Find research datasets worth reusing

opencc-by-4.0Oct 2022View details →

Long-Term Survival and Curative-Intent Treatment in Hepatitis B or C Virus-Associated Hepatocellular Carcinoma Patients Diagnosed during Screening

We uploaded the image of the mansucript Long-Term Survival and Curative-Intent Treatment in Hepatitis B or C Virus-Associated Hepatocellular Carcinoma Patients Diagnosed during Screening accepted on Biology.

opencc-by-4.0Nov 2022View details →

Supplementary materials for "SPAG9 expression predicts a good prognosis in patients with clear cell renal cell carcinoma: A bioinformatics integrative analysis"

Supplementary materials for "SPAG9 expression predicts a good prognosis in patients with clear cell renal cell carcinoma: A bioinformatics integrative analysis".

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STRA6 promotes thyroid carcinoma progression via activation of the ILK/AKT/mTOR axis in cells and female nude mice

Background: Metastasis has emerged to be an important cause for poor prognosis of thyroid carcinoma (TC) and its molecular mechanisms are not fully understood. STRA6 is a multifunctional membrane protein widely expressed in embryonic and adult tissues. The function and mechanism of STRA6 in TC remain elusive. Objective: We aimed to explore the role of STRA6 in TC progression and provide a therapeutic target for TC. Methods: The expression and clinicopathological relevance of STRA6 were explored in TC. Stable STRA6-knockdown TC cells were established and used to determine the biological function of STRA6 in vitro and in vivo. RNA-sequencing and Co-immunoprecipitation were performed to unveil the molecular mechanism of STRA6 in TC progression. The potential of STRA6 as a therapeutic target was evaluated by lipid nanoparticles (LNPs) containing siRNA. Results: STRA6 was upregulated in TC and correlated with aggressive clinicopathological features including extrathyroidal extension and lymph node metastasis, which contributed to the poor prognosis of TC. STRA6 facilitated TC progression by enhancing proliferation and metastasis in vitro and in vivo. Mechanistically, STRA6 could interact with ILK and subsequently activate the AKT/mTOR signaling pathway. We further unveiled that STRA6 reprogrammed lipid metabolism through SREBP1, which was crucial for the metastasis of TC. Moreover, STRA6 siRNA delivered by LNP significantly inhibited cell growth in xenograft tumor models. Conclusions: Our study demonstrates the critical roles of STRA6 contributing to TC progression via the ILK/AKT/mTOR axis, which may provide a novel prognostic marker as well as a promising therapeutic target for aggressive TC.

opencc-zeroFeb 2023View details →

opencc-by-4.0Feb 2023View details →

Raw Data for the article: How important is the role of iterative liver direct surgery in patients with hepatocellular carcinoma for a transplant center located in an area with a low rate of deceased donation?

Introduction: Hepatocellular carcinoma (HCC) accounts for nearly 90% of primary liver cancers, with estimates of over 1 million people affected by 2025. We aimed to explore the impacting role of an iterative surgical treatment approach in a cohort of HCC patients within the Milan criteria, associated with clinical risk factors for tumor recurrence (RHCC) after liver transplant (LT) and loco-regional therapies (LRT), as well as liver resection (LR) and/or microwave thermal ablation (MWTA). Methods: We retrospectively analyzed our experience performed during an 8-year period between January 2013 and December 2021 in patients treated for HCC, focusing on describing the impact on preoperative end-stage liver disease severity, oncologic staging, tumor characteristics, and surgical treatments. The Cox model was used to evaluate variables that could predict relapse risks. Relapse risk curves were calculated according to the Kaplan-Meier method, and the log-rank test was used to compare them. Results: There were 557 HCC patients treated with a first-line approach of LR and/or LRTs (n = 335) or LT (n = 222). The median age at initial transplantation was 59 versus 68 for those whose first surgical approach was LR and/or LRT. In univariate analysis with the Cox model, nodule size was the single predictor of recurrence of HCC in the posttreatment setting (HR: 1.61, 95% CI: 1.05-2.47, p = 0.030). For the LRT group, we have enlightened the following clinical characteristics as significantly associated with RHCC: hepatitis B virus infection (which has a protective role with HR: 0.34, 95% CI: 0.13-0.94, p = 0.038), number of HCC nodules (HR: 1.54, 95% CI: 1.22-1.94, p < 0.001), size of the largest nodule (HR: 1.06, 95% CI: 1.01-1.12, p = 0.023), serum bilirubin (HR: 1.57, 95% CI: 1.03-2.40, p = 0.038), and international normalized ratio (HR: 16.40, 95% CI: 2.30-118.0, p = 0.006). Among the overall 111 patients with RHCC in the LRT group, 33 were iteratively treated with further curative treatment (12 were treated with LR, two with MWTA, three with a combined LR-MWTA treatment, and 16 underwent LT). Only one of 18 recurrent patients previously treated with LT underwent LR. For these RHCC patients, multivariable analysis showed the protective roles of LT for primary RHCC after IDLS (HR: 0.06, 95% CI: 0.01-0.36, p = 0.002), of the time relapsed between the first and second IDLS treatments (HR: 0.97, 95% CI: 0.94-0.99, p = 0.044), and the impact of previous minimally invasive treatment (HR: 0.28, 95% CI: 0.08-1.00, p = 0.051). Conclusion: The coexistence of RHCC with underlying cirrhosis increases the complexity of assessing the net health benefit of ILDS before LT. Minimally invasive surgical therapies and time to HCC relapse should be considered an outcome in randomized clinical trials because they have a relevant impact on tumor-free survival.

opencc-by-4.0Apr 2023View details →

Hepatocellular carcinoma (HCC) Tumor microenvironment is more suppressive than colorectal cancer liver metastasis (CRLM) Tumor microenvironment.

Background and purpose: While HCC is an inflammation-associated cancer, CRLM develop on permissive healthy liver microenvironment. To evaluate the immune aspects of these two different environments, peripheral blood-(PB), peritumoral-(PT) and tumoral tissues-(TT) from HCC and CRLM patients were evaluated. Methods: 40 HCC and 34 CRLM were enrolled and freshly TT, PT and PB were collected at the surgery. PB-, PT- and TT-derived CD4+CD25+ Tregs, M/PMN-MDSC and PB-derived CD4+CD25− Teffector cells (Teffs) were isolated and characterized. Tregs function was also evaluated in the presence of the CXCR4 inhibitor, Peptide-R29, AMD3100 or anti-PD1. RNA was extracted from PB/PT/TT-tissues and tested for FOXP3, CXCL12, CXCR4, CCL5, IL-15, CXCL5, Arg-1, N-cad, Vim, CXCL8, TGFβ and VEGF-A expression. Results: In HCC/CRLM-PB higher number of functional Tregs, CD4+CD25hiFOXP3+ were detected, although PB-HCC Tregs exert a more suppressive function as compared to CRLM-Tregs. In HCC/CRLM-TT Tregs were highly represented with Activated/ENTPD-1+Tregs prevalent in HCC. As compared to CRLM, HCC overexpressed CXCR4 and N-cadherin/Vimentin in a contest rich of arginase and CCL5. Monocytic-MDSCs were highly represented in HCC/CRLM while high Polymorphonuclear-MDSCs were detected only in HCC. Interestingly, CXCR4-PB-Tregs function was impaired in HCC/CRLM by the CXCR4 inhibitor R29. Conclusion: In HCC and CRLM, peripheral blood, peritumoral and tumoral tissues-Tregs are highly represented and functional. Nevertheless, HCC display a more immunosuppressive TME due to Tregs, MDSCs, intrinsic tumor features (CXCR4, CCL5, arginase) and the contest in which it develops. As CXCR4 is overexpressed in HCC/CRLM tumor/TME cells, CXCR4 inhibitors may be considered for double hits therapy in liver cancer patients.

opencc-by-4.0Mar 2023View details →

Development and validation of metabolic models for predicting survival and immune status of hepatocellular carcinoma patients

Supplementary materials for the article titled “Development and validation of metabolic models for predicting survival and immune status of hepatocellular carcinoma patients”

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Response to primary chemoradiotherapy of locally advanced oropharyngeal carcinoma is determined by the degree of cytotoxic T cell infiltration within tumor cell aggregates

Background: Effective anti-tumor immune responses are mediated by T cells and require organized, spatially coordinated interactions within the tumor microenvironment (TME). Understanding coordinated T-cell behavior and deciphering mechanisms of radiotherapy resistance mediated by tumor stem cells will advance risk stratification of oropharyngeal cancer (OPSCC) patients treated with primary chemoradiotherapy (RCTx). Methods: To determine the role of CD8 T cells (CTL) and tumor stem cells in response to RCTx, we employed multiplex immunofluorescence stains on pre-treatment biopsy specimens from 86 advanced OPSCC patients and correlated these quantitative data with clinical parameters. Multiplex stains were analyzed at the single-cell level using QuPath and spatial coordination of immune cells within the TME was explored using the R-package Spatstat. Results: Our observations demonstrate that a strong CTL-infiltration into the epithelial tumor compartment (HR for overall survival, OS: 0.35; p<0.001) and the expression of PD-L1 on CTL (HR: 0.36; p<0.001) were both associated with a significantly better response and survival upon RCTx. As expected, p16 expression was a strong predictor of improved OS (HR: 0.38; p=0.002) and correlated with overall CTL infiltration (r: 0.358, p<0.001). By contrast, tumor cell proliferative activity, expression of the tumor stem cell marker CD271 and overall CTL infiltration, regardless of the affected compartment, were not associated with response or survival. Conclusion: In this study, we could demonstrate the clinical relevance of the spatial organization and the phenotype of CD8 T cells within the TME. In particular, we found that the infiltration of CD8 T cells specifically into the tumor cell compartment was an independent predictive marker for response to chemoradiotherapy, which was strongly associated with p16 expression. Meanwhile, tumor cell proliferation and the expression of stem cell markers showed no independent predictive effect in response to RCTx and require further study.

opencc-zeroApr 2023View details →

TCGA Bladder Urothelial Carcinoma (BLCA) Gene Expression

Abstract: The Cancer Genome Atlas (TCGA) was a large-scale collaborative project initiated by the National Cancer Institute (NCI) and the National Human Genome Research Institute (NHGRI). It aimed to comprehensively characterize the genomic and molecular landscape of various cancer types. This dataset's gene expression profile was measured experimentally using the Illumina HiSeq 2000 RNA Sequencing platform by the University of North Carolina TCGA genome characterization center. The Sample IDs serve as unique identifiers for each sample. The dataset contains information about 426 samples and 20530 genes.  Inspiration: This dataset was uploaded to UBRITE for GTKB project.  Instruction: The log2(x+1) normalization was removed, and z-normalization was performed on the dataset using a Python script. Acknowledgments: Goldman, M.J., Craft, B., Hastie, M. et al. Visualizing and interpreting cancer genomics data via the Xena platform. Nat Biotechnol (2020). https://doi.org/10.1038/s41587-020-0546-8 The Cancer Genome Atlas Research Network., Weinstein, J., Collisson, E. et al. The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet 45, 1113–1120 (2013). https://doi.org/10.1038/ng.2764 U-BRITE last update: 07/13/2023

TCGA Kidney Renal Clear Cell Carcinoma (KIRC) Clinical Data

Abstract: The Cancer Genome Atlas (TCGA) was a large-scale collaborative project initiated by the National Cancer Institute (NCI) and the National Human Genome Research Institute (NHGRI). It aimed to comprehensively characterize the genomic and molecular landscape of various cancer types. This dataset includes curated survival data from the Pan-cancer Atlas paper titled <a href="http://www.cell.com/cell/fulltext/S0092-8674(18)30229-0">"An Integrated TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR) to drive high quality survival outcome analytics"</a>. The paper highlights four types of carefully curated survival endpoints, and <a href="http://www.cell.com/action/showFullTableImage?isHtml=true&tableId=tbl3&pii=S0092867418302290">recommends the use of the endpoints of OS, PFI, DFI, and DSS for each TCGA cancer type</a>. The dataset also includes phenotypic information about KIRC. The Sample IDs are unique identifiers, which can be paired with the gene expression dataset.  Inspiration: This dataset was uploaded to UBRITE for GTKB project.  Instruction: The survival and phenotype data were merged into one file. Empty columns were removed. Columns with the same value for every sample were also removed.  Acknowledgments: Goldman, M.J., Craft, B., Hastie, M. et al. Visualizing and interpreting cancer genomics data via the Xena platform. Nat Biotechnol (2020). https://doi.org/10.1038/s41587-020-0546-8 Liu, Jianfang, Caesar-Johnson, Samantha J. et al. An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics. Cell, Volume 173, Issue 2, 400 - 416.e11. <a href="https://doi.org/10.1016/j.cell.2018.02.052">https://doi.org/10.1016/j.cell.2018.02.052</a> The Cancer Genome Atlas Research Network., Weinstein, J., Collisson, E. et al. The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet 45, 1113–1120 (2013). https://doi.org/10.1038/ng.2764 U-BRITE last update: 07/13/2023

TCGA Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (CESC) Clinical Data

Abstract: The Cancer Genome Atlas (TCGA) was a large-scale collaborative project initiated by the National Cancer Institute (NCI) and the National Human Genome Research Institute (NHGRI). It aimed to comprehensively characterize the genomic and molecular landscape of various cancer types. This dataset includes curated survival data from the Pan-cancer Atlas paper titled <a href="http://www.cell.com/cell/fulltext/S0092-8674(18)30229-0">"An Integrated TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR) to drive high quality survival outcome analytics"</a>. The paper highlights four types of carefully curated survival endpoints, and <a href="http://www.cell.com/action/showFullTableImage?isHtml=true&tableId=tbl3&pii=S0092867418302290">recommends the use of the endpoints of OS, PFI, DFI, and DSS for each TCGA cancer type</a>. The dataset also includes phenotypic information about CESC. The Sample IDs are unique identifiers, which can be paired with the gene expression dataset.  Inspiration: This dataset was uploaded to UBRITE for GTKB project.  Instruction: The survival and phenotype data were merged into one file.  Acknowledgments: Goldman, M.J., Craft, B., Hastie, M. et al. Visualizing and interpreting cancer genomics data via the Xena platform. Nat Biotechnol (2020). https://doi.org/10.1038/s41587-020-0546-8 Liu, Jianfang, Caesar-Johnson, Samantha J. et al. An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics. Cell, Volume 173, Issue 2, 400 - 416.e11. <a href="https://doi.org/10.1016/j.cell.2018.02.052">https://doi.org/10.1016/j.cell.2018.02.052</a> The Cancer Genome Atlas Research Network., Weinstein, J., Collisson, E. et al. The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet 45, 1113–1120 (2013). https://doi.org/10.1038/ng.2764 U-BRITE last update: 07/13/2023

Sarcopenia index predicts short-term prognosis of head and neck squamous cell carcinoma

Dataset of "Sarcopenia index predicts short-term prognosis of head and neck squamous cell carcinoma"

BriTROC-1 study: genomic landscape of recurrent ovarian high grade serous carcinoma - pre processed data

Dataset containing pre-processed data files required to replicate analysis performed in the publication "The genomic landscape of recurrent ovarian high grade serous carcinoma: the BriTROC-1 study" (<a href="https://doi.org/10.1038/s41467-023-39867-7">Smith & Bradley et al. 2023</a>).

Radiation Therapy With or Without Trastuzumab in Treating Women With Ductal Carcinoma In Situ Who Have Undergone Lumpectomy

ClinicalTrials.gov study NCT00769379. IPD Sharing: Not stated. Countries: 4. Publications: 2.

closedIPD-NOFeb 2026View details →

Window Study of Nivolumab With or Without Ipilimumab in Squamous Cell Carcinoma of the Oral Cavity

ClinicalTrials.gov study NCT02919683. IPD Sharing: NO. Countries: 1. Publications: 2.

closedIPD-NOFeb 2026View details →

Re-irradiation With Fractionated Stereotactic Radiosurgery Plus Cetuximab in Patients With Recurrent Squamous Cell Carcinoma of the Head and Neck

ClinicalTrials.gov study NCT01104922. IPD Sharing: NO. Countries: 1. Publications: 1.

An Investigational Immuno-therapy Study of Nivolumab Compared to Sorafenib as a First Treatment in Patients With Advanced Hepatocellular Carcinoma

ClinicalTrials.gov study NCT02576509. IPD Sharing: Not stated. Countries: 22. Publications: 4.

Doxorubicin and Gemcitabine in Treating Patients With Locally Recurrent or Metastatic Unresectable Renal Cell Carcinoma

ClinicalTrials.gov study NCT00068393. IPD Sharing: Not stated. Countries: 1. Publications: 1.

controlledIPD-YESFeb 2026View details →

Anti-PD-L1/TGF-beta Trap (M7824) Alone and in Combination With TriAd Vaccine and N-803 for Resectable Head and Neck Squamous Cell Carcinoma Not Associated With Human Papillomavirus Infection

ClinicalTrials.gov study NCT04247282. IPD Sharing: YES. Countries: 1. Publications: 3.

controlledIPD-YESFeb 2026View details →

A Study of Belzutifan (MK-6482) in Participants With Advanced Renal Cell Carcinoma (MK-6482-013)

ClinicalTrials.gov study NCT04489771. IPD Sharing: YES. Countries: 9. Publications: 1.

Study of Dovitinib Versus Sorafenib in Patients With Metastatic Renal Cell Carcinoma

ClinicalTrials.gov study NCT01223027. IPD Sharing: Not stated. Countries: 27. Publications: 1.