bluuebunny/crossref_metadata_2025_split huggingface dataset:
A pancancer analysis of CDK12 alterations in Chinese population.
Authors: Lou Luyan , Zhang Yanrui , Liu Huanhuan , Liang Xiayuan , Lou Feng , Cao Shanbo , Wang Huina 
Published: June 2022

e15068 Background: Cyclin-dependent kinases ( CDKs) are key regulators of both cell cycle progression and transcription. Analysis of mutation detection of CDK12 in pan-cancer could contribute to understand the complexity and diversity of genetic alterations present in CDK12 mutant cancers. Herein, we provide a pan-cancer analysis of CDK12 alterations in Chinese population. Methods: Using gene-panel target-capture next generation sequencing, we analyzed 17509 tumor tissue or plasma ctDNA samples from different patients. Testing included analysis of single nucleotide variants, insertions/deletions, fusions and amplifications. CDK12 variants of uncertain significance and synonymous variants excluded. Results: In total, 0.95% (167/17509) of pan-cancer patients harbored CDK12 mutation, and 32 patients carried at least two CDK12 mutations. The most common genetic alteration type was truncating mutations (128, 64%), followed by amplications (53, 26%), missense mutations (9, 5%) and splicing mutations (9, 5%). In our cohort, the highest CDK12 mutation frequency tumor type was prostate cancer(11.30%), followed by breast cancer (3.96%), bladder cacner (3.16%), stomach cancer (1.84%) and colorectal cacner (1.13%). The TCGA pan-cancer cohort confirmed that the CDK12-altered cancer was associated with shorter overall survival (81.11 vs 133.00 mos, p = 5.30×10−18) in prostate cancer. Tumor mutation burdens(TMB) were calculated for 137 samples of all the 167 samples. The median TMB was 7.66 mut/Mb with 38%≥10 mut/Mb and 17%≥20 mut/Mb. including a patient with hypermutated in colorectal cancer(TMB: 88.24 Mut/Mb), harboring three CDK12 mutations. Conclusions: Genomic alterations in CDK12 are widespread among Chinese patients, with alteration rates and alteration types varying by cancer type. We identified prostate cancer as the cancer type with the highest prevalence of CDK12 oncogenic alterations. Additional analyses are ongoing.
Predictive factors for successful growth of patient derived xenografts (PDX).
Authors: Hernandez-Guerrero Tatiana , Doger Bernard , Garcia-Foncillas Jesus , Wick Michael Jude , Moreno Victor 
Published: June 2022

e15069 Background: PDXs have become a core component of translational cancer research. Developing these models can become challenging since little is known about which factors influence engraftment rates. We sought to determine which clinical, pathological, or molecular factors may predict better engraftment rates in PDXs. Methods: Between March 2017 and January 2021, biopsies obtained from patients with primary or metastatic cancer were implanted into athymic nude mice. Statistical analyses were performed to identify factors that could correlate with final engraftment defined as achievement of at least three passes and sampling of PDXs tumors. We focused on clinical (patient factors) pathological (patients’ tumor samples) and molecular characteristics (patients’ tumor samples) analyzed either by immunohistochemistry (IHC) or next generation sequencing (NGS). Results: 585 tumor samples were collected and implanted. 21 failed to engraft due lack of malignant cells. Of 564 tumor-positive samples, 187 (33.2%) PDXs achieved successful growth at time of analysis (Feb, 21). The following clinical characteristics were correlated with engraftment: systemic antibiotics within 2 weeks of sampling: (38.1% (72/117) antibiotics- group vs 30.7% (115/260) no-antibiotics) (p = 0.048); systemic steroids within 2 weeks (41.5% (34/48) the steroids-receiving group vs 31.7% (153/329) no-steroids) (p: 0.05). For women, menopausal status was predictive: 34.9% (95/177) in postmenopausal achieved growth, Vs 20,4% (10/39) for premenopausal (p = 0.031). Baseline LDH levels: 74.9% (140/187) LDH levels above the upper limit of normality (ULN) against 25.1% (47/187) with normal LDH (p = 0.034). Tumor grade: Grade 1: 25.4% (47/187); grade 2: 34.8% (65/187) and grade 3: 40.1% (75/187) tumors achieved successful growth (p = 0.043). Similarly, higher ki67 levels were also correlated with better engraftment rates: (low (Ki67 < 15%): 8.9% (9/45) achieved growth, Vs high (Ki67 > 15%): 31% (35/113) (p:0.002). Presence of lymphovascular invasion in tumor sample was also predictive: 42.2% (97/230) with lymphovascular Vs 26.9% (90/334) of samples with no invasion (p = 0.0001). Likewise, 41.8% (59/141) of neural invasion-positive samples achieved growth against 30.3% (128/428) (p = 0.008). Mismatch repair deficient tumors showed better engraftment rates: 62.1% (18/29) achieved growth vs 40.8% (75/184) of proficient tumors (p = 0.026). 84 PDX were breast models, among which 57.9% (11/19) ER negative models grew, Vs 15.4% (10/65) of ER positive models (p = 0.0001). Conclusions: tumors with higher grade and Ki67, lymphovascular and/or perineural invasion, with dMMR and ER expression negative have higher chance of PDX development. Some clinical characteristics can also interfere with PDXs development such as use of steroids or antibiotics prior sampling.
Paeoniflorin, ASK1-TF, and SOCS3 and association with radiation enteritis.
Authors: Yang Mi , Sheng Lei , Fei Wenjing , Hu Liang , Liu Wen-Tao , Ma Jianxin 
Published: June 2022

e15076 Background: Radiation enteritis is one of the main adverse effects of radiotherapy, presenting with a poorly understood etiology and limited options for therapy. Intestinal inflammation and ischemia are the core mechanisms of radiation enteritis. Suppressor of cytokine signaling 3 (SOCS3) is an endogenous “inflammation brake”. We hypothesized that paeoniflorin, a pinane monoterpene bitter glycoside, could increase SOCS3 expression to reduce inflammation and ischemia and improve enteritis in mice. Methods: Laser doppler flowmetry was used to detect changes in intestinal blood flow. RAW264.7 and human umbilical vein endothelial cells were used to investigate the mechanism of action of paeoniflorin. Results: It was observed that radiation caused high mortality, intestinal inflammatory responses, and low blood flow in mice. Paeoniflorin effectively alleviated intestinal atrophy, prevented thrombosis, improved radiation enteritis, and reduced mortality in mice undergoing radiotherapy. In addition, paeoniflorin increased the release of growth arrest-specific gene 6 (Gas 6) and phosphorylation of the Axl receptor, subsequently inducing the expression of SOCS3 and inhibiting the expression of p-apoptosis signal-regulating kinase 1 and tissue factor in vivo and vitro. Conclusions: we suggest that paeoniflorin is potentially effective in alleviating radiation enteritis via the activation of the Gas6/Axl/SOCS3 axis and subsequent reduction in intestinal inflammation and ischemia.
The combination of the IAP antagonist, tolinapant and hypomethylating agents (HMA) is highly synergistic in in vitro models of T-cell lymphoma (TCL).
Authors: Manavalan John , Pal Ipsita , Pursley Aidan , Ward George , Smyth Tomoko , Sims Martin , Feith David , Loughran Thomas , O’Connor Owen , Marchi Enrica 
Published: June 2022

e15088 Background: Peripheral T-cell lymphoma (PTCL) are a highly aggressive and heterogeneous group of non-Hodgkin lymphomas that often carry a poor prognosis with standard chemotherapy. Tolinapant is a potent antagonist of inhibitors of apoptosis proteins (cIAP1/2 and XIAP). In a phase 2 trial (NCT02503423), tolinapant showed activity against heavily pre-treated patients with TCL. We explored the sensitivity of a range of TCL lines to tolinapant, established the synergy coefficient and interrogated the mechanism of synergy between tolinapant and drugs active against PTCL including romidepsin, pralatrexate, and the HMAs; azacytidine and decitabine. Methods: A panel of 10 human TCL lines were tested in proliferation assays (CellTiterGlo) for sensitivity to tolinapant in the presence or absence of 10 ng/ml of TNFα. For combination studies, each drug was tested, in the presence or absence of TNFα. Synergy coefficient was calculated using Excess over Bliss. Additionally, the on-target effects of the drugs were measured by analyzing levels of the IAPs, acetylated histones, DNMTs and key apoptosis and necroptosis markers by Western blotting. Results: TCL Lines demonstrated varying sensitivities to tolinapant with the most sensitive cell line, ALK+ ALCL SUP-M2, having an IC50 as low as 20 nM ± 1 nM while a resistant CTCL cell line HH had an IC50 of over 20 µM. In combination experiments using both cell lines, tolinapant plus azacytidine or decitabine displayed the highest degree of synergism, compared to romidepsin or pralatrexate. Of note, a high degree of synergism was also seen with concentrations 10 folds lower of azacytidine or 100 folds lower of decitabine, added daily (Table). The combination of tolinapant and the HMAs led to a decrease in the levels of cIAP1 and DNMT3a in TCL lines, demonstrating on-target activity of tolinapant and the HMAs, respectively. In addition, both azacytidine and decitabine increased the levels of RIPK3 and MLKL by western blot analysis, indicating activation of the necroptosis pathway. Conclusions: Tolinapant has demonstrated varying cytotoxic effects against a range of TCL lines as a monotherapy and displays a very high degree of synergism in combination with the HMAs, azacytidine and decitabine, also at low concentration, in vitro. The HMAs were also able to activate the necroptosis pathway, providing a possible mechanism for the high degree of synergism displayed when combined with tolinapant in the TCL lines in vitro. These data provide the rationale to initiate phase I trials with the combination of tolinapant and HMAs. Average synergy scores at 48 hrs for drugs used in combination with tolinapant in a CTCL line HH and ALK+ ALCL line SUP-M2. Above 10 indicates synergy.[Table: see text]
Inhibition of cancer stem cells with TACH101, a first-in-class inhibitor of KDM4 histone lysine demethylase.
Authors: Perabo Frank , Chandhasin Chandtip , Dang Van , Del Rosario Joselyn , Chen Young K , Filvaroff Ellen , Stafford Jeffrey , Quake Stephen , Clarke Michael F. 
Published: June 2022

e15105 Background: Cancer stem cells (CSCs) are believed to be responsible for both therapy resistance and metastasis. Until now, these resistant CSCs have not been well-characterized, and potential treatments targeting these cells have yet to be identified. Epigenetic modifiers, such as KDM4 histone demethylase, have been shown to play an important role in CSC renewal and maintenance. TACH101 is a novel, first-in-class pan inhibitor of KDM4 that has promising pre-clinical and pharmacologic properties as a possible cancer therapeutic. Methods: Effects of TACH101 on CSC population were evaluated in the colorectal cancer SU60 xenograft model. Mice engrafted with SU60 cells were treated with TACH101 or vehicle. The day after the last dose, tumors from each group were dissociated into single cells and used to perform (1) flow cytometry analysis of the tumorigenic cell population using markers CD44 and EpCAM, (2) single cell gene expression analysis using quantitative reverse transcription polymerase chain reaction (RT-qPCR), and (3) functional tumorigenicity assays (limiting dilution assays). Results: TACH101 administration reduced SU60 tumor growth by 62% compared to vehicle-treated mice (p < 0.0005). Flow cytometry analysis of SU60 tumor cells showed the proportion of cells with cancer stem cell features (CD44HighEpCAM+) was 2.5-fold lower in TACH101-treated mice as compared to vehicle-treated animals. Single cell gene expression analysis followed by hierarchical clustering based on expression of immature and mature cell markers showed that TACH101-treated tumors had a significant reduction in the proportion of progenitor-like cells (p = 0.01) and an increase in number of both intermediate-like and differentiated-like cells although the increase was not significant (p = 0.07). In limiting dilution assay experiments, result showed that tumors were bigger/grew faster in animals receiving tumor cells derived from vehicle-treated animals compared to TACH101-treated animals. Furthermore, TACH101 was shown to reduce the number of tumor-initiating cancer stem cells by 4.4-fold. Further evaluation of TACH101 across additional xenograft models including esophageal, gastric, breast, and lymphoma showed tumor growth inhibition of up to 100%. TACH101 demonstrated favorable cell permeability, good oral bioavailability, and high metabolic stability. Toxicity studies in rats and dogs identified potential target tissues and provided safety guidance for the use of TACH101 in human trials. Conclusions: TACH101 inhibited proliferation of and tumor initiation by CSCs. As therapy resistance and metastatic dissemination are grave consequences of CSC activity, TACH101 provides a novel approach to eradicating this population and shows broad applicability as a potential therapeutic agent. Preparations to advance TACH101 into clinical trials are underway.
An AI-based, automated workflow for identification and scoring of invasive tumors in Ki-67 stained breast cancer specimens.
Authors: Patel Bhavika , Allen Stephanie , Talwalkar Sameer S. , Mehra Navi , Thagaard Jeppe , Ramsing Thomas W. , Overgaard Agnete , Caldara Jeni 
Published: June 2022

e15108 Background: Understanding the rate of tumor cell growth in breast cancer specimens may be indicative of disease aggressiveness, a tumor characteristic which can be used to make an informed treatment decision. The nuclear protein Ki-67 is increased in cells as they prepare to divide or proliferate and is therefore widely used as a proliferation marker for tumor progression. This degree of tumor cell proliferation, or the proliferative index, is commonly detailed in pathology reports shared with the patient care team. Methods: In this study, we utilized the Ki-67 [K2] immunohistochemistry (IHC) assay to stain 10 breast cancer specimens. Stained slides were imaged using the AT2 scanner (Leica Biosystems, Buffalo Grove, IL) and analyzed using the Visiopharm Image Analysis platform. Results: Previous efforts to assess Ki-67 positivity utilizing image analysis have relied on the use of a secondary stain or manual effort by the pathologist to exclude non-invasive tumor regions. These antiquated methods are costly to the lab as they require additional materials or valuable pathologist time. Our novel image analysis approach utilizes artificial intelligence (AI) to automatically denote non-invasive verses invasive tumor regions, which can then be used to quantify the Ki-67 proliferative index. Conclusions: This valuable tool will allow for greater accuracy, cost-savings, and time efficiency when analyzing breast cancer samples compared to traditional methods.
The pattern of KRAS mutations in non-small cell lung cancer (NSCLC): A retrospective study from south-eastern Georgia.
Authors: Matosz Sabrina , Elzaidy Mostafa , Abdel Karim Nagla Fawzy 
Published: June 2022

e15110 Background: Carcinogenic Kirsten rat sarcoma viral oncogene homolog (KRAS) mutation is a common oncogenic mutation found in lung cancer. It is a gain-of-function mutation that is the most commonly mutated oncogene in NSCLC; occurs in about 30% of all lung adenocarcinomas. A lot of progress has been made in targeted therapies against other oncogenic drivers, such as EGFR, HER2, MET, BRAF mutations. However, KRAS mutant lung cancer is still very difficult to manage and options are limited. Most recently, K-ras G12C has a newly approved novel targeted therapy. Different KRAS mutations may also represent different outcomes. Multiple studies have been looking into mutant KRAS and investigating it in the clinical relevance in lung cancer. Here we characterize a cohort of KRAS subtypes in all tumor types of lung cancer from south-eastern Georgia. Methods: This is a retrospective study that evaluated patients with K-ras mutant lung cancer from Augusta, Georgia geographical area. Samples were obtained from May 15th, 2015 to January 4th, 2022 and patients with KRAS mutant lung cancers were identified via Guardant platform. Results: In our cohort of patients, a total of 622 patients were evaluated in which 531 patients had a lung cancer diagnoses. Of those 531 patients, 383 had lung adenocarcinoma, 109 lung squamous cell, 34 NSCLC, 3 small cell, 1 lung carcinoid, and 1 large cell lung carcinoma. Of the 531 lung cancer patients, 14 (2.6%) patients expressed KRAS mutation with 12 (3.1%) patients expressing KRAS with lung adenocarcinoma. NRAS was expressed separately in 2 patients and HRAS was expressed separately in 1 patient. Our cohort of patients with K-ras mutant NSCLC had TP53 co-mutation in 78 (14%), MSI-High mutation in 60 (11%) patients, and EGFR mutation in 23 (4.3%) patients. The most common KRAS subtype in lung adenocarcinoma was G12V (42%), G12C (42%), and Y64D (8.3%). Two patients were unable to identify the type of the K-ras mutation. In addition, 92% of the carriers for KRAS mutation in lung adenocarcinoma were males. Its been noted that G12C mutation is the most common; however, in south-east Georgia, G12V is as common as G12C. Conclusions: KRAS mutation subtypes have distinct genomic landscape which requires further assessment to guide future therapeutic development. In the geographical area of Augusta, Georgia, KRAS subtype G12V is as common as G12C.
Identification of biomarker associated with Trop2 expression in breast cancer: Potential implication for targeted therapy.
Authors: Liao Ning , Lai Jianguo , Luo Yuting , Qi Xiaofang , Li Cheukfai 
Published: June 2022

e15120 Background: Trop2 has been confirmed to enhance tumor proliferation, metastasis and invasion in various epithelial tumors. Breast cancer (BC) patients with high Trop2 protein expression have better prognosis and objective response rates. Thus, this study aimed to explore potential biomarker associated with Trop2 protein expression in BC. Methods: BC patients with complete clinical parameters were enrolled, including age, estrogen receptor (ER) status, progesterone receptor (PR) status, human epithelial growth factor receptor 2 (HER2 status), molecular subtype, Ki67 status, T stage, N stage, TNM stage, PD-L1 and Trop2 protein expression level. Univariate and multivariate ordinal logistic regression analyses were performed to identify the independent factor for Trop2 protein expression level. Immunohistochemical analysis was conducted to detect the protein expression level of Trop2 in BC. Kaplan–Meier analysis and the log-rank test were executed to assess the survival difference between low- and high- gene expression level of Trop2. Results: A total of 65 BC patients from the Guangdong Provincial People’s Hospital were included. Based on the univariate and multivariate ordinal logistic regression analyses, Ki67 status was the only independent factor for Trop2 protein expression level (P < 0.05). This finding revealed that BC patients with higher Ki67 status may harbor higher Trop2 protein expression level. According to cBioPortal database, the mutation rate of Trop2 was 2.1% and mutation type was amplification. BC patients with low Trop2 gene expression level had significantly greater survival prognosis (P < 0.05). Conclusions: We performed the comprehensive analysis of the Trop2 in BC patients. It has the potential to guide individualized targeted treatment in BC patients.
MiRNAs hsa-miR-30a-5p and hsa-miR-99b-5p regulate chemokine-mediated immune response in colorectal cancer.
Authors: Kit Oleg I. , Pushkin Anton A. , Gvaldin Dmitry Yu. , Novikova Inna A. , Timoshkina Natalya N. , Soldatkina Natalya V. , Gevorkyan Yuriy A. , Petrov Dmitriy S. , Kolesnikov Vladimir E. , Savchenko Dmitriy A. , Tolmakh Roman E. , Dashkov Andrey V. , Katelnitskaya Oksana V. , Ilchenko Sergei A. , Dzhenkova Elena A. , Kolesnikov Evgeniy N. , Maksimov Aleksey Yu. , Shaposhnikov Aleksandr V. 
Published: June 2022

e15500 Background: The immune response plays a key role in the oncogenesis of colorectal cancer. The heterogeneity of the tumor environment determines the need for immunogenetic profiling to identify associations with the implementation of tumor-specific immune responses in colorectal cancer. The purpose of our study was to describe the expression profiles of miRNAs and genes involved in the regulation of the immune response in colorectal cancer. Methods: The study included 18 patients (median age 66 years) diagnosed with colorectal cancer who were treated at the National Medical Research Centre for Oncology in 2018-2019. Total RNA was isolated using TRIzol (Thermo Fisher, USA) followed by treatment with DNase 1 (ThermoFisher, USA). Sequencing of RNA samples was performed using two approaches: AmpliSeq for Illumina Immune Response Panel (Illumina, USA) and TruSeq Small RNA Library Prep Kit -Set A (Illumina, USA) according to the manufacturer's instructions on a NextSeq 550 device (llumina, USA). Results: The study revealed 168 differentially expressed genes and 46 differentially expressed miRNAs (p < 0.05). 29 miRNA-mRNA pairs were identified. It has been established that the key signaling mechanism involved in the regulation of the tumor-specific immune response is chemokine signaling pathway (hsa04062). Expression of the CXCL1 and CXCL10 genes encoding the chemokines of the same name is increased in tumor cells (logFC = 1.51, p = 0.006 and logFC = 2.67, p < 0.001, respectively). At the same time, the level of hsa-miR-30a-5p and hsa-miR-99b-5p, which negatively regulate the expression of CXCL1 and CXCL10, is decreased (logFC = -2.26, p < 0.001 and logFC = -1.57, p < 0.001). Conclusions: Activation of expression CXCL1 and CXCL10 with simultaneous loss of negative regulators hsa-miR-30a-5p and hsa-miR-99b-5p was determined in colorectal tumors by NGS-sequencing, which seems promising for the development of personalized therapy, based on the immunogenetic features of colon tumors.