Browsing by Subject "Neoplasms"
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Item Advances in translational bioinformatics facilitate revealing the landscape of complex disease mechanisms(Springer (Biomed Central Ltd.), 2014) Yang, Jack Y.; Dunker, A. Keith; Liu, Jun S.; Qin, Xiang; Arabnia, Hamid R.; Yang, William; Niemierko, Andrzej; Chen, Zhongxue; Luo, Zuojie; Wang, Liangjiang; Liu, Yunlong; Xu, Dong; Deng, Youping; Tong, Weida; Yang, Mary Qu; Department of Biochemistry and Molecular Biology, IU School of MedicineAdvances of high-throughput technologies have rapidly produced more and more data from DNAs and RNAs to proteins, especially large volumes of genome-scale data. However, connection of the genomic information to cellular functions and biological behaviours relies on the development of effective approaches at higher systems level. In particular, advances in RNA-Seq technology has helped the studies of transcriptome, RNA expressed from the genome, while systems biology on the other hand provides more comprehensive pictures, from which genes and proteins actively interact to lead to cellular behaviours and physiological phenotypes. As biological interactions mediate many biological processes that are essential for cellular function or disease development, it is important to systematically identify genomic information including genetic mutations from GWAS (genome-wide association study), differentially expressed genes, bidirectional promoters, intrinsic disordered proteins (IDP) and protein interactions to gain deep insights into the underlying mechanisms of gene regulations and networks. Furthermore, bidirectional promoters can co-regulate many biological pathways, where the roles of bidirectional promoters can be studied systematically for identifying co-regulating genes at interactive network level. Combining information from different but related studies can ultimately help revealing the landscape of molecular mechanisms underlying complex diseases such as cancer.Item Allele-Specific Reprogramming of Cancer Metabolism by the Long Non-coding RNA CCAT2(Elsevier, 2016-02-18) Redis, Roxana S.; Vela, Luz E.; Lu, Weiqin; de Oliveira, Juliana Ferreira; Ivan, Cristina; Rodriguez-Aguayo, Cristian; Adamoski, Douglas; Pasculli, Barbara; Taguchi, Ayumu; Chen, Yunyun; Fernandez, Agustin F.; Valledor, Luis; Van Roosbroeck, Katrien; Chang, Samuel; Shah, Maitri; Kinnebrew, Garrett; Han, Leng; Atlasi, Yaser; Cheung, Lawrence H.; Huang, Gilbert Yuanjay; Monroig, Paloma; Ramirez, Marc S.; Ivkovic, Tina Catela; Van, Long; Ling, Hui; Gafà, Roberta; Kapitanovic, Sanja; Lanza, Giovanni; Bankson, James A.; Huang, Peng; Lai, Stephan Y.; Bast, Robert C.; Rosenblum, Michael G.; Radovich, Milan; Ivan, Mircea; Bartholomeusz, Geoffrey; Liang, Han; Fraga, Mario F.; Widger, William R.; Hanash, Samir; Berindan-Neagoe, Ioana; Lopez-Berestein, Gabriel; Ambrosio, Andre L.B.; Dias, Sandra M Gomes; Calin, George A.; Department of Surgery, IU School of MedicineAltered energy metabolism is a cancer hallmark as malignant cells tailor their metabolic pathways to meet their energy requirements. Glucose and glutamine are the major nutrients that fuel cellular metabolism, and the pathways utilizing these nutrients are often altered in cancer. Here, we show that the long ncRNA CCAT2, located at the 8q24 amplicon on cancer risk-associated rs6983267 SNP, regulates cancer metabolism in vitro and in vivo in an allele-specific manner by binding the Cleavage Factor I (CFIm) complex with distinct affinities for the two subunits (CFIm25 and CFIm68). The CCAT2 interaction with the CFIm complex fine-tunes the alternative splicing of Glutaminase (GLS) by selecting the poly(A) site in intron 14 of the precursor mRNA. These findings uncover a complex, allele-specific regulatory mechanism of cancer metabolism orchestrated by the two alleles of a long ncRNA.Item Assessment of folate receptor-β expression in human neoplastic tissues(Impact Journals, LLC, 2015-06-10) Shen, Jiayin; Putt, Karson S.; Visscher, Daniel W.; Murphy, Linda; Cohen, Cynthia; Singhal, Sunil; Sandusky, George; Feng, Yang; Dimitrov, Dimiter S.; Low, Philip S.; Department of Pathology & Laboratory Medicine, IU School of MedicineOver-expression of folate receptor alpha on cancer cells has been frequently exploited for delivery of folate-targeted imaging and therapeutic agents to tumors. Because limited information exists on expression of the beta isoform of the folate receptor in human cancers (FR-β), we have evaluated the immunohistochemical staining pattern of FR-β in 992 tumor sections from 20 different human cancer types using a new anti-human FR-β monoclonal antibody. FR-β expression was shown to be more pronounced in cells within the stroma, primarily macrophages and macrophage-like cells than cancer cells in every cancer type studied. Moreover, FR-β expression in both cancer and stromal cells was found to be statistically more prominent in females than males. A significant positive correlation was also observed between FR-β expression on stromal cells and both the stage of the cancer and the presence of lymph node metastases. Based on these data we conclude FR-β may constitute a good target for specific delivery of therapeutic agents to activated macrophages and that accumulation of FR-β positive macrophages in the stroma could serve as a useful indicator of a tumor's metastatic potential.Item Author Correction: Hypoxia-mediated downregulation of miRNA biogenesis promotes tumour progression(Nature, 2020-06-03) Rupaimoole, Rajesha; Wu, Sherry Y.; Pradeep, Sunila; Ivan, Cristina; Pecot, Chad V.; Gharpure, Kshipra M.; Nagaraja, Archana S.; Armaiz-Pena, Guillermo N.; McGuire, Michael; Zand, Behrouz; Dalton, Heather J.; Filant, Justyna; Miller, Justin Bottsford; Lu, Chunhua; Sadaoui, Nouara C.; Mangala, Lingegowda S.; Taylor, Morgan; van den Beucken, Twan; Koch, Elizabeth; Rodriguez-Aguayo, Cristian; Huang, Li; Bar-Eli, Menashe; Wouters, Bradly G.; Radovich, Milan; Ivan, Mircea; Calin, George A.; Zhang, Wei; Lopez-Berestein, Gabriel; Sood, Anil K.; Medicine, School of MedicineThis Article contains an error in Fig. 4. During the preparation of Fig. 4d, the image representing showing E-CADHERIN expression under hypoxia conditions in A2780 cells was inadvertently taken from the image in Supplementary Fig. 15C showing E-CADHERIN expression under hypoxia conditions in SKOV3 cells. The correct version of Fig. 4 is shown below. The error has not been corrected in the PDF or HTML versions of the Article.Item c-FLIP, a master anti-apoptotic regulator(Morion, 2012-10) Safa, A. R.; Department of Pharmacology and Toxicology, IU School of MedicineCellular FLICE (FADD-like IL-1β-converting enzyme)-inhibitory protein (c-FLIP) is a master anti-apoptotic regulator and resistance factor that suppresses tumor necrosis factor-α (TNF-α), Fas-L, and TNF-related apoptosis-inducing ligand (TRAIL)-induced apoptosis, as well as apoptosis triggered by chemotherapy agents in malignant cells. c-FLIP is expressed as long (c-FLIP(L)), short (c-FLIP(S)), and c-FLIP(R) splice variants in human cells. c-FLIP binds to FADD and/or caspase-8 or -10 and TRAIL receptor 5 (DR5) in a ligand-dependent and -independent fashion and forms an apoptosis inhibitory complex (AIC). This interaction in turn prevents death-inducing signaling complex (DISC) formation and subsequent activation of the caspase cascade. c-FLIP(L) and c-FLIP(S) are also known to have multifunctional roles in various signaling pathways, as well as activating and/or upregulating several cytoprotective and pro-survival signaling proteins including Akt, ERK, and NF-kB. Upregulation of c-FLIP has been found in various tumor types, and its silencing has been shown to restore apoptosis triggered by cytokines and various chemotherapeutic agents. Hence, c-FLIP is an important target for cancer therapy. For example, small interfering RNAs (siRNAs) that specifically knockdown the expression of c-FLIP(L) in diverse human cancer cell lines augmented TRAIL-induced DISC recruitment and increased the efficacy of chemotherapeutic agents, thereby enhancing effector caspase stimulation and apoptosis. Moreover, small molecules causing degradation of c-FLIP as well as decreasing mRNA and protein levels of c-FLIP(L) and c-FLIP(S) splice variants have been found, and much effort is focused on developing other c-FLIP-targeted cancer therapies. This review focuses on (1) the anti-apoptotic role of c-FLIP splice variants in preventing apoptosis and inducing cytokine and chemotherapy drug resistance, (2) the molecular mechanisms and factors that regulate c-FLIP expression, and (3) modulation of c-FLIP expression and function to eliminate cancer cells or increase the efficacy of anticancer agents. This article is part of a Special Issue entitled "Apoptosis: Four Decades Later".Item Cancer survivors' uptake and adherence in diet and exercise intervention trials: an integrative data analysis(Wiley, 2015-01-01) Adams, Rebecca N.; Mosher, Catherine E.; Blair, Cindy K.; Snyder, Denise C.; Sloane, Richard; Demark-Wahnefried, Wendy; Department of Psychology, School of ScienceBACKGROUND: The health benefits of diet and exercise interventions for cancer survivors are well documented. However, little is known regarding demographic and medical predictors of survivors' willingness to participate in diet and exercise intervention trials, study enrollment, intervention adherence, and study completion. To assist in interpreting the generalizability of trial findings and to improve the design of future trials, this study examined predictors of these process measures. METHODS: An integrative data analysis was performed on data from 3 of the largest home-based diet and exercise intervention trials for cancer survivors (n = 23,841). Demographic and medical factors (ie, sex, race, age, time since diagnosis, and cancer type) were examined as predictors of willingness to participate, study enrollment, intervention adherence, and study completion in the pooled sample. A 99% confidence interval was used to determine statistical significance. RESULTS: Across trials, 11.1% of contacted survivors were willing to participate, and 5.7% were eligible and enrolled. Among enrollees, 53.4% demonstrated ≥75% adherence to the intervention, and 91.1% completed the study. Race (Caucasian vs others), age, time since diagnosis, and cancer type predicted survivors' willingness to participate (P < .01). All examined predictors were associated with the likelihood of study enrollment (P < .01). No significant predictors of intervention adherence or study completion were found among study enrollees (P ≥ .01). CONCLUSIONS: Cancer survivors' demographic and medical characteristics predicted their interest and participation in diet and exercise intervention trials. These findings have implications for the generalizability of results and can help to guide procedures used in future trials to enhance patient representation.Item Comparative Responsiveness of Pain Measures in Cancer Patients(Elsevier, 2012-08) Kroenke, Kurt; Theobald, Dale; Wu, Jingwei; Tu, Wanzhu; Krebs, Erin E.; Department of Medicine, IU School of MedicineBrief measures to assess and monitor pain in cancer patients are available, but few head-to-head psychometric comparisons of different measures have been reported. Baseline and 3-month data were analyzed from 274 patients enrolled in the Indiana Cancer Pain and Depression (INCPAD) trial. Participants completed the Brief Pain Inventory (BPI), the PEG (a 3-item abbreviated version of the BPI), the short form (SF)-36 pain scale, and a pain global rating of change measure. The global rating was used as the criterion for standardized response mean and receiver operating characteristic curve analyses. To assess responsiveness to the trial intervention, we evaluated standardized effect size statistics stratified by trial arm. All measures were responsive to global improvement, discriminated between participants with and without improvement, and detected a significant intervention treatment effect. Short and longer measures were similarly responsive. Also, composite measures that combined pain severity and interference into a single score (BPI total, PEG, SF-36 pain) performed comparably to separate measures of each domain (BPI severity and BPI interference).Item Cost effectiveness of telecare management for pain and depression in patients with cancer: results from a randomized trial(Elsevier, 2014-11) Choi Yoo, Sung J.; Nyman, John A.; Cheville, Andrea L.; Kroenke, Kurt; Department of Medicine, IU School of MedicineOBJECTIVE: Pain and depression are prevalent and treatable symptoms among patients with cancer, yet they are often undetected and undertreated. The Indiana Cancer Pain and Depression (INCPAD) trial demonstrated that telecare management can improve pain and depression outcomes. This article investigates the incremental cost effectiveness of the INCPAD intervention. METHODS: The INCPAD trial was conducted in 16 community-based urban and rural oncology practices in Indiana. Of the 405 participants, 202 were randomized to the intervention group and 203 to the usual-care group. Intervention costs were determined, and effectiveness outcomes were depression-free days and quality-adjusted life years. RESULTS: The intervention group was associated with a yearly increase of 60.3 depression-free days (S.E. = 15.4; P < 0.01) and an increase of between 0.033 and 0.066 quality-adjusted life years compared to the usual care group. Total cost of the intervention per patient was US$1189, which included physician, nurse care manager and automated monitoring set-up and maintenance costs. Incremental cost per depression-free day was US$19.72, which yields a range of US$18,018 to US$36,035 per quality-adjusted life year when converted to that metric. When measured directly, the incremental cost per quality-adjusted life year ranged from US$10,826 based on the modified EQ-5D to US$73,286.92 based on the SF-12. CONCLUSION: Centralized telecare management, coupled with automated symptom monitoring, appears to be a cost effective intervention for managing pain and depression in cancer patients.Item Developing an organizing framework to guide nursing research in the Children’s Oncology Group (COG)(Elsevier, 2014-02) Kelly, Katherine Patterson; Hooke, Mary C.; Ruccione, Kathleen; Landier, Wendy; Haase, Joan E.; School of NursingObjectives To describe the development and application of an organizing research framework to guide COG Nursing research. Data Sources Research articles, reports and meeting minutes Conclusion An organizing research framework helps to outline research focus and articulate the scientific knowledge being produced by nurses in the pediatric cooperative group. Implication for Nursing Practice The use of an organizing framework for COG nursing research can facilitate clinical nurses’ understanding of how children and families sustain or regain optimal health when faced with a pediatric cancer diagnosis through interventions designed to promote individual and family resilience., The Children’s Oncology Group (COG) is the sole National Cancer Institute (NCI)-supported cooperative pediatric oncology clinical trials group and the largest organization in the world devoted exclusively to pediatric cancer research. It was founded in 2000 following the merger of the four legacy NCI-supported pediatric clinical trials groups (Children’s Cancer Group [CCG], Pediatric Oncology Group [POG], National Wilms Tumor Study Group, and Intergroup Rhabdomyosarcoma Study Group). The COG currently has over 200 member institutions across North America, Australia, New Zealand and Europe and a multidisciplinary membership of over 8,000 pediatric, radiation, and surgical oncologists, nurses, clinical research associates, pharmacists, behavioral scientists, pathologists, laboratory scientists, patient/parent advocates and other pediatric cancer specialists. The COG Nursing Discipline was formed from the merger of the legacy CCG and POG Nursing Committees, and current membership exceeds 2000 registered nurses. The discipline has a well-developed infrastructure that promotes nursing involvement throughout all levels of the organization, including representation on disease, protocol, scientific, executive and other administrative committees (e.g., nominating committee, data safety monitoring boards). COG nurses facilitate delivery of protocol-based treatments for children enrolled on COG protocols, and Nursing Discipline initiatives support nursing research, professional and patient/family education, evidence-based practice, and a patient-reported outcomes resource center. The research agenda of the Nursing Discipline is enacted through a well-established nursing scholar program.Item DNA repair targeted therapy: The past or future of cancer treatment?(Elsevier, 2016-04) Gavande, Navnath S.; VanderVere-Carozza, Pamela S.; Hinshaw, Hilary D.; Jalal, Shadia I.; Sears, Catherine R.; Pawelczak, Katherine S.; Turchi, John J.; Department of Medicine, School of MedicineThe repair of DNA damage is a complex process that relies on particular pathways to remedy specific types of damage to DNA. The range of insults to DNA includes small, modest changes in structure including mismatched bases and simple methylation events to oxidized bases, intra- and interstrand DNA crosslinks, DNA double strand breaks and protein-DNA adducts. Pathways required for the repair of these lesions include mismatch repair, base excision repair, nucleotide excision repair, and the homology directed repair/Fanconi anemia pathway. Each of these pathways contributes to genetic stability, and mutations in genes encoding proteins involved in these pathways have been demonstrated to promote genetic instability and cancer. In fact, it has been suggested that all cancers display defects in DNA repair. It has also been demonstrated that the ability of cancer cells to repair therapeutically induced DNA damage impacts therapeutic efficacy. This has led to targeting DNA repair pathways and proteins to develop anti-cancer agents that will increase sensitivity to traditional chemotherapeutics. While initial studies languished and were plagued by a lack of specificity and a defined mechanism of action, more recent approaches to exploit synthetic lethal interaction and develop high affinity chemical inhibitors have proven considerably more effective. In this review we will highlight recent advances and discuss previous failures in targeting DNA repair to pave the way for future DNA repair targeted agents and their use in cancer therapy.