bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 10: Sclareol induces apoptosis and inhibits notch signaling in hamster oral carcinogenesis
Authors: Chinnaiyan Aiyavu , Nallu Anandhi , Kathiresan Suresh
Published: September 2020

The Notch signaling pathway is an evolutionarily conserved cell signaling pathway. It plays a central role in cell fate decisions and differentiation. The bioavailability of sclareol has been widely studied due to its anti-carcinogenic and antioxidant effects. However, chemo preventive effects of sclareol on notch signaling in 7, 12-dimethylbenz [a] anthracene (DMBA) induced hamster buccal pouch(HBP) carcinogenesis remain to be fully elucidated. In the present study, tumors were induced by applying 0.5% DMBA topically to HBP thrice a week for 14 weeks and sclareol was orally administered at a dose of 20mg/kg body weight on alternate days of DMBA painting. We analyzed expression of Notch signaling in DMBA induced oral squamous cell carcinoma (OSCC) in experimental oral carcinogenesis and inhibition of notch signaling by sclareol. This study thus observed up regulation of Notch1, Notch2, Jagged1, Hes1 and Hey1 in DMBA alone induced hamsters. Furthermore, oral administration of sclareol led to reduced Notch1, Notch2 activation and expression of Jagged-1 and its downstream targets of Hes-1 and Hey-1 in tumor bearing hamsters. In addition, sclareol treatment increased pro-apoptotic and decreased anti-apoptotic proteins survival indicating apoptosis through activation of caspase 3, and promoting cell death by dysregulation of cyclin D1 levels in tumor bearing hamsters. Immunohistochemical examination showed that Notch intracellular domain accumulates in the nucleus of cells in DMBA induced hamster buccal pouch carcinogenesis, and Jagged1 was found to be dysregulated in sclareol treated tumor animals. In conclusion, the results provide an important new insight of Notch signaling pathway for a potential therapeutic target for oral cancer.

Citation Format: Aiyavu Chinnaiyan, Anandhi Nallu, Suresh Kathiresan. Sclareol induces apoptosis and inhibits notch signaling in hamster oral carcinogenesis [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 10.
Abstract 101: Studies on the flavonoid metabolite 2,4,6-trihydroxybenzoic acid as a CDK inhibitor and anti-proliferative agent: Potential role in cancer prevention
Authors: Sankaranarayanan Ranjini , Valiveti Chaitanya K. , van Slambrouck Severine , Kesharwani Siddharth S. , Kumar D. Ramesh , Seefeldt Teresa , Tummala Hemachand , Gunaje Jayarama B.
Published: September 2020

Colorectal cancer (CRC) is the second highest cause of cancer deaths in the United States according to Center for Disease Control. Increasing evidences suggest that a diet rich in fruits and vegetables will reduce incidences of colorectal adenomas. We hypothesize that the natural compounds present in fruits and vegetables, along with their metabolites generated by the gut microbiota, could be responsible for cancer prevention by targeting the cell cycle proteins. Previous studies conducted in the laboratory have identified 2,4,6- Trihydroxybenzoic acid (2,4,6-THBA), one of the degradation products of flavonoids, as a potential chemo-preventive agent mediating its effect through inhibition of cyclin dependent kinases (CDKs). Transport of monocarboxylic acids like 2,4,6-THBA is mediated by the Solute Ligand Carrier (SLC) family of transporters; in particular SLC5A8 and SLC5A12 have been implicated as tumor suppressor proteins that are down-regulated/non-functional in various cancers. In this study, we investigated the ability of the monocarboxylic acid transporter SLC5A8 to transport 2,4,6-THBA into the mammalian cells. Our pilot studies show that the cells expressing SLC5A8 transporters have the capacity to transport 2,4,6-THBA leading to upregulation of p21 and p27 as measured by western blots and qPCR. This was associated with decreased cell number as well as decreased colony formation as measured through clonogenic assays. We suggest that chemo-preventive actions of dietary compounds containing flavonoids may occur through 2,4,6-THBA, contributing largely to the prevention of CRC.

Citation Format: Ranjini Sankaranarayanan, Chaitanya K. Valiveti, Severine van Slambrouck, Siddharth S. Kesharwani, D. Ramesh Kumar, Teresa Seefeldt, Hemachand Tummala, Jayarama B. Gunaje. Studies on the flavonoid metabolite 2,4,6-trihydroxybenzoic acid as a CDK inhibitor and anti-proliferative agent: Potential role in cancer prevention [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 101.
Abstract 1115: Patient-derived explant cultures (PDECs) as a model system for immuno-oncology studies
Authors: Turpin Rita , Munne Pauliina , Suleymanova Ilida , Mustjoki Satu , Pouwels Jeroen , Klefström Juha
Published: September 2020

Despite the great promise of immunotherapy, only relatively few patients show long-term complete remission. In addition, immunotherapy is not effective against every cancer type. Cancer types with low mutational burden such as breast cancer (BCa), for example, are thought to not elicit an immune reaction and are therefore considered non-immunogenic. A major hurdle in the advancement of immunotherapy is the lack of preclinical models that faithfully preserve the tumor microenvironment and recapitulate human disease. We have developed a method to grow 3D cultures of intact fragments of patient-derived tissue (Patient-Derived Explant Cultures; PDECs), which has been used to assess the efficacy of novel treatment regimens on real human tumors (Haikala et al., Nature Comm. 2019; Tervonen et al., Oncogene 2016). PDECs offer many advantages over other cancer model systems; PDECs preserve the human tumor microenvironment, reflect inter- and intra-patient tumor heterogeneity and results are obtained within one week. Up to 16 experimental samples can be obtained from one clinical sample, allowing the same ‘patient' to be experimentally treated with different drug regimens and/or measurement of more than one endpoint.To assess whether PDECs are also a suitable model for IO studies we performed immunoprofiling experiments using FACS, RT-PCR, cytokine profiling and immunofluorescence, showing that the immune-contexture, i.e. the number and activation status of different immune cell types, is similar in PDECs than in the primary tumor they were derived from. Subsequently, we addressed whether the resident immune cells in PDECs were functional. Preliminary data showed that direct T cell activation in PDECs led to apoptosis of cancer cells and invoked a complex immune response, as assessed using cytokine profiling and FACS. Treatment with the immune checkpoint inhibitor anti-PD-1 had more moderate effects. These data reflect the clinical reality where very few BCa patients respond to immune checkpoint monotherapy, but also show that T cells in BCa can be activated to kill the cancer cells, suggesting that with the right treatment strategies, BCa can be targeted with immunotherapy. All in all, our data show that the tumor's immunocontexture is conserved in PDECs and that resident immune cells in PDECs can be activated to attack cancer cells, and thus support the use of PDECs as an ex vivo model system to study immuno-oncology in real human cancers for the development of the immunotherapies of tomorrow.

Citation Format: Rita Turpin, Pauliina Munne, Ilida Suleymanova, Satu Mustjoki, Jeroen Pouwels, Juha Klefström. Patient-derived explant cultures (PDECs) as a model system for immuno-oncology studies [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 1115.
Abstract 1129: CADM1 is a novel serum marker for small cell lung cancer
Authors: Ito Takeshi , Funaki Toko , Tanaka Goh , Nagase Takahide , Murakami Yoshinori
Published: September 2020

Small cell lung cancer (SCLC) accounts for about 15% of lung cancer. Although SCLC often responds favorably to combined-modality chemotherapy at the initial treatment, resistant tumors develop rapidly, which makes SCLC one of the representative cancers refractory to any therapeutic approaches. Moreover, molecular targeting therapy has not been developed for SCLC so far. Therefore, novel approaches to the diagnosis and treatment of SCLC on the basis of molecular understanding would be prerequisite to control this refractory cancer. One of the most critical issues of SCLC is its early detection in the initial screening and after chemotherapy. For this purpose, pro-gastrin releasing peptide (ProGRP) and neuron specific enolase (NSE) are widely used for serum markers for detection of SCLC, although combination of ProGRP and NSE can detect at most 60% of SCLC. We have previously demonstrated that CADM1, a member of the immunoglobulin superfamily cell adhesion molecules, is highly expressed in around 75% of SCLC. In addition, SCLC expresses a splicing variant, CADM1v8/9, which is observed specifically in normal testis. Here, we report that the extracellular fragment of CADM1v8/9 is digested by ADM17 and released into cell medium or human serum. So, we generated specific monoclonal antibody against CADM1v8/9 using Cadm1-deficient mice and developed a serum diagnostic marker system for SCLC. Preliminary study shows that CADM1v8/9 detects 47% of SCLC with specificity of 92%, which is independent of and partly overlapped with the cases detected by ProGRP or NSE. CADM1v8/9 can detect 25% of patients with limited disease and 77% of patients with extensive disease of SCLC. Furthermore, the amount of CADM1v8/9 fragments well correlates with the disease activity of SCLC before and after chemotherapy. These findings indicate that detection of CADM1v8/9 in serum from patients is a novel and promising approach to detect and follow up SCLC patients. Since CADM1 is highly expressed in cell membrane of SCLC, CADM1 would also provide a promising target for the treatment of SCLC.

Citation Format: Takeshi Ito, Toko Funaki, Goh Tanaka, Takahide Nagase, Yoshinori Murakami. CADM1 is a novel serum marker for small cell lung 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 1129.
Abstract 1164: Targeted next generation sequencing microbiome assay design
Authors: Ewing Aren
Published: September 2020

Background: Targeted Next Generation Sequencing may provide a lower cost approach for characterizing the Microbiome. Sequencing of 16S rRNA is one approach to characterize microbial diversity. However, 16S sequencing alone is often insufficient to gain species level information. Here we describe the design capabilities of targeted sequencing panels comprising both 16S and species-specific primers using Ion AmpliSeqTM technology. These types assay can be used to understand the composition and diversity of the microbiomes at the species level for human health and other applications.

Method:

Our assays include the capability to customize primers to multiple hypervariable regions of the 16S region. However, 16S alone can still be insufficient in distinguishing highly homologous organisms. To address this we can design species-specific primers that provide high strain coverage and high specificity performance. We have developed and tested example assays that include primers for a variety of species identification. With this approach, we can generate reads from sequencing to report taxonomic classifications and relative abundance for organisms in the sample with high specificity and sensitivity.

Results: We designed many a multiplexed Ion AmpliSeqTM assays including 16S targets and species-specific markers targeting important microbial species that can be adapted to new species of interest. This approach is proven as example of our fixed panels including Ion AmpliSeq Microbiome Health research Panel, Pan Bacterial and Anti-Microbial Resistance (AMR) community panels using the Ion Genestudio S5™ system. With the data generated from the species-specific primers, we identified all the targeted species in the ATCC samples at the Species level. We also created mixed population pools using DNA from clonal isolates of different bacterial strains. We are able to identify most microbes at Genus level with 100% sensitivity using 16S alone. We improved the detection resolution to the Species level through the application of our species-specific primers.

Conclusions: Using the Ion AmpliSeq™ technology, we can create highly sensitive and specific assays for robust characterization of microbiota customized to an individual labs needs. This highly multiplexed PCR approach enables an efficient and affordable means for conducting extensive analyses of the microbiomes having applications in the study of the etiology of phenotypic variability.

For research use only. Not for use in diagnostic procedures.

Citation Format: Aren Ewing. Targeted next generation sequencing microbiome assay design [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 1164.
Abstract 1217A: Serine threonine kinase 11/liver kinase B1 mutation in sporadic scirrhous-type gastric cancer cells
Authors: Nishimura Sadaaki , Yashiro Masakazu , Sera Tomohiro , Yamamoto Yurie , Sugimoto Atsushi , Kushiyama Shuhei , Togano Shingo , Kuroda Kenji , Okuno Tomohisa , Ohira Masaichi
Published: September 2020

Background: Scirrhous-type gastric carcinoma (SGC), which is characterized by the rapid proliferation of cancer cells accompanied by extensive fibrosis, shows extremely poor survival. No driver gene responsible for the malignant potential of SGC has not been identified. Next-generation sequencing (NGS) technology has defined as the genomic landscape of various types of cancers, and has elucidated a number of novel driver mutations of gastric cancer. RHOA and CDH1 are characteristic mutations for SGC, but these mutations are not druggable. Novel molecular target therapy has been necessary for SGC based on its biological behavior.

Objective: We sought to identify the characteristic driver gene which is responsible for SGC.

Methods: DNA was isolated from six human SGC cell lines: OUCM-1, OCUM-2M, OCUM-8, OCUM-9, OCUM-12, and OCUM-14. The mutational status of 90 cancer-associated genes was examined by next-generation sequencing. The expression level of serine threonine kinase 11/liver kinase B1 (STK11/LKB1) in 708 gastric cancers was examined immunochemically, and the correlations between STK11/LKB1 expression and clinicopathologic features of gastric cancer were analyzed.

Results: The nonsynonymous mutations of STK11/LKB1 gene were found in three of the six SGC cell lines. Nonsense mutation of STK11/LKB1, which was associated with STK11/LKB1 loss (Y253*), was found in OCUM-12 cells, and missense mutation of STK11/LKB1 (F354L) was found in OCUM-2M cells and OCUM-14 cells. Rapamycin, an inhibitor of STK11/ AMP-activated protein kinase (AMPK)/mammalian target of rapamycin signaling (mTOR), showed inhibitory effects of SGC cells harboring STK11/LKB1 mutation. The low STK11/LKB1 expression group was significantly associated with SGC, high invasion depth, and nodal involvement, in compared to the high STK11/LKB1 expression group. The 5-year survival rate of patients with low STK11/LKB1 expression was significantly poorer compared to those with high STK11/LKB1 expression (p<0.001). A conditional multivariate analysis showed that STK11/LKB1 expression status was an independent prognostic factor.

Conclusion: SGC cells frequently showed the nonsynonymous mutations of STK11/LKB1. STK11/LKB1 mutation might be responsible for the malignant potential of SGC. STK11/AMPK/mTOR signaling might be one of the therapeutic targets for patients with SGC.1

Citation Format: Sadaaki Nishimura, Masakazu Yashiro, Tomohiro Sera, Yurie Yamamoto, Atsushi Sugimoto, Shuhei Kushiyama, Shingo Togano, Kenji Kuroda, Tomohisa Okuno, Masaichi Ohira. Serine threonine kinase 11/liver kinase B1 mutation in sporadic scirrhous-type gastric cancer cells [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 1217A.
Abstract 1218: Pimavanserin induces autophagy mediated apoptosis in pancreatic cancer and suppresses pancreatic tumor growth
Authors: Ramachandran Sharavan , Srivastava Sanjay K.
Published: September 2020

Pancreatic cancer patients have limited treatment options in spite of several advanced treatment strategies. Pancreatic tumors exhibit high basal autophagy compared to other cancers. Several studies including from our lab reported that enhanced autophagy can lead to apoptosis in cancer cells. In this study, we have demonstrated that pimavanserin (PVT) suppresses pancreatic tumor growth by inducing autophagy-mediated apoptosis. Our results indicated that PVT induced apoptosis and reduced the proliferation of pancreatic cancer cells with IC50 ranging between 3-9µM after 24, 48 and 72 hours of treatment. In addition, PVT inhibited the colony formation of pancreatic cancer cells. Treatment of pancreatic cancer cells with increasing concentrations of PVT resulted in a concentration-dependent increase in autophagy as evaluated by acridine orange assay by flow cytometry. PVT induced the expression of autophagy markers ULK1, FIP200, Atg101, Beclin-1, LC3B and p62 in a concentration-dependent manner in several pancreatic cancer cells. Apoptotic effects of PVT in pancreatic cancer cells was validated by increase in cleavage of caspase3 and PARP. Oral administration of PVT suppressed BxPC3 tumor xenografts by 50% in athymic nude mice. In another in vivo experiment, PVT treatment inhibited the growth of orthotopicaly implanted PANC1 tumors by 75%. Autophagy and apoptosis was confirmed in the tumors of PVT treated mice by immunohistochemistry and western blotting. Chronic administration of PVT did not exhibit any general signs of toxicity or behavioral side effects in mice. Moreover, long-term administration of PVT did not alter the clinical chemistry parameters like ALT, AST, total serum protein, calcium and albumin. Collectively, our results indicate that PVT mediated pancreatic tumor growth suppression was associated with induction of autophagy and apoptosis. Since PVT is already available in the clinic with an established safety profile, our results will accelerate its clinical development for pancreatic cancer therapy.

Citation Format: Sharavan Ramachandran, Sanjay K. Srivastava. Pimavanserin induces autophagy mediated apoptosis in pancreatic cancer and suppresses pancreatic tumor growth [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 1218.
Abstract 129: Apoptosis & anti-proliferative nature of Aescin on 7,12 dimethylbenz[a]anthracene (DMBA) induced hamster buccal pouch carcinogenesis via downregulating Notch signaling
Authors: Ramadoss Hemavardhini , Kathiresan Suresh , Gupta Sanjay
Published: September 2020

Worldwide, oral squamous cell carcinoma (OSCC) is the sixth most common cancer & ranked as second most common cancer in India. The most implicated etiologic factors in the development of oral cancer is the use of tobacco, alcohol & also HPV infection. Aescin, a pentacyclic triterpenoid saponin mixtures derived from Aesculus hippocastanum L (horse chestnut) that has been used as traditional herbal medicine, exists the pharmacodynamic properties, anti- edematous, anti-inflammatory & antitumor. The present study, Tumors were induced by applying 0.5% DMBA topically to hamster buccal pouch (HBP) thrice a week for 14 weeks & Aescin was orally administered at a various dose of 40 mg/kg body weight on alternate days of DMBA painting. We observed, reduced the tumor incidence, diminished lipid peroxidation, & elevation of antioxidants, liver marker enzymes by Aescin. Furthermore, aescin induced apoptosis in DMBA induced tumor bearing animals significantly inhibited cell to cell communication of Notch-1, Notch-2 & its ligand & Jagged-1 leads to inhibited expression of the Notch downstream signaling target Hes-1 & Hey-1 analyzed by immunohistochemical analysis. These results clearly suggest that Aescin prevents lipid peroxidation, protects the antioxidant defense system, prohibit the dysplasia & anti-carcinogenic potential. we concluded; the results provide an important new insight of Notch signaling pathway & aescin might be developed as a potential chemo preventive agent for oral cancer.

Key words: Oral cancer, aescin, antioxidant, apoptosis, chemopreventive, Notch signaling

Citation Format: Hemavardhini Ramadoss, Suresh Kathiresan, Sanjay Gupta. Apoptosis & anti-proliferative nature of Aescin on 7,12 dimethylbenz[a]anthracene (DMBA) induced hamster buccal pouch carcinogenesis via downregulating Notch signaling [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 129.
Abstract 130: CpG binding protein promotes cell proliferation through H3K4 methylation in ovarian cancer
Authors: Yang Liu-qing , Hu Han-yin , Han Yao , Zhu Heng-Yan , Wang Xiao-min , Ao Lei , Xu Ying , Huang Xuan , Che Xuan , Wang Li-Zhong , Jiang Ya-Bo , Xu Chun-wei , Cheng Shu-Qun , Heger Michal , Pan Wei-wei
Published: September 2020

E3 ubiquitin ligase CRL4 complex activation requires cullin neddylation. MLN4924, a NEDD8-activating enzyme (NAE) inhibitor, reportedly blocked cullin neddylation and inactivated cullin (CUL)-RING E3 ligases (CRLs). Studies have shown that MLN4924 inhibits cell proliferation and survival. We examined the oncostatic and cytotoxic properties of MLN4924 in ovarian cancer. MLN4924 blocked human cancer cell proliferation in nude mice by inhibiting CpG binding protein CFP1 expression. Loss of CFP1 reduced cell growth, promoted apoptosis, and increased senescence. CFP1-dependent H3K4 trimethylation is necessary to maintain the expression of target genes in ovarian cancer cells. We identified bone marrow stromal cell antigen 2 (BST2) and noggin (NOG) as direct targets of CFP1. Their expression was selectively induced by CFP1 deletion. Furthermore, deletion of NOG and overexpression of BST2 prevented the growth-inhibitory effect of CFP1 loss. Our study further demonstrated that CRL4 inactivation reduced CFP1 transcription and trimethylation on lysine 4 of histone H3, which in turn inhibited cell proliferation and induced apoptosis. Therefore, CRL4 constitutes a druggable target in ovarian cancer.

Citation Format: Liu-qing Yang, Han-yin Hu, Yao Han, Heng-Yan Zhu, Xiao-min Wang, Lei Ao, Ying Xu, Xuan Huang, Xuan Che, Li-Zhong Wang, Ya-Bo Jiang, Chun-wei Xu, Shu-Qun Cheng, Michal Heger, Wei-wei Pan. CpG binding protein promotes cell proliferation through H3K4 methylation in ovarian 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 130.
Abstract 1332: Cancer-Immu portal: An open resource for exploring immunotherapy-related multidimensional cancer genomic profiles
Authors: Yang Jing , Liu Qi , Shyr Yu
Published: September 2020

Cancer immunotherapy that blocks immune checkpoint molecules, such as cytotoxic T lymphocyte-associated antigen-4 (CTLA-4) and programmed cell death protein-1 /ligand-1 (PD-1/PD-L1), has revolutionized anticancer therapy. Since the first approval of ipilimumab (anti-CTLA-4) for the treatment of unresectable or metastatic melanoma, FDA has granted dozens of approval of immune checkpoint blockade (ICB) drugs for many cancers, including non-small cell lung cancer, urothelial cancer, renal cell carcinoma, Hodgkin's lymphoma, head and neck cancer, microsatellite instability or mismatch repair deficient cancers, gastric cancer, colorectal cancer, hepatocellular carcinoma and Merkel cell carcinoma. Although patients with advanced-stage cancers have opportunity to get durable benefits from ICB treatment, only a minority of them responds to ICB, which highlights the need of the predictive biomarkers for guiding the selection of patients. Meanwhile, driven by the advances of technologies, such as next-generation sequencing and single-cell technologies, the field of immunotherapy-related cancer genomic is evolving rapidly, providing unprecedented opportunities to draw a comprehensive picture about immuno-genomic connection. In recent years, large amount of immuno-genomic data were generated, however, most of them are scattered in literatures and are not readily accessible to the community. To provide easy access to those valuable immuno-genomic datasets, we developed Cancer-Immu (http://bioinfo.vanderbilt.edu/database/Cancer-Immu/), which collected 2799 samples from 13 cancer types with both ICB response outcome and genomic profiling by either bulk sequencing or single-cell technologies Cancer-Immu allows interactive exploration of associations between ICB responsiveness and a variety of known and novel genomic features (genetic, transcriptomics, immune cell, and single cell populations) across multiple cancer types. Additionally, Cancer-Immu enables users to analyse their own datasets independently or co-analyse with existing data to identify and validate signatures of interest. Cancer-Immu, provides a platform for immunotherapy response evaluations, reduces barriers between researchers and complex genomic data, and facilitates discoveries in cancer immunotherapy, such as guiding combination treatments, repositioning existing drugs, and even developing novel agents.

Citation Format: Jing Yang, Qi Liu, Yu Shyr. Cancer-Immu portal: An open resource for exploring immunotherapy-related multidimensional cancer genomic profiles [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 1332.
Abstract 1333: High-quality multi-omic analysis of FFPE samples
Authors: Lund Jim , Bailey Shannon , Ekram Muhammad , Shahbazian David , Memeo Lorenzo , Hofman Paul , Williams Richard , Gulcher Jeff
Published: September 2020

Next-generation sequencing analysis of formalin-fixed, paraffin-embedded (FFPE) samples has the potential to lead to major advances in cancer treatment and prevention. These samples present a great opportunity for research because they are associated with clinical records, and millions of samples exist that can be used for retrospective analyses. We previously reported high quality whole-genome sequencing (WGS) results from FFPE tissue with an average of 98% of the genome covered at 20X or greater depth for samples as old as 15 years. In this study, we show high-quality results from performing multi-omic analysis including RNA sequencing (RNA-seq), WGS, methylation array, and microRNA sequencing (miRNA-seq) from the same archival sample. This demonstrates that multiomic analysis of existing cancer samples is technically feasible and opens up multi-omic analysis of these archival FFPE tissues.

Using archival samples derived from breast, non small-cell lung, colorectal, and melanoma tumors, we extracted high-quality, high molecular weight DNA using the WuXi NextCODE SeqPlus method, and RNA was extracted using a rRNA depletion method. Using these extracts, we performed WGS, methylation chip array, RNA-seq, and miRNA-seq analyses. The resulting WGS data had high uniform coverage, and high-quality data was produced from the methylation chips. Results from the FFPE samples were compared to those found in the TCGA data. Analysis of mutation calls in these WGS samples revealed high concordance with those produced from the fresh-frozen whole-exome sequenced TCGA samples. Methylation patterns from our data clustered with samples of the same cancer type in the TCGA dataset. We also saw a similar clustering with the RNA-seq and miRNA-seq results when compared to the TCGA data. In addition, we found that RNA expression was correlated with promoter methylation, and gene expression changes affected by mutation and methylation were identified. In summary, we found an overall clustering of the FFPE samples with samples of the same cancer type and no systemic differences between fresh and FFPE samples were observed. These data demonstrate the feasibility of performing comprehensive, multi-omic profiling of archival FFPE tissues.

Citation Format: Jim Lund, Shannon Bailey, Muhammad Ekram, David Shahbazian, Lorenzo Memeo, Paul Hofman, Richard Williams, Jeff Gulcher. High-quality multi-omic analysis of FFPE samples [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 1333.
Abstract 134: Targeting NLMP prevents drug adaptive prostate cancer evolution
Authors: Xie Yingqiu , Fan Haiyan , Manarbek Limara , Nurkesh Ayan A. , Yang Qing , Maipas Aisulu , Chen Zhenbang
Published: September 2020

We recently reported that nuclear localized membrane proteins (NLMP) play essential roles in drug adaptive mediated cancer evolution. Nuclear receptor tyrosine kinases (nRTKs), one of NLMP family, are aberrantly elevated in many human cancers. For example, nMET promotes cancer evolution through stem cell mediated drug resistance and homeostasis of cell survival. However, MET inhibitor mediated adaptive resistance frequently occurs by which nMET induction and other signaling mechanisms are involved. We previously showed androgen deprivation therapy (ADT) can induce nMET accumulation in castration resistant prostate cancer (CRPC) patient specimens, while membrane MET is primarily elevated in naïve prostate cancer (PCa) tumors. In addition to androgen deprivation enhanced NLMP, DNA damage targeting chemotherapy can also induce adaptive escape for survival while nonstem cell-like nMET expressing cells may undergo clearance by cell death through cell cycle arrest induced by p21 and DNA damage response as we reported previously. Here we further applied carbon nanodots to examine the combination effect on CRPC cells survival to target NLMP. We found beet derived carbon nanodots can enter into nucleus and induce DNA damage in PC3 cells. The DNA damage is prevented in nucleolus region and opposed by BRCA1 in nucleus. Most importantly, carbon nanodots suppressed tumor growth of PC3 cells in xenograft models in vivo in a PARP-dependent manner. Finally, we found beet derived carbon nanodots exhibit stem cell marker, phosphatase-like nanozyme activity and promote phosphatase activity. Thus, potential stemness induced by carbon nanodots may interfere the efficiency of anti-cancer by DNA damage. Then we applied phosphatase inhibitor for further enhanced inhibition of cell growth by targeting PARP with AZD-2281 in combination of carbon nanodots and phosphatase inhibitor. Our findings reveal for the first time that targeting CRPC by carbon nanodots can be a novel avenue for inhibiting RTK/nRTK/nMET in nucleus of prostate cancer cells. Taken together, our data suggest green carbon nanozyme mediated combination therapy with RTK/MET/NLMP inhibitors would be an innovation in targeted therapy to prevent drug resistance.

Citation Format: Yingqiu Xie, Haiyan Fan, Limara Manarbek, Ayan A. Nurkesh, Qing Yang, Aisulu Maipas, Zhenbang Chen. Targeting NLMP prevents drug adaptive prostate cancer evolution [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 134.
Abstract 1348: Optimizing experimental design for high-parameter protein analysis using BD AbSeq technology
Authors: Narayan Punya , Song Hye-Won , Nakamoto Margaret , Walczak Elisabeth , Lazaruk Katherine , Mortimer Stefanie
Published: September 2020

High-throughput single cell RNA sequencing (RNA-seq) has recently emerged as a powerful tool for profiling complex cell populations. While traditional single cell RNA-seq captures information about transcript expression, recent technological advances using oligo-conjugated antibodies enable simultaneous detection of proteins alongside mRNA in high-throughput sequencing. This multiomic technology enables high parameter protein analysis that can simultaneously discriminate 100 protein markers. However, experiment workflow time and cost can escalate quickly with high plexy assays. To address these issues we investigated a number of methods to decrease cost and assay time while maintaining data quality using the BD® AbSeq on the BD Rhapsody™ Single-Cell Analysis sequencing system. To begin, we investigated the performance of 20 core proteins when used in a 20plex, 40plex, 60plex, 80plex, or 100plex in model cells. Results from 3 experiments showed that performance was maintained as plexy increased, however rigorous experimental approaches must be followed to minimize impact on specificity or sensitivity. After establishing performance of this 20plex we investigated pre-cocktailing of antibodies as a method to shorten the day-of-experiment workflow, and mixing of oligo-labeled and unlabeled antibodies to high-expressing proteins (“signal muting”) as a way to decrease sequencing costs. Results showed a decrease in specificity as soon as 24 hours after the cocktailing of antibodies and increasing non-specific binding with longer cocktail storage times. On the other hand, signal muting was effective at decreasing sequencing requirements by up to 70%, without impacting data for high expressors. Together these results can be used to aid in optimizing experimental design when working with high-plex AbSeq protein panels, to better harness the information gained from multiomic single cell sequencing data. For Research Use Only. Not for use in diagnostic or therapeutic procedures.BD, the BD Logo, and Rhapsody are trademarks of Becton, Dickinson and Company or its affiliates. © 2019 BD. All rights reserved.

Citation Format: Punya Narayan, Hye-Won Song, Margaret Nakamoto, Elisabeth Walczak, Katherine Lazaruk, Stefanie Mortimer. Optimizing experimental design for high-parameter protein analysis using BD AbSeq technology [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 1348.
Abstract 1349: Improved human exome sequencing workflow with the most complete coverage
Authors: Hong Manqing , Min Bosun , Roseman Nicole , Star Ekaterina , Rusch Timothy , Datta Krishnalekha , Groenewold Steve , Ren Longhui , Zhou Jinglie , Lai Kevin , Wang Xiaohui , Downey Nick , Giorda Kristina , Wang Alexandra , Wang Yu , Lewis Lynette A. , Lau Patrick J. , Henck Steven
Published: September 2020

Consisting of only ~2% of the human genome, the exome accounts for ~85% of genetic disorders. Efficient sequencing of the human exome with complete and high coverage depth at low cost is invaluable for furthering research in clinical applications. IDT's xGen Exome Panel has proven to be a high performing option. Here, we present the updated xGen Exome Research Panel v2.0 in direct comparison with two other leading commercial human exome panels, using workflows per manufacturer's specifications.

NA12878 genomic DNA libraries were pooled together for 8-plex captures for all three platforms and sequenced on the Illumina NextSeq 500. Equivalent number of reads per sample were analyzed against a universal human exome target space to compare across the different exome panels. IDT's Exome NGS solution provided significantly highest on-target percentage at >90% as well as the greatest depth of coverage at >96% bases covered at >20X and >98% bases covered at >10X. Importantly, IDT's platform also reported the most complete gene-level coverage, demonstrated by minimal exon drop-outs in difficult-to-target genes.

While 8-plex is the upper limit supported by other suppliers, IDT's platform supports 12-plex workflow. The higher multiplex in combination with high coverage and on-target performance enables IDT to present the lowest total sequencing cost per sample. Since IDT hybridization capture baits are individually synthesized and qualified with the same high standards as standalone oligonucleotide products, lot-to-lot variability is negligible. This presents researchers with an option they can rely on for long-term use and places the focus on the true variabilities of the sample. In conclusion, this study demonstrates xGen Exome Research Panel v2.0, when combined with IDT's DNA Library Prep Kit, provides researchers with a complete Exome NGS solution that is competitive both in performance and sequencing cost.

Citation Format: Manqing Hong, Bosun Min, Nicole Roseman, Ekaterina Star, Timothy Rusch, Krishnalekha Datta, Steve Groenewold, Longhui Ren, Jinglie Zhou, Kevin Lai, Xiaohui Wang, Nick Downey, Kristina Giorda, Alexandra Wang, Yu Wang, Lynette A. Lewis, Patrick J. Lau, Steven Henck. Improved human exome sequencing workflow with the most complete coverage [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 1349.
Abstract 1395: Hsa_circ_005379 competitively binds to miR-182-5p to mediate PTEN expression in oral squamous cell carcinoma
Authors: Shen Yuehong , Su Wen , Yang Hongyu
Published: September 2020

Background: Oral squamous cell carcinoma (OSCC) is an oral and maxillofacial malignancy with a high incidence worldwide. Accumulating evidence indicates that circular RNAs (circRNAs) play a vital role in modulating tumor development. However, the mechanism of circRNA action in human OSCC remains largely unknown.

Methods: By using high-throughput transcriptome sequencing technology, we conducted a comprehensive study of circRNAs in human OSCC. The effect of CircRNA hsa_circ_0005379 on OSCC tissues and cell lines were monitored by qRT-PCR, transwell assay and western blot analysis. Xenograft mouse models were used to assess tumor growth and animal survival.

Results: CircRNA hsa_circ_0005379 was found to express significantly lower in OSCC tissue compared to paired non-cancerous matched tissue and is associated with tumor size and differentiation. Overexpression of has_circ_0005379 effectively inhibits migration, invasion, and proliferation of OSCC cells in vitro, and suppresses OSCC growth in nude mice. Mechanistic studies revealed that hsa_circ_0005379 may be involved in the regulation of epidermal growth factor receptor (EGFR) pathway.

Conclusions: Our findings provide evidence that hsa_circ_0005379 exerts regulatory functions and may be a new therapeutic target for OSCC treatment.

Citation Format: Yuehong Shen, Wen Su, Hongyu Yang. Hsa_circ_005379 competitively binds to miR-182-5p to mediate PTEN expression in oral squamous cell carcinoma [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 1395.
Abstract 1401: PVT1 exon 9 transcript regulates claudin 4 expression and migration in triple negative breast cancer
Authors: Levine Fayola A. , Ogunwobi Olorunseun O.
Published: September 2020

Breast cancer (BC) is a heterogeneous disease that is classically driven by the estrogen receptor (ER), progesterone receptor (PR) and human epithelial growth factor receptor 2 (EGFR2/HER2) signaling pathways. Triple negative breast cancer (TNBC), is a lethal subtype of invasive BC tumors that are ER-, PR- and HER2-. A subtype of TNBC is claudin low (CL). Dysregulation of claudin proteins disrupts tight junctions, consequently inducing the epithelial-to-mesenchymal transition (EMT) in cancers. This leads to enhanced motility and metastasis. Patients with CL TNBC have worse prognosis than patients with other BC subtypes. PVT1 is a long noncoding RNA (lncRNA) transcribed from the 8q24 genomic locus that has been implicated in multiple cancers including BC. Amplification of the 8q24 gene locus is a common event in many malignant diseases and is associated with poor clinical outcomes. Although previous research has implicated PVT1 as an important player in BC, the underlying molecular mechanisms of PVT1 in CL TNBC was previously unknown. We assessed PVT1 expression in BC, and we observed that PVT1 exons 4A, 4B, and 9 are significantly upregulated in MDA MB 231 cells (claudin low) and significantly downregulated in MDA MB 468 cells (claudin high), in comparison to T47D (ER+). We have confirmed that claudin expression, specifically claudins 1, 3, 4 and 7, are significantly higher in MDA MB 468 cells and significantly lower in MDA MB 231 cells. Knockdown of PVT1 exon 9 expression in the MDA MB 231 cell line, led to a significant reduction in migration when compared to cells transfected with a control scramble siRNA, indicating that PVT1 exon 9 regulates migration in CL TNBC. Interestingly, we observed that claudin 4 expression, and not claudins 1, 3 and 7, was increased in cells where PVT1 exon 9 was knocked down when compared to the control cells. This indicates that PVT1 exon 9 regulates claudin 4 protein stability in CL TNBC. We also assessed the expression of EMT markers (vimentin, fibronection, and caveolin) in MDA MB 231 cells. We observed no changes in EMT markers when PVT1 exon 9 is knocked down; however, our data suggests that EMT markers are more highly expressed in MDA MB 231 cells in comparison to MDA MB 468 cells. Taken together, our data indicate that PVT1 exon 9 regulates claudin expression and migration in CL TNBC, and may have implications for clinical outcomes in TNBC.

Citation Format: Fayola A. Levine, Olorunseun O. Ogunwobi. PVT1 exon 9 transcript regulates claudin 4 expression and migration in triple negative 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 1401.
Abstract 1416: Long non-coding RNA GAN1 inhibits tumor progression by regulating the mir-26a/PTEN axis in lung cancer
Authors: Wang Rui-qi , Long Xiao-Ran , Zhang Mei-Yin , Chen Dong-Ni , Wen Zhe-Sheng , Mai Shi-Juan , Wang Hui-Yun
Published: September 2020

Background: Long non-coding RNA has been reported to be involved in many cancers. To explore the role of lncRNA in non-small-cell lung cancer (NSCLC), we detected lncRNA expression profile with a custom microarray and found that lnc-GAN1 was significantly downregulated in NSCLC. In this study, we aimed to explore the clinical significance, biological function and mechanism of lnc-GAN1 in NSCLC.

Methods: We firstly analyzed relationship between the lncGAN1 expression and clinical features and survival in NSCLC patients from two medical centers. We secondly examined the biological function of lncGAN1 in lung cancer cells with Cell viability, colony formation, migration, invasion, cell cycle and apoptosis assays. Then, we localized the distribution of lnc-GAN1 in lung cancer cells using RNA-FISH and analyzed the interaction between lnc-GAN1 and mir-26a-5p with Dual luciferase reporter and RNA immunoprecipitation (RIP) assay. Finally, the xenograft tumor model was employed to assess tumor suppression role of GAN1.

Results: lnc-GAN1 is notably downregulated in NSCLC tissues compared with normal lung tissues and associated with small tumor size, poor overall survival (OS) and disease-free survival in NSCLC patients. In vitro experiments, lnc-GAN1 expression suppresses proliferation, colony formation, cell cycle progression and apoptosis of lung cancer cells. lnc-GAN1 was mainly observed in cytoplasm of lung cancer cells with FISH and subcellular fraction analysis. RNA-seq analysis showed that the genes in cell cycle pathway were changed obviously when lnc-GAN1 was overexpressed. Mechanistically, lnc-GAN1 functions as a sponge of miR-26a-5p, which directly targets PTEN. Ectopically expressed lnc-GAN1 increased the mRNA and protein levels of PTEN and decreased miR-26a-5p level in lung cancer cells. Furthermore, mir-26a-5p mimics caused a decrease in both lnc-GAN1 and PTEN expressions while mir-26a-5p inhibitors led to an increase in both lnc-GAN1 and PTEN levels. Finally, In vivo experiments demonstrated that lnc-GAN1 could suppress tumor growth compared with control vector in nude mice.

Conclusions: our study discovered that lnc-GAN1 is significantly downregulated and associated with survival in NSCLC patients, and plays a tumor suppressor role by inhibiting miR-26a-5p and upregulating PTEN expression in lung cancer, which suggest that lnc-GAN1 is a potential prognostic biomarker and innovative therapeutic target in NSCLC.

Citation Format: Rui-qi Wang, Xiao-Ran Long, Mei-Yin Zhang, Dong-Ni Chen, Zhe-Sheng Wen, Shi-Juan Mai, Hui-Yun Wang. Long non-coding RNA GAN1 inhibits tumor progression by regulating the mir-26a/PTEN axis in lung 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 1416.
Abstract 1436: Determination of antibody's specificity towards phosphorylated protein targets with automated in-capillary enzyme treatment and immunoassay
Authors: Taketa Daryl A. , Grant Rainer , Aydogdu Tufan
Published: September 2020

Protein phosphorylation is a reversible reaction that is integral in numerous signaling cascades. Characterization of signaling cascades has been largely detected by immunoblotting with phospho-specific antibodies, which may or may not have enough specificity or affinity. Currently, a separate lysate without any phosphatase inhibitors or a separate blot is needed to determine an antibody's specificity. Here we describe a simple assay that leverages automation and quantitation with capillary electrophoresis-based immunoassay (CEIA) to assess the specificity of these antibodies with a single lysate preparation. In this study, three lysate models are used: K562 ± TNFα treatment, 50 ng/mL phorbol myristate acetate (PMA) differentiated THP-1 ± 1 μg/mL lipopolysaccharide (LPS) treatment, and cytotoxic T lymphocytes (CTL) ± 10 ng/mL PMA and 500 ng/mL ionomycin treatment. K562 cell lysates are commercially purchased whereas THP-1 lysates are generated in-house. For CTL cells, whole blood cells from a single donor are isolated and expanded with commercially available kits. Expanded CTL cells are then stimulated with PMA and ionomycin for 15 minutes. Untreated and treated lysate samples are separated and captured to the inner lumen of the capillary wall with UV activated crosslink chemistry. Cross-linked proteins are treated with lambda phosphatase for 1 hour followed by the immunoassay to investigate the specificity of antibodies against phosphorylated protein targets respective to each activated pathway using either chemiluminescent or fluorescent detection. Preliminary data suggest phospho-specific signal decreased >90% with no significant changes to the non-specific noise. The method described here eliminates the need for multiple lysate preparations or an additional blot to assess an antibody's specificity to a phosphorylated protein target.

Citation Format: Daryl A. Taketa, Rainer Grant, Tufan Aydogdu. Determination of antibody's specificity towards phosphorylated protein targets with automated in-capillary enzyme treatment and immunoassay [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 1436.