Zhengdeng Lei, PhD

Zhengdeng Lei, PhD

2009 - Present Research Fellow at Duke-NUS, Singapore
2007 - 2009 High Throughput Computational Analyst, Memorial Sloan-Kettering Cancer Center, New York
2003 - 2007 PhD, Bioinformatics, University of Illinois at Chicago

Saturday, April 28, 2012

Patients with a HER2-positive breast cancer benefited from paclitaxel, regardless of estrogen-receptor status, but paclitaxel did not benefit patients with HER2-negative, estrogen-receptor-positive cancers.


http://www.ncbi.nlm.nih.gov/pubmed/17928597?dopt=Abstract


HER2 and response to paclitaxel in node-positive breast cancer.


Abstract

BACKGROUND:

The status of human epidermal growth factor receptor type 2 (HER2) in breast-cancer cells predicts clinical outcomes in women who receive adjuvant anthracycline-based chemotherapy. We hypothesized that HER2 positivity predicts a benefit from adjuvant doxorubicin doses above standard levels, from the addition of paclitaxel after adjuvant chemotherapy with doxorubicin plus cyclophosphamide, or from both.

METHODS:

We randomly selected 1500 women from 3121 women with node-positive breast cancer who had been randomly assigned to receive doxorubicin (60, 75, or 90 mg per square meter of body-surface area) plus cyclophosphamide (600 mg per square meter) for four cycles, followed by four cycles of paclitaxel (175 mg per square meter) or observation. Tissue blocks from 1322 of these 1500 women were available. Immunohistochemical analyses of these tissue specimens for HER2 with the CB11 monoclonal antibody against HER2 or with a polyclonal-antibody assay kit and fluorescence in situ hybridization for HER2 amplification were performed.

RESULTS:

No interaction was observed between HER2 positivity and doxorubicin doses above 60 mg per square meter. HER2 positivity was, however, associated with a significant benefit from paclitaxel. The interaction between HER2 positivity and the addition of paclitaxel to the treatment was associated with a hazard ratio for recurrence of 0.59 (P=0.01). Patients with a HER2-positive breast cancer benefited from paclitaxel, regardless of estrogen-receptor status, but paclitaxel did not benefit patients with HER2-negative, estrogen-receptor-positive cancers.

CONCLUSIONS:

The expression or amplification, or both, of HER2 by a breast cancer is associated with a benefit from the addition of paclitaxel after adjuvant treatment with doxorubicin (<60 mg per square meter) plus cyclophosphamide in node-positive breast cancer, regardless of estrogen-receptor status. Patients with HER2-negative, estrogen-receptor-positive, node-positive breast cancer may gain little benefit from the administration of paclitaxel after adjuvant chemotherapy with doxorubicin plus cyclophosphamide.

Women with aggressive intrinsic subtypes such as HER-2–positive and basal breast cancer benefited from the addition of paclitaxel


http://www.healio.com/hematology%20oncology/breast%20cancer/news/online/%7B699585D0-A0E1-4E74-ACF9-ED2D6B686F2C%7D/Tissue-microarrays-identified-intrinsic-subtype-predicted-value-of-chemotherapy-in-breast-cancer


Tissue microarrays identified intrinsic subtype, predicted value of chemotherapy in breast cancer

  • October 16, 2009
2009 ASCO Breast Cancer Symposium
Using tissue microarrays collected from women who participated in CALGB 9344, researchers found the addition of adjuvant paclitaxel to doxorubicin and cyclophosphamide improved survival in patients with early node-positive breast cancer.
Torsten O. Nielsen, MD, PhD, an associate professor in the department of pathology and laboratory medicine at the University of British Columbia in Vancouver, presented the results at the 2009 Breast Cancer Symposium. Women with aggressive intrinsic subtypes such as HER-2–positive and basal breast cancer benefited from the addition of paclitaxel (Taxol, Bristol Myers Squibb), but that was not the case for all women in the study.
“In the luminal A women, the most common group, we saw no benefit from adding paclitaxel,” Nielsen said. “There is no apparent benefit to adding paclitaxel to these node-positive women on top of the AC chemotherapy backbone.”
There were 790 women with luminal A tumors, 340 with luminal B, 444 with core basal, 221 with HER-2– enriched and 93 with ER-negative/HER-2/nonbasal disease.
Nielsen said results from the tissue microarrays showed substantial agreement with previous whole-section HER-2 and clinical ER data. He added that multivariate analysis showed intrinsic subtype was prognostically significant (P<.001).
Core basal status also predicted benefit from the addition of paclitaxel (P=.003). Ki67 status was prognostic but not predictive.
“The tissue microarray approach gives similar results to what could be obtained with more tedious, expensive and slower work on whole sections,” Nielsen said. – by Jason Harris

Friday, April 27, 2012

Proliferative

http://www.ncbi.nlm.nih.gov/pubmed/14985451


Mol Cancer Ther. 2004 Feb;3(2):111-21.

Gene expression correlating with response to paclitaxel in ovarian carcinoma xenografts.

Source

Mario Negri Institute for Pharmacological Research, Bergamo and Milan, Italy.

Abstract

We have investigated gene expression profiles of human ovarian carcinomas in vivo during Taxol(R) (paclitaxel) treatment and observed a difference in expression. Nude mice bearing 1A9 or 1A9PTX22 xenografts were given 60 mg/kg of paclitaxel. Therapeutic efficacy was achieved for 1A9, while 1A9PTX22 did not respond. Tumor tissues harvested 4 and 24 h after treatment were evaluated by cDNA microarray against untreated tumors. Paclitaxel caused the modulation of more genes in 1A9 than in 1A9PTX22 tumors, in accordance to their therapeutic response. Most gene expression alterations were detected 24 h after paclitaxel administration and affected genes involved in various biological functions including cell cycle regulation and cell proliferation (CDC2, CDKN1A, PLAB, and TOP2A), apoptosis (BNIP3 and PIG8), signal transduction and transcriptional regulation (ARF1, ATF2, FOS, GNA11, HDAC3, MADH2, SLUG, and SPRY4), fatty acid biosynthesis and sterol metabolism (FDPS, IDI1, LIPA, and SC5D), and IFN-mediated signaling (G1P3, IFI16, IFI27, IFITM1, and ISG15). The modulation of two representative genes, CDKN1A and TOP2A, was validated by Northern analyses on a panel of seven ovarian carcinoma xenograft models undergoing treatment with paclitaxel. We found that the changes in expression level of these genes was strictly associated with the responsiveness to paclitaxel. Our study shows the feasibility of obtaining gene expression profiles of xenografted tumor models as a result of drug exposure. This in turn might provide insights related to the drugs' action in vivo that will anticipate the response to treatment manifested by tumors and could be the basis for novel approaches to molecular pharmacodynamics.

Monday, April 23, 2012

Expression data from the Cancer Cell Line Encyclopedia (CCLE)

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36133

 www.broadinstitute.org/ccle

mesenchymal/invasive

Loss of PTEN expression (e.g. mutation/LOH) in mesenchymal/invasive subtype???
Targeting mTORC2 in mesenchymal cancer cells????

Tuesday, April 17, 2012

MRT first last train





JURONG EAST  
North-South East-West line last train service to:
Joo KoonDaily0017 HRS
Pasir RisDaily2345 HRS
Marina BayDaily2253 HRS
Toa PayohDaily2328 HRS
Ang Mo KioDaily0017 HRS








Boon Lay station
301 Boon Lay Way
Singapore 649846
Train service terminating at Pasir Ris
First train serviceMonday to Saturday0536 HRS
Sunday & Public Holiday0606 HRS
Last Train daily2338 HRS
 
Train service terminating at Joo Koon
First train serviceMonday to Saturday0524 HRS
Sunday & Public Holiday0553 HRS
Last Train daily 0024 HRS

Tuesday, April 10, 2012

Run R GUI from server

1. install Xming
http://ncu.dl.sourceforge.net/project/xming/Xming/6.9.0.31/Xming-6-9-0-31-setup.exe
or
http://www.straightrunning.com/XmingNotes/

2. install fonts
http://sourceforge.net/projects/xming/files/Xming-fonts/7.5.0.34/Xming-fonts-7-5-0-34-setup.exe
or
http://www.straightrunning.com/XmingNotes/

3. run Xming with localhost:0

4. (1) if use SSH secure shell, edit profile,
enable X11 connection
(2) if use PuTTY, connection->ssh-> X11, enable X11, display location: localhost:0

5.  go to ./R/bin, run R --gui=Tk