bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 6685: A retrospective observational study of telomerase peptide immunotherapy in heavily treated solid cancer patients
Authors: Choi Jonggwon
Published: September 2020

Background: Telomerase is an active enzyme that produces and maintains telomere which is located at the end of chromosomes. In general, telomere become shorter as the number of cells divide increases, leading to apoptosis. However, telomerase prolongs and maintains the length of the telomere so that tumor cells continue proliferation without cell death. When the telomerase is reduced, the telomere DNA is not produced and maintained and the chromosomes become shorter and shorter. Telomerase is not well observed in normal cells and known to act as a specific antigen by over-expression in various cencer cell types. The riavex(GV1001) which is 16 amino acid sequences from the telomere combines with HLA classI to induce an immune response through activates the CD4 T cell.

Methods: We analyzed 50 patients who were injected riavex. The riavex was provided through the application for emergency medication from the korea food and drug administration. Most patient who were given riavex failed several standard chemotherapy. The administration methods was injected riavex 0.2mili-liter in intradermal three times at first week and one time at 2weeks, 3weeks, 4 weeks, 6 weeks and then once per 28 days. A total of 12 doses were given to each patient. After the end of the administration, we evaluated anti-tumor response by RECIST 1.1 and quality of life by EORTC QLO-C30 and EQ-5D.

Results: Partial response was founded in one patient with renal cell carcinoma. The rest of the patients showed a stable or progress response. However, quality of life was significantly improved in 19 patient and fifteen of them have applied for re-treatment. Only three patients had a fever of more than 38 celsius degree and no significant side effects were observed in other patients

Conclusion:, Riavex as a anti-cancer vaccine is relatively safe to heavily treated solid cancer patient and is assessed to improve quality of life, although the treatment response is not promising.

Keywords: Telomerase, Riavex, Quality of life, Safety

Citation Format: Jonggwon Choi. A retrospective observational study of telomerase peptide immunotherapy in heavily treated solid cancer patients [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 6685.
Abstract 6686: SO-C101 displays strong anti-tumor effect in TC-1 and TRAMP-C2 tumor mice and in combination with PD-1 blockade prevents tumor development in a NK and CD8+ T cells dependent manner
Authors: Adkins Irena , Mikyskova Romana , Hradilova Nada , de Martynoff Guy , Bechard David , Moebius Ulrich , Reinis Milan , Spisek Radek
Published: September 2020

SO-C101 (RLI-15) is a superagonist fusion protein of interleukin (IL)-15 and the IL-15 receptor α (IL-15Rα) sushi+ domain designed to bypass the need of endogenous IL-15Rα, thereby leveraging the activity of IL-15 in vivo on target immune cells and reducing the toxicity of IL-15 as such. SO-C101 was previously shown to exhibit a potent anti-metastatic activity in Renca, B16F10 melanoma and delayed tumor growth in T cell-based mouse tumor models (CT26, MC38). Here we investigated the anti-tumor efficacy in predominantly natural killer (NK)-cell based mouse tumor models TC-1 and TRAMP-C2. We showed that SO-C101 monotherapy was effective in the treatment of established TC-1 tumors, which was dependent on the presence of both NK and CD8+ T cells, but not CD4+ T cells. In an early treatment setting SO-C101 significantly decreased the rate of tumor development also in dependence on NK and CD8+ T cells. SO-C101 effectively reduced tumor growth in TRAMP-C2 mice in early and advanced treatment settings. However, only in combination with anti-PD-1 antibody treatment the tumor development was prevented in majority of mice. This effect was durable, and the new tumor development was further significantly delayed after a tumor cell re-challenge, which suggests the involvement of memory T cells despite an important NK cell role in anti-tumor efficacy in these models. The efficacy of SO-C101 and anti-PD-1 treatment was not dependent on CD4+ T cells, but mainly on NK and CD8+ T cells. Interestingly, SO-C101 and anti-PD-1 treatment in double NK/CD8+ T cell-depleted mice decreased tumor growth which suggests an involvement of other immune cell populations in the anti-tumor efficacy. SO-C101 stimulated the proliferation and the cytotoxic activity of NK cells and memory CD8+ T cells without significant expansion of regulatory T cells. These data show the importance of various immune cell populations during SO-C101 monotherapy and the treatment in combination with anti-PD-1 antibodies, and set a base for further complex analysis of SO-C101 behavior. The therapeutic potential of SO-C101 is currently being tested in an ongoing Phase I clinical study in cancer patients.

Citation Format: Irena Adkins, Romana Mikyskova, Nada Hradilova, Guy de Martynoff, David Bechard, Ulrich Moebius, Milan Reinis, Radek Spisek. SO-C101 displays strong anti-tumor effect in TC-1 and TRAMP-C2 tumor mice and in combination with PD-1 blockade prevents tumor development in a NK and CD8+ T cells dependent manner [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 6686.
Abstract 669: Combined inhibition of AKT & TBK1 for the treatment of breast cancer
Authors: Habelhah Hasem , Zhnag Laiqun
Published: September 2020

Breast cancer (BC) is the most frequently diagnosed malignancy and the second leading cause of cancer mortality in Western women. In ~80% of BC cases, the PI3K-AKT pathway is aberrantly activated, due to the alterations in genes encoding the pathway components, such as Ras, Her2, PTEN, PIK3C and AKT. This pathway regulates multiple cellular processes to promote BC development, growth, metastasis, and drug resistance. Consequently, over 100 clinical trials are currently underway worldwide to evaluate the therapeutic efficacy of PI3K and AKT inhibitors in BC; however, initial data reported so far revealed that inhibition of this pathway is either not effective or often results in development of resistance and relapse of the disease. Thus, identification of additional targets and therapeutic combinations are urgently needed. We previously mapped TRAF2 phosphorylation sites (Ser-11 and Ser-55), identified PKC and TBK1 are the relevant kinases, and reported that TRAF2 phosphorylation enhances NF-κB activation to promote cancer cell survival under conditions of cellular stresses. Recently, we discovered that inhibition of AKT leads to increased phosphorylation of TRAF2 at Ser-11 by TBK1 in 4 out of 6 commonly used BC cell lines. TBK1 (aka T2K for TRAF2-associated kinase) and its close homologue IKKϵ are serine/threonine kinases overexpressed in ~70% of BC and play critical roles in BC cell survival. Interestingly, all 4 BC cell lines that exhibited enhanced TRAF2 phosphorylation were completely resistant to AKT inhibition-induced apoptosis in vitro, and combined inhibition of both AKT and TBK1/IKKϵ synergistically induced apoptosis in these BC lines. Importantly, combined inhibition of AKT and TBK1/IKKϵ also significantly suppresses xenograft BC tumor growth in vivo. Mechanistically, AKT did not directly inhibit TBK1, IKKϵ or TRAF2; it seems that an unknown kinase suppressed by AKT in cancer cells in normal culture conditions enhances TBK1-mediated TRAF2 Ser-11 phosphorylation in BC cells upon AKT inhibition. Nevertheless, our data suggest that inhibition of the PI3K-AKT pathway derepresses the pro-survival TBK1-TRAF2 pathway, which in turn confers resistance to PI3K-AKT inhibition in BC, and that combined inhibition of AKT and TBK1 effectively suppresses BC tumor growth. These findings also provide strong rationales for PDX and clinical investigation of combined AKT and TBK1 inhibition for the treatment of human BCs.

Citation Format: Hasem Habelhah, Laiqun Zhnag. Combined inhibition of AKT & TBK1 for the treatment of 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 669.
Abstract 671: mTORC1 suppression in Paneth cells prevents tumors in a mouse model of intestinal cancer
Authors: Parihar Manish , Dodds Sherry G. , Hasty Paul , Sharp Zelton Dave
Published: September 2020

The mechanistic (or mammalian) target of rapamycin, mTOR, is a highly conserved PI3K-related kinase that regulates cell growth, proliferation, survival, transcription, and protein synthesis. It forms two different complexes, mTOR complex-1 (mTORC1) and -2 (mTORC2). Rapamycin is an allosteric inhibitor specific to mTORC1 and extends life and health span with chronic use. Previous research from our lab shows that an enteric release formulation of rapamycin, eRapa, enhances the lifespan of mice mutated for adenomatous polyposis coli (Apc) tumor suppressor (ApcMin/+ mice), which normally develop intestinal cancer. These mice model familial adenomatous polyposis (FAP) in humans. eRapa restored a normal (and in 60% of the mice longer) life span in female ApcMin/+ mice. Mutations in Apc, a part of the Wnt/β-catenin pathway, accelerate the initiation of the adeno-carcinoma in FAP, resulting in numerous colorectal polyps at a young age, and if left untreated these polyps progress to colorectal cancer.eRapa treatment prevents polyposis in ApcMin/+ mice but the precise mechanism of action remains to be determined. We used a cross sectional and survival approach to test the preventive effects of eRapa and gain mechanistic insights. Four-week-old male and female animals were put on a diet containing either 42 ppm of eRapa or empty microcapsules. A subset of the animals was sacrificed to harvest tissue for analysis at 16 weeks of age and the rest were allowed to live out their lifespans.eRapa prevented polyposis in the small intestine of ApcMin/+ mice with only a few to no tumors in both males and females. In addition to adenomas in the intestine, ApcMin/+ mice also suffer from severe anemia. Hematocrits from the animals showed anemia in the control mice, however, eRapa treated animals did not have anemia. There was a reduction in phosphorylation of ribosomal protein S6 in the small intestine tissue, showing suppression of mTORC1 activity with eRapa. Histological analysis revealed that this suppression occurred in the Paneth cells of the small intestinal crypt. The Paneth cells, along with the stem cells at the base of the crypt form a niche and signaling between this niche maintains homeostasis in the crypt. Although the polyps are believed to originate from stem cells, our results suggest involvement of Paneth cells in tumor prevention perhaps by signaling changes in the niche. These are novel effects of rapamycin and help define its mechanisms of cancer prevention.

Citation Format: Manish Parihar, Sherry G. Dodds, Paul Hasty, Zelton Dave Sharp. mTORC1 suppression in Paneth cells prevents tumors in a mouse model of intestinal 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 671.
Abstract 685: Sortilin receptor-mediated novel cancer therapy: A targeted approach to inhibit vasculogenic mimicry in ovarian and breast cancers
Authors: Currie Jean-Christophe , Demeule Michel , Larocque Alain , Zgheib Alain , Béliveau Richard , Marsolais Christian , Annabi Borhane
Published: September 2020

Rational: Vasculogenic mimicry (VM) is defined as the formation of microvascular channels by aggressive, metastatic and genetically deregulated tumor cells. This microcirculation system, independent of endothelial cells, provides oxygen and nutrients to tumor cells. Such system contributes, in part, to current chemoresistance and facilitates tumor progression as well as dissemination of cancer metastases. VM is a process associated with aggressive ovarian cancer and triple-negative breast cancer (TNBC) and is shown to correlate with decreased overall cancer patient survival.

Procedures: Targeting VM in ovarian and TNBC tumors, in addition to targeting tumor cells, may thus help circumvent chemoresistance and contribute to more efficient cancer treatments. Sortilin receptor (SORT1) is essential for VM in ovarian and TNBC tumors and high expression of SORT1 in many types of cancers has been associated with their invasion and progression.

Results: SORT1 was detected in 3D-tubular structures of ES-2 ovarian cancer and MDA-MB-231 TNBC cells when grown on Matrigel. Peptide-drug conjugates targeting SORT1 significantly decreased the formation of new 3D-structures by 50% (IC50) at low nM concentrations (5-10 nM). In fact, the Doxorubicin-peptide conjugate (TH1904) abolished the formation of 3D-tubular structures of ovarian cancer cells in an in vitro model, whereas unconjugated Doxorubicin or liposomal Doxorubicin (up to 20 µM) had no effect on the formation of the VM structure. Moreover, a Docetaxel-peptide conjugate (TH1902) also showed very potent in vitro activity against the formation of VM in TNBC. IC50 values for VM 3D-tubular structures inhibition was about 30 pM for TH1902 compared to 0.5 nM for Docetaxel.

Conclusion: Our results provide insight into future potent ovarian and TNBC therapeutic treatments. Targeting this receptor's functions with peptide-drug conjugates may provide an efficient strategy to increase the binding/internalization of cancer drugs within tumor cells, thereby improving the efficacy of standard anticancer treatments. Our results indicate that peptide-drug conjugates targeting SORT1 strongly inhibit the formation of VM, a phenomenon associated with a more aggressive tumor phenotype and poor prognosis in patients with TNBC or ovarian cancer.

Citation Format: Jean-Christophe Currie, Michel Demeule, Alain Larocque, Alain Zgheib, Richard Béliveau, Christian Marsolais, Borhane Annabi. Sortilin receptor-mediated novel cancer therapy: A targeted approach to inhibit vasculogenic mimicry in ovarian and breast 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 685.
Abstract 689: Anti-tumor activity of Bifidobacterium secreting dual specific T cell redirecting antibody against EGFR/HER3-expressing cancer
Authors: Kobayashi Satoshi , Shioya Koichiro , Seki Yuji , Matsumura Tomio , Kanari Yasuyoshi , Shimatani Yuko , Nakazawa Hikaru , Umetsu Mitsuo , Kataoka Shiro , Nakamura Takaaki
Published: September 2020

Anti-cancer therapies targeting EGFR family, including monoclonal antibodies and kinase inhibitors, are the state of art for solid tumors such as colorectal and non-small cell lung cancers. T cell redirecting bispecific antibodies are a promising approach for cancer immune therapy, whereas their application is limited to hematological malignancy due to adverse events caused by the systemic exposure to highly immunologically active molecule.

To avoid the immunological adverse events, we have created a recombinant Bifidobacterium (APS002) that specifically colonizes in solid tumor and continuously secretes T cell redirecting antibody. The antibody was designed to form a diabody based on the sequence of dual specific antibody for EGFR/HER3 and CD3.

The diabody (termed DBERB1) comprises the equal amount of two polypeptides, anti-h CD3 (VL) - anti-EGFR/hHER3 (VH) and anti-hEGFR/hHER3 (VL) - anti-hCD3 (VH), respectively. DBERB1 bound to human EGFR and HER3, and human CD3. DBERB1 demonstrated potent cytotoxic activities against EGFR- and HER3-expressing human colon cancer HCT116 cells in the presence of human peripheral blood mononuclear cells (hPBMC) with EC50 values of 3 - 9 × 10−12 M. When APS002 was i.v. dosed to HCT116 tumor-bearing SCID mice inoculated with hPBMC, APS002 colonized only in the tumor and DBERB1 was detected in the tumors but not in the plasma. The growth of HCT116 tumors was significantly suppressed by APS002 but not by Bifidobacterium transfected with control vector.

In conclusion, our study in the mouse model indicates that APS002 is a novel and an extremely potent anti-cancer agent distributed only in the tumor. We are currently preparing for pre-clinical studies for the future clinical trials.

Citation Format: Satoshi Kobayashi, Koichiro Shioya, Yuji Seki, Tomio Matsumura, Yasuyoshi Kanari, Yuko Shimatani, Hikaru Nakazawa, Mitsuo Umetsu, Shiro Kataoka, Takaaki Nakamura. Anti-tumor activity of Bifidobacterium secreting dual specific T cell redirecting antibody against EGFR/HER3-expressing 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 689.
Abstract 701: Immunogenicity risk assessment and mitigation tools
Authors: Osmani Amin , Pattijn Sofie , Schockaert Jana , Mazy Aurélie , Ackaert Chloé
Published: September 2020

New immuno-oncology mAbs or agents with other structures have revolutionized treatment options for several malignancies in the past few years, and more are currently being evaluated in the clinic. The development of new therapeutics comes with a series of challenges and questions, of which one is the risk for unwanted immunogenicity which can lead to decreased efficacy and safety concerns. Today, both in silico and in vitro preclinical tools are available to identify early on therapeutic candidates with a high immunogenicity risk potential. Additionally, certain tools can be used to mitigate the immunogenicity potential, and thus improve and accelerate therapeutic drug development and reduce the number of clinical failures. Often used as a first step is an in silico T cell epitope prediction algorithm such as NetMHCIIpan which can be used to assess and compare the immunogenic potential of the lead candidates and guide de-immunization strategies. Further monitoring of the immunogenic risk can be performed using different in vitro assays: a peptide screen assay, to enable the exclusion of immunogenic peptides and the inclusion of low risk sequences; a dendritic cell activation assay to assess immunogenicity signals for the whole product; the MAPPs or MHC Associated Peptide Proteomics, assay to follow uptake, processing and presenting of biotherapeutics by dendritic cells and identify specific regions of concern, and; in vitro T cell proliferation and activation assays to determine and rank the immunogenic risk of the test proteins. The compilation of the different datasets and translation of the results into a comprehensive risk management plan, allows selection of the best candidates to move forward into humans, deimmunization of test candidates and identification and discontinuation of the high-risk candidates as early as possible.

Citation Format: Amin Osmani, Sofie Pattijn, Jana Schockaert, Aurélie Mazy, Chloé Ackaert. Immunogenicity risk assessment and mitigation tools [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 701.
Abstract 710: Exosomal DNA has the potential to detect circulating tumor DNA in patients with colorectal cancer
Authors: Kuriyama Sho , Yamada Takeshi , Koizumi Michihiro , Shinji Seiichi , Matsuda Akihisa , Ohta Ryo , Takahashi Goro , Hotta Masahiro , Hara Keisuke , Takeda Kohki , Ueda Koji , Yoshida Hiroshi
Published: September 2020

[Introduction] Exosomes are small vesicles of endosomal origin, which are released by all cell types, and are involved in physiological and pathological processes including cancer progression and metastasis. Exosomes comprise proteins, lipids, and nucleic acids such as RNA and DNA (exoDNA). Circulating exoDNAs harboring mutations are detected in patients with pancreatic or colorectal cancer. [Objective] To evaluate the clinical utility of detecting RAS mutations in exoDNAs of patients with colorectal cancers.

[Methods] We prospectively recruited 25 patients with RAS mutations in cells of their colorectal tissues. Circulating exoDNA was extracted from exosomes in 1 ml of preoperative plasma. Circulating cell-free DNA (ccfDNA) was concurrently extracted from 1 ml of plasma. We identified RAS mutations in exoDNAs and ccfDNAs using droplet digital PCR (ddPCR, Biorad).

[Results] We analyzed the exoDNAs of patients with right-sided (n = 13) and left-sided (n = 12) colon cancers (Stage II, [n = 9]; Stage III, [n = 9], Stage IV, [n = 7]). The median concentrations of exoDNA and ccfDNA were 52.3 ng/ml (32.1-223 ng/ml) and 132 ng/ml (41.3-4333 ng/ml). RAS mutations were detected in exoDNAs of 13 patients (52.0%) and in the ccfDNAs of 5 patients (20%) (P=0.03). The sensitivities of exoDNAs and ccfDNAs were equivalent (57.1%). However, for Stages II and III, the sensitivities of exoDNAs were higher compared with those of ccfDNAs. Notably, the sensitivity of exoDNA of Stage III was 77.8%. RAS mutations were undetectable in ccfDNAs of patients without detectable mutations in exoDNAs. The median mutation allele frequencies of exoDNA and ccfDNAs were 12.1% and 18.0%, respectively.

[Conclusion] Previously reported mutation-detection rates using Stages VI and III ccfDNAs are 90% and 15%, respectively. Here, the sensitivities using ccfDNAs for Stage II or III were low as well. Conversely, the sensitivities using exoDNAs were equivalently high in Stages III and Stage IV. These findings indicate that exoDNA has superior potential for detecting circulating tumor DNA compared with that of ccfDNA

Citation Format: Sho Kuriyama, Takeshi Yamada, Michihiro Koizumi, Seiichi Shinji, Akihisa Matsuda, Ryo Ohta, Goro Takahashi, Masahiro Hotta, Keisuke Hara, Kohki Takeda, Koji Ueda, Hiroshi Yoshida. Exosomal DNA has the potential to detect circulating tumor DNA in patients with colorectal 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 710.
Abstract 72: PARK2 enhances chemosensitivity of antimicrotubule drugs in breast cancer via promoting degradation of BCL-2
Authors: Chen Hengxing , Li Yun , Li Yu , Chen Zhen , Xie Limin , Li Wenjia , Zhu Yuanxin , Lu Daning , Hong Xue , Koeffler H. Phillip , Wu Wenjing , Hu Kaishun , Yin Dong
Published: September 2020

Chemotherapy is applied in over 70% of breast cancer patients. Antimicrotubule drugs and DNA-damaging drugs are the most popular medicine used for chemotherapy. However, it still lack of predictor for indicating which chemotherapy drug will benefit to patients. An urgent need is to develop biomarker used to determine which chemotherapy will work for individual patient. Antimicrotubule drugs such as docetaxel and vinorelbine are prescribed widely for breast cancer, nevertheless, about one-third of breast cancer patients suffer from the side effects of anti-microtubule drugs chemotherapy without benefit from it. Here, we report that PARK2 is a potential biomarker for chemosensitivity to antimicrotubule drugs in breast cancer. PARK2 gene encodes an E3 ubiquitin ligase. 34% of breast cancer patients exhibited PARK2 deletion. Interestingly, high PARK2 expression was positively correlated with favorable survival in breast cancer patients receiving chemotherapy, but not in those not receiving chemotherapy. Moreover, PARK2 overexpression specifically rendered cells more sensitive to antimicrotubule drugs, but not to DNA-damaging drugs. Depletion of PARK2 augmented resistance to antimicrotubule drugs. Mechanistically, PARK2 markedly activated the mitochondrial pathway of apoptosis after exposure to antimicrotubule drugs. This occurred through downregulating the antiapoptotic protein BCL-2. Notably, PARK2 physically interacted with BCL-2 and promoted ubiquitination of BCL-2 in an E3 ligase-dependent manner. Hence, PARK2 significantly enhanced the chemosensitivity of antimicrotubule drugs both in vitro and in vivo, while loss-of-function PARK2 mutants failed to enhance the sensitivity of antimicrotubule drugs. Taken together, we identified PARK2 as a novel mediator of antimicrotubule drug which provides a predictor for the chemosensitivity of antimicrotubule drugs in breast cancer.

Citation Format: Hengxing Chen, Yun Li, Yu Li, Zhen Chen, Limin Xie, Wenjia Li, Yuanxin Zhu, Daning Lu, Xue Hong, H. Phillip Koeffler, Wenjing Wu, Kaishun Hu, Dong Yin. PARK2 enhances chemosensitivity of antimicrotubule drugs in breast cancer via promoting degradation of BCL-2 [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 72.
Abstract 720: Analysis of circulating tumor DNA after neoadjuvant therapy to predict disease relapse in patients with stage II-III breast cancer
Authors: Lin Po-Han , Kuo Sung-Sheng , Huang Chiun-Sheng
Published: September 2020

The therapeutic efficacy of neoadjuvant chemotherapy for patients with breast cancer is usually assessed by the reduction of tumor size and lymph nodes. The pathologic complete response (pCR) is considered as a marker related to good prognosis. However, patients who can achieve pCR is a minor population, and pCR may be not a robust marker predicting prognosis in patients with ER-positive breast cancer. Additional markers allowing the assessment of prognosis is needed. Circulating tumor DNA (ctDNA) has been proved as a marker to detect disease progression in metastatic breast cancer and predict relapse in patients after resection of breast cancer. Therefore, we would like to assess the value of ctDNA in breast cancer patients receiving neoadjuvant therapy. The ctDNA was collected before and after completion of the neoadjuvant chemotherapy (Tend). The presence of ctDNA was detected by ultra-deep targeted next-generation sequencing. We enrolled 82 patients and 62 patients were found to have ctDNA as the biomarkers. The presence of ctDNA included nonsynonymous variants and copy number variations in TP53, PIK3CA, HER2, CDH1, PTEN, S100A, CCND1 and c-MYC. Among the 62 patients, there were 24 patients with hormone receptor (+)/Her2(-), 20 with Her2(+) and 18 with triple-negative breast cancer (TNBC). Pathologic complete response (pCR) occurred in 9 patients, partial response in 32 patients and stable/progression in 21 patients, according to the RECIST 1.1 criteria. Univariate analysis showed tumor reduction>50% (p=0.032), number of metastatic lymph node (p=0.039), and status of ctDNA at Tend (p<0.001) were significantly associated with disease-free survival (DFS). The 5-year DFS of patients with undetectable ctDNA at Tend (74.0%, 95% confidence interval (CI) range 98%-50%) was significantly superior to those with detected ctDNA (16.8%, 95% CI range 36.1%-0%). Multivariate analysis revealed that status of ctDNA at Tend was the only one independent factor predicting relapse (hazard ratio 7.74, 95% CI 2.81-21.35). Two patients had pCR and were found to have alterations of ctDNA at Tend; one with TNBC had distant metastases at 6 months after mastectomy and the other with Her2 (+) breast cancer had brain metastasis at the end of adjuvant trastuzumab treatment. Therefore, we concluded that the presence of ctDNA at the end of the neoadjuvant chemotherapy was a poor prognostic factor predicting relapse in patients with stage II-III breast cancer.

Citation Format: Po-Han Lin, Sung-Sheng Kuo, Chiun-Sheng Huang. Analysis of circulating tumor DNA after neoadjuvant therapy to predict disease relapse in patients with stage II-III 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 720.
Abstract 738: Utility of Assessing HER2 RNA expression for precision medicine
Authors: Shen Yifei , Pico Christian Cruz , Mohanty Vakul , Johnson Amber , Zeng Jia , Shaw Kenna Mills , Chen Ken , Meric-Bernstam Funda
Published: September 2020

Genomic analysis of tumors is rapidly becoming routine clinical practice. Most of the next generation sequencing (NGS)-based oncology assay focused on DNA alteration data for single nucleotide variants (SNVs), insertions and deletions (indels) and copy number variants (CNVs) of genes which have targeted drug. Although RNA sequencing technology is increasingly being explored, its clinical utility still needs to be clarified. As there is a growing number of HER2-targeted therapies, in this study, we dissected the association between HER2 amplification, RNA overexpression, HER2 protein expression by immunohistochemistry (IHC) and reverse phase proteomic arrays (RPPA) in 618 breast tumors in the TCGA. We conducted unsupervised clustering analysis based on HER2 RNA-seq gene expression and RPPA protein data to identify HER2 overexpression samples. As expected there was a strong correlation with ERBB2 copy number with HER2 RNA expression (R2 = 0.56, P <0.001), and HER2 protein expression by IHC (R2 = 0.25, P < 0.001). RNA expression also correlated with HER2 IHC (R2 = 0.40, P < 0.001) and HER2 protein expression by RPPA (R2 = 0.68, P < 0.001). We performed unsupervised clustering analysis based on RPPA protein data and gene expression data of the HER2 gene, all the breast cancer samples were classified as two distinct clusters. Among the two subgroups, one subgroup had significantly higher expression and protein level of HER2 gene. The clustering results of most breast tumors were consistent with the IHC score and copy number data. The gene expression cutoff value to distinguish the HER2 overexpression subgroup from the other was about 204 FPKM. In addition, we identified two HER2 overexpression tumors which were classified as HER2 negative based on IHC. Studies are planned to test transcriptomic based actionability in patient derived models.

Our results suggest that RNA-seq gene expression data may identify patients with HER2 overexpression that may be classified as HER2 negative based on IHC. Further studies are needed to determine the role of HER2 RNA overexpression as a predictive marker and to determine HER2 RNA expression across tumor types.

Citation Format: Yifei Shen, Christian Cruz Pico, Vakul Mohanty, Amber Johnson, Jia Zeng, Kenna Mills Shaw, Ken Chen, Funda Meric-Bernstam. Utility of Assessing HER2 RNA expression for precision medicine [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 738.
Abstract 745: Landscape of FGFRactivating aberrations in Chinese non-small cell lung cancer
Authors: Zhou Zhen , Liu Zichuan , Ou Qiuxiang , Wu Xue , Wang Xiaonan , Shao Yang , Liu Hongyan , Yang Yu
Published: September 2020

Background Dysfunction in fibroblast growth factor receptor (FGFR) signaling has been reported in non-small cell lung cancer (NSCLC), particularly in lung squamous cell carcinoma (LUSC). We hereby assessed the frequency of FGFR aberrations in a large Chinese NSCLC population.

Methods A total of 10,966 NSCLCs whose tumor specimen and/or circulating cell-free DNA (cfDNA) underwent hybridization capture-based next-generation sequencing (NGS) of 400+ cancer-related genes were retrospectively reviewed. Patients' clinical characteristics and treatment histories were further evaluated.

Results FGFR aberrations, including mutations, fusions, and gene amplifications, were detected in approximately 1.9% (210/10,966) of the population. FGFR abnormalities were more frequently observed in LUSCs (6.8%, 65/954) than lung adenocarcinomas (1.3%, 128/9596). Previously reported FGFR oncogenic mutations were identified in 19 patients (~0.17%), of which, 68% were male LUSC patients. Eleven out of the 19 patients (58%) had concurrent altered PI3K signaling, thus, highlighting an intriguing molecular characteristic and potential combination therapeutic strategy of dual-targeting FGFR and PI3K signaling in those patients. Furthermore, FGFR fusions retaining the intact kinase domain were identified in 12 patients (0.11%), including nine FGFR3-TACC3 cases, one FGFR2-INA fusion, one novel FGFR4-RAPGEFL1 rearrangement event, and one novel gene fusion between FGFR1 and the SLC20A2 5'-untranslated region, which may result in FGFR1 overexpression. Concomitant EGFR mutations or EGFR amplifications were observed in six patients, four of whom were previously treated with EGFR tyrosine kinase inhibitors, suggesting that FGFR fusions may act as acquired resistance to anti-EGFR therapies. In addition, FGFR amplification was detected in 24 patients, with FGFR1 amplification being the most common event. Notably, FGFR oncogenic mutations, fusions, and gene amplifications were almost always mutually exclusive events.

Conclusion We herein report an incidence of FGFR anomalies in a large Chinese NSCLC population, including mutations, gene amplifications, and previously characterized and novel FGFR fusions involving TACC3, INA, RAPGEFL1, and SLC20A2.

Keywords: FGFR, activating mutation, fusion, gene amplification, NSCLC, FGFR inhibitors

Citation Format: Zhen Zhou, Zichuan Liu, Qiuxiang Ou, Xue Wu, Xiaonan Wang, Yang Shao, Hongyan Liu, Yu Yang. Landscape of FGFRactivating aberrations in Chinese non-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 745.
Abstract 747: Pak1, TGFα, Ki 67 and survival in human gastric and gastroesophageal junction adenocarcinomas
Authors: Douglass Larry E. , Parritt Michael , Neltner Adam , Dooley Mariah , Robillard Michelle , Frydl Molly , Focke Leah , Damen Kyle , Deddens James A. , Carter Julia H.
Published: September 2020

Stomach cancer is the third most common cause of cancer mortality worldwide. Most are adenocarcinomas. Adenocarcinomas of the stomach fall into two obvious groups based on site of origin; those arising in the area of the gastroesophageal junction (GEJ) and those arising from a more distal location, which we term gastric in this study. Adenocarcinomas of the stomach fall into four obvious groups based on a combination of genomic, molecular biologic, clinical and histopathologic characteristics (Nagara A, Kikuchi O, Bass AJ, Cancer Discovery 2019; DOI: 10.1158/2159-8290.CD-19-0487). We are reporting herein a study of 99 patients with adenocarcinoma of the stomach. This study evaluates the location of the tumor, the histopathologic features of the tumor, the immunohistochemically determined nuclear and cytoplasmic expression of P21 activated kinase (Pak 1), Transforming Growth Factor α (TGFα), and Ki67, a marker of cell proliferation. This study correlates these findings with patient survival. The study reveals:

1. significantly lower survival in patients with diffuse type adenocarcinoma compared to intestinal type, in both GEJ and gastric locations.

2. both GEJ and gastric adenocarcinomas had a poor prognosis.

3. increased expression of both TGFα and Pak1 in GEJ adenocarcinomas.

4. Ki67 expression is significantly less in diffuse type than the intestinal type (p=0.01 for GEJ and 0.03 for gastric).

5. cytoplasmic Pak1 and cytoplasmic TGFα were highly positively correlated (p=0.0001).

6. Ki67 expression was significantly inversely correlated with both nuclear Pak1 (p=0.04) and nuclear TGFα (p=0.02).

7. significantly increased expression of nuclear Pak1 in gastric diffuse type compared with gastric intestinal (p=0.0002) and GEJ intestinal (p=0.0001).

These data suggest that Pak1 and TGFα might serve as diagnostic biomarkers of subtypes of adenocarcinomas of the stomach and gastroesophogeal junction.

Citation Format: Larry E. Douglass, Michael Parritt, Adam Neltner, Mariah Dooley, Michelle Robillard, Molly Frydl, Leah Focke, Kyle Damen, James A. Deddens, Julia H. Carter. Pak1, TGFα, Ki 67 and survival in human gastric and gastroesophageal junction adenocarcinomas [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 747.
Abstract 759: RNA Complete BCT: A novel blood collection tube targeting circulating RNA and extracellular vesicles
Authors: George Nicholas M. , Bartron Lisa , Binbuga Nursen , Salamifar Sean , Seong Eunju
Published: September 2020

Precision medicine, specifically in medical oncology, has been significantly enabled and the pace accelerated with the advent of liquid biopsy-based diagnostics. While liquid biopsy assays targeting circulating cell-free DNA (cfDNA) provide useful diagnostic information, such as mutational burden, they are limited to a static assessment of the disease state due to cfDNA derivation from dying cells. Assays exploiting circulating extracellular vesicles (EVs) and EV-associated cargo, such as cell-free RNA (cfRNA), provide a comprehensive and dynamic view of the disease as these analytes derive from both living and dying cells. A significant hurdle in making liquid biopsy testing with EVs and cfRNA commonplace is donor specimen integrity. Collected patient blood samples undergo time-dependent degradation leading to increases in disease non-specific EVs and cfRNA thereby compromising the accuracy and reproducibility of analyte measurement. To overcome this vulnerability we have developed the Streck RNA Complete BCT, a first of its kind blood collection tube intended for stabilizing draw-time concentrations of extracellular vesicles and cell-free RNA. Intended uses include direct analysis of EV populations and indirect analysis of cfRNA through RT-PCR or Next-generation Sequencing-based methods. Incorporation of this blood collection tube into the pre-analytical workflow will allow for delayed sample processing without effect on sample integrity or downstream analyte analysis.

Citation Format: Nicholas M. George, Lisa Bartron, Nursen Binbuga, Sean Salamifar, Eunju Seong. RNA Complete BCT: A novel blood collection tube targeting circulating RNA and extracellular vesicles [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 759.
Abstract 789: Development and validation of a capture based NGS assay that enables the detection of Epstein Barr virus from gastric cancer patients' tumor tissues
Authors: Hu Yajie , Yang Bo , Wang Lei , Liu Shiyi , Liang Lei , Wang Jie , Li Fugen , Sun Yu
Published: September 2020

Background: Gastric cancer patients with positive test for Epstein Barr virus (EBV) in their tumors have been reported to benefit significantly from anti-PD-1 therapy. Current clinical testing relies on fluorescent in situ hybridization of EBV-encoded small RNA (EBER). NGS assays have been increasingly used in the clinical settings to make therapeutic recommendations to cancer patients due to its versatility in detecting various types of genomic alterations. Detecting EBV by NGS is highly desired.

Method: DNA was extracted from the FFPE samples of 214 gastric cancer patients' tumors, and profiled by the comprehensive NGS assay. A classification algorithm was developed using 131 gastric cancer samples (EBV Pos, n = 31; EBV Neg, n = 100) with known EBV status derived from EBER. The algorithm and the predetermined cutoff was then applied to an independent sample set (EBV Pos, n = 30; EBV Neg, n = 53) to evaluate the test performance.

Results: In the training set, we achieved a sensitivity of 93.5% at a specificity of 100%. In the validation set, we achieved a sensitivity of 93.3% at a specificity of 100%. Using the same algorithm and cutoff, in the patients with tumor content above 20%, we achieve a sensitivity of 97.9% at a specificity of 100%.

Conclusion: We developed a method to detect EBV in gastric tumors' FFPE samples through a capture-based NGS assay. We also demonstrated strong concordance with an orthogonal assay (EBER) in detecting EBV.

Citation Format: Yajie Hu, Bo Yang, Lei Wang, Shiyi Liu, Lei Liang, Jie Wang, Fugen Li, Yu Sun. Development and validation of a capture based NGS assay that enables the detection of Epstein Barr virus from gastric cancer patients' tumor tissues [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 789.
Abstract 824: Uncommon EGFR mutations are associated with higher tumor mutation burden (TMB) in non-small cell lung cancer patients
Authors: Shen Xudong , Zhang Hushan , Huang Depei
Published: September 2020

Background: Epidermal growth factor receptor (EGFR) mutation is regarded as a predictor for poor clinical response to immunotherapy in non-small cell lung cancer (NSCLC), for which common EGFR mutations (the L858R point mutation and exon 19 deletions) generally exist lower tumor mutation burden (TMB) level. On the other side, uncommon EGFR mutations exist variable efficacy to tyrosine kinase inhibitors (TKIs) and the treatment for these patients is still controversial. Therefore, we conducted this study to investigate the correlation between uncommon EGFR mutations and TMB.

Methods: The tissue samples from a Chinese cohort of 2177 lung adenocarcinoma (LAC) and 500 lung squamous cell carcinoma (LSCC) patients were detected by a 381 genes NGS panel from 3D Medicines, and TMB values were obtained from the NGS sequencing data. We evaluated the correlation between common and uncommon mutations in EGFR and TMB in lung adenocarcinoma and squamous cell carcinoma, respectively.

Results: In lung adenocarcinoma, patients with uncommon EGFR mutations (n = 208) had a higher TMB level compared with common EGFR mutations (n = 1027) (medium TMB 6.14 Muts/Mb vs 4.84 Muts/Mb, P = 0.0016), but a lower TMB level than patients without EGFR mutations (n = 942) (medium TMB 6.14 Muts/Mb vs 7.26 Muts/Mb, P = 0.0176). In lung squamous cell carcinoma, the TMB level of uncommon EGFR mutations (n = 21) was significantly higher than common EGFR mutations (n = 20) (medium TMB 12.90 Muts/Mb vs 5.40 Muts/Mb, P < 0.0001). Meanwhile, the medium value of TMB in uncommon mutations group was slightly higher than non-mutations group (n = 459), however, there was no significant difference between the two groups (medium TMB 12.90 Muts/Mb vs 11.29 Muts/Mb, P = 0.2186).

Conclusions: Uncommon mutations in EGFR are associated with higher TMB level than common mutations in both lung adenocarcinoma and squamous cell carcinoma.

Citation Format: Xudong Shen, Hushan Zhang, Depei Huang. Uncommon EGFR mutations are associated with higher tumor mutation burden (TMB) in non-small cell lung cancer patients [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 824.
Abstract 832: Construction and optimization of gene expression signatures for prediction of survival in two-arm clinical trials
Authors: Theilhaber Joachim , Chiron Marielle , Dreymann Jennifer , Bergstrom Donald , Pollard Jack
Published: September 2020

Gene expression signatures for the prediction of differential survival of patients undergoing anti-cancer therapies are of great interest because they can be used to prospectively stratify patients entering new clinical trials, or to determine optimal treatment for patients in more routine clinical settings. Unlike prognostic signatures however, predictive signatures require training set data from clinical studies with at least two treatment arms, and the methodology for constructing and optimizing predictive signatures has been less prominently explored. Focusing on the “use case” of a two-arm clinical trial for metastatic colorectal cancer (CRC) patients treated with the anti-angiogenic molecule aflibercept, we present tools for the construction of signatures predictive of progression-free survival based on cross-validated multivariate Cox models. The work is organized around a specific approach called subtype correlation, which leverages a priori knowledge of molecular subtypes of tumors for a given indication. The tools and concepts presented here include the so-called differential log-hazard ratio, the survival scatter plot, the hazard ratio receiver operating characteristic, the area between curves and the patient selection matrix. In the CRC use case, the resulting signature stratifies the patient population into “sensitive” and “relatively-resistant” groups achieving a more than two-fold difference in the aflibercept-to-control hazard ratios across signature-defined patient groups. Through cross-validation and resampling the probability of generalization of the signature to similar CRC data sets is predicted to be high. The tools presented here should be of general use for building and using predictive multivariate signatures in oncology and in other therapeutic areas.

Citation Format: Joachim Theilhaber, Marielle Chiron, Jennifer Dreymann, Donald Bergstrom, Jack Pollard. Construction and optimization of gene expression signatures for prediction of survival in two-arm clinical trials [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 832.
Abstract 840: Pathway enrichment analysis of gene expression data from formalin-fixed paraffin embedded (FFPE) samples using the GeoMx™ DSP Platform
Authors: Hood Tressa R. , Reeves Jason , Norgaard Zach , Hoang Margaret , Warren Sarah , Piazza Erin , Boykin Rich , Beechem Joseph
Published: September 2020

The GeoMx Digital Spatial Profiling (DSP) Platform enables robust detection of high-plex protein and RNA expression from user-defined sections within FFPE samples. As the number of targets detected within such tissues increases, it becomes important to apply systems biology strategies in order to better interpret the complex biology of the tumor microenvironment.

In this study, we investigated the expression profiles of more than 1600 genes by utilizing more than 10,000 DSP-specific in situ hybridized (ISH) probes on FFPE samples. The bioinformatics tools we have development are enabling us to move beyond single-gene profiling to a better understanding of pathway-based expression. Our study includes colorectal cancer patient samples from which we have matching bulk RNA sequencing and NanoString analysis to compare. The panel of genes profiled have a strong focus around capturing biological signaling along canonical signaling pathways and cell-intrinsic signaling from immune cells and other cell types. We demonstrate the ability to leverage foundational pathway interrogation tools, including Reactome, with the data to capture spatially-resolved pathway interactions and signaling within FFPE tissues.

As we look towards the future of the GeoMx platform and high-plex RNA profiling of tissue samples, these experiments highlight not only the need but the capacity for this platform to derive deep understanding of the biology within and across a single slide of tissue. These experiments are being used to drive development of the software features within the GeoMx ecosystem, which will provide further support for pathway-level exploration of expression when working with highly multiplexed reagents in future platform offerings.

GeoMx™ DSP technology is for Research Use Only and not for use in diagnostic procedures.

Citation Format: Tressa R. Hood, Jason Reeves, Zach Norgaard, Margaret Hoang, Sarah Warren, Erin Piazza, Rich Boykin, Joseph Beechem. Pathway enrichment analysis of gene expression data from formalin-fixed paraffin embedded (FFPE) samples using the GeoMx™ DSP Platform [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 840.