papadimitrakopoulou Vassiliki A. , Hong David S. , Meric-Bernstam Funda , Heymach John , Subbiah Vivek
Published: August 2019

Background: The RET receptor tyrosine kinase can be oncogenically activated by gene fusions or point mutations. Multikinase inhibitors such as cabozantinib, lenvatinib, and vandetanib have demonstrated activity in RET dependent (RET+) malignancies. Recent development of selective RET inhibitors is poised to alter their treatment paradigm. However, the responsiveness of RET+ malignancies to immune checkpoint inhibition (ICI) is unknown. We compared the time to progression (TTP) on ICI with non-ICI therapy in patients with malignancies harboring activating RET mutations/fusions.

Methods: A retrospective chart review of all RET+ patients who were referred to the phase 1 clinical trials program at MD Anderson Cancer Center between September 2014 and October 2018 was conducted. Patients who had not discontinued treatment or had discontinued treatment for reasons besides disease progression were censored. Time to progression was estimated using Kaplan-Meier analysis.

Results: Out of 72 patients who had received systemic therapy for RET+ malignancies, 39 (54.2%) harbored RET mutations (RETm) and 33 (45.8%) harbored RET fusions (RETf). Nineteen patients (26.4%) received ICI and 53 (73.6%) received non-ICI therapy. Thirty four patients (47.2%) had medullary thyroid cancer, 29 (40.3%) had NSCLC and 9 (12.5%) had other types of cancer. PD-L1 expression was only available for 7 patients of which 5 (71.4%) were positive (≥ 1%). Patients had received a median of 1 (1-7) prior lines of therapy. Overall median TTP (mTTP) was 10.5 months (95% CI 6.7-30.1). Hazard ratio for ICI vs. non-ICI therapy was 1.73 (0.70, 4.26) p=0.25 in patients with RETf and 8.0 (2.27, 28.2) p=0.0025 in patients with RETm.

Conclusions: In patients with RET+ malignancies, mTTP was shorter with ICI compared to non-ICI therapy. The effect of type of therapy was dependent on the type of RET pathway aberration, with a statistically significant higher risk of progression in RETm malignancies treated with ICI compared to non-ICI therapy.

Time to ProgressionRETTherapyNmTTP (months)Freedom from Progression at 6 months (%)Freedom from Progression at 12 months (%)FusionNon-ICI218.36335FusionICI123.03624MutationNon-ICI3231.98273MutationICI75.6430

Citation Format: Aparna Hegde, Le Huang, Shuang Liu, Kenneth Hess, Maria Cabanillas, Mimi Hu, Naifa Busaidy, Steven Sherman, George Simon, George Blumenschein, Vassiliki A. Papadimitrakopoulou, David S. Hong, Funda Meric-Bernstam, John Heymach, Vivek Subbiah. Responsiveness to immune checkpoint inhibitors in RET dependent cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4997.
Abstract 5012: Targeting CD39 with a first-in-class inhibitory antibody prevents ATP processing and increases T-cell activation
Authors: Lerner Alana G. , Kovalenko Maria , Welch Megan , Cruz Tracy dela , Jones Jeff , Wong Clifford , Spatola Bradley , Eberhardt Meghan , Wong Andrew , Fung Wanchi , Lagpacan Leanna , Losenkova Karolina , Yegutkin Gennady , Soros Vanessa , Corbin John , Beers Courtney , Moesta Achim K.
Published: August 2019

The ATP/Adenosine pathway in the tumor microenvironment (TME) has emerged as an important immune-regulatory pathway. The ATPase CD39 is highly expressed in the TME, both on infiltrating immune cells and tumor cells across a broad set of cancer indications. CD39 processes pro-inflammatory extracellular ATP to ADP and AMP, which is then processed by CD73, to immunosuppressive adenosine. Inhibiting the enzymatic function of CD39 has the potential to shift the immunosuppressive milieu of the TME in a 2-pronged fashion: 1) Enhancement of immunostimulatory extracellular ATP released by damaged and/or dying tumor cells and 2) Inhibition of the generation and accumulation of suppressive adenosine within the TME, thereby unleashing an immune-mediated anti-tumor response.

Tizona has generated a novel first-in-class fully human anti-CD39 antibody, TTX-030, that inhibits CD39 ATPase enzymatic function with sub-nanomolar affinity and potency. TTX-030 is specific for CD39 and binds to CD39+ cancer cell lines and primary human leukocytes with high affinity. TTX-030 is capable of inhibiting CD39 at elevated ATP concentrations reported in the TME. Enzymatic inhibition by TTX-030 has demonstrated: preservation of pro-inflammatory extracellular ATP, reduction of adenosine accumulation, and inhibition of phosphate release by a variety of CD39-expressing cells, including tumor cells and immune cells. In vitro functional assays using stimulated PBMCs exposed to exogenous ATP demonstrated increased proliferation of both CD4+ and CD8+ T cells in the presence of TTX-030 and increased secretion of the pro-inflammatory cytokines IFN-γ, TNF-α, and IL-2. Treatment of mice with a mouse-specific CD39 inhibitory antibody in a syngeneic tumor model significantly decreased tumor growth.

In summary, TTX-030 is a selective and potent CD39 enzymatic inhibitor, capable of preventing adenosine-mediated immune suppression and increasing T-cell activation. Inhibition of CD39 with TTX-030 represents a unique therapeutic target aimed at modulating the immunosuppressive TME in cancer.

Citation Format: Alana G. Lerner, Maria Kovalenko, Megan Welch, Tracy dela Cruz, Jeff Jones, Clifford Wong, Bradley Spatola, Meghan Eberhardt, Andrew Wong, Wanchi Fung, Leanna Lagpacan, Karolina Losenkova, Gennady Yegutkin, Vanessa Soros, John Corbin, Courtney Beers, Achim K. Moesta. Targeting CD39 with a first-in-class inhibitory antibody prevents ATP processing and increases T-cell activation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5012.
Abstract 5029: OT-101/Chemotherapy- A novel mechanism of action (MOA) in glioblastoma immunization therapy
Authors: Hwang Larn , Nam David , Uckun Fatih , Trieu Vuong
Published: August 2019

Background: Escalating Intratumoral heterogeneity (IH) resulting in xenogenization which is countered by overexpression of TGF-β2. OT-101 is a TGF-β2-specific Phosphorothioate Antisense. Here we report the results of a randomized Phase 2b clinical trial (NCT00431561) comparing the safety and efficacy of OT-101 versus temozolomide (TMZ) in adult patients with WHO grade III/IV high-grade glioma. We took advantage of the known xenogenization activity of alkylating agent such TMZ to explore the impact of xenogenization on survival on treatment with OT-101.

Methods: This is a phase 2b, multi-national, multi-center, open-label, active-controlled, randomized parallel group dose-finding study to evaluate the efficacy and safety of OT-101 in adult patients with recurrent high-grade glioma, administered intratumorally as continuous high-flow microperfusion over a 7-day period every other week.

Results: A total of 134 patients, 89 patients in the OT-101 test group and 45 patients in the temozolomide (TMZ) group. OT-101 was superior to TMZ in doubling the number of pts in the good survival group, 64 of 97 pts (66%); whereas, only 14 of 45 pts (31%) treated with TMZ did (p=0.0001).

mOSOT-101TMZSubseq. TMZSubseq. TMZ (or other alkylating agent)Prev. TMZNoYesNoYesNo4.2mos (N=14)26.2mos (N=30)5.6mos (N=8)13.2mos (N=9)Yes4.8mos (N=19)29.5mos (N=34)6.6mos (N=14)36.6 mos (N=14)

There were two cases of neutropenia in the 90 pts treated with OT-101 versus 8, 10, and 8 pts with leukopenia, neutropenia, and thrombocytopenia, respectively, among 45 pts treated with TMZ (2% vs. 56%, p<0.0001).

Conclusions: Improved survival was achieved by repeated exposure to TMZ/alkylating agent. This was further enhanced by OT-101 and consistent with the proposed MOA of OT-101/Chemo as reactivation of immunity during TGF-β suppression and subsequent xenogenization by TMZ.

Citation Format: Larn Hwang, David Nam, Fatih Uckun, Vuong Trieu. OT-101/Chemotherapy- A novel mechanism of action (MOA) in glioblastoma immunization therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5029.
Abstract 5033: The role of the epigenetic regulator SATB2 in colon cancer progression
Authors: Brennan Donal J. , Naicker Kirsha , Das Sudipto , Moran Bruce , Klinger Rut , Ponten Fredrik , Hewitt Stephen , Jirström Karin , Byrne Annette T. , O'Sullivan Jacintha , Gallagher William M. , O'Connor Darran P.
Published: August 2019

SATB2 is a nuclear matrix-associated transcription factor that orchestrates gene expression by regulating higher-order chromatin structure. Using antibody-based screening of 48 normal human tissues and 20 cancer types, we identified SATB2 as a protein almost exclusively expressed in gastrointestinal tissue. We confirmed this observation at the mRNA level in 10,533 human tissue samples. Differential expression of SATB2 was observed in colorectal cancer, with loss of expression occurring along the adenoma-carcinoma sequence. Additionally, SATB2 expression was markedly decreased in metastatic SW620 colon cancer cells and siRNA knockdown of SATB2 expression in parental SW480 cells increased their growth and migratory capacity. Ectopic expression of SATB2 in the metastatic variant reversed the observed phenotype. Using tissue microarray and automated image analysis of SATB2 expression in colorectal cancers (n=309), SATB2 was demonstrated by multivariate Cox regression analysis to be an independent predictor of disease-specific survival (HR=0.52, 95% CI 0.32-0.83, p=0.006). SATB2 mRNA levels were examined in a second cohort (n=290) and again, SATB2 was demonstrated to be an independent predictor of disease-specific survival (HR=0.40, 95% CI 0.18-0.92, p=0.031). Interestingly, in colorectal cancer patients, SATB2 levels significantly correlated with CD3+ T-cell infiltrates in the tumours (p=0.006) and inversely correlated with COX2 expression (p=0.019). In two independent colorectal cancer cohorts (n=467), SATB2-low tumours were found to be significantly enriched in the CMS1 (immune-related) subtype (p<0.001). Gene set enrichment analysis revealed that SATB2 low tumours demonstrated altered immune signalling with significant increases in IFNγ (p=0.001), IL6 (p=0.001), IL8 (p<0.001) TFGβ (p<0.001), which was mirrored by in vitro manipulation of SATB2 expression in colon cancer cells. Furthermore, in a longitudinal cohort of patients with ulcerative colitis, we observed a significant correlation between loss of SATB2 expression and occurrence of future cancers (p=0.013). We therefore postulate that SATB2 acts as a master regulator of the inflammatory response in the gut and loss of expression is significantly associated with the progression of colorectal cancer.

Citation Format: Donal J. Brennan, Kirsha Naicker, Sudipto Das, Bruce Moran, Rut Klinger, Fredrik Ponten, Stephen Hewitt, Karin Jirström, Annette T. Byrne, Jacintha O'Sullivan, William M. Gallagher, Darran P. O'Connor. The role of the epigenetic regulator SATB2 in colon cancer progression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5033.
Abstract 5045: Pineal gland volume and risk of prostate cancer
Authors: Bazzi Latifa A. , Sigurdardottir Lara , Sigurdsson Sigurdur , Valdimarsdottir Unnur , Torfadottir Johanna , Aspelund Thor , Launer Lenore , Harris Tamara , Gudnason Vilmundur , Mucci Lorelei , Markt Sarah
Published: August 2019

Background: The parenchyma of the pineal gland, an endocrine gland in the brain, produces the circadian hormone melatonin. Previously, we found low levels of melatonin were associated with an increased risk for advanced prostate cancer. This study used data from men in the Age, Gene/Environment Susceptibility-Reykjavik (AGES-Reykjavik) Study to evaluate the relationship between pineal volume, melatonin levels, and prostate cancer risk.

Methods: Participants were enrolled in the AGES-Reykjavik Study from 2002 to 2006 and underwent detailed clinical assessments at baseline that included biospecimen collection, MRI of the brain, medical history, and health questionnaires on dietary and lifestyle factors. We included 802 men who had information on pineal size, where parenchyma, calcification, and cyst volume were estimated individually and manually from the MRIs. Cox proportional hazards regression was used to calculate hazard ratios and 95% confidence intervals for risk of prostate cancer during follow-up through 2014, comparing parenchyma volume tertiles.

Results: There was a positive association between pineal parenchyma volume and urinary levels of melatonin. During follow-up, 135 men were diagnosed with prostate cancer, 30 of which were advanced prostate cancer. Men with volumes in the upper tertile had no statistically significant increased risk of prostate cancer compared to men with volumes in the lowest tertile (HR: 1.0, 95% CI: 0.7, 1.5), and men with volumes in the middle tertile had only a borderline statistically significant decreased risk of prostate cancer compared to men with volumes in the lowest tertile (HR: 0.7, 95% CI: 0.4, 1.0). Compared to men without pineal cysts, there was a borderline statistically significant association between men with pineal cysts and decreased risk of prostate cancer (HR: 0.7, 95% CI: 0.5, 1.0). Compared to men without pineal calcifications, there was no statistically significant association between men with pineal calcifications and increased risk of prostate cancer (HR: 1.1, 95% CI: 0.7, 1.6).

Conclusions: Pineal parenchyma volume was associated with melatonin levels, but there was no statistically significant association between parenchyma volume alone and prostate cancer risk. Further studies are needed to investigate the relationship between pineal parenchyma volume, presence of calcifications and cysts, melatonin, and prostate cancer.

Citation Format: Latifa A. Bazzi, Lara Sigurdardottir, Sigurdur Sigurdsson, Unnur Valdimarsdottir, Johanna Torfadottir, Thor Aspelund, Lenore Launer, Tamara Harris, Vilmundur Gudnason, Lorelei Mucci, Sarah Markt. Pineal gland volume and risk of prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5045.
Abstract 5058: The association between smoking status at diagnosis and breast cancer specific mortality in Ireland: A population based study
Authors: Kiely Maeve , McDevitt Joesph , Sharp Linda
Published: August 2019

Background: Breast cancer is the most commonly diagnosed cancer worldwide and is a leading cause of breast cancer mortality in females. In recent years, 5 year survival rates have greatly improved for breast cancer however a clear disparity exists between survival in countries of high income compared to low and middle income. Disparity in survival also exists within individual countries. The identification of modifiable lifestyle factors can be an impactful and cost effective way to improve breast cancer outcomes worldwide, particularly in low income counties. An association between active smoking at diagnosis and breast cancer specific mortality has been reported by a number of studies to date. However, there is a paucity of studies undertaken in European populations. This large study was conducted to investigate whether smoking status at diagnosis is an independent prognostic factor for breast cancer specific mortality in the Irish female population.

Methods: All data was derived from the National Cancer Registry Ireland database which records all incident cancers in the Republic of Ireland. Completeness of case ascertainment at 5 years after diagnosis is estimated to be at 98%. Multivariable Cox proportional Hazards models were used to compare breast cancer specific mortality in current smokers, ex-smokers and never smokers. Subgroup analyses by breast cancer molecular subtype was also conducted.

Results: Data for women with known smoking status at time of diagnosis included 37,711 invasive breast cancer cases that accrued 263,626 women-years. Current smokers had a significantly increased risk of breast cancer specific mortality compared to never smokers (multi-variable HR, 1.3; 95% CI, 1.19, 1.41). Ex-smokers did not have a significantly different hazard ratio compared to never smokers (HR, 1.02; 95% CI, 0.92, 1.12). In subgroup analyses, risk of dying from breast cancer was increased most for current smokers with HER2+ disease compared to never smokers in the 5 years post diagnosis (HR, 1.53; 95% CI, 1.11, 2.12). This was followed by luminal A disease (HR, 1.39: 95% CI, 1.17, 1.65).

Conclusion. Breast cancer patients who are current smokers at diagnosis have a statistically significant increased risk of breast cancer specific mortality. This risk differs depending on molecular subtype of disease.

Citation Format: Maeve Kiely, Joesph McDevitt, Linda Sharp. The association between smoking status at diagnosis and breast cancer specific mortality in Ireland: A population based study [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5058.
Abstract 5069: Breast cancer prevention by triterpenoids from allspice
Authors: Gao Jie , Mamouni Kenza , Kallifatidis Georgios , Panda Siva , Thangaraju Muthusamy , Lokeshwar Bal L.
Published: August 2019

Breast cancer ranks second as a lethal cancer in women. Although survival following initial diagnosis is ~ 100% in first five years, cancer progression and mortality is imminent in subsequent years. The slow progression to the lethal form of breast cancer has prompted development of multiple avenues to delay the progression, metastasis and mortality using potent prevention strategies, including the use of nutraceuticals. Oleanolic acid (OA) and ursolic acid (UA) are two triterpenoids found in edible plant parts-fruits and seeds with potent cancer preventive, and selective cytotoxic activities against multiple cancers including breast cancer. We conducted cytotoxic assays of the combination of OA and UA. We found the combination has enhanced efficacy as compared to OA or UA alone. The combination of OA and UA and UA alone caused cell death by increased autophagy but not apoptosis in both MCF7 and MB231 human breast cancer cells. Further analysis revealed increased autopagosomes and autophagic flux, inhibition of either process reduced cytotoxicity, indicating cytotoxic autophagy is the primary mechanism of their action. Therefore, a combination of OA and UA with conventional therapies could enhance their therapeutic efficacy while limiting systemic toxicities of existing therapies.

Citation Format: Jie Gao, Kenza Mamouni, Georgios Kallifatidis, Siva Panda, Muthusamy Thangaraju, Bal L. Lokeshwar. Breast cancer prevention by triterpenoids from allspice [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5069.
Abstract 509: Acarbose, but not metformin, reduces tumor burden and improves intra-tumoral immune responses in a pre-clinical breast cancer model
Authors: Turbitt William J. , Orlandella Rachael M. , Gibson Justin T. , Norian Lyse A.
Published: August 2019

Finding ways to enhance T cell infiltration into tumors and boost effector function remains a critical knowledge gap that must be addressed to improve responses to immune-stimulatory therapies. Acarbose and metformin are FDA-approved drugs for the treatment of type two diabetes that display potent anti-hyperglycemic activity. A treatment strategy that decreases intra-tumoral glucose could reduce cancer cell viability and render tumors more susceptible to immunotherapy-mediated clearance. The goal of the current study was to determine if acarbose and/or metformin reduce tumor burdens and promote anti-tumor immunity in a preclinical model of breast cancer. Eight-week-old female C57BL/6 mice were orthotopically injected with EO771-Fluc mammary tumor cells then randomized to control (CTRL), CTRL+acarbose (ACA), CTRL+metformin (MET), or acarbose+metformin (ACA+MET) for four weeks. Compared to CTRL, single-agent ACA reduced primary tumor growth (50% decrease; p<0.001) and spontaneous lung metastases (48% decrease; p=0.035) without altering body weight. No effects of single-agent MET or the combination of ACA+MET on EO771 tumor growth or spontaneous lung metastases were observed. nanoString analysis of whole-tumors revealed increased dendritic cell-, T cell-, T helper 1 cell-, CD8+ T cell-, and exhausted CD8+ T cell-based gene signature scores in ACA compared to CTRL-fed mice. Cellular analysis revealed an ACA-induced increase in the percent of tumor-infiltrating PD-1+CD8+ T cells (p=0.042) and a trend toward decreased tumor-infiltrating myeloid-derived suppressor cells, resulting in improved CD8:MDSC ratios. The beneficial effects of ACA on intra-tumoral immunity, specifically promoting T cell immunity within the tumor microenvironment, illustrate the potential for future combined use of ACA with immunotherapies, such as PD-1 or CTLA-4 blockade.

Citation Format: William J. Turbitt, Rachael M. Orlandella, Justin T. Gibson, Lyse A. Norian. Acarbose, but not metformin, reduces tumor burden and improves intra-tumoral immune responses in a pre-clinical breast cancer model [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 509.
Abstract 5100: Optimization of amplicon design for polymerase chain reaction
Authors: He Bolong , Qin Hao , Li Fugen , Yang Hanyan
Published: August 2019

Amplicon design is critical important in DNA sequencing technology. Previously the amplicon designer uses exhaustive trial and error method, relying on the individual experience to compare the cost of different amplicon combinations. However, optimization of amplicon design has remained challenging due to the lack of a systematic method. As the magnitude of target DNA region and amplicon combination increases, the complexity of manual calculation and judgment will grow exponentially. In this study, our aim was to design a mathematical model to minimize the cost of amplicon combination. For given amplicon design problem, a linear integer programming model is constructed according to the optimization target and the restrictions. Let’s denote our target regions by R_1⋯ R_M, and amplicon by A_1,⋯, A_N, and conflict value c_ij for the amplicon pair A_i and A_j. The model’s restriction is to find a set of amplicons that could cover the target regions as much as possible, and for each R_i we have at most two A_j which will cover it simultaneously. The model’s optimization target is to minimize the total conflict value. The model is implemented by Python programming and uses Gurobi optimization software. In a project to design amplicon for DNA sequencing, the target regions consist of about 90,000 bits, and there are about 35,000 amplicon available. The above optimization method running on the personal computer with 8GB and 2.2GHz Intel i5-5200 CPU, take about 24 hours and produce total conflict value of 1374. The best trial and error practice took more than one week and produced total conflict value of 4527. Optimization of amplicon design for polymerase chain reaction proves to be more precise and efficient than the exhaustive trial and error method. Using optimization method will help standardize the product design for DNA sequencing.

Citation Format: Bolong He, Hao Qin, Fugen Li, Hanyan Yang. Optimization of amplicon design for polymerase chain reaction [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5100.
Abstract 5109: National cyberinfrastructure and bioinformatic analysis support available to the cancer research community
Authors: Papudeshi Bhavya , Ganote Carrie , Sanders Sheri , Doak Thomas G.
Published: August 2019

National Center for Genomic Analysis Support (NCGAS) is an NSF-funded center whose goal is to help biologists optimize their bioinformatic pipelines to best address their research questions. To help reach these goals, NCGAS provides a range of services based on the researchers needs. We currently host gateways, Trinity Galaxy and Genepattern, with built-in workflows to support cancer researchers who have little background in command line work. Both these gateways are projects funded by the Information Technologies in Cancer Research (ITCR) program of NIH, NCI, to aid in the genomic and transcriptomic characterization of cancers. NSF-funded researchers comfortable in command line can gain access to IU cyberinfrastructure (HIPAA compliant), to run or develop bioinformatic workflows. Bioinformatic packages are already installed system wide, with reference databases, and new programs are always added upon user’s request. NCGAS is also an ambassador of Extreme Science and Engineering Discovery Environment (XSEDE) resources, providing access to other HIPAA compliant national cyberinfrastructure (Texas Advanced Computing Center, Pittsburgh Supercomputing Center, etc.), available to the entire research community. XSEDE resources include the Jetstream cloud, based at IU and TACC, allowing researchers to use preconfigured virtual machines (VMs) already setup, create custom VM environments for their own work, and to share with classes and collaborators. Data can be transferred and managed between all of these resources securely with already available Globus endpoints which allows transfer for terabytes of data quickly. Additionally, NCGAS hosts workshops to help researchers get started. These training events can be scheduled online or at your local university upon request. NCGAS currently supports projects working on transcriptome, genome-level assembly, phylogenetics, metagenomics, and meta-transcriptomics analysis through providing a range of compute resources that best serve the research project.

Citation Format: Bhavya Papudeshi, Carrie Ganote, Sheri Sanders, Thomas G. Doak. National cyberinfrastructure and bioinformatic analysis support available to the cancer research community [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5109.