bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development and validation of a five-immune gene prognostic risk model in colon cancer
Authors: Chen Haitao , Luo Jun , Guo Jianchun 
Published: May 2020

Abstract
Background
Colon cancer is a common and highly malignant cancer. Its morbidity is rapidly increasing, and its prognosis is poor. Currently, immunotherapy is a rapidly developing therapeutic modality of colon cancer. This study aimed to construct a prognostic risk model based on immune genes for the early diagnosis and accurate prognostic prediction of colon cancer.

Methods
Transcriptomic data and clinical data were downloaded from The Cancer Genome Atlas database. Immune genes were obtained from the ImmPort database. Differentially expressed (DE) immune genes between 473 colon cancer and 41 adjacent normal tissues were identified. The entire cohort was randomly divided into the training and testing cohort. The training cohort was used to construct the prognostic model. The testing and entire cohorts were used to validate the model. The clinical utility of the model and its correlation with immune cell infiltration were analyzed.

Results
A total of 333 DE immune genes (176 up-regulated and 157 down-regulated) were detected. We developed and validated a five-immune gene model of colon cancer, including LBP, TFR2, UCN, UTS2, and MC1R. This model was approved to be an independent prognostic variable, which was more accurate than age and the pathological stage for predicting overall survival at five years. Besides, as the risk score increased, the content of CD8+ T cells in colon cancer was decreased.

Conclusions
We developed and validated a five-immune gene model of colon cancer, including LBP, TFR2, UCN, UTS2, and MC1R. This model could be used as an instrumental variable in the prognosis prediction of colon cancer.
The prognostic value of preoperative fibrinogen-to-prealbumin ratio and a novel FFC score in patients with resectable gastric cancer
Authors: Tang Shuli , Lin Lin , Cheng Jianan , Zhao Juan , Xuan Qijia , Shao Jiayue , Zhou Yang , Zhang Yanqiao 
Published: May 2020

Abstract
Background
Chronic inflammation is considered as a hallmark of gastric cancer (GC) and plays a critical role in GC progression and metastasis. This study aimed to explore the prognostic values of preoperative fibrinogen-to-prealbumin ratio (FPR), fibrinogen-to-albumin ratio (FAR), and novel FPR-FAR-CEA (FFC) score in patients with GC undergoing gastrectomy.

Methods
A total of 273 patients with resectable GC were included in this retrospective study. We performed Kaplan-Meier and Cox regression analyses to assess the prognostic role of preoperative FPR, FAR, and FFC score in patients with GC and analyze their relationships with clinicopathological features.

Results
Receiver operating characteristic curve (ROC) analysis revealed that the optimal cutoff values for FPR and FAR were 0.0145 and 0.0784, respectively. The FFC score had a higher area under the ROC curve than FAR and CEA. Elevated FPR (≥ 0.0145) and FAR (≥ 0.0784) were significantly associated with old age, large tumor size, tumor invasion depth, lymph nodes metastasis, advanced TNM stage, large Borrmann type, and anemia status. Kaplan-Meier analysis showed that high FPR, FAR, and FFC score were related to poor survival. Multivariate analyses indicated that FPR, FFC score, TNM stage, and tumor size were significant independent factors for survival.

Conclusions
Preoperative FPR and FFC score could be used as prospective noninvasive prognostic biomarkers for resectable GC.
Inferring the role of the microbiome on survival in patients treated with immune checkpoint inhibitors: causal modeling, timing, and classes of concomitant medications
Authors: Spakowicz Daniel , Hoyd Rebecca , Muniak Mitchell , Husain Marium , Bassett James S. , Wang Lei , Tinoco Gabriel , Patel Sandip H. , Burkart Jarred , Miah Abdul , Li Mingjia , Johns Andrew , Grogan Madison , Carbone David P. , Verschraegen Claire F. , Kendra Kari L. , Otterson Gregory A. , Li Lang , Presley Carolyn J. , Owen Dwight H. 
Published: May 2020

Abstract
Background
The microbiome has been shown to affect the response to Immune Checkpoint Inhibitors (ICIs) in a small number of cancers and in preclinical models. Here, we sought to broadly survey cancers to identify those in which the microbiome may play a prognostic role using retrospective analyses of patients with advanced cancer treated with ICIs.

Methods
We conducted a retrospective analysis of 690 patients who received ICI therapy for advanced cancer. We used a literature review to define a causal model for the relationship between medications, the microbiome, and ICI response to guide the abstraction of electronic health records. Medications with precedent for changes to the microbiome included antibiotics, corticosteroids, proton pump inhibitors, histamine receptor blockers, non-steroid anti-inflammatories and statins. We tested the effect of medication timing on overall survival (OS) and evaluated the robustness of medication effects in each cancer. Finally, we compared the size of the effect observed for different classes of antibiotics to taxa that have been correlated to ICI response using a literature review of culture-based antibiotic susceptibilities.

Results
Of the medications assessed, only antibiotics and corticosteroids significantly associated with shorter OS. The hazard ratios (HRs) for antibiotics and corticosteroids were highest near the start of ICI treatment but remained significant when given prior to ICI. Antibiotics and corticosteroids remained significantly associated with OS even when controlling for multiple factors such as Eastern Cooperative Oncology Group performance status, Charlson Comorbidity Index score, and stage. When grouping antibiotics by class, β-lactams showed the strongest association with OS across all tested cancers.

Conclusions
The timing and strength of the correlations with antibiotics and corticosteroids after controlling for confounding factors are consistent with the microbiome involvement with the response to ICIs across several cancers.
Reduction of cycles of neoadjuvant chemotherapy for advanced epithelial ovarian, fallopian or primary peritoneal cancer (ROCOCO): study protocol for a phase III randomized controlled trial
Authors: Park Soo Jin , Shim Seung-Hyuk , Ji Yong-Il , Kwon Sang-Hoon , Lee Eun Ji , Lee Maria , Chang Suk Joon , Park Samina , Kim Sang Youn , Lee Sung Jong , Kim Jae-Weon , Roh Ju-Won , Lee San Hui , Song Taejong , Kim Hee Seung 
Published: May 2020

Abstract
Background
Primary debulking surgery (PDS) and adjuvant chemotherapy is the standard treatment for advanced ovarian, fallopian or primary peritoneal cancer. However, neoadjuvant chemotherapy (NAC) followed by interval debulking surgery (IDS) has been introduced as an alternative, showing similar efficacy and decreased postoperative complications compared with PDS. Although there is still no evidence for whether three or four cycles of NAC used clinically could be adequate, reducing one cycle of NAC is expected to remove more visible tumours and thereby improve prognosis. Thus, we proposed with this study to evaluate the efficacy and safety of reducing one cycle of NAC for advanced ovarian, fallopian or primary peritoneal cancer.

Methods
This study is a prospective, multi-centre, open-label, randomized phase III trial. A total of 298 patients with advanced ovarian, fallopian or primary peritoneal cancer will be recruited and randomly assigned to either three (control group) or two cycles of NAC (experimental group). After the NAC, we will conduct IDS with maximal cytoreduction and then administer the remaining three or four cycles for a total of six cycles of adjuvant chemotherapy. The primary end point is progression-free survival, and the secondary end points are time to tumour progression, overall survival, tumour response after NAC, IDS and adjuvant chemotherapy, radiologic investigation after IDS, tumour response by positron emission tomography-computed tomography after NAC, quality of life, adverse events, success rate of optimal cytoreduction, surgical complexity, postoperative complications and safety of IDS. We will assess these factors at screening, at every cycle of chemotherapy, at IDS, after the completion of chemotherapy, every 3 months for the first 2 years after the planned treatment and every 6 months thereafter for 3 years.

Discussion
We hypothesize that reducing one cycle of NAC will contribute to more resection of visible tumours despite 10% reduction of optimal cytoreduction, which could improve survival. Moreover, two cycles of NAC may increase postoperative complications by 5% compared with three cycles, which may be acceptable.

Trial registration
This study has been prospectively registered at ClinicalTrials.gov on Oct. 2nd, 2018 (NCT03693248, URL: https://clinicaltrials.gov/ct2/show/NCT03693248).
Primary surgery versus no surgery in synchronous metastatic breast cancer: patient-reported quality-of-life outcomes of the prospective randomized multicenter ABCSG-28 Posytive Trial
Authors:   on behalf of the ABCSG, Bjelic-Radisic V. , Fitzal F. , Knauer M. , Steger G. , Egle D. , Greil R. , Schrenk P. , Balic M. , Singer Ch. , Exner R. , Soelkner L. , Gnant Michael 
Published: May 2020

Abstract
Background
The ABCSG-28 trial compared primary surgery followed by systemic therapy versus primary systemic therapy without surgery in patients with de novo stage IV BC. The present report describes QoL results of this trial.

Methods
Ninety patients with primary operable MBC were randomised to surgery of the primary tumor followed by systemic therapy or to primary systemic therapy without surgery. QoL analyses covering the results at baseline, 6,12,18 and 24 months follow up of 79 (88%) patients, was assessed with the EORTC QLQ-C30 and QLQ-BR23 questionnaires.

Results
There were no statistically significant differences in any of the scales of the QLQ-C30 and QLQ-BR23 questionnaires between the two groups over the time. Baseline global health status and physical functioning were predictors for OS (patients with a higher score lived longer (p=0.0250, p=0.0225; p=0.0355, p=0.0355)). Global health status, social functioning scale, breast symptoms and future perspective were predictors for longer TTPd (p=0.0244; p=0.0140, p=0.020; p=0.0438, p=0.0123). Patients in both arms reported significant improvement on the emotional functioning scale. Cognitive functioning decreased over time in both groups. Younger women had clinically relevant better physical and sexual functioning scores (p=0.039 and 0.024).

Conclusion
Primary surgery does not improve nor alter QoL of patients with de novo stage IV BC. Global health status and physical functioning were predictors for OS and could be use as additional marker for prediction of OS and TTTd in patients with de novo stage IV BC.

Trial registration
The trial is registered on clinicaltrial.gov (NCT01015625, date of registration:18/11/2009).
ALDH1A3 serves as a predictor for castration resistance in prostate cancer patients
Authors: Wang Shangqian , Zhou Xiang , Liang Chao , Bao Meiling , Tian Ye , Zhu Jundong , Zhang Tongtong , Yang Jie , Wang Zengjun 
Published: May 2020

Abstract
Background
Aldehyde dehydrogenase 1A3 (ALDH1A3) has been implicated in the survival and proliferation of prostate cancer cells.

Methods
We retrospectively reviewed our patients with advanced disease on adjuvant hormonal therapy after prostatectomy. Time to castration resistance stage was documented. And Immunohistochemistry analysis for ALDH1A3 was performed for those patient samples on tissue microarray. Bioinformatics anslysis was used for RNA sequencing data of both primary prostate cancer and metastatic castration resistance prostate cancer (mCRPC) from online datasets. Crispr-Cas9 was used to knock out ALDH1A3 in prostate cancer luminal cells, and morphologic analysis as well as the Gene Set Enrichment Analysis (GSEA) were facilitated to discover the mechanisms of the resistance phenotype.

Results
We found that the patients with ALDH1A3 low expression had shorter time to progression to castration resistance compared with those of higher expression group on adjuvant hormonal therapy after radical prostatectomy. The ALDH1A3 knockout cells gradually acquired resistance to androgen deprivation therapy, a few cells have been found in knockout group showing as that the spindle-like luminal cells in charcoal stripped medium. Furthermore, PI3K pathway activation has been confirmed by Western blot. The PI3K pathway inhibitor BEZ235 has been demonstrated that the acquired ADT resistance by ALDH1A3 down regulation could be rescued by PI3K pathway inhibitor.

Conclusion
These results suggested a novel function for ALDH1A3 in development of mCRPC, and indicated PI3K pathway inhibitor has the potential in the treatment of a subgroup of mCRPC patients.
Integrated analysis of genome-wide miRNAs and targeted gene expression in esophageal squamous cell carcinoma (ESCC) and relation to prognosis
Authors: Yang Howard , Su Hua , Hu Nan , Wang Chaoyu , Wang Lemin , Giffen Carol , Goldstein Alisa M. , Lee Maxwell P. , Taylor Philip R. 
Published: May 2020

Abstract
Background
Esophageal squamous cell carcinoma (ESCC) is a leading cause of cancer death worldwide and in China. We know miRNAs influence gene expression in tumorigenesis, but it is unclear how miRNAs affect gene expression or influence survival at the genome-wide level in ESCC.

Methods
We performed miRNA and mRNA expression arrays in 113 ESCC cases with tumor/normal matched tissues to identify dysregulated miRNAs, to correlate miRNA and mRNA expressions, and to relate miRNA and mRNA expression changes to survival and clinical characteristics.

Results
Thirty-nine miRNAs were identified whose tumor/normal tissue expression ratios showed dysregulation (28 down- and 11 up-regulated by at least two-fold with P < 1.92E-04), including several not previously reported in ESCC (miR-885-5p, miR-140-3p, miR-708, miR-639, miR-596). Expressions of 16 miRNAs were highly correlated with expressions of 195 genes (P < 8.42E-09; absolute rho values 0.51–0.64). Increased expressions of miRNA in tumor tissue for both miR-30e* and miR-124 were associated with increased survival (P < 0.05). Similarly, nine probes in eight of 818 dysregulated genes had RNA expression levels that were nominally associated with survival, including NF1, ASXL1, HSPA4, TGOLN2, BAIAP2, EZH2, CHAF1A, SUPT7L.

Conclusions
Our characterization and integrated analysis of genome-wide miRNA and gene expression in ESCC provides insights into the expression of miRNAs and their relation to regulation of RNA targets in ESCC tumorigenesis, and suggest opportunities for the future development of miRs and mRNAs as biomarkers for early detection, diagnosis, and prognosis in ESCC.
Spatial patterns in prostate Cancer-specific mortality in Pennsylvania using Pennsylvania Cancer registry data, 2004–2014
Authors: Wang Ming , Wasserman Emily , Geyer Nathaniel , Carroll Rachel M. , Zhao Shanshan , Zhang Lijun , Hohl Raymond , Lengerich Eugene J. , McDonald Alicia C. 
Published: May 2020

Abstract
Background
Spatial heterogeneity of prostate cancer-specific mortality in Pennsylvania remains unclear. We utilized advanced geospatial survival regressions to examine spatial variation of prostate cancer-specific mortality in PA and evaluate potential effects of individual- and county-level risk factors.

Methods
Prostate cancer cases, aged ≥40 years, were identified in the 2004–2014 Pennsylvania Cancer Registry. The 2018 County Health Rankings data and the 2014 U.S. Environmental Protection Agency’s Environmental Quality Index were used to extract county-level data. The accelerated failure time models with spatial frailties for geographical correlations were used to assess prostate cancer-specific mortality rates for Pennsylvania and by the Penn State Cancer Institute (PSCI) 28-county catchment area. Secondary assessment based on estimated spatial frailties was conducted to identify potential health and environmental risk factors for mortality.

Results
There were 94,274 cases included. The 5-year survival rate in PA was 82% (95% confidence interval, CI: 81.1–82.8%), with the catchment area having a lower survival rate 81% (95% CI: 79.5–82.6%) compared to the non-catchment area rate of 82.3% (95% CI: 81.4–83.2%). Black men, uninsured, more aggressive prostate cancer, rural and urban Appalachia, positive lymph nodes, and no definitive treatment were associated with lower survival. Several county-level health (i.e., poor physical activity) and environmental factors in air and land (i.e., defoliate chemical applied) were associated with higher mortality rates.

Conclusions
Spatial variations in prostate cancer-specific mortality rates exist in Pennsylvania with a higher risk in the PSCI’s catchment area, in particular, rural-Appalachia. County-level health and environmental factors may contribute to spatial heterogeneity in prostate cancer-specific mortality.
Metastatic breast cancer patient perceptions of somatic tumor genomic testing
Authors: Adams Elizabeth J. , Asad Sarah , Reinbolt Raquel , Collier Katharine A. , Abdel-Rasoul Mahmoud , Gillespie Susan , Chen James L. , Cherian Mathew A. , Noonan Anne M. , Sardesai Sagar , VanDeusen Jeffrey , Wesolowski Robert , Williams Nicole , Shapiro Charles L. , Macrae Erin R. , Pilarski Robert , Toland Amanda E. , Senter Leigha , Ramaswamy Bhuvaneswari , Lee Clara N. , Lustberg Maryam B. , Stover Daniel G. 
Published: May 2020

AbstractBackgroundTo assess metastatic breast cancer (MBC) patient psychological factors, perceptions, and comprehension of tumor genomic testing.MethodsIn a prospective, single institution, single-arm trial, patients with MBC underwent next-generation sequencing at study entry with sequencing results released at progression. Patients who completed surveys before undergoing sequencing were included in the present secondary analysis (n = 58). We administered four validated psychosocial measures: Center for Epidemiologic Studies Depression Scale, Beck Anxiety Inventory, Trust in Physician Scale, and Communication and Attitudinal Self-Efficacy scale for Cancer. Genetic comprehension was assessed using 7-question objective and 6-question subjective measures. Longitudinal data were assessed (n = 40) using paired Wilcoxon signed rank and McNemar’s test of agreement.ResultsThere were no significant differences between the beginning and end of study in depression, anxiety, physician trust, or self-efficacy (median time on study: 7.6 months). Depression and anxiety were positively associated with each other and both negatively associated with self-efficacy. Self-efficacy decreased from pre- to post-genomic testing (p = 0.05). Objective genetics comprehension did not significantly change from pre- to post-genomic testing, but patients expressed increased confidence in their ability to teach others about genetics (p = 0.04). Objective comprehension was significantly lower in non-white patients (p = 0.02) and patients with lower income (p = 0.04).ConclusionsThis is the only study, to our knowledge, to longitudinally evaluate multiple psychological metrics in MBC as patients undergo tumor genomic testing. Overall, psychological dimensions remained stable over the duration of tumor genomic testing. Among patients with MBC, depression and anxiety metrics were negatively correlated with patient self-efficacy. Patients undergoing somatic genomic testing had limited genomic knowledge, which varied by demographic groups and may warrant additional educational intervention.Clinical trial informationNCT01987726, registered November 13, 2013.
The efficacy and safety of induction chemotherapy combined with concurrent chemoradiotherapy versus concurrent chemoradiotherapy alone in nasopharyngeal carcinoma patients: a systematic review and meta-analysis
Authors: Wang Bi-Cheng , Xiao Bo-Ya , Lin Guo-He , Wang Chang , Liu Quentin 
Published: May 2020

Abstract
Background
Induction chemotherapy (IC) combined with concurrent chemoradiotherapy (CCRT) has been recommended as the first-line therapy for locoregional nasopharyngeal carcinoma (NPC). Due to the different chemotherapeutic drugs used in the IC and CCRT, the results remain controversial.

Methods
PubMed, EMBASE, Web of Science, and Cochrane Library databases were systematically retrieved to search potentially eligible clinical trials up to Sep 11, 2019. Eligible studies were registered and prospective randomized controlled clinical trials.

Results
From 526 records, nine articles including seven randomized controlled clinical trials were eligible, with a total of 2311 locoregional advanced NPC patients. IC + CCRT had significantly lower risks of death (3-year hazard ratio [HR]: 0.70, 95% confidence interval [CI] 0.55–0.89, p = 0.003; 5-year HR: 0.77, 95% CI 0.62–0.94, p = 0.01), disease progression (3-year HR: 0.67, 95% CI 0.55–0.80, p < 0.001; 5-year HR: 0.70, 95% CI 0.58–0.83, p < 0.0001), distant metastasis (3-year HR: 0.58, 95% CI 0.45–0.74, p < 0.0001; 5-year HR: 0.69, 95% CI 0.55–0.87, p = 0.001) and locoregional relapse (3-year HR: 0.69, 95% CI 0.50–0.95, p = 0.02; 5-year HR: 0.66, 95% CI 0.51–0.86, p = 0.002) than CCRT. Compared with CCRT, IC + CCRT showed higher relative risks of grade 3 or more neutropenia, thrombocytopenia, nausea, vomiting and hepatotoxicity throughout the course of treatment, and higher relative risks of grade ≥ 3 thrombocytopenia and vomiting during CCRT.

Conclusion
IC combined with CCRT significantly improved the survival in locoregional advanced NPC patients. Moreover, toxicities were well tolerated during IC and CCRT. Further clinical trials are warranted to confirm the optimal induction chemotherapeutic regimen in the future.
The contribution of large genomic rearrangements in BRCA1 and BRCA2 to South African familial breast cancer
Authors: van der Merwe Nerina C. , Oosthuizen Jaco , Theron Magdalena , Chong George , Foulkes William D. 
Published: May 2020

Abstract
Background
Pathogenic variants that occur in the familial breast cancer genes (BRCA1/2) lead to truncated ineffective proteins in the majority of cases. These variants are mostly represented by small deletions/insertions, nonsense- and splice-site variants, although some larger pathogenic rearrangements occur. Currently, their contribution to familial breast cancer (BC) and ovarian cancer (OVC) in South Africa (SA) is unknown.

Methods
Seven hundred and forty-four patients affected with BC or OVC were screened for larger genomic rearrangements (LGRs) by means of multiplex ligation-dependent probe amplification or Next Generation Sequencing using the Oncomine™ BRCA research assay.

Results
The patients represented mostly medium to high-risk families, but also included lower risk patients without a family history of the disease, diagnosed at an early age of onset (< 40 years). Eight LGRs were detected (1.1%); seven in BRCA1 with a single whole gene deletion (WGD) detected for BRCA2. These eight LGRs accounted for 8.7% of the 92 BRCA1/2 pathogenic variants identified in the 744 cases. The pathogenic LGRs ranged from WGDs to the duplication of a single exon.

Conclusions
Larger rearrangements in BRCA1/2 contributed to the overall mutational burden of familial BC and OVC in SA. Almost a quarter of all pathogenic variants in BRCA1 were LGRs (7/30, 23%). The spectrum observed included two WGDs, one each for BRCA1 and BRCA2.