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Biomedical subjects

Yixin Wang

Publications and source records attributed to Yixin Wang.

At least 19 recordsLinked to original sources

Early Cardiomyopathy in Prediabetic NDPK-B-Deficient Mice Is Associated with Remodeling of the Mitochondrial O-GlcNAc Proteome.

Diabetic cardiomyopathy (DCM) is characterized by myocardial remodeling that may already be evident during prediabetes, yet the molecular alterations accompanying these early changes remain poorly understood. The present study examined mouse models of Nucleoside diphosphate kinase B (NDPK-B)-deficient prediabetes and streptozotocin-induced diabetes using O-GlcNAc-associated proteomic profiling to define stage-specific molecular alterations during the progression from prediabetic to diabetic cardiomyopathy. Both models exhibited increased left ventricular extracellular matrix deposition and impaired diastolic function, together with activation of the hexosamine biosynthesis pathway. Profiling of O-GlcNAc-associated proteins uncovered extensive remodeling of the mitochondrial proteome already at the prediabetic stage, with respiratory complex I among the most prominently altered targets, alongside changes in substrate metabolism and inflammatory signaling. In overt DCM, the putative O-GlcNAc proteomic profile was associated with a shift toward wider lipid-dependent metabolic reprogramming and remodeling of mitochondrial proteins. These findings identify early remodeling of the mitochondrial O-GlcNAc-associated proteome as a molecular signature of prediabetic cardiomyopathy and highlight respiratory complex I proteins as candidate targets for future mechanistic investigations.

Animals↗

Establishment of a prognostic model based on ER stress-related cell death genes and proposing a novel combination therapy in acute myeloid leukemia.

BACKGROUND: Acute myeloid leukemia (AML) is a highly heterogeneous malignancy, presenting significant challenges in accurately predicting patient prognosis. Dysregulation of endoplasmic reticulum (ER) stress and resistance to programmed cell death (PCD) are hallmarks of AML cells. However, the prognostic significance of the interplay between ER stress and cell death pathways in AML remains largely unexplored. METHODS: We analyzed RNA sequencing and clinical data from 887 AML patients across 4 cohorts to develop an ER stress-related cell death index (ERCDI) using 10 machine-learning algorithms with 117 unique combinations. Survival and time-dependent Receiver Operating Characteristic Curve (ROC) analyses were performed to assess the model's efficacy. Clinical characteristics, the tumor immune microenvironment, and drug sensitivity differences between the high- and low-risk groups were also analyzed. The CMap database was used to identify potential therapeutic drugs. In vitro and in vivo experiments, including CCK-8, colony formation, flow cytometry, Transwell assays, and xenograft mouse models, were conducted to evaluate the effects of the target genes and candidate drugs. RESULTS: The ERCDI demonstrated strong prognostic and predictive performance for prognosis in AML patients. Furthermore, the ERCDI effectively predicted immunotherapy and chemotherapy outcomes and was associated with the immune features of the different risk groups. DNA damage-inducible transcript 4 protein (DDIT4), a key gene associated with ERCDI, is related to poor prognosis in AML patients with high expression. Additionally, the knockdown of DDIT4 significantly inhibited AML cell proliferation, induced cell apoptosis, and promoted cell cycle arrest. Chaetocin was subsequently identified as a candidate compound for AML treatment. Subsequent experiments suggested that combining chaetocin and venetoclax is a potentially promising therapeutic strategy for AML. CONCLUSION: The ERCDI provides personalized risk assessment and treatment recommendations for individual AML patients. The combined use of chaetocin and venetoclax can potentially be repurposed for AML therapy.

Humans↗

Gene expression signatures for predicting prognosis of squamous cell and adenocarcinomas of the lung.

Non-small-cell lung cancers (NSCLC) compose 80% of all lung carcinomas with squamous cell carcinomas (SCC) and adenocarcinoma representing the majority of these tumors. Although patients with early-stage NSCLC typically have a better outcome, 35% to 50% will relapse within 5 years after surgical treatment. We have profiled primary squamous cell lung carcinomas from 129 patients using Affymetrix U133A gene chips. Unsupervised analysis revealed two clusters of SCC that had no correlation with tumor stage but had significantly different overall patient survival (P = 0.036). The high-risk cluster was most significantly associated with down-regulation of epidermal development genes. Cox proportional hazard models identified an optimal set of 50 prognostic mRNA transcripts using a 5-fold cross-validation procedure. Quantitative reverse transcription-PCR and immunohistochemistry using tissue microarrays were used to validate individual gene candidates. This signature was tested in an independent set of 36 SCC samples and achieved 84% specificity and 41% sensitivity with an overall predictive accuracy of 68%. Kaplan-Meier analysis showed clear stratification of high-risk and low-risk patients [log-rank P = 0.04; hazard ratio (HR), 2.66; 95% confidence interval (95% CI), 1.01-7.05]. Finally, we combined the SCC classifier with our previously identified adenocarcinoma prognostic signature and showed that the combined classifier had a predictive accuracy of 71% in 72 NSCLC samples also showing significant differences in overall survival (log-rank P = 0.0002; HR, 3.54; 95% CI, 1.74-7.19). This prognostic signature could be used to identify patients with early-stage high-risk NSCLC who might benefit from adjuvant therapy following surgery.

Adenocarcinoma↗

Genes associated with breast cancer metastatic to bone.

PURPOSE: The biology of tumors relapsing to bone is poorly understood. In this study, we initiated a search for genes that are implicated in tumors relapsing to bone in breast cancer. PATIENTS AND METHODS: We analyzed 107 primary breast tumors in patients who were all lymph node negative at the time of diagnosis and all had experienced relapse. Total RNA isolated from frozen tumor samples was used to gather gene expression data using oligo microarrays. RESULTS: A panel of 69 genes was found significantly differentially expressed between patients who experienced relapse to bone versus those who experienced relapse elsewhere in the body. The most differentially expressed gene, TFF1, was confirmed by quantitative reverse transcriptase polymerase chain reaction in an independent cohort (n = 122; P = .0015). Our differentially expressed genes, combined with a recently reported gene set relevant to tumors relapsing to bone in an animal model system, pointed to the involvement of the fibroblast growth factor receptor signaling pathway in preference of tumor cells that relapse to bone. Given that patients who experience relapse to bone may benefit from bisphosphonate therapy, we developed a classifier of 31 genes, which in an independent validation set correctly predicts all tumors relapsing to bone with a specificity of 50%. CONCLUSION: Our study identifies a panel of genes relevant to bone metastasis in breast cancer. The subsequently developed classifier of tumors relapsing to bone could, after thorough confirmation on an extended number of independent samples, and in combination with our previously developed high-risk profile, provide a diagnostic tool for the recommendation of adjuvant bisphosphonate therapy in addition to endocrine therapy or chemotherapy.

Adult↗

Multicenter validation of a gene expression-based prognostic signature in lymph node-negative primary breast cancer.

PURPOSE: We previously identified in a single-center study a 76-gene prognostic signature for lymph node-negative (LNN) breast cancer patients. The aim of this study was to validate this gene signature in an independent more diverse population of LNN patients from multiple institutions. PATIENTS AND METHODS: Using custom-designed DNA chips we analyzed the expression of the 76 genes in RNA of frozen tumor samples from 180 LNN patients who did not receive adjuvant systemic treatment. RESULTS: In this independent validation, the 76-gene signature was highly informative in identifying patients with distant metastasis within 5 years (hazard ratio, [HR], 7.41; 95% CI, 2.63 to 20.9), even when corrected for traditional prognostic factors in multivariate analysis (HR, 11.36; 95% CI, 2.67 to 48.4). The actuarial 5- and 10-year distant metastasis-free survival were 96% (95% CI, 89% to 99%) and 94% (95% CI, 83% to 98%), respectively, for the good profile group and 74% (95% CI, 64% to 81%) and 65% (53% to 74%), respectively for the poor profile group. The sensitivity for 5-yr distant metastasis-free survival was 90%, and the specificity was 50%. The positive and negative predictive values were 38% (95% CI, 29% to 47%) and 94% (95% CI, 86% to 97%), respectively. The 76-gene signature was confirmed as a strong prognostic factor in subgroups of estrogen receptor-positive patients, pre- and postmenopausal patients, and patients with tumor sizes 20 mm or smaller. The subgroup of patients with estrogen receptor-negative tumors was considered too small to perform a separate analysis. CONCLUSION: Our data provide a strong methodologic and clinical multicenter validation of the predefined prognostic 76-gene signature in LNN breast cancer patients.

Adult↗

Epidemiology of hepatitis B, C, D and G viruses and cytokine levels among intravenous drug users.

To investigate the features of various hepatitis virus infection in intravenous drug users (IVDU), we conducted an epidemiological survey of hepatitis viruses including hepatitis B virus (HBV), hepatitis C virus (HCV), hepatitis D virus (HDV) and hepatitis G virus (HGV) in IVDU. The correlation of TH lymphocyte cytokine and hepatitis virus infection was examined. A study population of 406 IVDU consisted of 383 males and 23 females. HBV-DNA and HCV-RNA were detected by fluorescence quantitative polymerase chain reaction. HBsAg, HBeAg, anti-HBc, anti-HCV, HDV-Ag and anti-HGV were assayed by ELISA. The levels of cytokines of TH1 and TH2 were measured by ELISA. The similar indices taken from 102 healthy persons served as controls. The infection rate of each virus among IVDU was 36.45 % for HBV, 69.7 % for HCV, 2.22 % for HDV, and 1.97 % for HGV, respectively. The co-infection rate of HBV and HCV was detected in 113 of 406 (27.83 %). In contrast, among controls, the infection rate was 17.65 % for HBV and 0 % for the other hepatitis viruses. The levels of PHA-induced cytokines (IFN-gamma and IL-4) and the level of serum IL-2 were obviously decreased in IVDU. On the other hand, the level of serum IL-4 was increased. The IFN-gamma level was continuously decreased when the IVDU was infected with HBV/HCV. In conclusion, HBV and HCV infection were common in this population of IVDU and they had led to a high incidence of impaired TH1 cytokine levels.

Adolescent↗

Gene-expression signatures in oncology diagnostics.

The advent of DNA microarray technologies has enabled the development of gene expression signatures that can be used for prognostic and predictive purposes. This new information can change the paradigm of how medicine is practiced, coupling physical examination, pathology and clinical tests with new molecular information. However, many unanswered questions regarding sample acquisition, platform development, signature validation and clinical trial design will need to be addressed before this new medical content will have an impact on the clinical setting. This article will examine some of these issues in greater detail, focusing on tissue type, platform comparison, biospecimen collection and signature validation.

Gene Expression Profiling↗

Prognostic gene expression signatures can be measured in tissues collected in RNAlater preservative.

Gene expression signatures have the ability to serve in both prognostic and predictive capacities in patient management. The use of RNA as the starting material and the lability of this analyte, however, dictate that tissues must be snap-frozen or stored in a solution that can maintain the integrity of the RNA. We compared pairs of snap-frozen and RNAlater preservative-suspended tissue from 30 such paired lymph node-negative breast tumors and 21 such paired Dukes' B colon tumors. We assessed the correlation of gene expression profiles and prediction of recurrence based on two prognostic algorithms. Tissues stored in RNAlater preservative generated expression profiles with excellent correlation (average Pearson correlation coefficients of 0.97 and 0.94 for the breast and colon tumor pairs, respectively) compared to those produced by tissues that were snap-frozen. The correlation in the prediction of recurrence was 97% and 95% for the breast and colon tumor pairs, respectively, between these two types of tissue handling protocols. This novel finding demonstrates that prognostic signatures can be obtained from RNAlater preservative-suspended tissues, an important step in bringing gene expression signatures to the clinic.

Algorithms↗

A quantitative reverse transcriptase-polymerase chain reaction assay to identify metastatic carcinoma tissue of origin.

Identifying the primary site in patients with metastatic carcinoma of unknown primary origin can enable more specific therapeutic regimens and may prolong survival. Twenty-three putative tissue-specific markers for lung, colon, pancreatic, breast, prostate, and ovarian carcinomas were nominated by querying a gene expression profile database and by performing a literature search. Ten of these marker candidates were then selected based on validation by reverse transcriptase-polymerase chain reaction (RT-PCR) on 205 formalin-fixed, paraffin-embedded metastatic carcinoma specimens originating from these six and from other cancer types. Next, we optimized the RNA isolation and quantitative RT-PCR methods for these 10 markers and applied the quantitative RT-PCR assay to a set of 260 metastatic tumors. We then built a gene-based algorithm that predicted the tissue of origin of metastatic carcinomas with an overall leave-one-out cross-validation accuracy of 78%. Lastly, our assay demonstrated an accuracy of 76% when tested on an independent set of 48 metastatic samples, 37 of which were either a known primary or initially presented as carcinoma of unknown primary but were subsequently resolved.

Algorithms↗

Novel genes associated with malignant melanoma but not benign melanocytic lesions.

PURPOSE: Cutaneous melanoma is a common, aggressive cancer with increasing incidence. The identification of melanoma-specific deregulated genes could provide molecular markers for lymph node staging assays and further insight into melanoma tumorigenesis. EXPERIMENTAL DESIGN: Total RNA isolated from 45 primary melanoma, 18 benign skin nevi, and 7 normal skin tissue specimens were analyzed on an Affymetrix Hu133A microarray containing 22,000 probe sets. RESULTS: Hierarchical clustering revealed a distinct separation of the melanoma samples from the benign and normal specimens. Novel genes associated with malignant melanoma were identified. Differential gene expression of two melanoma-specific genes, PLAB and L1CAM, were tested by a one-step quantitative reverse transcription-PCR assay on primary malignant melanoma, benign nevi, and normal skin samples, as well as on malignant melanoma lymph node metastasis and melanoma-free lymph nodes. The performance of the markers was compared with conventional melanoma markers such as tyrosinase, gp100, and MART1. CONCLUSION: Our study systematically identified novel melanoma-specific genes and showed the feasibility of using a combination of PLAB and L1CAM in a reverse transcription-PCR assay to differentiate clinically relevant samples containing benign or malignant melanocytes.

Adolescent↗

Identification and characterization of optimal gene expression markers for detection of breast cancer metastasis.

Sentinel lymph node (SLN) status is highly predictive of overall axillary lymph node involvement in breast cancer. Historically, SLN-positive patients have undergone axillary lymph node dissection in a second surgery. Intraoperative SLN analysis could reduce the cost and complications of a second surgery; however, existing histopathological methods lack standardization and exhibit poor sensitivity. Rapid molecular methods may lead to improved intraoperative diagnosis of SLN metastasis. In this study, we used a genome-wide gene expression analysis of breast and other tissues to identify seven putative markers for detecting breast cancer metastasis. We assessed the utility of these markers for identifying clinically actionable metastases in lymph nodes through reverse transcriptase-polymerase chain reaction analysis of SLNs from 254 breast cancer patients. Polymerase chain reaction signals were compared to pathology on a per-patient basis. The optimal two-gene combination, mammaglobin and cytokeratin 19, detected clinically actionable metastasis in breast SLNs with 90% sensitivity and 94% specificity. Application of stringent criteria for identifying presumptive hematoxylin- and eosin-positive samples increased sensitivity and specificity to 91 and 97%, respectively. This study represents the first comprehensive demonstration of the utility of gene expression markers for detecting clinically actionable breast metastases. An intraoperative molecular assay using these markers has the potential to significantly reduce second surgeries for patients undergoing SLN dissection.

Biomarkers, Tumor↗

Gene expression-driven diagnostics and pharmacogenomics in cancer.

The advancement of microarray technologies for characterizing tumors at the gene expression level has made a significant impact on the field of oncology. Profiling gene expression of various human tumors has led to the identification of gene expression patterns or signatures related to tumor classification, disease outcome and response to therapy. This technology can also be used to study the mechanism of action of specific therapeutics. Routine application of microarrays in clinical practice will require significant efforts to standardize the array manufacturing techniques, assay protocols and analytical methods used to interpret the data. Extensive, independent validation using large, statistically sound datasets will also be necessary. Studies on gene expression profiling of clinically relevant tissue samples with the aim of finding gene markers to support disease prognosis and therapy decisions are reviewed.

Animals↗

Microarray analysis reveals genetic pathways modulated by tipifarnib in acute myeloid leukemia.

BACKGROUND: Farnesyl protein transferase inhibitors (FTIs) were originally developed to inhibit oncogenic ras, however it is now clear that there are several other potential targets for this drug class. The FTI tipifarnib (ZARNESTRA, R115777) has recently demonstrated clinical responses in adults with refractory and relapsed acute leukemias. This study was conducted to identify genetic markers and pathways that are regulated by tipifarnib in acute myeloid leukemia (AML). METHODS: Tipifarnib-mediated gene expression changes in 3 AML cell lines and bone marrow samples from two patients with AML were analyzed on a cDNA microarray containing approximately 7000 human genes. Pathways associated with these expression changes were identified using the Ingenuity Pathway Analysis tool. RESULTS: The expression analysis identified a common set of genes that were regulated by tipifarnib in three leukemic cell lines and in leukemic blast cells isolated from two patients who had been treated with tipifarnib. Association of modulated genes with biological functional groups identified several pathways affected by tipifarnib including cell signaling, cytoskeletal organization, immunity, and apoptosis. Gene expression changes were verified in a subset of genes using real time RT-PCR. Additionally, regulation of apoptotic genes was found to correlate with increased Annexin V staining in the THP-1 cell line but not in the HL-60 cell line. CONCLUSIONS: The genetic networks derived from these studies illuminate some of the biological pathways affected by FTI treatment while providing a proof of principle for identifying candidate genes that might be used as surrogate biomarkers of drug activity.

Acute Disease↗

Gene expression profiles and molecular markers to predict recurrence of Dukes' B colon cancer.

PURPOSE: The 5-year survival rate of patients with Dukes' B colon cancer is approximately 75%. Identification of the patients at high risk of recurrence in this group would allow better staging and more informed use of adjuvant chemotherapy. In this study, we used DNA chip technology to systematically identify new prognostic markers for tumor relapse in Dukes' B patients. PATIENTS AND METHODS: Using Affymetrix U133a GeneChip containing approximately 22,000 transcripts (Affymetrix, Santa Clara, CA), RNA samples from 74 patients with Dukes' B colon cancer were analyzed. Thirty-one patients developed tumor relapse in less than 3 years, whereas 43 patients remained disease-free for more than 3 years after surgery. Two supervised class prediction approaches were used to identify gene markers that can best discriminate between patients who would experience relapse and patients who would remain disease-free. A multivariate Cox model was built to predict recurrence. RESULTS: Gene expression profiling identified a 23-gene signature that predicts recurrence in Dukes' B patients. This signature was validated in 36 independent patients. The overall performance accuracy was 78%. Thirteen of 18 relapse patients and 15 of 18 disease-free patients were predicted correctly, giving an odds ratio of 13 (95% CI, 2.6 to 65; P =.003). The log-rank test indicated a significant difference in disease-free time between the predicted relapse and disease-free patients (P =.0001). CONCLUSION: The clinical value of these markers is that the patients at a high predicted risk of relapse (13-fold risk) could be upstaged to receive adjuvant therapy, similar to Dukes' C patients. Our data highlight the feasibility of a prognostic assay that could focus more intensive treatment for localized colon cancer.

Algorithms↗

Quantitative gene expression profiling in formalin-fixed, paraffin-embedded tissues using universal bead arrays.

We recently developed a sensitive and flexible gene expression profiling system that is not dependent on an intact poly-A tail and showed that it could be used to analyze degraded RNA samples. We hypothesized that the DASL (cDNA-mediated annealing, selection, extension and ligation) assay might be suitable for the analysis of formalin-fixed, paraffin-embedded tissues, an important source of archival tissue material. We now show that, using the DASL assay system, highly reproducible tissue- and cancer-specific gene expression profiles can be obtained with as little as 50 ng of total RNA isolated from formalin-fixed tissues that had been stored from 1 to over 10 years. Further, tissue- and cancer-specific markers derived from previous genome-wide expression profiling studies of fresh-frozen samples were validated in the formalin-fixed samples. The DASL assay system should prove useful for high-throughput expression profiling of archived clinical samples.

Algorithms↗

[Culture and identification of human and rabbit corpus cavernosum smooth muscle cells].

OBJECTIVE: To investigate an effective method to produce large numbers of pure corporal smooth muscle cells in vitro according to the requirement of study. METHODS: In this study, we used the primary tissue culture technique to isolate and culture the corpus cavernosum smooth muscle cells (CCSM) from human males with normal erectile function and New Zealand white rabbits. The cells were identified in regard to morphological and growing characteristics via immunohistochemical methods (including alpha-smooth muscle actin, desmin, myocin and factor VIII related antigen), special dye techniques (including Masson and Van Gieson) and transmission electron microscope. RESULTS: CCSM were isolated and cultured successfully with high purity. Morphologically, the cells were spindle shaped and grow on top of each other, resembling a "hill and valley" in appearance. When characterized in immunohistochemistry, the cells were stained with alpha-smooth muscle actin, desmin and myocin, but not with anti-factor VIII, an endothelial marker. CONCLUSION: The CCSM, which can be isolated and cultured successfully, may be used for further studying their biological function. The CCSM cultured in vitro was proved to be useful to evaluate and investigate the effect of some new medicine for penile erection. There is also a clinical and theoretical significance in further studying the experimental mechanisms of erectile dysfunction.

Animals↗

[Brachytherapy of 125I implantation for localized prostate cancer (report of 41 cases)].

OBJECTIVE: To observe the effect of brachytherapy of 125I implantation on localized prostate cancer. METHODS: Two-step technique was engaged in the implantation of 125I into the prostate for 41 localized prostate cancer patients. The prescription dosage of 125I was 160 Gy. TRUS and C-Arm X-ray were used for the confirmation of seeds location in the prostate. RESULTS: Thirty-three patients were followed up for 3 to 4 years. Abnormal PSAs were found in 2 patients by positive biopsy. No patients died in this investigation. The early stage complications were urinary irritation symptoms that were severe within 6 months and disappeared after 1 year. CONCLUSION: Brachytherapy of 125I implantation increases long-term tumor-free survival rate, with few long-term complications and some short-tern urinary stimulating symptoms.

Aged↗

[Questionnaire and pad-test in assessment of incontinence after radical retro-pubic prostatectomy].

OBJECTIVE: To confirm urinary incontinence after radical retro-pubic prostatectomy by questionnaire and pad-test, observe the influence of radical prostatectomy on the patient's quality of life (QOL), and study the effect of urethral sphincter preservation and the patient's age on incontinence. METHODS: Questionnaire and pad-test were conducted in 165 consecutive prostate cancer patients who underwent radical prostatectomies. The mean follow-up time was 13 months (12-14 months). Each patient was kept in contact with our incontinence advisor by telephone or direct interview. At 12 months after operation, the patients were asked to the clinic to fill in the questionnaire and underwent the pad-test. In accordance to different operative techniques, the patients were divided into a sphincter repairing group (19 cases) and a sphincter preservation group (146 cases). RESULTS: All the 165 patients were kept in contact with us, underwent the pad-test and filled in the questionnaire. Of the 7 patients diagnosed as incontinence for admitting using pads, only 1 had urinary leakage, and the other 6, who did not use pads very often, showed slight change of QOL. In the pad-test, 5 patients were considered to be incontinent since the pad weight gained > 1 grams. Between the questionnaire and the pad-test there was a high concordant rate (98.8%). Within 3 months after operation, younger patients seemed to return to continence sooner. The continence rate at 12 months after operation was 99.3% in the sphincter preservation group and 94.7% in the sphincter-repairing group. The incontinence rates at the removal of the urinary catheter after operation were 60% and 82% in patients aged 51-60 and 61-70, respectively. At 3 months after operation, the incontinence rates were similar in both groups. CONCLUSION: Both the questionnaire and the pad-test are recommendable in the assessment of post-operative incontinence since it can accurately document patients' incontinent status. Preservation of the urethral sphincter and its possible innervations can improve the incontinence rate. Younger patients seem to return to continence sooner than the elders.

Adult↗