bluuebunny/crossref_metadata_2025 huggingface dataset:
Greater than two coexisting mutations in KRAS and NRAS identified in the circulating tumor DNA fraction of liquid biopsies by NGS and confirmed with ddPCR.
Authors: Boulos Hala , Tell Robert , Beaubier Nike , Blidner Richard
Published: May 2020

e15563

Background: Liquid biopsies are increasingly utilized as a non-invasive tool in precision oncology to assess tumor mutational profiles in order to select targeted therapies, detect treatment resistance, and monitor disease progression in cancer patients. Additionally, liquid biopsies may provide a more comprehensive representation of tumor heterogeneity than standard tissue biopsies. However, limitations such as scarcity of circulating tumor DNA (ctDNA) and/or variants at low frequencies can be technically challenging to detect by next-generation sequencing (NGS) assays. Here, we use NGS to detect greater than two KRAS/NRAS mutations coexisting in single samples at low variant allele frequencies (VAFs). Methods: The Tempus xF liquid biopsy NGS assay is designed to detect actionable oncologic targets spanning 105 genes in plasma. The assay was validated to reliably detect single-nucleotide variants at 0.25% VAF, indels and copy number variants at 0.5% VAF, and fusions at 1% VAF with 96.2%-100% specificity and 97.4%-100% sensitivity. Pre-designed digital PCR assays were modified to measure 10ng of cell-free DNA (cfDNA) on a droplet-digital PCR (ddPCR) platform. Results: Overall, we report 100% positive predictive value and high correlation between ddPCR results and xF VAF, as well as in individual variants, such as KRAS G12D. Unexpectedly, we detected more than two coexisting KRAS/NRAS mutations at a low VAF in the plasma samples. To orthogonally confirm these results, ddPCR was deployed to independently measure the presence of each cfDNA variant with a sensitivity of 0.09% VAF. Subsequent ddPCR analysis of all targeted variants were concordant with NGS results. Conclusions: The occurrence of multiple KRAS and NRAS mutations in a single sample is quite uncommon and may be falsely interpreted as an NGS artifact. However, verification of this phenomenon by ddPCR confirmed the validity of the NGS liquid biopsy approach. These results highlight the capability of the Tempus xF assay to detect low-frequency variants, including those that fall below the validated detection threshold, which is essential for the diagnosis of early disease.
Assessment of 5-methylcytosine and 5-hydroxymethylcytosine technologies in contrived ctDNA-like samples.
Authors: Raiber-Moreau Eun-Ang , Hadfield James , Hodgson Darren , Wijdicks Marilou
Published: May 2020

e15585

Background: Epigenomic changes to DNA are early driving events in tumorigenesis and are specific markers of the tumour and its microenvironment. Cell-free DNA that is released from the tumour microenvironment can potentially be used for the detection of tumour-specific epigenomic changes for cancer liquid biopsy testing. In this study, we assessed the robustness of 5-methylcytosine and 5-hydroxymethylcytosine technologies in contrived ctDNA-like samples from NSCLC. Additionally, we assessed the limit of detection of the tumour fraction within the tested dilution range looking at a subset of differential epigenomic marks. Methods: 4 NSCLC tumour and buffy coat DNA samples were commercially obtained and processed to generate contrived tumour DNA dilution mimicking circulating tumour DNA at varying tumour fractions. Samples were sent in triplicate to multiple epigenomic assay providers for analysis. The robustness i.e. reproducibility and limit-of-detection within the tested range was determined. Results: Technical replicates all passed method-specific quality controls and were highly reproducible. Cancer specific differentially-methylated or hydroxymethylated regions were determined for each individual tumour sample as a “sample-specific cancer signature”; when applied to the tumour dilution samples, these signatures were capable of distinguishing all tumour dilutions down to 0.05% from normal background DNA. Detection of differential methylation and hydroxymethylation regions was reproducible across technical replicates for all four NCSLC samples at > 0.05%. Generation of pooled methylation “signatures” derived from commercially available healthy plasma and cancer tissue datasets could still detect cancer DNA in these four NCSLC samples at > 0.1% tumour fraction. Conclusions: Our pilot study showed that all assessed technologies generated reproducible, robust data and could detect ctDNA at even clinically relevant levels for early stage cancer. One limitation of this study was the small number of “n” and the use of sonicated contrived sample that may induce artificial bias and reduce sensitivity highlighting a requirement for the development of reference material in the community. The ability to detect cancer-specific epigenomic changes from liquid biopsy with high sensitivity offers new promising avenues for early detection of cancer, which can increase the chances of successful treatment.
Distinct molecular profiles of interval and screen-detected tumors in a real-world breast cancer registry.
Authors: Wilks Sharon , McIntyre Kristi , Han Linda K. , Cairo Michelina Marie , Barone Julie , Haan Josien , Mittempergher Lorenza , Yoder Erin , Menicucci Andrea , Wang Shiyu , Audeh William ,   FLEX Investigators' Group
Published: May 2020

e15587

Background: Interval breast cancers (BC) are detected between routine screening mammograms and are associated with worse prognosis, requiring more aggressive treatment compared to screen-detected BC identified during scheduled mammograms. Identifying molecular differences between interval BC and screen detected BC may lay the foundation for developing novel therapies. In this study, we compared gene expression profiles of interval BC to screen-detected BC. Methods: This analysis included a subset of 2260 patients enrolled in the FLEX Registry (NCT03053193), an ongoing, prospective study evaluating primary tumor samples from stage I-III BC patients who receive 70-gene risk of recurrence testing (70GS), 80-gene molecular subtyping (80GS), and consent to collection of clinically annotated full genome data. Interval BC were diagnosed < 12 months following a normal screening mammogram. Breast tumors were classified by 70GS as having a Low Risk (LR) or High Risk (HR) of distant metastases. Tumors were classified as Luminal, HER2, or Basal type by 80GS. Differential gene expression analysis was performed with limma and subsequent pathway analysis with DAVID and GSEA. Differences in the proportion of 70GS or 80GS results, 70GS index, and Ki67 were assessed by Chi-squared test or t-test. Results: In this study, 81% (1834/2260) of patients had screen-detected BC and 19% (426) had interval BC. A higher proportion of interval BC (51%) were HR compared to screen-detected BC (44%; p = 0.01). Most LR tumors were invasive ductal carcinoma (78% interval and 73% screen-detected) and over 99% were Luminal type. Between the two LR groups, 70GS indices were similar and there was no significant difference in transcriptional profiles. Basal and HER2 subtypes were more frequent among HR interval BC compared to screen-detected BC (p = 0.03). HR interval BC had 70GS indices of higher risk compared to HR screen-detected BC (p = 0.02). Differentially expressed genes in HR interval BC compared to HR screen-detected BC were associated with MYC signaling and mitosis, which was concordant with higher Ki67 by IHC (p = 0.007). Conclusions: This real-world data analysis shows interval BC are not all biologically High Risk and can be further stratified by the 70GS, aiding in treatment decisions. Preliminary results suggest that following 70GS LR classification, there is no biological difference between interval BC and screen-detected BC. In contrast, there are distinct biological processes associated with HR interval BC, which may have implications in the management of these cancers. Clinical trial information: NCT03053193.
The genes CNV and expression as a factors of HT-29 cells radioresistance.
Authors: Kosheleva Natalia G , Gusareva Marina A. , Balitsky Gennady V. , Lyman Natalia A. , Gabrichidze Peter N. , Gaziev Umar Muhmadovich , Solntseva Anna A. , Karnauhova Elena A. , Krokhmal Julia N. , Vasilyeva Ekaterina O. , Vladimirova Liubov Yu , Zinkovich Mikhail S. , Kutilin Denis S.
Published: May 2020

e15590

Background: The initial radioresistance of tumor cells associated with certain molecular genetic features has a great influence on the effectiveness of radiation therapy (RD). These features include the transcriptional activity of genes that regulate DNA repair, cell cycle and apoptosis, and their copy number variation (CNV). The aim of the study was to analyze the expression and CNV of genes that regulate DNA repair, cell cycle and apoptosis in HT-29 cells subjected to RD. Methods: HT-29 cell culture was used in the study. For the model experiment, doses of 5 and 7 Gy were used (irradiation was performed 5 times every 24 hours on a Novalis TX linear accelerator). Cell counting was carried out in Goryaev chamber (0.4% trypan blue solution). On the 5th day of irradiation, HT-29 was removed from the substrate with Trypsin / Versen solution. RNA was isolated according to the method of Chomczynski&Sacchi. For cDNA synthesis was used a "REVERTA-L". reagent. The phenol-chloroform method was used to DNA isolate. The RT-qPCR method was used to determine the CNV and expression of 32 genes: AKT, ATM, BRIP, BRCA1, BRCA2, CDK1, CDKN1B, CCND1, CCND3, EXO1, FGFR2, HIST1, H2AX, KU70, PTEN, RAD50, RAP80, RIF1, RNF8 TOPB1, TP53, XRCC4, BAX, CASP8, CASP3, CASP9, MDM2, BCL2, RBBP8, EP300, LIG4, C-FLIP. Statistical analysis was performed using ANOVA and Spearman's rank correlation coefficient (r). Results: After irradiation, only a specific pool of HT-29 cells remained viable: 32% for 5 Gy and 20% for 7 Gy of the initial number of cells. In HT-29 cells irradiated with 7 Gy, the CNV of the BRCA2, H2AX, CASP9 and RBBP8 genes was increased (p < 0.05) and the CNV of BCL2 gene was reduced (p < 0.05) relative to intact cells. In cells irradiated with 5 Gy only CASP9 and RBBP8 CNV was statistically significantly (p < 0.05) increased. In cells irradiated with 5 and 7 Gy, expression of BRCA2, H2AX, CASP9 and RBBP8 genes was statistically significantly (p < 0.05) increased and the expression of the BCL2 gene was reduced relative to intact cells. A strong positive correlation was observed between CNV and expression of the studied genes: r = 0.998 for control, r = 0.989 for cells irradiated at 5 Gy, and r = 0.993 for cells irradiated at 7 Gy. Conclusions: The study showed that 5 day RD at 5 and 7 Gy leads to selective survival of 32% and 20% of cells, respectively, with increased CNV and expression of BRCA2, H2AX, RBBP8 CASP9 genes and reduced CNV and expression of BCL2 gene.
CSNK2 in cancer: Pathophysiology and translational applications.
Authors: Strum Scott , Gyenis Laszlo , Litchfield David W
Published: May 2020

e15594

Background: Protein kinase CSNK2 (CK2) is a pleiotropic serine/threonine kinase whose expression levels are frequently elevated in solid and hematologic malignancies. CSNK2 has been discovered to hold prognostic and therapeutic significance across multiple cancers and is an excellent target for oncology research. This systematic review summarizes the current knowledge from in vitro and in vivo studies on the biology of this kinase in cancer alongside pre-clinical/clinical investigations from 24 different human cancer types. Methods: PRISMA methodology was used to generate a study protocol and building-block search strategy, from which a total of 796 publications in PubMed were retrieved across 24 human cancers. 245 of these publications met both screening and inclusion criteria. Data was then systematically extracted, including information about CSNK2 subunit mRNA/protein/activity levels, phosphorylation targets, phenotypic changes, in vivo studies, and prognostic/therapeutic data. The data was thereafter summarized and analyzed. Results: Five targets phosphorylated by CSNK2 were identified in at least 4 cancers: AKT, STAT3, RELA, PTEN, and TP53. The most heavily cited was AKT, identified in 15 cancers. Phenotypically, behaviors influenced by CSNK2 that were reported in 11 or more cancers included: evasion of apoptosis, enhancement of proliferation, enhancement of invasion/metastasis, and cell cycle control. Interestingly, these pathways correlated heavily with the most commonly cited CSNK2 targets. From a clinical perspective, CSNK2 held prognostic significance in 17 of the cancers. Additionally, xenograft experiments were found to have been performed in 13 cancers where CSNK2 inhibition resulted in a positive response to treatment. Lastly, early studies have shown promising results through the clinical application of CSNK2-specific inhibitors, with several clinical trials now underway for further assessment. Conclusions: Overall, our analysis supports CSNK2 as an attractive target for cancer therapy and points to specific areas where additional investigation is critical to advance our understanding of CSNK2 biology. The design of targeted therapies by exploiting the pathophysiology of CSNK2 has the potential to generate impactful treatment strategies across a wide range of cancers, promising exciting new discoveries scientifically and clinically.
Cytotoxic effect of unclassified group K rotaviruses on T98G and U87MG glioblastoma cells in vitro.
Authors: Sitkovskaya Anastasia O. , Kit Oleg I. , Kolpakov Sergey A. , Kolpakova Elena P. , Zlatnik Elena Yu. , Filippova Svetlana Yu. , Mezhevova Irina V. , Bondarenko Elena S. , Rostorguev Eduard E. , Ignatov Sergey N. , Kuznetsova Natalya S. , Atmachidi Dmitriy P. , Kavitskiy Sergey E. , Novikova Inna A. , Vladimirova Liubov Yu
Published: May 2020

e15597

Background: Oncolytic virotherapy is developing intensively in modern oncology. Viruses demonstrate the ability to the direct oncolysis and to the stimulation of antitumor immune activity; this experiment was aimed at solving the question of the prevalence of one of them. Glial tumors are the most common brain tumors; oncolytic viruses show certain prospects in their treatment due to the ability to penetrate the blood-brain barrier. The aim of the study was to determine the possible oncolytic effect of new unclassified group K rotaviruses (RVK) on T98G and U87MG glioblastoma cells in vitro. Methods: T98G and U87MG cell cultures were received from Russian banks of cell lines of human and animal tissues. Standard culturing was performed with attenuated apatogenic RVK strains No. 100 and No. 228 at a concentration of 108, 107, 106 and 105 particles/mL. The cytotoxic effect was determined with MTT and Annexin V assays, cell morphology was evaluated by the light-optical method. Results: Both RVK strains demonstrated a dose-dependent cytotoxic activity; the maximal effect was observed in strain No.100 at a dose of 108 particles/mL on U87MG cells (predominantly apoptosis). Studies of cell morphology showed a pronounced effect of RVK on the cell culture: significant degenerative changes in cells, a tendency to a decrease in cluster size, a change in their shape and granularity. Cluster formation in culturing in the serum-free medium is considered in the literature as a property of cancer stem cells responsible in vivo for tumor recurrence and its chemo- and radio-resistance. T98G cells demonstrated morphological changes: nuclear segmentation, diffused cytoplasm, indistinct cell borders with signs of syncytium formation. Conclusions: The established oncolytic effect of RVK strain No. 100 in vitro on glioma cells, presumably with tumor stem cells, indicates a significant potential for the use of these rotaviruses in treatment of glial tumors.
Lipocalin 2 – Devil or Angel? A pan cancer study.
Authors: Srinivasalu Vijay Kumar , Subramaniam Narayana , Das Manjula , Dhar Sujan Kumar
Published: May 2020

e15609

Background: Lipocalin2 (LCN2, also known as neutrophil gelatinase-associated lipocalin), is a protein that in humans is encoded by the LCN2 gene. It’s abnormal expression serves critical roles in the EMT transition process, angiogenesis, cell migration and invasion in many cancers. We aim to study the expression of LCN2 in tumours with respect to normal and its association with survival in multiple forms of cancer. Methods: On analysis of 23 TCGA datasets containing gene expression data for both tumour and adjacent normal samples, normalized RNAseq RSEM values of LCN2 were compared and differences between median expression levels were assessed using Wilcoxon rank sum test. Effect of LCN2 expression (lowest and highest tertiles) in tumour samples were estimated using Kaplan-Meier survival model. Correlation of LCN2 expression with immune cell population estimated using MCP Counter tool in Colonic Adenocarcinoma (CAC) and Head and Neck Squamous Cell Carcinoma (HNSCC) dataset were assessed. Results: LCN2 overexpression in tumour over normal was seen in 11 cancers viz. CAC, Cholangiocarcinoma, Esophageal ca, Kidney chromophobe, Kidney renal papillary cell ca, HCC, Lung adenoca, Rectum adenoca, Skin cutaneous melanoma, Thyroid ca and endometrial ca whereas LCN2 under-expression in tumour over normal was observed in 4 including HNSCC, Breast invasive ca, RCC and Prostate adenoca. For 8 cancers (Urothelial ca, Cervical and endocervical ca, Glioblastoma, Lower grade glioma, Lung squamous cell ca, Pancreatic adenoca, Phenochromocytoma and Stomach adenoca) no significant difference was observed between normal and tumour samples. LCN2 expression shows hazardous effect on OS in Renal Clear Cell ca (HR = 2.38, p = 0.00027), Glioblastoma (HR = 1.57, p = 0.036) and Pheochromocytoma (HR = 8.03, p = 0.03). On the other hand, high expression of LCN2 shows very mild protective effect on tumour progression in HNSCC (HR = 0.71, p = 0.05) and Prostate ca (HR = 0.46, p = 0.06). In CAC, the normal samples show a correlation between LCN2 expression and T-cells (Pearson r = 0.45, p = 0.0028) and with the T-cell chemo attractant CXCL10 (Pearson r = 0.5, p < 0.0001). Such correlations are broken in tumour samples. In HNSCC no correlations are visible between LCN2 expression and immune cell population estimate in either tumour or normal samples. Conclusions: Literature shows LCN2 as a potential therapeutic target. However, initial analysis of TCGA data fails to establish its role as pro- or anti-tumorigenic in multiple cancers. Further tissue-specific analysis including in vitro and invivo studies are needed to confirm its role in cancer.
Improvement of subcutaneous CDX model of lung cancer using A549 cell line.
Authors: Protasova Tatiana P. , Goncharova Anna S. , Gusareva Marina A. , Karnaukhova Elena A. , Leyman Igor A. , Sitkovskaya Anastasia O. , Volkova A. V. , Mindar M. V. , Tkachev Sergey Yu. , Zaikina Ekaterina V. , Khodakova D. V. , Lukbanova Ekaterina A. , Mezhevova Irina V. , Vladimirova Liubov Yu , Maksimov Aleksey Yu. , Kit Oleg I.
Published: May 2020

e15618

Background: Lung cancer is a challenging cancer problem, despite significant progress in its therapy. The search of drugs for the treatment of lung cancer is an urgent task. The creation of animal models of lung cancer plays a key role in preclinical trials and in understanding the mechanisms of tumor pathogenesis. The purpose of the study was to create a subcutaneous cell line-derived xenograft (CDX) model of lung cancer using the human lung cancer cells A459 and to compare results of subcutaneous injections of a cell suspension with different numbers of cells in two groups of animals. Methods: A CDX model of lung cancer was created using the human lung cancer cells A459 and male BALB/c Nude mice divided into two groups (n = 4 and n = 6) with subcutaneous injections of a mix of a cell suspension with Matrigel (200 μl). The injection mix contained 5*106 cells in 100 μl of serum-free RPMI-1640 medium and 100 μl of Matrigel (n = 4) and 10*106 cells in 100 μl of serum-free RPMI-1640 medium and 100 μl of Matrigel (n = 6). Results: Animal models receiving a suspension of 10*106 cells in 100 μl of serum-free RPMI-1640 medium and 100 μl of Matrigel were characterized by a higher tumor growth index compared to animals receiving 5*106 cells in 100 μl of serum-free RPMI-1640 medium and 100 μl of Matrigel. Models created with the injections of 10*106 cells showed a larger volume of tumor nodes: 65.33±1, 39.2±1, 41.79±1, 36.64±1, 75.87±1 and 43.13±1 mm3. CDX models created with the injections of 5*106 cells were characterized by a division of the single tumor node by the 30th day of the experiment which complicated the measurement. Conclusions: The creation of a CDX model with injections of 5*106 cells is undesirable due to the nonlinear growth of the xenograft and its division into several tumor nodes. Subcutaneous CDX models of lung cancer created with injections of 10*106 cells showed the linear growth and the formation of the single tumor node.
Multi-analyte liquid biopsies based treatment in advanced refractory cancers.
Authors: Limaye Sewanti , Patil Darshana , Akolkar Dadasaheb B , Crook Timothy , Ranade Anantbhushan , Bhatt Amit , Datta Vineet , Schuster Stefan , Sims Cynthe , Srivastava Navin , Fulmali Pradip , Devhare Pradip , Patil Sanket , Apurwa Sachin , Srinivasan Ajay , Datar Rajan
Published: May 2020

e15623

Background: Tumor tissue profiling following invasive biopsies is presently the standard approach for indication-based therapy management in solid organ cancers. However, challenges in biopsy are traditionally described due to proximity to vital organs, or patients’ co-morbidities or unwillingness for an invasive procedure. Liquid biopsies for evaluation of cancers are also largely restricted to single gene testing for selection of targeted therapy agents. We developed a comprehensive liquid biopsy based multi-analyte (molecular and functional) investigation of the cancer (eLBx: Encyclopedic Liquid Biopsy) for selection and management of individualised treatments in a cohort of advanced refractory cancers. Methods: We obtained 20 mL blood from 65 patients with solid organ cancers where the disease had progressed following failure of at least two lines of systemic therapies and where biopsy to obtain tumor tissue for molecular profiling of tumor was unviable. Cell free tumor DNA (ctDNA) was interrogated for mutations, while exosomal mRNA was profiled for gene expression. Viable circulating tumor associated cells (C-TACs) were tested in vitro for chemoresistance and used to determine expression of cell surface signalling receptors by immunocytochemistry (ICC). The findings were integrated to generate patient-specific treatment regimens. In patients who received treatment, response was determined radiologically. Results: Fifty-one patients received eLBx-guided personalized treatments with combinations of cytotoxic, targeted and endocrine agents. No two patients received the same treatment regimen. Forty-three patients were evaluable for treatment response per protocol among whom Partial Response (PR) was observed in 14 patients yielding an Objective Response Rate (ORR) of 32.6%. Additionally, 23 patients showed Stable Disease thus yielding an overall Disease Control rate of 86.1%. Median Progression Free Survival (PFS) was 108 days. There were no Grade IV therapy related Adverse Events or therapy related deaths. Conclusions: The ability to make informed treatment choices from a convenient blood draw implies a reduced dependence on invasive biopsies for disease management. We demonstrate successful management of advanced refractory solid tumor malignancies using an integrational non-invasive multi-analyte liquid biopsy approach. Clinical trial information: CTRI/2019/02/017548.
Preclinical evaluation of SC0191, a small molecule inhibitor of Wee1 kinase.
Authors: Yang Chundao , Li Zhengwei , Li Qi , Xia Yuanfeng , Chan Chi-Chung , Yuan Xusheng , Wang Yiwei , Chen Shuhui , Qian Wenyuan
Published: May 2020

e15637

Background: TP53 mutation is common in cancer cells, especially in small cell lung cancer (SCLC) and pancreatic cancer (PC). The G1 checkpoint function is lost in these cancer cells, which more rely on G2 checkpoint to repair damaged DNA. Wee1 is a serine/threonine kinase, which phosphorylates the Tyr15 locus of CDC2, inhibits the activity of CDC2, and stays in the G2 phase. Wee1 inhibition can promote the cells with DNA damage into the M phase, thus driving the TP53 mutant cancer cells to apoptosis. The purpose of this study was to investigate the in vitro and in vivo antitumor activity of SC0191, a small molecule inhibitor of Wee1 kinase, in preclinical models of SCLC and PC with TP53 mutation. Methods: The kinase inhibiting activity of SC0191 was determined using the Wee1 kinase assays. The cellular anti-proliferative activity was evaluated with TP53 mutant NCI-H446 SCLC and BxPC-3 PC cell lines. The in vivo antitumor activity of SC0191 was evaluated in the NCI-H446 and BxPC-3 cells-derived xenograft (CDX) mouse models, respectively. Results: SC0191 displayed potent kinase inhibiting activity for Wee1 with IC50 22.3 nM. SC0191 significantly inhibited tumor cell proliferation in TP53 mutant NCI-H446 cells with IC50 231.1 nM and BxPC-3 cells with IC50 223.8 nM. Moreover, SC0191 oral administration showed significant antitumor efficacy which was better than AZD1775, in the NCI-H446 and BxPC-3 CDX mouse models, respectively. Conclusions: A novel Wee1 inhibitor, SC0191, has demonstrated excellent antitumor efficacy in TP53 mutant solid cancer preclinical studies, and represents a promising clinical candidate for treating solid tumors, such as SCLC and PC.
Preclinical evaluation of SC0245, a small molecule inhibitor of ATR kinase.
Authors: Wang Jian , Li Qi , Xia Yuanfeng , Chan Chi-Chung , Yuan Xusheng , Wang Yiwei , Chen Shuhui , Qian Wenyuan
Published: May 2020

e15642

Background: The ataxia telangiectasia and Rad3-related (ATR) kinase is a member of the phosphoinositide 3-kinase related kinase (PIKK) family. ATR plays an important role in maintaining genome integrity during DNA replication through the activation of Chk1, and regulation of the DNA damage response (DDR). Replication stress (RS) is a major source of genomic instability in cancer, and targeting the RS-response kinase ATR has emerged as a promising antitumor approach. The purpose of this study was to investigate the antitumor activity of SC0245, a small molecule inhibitor of ATR kinase, in preclinical models of ATM pathway or ARID1A deficient solid tumors. Methods: The kinase inhibiting activity of SC0245 was determined using the ATR/ATRIP(h) complex assays. The cellular anti-proliferative activity was evaluated with tumor cells which was ATM pathway or ARID1A deficient. The in vivo antitumor activity of SC0245 was evaluated in ATM pathway or ARID1A deficient cell-derived xenograft (CDX) mouse models of gastric cancer (SNU-601) and colorectal adenocarcinoma (LoVo). Results: SC0245 displayed potent kinase inhibiting activity for ATR/ATRIP complex with IC50 14 nM, and had outstanding selectivity in the 104 onco-kinase panels. SC0245 significantly inhibited cell proliferation in ATM pathway or ARID1A deficient LoVo cells with IC50 0.163 μM, SNU-601 cells with IC50 0.218 μM. SC0245 showed excellent pharmacokinetics (PK) features with oral bioavailability ( > 80%) in mouse, rat and dog. Moreover, in the SNU601 and LoVo CDX mouse models, SC0245 oral administration significantly inhibited tumor growth, with better efficacy than AZD6738. Conclusions: SC0245, a novel potent ATR kinase inhibitor, has marked antitumor efficacy in the ATM pathway or ARID1A deficient solid tumor animal models, and has outstanding PK properties. SC0245 represents a promising clinical candidate for treating solid cancers, such as gastric and colorectal cancers.
A first-in-human phase I study of CYH33, a phosphatidylinositol 3-kinase (PI3K) α selective inhibitor, in patients with advanced solid tumors.
Authors: Wei Xiao-Li , Xu Rui-hua , Zhao Hongyun , Zhang Yang , Zou Ben-Yan , Wang Feng , Liu Jihong , Wang Zhiqiang , Qiu Miao-Zhen , Yu Qiuqiong , Liu Yun
Published: May 2020

e15645

Background: PI3Kα is the only subtype in PI3K family of which activated mutations occur frequently in tumors. CYH33 is a potent PI3Kα–selective inhibitor with anti-tumor activity in xenograft models. An open-label, Phase I dose-escalation & expansion study of CYH33 monotherapy (NCT03544905) is underway in patients (pts) with advanced solid tumors. Methods: This study evaluates the safety, pharmacokinetics (PK), and anti-tumor activity of CYH33 administered daily orally in 28-day cycles until intolerable toxicity or disease progression (PD). Adult pts with advanced solid tumors who have progressed despite standard therapies are enrolled to this trial, and pts with or without PIK3CA mutant are eligible for dose-escalation and pts with PIK3CA mutant are eligible for dose-expansion. Results: As of the cut-off date 20 Dec 2019, 17 pts (median age 47.0 y) were enrolled in the first 6 dose levels (1mg, 5mg, 10mg, 20mg, 40mg and 60mg) of the dose-escalation cohorts, and 3 pts were enrolled in expansion cohort of 40 mg. Cohorts 1 mg to 20 mg were completed without dose-limiting toxicities (DLT), cohort 40mg was completed with 1 DLT (Grade 3 hyperglycemia) out of 6 evaluable pts, and 3 enrolled pts at 60 mg are still in the DLT evaluation. Most frequent treatment-related adverse events (TRAEs) (all grades, ≥ 20%) included hyperglycemia (17 pts, 85%), decreased appetite (5 pts, 25%), diarrhea (4 pts, 20%). Grade≥3 TRAEs were hyperglycemia (8 pts, 40%), nausea (1 pt, 5%) and decreased appetite (1 pt, 5%). Hyperglycemia was generally manageable with anti-hyperglycemic medications. The preliminary PK profile of CYH33 showed dose proportionality across the tested dose levels, half-life (t1/2) was about 20 hours with minimum accumulation, and the maximum concentration (Cmax) achieved 2-4 hours after dosing. Over all, among 15 tumor response evaluable pts, partial response (PR) was observed in 2 pts treated with 40mg (1 colorectal cancer with unknown PIK3CA mutation status, 1 breast cancer with PIK3CA mutant), and stable disease (SD) was observed in 3 pts with unknown PIK3CA mutation status. After the cut-off date, 1 more pt (ovarian cancer with PIK3CA mutation) treated with 40mg achieved PR, so that 2 out of 3 enrolled PIK3CA mutant pts treated with 40mg achieved PR. Conclusions: The first-in-human study of the PI3Kα selective inhibitor CYH33 demonstrated a manageable safety profile, linear PK, and encouraging preliminary anti-tumor activity. CYH33 single agent and in combination with other anti-tumor agents have be planned in future studies. Clinical trial information: 03544905.
Anlotinib, a multitarget tyrosine kinase inhibitor, for advanced lung cancer patients: Efficacy in real-world study.
Authors: Feng Jifeng , Qian Lei
Published: May 2020

e15652

Background: Anlotinib is an novel small molecule multi-target tyrosine kinase inhibitor, which has been approved as a third-line therapy for patients with advanced NSCLC by CFDA in May 2018, and also approved as third-line therapy for patients with advanced SCLC in China in 2019. The objective of this study was to assess the efficacy of Anlotinib for patients with advanced lung cancer in the real world. Methods: We reviewed the patients who were diagnosed as advanced lung cancer and had received anlotinib in Jiangsu Caner Hospital from May 2018 to Sep 2019. The primary endpoint was progression-free survival (PFS) and the secondary endpoint was objective response rate (ORR), disease control rate (DCR) and safety. Results: A total of 465 patients were included in our study, containing 384 cases of NSCLC and 81 cases of SCLC. Among patients with NSCLC, 85 cases received anlotinib alone or anlotinib based therapy as first-line and second-line treatment, whereas 299 cases received anlotinib alone or anlotinib based therapy as third-line or later treatment. There were no significant differences in PFS, ORR and DCR between cohort of 1st /2nd line treatment and those with 3rd /later treatment. However, patients received combination therapy (including anlotinib combined with PD1 inhibitors such as Nivolumab, pembrolizumab, or chemotherapy such as platinum, docetaxel, pemetrexed, paclitaxel, tegafur, etc.) showed a significant longer PFS and higher ORR and DCR (P < 0.001, table). In patients with SCLC, 44 cases received anlotinib alone or anlotinib based therapy as first-line and second-line treatment. There were no significant differences in PFS, ORR and DCR between cohort of anlotinib monotherapy and other combination therapies (P > 0.05, table). No additional safety profile was observed. Conclusions: Anlotinib shows similar effect in patients with NSCLC and SCLC in real world. Anlotinib provides more significant benefits when combining with PD1 inhibitor or chemotherapy comparing with monotherapy in patients with advanced NSCLC. [Table: see text]
Correlation of MYC gene signature variations with clinical response to fimepinostat in patients with aggressive B-cell lymphoma.
Authors: Parker Jefferson , Grayson Dena , Von Roemeling Reinhard W.
Published: May 2020

e15654

Background: Fimepinostat (F), a small molecule dual inhibitor of PI3K α, β, and δ isoforms and Class I and II histone deacetylases (HDACs), is currently under investigation for the treatment of aggressive hematological cancers. Preclinical studies demonstrated that F both decreases transcription of myc and MYC-targeted genes (via HDAC inhibition) and increases destruction of MYC protein (via PI3K inhibition). This study sought to identify differences in transcript-level signatures of gene networks in pre-treatment tumor samples associated with future clinical response to F. Methods: Among 105 patients (pts) with relapsed or refractory (R/R) diffuse large B-cell lymphoma (DLBCL) treated in phase 1/2 clinical trials of F (± rituximab), 33 pts had pre-treatment tumor biopsy samples available for molecular testing. All pts had measurable disease at baseline and had at least 1 post-baseline tumor assessment. To be included in the analysis set, pts must have been on study for ≥42 days. RNA libraries were created and sequenced on the Illumina HiSeq platform. Gene Set Enrichment Analysis (GSEA; Subramanian et al., 2005) was used to study changes in transcript expression patterns that correlate with responder (complete/partial response) or non-responder (progressive disease) pt populations. ~20,000 genes were rank-ordered by log2-fold change and tested against the MSigDB (Liberzon et al., 2011) collection of gene expression signatures. Results: > 1500 Gene Sets with False Discovery Rate (FDR) < = 0.05 and Normalized Enrichment Score (NES) > 1.3 for genes upregulated in the F-responder population were identified. These Gene Sets represent transcriptional activity associated with well characterized biological pathways or gene expression signatures determined empirically. The top 20 signatures by NES were associated with general transcription functions (E2F, RNA polymerase), chromosomal structure (meiotic recombination, telomere maintenance) and specifically, MYC transcription targets (NES: 2.7; FDR q-val: 0). Additional signatures consistent with PI3K (GSK3b) and HDAC activity in the responder population were also identified, as would be expected for a dual inhibitor of PI3Ks and HDACs. Conclusions: GSEA analysis of genes upregulated in the F-treated responder DLBCL pts are consistent with preclinical data showing that F functions to suppress MYC in tumor cells. F is currently undergoing active clinical study in combination with venetoclax for the treatment of R/R DLBCL or high grade B-cell lymphoma (HGBL): NCT01742988.
Pan-cancer analysis to identify a novel class of glucocorticoid and androgen receptor antagonists with potent anti-tumor activity.
Authors: Tatman Philip , Fringuello Anthony , Graner Michael , Lillehei Kevin , Parasido Erika , Albanese Christopher , Tewari Ashutosh K. , Chakravarty Dimple , Nair Sujit , Theise Neil
Published: May 2020

e15663

Background: Large public cancer databases have allowed identification of novel mechanisms of oncogenesis and development of pharmacotherapies targeting these pathways. Examples are the androgen receptor (AR) and glucocorticoid receptor (GR). The Cancer Genome Atlas (TCGA) shows these receptors to have significantly increased expression over matched, normal tissue in several cancer types including: glioblastoma (AR and GR tumor-to-tissue ratios: AR = 6.53, GR = 1.42), low-grade gliomas (AR = 5.08, GR = 1.8), kidney clear cell carcinoma (AR = 1.89, GR = 1.82), kidney papillary cell carcinoma (AR = 3.64, GR = 1.2), and pancreatic adenocarcinoma (AR = 3.77, GR = 3.31). Methods: To investigate the therapeutic potential of targeting these receptors, we produced a series of analogues from a known GR inhibitor that all have the ability to target both the GR and the AR. Of these, PT150 is a clinical stage small molecule and PT157 is a preclinical stage small molecule. We began investigating the potential of these compounds to inhibit tumor growth using the NIH 60 cell lines panel with follow up in vitro testing and validation in clinically derived samples and established cell lines, including some cancers not include in the NIH 60 cell line panel or TCGA. Results: NIH 60 panel disclosed sensitivity towards gliomas, pancreatic cancer, and prostate cancer. For brain tumors, we investigated the effects of these inhibitors on glioblastoma, meningioma, and brain metastases. One analogue in particular, PT157, was able to significantly reduce cell viability after three days in culture in a dose dependent manor for each of the three tumor types and do so at a dose that is safely achievable in humans. Dose-dependent effects of PT150 and PT157 were observed in both androgen dependent and independent prostate cell lines, reducing viability of LNCaP, 22RV1 and DU145 cells. Similar data were also achieved in an in vitro pancreatic cancer model. Using patient-derived, primary pancreatic ductal adenocarcinoma (PDAC) cells, we found that both PT150 and PT157 were effective as monotherapies, inducing cell death in a dose dependent manner. In addition, both PT150 and PT157 significantly increased nab-paclitaxel sensitivity in nab-paclitaxel-resistant isogenic PDAC cells. Based on these in vitro data, we have begun pre-clinical experiments using in vivo mouse models. Conclusions: Our work has identified previously undescribed mechanisms of oncogenesis in several cancer types, as well as an efficacious class of novel compounds with the potential to inhibit them.
Whole exome and transcriptome sequencing of colorectal and pancreatic cancer.
Authors: Basu Gargi D. , Drenner Kevin , Ozols Audrey , Bair Candyce M , White Tracey , LoBello Janine R , Royce Thomas , Sharma Sunil
Published: May 2020

e15666

Background: Integration of Whole Exome Sequencing (WES) into clinical cancer therapeutics has revolutionized medicine in recent years. DNA sequencing alone may miss clinically actionable variants or identify aberrations that are not being transcribed. In this study we investigated the utility of integrating DNA and RNA sequencing in clinical samples. Methods: A cohort of 32 patient samples were analyzed by WES and RNA sequencing. Differential expression analysis was performed using a cohort of controls. Pathway analysis was performed using Ingenuity Pathway Analysis. WES and RNA analysis detected alterations including SNVs, indels, copy number events, fusions, alternate transcripts, TMB, MSI status and differential expression. Results: A total of 25 CRC (39-78yrs) and 7 pancreatic cancers (PCs) (51-91 yrs) were profiled by WES and RNA seq. A 66 yr old pt with neoplasm of rectosigmoid junction tumor was found to be KRAS wildtype and was treated with cetuximab plus FOLFIRI. Patient failed therapy after 2 yrs and sequencing revealed MET amplification which is a known mechanism of resistance to cetuximab treatment. Further, RNA expression analysis showed 44-fold increase in MET expression along with overexpression of AREG and EREG. Out of the 7 PCs, 3 cases that did not harbor KRAS mutation were found to harbor VTCN1/NRG1 fusion, FGFR1/G3BP2 fusion and BRAF V600E mutation respectively. A 50 year-old stage IV metastatic (met) PC pt was treated with standard of care regimens. Upon relapse the sample was found to harbor VTCN1/NRG1 fusion along with a TERT promoter mutation. RNA expression analysis revealed 54-fold increased expression of NRG1 which may lead to clinical trial enrollment. A 52 year-old male met Stage IV PC, was treated with rucaparib and irinotecan based on prior sequencing data. Upon relapse, the pt went on ATR inhibitor (BAY1895344) and progressed very quickly. Sequencing of the met lesion was found to harbor FGFR1/G3BP2 fusion which was also confirmed by RNA expression. A 55 year-old met pt with PC was treated with standard chemotherapy. Upon disease progression pt was sequenced and based on presence of BRAF V600E, pt was treated with trametinib and dabrafenib. Following disease progression on BRAF/MEKi, met sample was resequenced and RNA expression analysis found increased expression of MET, MACC1 and SMAD7 and 4-fold decrease in PTEN which could potentially cause resistance to BRAF/MEKi therapy. Conclusions: Our study highlights the utility of comprehensive testing integrating genomic and transcriptomic data, in identifying targeted therapy options for cancer patients.
Trends in primary surgical resection and chemotherapy for metastatic colorectal cancer, 2000-2016.
Authors: Sanford Nina Niu , Folkert Michael Ryan , Aguilera Todd Anthony , Beg Muhammad Shaalan , Kazmi Syed Mohammad Ali , Sanjeevaiah Aravind , Farkas Linda
Published: May 2020

e16000

Background: When, whether and in whom resection of the primary tumor for patients with metastatic colorectal cancer (CRC) is indicated remains incompletely elucidated, although a recent randomized trial (JCOG1007, presented at GI ASCO 2020) showed no survival benefit in resection of asymptomatic primary tumors in this population. Given the emergence of multiagent chemotherapy, surgery may be used less, but patterns of care for metastatic CRC have not been reported. As such, we sought to evaluate trends in use of primary surgical resection and chemotherapy among patients with metastatic CRC. Methods: Patients diagnosed with metastatic CRC between 2000-2016 were identified from the Surveillance, Epidemiology and End Results (SEER) registry. Multivariable logistic regression defined odds of undergoing primary surgical resection, with year of diagnosis as the primary independent variable. The cohort analysis was also stratified by primary site (colon versus rectum), age ( < 50 vs. >50 years) and whether patients also underwent resection of metastatic sites (yes versus no). The secondary endpoint of interest was receipt of any chemotherapy, also assessed by multivariable logistic regression. Results: Among 99,835 patients with metastatic CRC, 55,527 (55.7%) underwent resection of their primary tumor. The odds of undergoing primary surgery decreased with later year of diagnosis, with patients diagnosed in 2016 61.1% less likely to undergo surgery than those diagnosed in 2000 (AOR 0.39, 95% CI 0.36-0.42, p < 0.0001; absolute percent 62.3% to 43.8%). Black patients and women were also less likely to have surgery (p < 0.001). Similar trends by year for primary surgery were observed among each of the subgroups, although patients with colon primary, young adults (age < 50), and patients also undergoing metastatectomy were more likely to undergo primary surgery (p < 0.001 for all). In contrast, the odds of receiving chemotherapy increased dramatically with later year of diagnosis, with patients diagnosed in 2016 221% more likely to receive chemotherapy than those diagnosed in 2000 (AOR 2.21, 95% CI 2.04 to 2.40, p < 0.0001; 45.5% to 64.0%). Conclusions: From 2000-2016, we observed a sharp decline in the rate of primary surgical resection for patients with metastatic CRC, while use of chemotherapy increased over the same period. Prospective studies are needed to define the optimal local treatment for patients with metastatic CRC, perhaps with stratification by molecular and clinical characteristics, in order to optimize both cancer-specific and symptomatic outcomes.
Real-world evidence: Adjuvant chemotherapy in colorectal cancer with liver metastases.
Authors: Kuan Feng-Che , Lin Gengping , Chin Chih-Chien , Huang Wen Shih , Fan Chung-Wei , Chiang Jy Ming , Chen Hong-Hwa , Chen Jinn-Shiun
Published: May 2020

e16008

Background: Systematic chemotherapy with biologics improves survival in metastatic colorectal cancer (mCRC). Oxaliplatin-based adjuvant chemotherapy is suggested in stage III and high-risk stage II CRC. However, whether adjuvant oxaliplatin-based chemotherapy remains standard treatment in CRC with liver metastases after hepatectomy is not elucidated. Methods: Medical records were searched in Chang-Gung Research Database from 2004 to 2017. Patients with CRC and liver metastases who received systematic therapies and salvage hepatectomy were included. The Kaplan-Meier method was used to estimate survival, and multivariate Cox proportional hazard models were used to estimate adjusted hazard ratios (HRs) and 95% confidence intervals (CIs). Results: Total 454 patients received upfront hepatectomy (cohort 1) and 232 patients received neoadjuvant chemotherapy +/- biologics and salvage hepatectomy (cohort 2) were included in this study. In cohort 1 or cohort 2, the baseline characteristics of those received either postoperative oxaliplatin-containing regimen or other systematic regimens were not statistically different in gender, age, primary site, and biologic drugs. In cohort 1, overall survival (OS) in those received postoperative oxaliplatin-containing chemotherapy was significantly better than that of those received non-oxaliplatin-containing chemotherapy (median OS: 6.6 vs. 4.5 years, Log-rank p = 0.032; 5-year survival rate: 57.5 vs. 47.0%). In cohort 2, OS in those received postoperative oxaliplatin-containing chemotherapy was similar with that of those received irinotecan or biologics-containing chemotherapy (median OS: 3.1 vs. 3.5 vs. 3.8 years, Log-rank p = 0.472; 5-year survival rate: 30.9 vs. 33.3 vs. 37.0%). Conclusions: Oxaliplatin-containing chemotherapy provides better OS and remains standard adjuvant treatment in CRC with liver metastases after upfront hepatectomy. However, adjuvant chemotherapy in those received neoadjuvant chemotherapy +/- biologics and salvage hepatectomy should be individualized. Further prospective studies are warranted to validate these findings.