Faculty Research - Experimental Pathology

PEOPLE IN THE LAB

Education and Training:

Positions:

Areas of interest: 

Experimental pathology –

Cancer Research, Lung cancer and development, Cancer genomics, Molecular study of oncogene mechanism, Oncogenic signaling, Functional screens for novel cancer genes, Developing function-based tools to rapidly evaluate multiple candidate cancer genes, DNA repair and cancer.

Research interests: 

The general areas of interest center on cancer research and are classified into these three areas (at this time):

I.  Mechanistic study of the 14q13.3 lung oncogenes

Oncogenes activated via gene amplification have a proven track record of being amenable to invention of new anti-cancer therapies.  The new generation of anti-cancer therapies such as Herceptin®, Erbitux®, Tarceva®, Iressa® all targets oncogenes that rely on gene amplification as an activation mechanism in cancers.  Regarding the cancer type to investigate, we’ve been focusing on lung cancer in view of its severe unmet medical needs in early diagnosis and treatment.  Prior to my arrival at Penn State University College of Medicine, we had collected genome-wide DNA copy number alteration (CNA) data using an array-based comparative genomic hybridization (aCGH) method from a collection of over 200 human lung tumor and cancer cell lines.  Analysis of the CNA data identified a frequent amplicon located at chromosome 14q13.3 and the minimal amplified region deduced from all the amplified samples covered these three genes that are related to fetal lung development – TTF1, NKX2-8, and PAX9.  TTF1 (thyroid transcription factor 1), NKX2-8 and PAX9 are transcription factors that regulate gene expression.  Our in vitro cell culture study found that these three coamplified genes could synergistically stimulate proliferation of premalignant lung epithelial cells (Kendall et al. PNAS 2007). We also have published loss-of-function data documenting their indispensability in the tumor maintenance of the lung cancer cell lines carrying the 14q13.3 amplicon.  It is very interesting that three functionally cooperating developmental transcription factors are coamplified by one specific amplicon to confer oncogenic advantage. Tumorigenesis and organogenesis share similar steps including rapid cell growth and vasculature restructuring. It is thus not surprising that the misappropriation of organ development and morphogenesis pathways may lead to malignant transformation. In our laboratory, we are particularly interested in dissecting the oncogenic mechanism of TTF1, NKX2-8, and PAX9 using biochemical, cell-based, and model organism-based tools.

II.  New cancer gene discovery and characterization

In addition to the 14q13.3 lung oncogenes, discovering additional novel lung cancer genes is of great interest to our laboratory.  To pursue this goal, we will use two different but complementary approaches – (i) genetics approach utilizing mutations of cancer genome as an entry point of cancer gene discovery (e.g., discovery of the coamplified 14q13.3 lung oncogenes) and (ii) function-based method relying on functional screens to identify genes with novel oncogenic property.  With regard to the genetics-based approach, we will use the in-house lung cancer genome database that led to the discovery of the 14q13.3 amplicon as well as the cancer genome database produced by the NIH-sponsored cancer genome project (also known as The Cancer Genome Atlas, TCGA). Regarding the function-based approach, we plan to create premaglinant lung epithelial cells as a host to screen cDNAs that exist in genomic regions known to undergo DNA copy number alteration. With the identified oncogenes, we intend to study the molecular mechanism of their activities as in the case of the 14q13.3 oncogenes.  Although our laboratory is currently focused on lung cancer, the principle and methodology employed in our laboratory are readily transposable to studying other cancer types.

III.  Developing loss-of-function tools to rapidly evaluate multiple candidate oncogenes

Most of the recurrent amplicons that we would like to study contain many candidate genes.  Within our lung CNA dataset of 261 lung cancer samples, 50% of all observed focal amplicons contain five or more genes.  The fact that many well-proven oncogenes like K-RAS and CCND1 exist in multigenic amplicons suggests that it would be a mistake not to pursue the identification of the driver genes of multigenic amplicons.  However, the gene-by-gene approach of identifying the driver gene is time-consuming and not practical for amplicons containing many genes.  In order to facilitate the study of multigenic amplicons, we wish to subject them directly to a loss-of-function screen using barcoded RNA interference (RNAi) technology (BRT).  The idea is based on the barcoded hairpin RNA (shRNA) library developed by Dr. Greg Hannon’s group in the Cold Spring Harbor Laboratory. The logical assumption is that the driver gene(s) of a complex amplicon must be providing a functional advantage to the host cells.  Blocking this functional advantage through RNAi-induced downregulation of the driver gene would impose a deleterious effect on the cancer cell.  Although the “addiction” of tumor cells to a single oncogene may not be a universal rule and can be highly dependent on the genetic context, well-controlled RNA interference experiments are a fast and powerful tool in assessing the roles of candidate amplified oncogenes. As a proof-of-principle experiment, we tested the C-MYC oncogene in a lung cancer cell line highly amplified for C-MYC.  Three different retrovirus-based shRNAs against C-MYC were designed and termed MYCA, MYCB, and MYCC.  MYCA reduced the endogenous protein expression level of C-MYC to 10% of wild-type level, whereas MYCB and MYCC hairpins did not significantly alter C-MYC protein expression. To create a simple model system, we infected MYCA and MYCB along with the empty retroviral vector (LMP) individually into the amplified cell line.  To move forward with this proof-of-principle experiment, we co-injected subcutaneously a 50:50 mixture of the amplified lung cancer cell line stably expressing MYCA- or MYCB- shRNA into nude mice.  In this way, the two populations of transfectant cells were forced to compete to form tumors in vivo.  By quantitative PCR (QPCR), the actual ratio of MYCB/MYCA shRNA in the 50:50 cell mixture used for injection was close to 0.5 (reflecting cell counting error in the preparation of the 50:50 cell mixture). However, the MYCB/MYCA shRNA ratio in a resultant tumor at day 25 post injection increased to from to 5, representing a 10-fold depletion of the effective MYCA shRNA from the original 50:50 cell mixture.  At day 40, the ratio increased to 11-fold.  This simple model system, consisting of 2 RNA hairpins to one driver gene (C-MYC), provides encouraging data.  We will expand the proof-of-principle model system by increasing the complexity in species of genes and shRNAs towards applying it to studying complex amplicons.

 Patent Applications:

1. “Amplification and Overexpression of Oncogenes”  2003. International Pub. NO. WO 03/100000 A2.

2. "Amplified Cancer Gene Hepsin" (2002) US serial NO. 10/073,060 (European Patent Office: application number 02706233.0-2402-US0204018). Pub. NO. US 2003/0049645 A1.

3. “Gene Amplification in Cancer”. US Provisional Application No. 10/742,442 (2003).

4. “Amplified Oncogenes and Their Involvement in Cancer”. Patent Cooperation Treaty International Publication Number WO 03/018770 A2 (2003). Pub. NO. US 2003/0092042 A1.

5. “Gene Amplification and Overexpression in Cancer (SALPR)” US Provisional Application No. 60/479,833 (2003).

Patent Granted:

1. “Diagnosis and treatment of cancer using mammalian pellino polypeptides and polynucleotides”. United States Patent # 7,115,368, issued Oct-3-2006.

2. “Nucleic acid encoding KCNB potassium channel”. United States Patent # 7,462,465, issued Dec-9-2008.

Publications (peer-reviewed):

1. Gene-Hsiang Lee, Shie-Ming Peng, Shie-Fu Lush, David Mu, Rai-Shung Liu. Reaction of iron-.eta.1-dienyl complexes with dienophiles. X-ray structures of the [4 + 2] cycloaddition adducts. Organometallics 7:1155-1161, 1988.  [View PDF]

2. Fu-Chen Liu, David Mu, Gene-Hsian Lee, Shie-Ming Peng, and Rai-Shung Liu. Preparation of Molybdenum-h3-Pentadienyl Complexes: Structural Characterization of a Delocalized Pentadienyl Ligand in Anti-h3 Geometry. Organometallics 8:402-407, 1989.  [View PDF]

3. Inn-Chu Tsing, David Mu, Gene-Hsian Lee, Shie-Ming Peng, and Rai-Shung Liu. Preparation and Properties of Molybdenum-Pentadienyl Complexes: A Facile h5<=>h3 Reversible Interconversion for a Pentadienyl Ligands. Organometallics 8:2248-2252, 1989.  [View PDF]

4. Susan Janes, David Mu, David Wemmer, Alan J. Smith, Surinder Kaur, David Maltby, Alma L. Burlingame, and Judith P. Klinman.  A New Redox Cofactor in Eukaryotic Enzyme: 6-Hydroxydopa at the Active Site of Bovine Serum Amine Oxidase.  Science  248:981-987, 1990.  [View PDF]

5. Doreen E. Brown, Michele A. McGuirl, David M. Dooley, Susan M. Janes, David Mu, and Judith P. Klinman.  The Organic Functional Group in Copper-containing Amine Oxidases: Resonance Raman spectra are consistent with the presence of topa quinone in the active site.   Journal of Biological Chemistry 266:4049-4051, 1991.  [View PDF]

6. David Mu, Susan M. Janes, Alan J. Smith, Doreen E. Brown, David M. Dooley, and Judith P. Klinman.  Tyrosine Codon Corresponds to Topa Quinone at the Active Site of Copper Amine Oxidases.   Journal of Biological Chemistry 267:7979-7982, 1992.  [View PDF]

7. David Mu, Katalin F. Medzihradszky, Greg Adams, Alan J. Smith, Alma L. Burlingame, Danying Cai, and Judith P. Klinman.   Primary Structures for Mammalian Intracellular and Serum Copper Amine Oxidases.  Journal of Biological Chemistry 269:9926-9932, 1994.  [View PDF]

8. David Mu, Elisabeth Bertrand-Burggraf, Juch-Chin Huang, Robert P.P. Fuchs, and Aziz Sancar.  Human and E.coli Excinucleases Are Affected Differently by the Sequence Context of Acetylaminofluorene-guanine Adduct.  Nucleic Acids Research 22:4869-4871, 1994. [View PDF]

9. Chi-Hyun Park, David Mu, Joyce T. Reardon, and Aziz Sancar.  The General Transcription Repair Factor TFIIH is Recruited to the Excision Repair Complex by the XPA Protein Independent of the TFIIE Transcription Factor.  Journal of Biological Chemistry 270:4896-4902, 1995.  [View PDF]

10. David Mu, Chi-Hyun Park, Tsukasa Matsunaga, David S. Hsu, Joyce T. Reardon, and Aziz Sancar.  Reconstitution of Human DNA Repair Excision Nuclease in a Highly Defined System.  Journal of Biological Chemistry 270:2415-2418, 1995.  [View PDF]

11. Tsukasa Matsunaga, David Mu, Chi-Hyun Park, Joyce Reardon, and Aziz Sancar.  Analysis of the Roles of the Subunits Involved in Dual Incisions by Using Anti-XPG and Anti-ERCC1 Antibodies.  Journal of Biological Chemistry 270:20862-20869, 1995.  [View PDF]

12. Aleksey Kazantsev, David Mu, Anne F. Nichols, Stuart M. Linn, and Aziz Sancar.   Functional Complementation of Xeroderma pigmentosum Group E by Replication Protein A (RPA) in an in vitro System.  Proc. Natl. Acad. Sci. USA  93:5014-5018, 1996.  [View PDF]

13. David Mu, David S. Hsu, and Aziz Sancar.  Reaction Mechanism of Human DNA Repair Excision Nuclease.   Journal of Biological Chemistry 271:8285-8294, 1996.  [View PDF]

14. Tsukasa Matsunaga, Chi-Hyun Park, Tadayoshi Bessho, David Mu, and Aziz Sancar.  The Replication Protein RPA Confers Structure-Specific Endonuclease Activities to the XPF-ERCC1 And XPG Subunits of Human DNA Repair Excision Nuclease.  Journal of Biological Chemistry 271:11047-11050. 1996.  [View PDF]

15. Joyce T. Reardon, David Mu, and Aziz Sancar.  Overproduction, Purification, and Characterization of the XPC Subunit of the Human DNA Repair Excision Nuclease.  Journal of Biological Chemistry 271:19451-19456, 1996.   [View PDF]

16. Deborah B. Zamble, David Mu, Joyce T. Reardon, Aziz Sancar, and Stephen J. Lippard.  Repair of Cisplatin-DNA Adducts by the Mammalian Excision Nuclease.  Biochemistry 35:10004-10013, 1996.   [View PDF]

17. David Mu, Mihray Tursun, Derek R. Duckett, James T. Drummond, Paul Modrich, and Aziz Sancar.  Recognition and Repair of Compound DNA Lesions (Base Damage and Mismatch) by Human Excision Repair and Mismatch Repair Systems.  Molecular and Cellular Biology 17:760-769, 1997.  [View PDF]

18. David Mu and Aziz Sancar.  Model for XPC-Independent Transcription-Coupled Repair of Pyrimidine dimers in Huamns.  Journal of Biological Chemistry 272:7570-7573, 1997.   [View PDF]

19. Tadayoshi Bessho, David Mu, and Aziz Sancar.  Initiation of DNA Interstrand Crosslink Repair in Humans: The Nucleotide Excision Repair System Makes Dual Incisions 5’ to the Crosslinked Base and Removes a 22-28 Nucleotide-long Damage-free Strand.  Molecular and Cellular Biology 17:6822-6830, 1997.  [View PDF]

20. David Mu, Mitsuo Wakasugi, David S. Hsu, and Aziz Sancar.  Characterization of Reaction Intermediates of Human DNA Excision Repair Nuclease.  Journal of Biological Chemistry 272:28971-28979, 1997.  [View PDF]

21. David Mu, Tadayoshi Bessho, Lubomir V. Nechev, David J. Chen, Thomas M. Harris, John E. Hearst, and Aziz Sancar.  DNA Interstrand Cross-Links Induce Futile Repair Synthesis in Mammalian Cell Extracts.   Molecular and Cellular Biology 20:2446-2454, 2000.  [View PDF]

22. David Mu, Liyun Chen, Xiping Zhang, Lei-Hoon See, Christina M. Koch, Clifford Yen, James Jiayuan Tong, Lori Spiegel, Ken C. Q. Nguyen, Allyson Servoss, Yue Peng, Lin Pei, Jeffrey R. Marks, Scott Lowe, Timothy Hoey, Lily Yeh Jan, W. Richard McCombie, Michael H. Wigler and Scott Powers.   Genomic amplification and oncogenic properties of the KCNK9 potassium channel gene.  Cancer Cell 3:297-302, 2003.   [View PDF]

23. Lin Pei, Ofer Wiser, Anthony Slavin, David Mu, Scott Powers, Lily Yeh Jan, and Timothy Hoey.  Oncogenic potential of TASK3 (Kcnk9) depends on K⁺ channel function.  Proc. Natl. Acad. Sci. USA 100:7803-7807, 2003.  [View PDF]

24. Lin He, J. Michael Thomson, Michael T. Hemann, Eva Hernando-Monge, David Mu, Summer Goodson, Scott Powers, Carlos Cordon-Cardo, Scott W. Lowe, Gregory J. Hannon, and Scott M. Hammond.  A microRNA polycistron as a potential human oncogene. Nature 435:828-833, 2005.  [View PDF]

25. E. Galteland, E.A. Sivertsen, D.H. Svendsrud, L. Smedshammer, S.H. Kresse, L.A. Meza-Zepeda, O. Myklebost, Z. Suo, D. Mu, P.M. DeAngelis, and T. Stokke.  Translocation t(14;18) and gain of chromosome 18/BCL2: effects on BCL2 expression and apoptosis in B-cell non-Hodgkin's lymphomas.  Leukemia 19:2313–2323, 2005.  [View PDF]

26. E.A. Sivertsen, E. Galteland, D. Mu, H. Holte, L. Meza-Zepeda, O. Myklebost, S. Patzke, E.B. Smeland and T. Stokke.  Gain of chromosome 6p is an infrequent cause of increased PIM1 expression in B-cell non-Hodgkin's lymphomas.  Leukemia 20:539–542, 2006.  [View PDF]

27. Lars Zender, Mona S. Spector, Wen Xue, Peer Flemming, Carlos Cordon-Cardo, John Silke, Sheung-Tat Fan, John M. Luk, Michael Wigler, Gregory J. Hannon, David Mu, Robert Lucito, Scott Powers, and Scott W. Lowe. Identification and Validation of Oncogenes in Liver Cancer Using an Integrative Oncogenomic Approach.  Cell 125:1253-1267, 2006.  [View PDF]

28. Aaron M. Geurts, Lara S. Collier, Jennifer L. Geurts, Leann L. Oseth, Matthew L. Bell, David Mu, Robert Lucito, Susan A. Godbout, Laura E. Green, Scott W. Lowe, Betsy A. Hirsch, Leslie A. Leinwand, David A. Largaespada. Gene Mutations and Genomic Rearrangements in the Mouse as a Result of Transposon Mobilization from Chromosomal Concatemers.  PLoS Genetics Vol. 2, No. 9, e156 doi:10.1371, 2006.  [View PDF]

29. Robert J. Pelham, Linda Rodgers, Ira Hall, Robert Lucito, Ken C. Q. Nguyen, Nicholas Navin, James Hicks, David Mu, Scott Powers, Michael Wigler, and David Botstein.  Identification of alterations in DNA copy number in host stromal cells during tumor progression.  Proc. Natl. Acad. Sci. USA 103:19848-19853, 2006.  [View PDF]

30. David MacPherson, Karina Conkrite, Mandy Tam, Shizuo Mukai, David Mu, and Tyler Jacks.  Murine bilateral retinoblastoma exhibiting rapid onset, metastatic progression and N-myc gene amplification.  EMBO J  26:784-794, 2007.  [View PDF]

31. R. Karni, E. de Stanchina, S.W. Lowe, R. Sinha, D. Mu, and A.R. Krainer.  The splicing factor SF2/ASF is an oncogene.  Nature Struct. Mol. Biol. 14:185-193, 2007.  [View PDF]

32. C.L. Scott, J. Gil, E. Hernando, J. Teruya-Feldstein, M. Narita, D. Martinez, T. Visakorpi, D. Mu, C. Cordon-Cardo, G. Peters, D. Beach, and S.W. Lowe.  Oncogenic properties of the polycomb protein CBX7.  Proc. Natl. Acad. Sci. USA  104:5389-5394, 2007.  [View PDF]

33. Jude Kendall, Qing Liu, Amy Bakleh, Alex Krasnitz, Ken Nguyen, B. Lakshmi, William Gerald, Scott Powers, and David Mu.  Oncogenic cooperation and co-amplification of developmental transcription factor genes in lung cancer. Proc. Natl. Acad. Sci. USA  104:16663-16668, 2007.  [View PDF]

34. Jiangyong Miao, David Mu, Burce Ergel, Rajasekhar Singavarapu, Zhenfeng Duan, Scott Powers, Esther Oliva, Sandra Orsulic. Hepsin colocalizes with desmosomes and induces progression of ovarian cancer in a mouse model.  Int. J. Cancer. 123:2041-2047, 2008.  [View PDF]

35. Navneet Sangha, Rong Wu, Rork Kuick, Scott Powers, David Mu, Diane Fiander, Kit Yuen, Hidetaka Katabuchi, Hironori Tashiro, Eric R. Fearon, and Kathleen R. Cho. Neurofibromin 1 (NF1) Defects are Common in Human Ovarian Serous Carcinomas and Co-Occur with TP53 Mutations.  Neoplasia  10:1362-1372, 2008.  [View PDF]

36. David S. Hsu, Chaitanya R. Acharya, Bala S. Balakumaran, Richard F. Riedel, Mickey K. Kim, Marvaretta Stevenson, Sascha Tuchman, Sayan Mukherjee, William Barry, Holly K. Dressman, Joseph R. Nevins, Scott Powers, David Mu, and Anil Potti (D.M. & A.P., equal senior authorship).  Characterizing the Clinical Relevance of Developmental Pathways in Lung Cancer.  Proc. Natl. Acad. Sci. USA 106:5312-5317, 2009.   [View PDF]

Review Articles and Book Chapters:

1. Judith P. Klinman  and  David Mu.  Quinoenzymes in Biology.  Annual  Review of  Biochemistry 63:299-344, 1994.  [View PDF]

2. David Mu and Judith P. Klinman.  Cloning of Mammalian Topa Quinone-Containing Enzymes.  Methods in Enzymology 258:114-122, 1995.  [View PDF]

3. David Mu  and Aziz Sancar.  DNA Excision Repair Assays. Progress in Nucleic Acid Research and Molecular Biology 56:63-81, 1997.  [View PDF]

4. Xiaodong Zhao and David Mu.  (6-4) Photolyase: light-dependent repair of DNA damage.  Histology and Histopathology 13:1179-1182, 1998.  [View PDF] 

5. Scott Powers and David Mu. Genetic Similarities Between Organogenesis and Tumorigenesis of the Lung.  Cell Cycle 7:200-204, 2008.  [View PDF]

Frequently Asked Questions About
Dr. Mu's Lab

Dr. David Mu's Curriculum Vitae

(as of December 2009)

Expectation For Graduate Students and Postdoc Fellows

Research Grants Awarded