bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of Wnt pathway inhibitor on ovarian cancer tumors.
Authors: Mindar M. V. , Goncharova Anna S. , Volkova A. V. , Verenikina Ekaterina V. , Menshenina Anna P. , Zaikina Ekaterina V. , Khodakova D. V. , Lukbanova Ekaterina A. , Ardzha Anna Yu. , Kurbanova L. Z. , Adamyan M. L. 
Published: June 2021

e15010 Background: Ovarian cancer (OC) is the fourth most common cancer in women aged 40-54 years. Despite advances in cancer research, no existing methods provide effective early diagnosis and treatment of OC, so the search for new medications is an urgent task. The effectiveness of the XAV-939 pharmacological substance, which inhibits the Wnt signaling pathway, was studied in an orthotopic patient-derived xenograft of human ovarian cancer. Methods: A PDX model was created in 20 female immunodeficient Balb/c Nude mice. A tumor fragment was implanted into the ovary, and the ovary was transposed under the skin to better visualize the xenograft growth. When the average tumor volume was 67.4 mm3, animals were divided into 4 groups: group 1 – controls (n = 5); group 2 – animals receiving paclitaxel (n = 5); group 3 – animals with XAV-939 (n = 5); group 4 – animals with combined paclitaxel+XAV-939 (n = 5). The control group received the carrier substance, and the test substances were administered at 10 mg/kg; the substances were administered intraperitoneally twice a week for 22 days. The tumor growth was assessed throughout the experiment by measuring its linear dimensions (length and width), and the volume and tumor growth index were calculated. The data were statistically processed using Microsoft Excel and STATISTICA 10. The Mann-Whitney nonparametric test was used to assess the differences between the control and experimental groups. Results: No statistically significant differences were observed in the indices of tumor growth between groups 2 (paclitaxel) and 1 (control), and groups 3 (XAV-939) and 1 (control). However, the difference was statistically significant between groups 4 (paclitaxel+XAV-939) and 1 (control). The tumor growth inhibition index was calculated at the end of the experiment. It was maximal in group 4 (paclitaxel+XAV-939) – 67.78%; in groups 2 (paclitaxel) and 3 (XAV-939), it was 21.39% and 30.33%, respectively. Conclusions: An orthotopic PDX model of ovarian cancer was generated, and the activity of XAV-939 towards the OC xenograft was studied; the greatest efficacy of the preparation was noted in combination with paclitaxel.
Association of genes copy number in extracellular DNA in patients with prostate cancer and sensitivity to radiotherapy.
Authors: Kutilin Denis S. , Zinkovich Mikhail S. , Gusareva Marina A. , Faenson Aleksandr V. , Karnauhova Elena A. , Solntseva Anna A. , Fatkina Natalya B. , Krokhmal Julia N. , Vasilieva Ekaterina O. , Shevchenko Alexey N. , Filatova Elena V. , Khomutenko Irina A. , Rozenko Lyudmila Ya. , Udalenkova Irina A. , Gappoeva M. A. , Donskaya Aliya K. 
Published: June 2021

e15014 Background: Radiotherapy (RT) is one of the main treatments for prostate cancer (PC). The effectiveness of such therapy depends on the initial radioresistance of tumor cells, which is ensured by their certain molecular features, which include the genes copy number variation (CNV). Model experiments on cell cultures (obtained from surgical material) have shown that CNVs have high potential as predictors of RT sensitivity. However, this potential is limited by the high level of invasiveness in obtaining biomaterials. A possible solution to this problem lies in the transition to CNV study in the extracellular DNA (cfDNA) of blood plasma. The aim of the study was to screen predictors of radioresistant PC based on the genes CNV in cfDNA. Methods: The study included 400 patients with diagnosed PC (T2a-3bN0M0, st. II-III), 40 of them after RT had a state of biochemical relapse (RT was performed on a Novalis TX linear accelerator (Varian, USA) (TFDisoeff = 75 Gr), mean time to biochemical relapse 7.5 months). Blood samples were separated into plasma and cell fraction by centrifugation. Isolation of cfDNA from blood plasma was performed using a set of reagents “DNA-Plasma-M” (Russia). Determination of the relative CNV of 13 genes (CDK1, CCND3, CDKN1B, TP53, PTEN, BCL2, XRCC4, BAX, RBBP8, H2AX, BRCA2, RAD50, EP300) was performed using the Real-Time qPCR method. Differences were assessed using the Mann-Whitney test; the Benjamin-Hochberg correction was used to correct multiple comparisons. Results: In the group with biochemical relapse (n = 40), the CNV of genes CDK1, CDKN1B, RBBP8, XRCC4, BRCA2 and RAD50 was statistically significantly (p < 0.05) higher by 2.0 times, 2.3 times, 2.1 times, 1.4 times, 2.4 times and 2.8 times, respectively, relative to the CNV of these genes in the cfDNA of the group without relapse (n = 360). Conclusions: Thus, it was found that the CNV of 6 genes (CDK1, CDKN1B, RBBP8, XRCC4, BRCA2 and RAD50) may be a potential molecular marker of radiosensitivity of prostate tumors. Based on the obtained data, a low invasive method for determining the prostate tumors sensitivity to RT has been developed.
Investigation of TLR4 and pSTAT3 expression on tumor and immune cells in the peripheral blood (PB) of patients with breast cancer (BC).
Authors: Papadaki Maria A , Monastirioti Alexia , Apostolopoulou Christina A , Aggouraki Despoina , Papadaki Chara , Michaelidou Kleita , Mavroudis Dimitrios , Agelaki Sofia 
Published: June 2021

e15015 Background: Toll-like receptor 4 (TLR4) and phosphorylated signal transducer and activator of transcription protein 3 (pSTAT3) hold a key role in inflammatory response and tumor immune evasion. Their role in the peripheral immune response and in tumor immune interactions in circulation needs further investigation. In the current report we evaluated the incidence of TLR4 and pSTAT3 expression on tumor and immune compartments within the peripheral blood (PB) of patients with early (eBC) and metastatic breast cancer (mBC). Methods: PB was obtained from patients with eBC (n = 99) and mBC (n = 100), prior to adjuvant and first-line therapy, respectively. Triple immunofluorescence staining for cytokeratins (CK), TLR4 and pSTAT3 was performed on peripheral blood mononuclear cell (PBMC) cytospins. Single cell-level expression of TLR4 and pSTAT3 was assessed on CK+ circulating tumor cells (CTCs) and PBMCs using the Ariol microscopy system. Results: CK+ CTCs were detected in 6.1% and 19% of patients with eBC and mBC, respectively (p = 0.006) (number of CTCs: n = 34 and n = 28, respectively). Higher TLR4 expression rates on CTCs were observed in mBC as compared to eBC (53.6% vs 7.7% of CTCs, 13% vs 3% of patients; p = 0.016). pSTAT3+ CTCs also prevailed in mBC (60.7% vs 10.3% of CTCs; 14% vs 5.1% of patients; p = 0.032). In the metastatic patients, CTC detection was associated with shorter overall survival (median OS: 24.9 vs 36.5 months; p = 0.042; Kaplan Meier), whereas the detection of TLR4+ CTCs predicted for shorter progression free survival (median PFS: 11.4 vs 12.6 months; p = 0.036). At the PBMC level, TLR4 expression was more frequent among patients with mBC as compared to eBC (34% vs 20.2%, respectively; p = 0.029), whereas pSTAT3 expression prevailed in eBC (89.9% vs 77% of patients, respectively; p = 0.014). The detection of TLR4+ PBMCs was associated with reduced disease-free survival (median DFS: not reached; p = 0.007) and shorter OS (median OS: not reached; p = 0.028) in patients with eBC. Conclusions: TLR4 and pSTAT3 expression is demonstrated on CTCs and PBMCs and significantly varies among eBC and mBC, suggesting that the inflammatory signaling through TLR4 and pSTAT3 in PB could be associated with BC progression. Our results further imply that their assessment in PB may hold significant prognostic implications in BC.
Targeting DNAJC19 overcomes tumor growth and metastasis in NSCLC by regulating AKT1 signaling.
Authors: Ren Tao 
Published: June 2021

e15024 Background: Some driver oncogenes are still unknown in non-small cell lung cancer (NSCLC). DNAJC19, known as a major component of the translocation machinery of mitochondrial membranes, is a disease-associated protein. Herein, we reported the role of DNAJC19 in NSCLC cell growth and metastasis. Methods: Immunohistochemistry (IHC) was performed to investigate DNAJC19 expression in NSCLC clinical samples. For knockdown or overexpression assays in A549 or NCI-H1299 lung cancer cells, lentiviral vectors were used. After assessment of cell functions, DNAJC19-knockdown A549 cells were further applied to establish mice xenograft and metastasis tumor models. STRING database, western, PCR, immunoprecipitation and IHC were performed for the mechanistic study. Results: Expression of DNAJC19 was higher in tumors than non-cancerous adjacent tissues. Survival analysis found that low DNAJC19 levels were correlated with increased progression-free survival rate. ShRNA-mediated knockdown of DNAJC19 markedly inhibited cell growth, viability, migration and invasion. Moreover, RNA-seq analysis explored that PI3K/AKT signaling pathway was involved in molecular events when A549 cells treated with shDNAJC19. And then DNAJC19 knockdown also decreased AKT1 expression in A549 cells. In addition, cellular functions were greatly rescued in DNAJC19-knockdown A549 cells by exotic overexpression of AKT1. Furthermore, tumor xenograft growth and metastasis were markedly repressed in the shDNAJC19 group than control group. As expected, DNAJC19 and AKT1 expression levels in xenograft mice samples were also lower in the shDNAJC19 group than in the shCtrl group. Conclusions: DNAJC19 greatly promotes NSCLC cell growth and metastasis via regulating AKT1 signaling, providing a novel therapeutic target for NSCLC patients.
Characterization of NTRK gene fusion events in solid tumors among Chinese patients.
Authors: Zhang Xuhui , Chen Dongsheng , Zhang Qin , Duan Qianqian , WANG Qing , Li Si , Xiao Mingzhe 
Published: June 2021

e15040 Background: NTRK fusions are actionable genomic alterations detected across tumor types. NTRK gene fusions involving either NTRK1, NTRK2 or NTRK3 (encoding the neurotrophin receptors TRKA, TRKB and TRKC, respectively) are oncogenic drivers of various adult and paediatric tumour types. Here, we update the detection of NTRK gene fusions across tumor types and further describe fusion partner characteristics among Chinese patients. Methods: Samples submitted for clinical molecular profiling were retrospectively analyzed for NTRK fusion events. Method for identifying NTRK fusions was DNA-based next-generation sequencing that tumour DNA is extracted from formalin-fixed paraffin-embedded tissue. All NTRK fusion partners were identified for intact functional domains, domain prediction, breakpoints, frame retention and co-occurring alterations. Results: A total of 64 NTRK fusion events (0.26% of 24,451) were identified. NTRK fusions are characteristic in a few rare types of cancer, such as melanoma, glioma and carcinomas of the thyroid, lung and colon, but they are also infrequently seen in some uncommon cancers, such as secretory carcinoma of the breast or salivary gland and infantile fibrosarcoma. Among the fusions, NTRK1 (0.08% of 24,430), NTRK2 (0.02% of 24,445), NTRK3 (0.15% of 24,414) were identified. Twenty-six unique fusion partners were identified, the most common in NTRK1 fusion being TPM3 (23.8%), NTRK2 fusion being AGTPBP1 (33.3%), and NTRK3 fusion being TFG (13.5%). Almost 53.8 % (14 of 26) of all fusion events are expected to include the transmembrane domain contributed by the NTRK fusion partner. The most commonly identified breakpoints occur in exon 14 and exon 17 and in exon 15 and exon 20, in NTRK1, NTRK3, respectively. Conclusions: NTRK fusion products are diverse across tumor types, but the significance of these variations is not clear. The biological and clinical implications of retaining certain domains of NTRK and of fusion partners warrants further investigation.
Discovery of HBW-3-20, the first potent reversible inhibitor of Bruton’s tyrosine kinase (BTK) with high brain exposure.
Authors: Lee Ning , Li Yingfu , Yuan Chester , Liu Guanfeng , Yue Chunchao 
Published: June 2021

e15068 Background: It has been an on-demand task to develop a BTK inhibitor of significant brain exposure, a critical property for extending its usages to treat Primary Central Nervous System Lymphoma (PCNSL) and autoimmune disorders. PCNSL is an aggressive extra nodal non-Hodgkin lymphoma that exclusively invades the central nervous system (CNS). Tirabrutinib, an irreversible BTK inhibitor with limited brain exposure, is the first BTK inhibitor approved for the treatment of recurrent or refractory primary central nervous system lymphoma recently. PRN2246 is another irreversible BTK inhibitor claimed to be of brain exposure, and is currently in clinical trials for the treatment of multiple sclerosis. Methods: New reversible BTK inhibitors were designed, synthesized and tested for enzymatic activities against wild-type and C481S-mutated BTK. Highly active compounds were confirmed for growth effects in diffuse large B-cell lymphoma derived TMD8 cells. Their microsomal stability and ADME properties were also assessed. Potent and bioavailable compounds were further measured for brain exposures in rats. Results: HBW-3-20 has excellent potency against both wild-type and C481S-mutated BTK, with IC50 of 2.5 and 3.8 nM, respectively. Its TMD8 cellular potency is 72 nM. In a head-to-head direct comparison of brain exposure experiment, HBW-3-20, tirabrutinib and PRN2246 were all dosed at 10mg/kg orally. The brain and plasma concentration were measured after 1 hour and the data are shown in the table below. The brain to plasma ratio for HBW-3-20, tirabrutinib and PRN2246 are 58%, 11.8% and 4.2% respectively. Our results show that HBW-3-20 has much greater brain permeability than tirabrutinib or PRN2246 in rats. Conclusions: HBW-3-20 is the first potent reversible BTK inhibitor that shows promisingly high brain permeability. HBW-3-20 provides a very valuable clinical candidate for treating B-cell malignancies in brain and autoimmune disorders![Table: see text]
Accurately estimating the homologous recombination deficiency based on low-pass whole-genome sequencing and target sequencing.
Authors: Lv Fang , Liu Yiqian , Zhang Yaxi , Liu Xiaoli , Zhihua Pei , Yu Jianing , Chen Weizhi , He Ji 
Published: June 2021

e15077 Background: Homologous recombination deficiency (HRD) is a promising biomarker for poly ADP-ribose polymerase (PARP) inhibitors. In the past, the HRD status was mainly estimated by summing the loss of heterozygosity (LOH), telomeric allelic imbalance (TAI), and large-scale state transition (LST) based on target sequencing. However, the heterozygous loci coverage and probe number are closely correlated to B allele frequency and copy number variations (CNVs). Here we developed a novel method to combine the data from low-pass whole-genome sequencing (WGS) and target sequencing to accurately estimate the genome-wide CNVs and allelic imbalance. Methods: We first performed low-pass WGS and target sequencing on 30 healthy controls, formalin-fixed and paraffin-embedded (FFPE) samples, and matched blood cell samples for 29 patients with breast cancer or ovarian cancer. Two HRD positive samples were diluted to 40%, 30%, 20%, and 10% tumor purity with matched blood cell samples, respectively. Each diluted sample was sequenced 20 times. The baseline for CNVs was built based on the sequencing data of healthy donors. To eliminate the artifacts resulted from the sequencing platform, models for each candidate single nucleotide polymorphism (SNP) in target regions were trained using the data from healthy donors. The mutations of BRCA1/BRCA2 of 29 patients were used to define the threshold of the HRD score. The numbers of LOH, LST, and TAI were evaluated by CNVs and B allele frequency. Results: We defined a cutoff of 42 for the HRD status based on the low-pass WGS and target sequencing data of 29 patients. Specifically, the original HRD scores for two selected HRD positive samples were 68 and 89. The median HRD scores for 40%, 30%, 20%, and 10% tumor purity samples were 69 and 88, 66.5 and 90, 61 and 68, 52 and 34.5, respectively. Conclusions: We developed a novel method for robustly inferring the HRD status using low-pass WGS and target sequencing with a limit of detection of 20%.
Transformation from non-small cell lung cancer to small cell lung cancer: A report of clinicopathological characteristics and prognoses.
Authors: Wang Jun , Liu Qing , Shang Yanhong , Xiao Linlin , Huo Ran 
Published: June 2021

e15084 Background: The transformation to small cell lung cancer (SCLC) is one of the mechanisms of drug resistance in non-small cell lung cancer (NSCLC). However, there are few reports on it. The study aims to analyze the clinicopathological characteristics of the patients, to explore the transformation factors and reasonable treatment strategy for them. Methods: A total of 9 patients with pathologically diagnosed NSCLC transformed into SCLC after first-line or multi-line treatment were involved in the study. Results: Among the 9 patients, there were 8 adenocarcinomas (ADC) and 1 squamous cell carcinoma (SCC), 7 of them were non-smokers. Epidermal growth factor receptor (EGFR) mutations were present in all ADC patients, including 7 with exon19 deletion (87.5%) and 1 with exon21 mutation (12.5%). All of them received EGFR tyrosine kinase inhibitors (TKIs) before the transformation, and the median transformation time was 19.5 months (95% CI, 14.1-32.7months). After first-line chemotherapy with paclitaxel and cisplatin, one SCC patient transformed to SCLC within 5 months. EGFR mutation was still maintained in 6 ADC patients when transformation occurred, of which 2 patients had a new TP53 mutation and 1 had RB1 gene mutation. Serum tumor markers were monitored in 6 patients, of them, progastrin releasing peptide (Pro-GRP) increased apparently at the time of disease progression in 5 patients, and neuron-specific enolase (NSE) also increased in 3 patients. This phenomenon occurred three to six months earlier than the transformation. The median survival time (MST) was 37 months from the initial diagnosis of NSCLC and 13 months after transformation. The median progression-free survival (mPFS) was only 2 months for those treated with chemotherapy (CT) after transformation, whereas 6 months treated with CT combined with TKIs as the first-line treatment. Three patients who received chemotherapy combined with programmed death receptor-1 (PD-1) inhibitor after multi-line therapy underwent progress within 2 months, nevertheless, 1 patient treated with the EP regimen combined with pembrolizumab as the first line treatment after transformation had a PFS of 12 months. After re-progression, the patients got another PFS of 5 months with a pemetrexed-platinum combined with atezolizumab. Conclusions: Phenotypic transformation is one of the mechanisms of drug resistance for NSCLC patients, especially for those with EFGR exon19 deletion received EGFR-TKIs. Tumor heterogeneity, TP53 gene and Rb gene mutation may be responsible for the transformation. The serum Pro-GRP over expression could as an early predictor of transformation. Classical chemotherapy is ineffective after SCLC transformation patients who still have sensitive mutation, it might be suitable to combine with EGFR-TKIs. The early application of immunotherapy could be attempted, but still needs to be explored further.
Profiling receptor tyrosine kinase fusions in Chinese breast cancers.
Authors: Tao Zhonghua , Hu Xichun , Cao Wen-Ming , Liu Jianxia , Li Ting , Xu Hong , Chen Kai , Zhang Jian , Zhou Hao , Sun Jie , Han Jinming , Yang Hua , Shao Lin , Xiang Jianxing , Guan Xiaoqian , Li Min 
Published: June 2021

e15092 Background: Receptor tyrosine kinases (RTKs) are a class of tyrosine kinases that regulate cell-to-cell communication and control a variety of complex biological functions. Dysregulation of RTK signaling partly due to chromosomal rearrangements leads to novel tyrosine kinase fusion oncoproteins which are possibly driver alterations to cancers. Targeting some RTK fusions with specific tyrosine kinases inhibitors (TKIs) is an effective therapeutic strategy across a spectrum of RTK fusion-related cancers. However, there is still a paucity of extensive RTK fusion investigations in breast cancer. We aimed to characterize RTK fusions in Chinese breast cancer patients. Methods: An in-house sequencing database of 1440 Chinese breast cancer patients using a 520-gene NGS sequencing panel was thoroughly reviewed. RTK fusion was defined as an in-frame fusion with the tyrosine kinase domain of the RTK completely retained with the only exception of ERBB2 fusion which was not counted due to its unclear significance. Concomitant mutations and TMB were also analyzed and calculated. Patients’ clinical characteristics were retrieved from case records. Results: 27 RTK fusion-positive breast cancers (12 tissues + 15 plasmas) were identified, patients had a median age of 52 years. Triple-negative breast cancer subtype comprised 37% with luminal and HER2 positive subtypes being 40.8% and 22.2%, respectively. 77.8% of patients were at stage IV and 22.2% at stage I-III. Ten were treatment naïve. RTK fusions occurred in 2% of breast cancers in our database, compared with the prevalence of 0.6% and 1.3% in MSKCC and TCGA, respectively. In the subset of stage IV patients, our database showed a significantly higher RTK fusion frequency than that in MSKCC (3.2% vs. 0.6%, p = 0.013). FGFR2 fusions were seen most commonly (n = 7), followed by RET (n = 4), ROS1 (n = 3), NTRK3 (n = 3), BRAF (n = 2), and NTRK1 (n = 2). Other RTK fusions including ALK, EGFR, FGFR1, FGFR3, MET, and NTRK2 were identified in one patient each. Of note, the normalized abundance of RTK fusion (fusion AF/max AF) correlated negatively with TMB (r = -0.48, p = 0.017). Patients with TMB < 4 (Muts/Mb) displayed a higher fusion abundance than those with TMB ≥ 4 (Muts/Mb) (p = 0.018), suggesting a higher likelihood of subclonal nature for RTK fusions in TMB-high patients. Moreover, CREBBP mutation only co-occurred with FGFR2 fusion (p = 0.012), while NTRK3 fusion and TP53 mutation were mutually exclusive (p = 0.019). Conclusions: This is the first study comprehensively delineating the prevalence and spectrum of RTK fusions in Chinese breast cancers. Further study is ongoing to identify the enriched subpopulation which may benefit from RTK fusion inhibitors.