bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 5356: Targeted in vivo delivery of NF-κB decoy oligodeoxynucleotide augments efficacy of radiation therapy against B-cell lymphomas
Authors: zhang Zhuoran , Zhao Xingli , Moreira Dayson , Su Yu-Lin , Swiderski Piotr , Forman Stephen , Kwak Larry , Kortylewski Marcin
Published: September 2020

Despite recent advances in the treatment of non-Hodgkin B-cell lymphoma (BCL), significant numbers of patients relapse or remain refractory to current therapies. Treatment resistance in BCL is associated with survival signaling via NF-κB transcription factor. While NF-κB is an attractive molecular target in BCL and many other human cancers, as a transcription factor it remains undruggable. Here, we describe a B-cell-selective NF-κB inhibitor consisting of a NF-κB-specific decoy oligodeoxynucleotide (dODN) conjugated to a type B CpG ODN sequence targeting Toll-like receptor-9 (TLR9)-expressing B-cell lymphoma cells. Bc-NFκBdODN showed efficient uptake by human diffuse large B-cell lymphoma (DLBCL) and mantle cell lymphoma (MCL), such as U2932, OCI-Ly3 and Jeko1, respectively. In addition, we confirmed that Bc-NFκBdODN inhibited nuclear translocation and DNA-binding activity of NF-κB together with the expression of CCND2 and MYC target genes. In vitro Bc-NFκBdODN enhanced direct and ionizing radiation-induced cytotoxicity in lymphoma cells. In xenotransplanted models of human U2932 and Ly3 lymphomas, local injections of Bc-NFκBdODN reduced NF-κB activity in whole tumors and effectively arrested lymphoma progression when combined with a single, local 3Gy or 10Gy dose of radiation. In immune-competent mice, intratumoral treatment with Bc-NFκBdODN abrogated growth of directly treated as well as distant A20 lymphomas and triggered CD8+ T cell-mediated anti-tumor immune responses. Bc-NFκBdODN but not control Bc-scrambled oligonucleotides downregulated PD-1 expression on CD8+ and CD4+ T cells, while reducing Treg percentage in tumor draining lymph nodes (TDLN). Bc-NFκBdODN treatment also downregulated PD-L1 on tumor-associated myeloid cells and reduced percentage of tumor-infiltrating M-MDSCs. Our results underscore clinical relevance of NF-κB-specific decoy strategy, which can restore efficacy of standard radiation therapy to benefit patients with resistant or relapsed BCL.

Citation Format: Zhuoran zhang, Xingli Zhao, Dayson Moreira, Yu-Lin Su, Piotr Swiderski, Stephen Forman, Larry Kwak, Marcin Kortylewski. Targeted in vivo delivery of NF-κB decoy oligodeoxynucleotide augments efficacy of radiation therapy against B-cell lymphomas [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5356.
Abstract 5372: HER2 expression on tumor-derived extracellular vesicles and circulating tumor cells in metastatic breast cancer
Authors: Nanou Afroditi , Zeune Leonie L. , Bidard Francois-Clement , Pierga Jean-Yves , Terstappen Leon W.
Published: September 2020

Tumor-derived extracellular vesicles (tdEVs) and circulating tumor cells (CTCs) in blood of metastatic cancer patients associate with poor outcome. In this study, we explored the human epidermal growth factor receptor 2 (HER2) expression on CTCs and tdEVs of metastatic breast cancer patients.

Blood samples from 98 patients (IC 2006-04 study) were originally processed with the CellSearch® system using the CTC kit and anti-HER2 as an additional marker in the staining cocktail. CTCs and tdEVs were automatically enumerated from the generated CellSearch image datasets using the open-source ACCEPT software. The HER2 status of the tissue was assessed by fluorescence in situ hybridization (FISH).

The inclusion of anti-HER2 increased the percentage of informative samples with ≥1 detectable CTC and tdEV from 89% and 99% to 95 and 100%, respectively. CTCs and tdEVs were subdivided based on their cytokeratin (CK) and HER2 phenotype into CK+HER2-, CK-HER2+ and CK+HER2+. Inter- and intra- patient heterogeneity was found regarding the phenotype of CTCs and tdEVs with the majority of patients having all different subclasses present. CK- CTCs and tdEVs correlated equally well with clinical outcome as CK+ CTCs and tdEVs. Use of ≥7% HER2+CK+ tdEVs can predict HER2 expression of the tissue with 74% sensitivity and specificity, whereas the respective use of ≥23% HER2+CK+ CTCs leads to 65% sensitivity and 66% specificity.

HER2 can be detected on CTCs and tdEVs not expressing CK, which have similar clinical relevance to CTCs and tdEVs expressing CK. tdEVs perform better than CTCs in predicting the HER2 status of the tissue.

Funded by the NWO Applied and Engineering Sciences Cancer-ID project #14190, the EUFP7 CTCTrap project #305341 and the EU IMI CANCER-ID project # 115749-1.

Citation Format: Afroditi Nanou, Leonie L. Zeune, Francois-Clement Bidard, Jean-Yves Pierga, Leon W. Terstappen. HER2 expression on tumor-derived extracellular vesicles and circulating tumor cells in metastatic breast cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5372.
Abstract 5374: Rapid microfluidic isolation and detection of circulating tumor cells/clusters with zero sample preparation
Authors: Zhou Jian , Liu Bin , Luan Qiyue , Mallisetty Apurva , Hulbert Alicia , Papautsky Ian
Published: September 2020

Background: Circulating tumor cells (CTCs) and clusters of liquid biopsy permits continual access to phenotypic and genotypic landscape of primary and metastatic tumors for optimized personalized therapy. In addition, it holds the promise of deciphering the tumor heterogeneity which is one of the major sources of treatment resistance. Due to the extreme rarity of CTCs in peripheral blood, rapid and reliable isolation remains challenging amid new technologies being tested. Herein, we developed and demonstrated a novel microfluidic approach capable of direct isolation of CTCs and clusters from untreated whole blood within 20 min.

Methods: Our microfluidic approach takes advantages of the intrinsic strong cell-cell interactions when whole blood flows in a microchannel, which leads to faster lateral migration of larger cells and thus label-free isolation of CTCs based on size. Our biochip integrates cell isolation and cell immobilization units and allows processing of untreated whole blood at high throughput (2 mL in 20 min). Immobilized CTCs and clusters were subsequently characterized onchip by immunocytochemistry as CD45-, CK+ and DAPI+.

Results: Blood samples of 9 deidentified patients diagnosed with non-small-cell-lung cancer (NSCLC) were directly processed through our microfluidic biochip. 2 mL whole blood of each sample were used without pretreatment. Immunofluorescence assay identified at least 1 CTC in the blood samples from all patients (100%). CTC count ≥ 5 was found in 8/9 samples (89%). The median of CTC count was 9 per 2 mL blood. A maximum of 38 CTCs per 2 mL whole blood was found in the sample of a late stage patient. Grape-like CTC cluster was also detected in one of the nine samples (11%).

Conclusions: These “proof of concept” results suggest that our novel, label-free microfluidic technology is capable of rapid isolation and detection of CTCs and clusters directly from patient peripheral blood without sample pretreatment. It completely spares the need of costly, time-consuming and laborious sample pretreatment required by other methods. Further validation studies with cases and controls using patient lung tumor compared to the obtained CTC from our microfluidic approach are required before its implementation in the real-world practice.

Citation Format: Jian Zhou, Bin Liu, Qiyue Luan, Apurva Mallisetty, Alicia Hulbert, Ian Papautsky. Rapid microfluidic isolation and detection of circulating tumor cells/clusters with zero sample preparation [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5374.
Abstract 5407: Novel imipridone combination therapies targeting oncohistone H3K27M mutant diffuse midline glioma (DMG)
Authors: Borsuk Robyn , Zhou Lanlan , Lulla Rishi , El-Deiry Wafik
Published: September 2020

Malignant glioma including diffuse midline glioma (DMG) is the leading cause of cancer related death in children. Recent advances in sequencing have identified the oncohistone H3K27M mutation in ~80% of pediatric DMG, which represents a target for new therapeutics. ONC201 is a first-in-class small molecule which upregulates TNF-related apoptosis inducing ligand (TRAIL) and its proapoptotic receptor DR5, independent of p53, selecting for apoptosis/growth arrest of many different tumor types including H3K27M mutant DMG. While single agent ONC201 along with RT is currently being tested in clinical trials for newly diagnosed and refractory DMG, there is an urgent need to evaluate ONC201 and other imipridone analogs in combination with other agents. Patient derived H3K27M mutant DMG cell lines (SU-DIPG-IV, SU-DIPG-13, SU-DIPG-25, SU-DIPG-27, SU-DIPG-29, SU-DIPG-36, and SF8628), were grown in culture and exposed to imipridones (ONC201, ONC206 and ONC212) alone, and in combination with other chemotherapeutic agents that have demonstrated pre-clinical activity against DMG (HDAC inhibitors and etoposide). Response to treatment was determined by Cell Titer-Glo cell viability assays as well as Western Immunoblotting for evidence of apoptosis and integrated stress response (ISR) activation. All H3K27M-mutant DMG cell lines tested to date exhibit a dose-dependent response to imipridone therapy. Mean IC50 values were significantly lower with the imipridone analogs ONC206 (0.11 µM) and ONC212 (0.03 µM) as compared to ONC201 (1.46 µM) when used as a single agent. ONC206 and ONC212 were associated with robust induction of apoptosis evidenced by increased expression of cleaved PARP, and ISR by increased expression ATF4. In the SU-DIPG-IV cell line, combination studies of ONC201 and panobinostat demonstrated a synergistic effect of both agents, as calculated by CompuSyn software. Combination indices below one were observed at concentrations of 0.003 - 0.05 µM of panobinostat with ONC201 at 0.156 - 5 µM, with the best combination index of 0.22. We similarly observed synergy between either ONC201 or ONC206 with Etoposide. Additional combination testing and synergy analysis is ongoing and will be presented. Our findings suggest that H3K27M DMG cells demonstrate increased sensitivity to imipridones ONC206 and ONC212 as single agents and combinational strategies with HDAC inhibitors and etoposide, and provide insights into novel therapies for further clinical testing.

Citation Format: Robyn Borsuk, Lanlan Zhou, Rishi Lulla, Wafik El-Deiry. Novel imipridone combination therapies targeting oncohistone H3K27M mutant diffuse midline glioma (DMG) [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5407.
Abstract 5415: Profiling cancer testis antigens in osteosarcomas
Authors: Zhang Zhongting , Wang Yifei , Zhang Wendong , Xu Zhaohui , Zhou Xin , Roth Michael , Gill Jonathan , Harrison Douglas , Hingorani Pooja , Jusu Sylvester , Kannan Sankar , Tian Xiangjun , Wang Jing , Lazcano Rossana N Segura , Lazar Alexander , Gorlick Richard
Published: September 2020

Cancer testis antigens (CTA) are reported to have restricted expression in placenta and testis, but they are also known to be expressed in some malignant tumors. Immunotherapy targeting CTAs in melanomas and certain types of soft tissue sarcomas have shown potential therapeutic value. However, the expression pattern of CTAs in osteosarcoma (OS) has not been fully elucidated. To characterize the CTA landscape of OS, we compared RNA sequencing data from 40 high-risk OS patients treated at MD Anderson Cancer Center and 111 OS patients available through a public online database. All of these tumor data are subsequently compared with testis/placenta and other normal tissue RNA-sequencing data from the NIH Genotype-Tissue Expression (GTEx) database as well as an online dataset which includes normal bone tissue. 53 genes that are significantly highly expressed in OS and testis/placenta (log fold change tumor versus normal >1.0 for each tissue, p < 0.01) are selected. Of those, 11 genes have been annotated in the Cancer Testis Database (CTdatabase) such as MAGEA3/A6 and LY6K. We also identified 42 genes that are not annotated in the CTdatabase. The co-expression pattern of CTAs in OS was also investigated by unsupervised hierarchical cluster analysis. The expression of selected CTAs was validated by IHC staining with an OS tissue microarray from 100 patients, and western blot using PDX models and patient-derived cell lines. Interestingly, the results demonstrated that multiple CTAs such as MAGEA3, LY6K and PAGE5 are also highly expressed in normal bone tissue. The current results suggest further development of immunotherapy approaches targeting CTAs in OS.

Citation Format: Zhongting Zhang, Yifei Wang, Wendong Zhang, Zhaohui Xu, Xin Zhou, Michael Roth, Jonathan Gill, Douglas Harrison, Pooja Hingorani, Sylvester Jusu, Sankar Kannan, Xiangjun Tian, Jing Wang, Rossana N Segura Lazcano, Alexander Lazar, Richard Gorlick. Profiling cancer testis antigens in osteosarcomas [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5415.
Abstract 5423: Multimodal prediction of diagnosis for cancers of unknown primary
Authors: Michuda Jackson , Leibowitz Benjamin , Amar-Farkash Shlomit , Bevis Crystal , Breschi Alessandra , Kapilivsky Joshuah , Igartua Catherine , Bell Joshua S. , Beauchamp Kyle A. , White Kevin , Stumpe Martin , Beaubier Nike , Taxter Timothy
Published: September 2020

Background: Tumors of unknown origin account for up to 5% of newly diagnosed cancers and the average survival time is 9 to 12 months from diagnosis. Establishing tumor type and subtype guides standard of care treatment for several NCCN targeted therapy guidelines.

Methods: Targeted DNA sequencing for more than 500 cancer-associated genes and exome-capture RNA sequencing was carried out in more than 25,000 fresh frozen or paraffin embedded tumor samples, including both primary and metastatic tumors. Mutations, copy number variants, and viral sequences were detected from DNA sequencing while gene expression and fusion events were determined from RNA sequencing. We aimed to predict cancer type by utilizing multiple machine learning models trained on individual data types and harmonize predictions across multiple data types.

Results: The transcriptome model predicts more than 60 unique diagnoses covering both solid and hematological cancers with >90% overall accuracy on a held-out test set. Of note, the model can accurately predict 10 subtypes of sarcoma and 6 subtypes of neuroendocrine tumors. Gene expression and splicing were the most informative data types, but a performant DNA-only model was also evaluated for application when only DNA data is available. Finally, we evaluated the model on an unlabeled cohort of poorly differentiated samples with inconclusive diagnosis.

Conclusions: The incorporation of multiple modes of omics data can improve the interpretability and robustness of machine learning models to predict cancer diagnosis.

Citation Format: Jackson Michuda, Benjamin Leibowitz, Shlomit Amar-Farkash, Crystal Bevis, Alessandra Breschi, Joshuah Kapilivsky, Catherine Igartua, Joshua S. Bell, Kyle A. Beauchamp, Kevin White, Martin Stumpe, Nike Beaubier, Timothy Taxter. Multimodal prediction of diagnosis for cancers of unknown primary [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5423.
Abstract 5431: Subungual melanoma: It may be a distinct entity
Authors: Holman Blair N. , Van Gulick Robert J. , Amato Carol , Couts Kasey , Robinson William A.
Published: September 2020

Subungual melanoma (SUM) is a type of malignant melanoma that arises beneath the nails of the hands and feet. Subungual melanomas represent a small subset of melanoma patients and have not been well characterized by current molecular techniques. In most studies they have been included in the category of acral melanoma (AM), but there are numerous reasons to believe that they may be different. New effective melanoma treatments rely on both clinical and molecular data to select therapy. In this study, we reviewed characteristics in 29 patients with subungual melanomas seen at our institution in an attempt to provide better understanding and treatment. The median age was 56, almost equally distributed between males and females, with a higher percentage of non-Caucasians than seen in cutaneous melanoma. The most common sites were the thumb (28%), big toe (21%), and index finger (17%). Most were deep at diagnosis (mean Breslow depth 4.21 mm), and 72% had, or developed, metastases and responded poorly to therapy of all kinds. In 12 of the 29 cases, molecular testing via targeted sequencing through Foundation Medicine was done on either a primary or metastatic lesion. These 12 cases were compared to 20 cases of AM seen at our institution. One BRAF mutation was found (1/12, 4%) in SUM, whereas BRAF mutations occurred in about 20% of patients with AM. No patients with SUM had an NRAS mutation, compared to a 45% mutation rate in AM. Two SUM patients had KRAS mutations (2/12, 17%), whereas no patients with AM had a KRAS mutation. Three SUM patients had mutations in KIT (3/12, 25%) compared to one (1/20, 5%) in AM. In addition, 3 patient tumors had a recurrent variant (K587R) in the tuberous sclerosis related gene TSC-1, which has not been described in patients with AM. While our profile of subungual melanoma has some similarities with non-subungual acral melanomas, the high number of KRAS, KIT and TSC1 mutations and lack of BRAF and NRAS mutations suggests that these melanoma may have unique characteristics, different causation, and need specific therapy different from acral melanomas.

Citation Format: Blair N. Holman, Robert J. Van Gulick, Carol Amato, Kasey Couts, William A. Robinson. Subungual melanoma: It may be a distinct entity [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5431.
Abstract 5434: Insulinoma-associated protein 1 (INSM1) expression in small cell neuroendocrine carcinoma of the urinary tract
Authors: Kim Isaac E. , Amin Ali , Wang Li Juan , Cheng Liang , Perrino Carmen M.
Published: September 2020

Introduction

Clinical guidelines including the American Urological Association (AUA) state that neoadjuvant chemotherapy should be administered prior to surgery in cases of muscle invasive urinary bladder small cell neuroendocrine carcinoma. Although the recently described marker insulinoma-associated protein 1 (INSM1) has been reported to be sensitive and specific for neuroendocrine differentiation in neuroendocrine tumors at several sites, its efficacy as a marker in urinary bladder small cell carcinoma has not been well established. This study aims to examine the immunohistochemical expression pattern of INSM1 on whole tissue sections of urinary bladder small cell neuroendocrine carcinoma and compare INSM1 expression to those of established markers of neuroendocrine differentiation.

Methods

Archived tissue from 32 cases of urinary bladder small cell neuroendocrine carcinoma were obtained from Rhode Island Hospital and The Miriam Hospital. Immunohistochemical stains for CD56, INSM1, synaptophysin, and chromogranin were performed. Staining was scored for intensity (0: no staining; 1: weak; 2: moderate; 3: strong) and proportion of cells stained (0: 0%; 1: >0 to 25%; 2: >25 to 50%; 3: >50 to 75%; 4: >75 to 100%).

Results

INSM1 was positive (intensity 1-3 or proportion 1-4) in 87% (28/32) of small cell neuroendocrine carcinoma cases (20 with intensity 2-3, 17 with proportion 3-4). CD56, synaptophysin, and chromogranin were positive in 75% (24/32), 60% (19/32), and 44% (14/32) of cases, respectively. While the rate of positivity was high, INSM1 was negative (n=4) or only showed weak intensity staining (n=7) in 34% (11/32) of cases.

Conclusion

INSM1 is a sensitive marker of small cell neuroendocrine differentiation of the urinary bladder. However, the findings in this study suggest that optimal utilization of INSM1 would be in a limited panel of stains rather than as a stand-alone screening marker given that it is negative or only shows weak intensity staining in a significant proportion of cases.

StainNegative [n (%)]Positive [n (%)]INSM14 (13)28 (87)CD568 (25)24 (75)Synaptophysin13 (40)19 (60)Chromogranin18 (56)14 (44)

Citation Format: Isaac E. Kim, Ali Amin, Li Juan Wang, Liang Cheng, Carmen M. Perrino. Insulinoma-associated protein 1 (INSM1) expression in small cell neuroendocrine carcinoma of the urinary tract [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5434.
Abstract 5439: Distinct genomic profile in H. pylori associated gastric cancer
Authors: Wang Ao , Bao Hua , Hu Pengfei , Wu Yong , Zhang Jinfeng , Wu Xue , Wang Xiaonan , Shao Yang
Published: September 2020

Background: Gastric cancer is one of the most common and deadly cancer types. Currently 4 subtypes have been identified with unique molecular alterations: Epstein-Barr virus (EBV)-positive, microsatellite instability (MSI), chromosomal instability (CIN), and genomic stable (GS) tumors. However, many gastric tumors are associated with the bacterium Helicobacter pylori but the genomic landscape of this subgroup of tumors remains largely unknown.

Methods: Targeted-sequencing covering 425 genes were performed retrospectively on 1759 gastric tumor tissues and matched normal blood samples. The mean sequencing depth of tumors was 1159X. Nonsynonymous mutations, copy-number variation (CNV) and MSI status were called from human DNA reads; non-human DNA reads were mapped to NCBI microbial reference genome using Kraken and significant species were identified.

Results: Overall, 37 (2.67%) samples were EBV-positive, 200 (11.37%) samples were H. pylori-positive, and 10 (0.57%) samples were positive for both. Other notable species identified in tumor samples were E. coli and C. acnes. No bacteria or viral reads were found in normal blood. Among the rest, 59 (3.35%) samples were MSI, 380 (21.6%) were CIN, and 1017 (57.82%) were GS. H. pylori-positive samples tend to be GS (85.5%, p < 0.001) and microsatellite stable (95%, p = 0.04). The most common mutations identified in H. pylori-positive tumors were TP53 (47%), CDH1 (12%) and ARID1A (8.5%). The top CNV events were amplification in MCL1 (14.5%), TERC (9%), CCNE1 (8.5%), PTPRD (8.5%), and MYC (7.5%). Compared to other GS tumors, mutation in AKT3 (p = 0.002) and amplification of TERC (p = 0.008) as well as MCL1 (p = 0.0.029) were significantly enriched in H. pylori-positive tumors. There was no difference in patients' sex or age among subtypes (p >= 0.05).

Conclusion: This study characterized the genomic landscape of H. pylori positive gastric tumors using targeted-sequencing, which allowed direct comparison with other subtypes of gastric cancer. Identification of DNA reads from infectious agents in the tumor samples indicates that deep sequencing platform has promising utility in uncovering the characteristics of microbial environment of tumor. Co-infection between H. pylori and EBV occurred at a low frequency. H. pylori-positive tumors were GS and microsatellite stable with unique molecular features. Future study examining difference in treatment response among these subtypes of gastric cancer are warranted.

Citation Format: Ao Wang, Hua Bao, Pengfei Hu, Yong Wu, Jinfeng Zhang, Xue Wu, Xiaonan Wang, Yang Shao. Distinct genomic profile in H. pylori associated gastric cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5439.
Abstract 5443: Modulating plasticity in aggressive variant prostate cancers
Authors: Soundararajan Rama , den Hollander Petra , Shepherd Peter , Navone Nora , Lorenzini Daniele , Laberiano-Fernandez Caddie , Lu Wei , Zhou Jianling , Liu Jingjing , Zhang Jianhua , Solis-Soto Luisa Maren , Mani Sendurai A. , Aparicio Ana
Published: September 2020

Aggressive Variant Prostate Cancers (AVPC) are a clinically and molecularly distinct subset of prostate cancers with a poor prognosis characterized by androgen-indifference, platinum-sensitivity and combined defects in Tp53, RB1 and PTEN, for which novel therapeutic approaches are urgently needed. Defects observed in these tumor suppressor pathways have been linked to lineage plasticity in genetically engineered mouse models. We hypothesized that this plasticity can be identified in human tumor samples, and can be modulated to serve as the foundation for effective combination therapies for the AVPC subset. We previously defined a gene expression signature derived from mouse embryonic day 6.5 that is representative of extensive cellular plasticity (PMID:26123483). We determined the plasticity scores in 12 patient-derived xenograft (PDX) models representative of the spectrum of prostate cancer biology (using available RNA sequencing profiles), and in 26 macrodissected tumor biopsies obtained from patients who received platinum-based chemotherapy for aggressive prostate cancer (using ALMAC Affymetrix gene expression microarray). As expected, the AVPC PDX models exhibited high plasticity scores as did 11 (42.3%) of the patient samples, associated with patient progression free- and overall survival. We next treated a well characterized AVPC PDX model (144-4) with the anti-EMT drug (p38MAPK inhibitor) SB203580 at 10mg/kg, and observed a decrease in stem-cell and EMT factors associated with plasticity. These data confirm the association between plasticity and AVPC in human tumor samples, and suggest that changes in plasticity can be measured in tumor samples to determine the value of its modulation in clinical trials.

Acknowledgments: ALMAC Diagnostics Services, UK, and UTMDACC ATGC Core Lab (CCSG-CA016672-ATGC) for RNA sequencing services; UTMDACC Prostate Cancer SPORE (RS, SAM, AA), UTMDACC IRG (RS), and the UTMDACC Prostate Cancer Moonshot Program (AA) for financial support.

Citation Format: Rama Soundararajan, Petra den Hollander, Peter Shepherd, Nora Navone, Daniele Lorenzini, Caddie Laberiano-Fernandez, Wei Lu, Jianling Zhou, Jingjing Liu, Jianhua Zhang, Luisa Maren Solis-Soto, Sendurai A. Mani, Ana Aparicio. Modulating plasticity in aggressive variant prostate cancers [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5443.
Abstract 5444: Clinical significance of tetraspanin CD63 in human ESCC
Authors: Matsumoto Yasunori , Kano Masayuki , Murakami Kentaro , Endo Satoshi , Toyozumi Takeshi , Shiraishi Tadashi , Kamata Toshiki , Ryuzaki Takahiro , Kinoshita Kazuya , Hirasawa Soichiro , Matsubara Hisahiro
Published: September 2020

Background: ESCC(Esophageal Squamous Cell Carcinoma) is highly aggressive due to its tendency to metastasize to the lymph nodes and organs. Our laboratory previously reported that the exosome amount in the peripheral blood could predict the prognosis of ESCC patients. CD63 is a tetraspanin family protein and is often used as a marker of exosome.CD63 highly express in early stage melanoma and thought to be a suppressive factor against EMT (epithelial-to-mesenchymal transition) in melanoma. On the other hand, some report confirmed CD63 as a prometastatic factor via regulating E cadherin expression. The function of CD63 are still controversial. We herein assessed CD63 expression and clinicopathological findings in ESCCpatient, and assessed molecular roles of CD63 in ESCC cell lines.

Materials and methods: The relationship between the CD63 expression in the resected ESCC specimen (from 1997 to 2006, n=86) and clinicathological features were assessed using immunohistochemical staining. Human ESCC cell lines (TE2,TE15) were used as high CD63 expression cell lines for in vitro analysis. CD63 was knockdown using siRNA, and CD63 down regulate was confirmed by western blot and PCR. The influence on the cell behavior and gene expressions were assessed by cell proliferation assay, mRNA microarray, and GSEA(Gene Set Enrichment Analysis).

Results: There were no statistically significant correlation between the CD63 expression and age, sex, tumor depth (T), lymph node metastasis (N), distant organ metastasis (M), differentiation of tumor, lymphatic vessel invasion (ly), venous invasion (v), the type of progression. As for the prognosis, the high CD63 expression patients have significantly poorer prognosis than the low expression of CD63 patients. (P=0.047, log rank test). In vitro study, cell proliferation assay showed down expression of CD63 reduce cell proliferation. Knock down of CD63 downregulates HER2 expression and influence on other ERBB signaling pathways.

Conclusions: High CD63 expression predicts poor prognosis in human ESCC. The molecular function of CD63 could have relationship to ERBB signaling pathways in human ESCC cells.

Citation Format: Yasunori Matsumoto, Masayuki Kano, Kentaro Murakami, Satoshi Endo, Takeshi Toyozumi, Tadashi Shiraishi, Toshiki Kamata, Takahiro Ryuzaki, Kazuya Kinoshita, Soichiro Hirasawa, Hisahiro Matsubara. Clinical significance of tetraspanin CD63 in human ESCC [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5444.
Abstract 5452: Neuroendocrine negative RB1 WT SCLC and LCNEC
Authors: Sonkin Dmitriy , Thomas Anish , Teicher Beverly A.
Published: September 2020

Background: Based on genomics data generated in last few years about 15% of tumors diagnosed as large cell neuroendocrine carcinomas (LCNEC) are actually neuroendocrine negative. Interestingly, approximately similar percentage of small cell lung cancers (SCLC) are also neuroendocrine negative, historically known as SCLC variant and are enriched for RB1 WT tumors. Here we compare the morphological, genomic and other features of neuroendocrine negative RB1 WT SCLC and LCNEC.

Methods: To comprehensively compare neuroendocrine RB1 WT SCLC and LCNEC, we examined morphological, genomic and other features of these rare lung cancer subtypes using publicly available data. From a genomics perspective, we payed special attention to key oncogenic genetic alterations and expression pattern of transcription factors known to play critical role in SCLC and LCNEC.

Results/Conclusions: The expression pattern of transcription factors ASCL1, POU2F3, NEUROD1, YAP1 in LCNEC has number of similarities to expression pattern of these transcription factors in SCLC. Neuroendocrine negative/low RB1 WT SCLC and neuroendocrine negative/low, RB1 WT, KEAP1 WT, STK11 WT LCNEC have similar genomics and morphological characteristics and might be in fact the same entity. Based on differences in distribution of different lung cell types at different anatomical locations such as: peripheral, midzone or central, collecting information on lung tumor location along with genomic information and neuroendocrine markers staining could be important for better understanding of rare lung tumor subtypes. Clinical trial NCT04010357 is going to investigate efficacy of CDK4/6 inhibitor abemaciclib in RB1WT SCLC. Based on our observations patients with neuroendocrine negative/low RB1 WT, KEAP1 WT, STK11 WT LCNEC subtype might be also candidates for clinical trial-based treatment with CDK4/6 inhibitors.

Citation Format: Dmitriy Sonkin, Anish Thomas, Beverly A. Teicher. Neuroendocrine negative RB1 WT SCLC and LCNEC [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5452.
Abstract 5457: Structural and functional assessment of mutations identified in different breast cancer genes
Authors: Mishra Neha , Khan Mudassar Ali , Kuligina Ekaterina S. , Hasan Syed , Varma Ashok K.
Published: September 2020

Atomic protein structure helps in understanding the functions associated with protein molecule. Therefore, it is very important to correlate the structural information from the biological functions of proteins for translational research. So far, BRCA1 and BRCA2 (Breast Cancer Susceptibility genes 1 and 2) genes have been extensively studied genes for hereditary breast and ovarian cancers. BRCA1 comprises 1863 amino acids and is involved in the tumour suppressor function. It also plays an important role in cell cycle checkpoint control and DNA damage repair process. Germ-line mutations discovered in BRCA1 and BRCA2 genes are distributed all over gene coding regions. BRCA1 encompasses different functional domains like RING-domain at N- terminus, DNA binding domain at the centre and tandem repeats of BRCT at C-terminus. RING-domain of BRCA1 interacts with BARD1, BAP1 whereas C-terminal region of BRCA1 interacts with BACH1, CtIP, Abraxas and controls the cell -cycle checkpoint through the protein-protein interactions. Germ-line mutations identified from the larger cohort of patients is available in different databases. However, unreported mutations are also regularly detected in clinical settings. We have evaluated the folding pattern of mutations discovered in different domains of BRCA1 and BRCA2 using in-silico, in-vitro and biophysical approaches. Furthermore, studies of protein-protein interactions (PPIs) with the binding partners of BRCA1 such as RAP80, MERIT40, and ABRAXAS have been explored using isothermal titration calorimetry. The slight differences between wild-type and mutant proteins of BRCA1 and BRCA2 have been observed. The data obtained from Circular- Dichroism, protein-protein interactions and structural analysis confirm that an alterations in protein folding pattern although not able to serve as a sole tool for mutation pathogenicity assessment, could provide valuable information to aid the classification of uncertain, potentially disease-causing, variants in the human cancer-relevant genes. Grant number: DST (Grant DST/INT/RUS/RSF/11), Russian foundation for Basic research (grant number 19-515-25001)

Citation Format: Neha Mishra, Mudassar Ali Khan, Ekaterina S. Kuligina, Syed Hasan, Ashok K. Varma. Structural and functional assessment of mutations identified in different breast cancer genes [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5457.
Abstract 5475: Evaluation of feature selection methods used for cluster analysis in identification of novel cancer subtypes
Authors: Vidman Linda , Källberg David , Rydén Patrik
Published: September 2020

Background: RNA-seq data from tumor samples can be used to identify novel cancer subtypes using cluster analysis. The number of features is often large compared to the number of samples and different clusters can appear in different subsets of the feature space. Feature selection techniques are therefore commonly used to reduce the dimension and remove redundant and irrelevant features before performing cluster analysis. An abundance of feature selection methods have been proposed in the literature, but it is unclear how the ability to identify novel subtypes of cancer using cluster analysis is affected by choice of feature selection method.

Method: We evaluated 13 feature selection methods on four publicly available cancer data sets from The Cancer Genome Atlas. RNA-seq data and associated clinical data were retrieved from Broad institute GDAC Firehose. Overlap and characterization of the highest ranked features (i.e. genes) were studied for top 100, 1000 and 3000 genes. Performance was measured by comparing known cancer subtypes to partitions obtained using hierarchical clustering with Euclidean distance and Ward´s linkage, based on the selected features. The result was compared to both a random selection (negative control) and a supervised approach (positive control) using adjusted Rand index.

Results: The relative performance of the feature selection methods varied heavily depending on number of included genes and the data set used. Based on all data, gene selection using the Dip-test statistic and the Bimodality index generated the overall highest clustering performance. The overlap of selected genes between the Bimodality index, the Dip-test and the supervised approach was relatively low. The Dip-test and Bimodality index tended to favor genes with relatively low expression values.

Conclusions: The choice of feature selection method can have a huge impact on the ability to identify cancer subtypes using cluster analysis, and the relative performance is highly dependent on the data. Low overlap of selected genes between the highest ranked methods suggests that the methods identify genes that contain complementary information, and that it might be beneficial to combine two or more feature selection methods.

Citation Format: Linda Vidman, David Källberg, Patrik Rydén. Evaluation of feature selection methods used for cluster analysis in identification of novel cancer subtypes [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5475.
Abstract 5508: BCMA-CD3 bispecific antibodies: A modeling framework to characterize kinetics of bispecific antibody, T cell, cytokines, and serum M-protein
Authors: Udata Chandrasekhar , Wei Dai , Jiang Sibo , Forgie Alison , Hooper Andrea , Qiao Wenlian , Musante Cynthia , Yin Donghua
Published: September 2020

The B-cell maturation antigen (BCMA) is an attractive target in multiple myeloma since it is more selectively expressed on myeloma cells. Meanwhile, T-cell-engaging bispecific antibodies (BsAbs) are an important class of antibody therapeutics in cancer therapy. BCMA-CD3 BsAbs simultaneously bind to CD3 on T cells and BCMA on tumor cells, activate T cells, and redirect T cells' cytotoxicity against tumor cells. BCMA is shed from the surface of plasma cells by gamma-secretase-mediated cleavage, leading to detectable, soluble BCMA (sBCMA) in circulation. Higher concentrations of sBCMA in patients with myeloma are associated with poorer clinical outcomes. Furthermore, sBCMA in circulation may act as a drug sink, especially when it is present in a relatively higher amount compared to the drug concentration, potentially attenuating the intended pharmacological mechanism and impacting pharmacokinetics and efficacious dose predictions. To address the complexities, we leveraged a quantitative systems model to characterize the kinetics of a model BsAb, T-cell, cytokines and serum M-protein upon BsAb treatment based on the literature data. This model incorporated T-cell activation, cytokine profiles as well as serum M-protein following various dosing regimens and baseline sBCMA levels. This model could assist in the design of clinical dosing strategies for BCMA-CD3 BsAb programs.

Citation Format: Chandrasekhar Udata, Dai Wei, Sibo Jiang, Alison Forgie, Andrea Hooper, Wenlian Qiao, Cynthia Musante, Donghua Yin. BCMA-CD3 bispecific antibodies: A modeling framework to characterize kinetics of bispecific antibody, T cell, cytokines, and serum M-protein [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5508.
Abstract 5509: Breaking the paradox breakers - RAF inhibitor mechanisms
Authors: Mendiratta Gaurav , McFall Thomas , Stites Edward
Published: September 2020

A number of ATP competitive inhibitors of RAF onco-protein have been successful in tumors with RAF V600 mutations but have failed for more common cases with upstream mutations. Instead, a paradoxical activation (PA) of downstream signaling is observed in response to these inhibitors when RAF is not the driver mutation. A detailed understanding of processes that potentiate PA would help in minimizing side effects, choosing appropriate mono- or combination treatments and guide future drug development. Several mechanisms of PA have been proposed in the past, such as negative co-operativity to additional drug binding and RAF dimer stabilization. However, the evidence for these mechanisms is indirect and does not explain PA for all the different types of drugs.

In our work, we created a mathematical model of RAF activation solely based on canonical RAF signal regulatory processes to show how autoinhibition provides a general mechanism of PA. We also used this model to show that 14-3-3 proteins could further potentiate PA by stabilizing autoinhibited RAF. Based on the computational work, we predicted that transfecting 14-3-3 proteins would potentiate PA even with drugs which are otherwise expected to provide minimal or no PA. Our experiments with these drugs in SKMEL2 melanoma cells and SW48 colon cancer cells validated our predictions thereby providing support for our general model of PA.

Citation Format: Gaurav Mendiratta, Thomas McFall, Edward Stites. Breaking the paradox breakers - RAF inhibitor mechanisms [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5509.
Abstract 5574: In vivo model development for immune cell-based therapeutics
Authors: McMichael Elizabeth , Jetley Utsav , Rudulier Christopher , Borah Minasri , Ganci Nicole , Ragothaman Vandhana , Balwani Ishina , Frain Amanda , Pajanirassa Priya , Miki Yuko , Jones Jeffrey , Luster Troy , Keenan Marie , Martinez Terina , Zhang Yong , Schultes Birgit
Published: September 2020

The implementation of various mouse models is critical to asses safety, efficacy, and short- and long-term persistence of therapeutic modalities, especially for cell-based therapies. To increase our repertoire of viable humanized murine models, we developed two in vivo models by taking advantage of Taconic's immunodeficient mice, one monitoring graft versus host disease (GvHD) and the other addressing human natural killer (NK) cell cytotoxicity. We utilized NOG mice to develop a model of GvHD, by transplanting human PBMCs at varying doses and monitoring mice for changes in body weight over time. We determined a dose of injected PBMCs that allowed for GvHD to occur yet provided a window of opportunity for potential therapies to slow progression. When human natural T regulatory cells (nTregs) were co-injected with PBMCs in NOG mice, there was prolonged survival and a less rapid loss of body weight as compared to PBMCs alone. To create an NK cytotoxicity model, we transplanted human primary NK cells into NOG-hIL15 mice, which are NOG mice that constitutively produce human IL-15. We showed successful engraftment and proliferation of NK cells, with peak engraftment occurring 4-5 weeks post injection, and that these human primary NK cells were able to persist without signs of xenogeneic GvHD. Utilizing K562 tumor cells that express luciferase, we found these engrafted NK cells have fast and potent cytotoxic activity using IVIS imaging, resulting in elimination of tumor cells as compared to non-engrafted mice. Our results collectively suggest that the two in vivo models developed here will be valuable tools for investigating the clinical benefit of immune cell-based therapeutics.

Citation Format: Elizabeth McMichael, Utsav Jetley, Christopher Rudulier, Minasri Borah, Nicole Ganci, Vandhana Ragothaman, Ishina Balwani, Amanda Frain, Priya Pajanirassa, Yuko Miki, Jeffrey Jones, Troy Luster, Marie Keenan, Terina Martinez, Yong Zhang, Birgit Schultes. In vivo model development for immune cell-based therapeutics [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5574.
Abstract 558: M6123, a selective FGFR1 antagonist, demonstrates anti-tumor activity as monotherapy and in combination with chemotherapy in mesothelioma models
Authors: Esdar Christina , Ross Edith , Sanderson Michael , Zimmermann Astrid
Published: September 2020

Malignant pleural mesothelioma is an aggressive, asbestos-related cancer most commonly arising from the mesothelial cells lining the pleural cavity surrounding the lung. Despite the poor prognosis and increasing incidence of this disease, the combination of pemetrexed with cisplatin currently remains the only available treatment option to patients. Molecular characterization of mesothelioma tumors indicates a potential dependency on autocrine FGF-FGFR signaling. Based on this information, the therapeutic activity of M6123, a potent and selective, monovalent antagonist of FGFR1, was investigated in preclinical mesothelioma models in vitro and in vivo. In a panel of mesothelioma cell lines, M6123 mediated cellular growth reduction was clearly correlated with the level of endogenous FGF2 ligand. M6123 monotherapy significantly inhibited FGFR1 signal transduction and tumor growth in a cell line derived mesothelioma model. Furthermore, combination benefit was observed for M6123 with standard of care (SoC) chemotherapy. In a panel of nine mesothelioma patient derived xenograft (PDX) models, 66% (6/9) were sensitive to the combination of M6123 plus pemetrexed/cisplatin compared to 33% (3/9) for chemotherapy alone. The expression of a focused set of FGF-FGFR pathway genes was examined in PDX models to elucidate potential predictive biomarkers of sensitivity to M6123. Sprouty homolog 2 (SPRY2), a negative regulator of FGFR1 signaling, was upregulated in non-sensitive PDX models, whilst positive regulators of FGFR1 signaling including the ligand FGF5, the coreceptor FGFRL1 (FGFR5) and the downstream transcription factor ELK3 were elevated in sensitive models. In summary, M6123 showed favorable anti-tumor activity in preclinical models of mesothelioma, in particular in combination with standard of care chemotherapy. Further preclinical testing is warranted to confirm a predictive biomarker signature for selection of mesothelioma patients that may benefit from addition of M6123.

Citation Format: Christina Esdar, Edith Ross, Michael Sanderson, Astrid Zimmermann. M6123, a selective FGFR1 antagonist, demonstrates anti-tumor activity as monotherapy and in combination with chemotherapy in mesothelioma models [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 558.