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Item A 61-year-old woman with osteomalacia and a thoracic spine lesion(Wiley, 2010-03) Marshall, Ann E.; Martin, Sarah E.; Agaram, Narasimhan P.; Chen, Jey-Hsin; Horn, Eric M.; Douglas-Akinwande, Annette C.; Hattab, Eyas M.; Pathology and Laboratory Medicine, School of MedicinePhosphaturic mesenchymal tumor, mixed connective tissue variant (PMT-MCT) is a rare, largely benign, mesenchymal neoplasm almost invariably associated with oncogenic osteomalacia. It is generally found in the soft tissue and bone of the extremities. We report a case of a 61-year-old female with long-standing osteomalacia who was found to have PMT-MCT of the thoracic spine. There have been very few previously reported cases of PMT involving the spinal vertebrae and neuropathologists should be aware of this lesion. Recognition of PMT-MCT is critical for optimal patient care since complete surgical resection without additional therapy is curative.Item A Systematic Review of Functional Outcomes in Cancer Rehabilitation Research(Elsevier, 2022) Sleight, Alix G.; Gerber, Lynn H.; Marshall, Timothy F.; Livinski, Alicia; Alfano, Catherine M.; Harrington, Shana; Flores, Ann Marie; Virani, Aneesha; Hu, Xiaorong; Mitchell, Sandra A.; Varedi, Mitra; Eden, Melissa; Hayek, Samah; Reigle, Beverly; Kerkman, Anya; Neves, Raquel; Jablonoski, Kathleen; Hacker, Eileen; Sun, Virginia; Newman, Robin; McDonnell, Karen Kane; L’Hotta, Allison; Schoenhals, Alana; Stout, Nicole L.; School of NursingObjective: To systematically review the evidence regarding rehabilitation interventions targeting optimal physical or cognitive function in adults with a history of cancer and describe the breadth of evidence as well as strengths and limitations across a range of functional domains. Data sources: PubMed, Cumulative Index to Nursing and Allied Health Plus, Scopus, Web of Science, and Embase. The time scope was January 2008 to April 2019. Study selection: Prospective, controlled trials including single- and multiarm cohorts investigating rehabilitative interventions for cancer survivors at any point in the continuum of care were included, if studies included a primary functional outcome measure. Secondary data analyses and pilot/feasibility studies were excluded. Full-text review identified 362 studies for inclusion. Data extraction: Extraction was performed by coauthor teams and quality and bias assessed using the American Academy of Neurology (AAN) Classification of Evidence Scheme (class I-IV). Data synthesis: Studies for which the functional primary endpoint achieved significance were categorized into 9 functional areas foundational to cancer rehabilitation: (1) quality of life (109 studies), (2) activities of daily living (61 studies), (3) fatigue (59 studies), (4) functional mobility (55 studies), (5) exercise behavior (37 studies), (6) cognition (20 studies), (7) communication (10 studies), (8) sexual function (6 studies), and (9) return to work (5 studies). Most studies were categorized as class III in quality/bias. Averaging results found within each of the functional domains, 71% of studies reported statistically significant results after cancer rehabilitation intervention(s) for at least 1 functional outcome. Conclusions: These findings provide evidence supporting the efficacy of rehabilitative interventions for individuals with a cancer history. The findings should be balanced with the understanding that many studies had moderate risk of bias and/or limitations in study quality by AAN criteria. These results may provide a foundation for future work to establish clinical practice guidelines for rehabilitative interventions across cancer disease types.Item Acceptance and commitment therapy for patient fatigue interference and caregiver burden in advanced gastrointestinal cancer: Results of a pilot randomized trial(Sage, 2022) Mosher, Catherine E.; Secinti, Ekin; Wu, Wei; Kashy, Deborah A.; Kroenke, Kurt; Bricker, Jonathan B.; Helft, Paul R.; Turk, Anita A.; Loehrer, Patrick J., Sr.; Sehdev, Amikar; Al-Hader, Ahmad A.; Champion, Victoria L.; Johns, Shelley A.; Psychology, School of ScienceBackground: Fatigue often interferes with functioning in patients with advanced cancer, resulting in increased family caregiver burden. Acceptance and commitment therapy, a promising intervention for cancer-related suffering, has rarely been applied to dyads coping with advanced cancer. Aim: To examine the feasibility, acceptability, and preliminary efficacy of acceptance and commitment therapy for patient-caregiver dyads coping with advanced gastrointestinal cancer. Primary outcomes were patient fatigue interference and caregiver burden. Design: In this pilot trial, dyads were randomized to six weekly sessions of telephone-delivered acceptance and commitment therapy or education/support, an attention control. Outcomes were assessed at baseline and at 2 weeks and 3 months post-intervention. Setting/participants: Forty patients with stage III-IV gastrointestinal cancer and fatigue interference and family caregivers with burden or distress were recruited from two oncology clinics and randomized. Results: The eligibility screening rate (54%) and retention rate (81% at 2 weeks post-intervention) demonstrated feasibility. At 2 weeks post-intervention, acceptance and commitment therapy participants reported high intervention helpfulness (mean=4.25/5.00). Group differences in outcomes were not statistically significant. However, when examining within-group change, acceptance and commitment therapy patients showed moderate decline in fatigue interference at both follow-ups, whereas education/support patients did not show improvement at either follow-up. Acceptance and commitment therapy caregivers showed medium decline in burden at 2 weeks that was not sustained at 3 months, whereas education/support caregivers showed little change in burden. Conclusions: Acceptance and commitment therapy showed strong feasibility, acceptability, and promise and warrants further testing.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 Asparagine bioavailability regulates the translation of MYC oncogene(Springer Nature, 2022) Srivastava, Sankalp; Jiang, Jie; Misra, Jagannath; Seim, Gretchen; Staschke, Kirk A.; Zhong, Minghua; Zhou, Leonardo; Liu, Yu; Chen, Chong; Davé, Utpal; Kapur, Reuben; Batra, Sandeep; Zhang, Chi; Zhou, Jiehao; Fan, Jing; Wek, Ronald C.; Zhang, Ji; Pediatrics, School of MedicineAmino acid restriction has recently emerged as a compelling strategy to inhibit tumor growth. Recent work suggests that amino acids can regulate cellular signaling in addition to their role as biosynthetic substrates. Using lymphoid cancer cells as a model, we found that asparagine depletion acutely reduces the expression of c-MYC protein without changing its mRNA expression. Furthermore, asparagine depletion inhibits the translation of MYC mRNA without altering the rate of MYC protein degradation. Of interest, the inhibitory effect on MYC mRNA translation during asparagine depletion is not due to the activation of the general controlled nonderepressible 2 (GCN2) pathway and is not a consequence of the inhibition of global protein synthesis. In addition, both the 5' and 3' untranslated regions (UTRs) of MYC mRNA are not required for this inhibitory effect. Finally, using a MYC-driven mouse B cell lymphoma model, we found that shRNA inhibition of asparagine synthetase (ASNS) or pharmacological inhibition of asparagine production can significantly reduce the MYC protein expression and tumor growth when environmental asparagine becomes limiting. Since MYC is a critical oncogene, our results uncover a molecular connection between MYC mRNA translation and asparagine bioavailability and shed light on a potential to target MYC oncogene post-transcriptionally through asparagine restriction.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 Baseline Features and Reasons for Nonparticipation in the Colonoscopy Versus Fecal Immunochemical Test in Reducing Mortality From Colorectal Cancer (CONFIRM) Study, a Colorectal Cancer Screening Trial(American Medical Association, 2023-07-03) Robertson, Douglas J.; Dominitz, Jason A.; Beed, Alexander; Boardman, Kathy D.; Del Curto, Barbara J.; Guarino, Peter D.; Imperiale, Thomas F.; LaCasse, Andrew; Larson, Meaghan F.; Gupta, Samir; Lieberman, David; Planeta, Beata; Shaukat, Aasma; Sultan, Shanaz; Menees, Stacy B.; Saini, Sameer D.; Schoenfeld, Philip; Goebel, Stephan; von Rosenvinge, Erik C.; Baffy, Gyorgy; Halasz, Ildiko; Pedrosa, Marcos C.; Kahng, Lyn Sue; Cassim, Riaz; Greer, Katarina B.; Kinnard, Margaret F.; Bhatt, Divya B.; Dunbar, Kerry B.; Harford, William V.; Mengshol, John A.; Olson, Jed E.; Patel, Swati G.; Antaki, Fadi; Fisher, Deborah A.; Sullivan, Brian A.; Lenza, Christopher; Prajapati, Devang N.; Wong, Helen; Beyth, Rebecca; Lieb, John G.; Manlolo, Joseph; Ona, Fernando V.; Cole, Rhonda A.; Khalaf, Natalia; Kahi, Charles J.; Kohli, Divyanshoo Rai; Rai, Tarun; Sharma, Prateek; Anastasiou, Jiannis; Hagedorn, Curt; Fernando, Ronald S.; Jackson, Christian S.; Jamal, M. Mazen; Lee, Robert H.; Merchant, Farrukh; May, Folasade P.; Pisegna, Joseph R.; Omer, Endashaw; Parajuli, Dipendra; Said, Adnan; Nguyen, Toan D.; Tombazzi, Claudio Ruben; Feldman, Paul A.; Jacob, Leslie; Koppelman, Rachel N.; Lehenbauer, Kyle P.; Desai, Deepak S.; Madhoun, Mohammad F.; Tierney, William M.; Ho, Minh Q.; Hockman, Heather J.; Lopez, Christopher; Carter Paulson, Emily; Tobi, Martin; Pinillos, Hugo L.; Young, Michele; Ho, Nancy C.; Mascarenhas, Ranjan; Promrat, Kirrichai; Mutha, Pritesh R.; Pandak, William M.; Shah, Tilak; Schubert, Mitchell; Pancotto, Frank S.; Gawron, Andrew J.; Underwood, Amelia E.; Ho, Samuel B.; Magno-Pagatzaurtundua, Priscilla; Toro, Doris H.; Beymer, Charles H.; Kaz, Andrew M.; Elwing, Jill; Gill, Jeffrey A.; Goldsmith, Susan F.; Yao, Michael D.; Protiva, Petr; Pohl, Heiko; Kyriakides, Tassos; CONFIRM Study Group; Medicine, School of MedicineImportance: The Colonoscopy Versus Fecal Immunochemical Test in Reducing Mortality From Colorectal Cancer (CONFIRM) randomized clinical trial sought to recruit 50 000 adults into a study comparing colorectal cancer (CRC) mortality outcomes after randomization to either an annual fecal immunochemical test (FIT) or colonoscopy. Objective: To (1) describe study participant characteristics and (2) examine who declined participation because of a preference for colonoscopy or stool testing (ie, fecal occult blood test [FOBT]/FIT) and assess that preference's association with geographic and temporal factors. Design, setting, and participants: This cross-sectional study within CONFIRM, which completed enrollment through 46 Department of Veterans Affairs medical centers between May 22, 2012, and December 1, 2017, with follow-up planned through 2028, comprised veterans aged 50 to 75 years with an average CRC risk and due for screening. Data were analyzed between March 7 and December 5, 2022. Exposure: Case report forms were used to capture enrolled participant data and reasons for declining participation among otherwise eligible individuals. Main outcomes and measures: Descriptive statistics were used to characterize the cohort overall and by intervention. Among individuals declining participation, logistic regression was used to compare preference for FOBT/FIT or colonoscopy by recruitment region and year. Results: A total of 50 126 participants were recruited (mean [SD] age, 59.1 [6.9] years; 46 618 [93.0%] male and 3508 [7.0%] female). The cohort was racially and ethnically diverse, with 748 (1.5%) identifying as Asian, 12 021 (24.0%) as Black, 415 (0.8%) as Native American or Alaska Native, 34 629 (69.1%) as White, and 1877 (3.7%) as other race, including multiracial; and 5734 (11.4%) as having Hispanic ethnicity. Of the 11 109 eligible individuals who declined participation (18.0%), 4824 (43.4%) declined due to a stated preference for a specific screening test, with FOBT/FIT being the most preferred method (2820 [58.5%]) vs colonoscopy (1958 [40.6%]; P < .001) or other screening tests (46 [1.0%] P < .001). Preference for FOBT/FIT was strongest in the West (963 of 1472 [65.4%]) and modest elsewhere, ranging from 199 of 371 (53.6%) in the Northeast to 884 of 1543 (57.3%) in the Midwest (P = .001). Adjusting for region, the preference for FOBT/FIT increased by 19% per recruitment year (odds ratio, 1.19; 95% CI, 1.14-1.25). Conclusions and relevance: In this cross-sectional analysis of veterans choosing nonenrollment in the CONFIRM study, those who declined participation more often preferred FOBT or FIT over colonoscopy. This preference increased over time and was strongest in the western US and may provide insight into trends in CRC screening preferences.Item Bevacizumab-induced hypertension and proteinuria: a genome-wide study of more than 1000 patients(Springer Nature, 2022) Quintanilha, Julia C.F.; Wang, Jin; Sibley, Alexander B.; Jiang, Chen; Etheridge, Amy S.; Shen, Fei; Jiang, Guanglong; Mulkey, Flora; Patel, Jai N.; Hertz, Daniel L.; Dees, Elizabeth Claire; McLeod, Howard L.; Bertagnolli, Monica; Rugo, Hope; Kindler, Hedy L.; Kelly, William Kevin; Ratain, Mark J.; Kroetz, Deanna L.; Owzar, Kouros; Schneider, Bryan P.; Lin, Danyu; Innocenti, Federico; Medicine, School of MedicineBackground: Hypertension and proteinuria are common bevacizumab-induced toxicities. No validated biomarkers are available for identifying patients at risk of these toxicities. Methods: A genome-wide association study (GWAS) meta-analysis was performed in 1039 bevacizumab-treated patients of European ancestry in four clinical trials (CALGB 40502, 40503, 80303, 90401). Grade ≥2 hypertension and proteinuria were recorded (CTCAE v.3.0). Single-nucleotide polymorphism (SNP)-toxicity associations were determined using a cause-specific Cox model adjusting for age and sex. Results: The most significant SNP associated with hypertension with concordant effect in three out of the four studies (p-value <0.05 for each study) was rs6770663 (A > G) in KCNAB1, with the G allele increasing the risk of hypertension (p-value = 4.16 × 10-6). The effect of the G allele was replicated in ECOG-ACRIN E5103 in 582 patients (p-value = 0.005). The meta-analysis of all five studies for rs6770663 led to p-value = 7.73 × 10-8, close to genome-wide significance. The most significant SNP associated with proteinuria was rs339947 (C > A, between DNAH5 and TRIO), with the A allele increasing the risk of proteinuria (p-value = 1.58 × 10-7). Conclusions: The results from the largest study of bevacizumab toxicity provide new markers of drug safety for further evaluations. SNP in KCNAB1 validated in an independent dataset provides evidence toward its clinical applicability to predict bevacizumab-induced hypertension.