Mass effect and signal intensity alteration in the suprapatellar fat pad: associations with knee symptoms and structure

OBJECTIVE

To describe cross-sectional associations between mass effect or signal intensity alteration of the suprapatellar fat pad (SPFP) with knee symptoms and structure in older adults.

METHODS

A cross-sectional sample of 904 randomly selected subjects (mean 62.4 years, 49.9% female) was studied. T1- or T2-weighted fat suppressed magnetic resonance imaging (MRI) was used to assess mass effect or signal intensity alteration of SPFP, cartilage volume, cartilage defects, and bone marrow lesions (BMLs). Knee pain was assessed by self-administered Western Ontario McMaster Osteoarthritis Index (WOMAC) questionnaire. The Osteoarthritis Research Society International (OARSI) atlas was used to assess knee osteophyte, joint space narrowing (JSN) and radiographic osteoarthritis (ROA). Univariable and multivariable linear or logistic regression analyses were used to examine the associations.

RESULTS

After adjustment for confounders including age, sex, body mass index (BMI), disease status, tibial bone area and/or ROA, the presence of SPFP mass effect was significantly associated with any knee pain (OR: 2.39; 95% confidence interval (CI): 1.54, 3.70) and ROA (OR: 2.10; 95% CI: 1.33, 3.31) but not with cartilage volume, cartilage defects or BMLs. The presence of SPFP signal intensity alteration was significantly associated with any knee pain (OR: 1.90; 95% CI: 1.43, 2.53), ROA (OR: 1.83; 95% CI: 1.37, 2.45), any BMLs (OR: 1.55; 95% CI: 1.17, 2.06) but not with cartilage volume and cartilage defects. Significant associations with knee pain and BMLs were more evident in subjects with ROA. Presence of SPFP mass effect and/or signal intensity alteration combined was associated with any tibial cartilage defects (OR: 1.45; 95% CI: 1.04, 2.04).

CONCLUSIONS

SPFP mass effect and/or signal intensity alterations are deleteriously associated with knee pain, radiographic OA and BMLs in this cross-sectional study, suggesting that SPFP abnormalities may contribute to pain and structural abnormalities in the knee.

Effects of high thoracic epidural anesthesia on ischemic cardiomyopathy cardiac function and autonomic neural function

We aimed at observing the effects of high thoracic epidural anesthesia (HTEA) on cardiac structure and function, heart rate variability (HRV), and QT interval variation (QTV) in ischemic cardiomyopathy (ICM) patients with chronic heart failure. We divided 30 ICM patients into HTEA (N = 16) and control (N = 14) groups.The control group was treated with medication, and the HTEA group was treated with HTEA and medication for 4 weeks. We measured the changes in the left-ventricular end-diastolic diameter (LVEDd) and left-ventricular ejection fraction (LVEF) before and after treatment by using echocardiography and examined changes in HRV and QTV using ambulatory electrocardiogram. HTEA significantly narrowed the LVEDd, improved LVEF, significantly increased the HRV, and significantly reduced the QTV in the ICM group compared to the control group. HTEA significantly narrowed the ventricular chamber diameter size of ICM patients, enhanced myocardial contractility, increased myocardial electrical stability, and improved the cardiac structure and function.

A novel eliminase from a marine bacterium that degrades hyaluronan and chondroitin sulfate

Lyases cleave glycosaminoglycans (GAGs) in an eliminative mechanism and are important tools for the structural analysis and oligosaccharide preparation of GAGs. Various GAG lyases have been identified from terrestrial but not marine organisms even though marine animals are rich in GAGs with unique structures and functions. Herein we isolated a novel GAG lyase for the first time from the marine bacterium Vibrio sp. FC509 and then recombinantly expressed and characterized it. It showed strong lyase activity toward hyaluronan (HA) and chondroitin sulfate (CS) and was designated as HA and CS lyase (HCLase). It exhibited the highest activities to both substrates at pH 8.0 and 0.5 m NaCl at 30 °C. Its activity toward HA was less sensitive to pH than its CS lyase activity. As with most other marine enzymes, HCLase is a halophilic enzyme and very stable at temperatures from 0 to 40 °C for up to 24 h, but its activity is independent of divalent metal ions. The specific activity of HCLase against HA and CS reached a markedly high level of hundreds of thousands units/mg of protein under optimum conditions. The HCLase-resistant tetrasaccharide Δ(4,5)HexUAα1-3GalNAc(6-O-sulfate)β1-4GlcUA(2-O-sulfate)β1-3GalNAc(6-O-sulfate) was isolated from CS-D, the structure of which indicated that HCLase could not cleave the galactosaminidic linkage bound to 2-O-sulfated d-glucuronic acid (GlcUA) in CS chains. Site-directed mutagenesis indicated that HCLase may work via a catalytic mechanism in which Tyr-His acts as the Brønsted base and acid. Thus, the identification of HCLase provides a useful tool for HA- and CS-related research and applications.

Clozapine directly increases insulin and glucagon secretion from islets: implications for impairment of glucose tolerance

Second generation antipsychotics cause derangements in glucose metabolism that are often interpreted as insulin resistance. In previous studies we have shown that this is not classical insulin resistance but the drugs were actually inducing a hyperglycaemic state associated with elevated hepatic glucose output (HGO) and increased levels of glucagon and insulin. However, it remains unclear whether these effects are directly elicited by drug actions in the liver and pancreas, or whether they are indirectly mediated. Here we investigated if clozapine is capable of inducing insulin resistance in the liver or enhancing insulin and glucagon secretion from the pancreas. It was observed that insulin signalling was elevated in livers from animals treated with clozapine indicating there was no insulin resistance in the early steps of insulin signalling. To explore whether the defects arise at later stages of insulin action we used an isolated perfused liver system. In this model, clozapine had no direct effect on insulin's counter regulatory effect on epinephrine-induced HGO. In isolated mouse islets clozapine significantly increased glucose-stimulated insulin secretion while simultaneously blocking glucose-induced reductions in glucagon secretion. We also show that the non-peptidic glucagon receptor like peptide-1 (GLP-1) receptor agonist Boc5 was able to overcome the inhibitory effects of clozapine on glucose metabolism. Taken together these results suggest that clozapine does not have any direct effect on glucose metabolism in the liver but it simultaneously stimulates insulin and glucagon secretion, a situation that would allow for the concurrent presence of high glucose and high insulin levels in treated animals.

Socioeconomic status in relation to incident fracture risk in the Study of Women's Health Across the Nation

We examined baseline and annual follow-up data (through annual follow-up visit 9) from a cohort of 2,234 women aged 42 to 52 years at baseline. Independent of financial status, higher educational level was associated with lower fracture incidence among non-Caucasian women but not among Caucasian women.

INTRODUCTION

This study was conducted to determine the associations of education and income with fracture incidence among midlife women over 9 years of follow-up.

METHODS

We examined baseline and annual follow-up data (through annual follow-up visit 9) from 2,234 participants of the Study of Women's Health Across the Nation, a cohort of women aged 42 to 52 years at baseline. We used Cox proportional hazards regression models to examine the associations of socioeconomic predictors (education, family-adjusted poverty-to-income ratio, and difficulty paying for basics) with time to first incident nontraumatic, nondigital, noncraniofacial fracture.

RESULTS

Independent of family-adjusted poverty-to-income ratio, higher educational level was associated with decreased time to first incident fracture among non-Caucasian women but not among Caucasian women (p(interaction) 0.02). Compared with non-Caucasian women who completed no more than high school education, non-Caucasian women who attained at least some postgraduate education had 87% lower rates of incident nontraumatic fracture (adjusted hazard ratio 0.13, 95% confidence interval [CI] 0.03-0.60). Among non-Caucasian women, each additional year of education was associated with a 16% lower odds of nontraumatic fracture (adjusted odds ratio 0.84, 95% CI 0.73-0.97). Income, family-adjusted poverty-to-income ratio, and degree of difficulty paying for basic needs were not associated with time to first fracture in Caucasian or non-Caucasian women.

CONCLUSIONS

Among non-Caucasian midlife women, higher education, but not higher income, was associated with lower fracture incidence. Elucidation of the mechanisms underlying the possible protective effects of higher educational level on nontraumatic fracture incidence may allow us to better target individuals at risk of future fracture.

HLA-haploidentical hematopoietic SCT from collateral related donors without in vitro T-cell depletion for hematological malignancies

HLA-haploidentical hematopoietic SCT (HSCT) provides an opportunity for almost all patients who lack HLA-matched sibling donors. The donor availability can be increased by including the collateral related donors (CRDs). We compared clinical outcomes of patients with hematological malignancies, who underwent haploidentical HSCT from CRD (n=30) and immediate related donors (IRDs; n=120). In CRDs, 29 (96.7%) patients achieved sustained engraftment. In CRDs and IRDs, the median times of myeloid recovery were 13 (range 10-20 days) and 14 days (range 12-23 days), and the median times of platelet recovery were 18 (range 7-270) and 15 days (range 7-132 days; P=0.027). The incidences of II-IV acute GVHD were 27.6% versus 39.4% (P=0.058). The 2-year cumulative incidences of chronic GVHD (cGVHD) were 63.3% versus 57.8% (P=0.365). The 2-year incidence of extensive cGVHD of CRDs was significantly higher than that of IRDs (36.7% versus 20.2%, P=0.03). The 2-year incidences of relapse, 3-year probability of OS and leukemia-free survival for the two groups were 26.7% versus 14.8% (P=0.17), 56.7% versus 70.4% (P=0.224) and 50.0% versus 65.4% (P=0.103), respectively. This study shows that haploidentical HSCT from CRDs can provide a safe and effective treatment for patients with hematological malignancies. CRDs could be an alternative when there was no suitable IRDs.

Promyelocytic leukaemia zinc finger maintains self-renewal of male germline stem cells (mGSCs) and its expression pattern in dairy goat testis

OBJECTIVES

Previous studies have shown that promyelocytic leukaemia zinc finger (PLZF) is a spermatogonia-specific transcription factor in the testis, required to regulate self-renewal and maintenance of the spermatogonia stem cell. Up to now, expression and function of PLZF in the goat testis has not been known. The objectives of this study were to investigate PLZF expression pattern in the dairy goat and its effect on male goat germline stem cell (mGSC) self-renewal and differentiation.

MATERIALS AND METHODS

Testis development and expression patterns of PLZF in the dairy goat were analysed by haematoxylin and eosin staining, immunohistochemistry and reverse transcription-polymerase chain reaction (RT-PCR). Furthermore, effects of PLZF overexpression on mGSC self-renewal and differentiation were evaluated by quantitative RT-PCR (QRT-PCR), immunofluorescence and BrdU incorporation assay.

RESULTS

Promyelocytic leukaemia zinc finger was essential for dairy goat testis development and expression of several proliferation and pluripotency-associated proteins including OCT4, C-MYC were upregulated by PLZF overexpression. The study demonstrated that PLZF played a key role in maintaining self-renewal of mGSCs and its overexpression enhanced expression of proliferation-associated genes.

CONCLUSIONS

Promyelocytic leukaemia zinc finger could function in the dairy goat as well as in other species in maintaining self-renewal of germline stem cells and this study provides a model to study the mechanism on self-renewal and differentiation of mGSCs in livestock.

Health-related quality of life of patients with newly diagnosed chronic myeloid leukemia treated with allogeneic hematopoietic SCT versus imatinib

To evaluate and compare the health-related quality of life (HRQOL) of patients with newly diagnosed CML in the first chronic phase (CML-CP1) receiving HLA-identical sibling donor (ISD) hematopoietic SCT (HSCT) or imatinib, a cross-sectional study that was part of a prospective cohort study at the Institute of Hematology, Peking University was performed. A total of 222 patients including 126 and 96 in the imatinib and ISD HSCT groups, respectively, were enrolled. HRQOL was measured using the Medical Outcomes Study 36-Item Short-Form Health Survey. The ISD HSCT group functioned significantly better on the role-physical functioning and mental health subscales, as well as the mental component summary (MCS) than the imatinib group. HRQOL was generally comparable to groups in the young population. Multivariate analysis showed that white blood cell count ≥ 30 × 10(9)/L and plts count ≥ 450 × 10(9)/L were the major adverse factors affecting HRQOL in long-term survivors. Imatinib therapy was also an adverse factor affecting the MCS (odds ratio=1.7, P=0.032). Thus, long-term CML-CP1 survivors receiving ISD HSCT can attain desirable HRQOL comparable to or better than that of patients receiving imatinib.

Physical activity as determinant of femoral neck strength relative to load in adult women: findings from the hip strength across the menopause transition study

Our objective was to examine associations of physical activity in different life domains with peak femoral neck strength relative to load in adult women. Greater physical activity in each of the domains of sport, active living, home, and work was associated with higher peak femoral neck strength relative to load.

INTRODUCTION

Our objective was to examine the associations of physical activity in different life domains with peak femoral neck strength relative to load in adult women. Composite indices of femoral neck strength integrate body size with femoral neck size and bone mineral density to gauge bone strength relative to load during a fall, and are inversely associated with incident fracture risk.

METHODS

Participants were 1,919 pre- and early perimenopausal women from the Study of Women's Health Across the Nation. Composite indices of femoral neck strength relative to load in three failure modes (compression, bending, and impact) were created from hip dual-energy X-ray absorption scans and body size. Usual physical activity within the past year was assessed with the Kaiser Physical Activity Survey in four domains: sport, home, active living, and work. We used multiple linear regression to examine the associations.

RESULTS

Greater physical activity in each of the four domains was independently associated with higher composite indices, adjusted for age, menopausal transition stage, race/ethnicity, Study of Women's Health Across the Nation study site, smoking status, smoking pack-years, alcohol consumption level, current use of supplementary calcium, current use of supplementary vitamin D, current use of bone-adverse medications, prior use of any sex steroid hormone pills or patch, prior use of depo-provera injections, history of hyperthyroidism, history of previous adult fracture, and employment status: standardized effect sizes ranged from 0.04 (p < 0.05) to 0.20 (p < 0.0001).

CONCLUSIONS

Physical activity in each domain examined was associated with higher peak femoral neck strength relative to load in pre- and early perimenopausal women.

Propensity for social interaction predicts nicotine-reinforced behaviors in outbred rats

Social and genetic factors can influence smoking behavior. Using olfactogustatory stimuli as the sensory cue for intravenous nicotine self-administration (SA), we previously showed that social learning of nicotine contingent odor cue prevented rats from developing conditioned taste aversion and allowed them to instead establish stable nicotine SA. We hypothesized that genetic factors influenced socially acquired nicotine SA. A heterogeneous stock (HS; N/NIH) of outbred rats was trained to self-administer nicotine using the social learning protocol. Both male and female HS rats acquired nicotine SA, but females self-administered more nicotine than males. After extinction, the context previously paired with nicotine SA, in conjunction with socially transmitted drug cues, was sufficient to cause reinstatement of drug-seeking behavior. Wide variation in both nicotine intake and reinstatement was observed. Using multiple regression analysis, we found that measures of social interaction were significant predictors of nicotine intake and reinstatement of drug seeking in both males and females. Furthermore, measures of depression were predictors of nicotine intake in both males and females, anxiety was a predictor only in males and response to novelty was a predictor only in females. In males, measures of both depression and anxiety predicted nicotine reinstatement. Together, these data supported the ideas that genetically determined propensities for emotional and social phenotypes are significant determinants for nicotine-reinforced behavior, and that the HS rat is a suitable tool for dissecting genetic mechanisms that may underlie the interaction between social behavior, anxiety, depression and smoking.

Abstract P6-06-08: Impact of initial surgical treatment delay on survival according to hormone responsiveness in breast cancer

Previous studies on the issue of the prognostic importance of treatment delay in breast cancer have shown inconsistent results. Furthermore, the association between the impact of treatment delay and molecular characteristics of tumors has not been adequately addressed. The purpose of this study is to examine the prognostic impact of initial surgical treatment delay after biopsy-proven cancer diagnosis in breast cancer patients.

A total of 1,393 consecutive invasive breast cancer patients, treated in Seoul National University Hospital, Seoul, Korea, between July 2006 and June 2008, were included in this study. Patients with in situ or metastatic carcinoma at the time of diagnosis and patients in whom the dates of the initial pathologic diagnosis were unknown were excluded.

The median time from biopsy-confirmed cancer diagnosis to initial surgical treatment was 25 days (range 0-134). When the patients were classified according to their treatment delay days (0 to 29, 30 to 59, and ≥60days), there was no difference in survival between ‘0-29days’ group and ‘30-59days’ group. However, for patients who experienced more than 60 days of initial delay in surgical treatment, the survival was significantly worse when compared to other groups (p = 0.034). The association between the treatment delay and poor outcome was only seen in patients with ER and PR negative tumors (p = 0.018) while patients with hormone-responsive tumors showed no such association. Patients with ER and PR negative tumors developed more recurrence and had shorter disease-free survival if they had treatment delay of more than 60 days. The prognostic importance of treatment delay of more than 60 days remained significant in predicting disease-free survival after adjusting for other known prognostic factors such as age, tumor size, nodal status, cancer stage, nuclear grade and Ki-67 expression (HR 5.127; 95% CI, 1.350 to 19.472; p = 0.016).

Our results suggest that having treatment delay of more than 60 days is associated with poor treatment outcome in patients with ER and PR negative breast cancer.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P6-06-08.

Abstract P3-14-20: Neoadjuvant chemotherapy in young age breast cancer: Survival benefit over adjuvant chemotherapy in clinically T2 node positive patients

Background: The downstaging of the primary tumor and the increase in breast conservation rates seems to be the only clinical benefit of Neoadjuvant systemic therapy(NST) in breast cancer treatment, given that several studies failed to demonstrate an improvement of overall survival compared with postoperative adjuvant chemotherapy. In Europe, S6 trial showed better early outcome in survival in favour of the neoadjuvant chemotherapy group compared to adjuvant chemotherapy group in premenopausal patients without significantly modifying long-term event rates. The aim of this study was to assess a potential advantage in survival by neoadjuvant as compared to adjuvant chemotherapy in young age breast cancer patients.

Methods: Between January 2001 and December 2008, 1169 consecutive patients with breast cancer aged under 40 underwent adjuvant chemotherapy before or after surgery. Prospectively collected medical records for all patients were reviewed retrospectively. For the comparison of survival between neoadjuvant versus adjuvant chemotherapy group, cinically T2 and node positive patients were retrieved. Survival curves were derived from Kaplan-Meier estimates and compared by log-rank test.

Results: Of the 1169 patients, 203(17.3%) patients were treated with neoadjuvant chemotherapy, and they were grouped as ‘NST’ and ‘non-NST’ according to initial treatment. About 47% patients in each group were clinically T2 patients. (99(47.8%) in NST group, 453(46.9%) in non-NST group) Among them, clinically T2 and node positive patients were 188, 97 patients in NST group, 91 patients in non-NST group each. The median age was 35.11±3.9 years old and HER2 amplification was observed as 23.5%, and they were not different between two groups.(p = 0.146 and 0.941 each) Significant lower hormone receptor expression rate and higher Ki-67 level were observed in NST group(p = 0.03 and &lt;0.0001 each) Breast conservation surgery rate was also significantly different between two groups, more favorable results in NST group.(67% in NST group, 37.4% in non-NST group, p&lt;0.0001) During median follow-up period of 61 months (range 44 to 148 months), we observed a statistically significant difference (p = 0.011) in survival in favour of the NST group. This benefit of survival was presented consistently regardless of hormone receptor expression. A similar trend was seen when the time to distant disease recurrence was evaluated (p = 0.176). And this trend was more prominent in hormone receptor negative patients, but still not statistically significant. (p = 0.144) The mean total dose of chemotherapy administered was similar in both groups. Improved survival figures in the NST group could be the result of the early initiation of systemic treatment, but the trend in favour of decreased metastases was not statistically significant.

Conclusion: A potential advantage of primary over adjuvant chemotherapy in young age breast cancer patients’ survival might be proposed by this results.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P3-14-20.

Abstract P3-07-09: Breast cancer susceptibility associated single nucleotide polymorphisms (SNPs) and prognosis: GG genotype of a SNP rs3803662 (TOX3/TNRC9) associated with better survival

Backgrounds: After completion of human genome project, some genetic variants are discovered and highlighted by genome-wide association studies (GWAS). Single nucleotide polymorphisms (SNP) are considered to be the key variations leading to the various breast cancer susceptibility between each individuals. In 2011, our group has validated 5 SNPs as significant risk factor of breast cancer in Korean women for the first time. Recently, there has been some attempts to find clinical meaning of SNPs in each breast cancer patient. But it was not successful.

Methods: Consecutive patients with histologically confirmed primary breast cancer subjected to operative procedures between 2002 and 2009 in Seoul National University Hospital were included for analysis. Patients diagnosed with noninvasive breast cancer (ductal carcinoma in situ and lobular carcinoma in situ) or stage IV breast cancer were excluded. Peripheral venous blood samples were obtained and stored at the time of operation. The SNPs genotyped included rs2046210 (6q25.1), rs2981582 (FGFR2), rs889312 (MAP3K1), rs3803662 (TOX3/TNRC9), and rs4973768 (SLC4A7). SNP genotyping was carried out on an Applied Biosystems 7900HT realtime PCR system (Applied Biosystems). We made collaboration with the Korean Central Cancer Registry (KCCR) to improve the validity of the mortality data. Total of 3,209 patients were included for survival and recurrence analysis.

Results: 492 (15.33%) patients had recurrence. And there were 277 (8.63%) mortalities overall. The median follow-up was for 85.59 month (±29.979). The GG genotype of SNP rs3803662 showed better survival than other AA, AG genotypes (Cumulative survival was 89% vs 84% at 120 months f/u). And it is validated at multivariate analysis (p = 0.024).

Conclusion: This study showed strong association between a certain genotype of single SNP and survival of breast cancer patients for the first time. Further lab investigation including functional study or studies on other races should be performed to find a novel or alternative hidden pathways of cancer progression.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P3-07-09.

Abstract P4-04-09: Extensive novel hybrid isoforms revealed by RNA sequencing of 120 primary breast cancer samples

Introduction

Recent studies of next generation sequencing (NGS) have highlighted the extensive transcriptional heterogeneity of cancer cells. Alternative splicing is one of the evolutionary process by which cells and tissues achieve their specificity within central dogma. Also it is highly assumed to contribute to oncogenesis and thought to be a critical mechanism how cancer cells gain resistance to therapeutic agents and adapt to various circumstances. Relevance of differential splicing in breast cancer biology is mostly unknown. We performed whole transcriptome sequencing (RNA-Seq) to reveal novel splicing alterations among 120 primary breast cancer samples.

Materials and Method

Total RNA was prepared using the Illumina TrueSeq™ RNA sample Preparation Kit and TrueSeq mRNA library was constructed. Clustering and sequencing was done using Illumina HiSeq 2000. RNA-Seq reads were aligned to human reference genome(hg19) using TopHat software and expression was measured using cufflinks software. We used tissues extracted from previously collected 120 fresh-frozen primary breast cancer samples obtained after surgical resection whose clinicopathological data are available. Patients undergone neoadjuvant systemic therapies or stage lV disease at diagnosis were excluded. Thirty-six(30%) cases occurred distant metastasis during follow up. Hormone receptor(HR) was positive in 61(50.8%) samples, 20(16.7%) had HER2 oncogene overexpression and 36(30%) were triple negative breast cancer.

Results and discussion

Total 11345 novel isoforms were detected among 120 tumors. Isoforms of pseudo-genes and exon skipping of the ‘non-coding exon’ were excluded. Splice variants detected in normal reference were sorted out as well. 4045 were in-frame exon skipping and 4960 were off-frame exon skipping which may lead to protein truncation. 5036 were private exon skipping and 3969 isoforms were detected recurrently in more than 2 samples. To minimize false positivity we confined ‘exon skipping’ analysis to those with the expression level (Fragments per kilo-base of exon per million fragments mapped, FPKM) of the skipped exon below 0.1 compared to the adjacent exons. Mean number of exon skipping events per sample was 196.8 (range 75-299, SD 35.9). There were no differences in numbers of exon skipping event among breast cancer subtypes nor distant metastasis. We have identified novel exon skipping in ESR1, CHEK2, EIF3E, FGFR, MAP2K, PIK3R2, TERT, VAV3 genes which is strongly suspected to be novel driver isoforms and is under validation process.

Conclusion We performed whole-transcriptome sequencing with a large set of primary breast cancer samples and revealed extensive transcriptional heterogeneity by isoform profiling. As distinguishing the natural transcriptomic dynamics from oncogenic ‘driver’ isoform is a major challenge, validation and functional studies are ongoing.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P4-04-09.

Abstract PD4-2: Whole exome and transcriptome sequencing of 120 primary breast cancer to discover novel therapeutic target

Introduction: Many somatic mutations, structural alterations, and gene expression changes are causally implicated in oncogenesis and tumor progression, and as a result, affect clinical outcome. Although majority of breast cancer patients have benefits from therapeutics targeting tumor biology, such as estrogen receptor and HER-2, still many patients suffer from disease recurrence and metastasis. More kind of specific target therapies are needed, especially for hormone-resistant tumor and triple-negative breast cancer.

Materials and Method: To find novel therapeutic target in breast cancer, here we examine the both whole exome and whole transcriptome of fresh-frozen primary breast cancer tissues from 120 patients whose clinical, pathological, and survival data are available. Patients with Stage IV disease or who received neoadjuvant chemotherapy were excluded. 36 patients had distant metastasis within 5 years from surgery, and 84 patients were NED at least 5 years. RNA and DNA were extracted and qualities were assessed in all samples. Exome and transcriptome sequencing were done using NGS technology (Illumina HiSeq 2000). As a control, exome sequencing was done for 93 normal DNA from matched patients. Single nucleotide variations (SNV) identified in cancer samples on exonic region, nonsynonymous SNV or stop gain/loss, whose quality ≥20, and not found in 93 normal samples were included. SNVs registered in dbSNP135_common or 1000 genome allele frequency &gt;0.001 were excluded.Results and Discussion: We identified 11,684 putative somatic mutations in 7,373 genes. Of them, 6,547 were deleterious or damaging mutation by Provean or SIFT analysis. Mutations were found in potential drug target genes, such as PIK3CA(25), PTEN(3), AKT1(3), ALK(3), ROS1(2), FGFR4(3), FGFR3(2), ERBB2(2), and IDH1(1) etc. In a pathway analysis, mutations in insulin signaling pathway were most dominant. We hypothesized that driver gene and therapeutic target has to have recurrent mutation and gene expression at least more than average expression. We calculated expression “Volume” according to the median normalized FPKM value of individual gene's RNA-seq data. With a cut-off of 3 or more mutations in each gene, 1,116 genes were selected. After the filtering of Volume&lt;0.3, 696 genes were selected. Finally, 55 genes were selected which are druggable or potentially druggable using drug database (DrugBank, TOCRIS, Ingenuity) and Pubmed. DriverNet analysis result was also considered for the selection. All 342 tumor suppressor genes were filtered out. Interestingly, 18 of the 55 were genes involved in metabolism (fatty acid, glucose, amino acids). 12 were kinases and 4 were involved in insulin pathway. Excluding the previously confirmed therapeutic target, PIK3CA, AKT1, and NOTCHs, and considering the patients’ clinical data, our primary candidates for hormone-resistant breast cancer were NQO2, CELSR1, GLUD2, MYH9, PSMD2, NADK, IRS2, MAP3K5, and for triple-negative breast cancer were HSPG2, PHGDH, MYLK, etc. Validation with Sanger sequencing and functional study is on-going.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr PD4-2.