bluuebunny/crossref_metadata_2025 huggingface dataset:
Mutational landscape of AKT1/2/3 in Chinese patients with solid tumors.
Authors: Kong Hui , Fang Weijia , Mou Haibo , Chen Feng Xiao , Liu Lingxiang , Wei Jia , Cui Shiyun , Wei Yongzhong , Li Juming , Du Juan , Ling Qi , Tang Xiaofeng , Qian Yigang , Yu Songfeng , Xue Liang , Wang Ting , Xiao Min , Pan Qiuyue , Zhang Shiyue , Zhang Lin
Published: May 2020

e15566

Background: As a central component of PI3K/AKT pathway, AKT serves as an attractive target of anti-cancer strategy with various AKT inhibitors, which show great promise in phase I/II clinical trials. This study aimed to investigate AKT1/2/3 status in different types of cancers by using next generation sequencing (NGS). Methods: Formalin-fixed, paraffin-embedded (FFPE) tumor samples were collected from 10,010 Chinese patients with solid tumors and subjected to next-generation sequencing (NGS)-based 450 gene panel testing carried out by a College of American Pathologists (CAP) accredited and Clinical Laboratory Improvement Amendments (CLIA) certified laboratory. Genomic alterations, tumor mutational burden (TMB) values, and microsatellite instability (MSI) status were assessed with a mean coverage of 1000X, including single base substitutions, short and long insertion/deletions, copy number variations, gene fusions, and rearrangements. Genomic data and immune checkpoint inhibitors (ICIs) treatment outcome of a cohort of 1610 patients with solid tumors were derived from cBioPortal (MSKCC, Nat Genet. 2019). Results: AKT1/2/3 were found to be mutually exclusive with each other and accounted for 3.4% in this cohort. The frequencies of AKT1/2/3 variations were 1.1%, 1.6%, and 0.8%, respectively. The most common co-altered genes associated with AKT1/2/3 variations were TP53 (69.4%), PIK3CA (19.3%), KRAS (19%), CCNE1 (18.4%), CDKN2A (16.6%), and 11q13 (6.5%). AKT1/2/3 variations were significantly associated with higher TMB, and independent of MSI status. Outcome data from the MSKCC cohort showed that patients with AKT1/2/3 variations had a remarkable clinical benefit to ICIs treatment compared to patients with wild-type AKT1/2/3 in overall survival (OS) (NA vs 18 months, p = 0.009). Furthermore, AKT1/2/3 variations were independent risk factors of OS (HR: 0.55, 95%CI: 0.34-0.87, p = 0.012). Conclusions: The prevalence of AKT1/2/3 somatic alterations across different types of solid tumors in China was 3.4%. AKT1/2/3 variations were associated with an increased TMB and favorable response to ICIs, suggesting that A KT1/2/3 variations may be biomarkers for guiding anti-AKT agents and ICI treatment.
Utilizing single-cell-subtype analysis via advanced microdissection methods and the impact on precision medicine.
Authors: Johann Donald Joseph , Laun Sarah , Stephens Owen , Weigman Robert , Shin Ikjae , Roberge Adam , Greisman Valerie , Steliga Matthew V , Muesse Jason , Peterson Erich , Emmert-Buck Michael , Tangrea Michael
Published: May 2020

e15571

Background: Improving the utilization of tumor tissue from diagnostic biopsies is an unmet medical need. This is especially relevant today in the rapidly evolving precision oncology field where tumor genotyping is essential for the indication of many advanced and targeted therapies. National Comprehensive Cancer Network (NCCN) guidelines now mandate molecular testing for clinically actionable targets in certain malignancies. Patients diagnosed with advanced non-small cell lung cancer (NSCLC) are commonly of an older age and have significant co-morbidities. This frequently causes clinical dilemmas regarding the ability to obtain adequate amounts of tissue for tumor genotyping. In these cases, the tumor tissue may have been obtained by an image-guided biopsy, and the diagnosis of NSCLC proper determined via cytology. In certain instances, adequate tissue for tumor genotyping and/or a more advanced mutational analysis to identify oncogenic drivers may not be available. Methods: Following pathology review, formalin fixed paraffin embedded (FFPE) specimens were subjected to advanced immuno-based laser capture microdissection (LCM), DNA was extracted and prepped for droplet digital PCR (ddPCR) and run with a series of positive and negative controls. Results: Utilizing advanced stage lung cancer as an example, an improved genotyping approach for solid tumors is possible. The strategy involves optimization of the microdissection process and analysis of a large number of identical target cells from FFPE specimens sharing similar characteristics, in other words, single-cell subtype analysis. The shared characteristics can include immunostaining status, cell phenotype, and/or spatial location within a histological section. Conclusions: Synergy between microdissection and ddPCR enhances the molecular analysis. We demonstrate a methodology that illustrates genotyping of a solid tumor from a small tissue biopsy sample in a time and cost-efficient manner, using immunostain targeting as an example.
Application of automated segmentation and classification of PD-L1 immunohistochemistry images in cancer treatment prediction.
Authors: Zhou Xinrui , Zhang Xiaochen , Wei Jinwang , Liu Jun , Dai Chun , Wang Guan , Xu Qiang
Published: May 2020

e15572

Background: Therapies targeting immune checkpoints, such as the programmed cell death-1 (PD-1) / programmed cell death ligand 1 (PD-L1) pathway, have become successful in treating several cancer types, particularly those with high PD-L1 expression. Patient response rates, however, are variable, demanding a more sensitive companion diagnostic test than the current method of manual scoring of PD-L1 immunohistochemistry images. The low predictive value of manual PD-L1 scoring is at least partially compounded by the pathologist-to-pathologist or hospital-to-hospital variation. To eliminate the variation caused by human factors, we developed an alternative PD-L1 scoring method based on automated image analysis and assessed its predictive and prognostic values. Methods: Archival or fresh tumor biopsies were analyzed for PD-L1 expression by immunohistochemistry. Digital images were automatically scored as PD-L1 positive or negative using a custom algorithm implemented in Python and Tensorflow, which uses a fine-tuned, ImageNet pre-trained, Inception-ResNet-V2 model as the binary classifier along with a modified U-net image segmentation model to determine the final prediction. Supervised machine learning was used to control for heterogeneity introduced by PD-L1 positive inflammatory cells in the tumor microenvironment. Samples from 256 patients were collected and used in algorithm training and verification by random assignment with an 8:2 split ratio. Results: In total, 10,000 images with balanced PD-L1 positive and negative distributions were obtained. A highly significant correlation of PD-L1 scores was found between pathologist-based consensus reading and automated analysis using our custom algorithm (R = 0.97, p < 0.0001). The automated analysis reached 0.94 sensitivity and 0.96 specificity. Additionally, it showed excellent reproducibility (R = 1.0, p < 0.0001) in independent trials executed on different workstations, which is far superior to the manual scoring performed by human examiners. Conclusions: Our automated PD-L1 evaluation algorithm significantly reduces scoring variability. It may help to identify cancer patients who can have optimal response to PD-1/PD-L1 related immune therapy and therefore facilitate patient stratification in clinical practice.
Enabling variant calling in challenging FFPE samples by coupling a novel library preparation chemistry with exome sequencing.
Authors: Min Bosun , Das Chakravarty Ushati , Hong Manqing , Star Ekaterina , Huang Hsiao-Yun , Barnes Tim , Chen Tzu-Chun , Lopez Ramses , Scott Karissa , Lewis Lynette A , Groenewold Steve , Ren Longhui , Zhou Jinglie , Lai Kevin , Sheu Jessica , Wang Xiaohui , Lau Patrick J , Henck Steven
Published: May 2020

e15584

Background: Comprehensive tumor profiling using NGS is fundamentally transforming oncology research. However, converting archival tissue samples into libraries is often challenging due to the low quantity and quality of DNA. Here we present accurate detection of variants in the human exome using the novel chemistry of the xGen Prism DNA library preparation kit, optimized for low-input and degraded samples, with xGen Research Exome v2.0 hybrid-capture enrichment. Methods: The IDT Exome v2 panel was used to carry out targeted sequencing of Prism DNA libraries generated from archival FFPE samples. The unique library preparation is enabled by an engineered mutant ligase and proprietary adapters that prevent chimeras and suppress dimer-formation, thereby maximizing the conversion of input DNA to sequencing libraries. Results: We achieved high yields of library (300-400 ng) from input amounts as low as 25 ng for severely damaged FFPE samples (DIN 1-3), > 90% on-target rates and uniform depth of coverage ( > 96% bases covered at > 20X and > 98% bases covered at > 10X) for FFPE samples across a wide range in quality. We also observed minimal exon drop-outs in difficult-to-target genes for severely damaged FFPE material. To validate the variant calling performance of the Prism-Exome workflow, we used the Horizon OncoSpan FFPE reference control which contains 1-92% AF SNVs and Indels and achieved > 98% sensitivity across ~250 SNVs and Indels. Conclusions: This study demonstrates that the xGen Exome Research v2, when combined with xGen Prism DNA library preparation, provides researchers with a complete human exome FFPE-sequencing solution with robust performance across FFPE samples of varying quality.
Treatment of breast, ovarian and lung cancer cells by inducing apoptosis with a deep eutectic solvent prepared from 2-deoxy-D-glucose and metformin: Cancer cell metabolism as a drug target.
Authors: Vuoti Sauli , Eemil Jaakko , Narasimha Kumar , Reinikainen Kai
Published: May 2020

e15599

Background: Targeting cancer cell metabolism has gained attention as a future strategy to fight cancer. A characteristic of tumor cells is the elevated aerobic glycolysis for energy production. It has been shown that 2-deoxy-D-glucose (2DG) inhibits glycolysis and induces apoptotic cell death in different tumor types. The anti-diabetic drug metformin has been used in combination to enhance the inhibitory effect. So far, the attempts to combine both compounds in a clinical setting have been limited by the requirement of concentrations higher than those accessible in blood plasma of human beings. Deep eutectic solvents (DES) are solvent mixtures prepared from hydrogen bond donors and acceptors, wherein pharmaceutically active compounds can also be one of the components. Besides having unique physicochemical properties, DESs have been reported to demonstrate or enhance anticancer properties. Methods: We developed a DES mixture from 2DG and MET using a method based in mechanical grinding. We investigated the anticancer activity of conventional and DES mixtures of MET and 2DG, and used the mixtures to inhibit the growth, migration and invasion of cancer cells, and induce cell cycle arrest in vitro. Results: MET and 2DG, alone and in combination, induced apoptosis in the H460, SKOV-3, MDA-MB-231 and HCC1806 (TNBC) cell lines. Induction of apoptosis was further quantified by measurement of the loss of mitochondrial membrane potential and cleavage of PARP. DES mixtures had the highest impact on cell viability, exceeding the effect of 2DG/MET as single agents or combinations at all clinically relevant concentrations. The DES mixture with the lowest concentration to induce apoptosis consisted of 100 µM 2DG and 200 µM MET. A conventional solution with similar concentrations showed no activity. Conclusions: We developed a DES from 2DG/MET, which significantly reduced the viability of several types of cancer cells, surpassing the effect of single components or mixtures. The DES does not necessitate the use of additional solvents and could be used to develop clinical applications for targeting cancer cell metabolism.
Preclinical evaluation of CLX-155, a novel prodrug of 5-FU for the treatment of cancer.
Authors: KB Sunil Kumar , Kandula Mahesh , P Sivanesan
Published: May 2020

e15614

Background: CLX-155 is a novel prodrug of 5-FU, developed by adding two acetyl groups (ester bond) and a caprylic acid moiety (amide bond) to 5'-DFCR ring structure. CLX-155 is designed to have a differentiated ADME profile, with improved safety and efficacy over capecitabine. Here, we present the preclinical data of CLX-155 in comparison with capecitabine. Methods: Solubility/stability of CLX-155 was studied in buffers, simulated gastrointestinal fluids and liver microsomes. In vitro metabolite profiling in hepatocytes was done following standard protocol. An oral (gavage) dose range finding (DRF) toxicity, comparative oral pharmacokinetic study and antitumor activity in HCT-116 human colon cancer cell xenograft model was conducted in mice. DRF study in mice evaluated the toxicity of CLX-155 when administered at once daily doses of 100 to 1000 mg/kg/day for 7-days. The oral pharmacokinetics CLX-155/metabolites (5'-DFCR, 5'-DFUR and 5-FU) was determined in mice at MTD dose of 500 mg/kg and for capecitabine at 1000 mg/kg. Antitumor activity of CLX-155 was evaluated in Foxn1 athymic mice at 125, 250 and 500 mg/kg/day and for capecitabine at 1000 mg/kg/day. Treatment was performed for three consecutive weeks (5 days on; 2 days off per week). Results: The results of in-vitro studies confirmed an acceptable profile for further development of CLX-155. Maximum tolerated dose of CLX-155 in mice was 500 mg/kg/day. The key toxicity findings were consistent with the mechanism of action and comparable with capecitabine. Oral PK study in mice showed a lower plasma Cmax for 5'-DFCR, 5'-DFUR and 5-FU. Plasma AUCs of the metabolites were close to or higher than that of capecitabine, indicating an extended absorption or altered metabolism in comparison with capecitabine. CLX-155 caused significant, tumor growth inhibition at all the dose levels tested. Complete tumor regression was seen in 2/10 animals at 500 mg/kg/day of CLX-155. CLX-155 was better tolerated in the mouse xenograft study, no mortality in CLX-155 versus 2/10 in capecitabine group. Conclusions: CLX-155 has an excellent safety and a differentiated ADME profile in relation to capecitabine. This translated into an improved in-vivo antitumor activity for CLX-155 in the HCT 116 xenograft model in relation to capecitabine. Overall data indicate that CLX-155 could offer significant improvements over the currently approved capecitabine in terms of dose size, frequency of administration, safety and interpatient variability in pharmacokinetics.
The multidirectional effects of some comorbid disorders on the malignant process and tumor-bearing organism in the experiment.
Authors: Zhukova Galina V. , Shikhlyarova Alla I. , Goncharova Anna S. , Tkachev Sergey Yu. , Protasova Tatiana P. , Triandafilidi Elena I. , Bykadorova Oksana V. , Shevchenko Alexey N. , Filatova Elena V. , Khomutenko Irina A. , Shashkina Larisa Yu. , Kit Oleg I.
Published: May 2020

e15616

Background: The question of the effects of comorbid diseases on oncogenesis has been little studied else. The increase in the frequency of dorsopathies and arthritis with age determines the important of the question about their influence on malignant process. The aim of the research was to study the features of the tumor growth and animal's condition under chronic neurogenic and inflammatory pain. Methods: In experiments on 54 white unbred male rats of 280-390 g, with transplantable Guerin's carcinoma (сG), two experimental models of chronic pain were used - unilateral sciatic nerve ligation (SNL) according to G.J. Bennet (neurogenic pain) and injections of formalin (Fm) into the ankle joint of the back paw (inflammatory pain). Formalin injection is known to be used to form both acute and chronic pain. The dynamics of tumors size, level of motor activity (MAL) in open field test, hematological parameters (by the blood analyzer «Exigo EOS vet», Sweden), adaptation status (AS) by Selye-Garkavi-Kvakina and also the lifespan of the animals (LS) were evaluated. Results: Unlike the unidirectional negative influence of chronic pain known in tumor-bearing animals in the cases of bilateral SNL, two opposite effects were observed with unilateral SNL and the formalin injection. Along with accelerated tumor growth in some animals (up to 62%), increase of LS of more than a third of the rats of the main groups by 3-30% in comparative with maximal LS in the control group was noted. In these cases, often the death of animals occurred with the larger tumors than in the control groups. In the cases of unilateral SNL, a relation between changes in the characteristics of the AS and the LS was noted. In the cases of Fm injections, animals with diverse LS differed in the features of the inflammatory reaction and the dynamics of the MAL. The prognostic value of shifts of the MAL in chronic inflammatory pain and tumor growth is assumed. Conclusions: A nonlinear relationship between the processes caused by chronic pain, oncogenesis, and individual characteristics of systemic regulation was shown. The question about the mechanisms of adaptation to the malignant process, promoting the body's viability in large tumors in conditions of chronic neurogenic and inflammatory pain is of interest.
Bstrongximab-MMAE, a novel antibody-drug-conjugate for metastatic gastric and pancreatic cancers.
Authors: Schopperle William Michael
Published: May 2020

e15620

Background: As of today, there are no current beneficial clinical therapeutic cancer treatments for advance metastatic gastric or pancreatic cancers. A new approach to finding effective and meaningful drugs to treat these cancers is based an emerging hypothesis that cancer is a reprogramming disease and its origin and development is due to retrograde-like malignant cells with primitive and embryonic characteristics which are responsible for the dissemination of the disease and the almost universal clinical response of tumor resistance when treated with standard current therapies. Methods: A pluripotent human germ cell tumor cell line, TERA-1, was used to isolate and purify embryonic antigens which where used to immunized mice and, with standard B-cell hybridoma technology, to generate monoclonal antibodies. Antibodies were screened by ELISA and SDS-PAGE Western blotting to identify antibodies specific to gastric and pancreatic cancers but not to normal tissues. A second assay was used to screen the potential of the antibodies to function as antibody-drug-conjugate therapeutics against cancer. Results: A lead therapeutic antibody, Bstrongomab, was identified in the antibody screens: it is positive for gastric and pancreatic cancers but does not react with normal tissues. Bstrongomab is an IgG1 monoclonal antibody which has high affinity and specificity to the embryonic target TRA-1-60. TRA-1-60 is a carbohydrate molecule which is highly expressed in normal embryonic stem cells and not expressed in normal tissues but is re-expressed in gastric and pancreatic cancers. Immunohistochemical tissue staining studies show TRA-1-60 is expressed in gastric and pancreatic cancers. Recent published scientific reports confirm this finding. A human/mouse therapeutic version of Bstrongomab was developed - Bstrongximab - and used to generate a novel therapeutic antibody-drug-conjugate with Bstongximab and the toxic payload MMAE (Monomethyl auristatin E). Pre-clinical i n-vitro and in-vivo studies show Bstrongximab-MMAE is a potent drug for gastric and pancreatic cancers. Conclusions: Bstrongximab is a novel IgG1 human/mouse chimeric therapeutic antibody that targets TRA-1-60, a novel and yet to be tried cancer target that is highly expressed in gastric and pancreatic cancers but not in normal tissues. Bstrongximab-MMAE has the potential to be a first-in-class cancer therapeutic that provides real and meaningful benefits to patients with metastatic gastric and pancreatic cancers.
A precision medicine tool “Knowledge Frames” to explain poor results of STING agonist trials.
Authors: Blunt Al , Messerschmidt Gerald L. , Gyorffy Steve
Published: May 2020

e15632

Background: STING activating cyclic-di-nucleotides result in the production of interferons, activating immune cells. We show that “Precision Medicine Knowledge Frames” (PMKF) are analyses inherently involving 2 processes: Frame 1 – Bench Science - biochemical functions of the experimental product, and Frame 2 - Human Organism Level - actions from product biochemical effects to tumor cell killing. Methods: STING agonists meet this PMK frame1 and activate STING (step 1) effectively. Activated STING binds TBK1 (step 2), then phosphorylates IRF3 (step 3), enters the nucleus (step 4), dimerizes (step 5) and binds specific regions of the DNA (step 6) for interferon transcription (step 7), which are secreted (step 8). Frame 2, the Human Organism Level - final common pathway requires many additional actions: Interferon must interact with immune cells (step 9) [within tumor or peripheral locations]. Very warm or hot tumors [contain functional immune cells] actively allow trafficking (homing) to the tumor (step 10) and infiltrating the tumor microenvironment (step 11). An activated immune cell can kill the tumor cell(s) (step 12). Cold tumors may not allow homing (step 10) to the tumor and/or infiltration (step 11) of the microenvironment. Results: PMKF modeling was applied to STING administration public data. Lack of efficacy was predicted if one of the critical pathway steps to tumor cell death are dysfunctional. Early steps (Frame 1) to interferon production and excretion into the environment occur within normal cells (antigen presenting cells) predictably. However, in the setting of malignancy, Frame 2 steps are often aberrant at the Organism Level. Cold tumors do not allow immune cell homing (step 10) and inhibit tumor infiltration (Step 11), tumor cell localization and killing of the tumor cell (step 12). Conclusions: STING Agonist are cutting edge therapies that perform PMKF Frame 1 well and increase interferon production. Application of the PMKF - Frame 2 demonstrate poor clinical activity may be explained by poor immune cell homing, infiltration and functional killing within the cold tumor microenvironment (dysfunctional steps 10, 11 and 12). Population selection may improve these results.
Preclinical evaluation of WXSH0011, a selective small molecule dual inhibitor of FGFR/c-Met.
Authors: Chen Zhengxia , Dai Meibi , Sun Deheng , Xia Yuanfeng , Zhang Yang , Chan Chi-Chung , Li Jian , Chen Shuhui
Published: May 2020

e15641

Background: FGFRs (fibroblast growth factor receptors) are a family of receptor tyrosine kinases. c-Met is a receptor tyrosine kinase with a high-affinity ligand, hepatocyte growth factor/scatter factor (HGF/SF). Aberrations in the FGFR pathway are associated with a variety of human cancers. c-Met and HGF have been implicated in carcinogenesis and metastatic tumor progression because of their ability to enhance angiogenesis, cancer cell proliferation, migration, and invasion. WXSH0011 is an orally bioavailable novel potent and selective FGFR/c-Met dual kinase inhibitor, which displayed significant antitumor activity in preclinical models of solid cancer with FGFRs/c-Met overexpression. Preclinical studies demonstrated that WXSH0011 has potential to be effective in solid cancer, such as HCC and Gastric. Methods: Kinase inhibiting activity of WXSH0011 was determined with FGFRs/ c-Met kinase assays. Cellular anti-proliferative activity was evaluated with FGFR overexpressed NCl-H1581, SNU-16, RT112/84, Hep3B, c-Met overexpressed MHCC97H, EBC-1 cell line and FGFR, c-Met both overexpressed PDC cell line (LI-03-0141 (HCC) and ST-02-0063 (Gastric) PDC). The antitumor activity of WXSH0011 was evaluated in vivo cell derived-xenograft (CDX) models of Gastric Cancer SNU-16 and HCC Hep3B. Results: WXSH0011 displayed potent kinase inhibiting activity for FGFR1/2/3/4 and c-Met/ with IC50 0.19 nM/0.21 nM/1.15 nM/1.49 nM /15.9 nM, respectively. WXSH0011 inhibited cell proliferation in FGFR overexpressed NCl-H1581, SNU-16, RT112/84, Hep3B with IC50 10 nM, 3 nM, 2 nM, 63 nM, c-Met overexpressed MHCC97H and EBC-1 cell line with IC50 0.832 µM, 0.52 µM, FGFR, c-Met dual overexpressed LI-03-0141 (HCC) and ST-02-0063 (Gastric) PDC with IC50 0.19 µM, 0.08 µM. Kinome panel screening revealed that WXSH0011 demonstrated good overall kinase selectivity. WXSH0011 showed antitumor efficacy in gastric cancer SNU-16 (TGI = 100% @5 mpk, BID), as well as in the liver cancer Hep3B model (TGI = 86.92% @20 mpk, QD). Conclusions: We have identified a novel selective and potent dual FGFR/c-Met inhibitor WXSH0011. Preclinical studies shows antitumor efficacy of WXSH0011 in gastric and liver cancer models. It is currently at IND submission stage.
Delivery of all-trans-retinoic-acid (ATRA) in liposomes modulated MDSCs and T-cell activities in the tumor microenvironment.
Authors: Xu Yuhong , Zheng Anjie , Jin Shanshan , Chen Xiaolong
Published: May 2020

e15644

Background: All-Trans-Retinoid-Acid (ATRA) is a naturally occurring vitamin A metabolite that participates in many biological processes. Beside its highly potent effect of promoting terminal differentiation of acute promyelocytic leukemia blasts into mature granulocytes, there have been many other studies suggesting its activity on the myeloid derived suppressor cells (MDSCs) and tumor specific CD8+ T cells in animal models as well as using clinical samples. But the use of ATRA as an immune-oncological agent in solid tumor therapy has been limited by the very poor solubility of the compound, its fast metabolism, and very limited exposure achieved after oral administration. Methods: We prepared a new dosage form by encapsulating ATRA inside PEGylated liposomes. The liposomes were shown to accumulate inside solid tumor tissues and deliver more ATRA with longer duration. Results: The effect and dose response of the liposomal ATRA on CT26 murine tumor growth were examined, as well as specific molecular signatures concerning tumor infiltrating myeloid cells. Notably, there was significant higher expression of CD86 and lower expression of PD-L1. These myeloid cells had very low inhibitory effect on ex vivo activated T cells, while on the other hand could promote specific antigen presentation to amplify CD8+ T cells. Furthermore, the liposomal ATRA was also shown to synergize with anti-PD-1 treatment to result in more CD8 T cell distribution in the tumor tissues. Conclusions: These data may suggest an exciting opportunity for targeting MDSCs using liposomal ATRA for combination with T cell based therapeutics in cancer immunotherapy.
Starting dose selection and dose escalation for oncology small molecule first-in-patient trials: Learnings from a survey of approved drugs.
Authors: Mittapalli Rajendar K , Yin Donghua , Beaupre Darrin M. , Palaparthy Rameshraja
Published: May 2020

e15648

Background: The ideal starting dose (SD) for an oncology first-in-patient (FIP) trial should be low enough to be safe but not too far removed from therapeutically relevant doses. A low SD combined with small dose increments could lead to a lengthy dose escalation (DE) and could expose patients unnecessarily to sub-therapeutic dosing. Over the past decade, the SD selection for oncology FIP trials was predominantly based on ICH S9 Guidance. This work attempts to assess the performance of current approaches in SD selection and DE methods for small molecule oncology drugs (SMOD), with an aim to identify potential opportunities for more efficient FIP DE methods and to minimize patients receiving sub-therapeutic dosing. Methods: A systematic review of the FIP trials of USFDA approved SMODs from 2010 to early 2019 was performed. The data sources included the FDA “USPI”, relevant “Summary basis of approval” documents, and published articles. The review focused on FIP trial data including the SD, DE design, the number of cohorts to the maximum tolerated dose (MTD) or the recommended phase 2 dose (RP2D), and the number of subjects in each cohort. These data were analyzed to evaluate the efficiency and appropriateness of current approaches for FIP SD selection and DE. Results: Of 53 SMODs approved between 2010 and early 2019, ~ 65% were kinase inhibitors and ~74% were approved for solid tumor indications. All SMODs appeared to follow ICH S9 Guidance for SD selection and none of SMODs had more than doubling for dose increments in the escalation. The median MTD to SD ratio was 8 (1 to 125). A majority (57%) of the trials used a 3+3 design for DE and had a median of 4 cohorts (0 to 11) to reach MTD or RP2D from the SD. About 30% of the FIP trials had ≥ 6 DE to reach the MTD or RP2D, and in this subset, greater than 55% of the trial participants received subtherapeutic dosing. Conclusions: The ICH S9 Guidance-based SD and the DE methods for SMODs have generally performed well in most cases; the SD was well tolerated and the MTD or RP2D were achieved with reasonable efficiency. However, for a portion of SMODs the SD appeared to be too low or the DE was too conservative, suggesting opportunities for improvement to minimize the number of patients dosed at sub-therapeutic doses.
FIH phase I dose escalation study of FN1501, an investigational FLT-3 inhibitor with multiple targets in patients with relapsed or refractory solid tumors and acute myeloid leukemia.
Authors: Richardson Gary Edward , Vaishampayan Ulka N. , Bozon Viviana , Hui Ai-Min , Williamson Stephen K.
Published: May 2020

e15656

Background: FN1501 inhibits various tyrosine kinases as CDK4/6, KIT, PDGFR, ALK and RET proteins, particularly potent on FLT3 and EGFR2. A Ph1 FIH trial for patients (pts) with solid tumors and Acute Myeloid Leukemia (AML) is on-going1. Preclinical data showed that FN1501 inhibits the phosphorylation of FLT3 and its downstream kinase STAT5 in human acute leukemia cell lines, arrests the cell cycle inducing apoptosis and inhibits growth and proliferation of leukemia cells. It has anti-proliferation activity against other leukemia cell lines bearing FLT3 mutations, and lymphoma cell lines2, 3. Methods: 26 pts with advanced solid tumors or AML enrolled in the escalation phase and received IV FN1501 on days 1, 3, 5, 8, 10 and 12 on 21-day cycles. Primary objectives are safety and MTD, secondary objectives include preliminary activity, PK and PD. Plasma PK were assessed at different timepoints pre and post dose in C1 and C2. Results: As of 6FEB20, 26 pts have been treated in 7 ascending doses of 2.5mg, 5mg, 10mg, 15mg, 22.5mg, 30mg and 40mg. A 54 mg dose cohort is on-going. No DLTs, no SAEs or deaths associated to FN1501 have been reported. 12 pts (46%) had one grade 3 or higher TEAE and 7 pts (27%) had dose interruptions due to a TEAE. Administration of FN1501 to pts with metastatic solid tumors has resulted in anti-tumor activity. 9 pts had durable stable disease across 4 doses in renal, endometrial, ovarian, gastric, appendix and thymic malignancies. One pt with serous endometrial carcinoma achieved a cPR after 2 cycles at 40mg with a 47% tumor size reduction (target lesions). As of 26Oct19 preliminary PK data showed a t1/2 of approximately 12.7-19.0 hours post-dose. Mean Cmax and AUC increased proportionally with dose and Clearance is consistent among all doses. Conclusions: This on-going Ph1trial of FN1501 is providing evidence of dose or exposure effects as a single agent in patients with solid tumors. Since FN1501 targets multiple kinases on addition to FLT3, antitumor activity beyond AML is also being observed, suggesting that the potent inhibitory effects of other tyrosine kinases, including EGFR2 may be playing a role in the regulation of cellular functions, cell growth, differentiation and angiogenesis effects. FN1501 has been well tolerated and AEs are manageable. Genomic alterations investigations are underway to identify candidate biomarkers useful for predicting sensitivity to the multiple FN1501 tyrosine kinases. Further development of FN1501 is warranted. Clinical trial information: NCT03690154.
An integrative molecular framework to predict homologous recombination deficiency.
Authors: Bell Joshua SK , Venkat Aarti , Parsons Jerod , Igartua Catherine , Leibowitz Benjamin D. , Tell Robert , White Kevin
Published: May 2020

e15664

Background: Homologous recombination deficiency (HRD) is the primary biomarker for sensitivity to PARP inhibitors, but identifying the genetic and transcriptomic characteristics that fully capture all HRD patients has remained difficult. For example, DNA-based approaches are limited to patients with pathogenic mutations and loss of heterozygosity (LOH) events, and can fail to properly classify patients with variants of unknown significance. To capture more dynamic cellular processes that arise immediately upon induction of HRD through silencing or loss of BRCA 1/2, a more integrated approach that includes both RNA and DNA based models is necessary. Methods: Using DNA sequencing we developed a genome-wide LOH score that combines pathogenic mutation status and LOH at the BRCA1/2 loci, and the proportion of bases sequenced in the Tempus xT panel that undergo LOH. We also developed three independent RNA-based models to predict BRCA deficiency: 1) An elastic net transcriptome model to predict DNA-based HRD scores derived from exome and SNP array data for each tumor type represented in TCGA; 2) A logistic model to detect BRCA1 promoter hypermethylation from the transcriptome in TCGA data; 3) A model that leveraged the mSigDB annotated gene sets to conduct single sample gene set enrichment analysis (ssGSEA) on Tempus-sequenced patients, selecting over a hundred gene sets that were predictive of BRCA-deficiency. These 4 features were combined to develop a stacked, linear-regression model to distinguish BRCA-intact from BRCA-deficient patients. Results: We found that the genome-wide LOH score alone is predictive of BRCA deficiency. However, our integrated model was highly accurate at distinguishing between BRCA-intact and BRCA-deficient patients and outperformed any single RNA- or DNA-based model. Using this model, we identified many patients that are likely to respond to PARP inhibitors that would have been overlooked using RNA or DNA-based inferences alone. Conclusions: Our approach highlights the strength of integrating diverse molecular features to refine diagnosis and enable oncologists to deliver the most effective therapies to patients.
The landscape of muti-PIK3CA variations of 10,000 Chinese solid-tumor patients.
Authors: Gu Weiguang , Zhou Chengzhi , Shen Zhuojian , Huang Jian , Qiao Chang , Hu Jinwei , Wang Weifeng , Yao Ming , Wang Kai
Published: May 2020

e15670

Background: PI3K/mTOR signaling pathway plays a central role in cancer biology. Our study aimed to explore the characteristics of multiple PIK3CA variations in the Chinese patient with solid tumors. Methods: Formalin fixed, paraffin embedded (FFPE) tumor samples and matched peripheral blood from 10,194 Chinese solid tumor patients were collected for next-generation sequencing based 450 genes panel assay. The testing was carried out by OrigiMed, a College of American Pathologists (CAP) accredited and Clinical Laboratory Improvement Amendments (CLIA) certified laboratory, Shanghai, China. Genomic alterations including SNV, short and long Indel, CNV, Fusion/Rearrangement were assessed. Microsatellite stable (MSS) status and TMB (tumor mutational burden) were also acquired by an NGS algorithm. Results: A total of 672 (6%) patients were identified harboring PIK3CA mutations, 93 (13.8%) of them had multiple PIK3CA mutations. Patients with multiple PIK3CA mutations included 51 females and 42 males with a mean age of 56 years old. Tumors with multiple PIK3CA mutations were composed of stage I (N = 14), II (N = 22), III (N = 18), IV (N = 25) and 14 without staging information. Cervical, breast, gastric and colorectal cancers were top ranked multiple-PIK3CA-mutant tumors (21%, 17%, 15%, 12% and 6%, respectively). TMB-H (≥10 mut/Mb) was significantly higher in multiple-PIK3CA-mutant tumors than that in single-PIK3CA-mutant tumors (60% vs 32%, P < 0.001). The MSS status was similar between multiple- and single-PIK3CA-mutant tumors (14% vs 11%). The most common PIK3CA alterations in both multiple- and single-PIK3CA-mutant tumors were E545 (36% vs 28%), H1047 (19% vs 24%) and E542 (16% vs 13%). Noticeably, the frequency of R88 (16% vs 3%, P < 0.0001), E726 (10% vs 0.8%, P < 0.0001), E453 (10% vs 1%, P < 0.0001), and M1043 (9% vs 0.8%, P < 0.0001) mutations were significantly higher in multiple-PIK3CA-mutant tumors than that in single-PIK3CA-mutant tumors. The top 3 most frequent PIK3CA dual mutation combinations were E545K+E726K, H1047R+E726K and E545K+R88Q. Among the co-mutated genes, copy numbers of ERBB2 were less altered in multiple-PIK3CA-mutant tumors than single-PIK3CA-mutant tumors (1% vs 6%, p < 0.05). Conclusions: This study, for the first time, revealed that approximately 13% PIK3CA positive Chinese solid tumor pts harboring multiple PIK3CA mutations. Several novel dual-PIK3CA-mutations were detected and multiple-PIK3CA-mutant pts more likely had high TMB, which may guide potential immunotherapy or PI3K-targeted therapy for multiple PIK3CA Chinese solid tumor patients.
A whole transcriptome sequencing (WTS)-based cMet dysregulation biomarker assay with correlates to cMet DNA mutations and cMet protein expression.
Authors: Zhang Xiaoling , Stafford Phillip , Baker Brian , Kimbrough Jeffery , Benedetti Fabio M.
Published: May 2020

e15676

Background: Selective cMet kinase inhibitors (cMet-i) have demonstrated promising clinical activity as single-agents in non-small cell lung cancer (NSCLC) with cMet exon-14 skip mutations (MET∆14). APL-101 (PLB-1001) is a selective cMet-i and has demonstrated single-agent anti-tumor activity in secondary glioblastoma (GBM) harboring MET∆14 and/or MET fusion with evidence of blood-brain barrier permeability (Cell. 2018, 175: 1665-1678). A WTS-based cMet biomarker assay is being developed under Caris MI Transcriptome platform to predict clinical response to monotherapy APL-101 in tumors with cMet dysregulation (NCT03175224). Methods: In a pilot study, we used Caris WTS to analyze 202 patient samples of NSCLC (78%) and other tumor types (22%) mostly GBM and gastrointestinal tumors to establish key parameters of Caris WTS in detection of cMet dysregulation. These samples were also analyzed by DNA-seq and IHC to understand the correlations of Caris WTS to DNA-based cMet mutation detection and cMet protein expression. The samples included 63 (31%) MET∆14, 48 (24%) MET fusions based on WTS and covered a broad dynamic range in cMet expression and copy number variations. In order to establish a stable baseline against which to compare MET mRNA expression, 123 unique tissue samples from 93 unique non-tumor tissues covering 27 unique tissue types were analyzed for wild-type MET expression. Results: Concordance between WTS and DNA-seq in detection of MET∆14 was 84% based on 67 cases analyzed by both methods. WTS identified 45% positive MET∆14, compared to 35% by DNA-seq. Out of 11 discordant cases, 9 were positive by WTS and 2 positive by DNA-seq. The number of transcripts carrying MET∆14 variants correlated with cMet wild type mRNA expression (n = 63, r = 0.88, p< 0.0001). cMet mRNA expression correlated with total cMet protein by IHC in MET fusion subset (n = 43, ρ = 0.65, p= < 0.0001), MET∆14 subset (n = 55, ρ = 0.64, p< 0.0001), and in all samples (n = 175, ρ = 0.75, p< 0.0001). In 175 cases with both WTS and IHC results, 9 MET∆14 positive cases had no detectable cMet protein on plasma membrane albeit all showed a detectable level of total cMet protein. Conclusions: A cMet WTS assay has been established to identify patients with cMet dysregulation including MET∆14 and MET fusion. cMet IHC and DNA-seq may offer secondary utility to differentiate WTS-identified METΔ14 patients to further strengthen the prediction of clinical response to a cMet inhibitor.
20q amplification defined by genomic and clinical characteristics as a subgroup with increased prevalence and better survival in metastatic colorectal cancer.
Authors: Maharaj Satish , Xue RuoBing , Cheema Anmol
Published: May 2020

e16003

Background: Genomic instability from 20q amplification is an oncogenic pathway in colorectal cancer (CRC). Several genes have been implicated, including BCL2L1, AURKA, SRC, ASXL1, GNAS and TOP1. There is a lack of data regarding 20q amplified group and one study implicating these genes suggested these patients have better overall survival. Next Generation Sequencing (NGS) has become widely used in metastatic CRC (mCRC) and easily identifies patients with 20q amplification. Nevertheless, most oncologists do not routinely consider 20q amplification status and this subgroup remains underinvestigated. This study aims to investigate genomic and clinical characteristics of 20q amplified mCRC using a single-center retrospective cohort and a multi-center genomic dataset. Methods: A cohort was identified comprising patients with mCRC who had NGS testing of tumor DNA and were treated between 2014-2019. Cases with and without 20q amplification were identified. Genomic, clinical and survival data were analyzed. Significant genomic findings were compared with all-stage CRC data using the AACR Genomic Evidence Neoplasia Information Exchange (GENIE) and The Cancer Genome Atlas (TCGA) databases. Results: Of the mCRC cohort ( n= 72), 15% ( n= 11) had 20q amplification. Amplified and non-amplified groups had no significant differences in age, sex or follow-up time. Patients with 20q amplification were more likely to have never smoked, and less likely to have treatment with targeted therapy. Survival analysis showed clear separation with longer overall survival for the amplified group. Eight genes at loci 20q11 to 20q13 were amplified - in order of frequency: ASXL1, GNAS, ARFRP1, ZNF217, AURKA, BCL2L1, SRC and TOP1. 20q amplification was significantly associated with wild-type RAS and BRAF, microsatellite stability, mutant TP53 and mutant APC. Using the GENIE and TCGA databases, it was found that metastatic disease had increased prevalence of all 20q amplified genes except TOP1, when compared to all-stage CRC. Conclusions: Clinical use of NGS identifies the 20q amplification subgroup that has increased prevalence in mCRC (compared to all CRC). Compared to non-20q amplified mCRC, this group had better survival, suggesting genomic pattern in mCRC is a novel independent prognostic marker. We believe mCRC patients would benefit from further studies defining a genomic prognostication model and development of therapy targeting the 20q amplification pathway.
Image-guided navigation for locally advanced primary and locally recurrent rectal cancer: Evaluation of its early cost-effectiveness.
Authors: Lindenberg Melanie , Kramer Astrid , Kok Esther , Retel Valesca P. , Ruers Theo , van Harten Wim
Published: May 2020

e16015

Background: Radical resection is an important prognostic factor in patients with locally advanced primary (LARC) and locally recurrent rectal cancer (LRRC), but achieving this can be challenging. Therefore, an intraoperative surgical navigation system has been developed, showing improved radical resection rates for LARC and LRRC. This study evaluates the early cost-effectiveness of navigated surgery in LARC and LRRC compared to standard surgery. Methods: Two Markov decision models; one for each indication, were used to estimate the expected costs and outcomes for navigated and standard surgery from a Dutch healthcare perspective over a 3-year time horizon. The models started with a decision tree resulting in a radical or non-radical resection. Subsequently, the Markov-models comprised the health states “stable disease”, “progression” and “death”. The input parameters were based on prospective (navigation cohort n = 33) and retrospective (control group n = 142) data collected at the Netherlands Cancer Institute, reference and unit prices and expert opinion. Quality-Adjusted Life Years (QALYs) were measured by the EQ5D-5L. Additionally, a probabilistic sensitivity analysis and a scenario analysis were performed. Results: Navigated surgery showed incremental costs of €3139 and €2857 in LARC and LRRC, respectively. For LARC, for navigation and standard surgery we found: 2.54 vs 2.52 Life Years (LYs), and 2.06 vs 2.04 QALYs. For LRRC we found 2.17 vs 2.11 LYs and 1.73 vs 1.67 QALYs. The base case analysis showed an Incremental Cost-Effectiveness Ratio (ICER) of €144,192 for LARC and €51,802 for LRRC per QALY gained. At a willingness to pay threshold of €80,000, navigated surgery is not cost- effective in LARC but is cost-effective in LRRC. When a hospital lacks a hybrid OR and needs to invest in one to use the navigation system, which will increase the ICERs for both indications. Finally, more utilization of the navigation system (12% to 50% utilization rate) shows ICERs of € 65,257 and €20,648 for LARC and LRRC, respectively. Conclusions: Based on the current data, the navigation system is expected to be cost-effective in LRRC and has the potential to become cost-effective in LARC. To decrease the costs, it is crucial to identify more surgical indications for image-guided navigation. Especially as in the near future, image-guided surgery is expected to be a standard option in surgical practice. As these findings are sensitive to uncertainty in the data, a randomized controlled trial is advised to perform for relevant indications.
The results of a study of the concordance of RAS status in liquid and invasive biopsies in patients with metastatic colorectal cancer in the Republic of Kazakhstan.
Authors: Smagulova Kaldigul , Kaidarova Dilyara , Ukolova Yelena , Orazgalieva Madina , Kurmankulova Anel
Published: May 2020

e16017

Background: Liquid biopsy is increasingly of interest as an alternative to invasive biopsy of solid tumors for predicting, making decisions about the treatment and monitoring of the disease. Particular preference is given to liquid biopsy in cases where it is not possible to obtain a sufficient amount of material or material of poor quality with a tumor biopsy. However, in order to find out the clinical significance of circulating tumor DNA (ctDNA), it is important to first establish the sensitivity of the method using tumor-plasma consistency studies. Methods: We selected 38 patients with a confirmed diagnosis of colorectal cancer (CRC), in whom was established the progression of the disease. All patients underwent two diagnostic methods, which we divided conditionally into 2 groups: A – invasive biopsy from available metastatic foci; to detect mutations in exons 2, 3, and 4 the KRAS gene used a reagent kit to detect 18 point mutations in codons 12,13,61,117,146 and a reagent kit to identify 10 mutations of the NRAS gene in codons 12,13,61,146 (Entrogen) on a Rotor-Gene 6000 Amplifier; B - liquid biopsy, to determine 21 mutations in the codons 12,13,59,61,117,146 of the KRAS gene, 18 mutations in the codons of 12,13,59,61,117,146 of the NRAS gene, was used Idylla automated molecular diagnostic system. Results: Of the 38 studied samples of group A: 22 (57.9%) had wild type KRAS, 16 (42.1%) were mutated, in group B: wild type had 25 (65.8%) patients, mutated - 13 (34, 2%). Thus, we see a discrepancy in the results in 3 (7.9%) of 38 cases. Conclusions: The results indicate a high degree of sensitivity (92.1%) of liquid biopsy as a diagnostic method, but confirmation of concordance with traditional tissue biopsy requires further in-depth study of this issue in a larger sample of patients.