Characteristics of cross-hybridization and cross-alignment of expression in pseudo-xenograft samples by RNA-Seq and microarrays.

BACKGROUND: Exploring stromal changes associated with tumor growth and development is a growing area of oncologic research. In order to study molecular changes in the stroma it is recommended to separate tumor tissue from stromal tissue. This is relevant to xenograft models where tumors can be small and difficult to separate from host tissue. We introduce a novel definition of cross-alignment/cross-hybridization to compare qualitatively the ability of high-throughput mRNA sequencing, RNA-Seq, and microarrays to detect tumor and stromal expression from mixed 'pseudo-xenograft' samples vis-à-vis genes and pathways in cross-alignment (RNA-Seq) and cross-hybridization (microarrays). Samples consisted of normal mouse lung and human breast cancer cells; these were combined in fixed proportions to create a titration series of 25% steps. Our definition identifies genes in a given species (human or mouse) with undetectable expression in same-species RNA but detectable expression in cross-species RNA. We demonstrate the comparative value of this method and discuss its potential contribution in cancer research. RESULTS: Our method can identify genes from either species that demonstrate cross-hybridization and/or cross-alignment properties. Surprisingly, the set of genes identified using a simpler and more common approach (using a 'pure' cross-species sample and calling all detected genes as 'crossers') is not a superset of the genes identified using our technique. The observed levels of cross-hybridization are relatively low: 5.3% of human genes detected in mouse, and 3.5% of mouse genes detected in human. Observed levels of cross-alignment are practically comparable to the levels of cross-hybridization: 6.5% of human genes detected in mouse, and 2.3% of mouse genes detected in human. We also observed a relatively high percentage of orthologs: 40.3% of cross-hybridizing genes, and 32.2% of cross-aligning genes.Normalizing the gene catalog to use Consensus Coding Sequence (CCDS) IDs (Genome Res 19:1316-1323, 2009), our results show that the observed levels of cross-hybridization are low: 2.7% of human CCDS IDs are detected in mouse, and 2.4% of mouse CCDS IDs are detected in human. Levels of cross-alignment using the RNA-Seq data are comparable for the mouse, 2.2% of mouse CCDS IDs detected in human, and 9.9% of human CCDS IDs detected in mouse. However, the lists of cross-aligning/cross-hybridizing genes contain many that are of specific interest to oncologic researchers. CONCLUSIONS: The conservative definition that we propose identifies genes in mouse whose expression can be attributed to human RNA, and vice versa, as well as revealing genes with cross-alignment/cross-hybridization properties which could not be identified using a simpler but more established approach. The overall percentage of genes affected by cross-hybridization/cross-alignment is small, but includes genes that are of interest to oncologic researchers. Which platform to use with mixed xenograft samples, microarrays or RNA-Seq, appears to be primarily a question of cost and whether the detection and measurement of expression of specific genes of interest are likely to be affected by cross-hybridization or cross-alignment.

Will periodic intravenous injections of conditioned bone marrow cells effectively reduce atherosclerosis?

Maintenance of healthy arteries requires a balance between injuries to the arterial wall and processes of intrinsic arterial repair. Such repair requires the availability of progenitor cells that are local to the wall itself. Progenitor cells from distant reservoirs like the bone marrow may also contribute to repair. Arterial repair seems to degrade over a lifetime, particularly with risk factors such as smoking and diabetes. Hence, a potential preventive/therapeutic strategy for atherosclerosis could be transfusion of competent bone marrow cells (BMCs) to restore effective repair in the face of arterial injury and depleted endogenous repair reservoirs. The challenge with this strategy has been the reliable collection and/or generation of BMCs that support arterial repair. In this study, we describe a set of experiments to elucidate a method of culturing BMCs that robustly retards atherosclerosis development in apolipoprotein E knockout mice. Identifying such a method would represent an important step in developing cell-based treatments for patients with proclivity for developing atherosclerosis.

The role of SATB1 in breast cancer pathogenesis.

BACKGROUND: SATB1 has been previously proposed as a key protein that controls the development and progression of breast cancer. We explored the potential of the SATB1 protein as a therapeutic target and prognostic marker for human breast cancer. METHODS: We used aggressive (MDA-MB-231 and BT549) and nonaggressive (SKBR3 and MCF7) breast cancer cell lines to investigate the potential of SATB1 as a therapeutic target. SATB1 mRNA expression was silenced in aggressive cells by use of short hairpin RNAs against SATB1. SATB1 was overexpressed in nonaggressive cells by use of SATB1 expression vectors. We assessed the effect of modifying SATB1 expression on the transformed phenotype by examining anchorage-independent cell proliferation, acinar morphology on matrigel, and migration by wound healing in cultured cells. We examined tumor formation and metastasis, respectively, by use of orthotopic mammary fat pad and tail vein xenograft mouse models (mice were used in groups of six, and in total, 96 mice were used). SATB1 mRNA expression was compared with outcome for patients with primary breast cancer from six previous microarray studies that included a total of 1170 patients. All statistical tests were two-sided. RESULTS: The transformed phenotype was not suppressed by SATB1 silencing in aggressive cells and was not enhanced by ectopic expression of SATB1 in nonaggressive cells. Modifying SATB1 expression did not alter anchorage-independent cell proliferation, invasive acinar morphology, or cell migration in cultured cells and did not affect tumor formation or metastasis in xenograft mouse models. In addition, SATB1 expression was not associated with decreased overall survival of patients with primary breast cancer in six previous independent microarray studies (overall odds ratio = 0.80, 95% confidence interval = 0.62 to 1.03, P = .10). CONCLUSION: In contrast to previous studies, we found that SATB1 expression did not promote breast cancer progression and was not associated with breast cancer outcome.

Final results of a phase II study of nab-paclitaxel, bevacizumab, and gemcitabine as first-line therapy for patients with HER2-negative metastatic breast cancer.

In order to examine the efficacy and safety of nanoparticle albumin-bound paclitaxel (nab-P) in combination with bevacizumab (B) and gemcitabine (G) for the first-line treatment of patients with HER2-negative metastatic breast cancer (MBC). In this single-center, open-label phase II trial, patients with HER2-negative MBC received gemcitabine 1500 mg/m(2), nab-paclitaxel 150 mg/m(2), and bevacizumab 10 mg/kg (each administered intravenously) on days 1 and 15 of a 28-day cycle. The primary end point was progression free survival (PFS); secondary end points were overall response rate (ORR), complete (CR) and partial (PR) response rates, clinical benefit (ORR + stable disease), overall survival (OS), and safety. Thirty patients were enrolled. One patient was ineligible and was not included in analysis. Median PFS was 10.4 months (95% CI: 5.6-15.2 months). ORR was 75.9%, comprising eight (27.6%) CRs and 14 (48.3%) PRs; five patients had stable disease (SD) and two patients (6.9%) had progressive disease (PD) as their best response. The clinical benefit rate was 93.1% (27/29) in the overall group and 84.6% in the triple-negative cohort (11/13). The 18-month survival rate was 77.2% (95% CI: 51.1-90.5%). Eight (27.6%) patients experienced grade 3 or 4 toxicity: grade 4 neutropenic fever (n = 1) and grade 3 infection (n = 6), leukopenia, thrombocytopenia, peripheral neuropathy, seizure, shortness of breath, hematuria, and cardiac tamponade (one each). First-line therapy with nab-P, B, and G demonstrated a median PFS of 10.4 months and a 75.9% ORR with acceptable toxicity; this novel combination warrants investigation in a randomized study.

Statistical expression deconvolution from mixed tissue samples.

MOTIVATION: Global expression patterns within cells are used for purposes ranging from the identification of disease biomarkers to basic understanding of cellular processes. Unfortunately, tissue samples used in cancer studies are usually composed of multiple cell types and the non-cancerous portions can significantly affect expression profiles. This severely limits the conclusions that can be made about the specificity of gene expression in the cell-type of interest. However, statistical analysis can be used to identify differentially expressed genes that are related to the biological question being studied. RESULTS: We propose a statistical approach to expression deconvolution from mixed tissue samples in which the proportion of each component cell type is unknown. Our method estimates the proportion of each component in a mixed tissue sample; this estimate can be used to provide estimates of gene expression from each component. We demonstrate our technique on xenograft samples from breast cancer research and publicly available experimental datasets found in the National Center for Biotechnology Information Gene Expression Omnibus repository. AVAILABILITY: R code (http://www.r-project.org/) for estimating sample proportions is freely available to non-commercial users and available at http://www.med.miami.edu/medicine/x2691.xml.

Geriatric oncology: past, present, future.

Efforts to integrate geriatric oncology principles in the training of all medical oncologists are underway.

Evaluation of agreement between physicians' notation of 'no evidence of disease' (NED) and patients' report of cancer status.

This study examines extent of agreement between oncologists' and cancer patients' reports of current cancer status. Participants with history of cancer were given a comprehensive geriatric assessment in which they were asked whether they had cancer at the present time. This was compared to cancer status concurrently recorded by their physicians in the chart. 75.5% of patients whose physicians reported 'no evidence of disease' (NED) reported that they currently had cancer. 30% of them were anxious and 27% were depressed. Among patients for whom both the patient and physician reported no cancer, only 12.5% were anxious and 7% depressed. Compared to patients with concordant responses, those who discrepantly reported they had cancer had significantly more comorbid illnesses, medications, and pain, and lower levels of social, emotional, and physical functioning. Moreover, equal levels of distress and dysfunction were found between those who reported cancer but had NED and those who reported cancer and did have active disease by physician notation. Although conclusions about cause and effect are limited due to study design, findings suggest that some patients might suffer unnecessarily from lack of understanding about current disease status. These findings also suggest the need for improved physician-patient communication and symptom recognition/management.

The association between oral health and general health and quality of life in older male cancer patients.

OBJECTIVES: To describe the long-term effects of oral health problems on quality of life (QoL), functional status, pain, and general health in older male cancer patients. DESIGN: Secondary analysis of a prospective observational study. SETTING: Community dwelling cancer patients served by a Department of Veterans Affairs hospital. PARTICIPANTS: One hundred fifty male cancer patients responded to the question "Do you have tooth or mouth problems making it hard to eat?" The relationship between patients answering "yes" and the following parameters was assessed: demographics, comorbid conditions, habits, activities of daily living, pain, anxiety, depression, social support, spirituality, QoL, and overall health ratings. MEASUREMENTS: Chi-square contingency tables for dichotomous variables, Cochran-Mantel-Haenszel for ordered categorical variables, and t tests for associations with continuous variables. RESULTS: The median age of respondents was 67. Those reporting tooth or mouth problems had had their cancer diagnosed on average 2.9 years before, and 83.3% were found clinically to be cancer free. Patients with these problems had significantly lower global (P=.003) and subscale scores on QoL analysis and higher levels of anxiety (P<.001) and depression (P=.01) than those without tooth or mouth problems; they also had significantly more pain (P<.001) and lower physical functioning (P<.001) and were more impaired in activities of daily living (P<.001). Those with tooth or mouth problems were more likely to describe their overall health as fair or poor (P=.01). Having cancer located in the head and neck region related significantly to having mouth or tooth problems (P=.005), but these problems were not associated with race, education, income, insurance coverage, age, comorbid conditions, alcohol consumption, tobacco or medication usage, type of cancer treatment, tumor stage at diagnosis or follow-up, perceived social support, or spirituality. CONCLUSION: Older male cancer patients with mouth or tooth problems making it hard to eat are more likely to have a lower QoL, poorer emotional health, lower levels of physical functioning, and greater pain than patients without these problems.

Retinoic acid receptor-beta2 promoter methylation in random periareolar fine needle aspiration.

Methylation of the retinoic acid receptor-beta2 (RARbeta2) P2 promoter is hypothesized to be an important mechanism for loss of RARbeta2 function during early mammary carcinogenesis. The frequency of RARbeta2 P2 methylation was tested in (a) 16 early stage breast cancers and (b) 67 random periareolar fine needle aspiration (RPFNA) samples obtained from 38 asymptomatic women who were at increased risk for breast cancer. Risk was defined as either (a) 5-year Gail risk calculation > or = 1.7%; (b) prior biopsy exhibiting atypical hyperplasia, lobular carcinoma in situ, or ductal carcinoma in situ; or (c) known BRCA1/2 mutation carrier. RARbeta2 P2 promoter methylation was assessed at two regions, M3 (-51 to 162 bp) and M4 (104-251 bp). In early stage cancers, M4 methylation was observed in 11 of 16 (69%) cases; in RPFNA samples, methylation was present at M3 and M4 in 28 of 56 (50%) and 19 of 56 (38%) cases, respectively. RPFNAs were stratified for cytologic atypia using the Masood cytology index. The distribution of RARbeta2 P2 promoter methylation was reported as a function of increased cytologic abnormality. Methylation at both M3 and M4 was observed in (a) 0 of 10 (0%) of RPFNAs with Masood scores of < or = 10 (nonproliferative), (b) 3 of 20 (15%) with Masood scores of 11 to 12 (low-grade proliferative), (c) 3 of 10 (30%) with Masood scores of 13 (high-grade proliferative), and (d) 7 of 14 (50%) with Masood scores of 14 of 15 (atypia). Results from this study indicate that the RARbeta2 P2 promoter is frequently methylated (69%) in primary breast cancers and shows a positive association with increasing cytologic abnormality in RPFNA.

Effects of cancer history and comorbid conditions on mortality and healthcare use among older cancer survivors.

BACKGROUND: Older cancer survivors use healthcare services to an increased extent relative to their counterparts who have no history of malignant disease. In the current study, the authors set out to assess the effects of cancer history and comorbid conditions on healthcare use and mortality. METHODS: Using information from the 1992 North Carolina Established Populations for Epidemiologic Study of the Elderly database, study participants were classified as having no history of malignant disease or as having a recent (cancer diagnosed < 1 year earlier), intermediate (cancer diagnosed 1-6 years earlier), or remote (cancer diagnosed > 6 years earlier) history of malignancy. Overall, 15 different comorbid conditions were ascertained. Logistic regression models adjusted for sociodemographic factors, tobacco and alcohol use, and functional measures were used to determine the risk of emergency room, hospital, and nursing home (NH) admission in 1992 and also in 1996 according to history of malignancy and presence of comorbid conditions. Using data from the National Death Registry, a similar controlled analysis of 7-year mortality also was performed. RESULTS: There were 2567 participants in the current study (mean age, 79 years; range, 71-102 years); 69% of all participants were women, 55% were African American, and 14% reported having a history of malignancy. Participants with a history of malignancy had an average of 3 comorbid conditions, and differences across groups in terms of cardiovascular and lung disease incidence were noted. Controlled analyses revealed that recent cancer history (odds ratio [OR], 15.5; 95% confidence interval [CI], 7.0-34.2) and intermediate cancer history (OR, 2.1; 95% CI, 1.4-3.3) were associated with same-year hospital admission. In addition, having a recent history of malignancy in 1992 was found to be correlated with NH admission 4 years later (OR, 3.1; 95% CI, 1.1-9.1). History of malignancy was not associated with mortality. CONCLUSIONS: Cancer history had limited influence on healthcare use and mortality. Efforts aimed at improving health-related outcomes in older cancer survivors should continue to focus on attenuating the impact of comorbid conditions.

Assessing a prostate cancer brachytherapy technique using early patient-reported symptoms: a potential early indicator for technology assessment?

Brachytherapy for early prostate cancer can cause long-term urinary, bowel, and sexual dysfunction. Modifying technique may mitigate complications, but definitive outcome assessment requires long-term follow-up. Although radiation dose plausibly mediates all treatment-related toxicity, short-term symptoms may indicate long-term outcomes. We sought an early indication of whether a modified brachytherapy technique successfully decreased toxicity in the anticipated direction by assessing changes in symptoms and symptom distress 3 months after treatment. In a prospective study of clinically localized prostate cancer using a validated, patient-reported questionnaire, we assessed 85 men, whose primary treatment was brachytherapy alone, prior to treatment and 3 months after the procedure. Twenty-two men received standard ultrasound-guided brachytherapy (SB), and 63 men received magnetic resonance imaging-guided brachytherapy (MB), a technique intended to decrease urinary toxicity by reducing urethral irradiation. Patient age and other sociodemographic variables were similar in the 2 groups. The MB group experienced a greater increase in urinary obstruction/irritation symptoms (P = 0.02) and sexual function distress, but not sexual dysfunction (P = 0.22), whereas the SB group reported a smaller increase in bowel symptoms (P = 0.04) and bowel distress (P = 0.02). We found reduced short-term urinary obstruction/irritation and increased bowel problems after MB consistent with the hypothesized effects of the modified technique, although no obvious mechanism explains the decreased sexual function distress in MB patients. Whether these short-term changes predict long-term outcome differences will require much longer follow-up. However, these results suggest that measuring early symptoms may indicate whether an altered brachytherapy treatment technique has intended favorable consequences, potentially accelerating technology assessment.

Geriatric assessment and comorbidity.

Elderly persons, a rapidly growing population segment, have an increased incidence of cancer. The older cancer patient's clinical evaluation and treatment is influenced by conditions such as disabilities, comorbidity, and functional status, along with tumor type and stage. These conditions and other geriatric syndromes can be identified by comprehensive geriatric assessment to guide therapy and affect prognosis and quality of life. Comprehensive geriatric assessment involves the medical, functional, affective, social, spiritual, and environmental assessments. The medical assessment, which includes a nutrition, vision, hearing, continence, gait and balance, and cognition evaluation, can provide additional information to performance status and comorbidity. Although there are many assessment domains using several instruments, comprehensive geriatric assessment can be focused and efficient, especially with a multidisciplinary team of nurses, social workers, pharmacists, and other personnel. Comorbid illnesses may have complex interactions, with the underlying cancer influencing cancer diagnosis, disease course, treatment-related side effects, and mortality. Many instruments are available for comorbidity measurement, and retrospective studies in elderly cancer cohorts have shown comorbidity to influence survival. However, the ultimate aim would be to use comorbidity and comprehensive geriatric assessments prospectively in the older cancer patient to help predict the suitability and success of treatment with various antineoplastic modalities.

Aging and cancer.

A substantial increase in the number of elderly people in the populations of developed nations in the coming years has been projected. Persons 65 years and older are at significantly higher risk of developing cancer when compared to younger individuals. There is a resulting increase in cancer incidence as well as mortality in this advanced age group. It is important to know how changes in physiological reserve and functional status in elderly patients, polypharmacy issues, comorbidities, and other age-related problems can affect cancer prognosis and management. Elderly patients are not adequately represented in clinical trials, thus creating a relative lack of information related to specific issues about elderly cancer patients and their care. Nevertheless, there is a substantial amount of guidance available, and in this review we will address selected issues of importance when considering the approach to the older cancer patient.

Function in elderly cancer survivors depends on comorbidities.

BACKGROUND: Factors associated with functional status in elderly cancer survivors, in particular, comorbidity, have been inadequately studied. METHODS: Of 4162 participants aged 65 and older enrolled in the Duke Established Populations for Epidemiologic Studies of the Elderly study in 1986, 376 of the participants self-reported a diagnosis of cancer. Participants were divided into 2 comorbidity groups and 4 cancer groups. Cancer groups included 132 participants diagnosed 0-4 years ago, 117 diagnosed 5-15 years ago, 127 diagnosed >15 years ago, and 3784 participants who had never been diagnosed with cancer. Comorbidity (self-reported stroke, diabetes, hypertension, and myocardial infarction) was classified as presence of 1 or no comorbidities (n = 3089) or 2 or more comorbidities (n = 1073). Function was assessed by Katz Activities of Daily Living, Rosow-Breslau, Nagi, and Instrumental Activities of Daily Living scales at the time of interview. RESULTS: In a two-way analysis of covariance model of comorbidity and cancer group controlling for age, race, sex, education, marital status, depression, and cognitive status, duration of cancer survivorship does not influence most measures of function. In the subset of 376 cancer survivors, comorbidity significantly correlates with the functional status of these older cancer survivors (<0.02, for all 4 measures of function). CONCLUSIONS: In the older cancer survivor, regardless of duration following diagnosis, the presence of comorbidity rather than the history of cancer per se correlates with impaired functional status.

Comprehensive assessment of the elderly cancer patient: the feasibility of self-report methodology.

PURPOSE: Comprehensive geriatric assessment (CGA) has aided the medical community greatly in understanding the quality-of-life issues and functional needs of older patients. With its professional team assessment approach, however, CGA may be time consuming and costly. The goal of the present study was to assess the ability of cancer patients to complete a self-administered CGA and then to characterize cancer patients across multiple domains and age groups. PATIENTS AND METHODS: Two hundred sixty-six male outpatient oncology patients at the Durham Veterans Affairs Medical Center were asked to fill out a survey assessing 10 domains (demographics, comorbid conditions, activities of daily living, functional status, pain, financial well being, social support, emotional state, spiritual well-being, and quality of life). RESULTS: Seventy-six percent of the patients who received their surveys and kept their appointments returned the assessment tool. Older oncology patients had significantly less education (P <.0001), income (P =.05), frequent exercise (P =.01), and chance of being disease free (P =.003) than younger patients. Other findings in older patients were a higher rate of marriage (P =.02), more difficulty in taking medications (P =.05), and less cigarette (P =.03) and alcohol (P =.03) use. Members of all age cohorts reported a sense of social support, with younger patients deriving this more from family and friends than older patients, and older patients deriving social support more from membership in religious communities than younger patients. No differences were found across age groups for number and impact of comorbid illnesses, number of medications, basic and instrumental activities of daily living, pain, overall health rating, financial adequacy, anxiety, depression, and quality of life. CONCLUSION: CGA can be conducted in an outpatient cancer community using a self-report format. Despite the fact that this population varied demographically across age groups and is limited to veterans, this study demonstrated remarkable similarities between younger and older cancer patients in terms of functional status, health states, and quality of life.