6048 results for "canc*"

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• Whole Exome and RNA Sequencing of 22 Patient-Derived Xenografts from Estrogen Receptor-Positive Breast Cancers

  We performed RNA and whole exome sequencing on 22 patient-derived xenografts (PDX) from estrogen receptor-positive (ER+) breast cancers, in the presence and absence of estradiol (E2) supplementation. Exome coverage across more than 3,500 clinically relevant genes that previously were covered below 20X (~2.72Mb) was achieved. On average, 11.2Gb of unique sequence data were generated with 95.3% of the bases in the exome design covered to 20x read depth or greater. RNA sequencing was generated from xenograft tumors. Between 50 and 85M total reads were performed. The average strand-specificity and rRNA rate was 98% and 1.5%, respectively. Transcripts for 17,000 to 27,087 genes were detected in these samples.

  Study phs003324

• NCTN: Randomized Phase III Study of Maintenance Therapy With Bevacizumab, Pemetrexed, or a Combination of Bevacizumab and Pemetrexed Following Carboplatin, Paclitaxel and Bevacizumab for Advanced Non-Squamous NSCLC (E5508)

  Study ID: E5508NCT Number: NCT01107626ECOG-ACRIN Cancer Research Group Submitted in collaboration with the NCTN/NCORP Data Archive Trial Title: NCTN: Randomized Phase III Study of Maintenance Therapy with Bevacizumab, Pemetrexed, or a Combination of Bevacizumab and Pemetrexed following Carboplatin, Paclitaxel and Bevacizumab for Advanced Non-Squamous NSCLC (E5508) Trial Description: RATIONALE: Drugs used in chemotherapy, such as paclitaxel and carboplatin, work in different ways to stop the growth of tumor cells, either by killing the cells or by stopping them from dividing. Monoclonal antibodies, such as bevacizumab, can block tumor growth in different ways. Some block the ability of tumor cells to grow and spread. Others find tumor cells and help kill them or carry tumor-killing substances to them. Bevacizumab may also stop the growth of non-small cell lung cancer by blocking blood flow to the tumor. Pemetrexed disodium may stop the growth of tumor cells by blocking some enzymes needed for cell growth. It is not yet known whether giving bevacizumab or pemetrexed disodium alone or in combination is more effective in treating non-squamous non-small cell lung cancer. PURPOSE: This randomized phase III trial is studying bevacizumab and pemetrexed disodium alone or in combination after induction therapy to see how well they work in treating patients with advanced non-squamous non-small cell lung cancer. Clinical data presented in the following publication(s): PMID 31361535 Disease type(s): Lung, Mediastinal and Pleural Neoplasm - Non-Small Cell Lung Cancer Clinical dataset(s) included: NCT01107626-D1 (PMID 31361535): There are two different datasets for PMID 31361535 from trial E5508. This dataset, NCT01107626-D1, contains baseline characteristics, treatment assignment, prior treatment, metastatic sites and efficacy data. Pemetrexed or bevacizumab is used for maintenance therapy of advanced no squamous non-small cell lung cancer (NSCLC). The combination of bevacizumab and pemetrexed has also demonstrated efficacy. This study contains two step registration, induction therapy step and maintenance therapy. All patients who were registered to at least one of the steps are included. Due to data cleaning efforts, data may contain slight discrepancies from that reported in Table 1 and Table 2 in the publication (PMID 31361535). The number of each metastatic site is incorrect in the publication: The data in this dataset is correct.NCT01107626-D2 (PMID 31361535): There are two different datasets for PMID 31361535 from trial E5508. This dataset, NCT01107626-D2, contains toxicity data. Pemetrexed or bevacizumab is used for maintenance therapy of advanced no squamous non‐small cell lung cancer (NSCLC). The combination of bevacizumab and pemetrexed has also demonstrated efficacy. This study contains two step registration, induction therapy step and maintenance therapy. All patients who were registered to at least one of the steps are included.You are encouraged to view the PDF data dictionaries found in the “Documents” tab of the dbGaP study page, which may contain additional information regarding the data or the associated publication(s).

  Study phs004240

• International Cancer Proteogenome Consortium (ICPC): Proteogenomics of Oral Squamous Cell Carcinoma in Taiwan

  Oral cavity squamous cell carcinoma (OSCC) is the major subtype (~90%) of oral cancer, which is leading cancer with high mortality worldwide. The environmental risk factors associated with OSCC are quite different in Taiwan as compared to other populations. In most non-Taiwanese populations, OSCC is often associated with tobacco chewing, cigarette smoking, alcohol drinking, or human papillomavirus (HPV) infection. In Taiwan, in contrast, the OSCC occurs mainly in males aged 30 years or older who have habitual betel nut chewing, cigarette smoking, and alcohol drinking. To uncover molecular mechanisms and identify new therapeutic strategies of oral squamous cell carcinoma, this study recruited 112 treatment-naïve OSCC patients and generated multi-omics data, including WES, RNA-Seq, TMT-labeled proteomes, and phosphoproteomes from paired normal/tumor tissues. We have investigated our multi-omics data, covering molecular characterizations such as mutation signatures, impacts of mutations on RNA/protein/phosphoprotein, RNA-protein correlation, somatic copy number alteration, and the relationship with RNA & protein, proteome, and phosphoproteome analysis (T vs NAT), novel peptides (somatic variants, neoantigens, CT antigens, T cell receptors, etc.), as well as molecular subtyping (& pathway analysis). Notably, we have discovered a higher frequency of APOBEC3B deletion polymorphism in the Taiwanese population, and APOBEC3A is a potential prognostic biomarker. Our proteogenomic data enable us to further stratify patients into four groups based on APOBE3A expression level, which is found inversely correlated with EGFR expression. Therefore, the patients with high EGFR and low APOBEC3A expression may benefit from anti-EGFR therapy, while those with low EGFR and high APOBEC3A expression may benefit from immunotherapy. To clarify if there is an interaction between genetic polymorphisms and betel nut chewing habit in Taiwanese OSCC, we plan to concurrently evaluate the effect of habitual betel nut chewing on the gene mutation pattern, the dysregulated protein/phosphoproteins as novel biomarkers and/or therapeutic targets, and the molecular subtyping of patients for effective treatments. 

  Study phs002580

• Evolution of Structural Rearrangements in Prostate Cancer Intracranial Metastases

  Intracranial metastases in prostate cancer are uncommon but clinically aggressive. We sought to characterize prostate cancer intracranial metastases in order to improve our understanding of their pathogenesis and to promote the search for new treatment strategies. We evaluated the clinical and molecular characteristics of 36 patients with metastatic prostate cancer to either the dura or brain parenchyma. We performed whole genome sequencing (WGS) on samples from 21 patients. The WGS samples include 10 intracranial prostate cancer metastases, as well as WGS of primary prostate tumors from men who later developed metastatic disease (n=6) and non-brain prostate cancer metastases (n=26).

  Study phs003357

• Genetic Factors Associated with Anthracycline-Induced Cardiomyopathy (COG-ALTE03N1)

  We investigated the genetic mechanisms underlying anthracycline-induced cardiomyopathy, a serious long-term complication among childhood cancer survivors. We focused on the role of DNA damage response and repair (DDR) genes, which had not been previously studied in this context. A gene-based and pathway-based approach was applied to assess both the main effects and gene-by-anthracycline interaction effects of DDR genes on cardiomyopathy risk. The analysis was conducted using a matched case-control design within the COG-ALTE03N1 study, including 113 cases and 226 controls, all of whom were non-Hispanic White childhood cancer survivors exposed to anthracyclines. For each case, we randomly selected 1-3 childhood cancer survivors with no cardiomyopathy, matched on primary cancer diagnosis, year of diagnosis (±10y), and race/ethnicity. The selected controls had to have a longer duration of follow-up compared with time from cancer diagnosis to cardiomyopathy for the corresponding case. Participants provided blood or saliva for germline DNA isolation and genotyping. Genotyping was performed using Illumina HumanOmniExpress-12 v1.0 (709,358 SNPs) and IlluminaOmni5Exome-4 v1.3 arrays (4,293,368 SNPs), with merging of genotype data from the two arrays (683,781 overlapped SNPs) and quality control (QC) using PLINK. Of the 220 genes in the MD Anderson DDR gene website, 187 genes with 2,220 single nucleotide polymorphisms [SNPs] identified on our array data were included in the analyses. A total of 2,170 SNPs were retained in the final gene-based and pathway-based analysis in 339 anthracycline-exposed non-Hispanic White (NHW) patients (113 cases; 226 controls). Key findings included significant associations for FANCC and XRCC5 with cardiomyopathy risk (main effect), and a significant gene-environment interaction involving MGMT. The study also confirmed the involvement of DDR-related biological pathways through both genetic association and interaction analyses.Data Available Through dbGaP: • Genotype data (GWAS) for all study participants • Phenotype data: age at primary cancer diagnosis, sex, race/ethnicity, case-control status This dataset supports further research into genetic susceptibility to chemotherapy-induced adverse outcomes and enables cross-cohort comparisons in cardio-oncology.

  Study phs003792

• The Role of E2F4 in Controlling Resistance to Irinotecan (CPT-11) in Human Colon Cancer

  This study reports the results of RNA sequencing (RNA-seq) experiments performed on three isogenic clones of the human HT29 colon cancer cell line, genetically engineered to achieve the selective inactivation of the adenovirus early 2 (E2) gene transcription factor 4 (E2F4) protein, a key functional component of the multimeric transcriptional repression complex known as the dimerization partner (DP), retinoblastoma-like (RB-like), E2F and multi-vulva class B (MuvB) complex (DREAM). In previous studies, we identified E2F4 as a key regulator of colorectal cancer (CRC) resistance to irinotecan (CPT-11), a cytotoxic agent that stands at the backbone of multiple chemotherapy regimens for the treatment of metastatic CRCs. The molecular mechanisms linking E2F4 to irinotecan resistance, however, remain poorly understood. The present study was designed to identify which genes are under the transcriptional control of E2F4, either at baseline or following exposure to SN38 (i.e., the active metabolite of irinotecan, generated in vivo by biotransformation in the liver) in order to clarify the role played by E2F4 in shaping colon cancer resistance to chemotherapy. The cell line used for this study (HT29) is aneuploid and contains three copies of the E2F4 gene, because of a trisomy of chromosome 16, where the E2F4 gene is located (Kawai et al., Genes, Chromosomes & Cancer, 34:1-8, 2002; PMID: 11921276). HT29 cells were infected with lentivirus vectors encoding for CRISPR/Cas9 constructs designed to selectively inactivate the E2F4 gene, using three distinct guide-RNAs (gRNAs), each targeting a different sequence within the proximal exons of the E2F4 gene (exon 1, exon 2). Lentivirus-infected cells were sub-cloned by single-cell fluorescence-activated cell sorting (FACS), based on the differential expression of a fluorescent reporter (EGFP) expressed in tandem with the gRNAs. Isogenic clones (EGFP+) were then screened to identify those with a tri-allelic knock-out, as revealed by both genetic sequencing of the E2F4 gene (revealing the presence of three distinct frameshift mutations) and Western blot (revealing complete loss of E2F4 protein expression). The study includes twelve (n=12) RNA-seq experiments, representative of 3 experimental replicates (i.e., three distinct isogenic clones of the HT29 cell line, each displaying complete loss of E2F4 expression) and 3 negative controls (i.e., three independent preparations of the parent HT29 cell line, infected with a lentivirus vector encoding for a non-targeting gRNA) exposed to 2 distinct in vitro cell culture conditions: a) treatment with SN38 resuspended in dimethyl sulfoxide (DMSO); or b) treatment with DMSO alone (negative control). The in vitro treatment regimen used for SN38 (32 nM, 24 hours) was designed so that the exposure to SN38 experienced in vitro by HT29 cells would mirror the exposure to SN38 experienced in vivo by malignant tissues, as measured, for example, in metastatic CRC patients receiving a standard dose of irinotecan (180 mg/m2) administered by intravenous infusion over 90 minutes (Deyme et al., Cancer Chemotherapy and Pharmacology, 88:247-258, 2021; PMID: 33912999).

  Study phs003560

• Proteogenomic Characterization Unveils Biomarkers Associated With Chemoresistance in Muscle Invasive Bladder Cancer

  Cisplatin-based neoadjuvant chemotherapy (NAC) combined with radical cystectomy has been used as a standard of care for patients with clinically non-metastatic muscle invasive urothelial bladder cancer, but 40-50% patients will benefit from the treatment. Molecular subtypes of muscle invasive bladder cancer (MIBC) provide a possible biomarker roadmap that may help identify patients who may or may not respond to NAC. Recently, by integrating Mass Spectrometry-based proteomics, proteogenomic studies from the Clinical Proteomic Tumor Analysis Consortium (CPTAC) have demonstrated the potential of this approach in prioritizing candidate driver genes and facilitating understanding of the chemotherapy resistance mechanisms. To demonstrate the proteogenomic workflow for investigating the mechanisms underlying chemotherapy resistance in MIBC, we conducted proteogenomic characterization of 46 pre- and 14 post- treatment tumors, including whole exome sequencing (WES), mRNA sequencing, Tandem Mass Tag (TMT)-proteomics, or TMT-phosphoproteomic. These samples were selected from an initial cohort of 143 MIBC tissues and filtered by tumor purity, clinical history, pathological response, and proteomic quality control metrics. The final cohort comprised samples from 53 patients, including 45 with both genomic and proteomic data and 8 with genomic data only.Our multi-omics-based clustering reveals subtypes associated with chemotherapy sensitivity. Protein abundance of a short isoform of ATAD1 and RAF family proteins were identified as biomarkers of chemosensitivity which highlights the importance of proteomics data. Integration of proteomic and phosphoproteomic data reveals Wnt signaling via GSK3B-S9 phosphorylation and the JAK/STAT pathway as potential targets to overcome chemoresistance. Correlations between PD-L1 and TROP-2/NECTIN-4 indicate an additive benefit of combination therapy targeting these proteins. Our data analysis clearly demonstrates that proteogenomic plays an important role in uncovering potential resistance mechanisms that operate only at protein and Post-Translational Modification (PTM) levels. Proteomics data can be accessed through PRIDE with ID PXD060290. RNA-seq and whole-exome sequencing (WES) FASTQ files are archived in the dbGaP database.

  Study phs004049

• Blood and Marrow Clinical Trials Network Trial of Non-Myeloablative Conditioning and Transplantation of Umbilical Cord Blood For Hematologic Malignancies (BMT CTN-0604-BioLINCC)

  Data Access NOTE: Please refer to the “Authorized Access” section below for information about how access to the data from this accession differs from many other dbGaP accessions.Objectives: To examine the safety and effectiveness of a non-myeloablative stem cell transplant using umbilical cord blood as a treatment option for patients with leukemia or lymphoma and no suitable related donor.Background: Chemotherapy is a common treatment option for patients with aggressive forms of the blood cancers leukemia and lymphoma, but other treatment methods may need to be considered if the cancer does not respond well to chemotherapy, or if the cancer returns. In such cases, it may be recommended that the patient receive a stem cell transplant, commonly using donated bone marrow. A first degree relative is likely to be the best candidate for donation if the human leukocyte antigen (HLA) markers are a sufficient match. For patients lacking a HLA-matched related donor, it is routine to initiate an unrelated donor search. However some patients, particularly ethnic minorities, experience disease progression while awaiting identification of a suitably HLA-matched donor. Recently, stem cell transplants using umbilical cord blood have become a viable alternative option to treat these types of cancers.Typically patients undergoing a stem cell transplant receive high doses of chemotherapy before the transplant to prepare their bodies to accept the donor stem cells. In this study, participants received a type of stem cell transplant called a non-myeloablative transplant, which is a reduced intensity conditioning (RIC) method of transplantation that does not require high doses of chemotherapy. RIC can be preferable in patients that are older and less clinically fit, and therefore less able to withstand the chemotherapeutic agents' toxicity levels.The BMT CTN 0604 study was one of two parallel multicenter phase 2 studies; the other of which was BMT CTN 0603, which used partially HLA-mismatched related bone marrow (Haplo-marrow) transplantation. The goal of these studies was to generate pilot multicenter data to support a future phase 3 randomized clinical trial.Participants: Patients less than 71 years of age with acute leukemia or lymphoma and lacking a suitable HLA-matched related donor were eligible to participate. Patients less than 22 years of age were eligible if they were ineligible for the BMT CTN 0501 trial. Acute leukemia was required to be in morphologic complete remission. Large-cell, mantle-cell, and Hodgkin lymphomas were required to have achieved at least a partial remission with treatment before allogeneic hematopoietic cell transplantation. Low-grade lymphoma patients were required to have failed two prior chemotherapy regimens. Patients who had undergone prior autologous transplantation were not excluded as long as three months had elapsed since the procedure. Participants were also required to have adequate organ function, including a left ventricular ejection fraction of at least 35% and specific liver, kidney, pulmonary, and physical functioning scores within acceptable ranges. A total of 54 individuals were enrolled in the study and 50 were included in the analysis.Design: Participants underwent a reduced intensity conditioning regimen prior to receiving the double umbilical cord blood (dUCB) transplant, which included two chemotherapeutic agents, cyclophosphamide and fludarabine, and a small dose of radiation. Cyclophosphamide was administered intravenously at 50 mg/kg six days before the transplant. Fludarabine was administered intravenously at 40 mg/m2 (adjusted for creatinine clearance) each day for five days before the transplant. A single dose of 200 cGy total body irradiation was performed one day prior to transplantation. Participants also received cyclosporine and mycophenolate mofetil (MMF) beginning three days before the transplant as prophylaxis for graft-versus-host-disease (GVHD). Participants could receive tacrolimus instead of cyclosporine.At transplantation, patients received two partially HLA-matched umbilical cord blood units from unrelated donors. The maximum allowable mismatch between the UCB unit and the recipient, or between the UCB units, was 2 of 6 HLA loci. Each unit contained a minimum of 1.5 × 107 nucleated cells, or 2.0 × 107 for units that were not red cell depleted, per kilogram of recipient weight. Units were thawed and infused per institutional practice after validation using methods approved by the study. After transplantation, filgrastim, a granulocyte-colony stimulating factor, was initiated at 5 μg/kg a day and continued until the absolute neutrophil count was at least 2000/μL for three consecutive days. Participants continued to receive MMF for 30 days after the transplant or 7 days after engraftment, whichever was later, and cyclosporine or tacrolimus until 180 to 200 days after the transplant. Supportive care, including blood product administration, prophylaxis, therapy for infection, and treatment of GVHD, was at the discretion of treating physicians and transplantation center practices.The primary outcome was participant survival from the time of transplant to 180 days. Secondary end points included progression-free survival and cumulative incidences of hematopoietic recovery, acute or chronic GVHD, relapse, and non-relapse mortality.Conclusions: Survival at 180 days after double umbilical cord blood transplant was 74%. Collectively, the results of BMT CTN 0603 and 0604 confirm the utility of dUCB and Haplo-marrow as alternative donor sources for reduced intensity conditioning hematopoietic cell transplantation, providing a rationale for an additional clinical trial to assess the relative efficacy of these two strategies.

  Study phs004890

• A Phase II Study: CRS207/GVAX Plus Anti-PD1 and Anti-CTLA4 Recruits Mesothelin- and KRAS-Specific T cells into PDAC

  This study examined immunologic correlatives from a phase II study evaluating CRS207/GVAX vaccines in combination with anti-PD1 and anti-CTLA4 in metastatic pancreatic cancer (NCT03190265). Arm A received CRS207/GVAX with anti-PD1 and anti-CTLA4 therapy; Arm B received CRS207 with anti-PD1 and anti-CTLA4 therapy. Patients undergoing treatment in this trial had peripheral blood mononuclear cells (PBMCs) and tumor tissue biopsied serially at pre-treatment and on-treatment timepoints. Single-cell RNA/TCR sequencing was employed on PBMCs. Bulk RNA/TCR sequencing was employed on tumor tissues. We identified treatment-enriched inflammatory pathways as well as T cell repertoires.

  Study phs003798

• Correlative Studies in Protocol GU16-287, which Studied Gemcitabine + (Carboplatin or Oxaliplatin) + Nivolumab in Metastatic Urothelial Cancer, which Included Collaboration with CIMAC-CIDC (Cohort 1 of 3)

  Purpose: Oxaliplatin has demonstrated the ability to sensitize tumors to immune checkpoint blockade through its immunomodulatory properties in model systems of cancer. This randomized trial aimed to evaluate gemcitabine/oxaliplatin and gemcitabine/carboplatin, each combined with nivolumab, in cisplatin-ineligible metastatic urothelial carcinoma (mUC) patients. Patients and Methods: Cisplatin-ineligible patients with mUC were randomized 1:1 to gemcitabine/carboplatin plus nivolumab or gemcitabine/oxaliplatin plus nivolumab for up to 6 cycles, followed by nivolumab monotherapy. A pick-the-winner design was employed with objective response rate (ORR) as the primary endpoint. Secondary endpoints included progression-free survival (PFS) and overall survival (OS). Exploratory analyses evaluated plasma protein analytes, circulating immune cell populations, and circulating tumor cells. Results: Forty-nine patients were enrolled (carboplatin arm, N = 25; oxaliplatin arm, N = 24). The ORR was 69.6% (95% confidence interval [CI] 0.48–0.87) for the carboplatin arm and 33.3% (95% CI 0.15–0.57) for the oxaliplatin arm. Median OS was 24.74 months and 16.43 months for the carboplatin group and oxaliplatin arms, respectively (hazard ratio 1.99, 95% CI 0.94–4.22; p = 0.07). Exploratory biomarker analyses revealed sustained adaptive immune activation in the carboplatin arm and features suggestive of tumor-promoting inflammation in the oxaliplatin arm. Conclusions:Oxaliplatin-based chemo-immunotherapy, versus carboplatin-based chemo-immunotherapy, did not yield a higher response rate, challenging assumptions based on preclinical data.

  Study phs004060