Research
Taking a basic science research approach to understanding cancer
Our research aims to define the mechanisms that control normal cell proliferation, differentiation, survival and genome maintenance to identify the aberrations in these processes that drive cancer. Our research focus areas include: Cellular and Molecular Mechanisms of Carcinogenesis; Cancer Genetics and Epigenetics; Genome Integrity - DNA Replication, Recombination and Repair; and Cancer Stem Cells, Apoptosis and Autophagy. Our department has laboratories and resources located on both the North and South MD Anderson Campuses in Houston, Texas.
Cellular and Molecular Mechanisms of Carcinogenesis
The overall goal of our carcinogenesis research is to understand the basic cellular and molecular mechanisms that allow the transformation of normal cells into cancer cells. Defining these mechanisms will help identify new cancer targets and novel strategies for identifying, treating, and preventing cancer.
Departmental carcinogenesis research includes:
- Discovering new genetic contributors and drivers of cancers
- Identifying genetic and/or therapeutic vulnerabilities in cancers (e.g. synthetic lethality)
- Defining genetic, epigenetic, immunologic, and transcriptional alterations accompanying cancer initiation and progression
- Investigating cell signaling pathways involved in cancer induction and progression
Developing novel computational approaches for cancer research
Enormous amounts of data have been generated from high-throughput, genome-wide experimental approaches, thus creating a pressing need for novel computational approaches to mine and interpret complex "-omics" data sets. Understanding these data sets will help define both the players in biological interaction networks and their functions. Research in the department is combining in-silico approaches with wet-lab experiments to identify drivers and attenuators of cancer. Likewise, the development of CRISPR technology has led to new high-throughput approaches such as genome-wide synthetic lethal screens that also benefit from computational approaches, like those being developed in the department to aid the design and interpretation of high-throughput screens.
Implementing cutting-edge animal models
Our research relies on the development of genetically engineered animal models for investigating the stepwise molecular changes that occur during carcinogenesis, the function of key genes and gene variants in cancer development, and preclinical prevention and therapeutic studies. A number of existing models are being used for these mechanistic studies, including models for skin, mammary gland, prostate, thymus and blood cancers, but we are also creating novel mouse models using modern knockout/knock-in technologies (e.g. CRISPR-Cas9) to study specific genes and pathways involved in cancer induction and progression.
Making discoveries at the intersection of immunology and systems biology
Immunotherapy has been hailed as the fourth pillar of cancer therapy joining surgery, chemotherapy, and radiation treatment. Yet, this treatment approach does not work for all patients. Collaborative departmental research has revealed that patients who respond to immunotherapy have antibody responses against their tumors and that the presence of B cells within a tumor may serve as a marker to predict patient immunotherapy response. These findings are leading to new questions about the role of B cells in immunotherapy response. Other departmental research combining systems-level approaches and wet-lab experiments has revealed that specific mismatch repair-deficient (dMMR) tumors rely on neddylation to remove misfolded or otherwise aberrant proteins, and this mechanism can be exploited by blocking neddylation-mediated protein degradation, which leads to in an increase in immunogenic cell death. These findings suggest that blocking neddylation may benefit patients with dMMR tumors who do not respond to treatment with immunotherapy alone.
Examples of faculty members who are defining the Cellular and Molecular Mechanisms of Carcinogenesis:
C. Marcelo Aldaz - Role of WWOX in cancer and disease; genomic determinants controlling development and progression of pre-invasive breast lesions
Shawn Bratton - Autophagy and prostate cancer; caspase-activating complexes
Sharon Dent - Chromatin remodeling and epigenetics in normal cell growth and in development of cancer and disease
David Johnson - Transcription factor responses in DNA damage and tumor development
Ellen Richie - Regulation of thymus development and homeostasis; role of thymic epithelial cells in regulating T-cell development and T-cell receptor repertoire selection
Kevin McBride - B cell function and antibody repertoire; B cell lymphoma; role of B cells in immunotherapy response
Nidhi Sahni - Systems-level functional and computational genomics, genetic and
epigenetic influencing susceptibility and resistance to human cancer and immune
system heterogeneity
Margarida Almeida Santos - Tumor promoting roles of genome guardians in leukemia
Richard Wood - Role of DNA polymerase zeta in skin and mammary carcinogenesis
Han Xu - Global view of transcriptional and epigenetic regulation using CRISPR screens; machine-learning and statistical algorithms for high-throughput experiments
Cancer Genetics & Epigenetics
Epigenetic factors that regulate DNA methylation, histone modification and chromatin organization can act as either oncogenes or tumor suppressors. Departmental epigenetics research seeks to define both the normal functions of these factors as well as their roles in cancer formation or suppression.
Readers, Writers and Erasers of Epigenetic Marks
Epigenetic marks include cytosine methylation and hydroxymethylation of DNA and methylation, acetylation, phosphorylation, and ubiquitination of histones. These marks are created by enzymes called "writers." Epigenetic "readers" are effector proteins that bear domains that recognize the specific marks left by the "writers," and epigenetic "erasers" can remove these marks. Thus, multiple epigenomes can be created from a single genome.
Uncovering how epigenetic changes and mutations in epigenetic proteins alter gene expression
The major outcome of epigenetic change is alterations in gene expression. Some epigenetic changes are required for normal development and stem cell differentiation, whereas others are aberrant and can lead to diseases, including immunodeficiency, centromeric region instability and facial anomalies syndrome (ICF) and leukemia and other cancers. Importantly, many epigenetic proteins are mutated in human disease, and epigenetic alterations may be just as important as DNA mutations in driving cancer. In addition to controlling gene transcription, these chromatin-modifying enzymes regulate other processes that require access to DNA, including DNA replication and repair.
Departmental epigenetic research areas include:
- Uncovering epigenetic factors controlling developmental reprogramming
- Discovering biological roles of histone lysine and arginine methylation
- Defining the structure and function of epigenetic proteins and epigenetic marks
- Revealing the cellular functions of ATP-dependent chromatin remodelers
- Identifiying and characterizing “readers” of epigenetic marks
- Understanding the role of histone modifications in DNA repair
- Deciphering crosstalk between: histone modifications; histone modifications and DNA methylation; and histone modifications and post-translational modifications of non-histone substrates
Epigenetics-based research provides new avenues for cancer treatment
Epimutations, unlike genetic mutations, can be reversed by chemotherapeutic intervention, which makes epigenetic therapy conceptually appealing. Researchers in the department are screening and identifying small-molecule regulators of epigenetic modifiers and evaluating their potential as anti-cancer drugs, providing clear translational relevance to this research.
As an example, multiple departmental research teams combined their expertise
to use cell culture experiments, computational approaches evaluating cancer
cell line RNAi screens, and animal xenograft models to show that small molecule
inhibition of an arginine methyltransferase (CARM1) in CREBBP/EP300-mutated
diffuse large B-cell lymphomas (DLBCLs) reduces histone acetyltransferase
activity and causes synthetic lethality through downregulation of CBP-target
genes. This synthetic interaction reveals the possibility that combination
therapy using CARM1 inhibitors with CBP/p300 inhibitors may be useful for
treating DLBCLs and other cancers with non-mutated CREBBP/EP300.
Examples of faculty engaged in epigenetics research:
Blaine Bartholomew - ATP-dependent chromatin remodelers influence on chromatin dynamics and non-coding RNA transcription
Mark Bedford - Arginine methylation in cellular processes; development of technologies to identify readers of proteins bearing specific epigenetic marks
Taiping Chen - Biological function of histone methylases and demethylases in development and disease
Xiaodong Cheng - Structure and function of readers, writers, and erasers of DNA modifications and their associated histone modifications
Francesca Cole - Epigenetic regulation of meiotic chromosome organization & pairing
Sharon Dent - Histone modifying proteins in development and disease
David Johnson - Recruitment of histone modifying enzymes by E2F1
Margarida Almeida Santos - Epigenetic regulators affecting hematopoietic stem cells
DNA Replication, Recombination & Repair - Genomic Stability
Understanding the mechanisms that damage and repair DNA is fundamental to cancer research
DNA breaks can result from molecularly programmed, intentional DNA damage or non-programmed, incidental DNA damage. Intentional breaks results from specialized cellular processes such as those needed for accurate segregation of chromosomes during meiosis and for creating immune system diversity. In contrast, incidental DNA damage results from exposure to DNA damaging agents from both external and internal sources. External sources include ultraviolet radiation from the sun and chemicals in the environment. Internal sources include reactive chemical species, such as oxygen and water as well as accidental DNA breaks formed during DNA replication. Moreover, many cancer therapies induce irreparable DNA damage leading to cell death. Therefore, investigating how cells respond to and repair DNA damage is important for understanding the causes of cancer and developing new treatments. Research in this area employs a broad range of approaches including studies using protein biochemistry, single-cell genomics, high-resolution microscopy, and genetically engineered mouse models.
Departmental research related to genomic stability includes:
- Defining molecular mechanisms of DNA double-strand break repair
- Discovering new DNA repair pathways and proteins
- Defining the functions of DNA polymerases in DNA repair
- Characterizing DNA damage and repair processes in normal cell function and in carcinogenesis
- Learning how DNA damage and repair contribute to immune system diversity
- Unraveling the relationships between DNA damage, chromatin remodeling, and DNA repair
- Understanding how DNA methylation influences DNA mutation and repair
When DNA damage causes cells to go awry
Department investigators are studying the protein machinery involved in several DNA repair pathways, including homologous recombination and DNA end-joining proccesses for the repair of DNA double-strand breaks, and nucleotide excision repair for the repair of ultraviolet radiation-induced DNA damage and other strand-distorting lesions.
Faculty are also uncovering how programmed DNA damage and repair are involved in normal cellular processes, such as meiosis and immune system B cell development, as well as how these normal processes go awry and contribute to cancer and disease.
Other active areas of research include investigations into the actions of DNA polymerases at repair sites, how chromatin-modifying proteins cooperate with the DNA repair machinery to facilitate repair in the context of chromatin, the mechanisms underlying the conversion of DNA damage into the mutations that cause cancer, and the mechanisms that allow cells to tolerate and survive DNA damage.
Examples of faculty members leading the way in DNA Replication, Recombination, and Repair :
Xiaodong Cheng - Role of DNA methylation in DNA mutation and repair
Francesca Cole - DSB repair by homologous recombination during meiosis
Kevin McBride - Role of programmed DNA damage in creating antibody diversity and leading to lymphomagenesis
Margarida Almeida Santos - DNA damage-induced differentiation of stem-like cancer cells
Richard Wood - Nucleotide excision repair, DNA crosslink repair, role of polymerases in DNA damage tolerance
Cancer Stem Cells & Programmed Cell Death
Stem cells are undifferentiated cells that are unique in their ability to self-renew to create more stem cells while also being able to create daughter cells that can differentiate into other cell types. Most, if not all, cancerous states reflect inappropriate or incomplete cellular differentiation. Aggressive, therapy resistant cancer cells often resemble stem cells in terms of their transcription profiles and self-renewal capacities. Likewise, unregulated growth, abnormal cell division, and defective apoptotic cell death pathways are hallmark features of tumors.
The goal of research in this area is to define normal stem cell biology and developmental pathways as well as to define genetic, molecular, and biochemical mechanisms that regulate cell proliferation, apoptosis and autophagy and relate these pathways to carcinogenesis.
Specific research in this area includes:
- Defining pathways that govern stem cell biology and embryo development
- Understanding DNA damage response in cancer stem cells
- Epigenetic modifications in embyronic, adult, and cancer stem cells
- Epigenetic mechanisms in early embryos and germ cells
- Role of caspases in apoptosis
- Apoptosis and autophagy in normal and disease processes
Using stem cells to learn about cancer
Our research using mouse embryonic and adult stem cells has led to several foundational discoveries. For example, research centered on GCN5, a histone acetyltransferase component of the SAGA complex, uncovered a Myc-SAGA axis that is critical for driving stem cells to pluripotency and is essential for the expression of cell-cycle genes driven by MYC overexpression in a mouse model of B cell lymphoma. Studies of SETDB1, a lysine methyltransferase that deposits the repressive H3K9me3 mark, revealed that SETDB1-dependent gene repression is essential for preserving intestinal stem cell identity by modulating the Wnt and Notch signaling pathways. Other research using mouse models of MLL-rearranged acute myeloid leukemia showed that protein arginine methyltransferase 5 (PRMT5) is essential for the initiation and maintenance of MLL-AF9-mediated leukemia and that inhibiting PRMT5 restores normal differentiation to hematopoietic stem cells.
Apoptosis and autophagy: cancer inhibitors and facilitators
Autophagy (self-cannibalism) and apoptosis (programmed cell death) are fundamental cellular processes that provide mechanisms for cell survival (autophagy) and cell death (apoptosis). Autophagy provides cells with means not only to survive cellular stress and to recycle cellular materials and organelles but also to rid themselves of damaged, malformed, or foreign material. Although autophagy helps suppress carcinogenesis, it can also promote tumor progression, metastasis, and cancer therapy resistance. Apoptosis is required for normal organismal development, but also provides a mechanism to stop cells with DNA damage from dividing. Many chemotherapeutics work by causing DNA damage and inducing apoptosis; however, defects in apoptosis contribute to both tumorigenesis and resistance to cancer treatment. Therefore, defining the molecular mechanisms guiding autophagy and apoptosis, and the pathways allowing cross-talk between them, will provide insights into how cells evade and succumb to cancer treatments.
Faculty with research interests in Cancer Stem Cells and Programmed Cell Death:
Blaine Bartholomew - Chromatin remodelers in pluripotency and development
Shawn Bratton - Heat shock- and tumor necrosis factor-related apoptosis-inducing ligand (TRAIL)- induced apoptosis; caspase-activating complexes and the apoptosome; structure and function of autophagosomes; role of autophagy in prostate cancer
Taiping Chen - Epigenetic regulation of embryonic and adult stem cell behavior and function
Sharon Dent - Chromatin modifiers in embryonic stem cells and somatic cell reprogramming
Margarida Almeida Santos - Epigenetic regulation of cancer stem cells
Selected Publications
2023
Amici DR, Cingoz H, Alasady MJ, Alhayek S, Phoumyvong CM, Sahni N, Yi SS, Mendillo ML. The HAPSTR2 retrogene buffers stress signaling and resilience in mammals. Nat Commun. 2023 Jan 11;14(1):152.
Chen Q, Sinha KM, de Crombrugghe B, Krahe R. Osteoblast-Specific Overexpression of Nucleolar Protein NO66/RIOX1 in Mouse Embryos Leads to Osteoporosis in Adult Mice. J Osteoporos. 2023 Jan 10;2023:8998556.
Gao G, Hausmann S, Flores NM, Benitez AM, Shen J, Yang X, Person MD, Gayatri S, Cheng D, Lu Y, Liu B, Mazur PK, Bedford MT. The NFIB/CARM1 partnership is a driver in preclinical models of small cell lung cancer. Nat Commun. 2023 Jan 23;14(1):363.
Hua X, Li Y, Pentaparthi SR, McGrail DJ, Zou R, Guo L, Shrawat A, Cirillo KM, Li Q, Bhat A, Xu M, Qi D, Singh A, McGrath F, Andrews S, Aung KL, Das J, Zhou Y, Lodi A, Mills GB, Eckhardt SG, Mendillo ML, Tiziani S, Wu E, Huang JH, Sahni N, Yi SS. Landscape of MicroRNA Regulatory Network Architecture and Functional Rerouting in Cancer. Cancer Res. 2023 Jan 4;83(1):59-73.
Thiyagarajan T, Ponnusamy S, Hwang DJ, He Y, Asemota S, Young KL, Johnson DL, Bocharova V, Zhou W, Jain AK, Petricoin EF, Yin Z, Pfeffer LM, Miller DD, Narayanan R. Inhibiting androgen receptor splice variants with cysteine-selective irreversible covalent inhibitors to treat prostate cancer. Proc Natl Acad Sci U S A. 2023 Jan 3;120(1):e2211832120.
Zhou J, Horton JR, Menna M, Fiorentino F, Ren R, Yu D, Hajian T, Vedadi M, Mazzoccanti G, Ciogli A, Weinhold E, Hüben M, Blumenthal RM, Zhang X, Mai A, Rotili D, Cheng X. Systematic Design of Adenosine Analogs as Inhibitors of a Clostridioides difficile-Specific DNA Adenine Methyltransferase Required for Normal Sporulation and Persistence. J Med Chem. 2023 Jan 12;66(1):934-950.
2022
Basu S, Dong Y, Kumar R, Jeter C, Tang DG. Slow-cycling (dormant) cancer cells in therapy resistance, cancer relapse and metastasis. Semin Cancer Biol. 2022 Jan;78:90-103.
Carvajal-Maldonado D, Drogalis Beckham L, Wood RD, Doublié S. When DNA Polymerases Multitask: Functions Beyond Nucleotidyl Transfer. Front Mol Biosci. 2022 Jan 7;8:815845
Chakravarty AK, McGrail DJ, Lozanoski TM, Dunn BS, Shih DJH, Cirillo KM, Cetinkaya SH, Zheng WJ, Mills GB, Yi SS, Jarosz DF, Sahni N. Biomolecular Condensation: A New Phase in Cancer Research. Cancer Discov. 2022 Sep 2;12(9):2031-2043.
Chen YC, Koutelou E, Dent SYR. Now open: Evolving insights to the roles of lysine acetylation in chromatin organization and function. Mol Cell. 2022 Feb 17;82(4):716-727.
Cheng X, Blumenthal RM. Mediating and maintaining methylation while minimizing mutation: Recent advances on mammalian DNA methyltransferases. Curr Opin Struct Biol. 2022 Aug;75:102433.
Dan J, Chen T. Genetic Studies on Mammalian DNA Methyltransferases. Adv Exp Med Biol. 2022;1389:111-136.
Darbaniyan F, Zheng H, Kanagal-Shamanna R, Lockyer P, Montalban-Bravo G, Estecio M, Lu Y, Soltysiak KA, Chien KS, Yang H, Sasaki K, Class C, Ganan-Gomez I, Do KA, Garcia-Manero G, Wei Y. Transcriptomic Signatures of Hypomethylating Agent Failure in Myelodysplastic Syndromes and Chronic Myelomonocytic Leukemia. Exp Hematol. 2022 Nov;115:44-53.
Fabre ML, Canzoneri R, Gurruchaga A, Lee J, Tatineni P, Kil H, Lacunza E, Aldaz CM*, Abba MC*. MALINC1 an Immune-Related Long Non-Coding RNA Associated with Early-Stage Breast Cancer Progression. Cancers (Basel). 2022 Jun 7;14(12):2819. (*co-correpsonding authors)
Fedoriw A#, Shi L#, O'Brien S, Smitheman KN, Wang Y, Hou J, Sherk C, Rajapurkar S, Laraio J, Williams LJ, Xu C, Han G, Feng Q, Bedford MT, Wang L, Barbash O, Kruger RG, Hwu P, Mohammad HP, Peng W. Inhibiting Type I arginine methyltransferase activity promotes the T cell mediated antitumor immune response. Cancer Immunol Res. 2022 Apr 1;10(4):420-436. (#equal contribution)
Fontes F, Rocha S, Sánchez R, Pessina P, Sebastian M, Benavides F, Breijo M. Detection of high antibodies titers against rat leukemia virus in an outbreak of reproductive disorders and lymphomas in Wistar rats. Lab Anim. 2022 Mar 31:236772221085356. doi: 10.1177/00236772221085356. Online ahead of print.
Fu* R, He W*, Dou J, Villarreal OD, Bedford E, Wang H, Hou C, Zhang L, Wang Y, Ma D, Chen Y, Gao X, Depken M, Xu H. Systematic decomposition of sequence determinants governing CRISPR/Cas9 specificity. Nat Commun. 2022 Jan 25;13(1):474. (*equal contribution)
Horton JR, Pathuri S, Wong K, Ren R, Rueda L, Fosbenner DT, Heerding DA, McCabe MT, Pappalardi MB, Zhang X, King BW, Cheng X. Structural characterization of dicyanopyridine containing DNMT1-selective, non-nucleoside inhibitors. Structure. 2022 Jun 2;30(6):793-802.e5.
Hou J, Liang S, Xu C, Wei Y, Wang Y, Tan Y, Sahni N, McGrail DJ, Bernatchez C, Davies M, Li Y, Chen R, Yi SS, Chen Y, Yee C, Chen K, Peng W. Single-cell CRISPR immune screens reveal immunological roles of tumor intrinsic factors. NAR Cancer. 2022 Dec 9;4(4):zcac038.
Huang P, Peslak SA, Ren R, Khandros E, Qin K, Keller CA, Giardine B, Bell HW, Lan X, Sharma M, Horton JR, Abdulmalik O, Chou ST, Shi J, Crossley M, Hardison RC, Cheng X, Blobel GA. HIC2 controls developmental hemoglobin switching by repressing BCL11A transcription. Nat Genet. 2022 Sep;54(9):1417-1426
Huang YH, Chen CW, Sundaramurthy V, Słabicki M, Hao D, Watson CJ, Tovy A, Reyes JM, Dakhova O, Crovetti BR, Galonska C, Lee M, Brunetti L, Zhou Y, Tatton-Brown K, Huang Y, Cheng X, Meissner A, Valk PJM, Van Maldergem L, Sanders MA, Blundell JR, Li W, Ebert BL, Goodell MA. Systematic Profiling of DNMT3A Variants Reveals Protein Instability Mediated by the DCAF8 E3 Ubiquitin Ligase Adaptor. Cancer Discov. 2022 Jan;12(1):220-235.
Iannelli G, Milite C, Marechal N, Cura V, Bonnefond L, Troffer-Charlier N, Feoli A, Rescigno D, Wang Y, Cipriano A, Viviano M, Bedford MT, Cavarelli J, Castellano S, Sbardella G. Turning Nonselective Inhibitors of Type I Protein Arginine Methyltransferases into Potent and Selective Inhibitors of Protein Arginine Methyltransferase 4 through a Deconstruction-Reconstruction and Fragment-Growing Approach. J Med Chem. 2022 Apr 28. doi: 10.1021/acs.jmedchem.2c00252. Online ahead of print.
Kannan S, Irwin ME, Herbrich SM, Cheng T, Patterson LL, Aitken MJL, Bhalla K, You MJ, Konopleva M, Zweidler-McKay PA, Chandra J. Targeting the NRF2/HO-1 Antioxidant Pathway in FLT3-ITD-Positive AML Enhances Therapy Efficacy. Antioxidants (Basel). 2022 Apr 5;11(4):717.
Khan FI, Rehman T, Sameena F, Hussain T*, AlAjmi MF, Lai D, Khan MKA. Investigating the binding mechanism of topiramate with bovine serum albumin using spectroscopic and computational methods. J Mol Recognit. 2022 Jul;35(7):e2958. (*postdoctoral fellow with C.M. Aldaz)
Kim KB, Kabra A, Kim DW, Xue Y*, Huang Y, Hou PC, Zhou Y, Miranda LJ, Park JI, Shi X, Bender TP, Bushweller JH, Park KS. KIX domain determines a selective tumor-promoting role for EP300 and its vulnerability in small cell lung cancer. Sci Adv. 2022 Feb 18;8(7):eabl4618. (*graduate student with X. Shi)
Koutelou E, Dent SYR. Navigating EMT with COMPASS and PRC2. Nat Cell Biol. 2022 Apr;24(4):412-414. (News & Views article)
Lancaster JN, Keatinge-Clay DE, Srinivasan J, Li Y, Selden HJ, Nam S, Richie ER, Ehrlich LIR. Central tolerance is impaired in the middle-aged thymic environment. Aging Cell. 2022 Jun;21(6):e13624. PMID: 35561351
Li J, Lu H, Ng PK, Pantazi A, Ip CKM, Jeong KJ, Amador B, Tran R, Tsang YH, Yang L, Song X, Dogruluk T, Ren X, Hadjipanayis A, Bristow CA, Lee S, Kucherlapati M, Parfenov M, Tang J, Seth S, Mahadeshwar HS, Mojumdar K, Zeng D, Zhang J, Protopopov A, Seidman JG, Creighton CJ, Lu Y, Sahni N, Shaw KR, Meric-Bernstam F, Futreal A, Chin L, Scott KL, Kucherlapati R, Mills GB, Liang H. A functional genomic approach to actionable gene fusions for precision oncology. Sci Adv. 2022 Feb 11;8(6):eabm2382.
Liao Y, Chen CH, Xiao T, de la Peña Avalos B, Dray EV, Cai C, Gao S, Shah N, Zhang Z, Feit A, Xue P, Liu Z, Yang M, Lee JH, Xu H, Li W, Mei S, Pierre RS, Shu S, Fei T, Duarte M, Zhao J, Bradner JE, Polyak K, Kantoff PW, Long H, Balk SP, Liu XS, Brown M, Xu K. Inhibition of EZH2 transactivation function sensitizes solid tumors to genotoxic stress. Proc Natl Acad Sci U S A. 2022 Jan 18;119(3):e2105898119.
Liu Y, Iqbal A, Li W, Ni Z, Wang Y, Ramprasad J, Abraham KJ, Zhang M, Zhao DY, Qin S, Loppnau P, Jiang H, Guo X, Brown PJ, Zhen X, Xu G, Mekhail K, Ji X, Bedford MT, Greenblatt JF, Min J. A small molecule antagonist of SMN disrupts the interaction between SMN and RNAP II. Nat Commun. 2022 Sep 16;13(1):5453.
Meng H, Gonzales NM, Jung SY, Lu Y, Putluri N, Zhu B, Dacso CC, Lonard DM, O'Malley BW. Defining the mammalian coactivation of hepatic 12-h clock and lipid metabolism. Cell Rep. 2022 Mar 8;38(10):110491.
Miglioranza Scavuzzi B, van Drongelen V, Kaur B, Fox JC, Liu J, Mesquita-Ferrari RA, Kahlenberg JM, Farkash EA, Benavides F, Miller FW, Sawalha AH, Holoshitz J. The lupus susceptibility allele DRB1*03:01 encodes a disease-driving epitope. Commun Biol. 2022 Jul 28;5(1):751.
Moyret-Lalle C, Prodhomme MK*, Burlet D, Kashiwagi A, Petrilli V, Puisieux A, Seimiya H, Tissier A. Role of EMT in the DNA damage response, double-strand break repair pathway choice and its implications in cancer treatment. Cancer Sci. 2022 May 9. doi: 10.1111/cas.15389. Online ahead of print. (*Prodhomme is a postdoc in the Wood lab)
Mustachio LM, Roszik J . Single-Cell Sequencing: Current Applications in Precision Onco-Genomics and Cancer Therapeutics. Cancers (Basel). 2022 Jan 28;14(3):657.
Ozirmak Lermi N, Gray SB, Bowen CM, Reyes-Uribe L, Dray BK, Deng N, Harris RA, Raveendran M, Benavides F, Hodo CL, Taggart MW, Colbert Maresso K, Sinha KM, Rogers J, Vilar E. Comparative molecular genomic analyses of a spontaneous rhesus macaque model of mismatch repair-deficient colorectal cancer. PLoS Genet. 2022 Apr 21;18(4):e1010163.
Pan X, Burgman B, Wu E*, Huang JH*, Sahni N*, Stephen Yi S*. i-Modern: Integrated multi-omics network model identifies potential therapeutic targets in glioma by deep learning with interpretability. Comput Struct Biotechnol J. 2022 Jun 30;20:3511-3521. (*co-corresponding authors)
Park D, Gharghabi M, Reczek CR, Plow R, Yungvirt C, Aldaz CM, Huebner K. Wwox Binding to the Murine Brca1-BRCT Domain Regulates Timing of Brip1 and CtIP Phospho-Protein Interactions with This Domain at DNA Double-Strand Breaks, and Repair Pathway Choice. Int J Mol Sci. 2022 Mar 28;23(7):3729.
Perez CJ, Mecklenburg L, Fernandez A, Cantero M, de Souza T, Lin K, Dent SYR, Montoliu L, Awgulewitsch A, Benavides, F. Naked (N) mutant mice carry a nonsense mutation in the homeobox of Hoxc13. Exp Dermatol. 2022 Mar;31(3):330-340.
Piya S, Yang Y, Bhattacharya S, Sharma P, Ma H, Mu H, He H, Ruvolo V, Baran N, Davis RE, Jain AK, Konopleava M, Kantarjian H, Andreeff M, You MJ, Borthakur G. Targeting the NOTCH1-MYC-CD44 axis in leukemia-initiating cells in T-ALL. Leukemia. 2022 May;36(5):1261-1273.
Ren R#, Horton JR#, Hong S, Cheng X. Recent Advances on DNA Base Flipping: A General Mechanism for Writing, Reading, and Erasing DNA Modifications. Adv Exp Med Biol. 2022;1389:295-315. (#equal contribution)
Soundararajan R, Viscuse P, Pilie P, Liu J, Logotheti S, Laberiano Fernández C, Lorenzini D, Hoang A, Lu W, Soto LMS, Wistuba II, Xu M, Song X, Shepherd PDA, Navone NM, Tidwell RSS, Lozano G, Logothetis C, Zhang J, Long JP, Estecio MR, Tzelepi V, Aparicio AM. Genotype-to-Phenotype Associations in the Aggressive Variant Prostate Cancer Molecular Profile (AVPC-m) Components. Cancers (Basel). 2022 Jun 30;14(13):3233.
Srour N, Villarreal OD, Hardikar S, Yu Z, Preston S, Miller WH Jr, Szewczyk MM, Barsyte-Lovejoy D, Xu H, Chen T, del Rincón SV, Richard S. PRMT7 ablation stimulates anti-tumor immunity and sensitizes melanoma to immune checkpoint blockade. Cell Rep. 2022 Mar 29;38(13):110582.
Tu SM, Estecio MR, Lin SH, Zacharias NM. Stem Cell Theory of Cancer: Rude Awakening or Bad Dream from Cancer Dormancy? Cancers (Basel). 2022 Jan 27;14(3):655.
Van HT, Harkins PR, Patel A, Jain AK, Lu Y, Bedford MT, Santos MA. Methyl-lysine readers PHF20 and PHF20L1 define two distinct gene expression-regulating NSL complexes. J Biol Chem. 2022 Mar;298(3):101588.
Vanson S, Li Y, Wood RD, Doublié S.Probing the structure and function of polymerase θ helicase-like domain. DNA Repair (Amst). 2022 Aug;116:103358.
Wang Y, Person MD, Bedford MT. Pan-methylarginine antibody generation using PEG linked GAR motifs as antigens. Methods. 2022 Apr;200:80-86.
Wang Z, Lu Y, Fornage M, Jiao L, Shen J, Li D, Wei P. Identification of novel susceptibility methylation loci for pancreatic cancer in a two-phase epigenome-wide association study. Epigenetics. 2022 Nov;17(11):1357-1372.
Wood RD, Doublié S. Genome Protection by DNA Polymerase θ. Annu Rev Genet. 2022 Nov 30;56:207-228.
Yan G, Luna A, Wang H, Bozorgui B, Li X, Sanchez M, Dereli Z, Kahraman N, Kara G, Chen X, Zheng C, McGrail D, Sahni N, Lu Y, Babur O, Cokol M, Lim B, Ozpolat B, Sander C, Mills GB, Korkut A. BET inhibition induces vulnerability to MCL1 targeting through upregulation of fatty acid synthesis pathway in breast cancer. Cell Rep. 2022 Sep 13;40(11):111304.
Yang J*, Gupta E*, Horton JR, Blumenthal RM, Zhang X, Cheng X. DNA Repair. Differential ETS1 binding to T:G mismatches within a CpG dinucleotide contributes to C-to-T somatic mutation rate of the IDH2 hotspot at codon Arg140. DNA Repair DNA Repair (Amst). 2022 Apr;298(4):101751. (*equal contribution)
Yu D, Dai N, Wolf EJ, Corrêa IR Jr, Zhou J, Wu T, Blumenthal RM, Zhang X, Cheng X. Enzymatic characterization of mRNA cap adenosine-N6 methyltransferase PCIF1 activity on uncapped RNAs. J Biol Chem. 2022 Apr;298(4):101751
Yu D, Zhou J, Chen Q, Wu T, Blumenthal RM, Zhang X, Cheng X. Enzymatic Characterization of In Vitro Activity of RNA Methyltransferase PCIF1 on DNA. Biochemistry. 2022 May 23;61(11):1005-13.
Zhou J, Horton JR, Yu D, Ren R, Blumenthal RM, Zhang X, Cheng X. Repurposing epigenetic inhibitors to target the Clostridioides difficile-specific DNA adenine methyltransferase and sporulation regulator CamA. Epigenetics. 2022 Sep;17(9):970-981.
Zhao S, Habib SL, Senejani AG, Sebastian M, Kidane D. Role of Base Excision Repair in Innate Immune Cells and Its Relevance for Cancer Therapy. Biomedicines. 2022 Feb 26;10(3):557.
Zhang Y, Li Y, Chachad D, Liu B, Godavarthi JD, Williams-Villalobo A, Lasisi L, Xiong S, Matin A. In silico analysis of DND1 and its co-expressed genes in human cancers. Biochem Biophys Rep. 2022 Jan 13;29:101206.
Zhang Y, Williams-Villalobo A, Godavarthi JD, Shakoor F, Xiong S, Liu B. Integrative bioinformatic analysis of p53 and pathway alterations in two different lung cancer subtypes. Biochem Biophys Rep. 2022 Dec 7;33:101404.
2021
Abba MC, Fabre ML, Lee J, Tatineni P, Kil H, Aldaz CM. HOTAIR Modulated Pathways in Early-Stage Breast Cancer Progression. Front Oncol. 2021 Nov 17;11:783211.
Bailey CP, Wang R, Figueroa M, Zhang S, Wang L, Chandra J. Computational immune infiltration analysis of pediatric high-grade gliomas (pHGGs) reveals differences in immunosuppression and prognosis by tumor location. Comput Syst Oncol. 2021 Sep;1(3):e1016.
Ben Yamin B#, Ahmed-Seghir S#, Tomida J#, Despras E, Pouvelle C, Yurchenko A, Goulas J, Corre R, Delacour Q, Droin N, Dessen P, Goidin D, Lange SS, Bhetawal S, Mitjavila-Garcia MT, Baldacci G, Nikolaev S, Cadoret JC*, Wood RD*, Kannouche PL*. DNA polymerase zeta contributes to heterochromatin replication to prevent genome instability. EMBO J. 2021 Nov 2;40(21):e104543. (#equal contributions as first authors, *equal contributions as senior authors)
Carvajal-Maldonado D, Wood RD. Regulating Polθ in Breast Cancer. Cancer Res. 2021 Mar 15;81(6):1441-1442.
Chen J, Horton J, Sagum C, Zhou J, Cheng X, Bedford MT. Histone H3 N-terminal mimicry drives a novel network of methyl-effector interactions. Biochem J. 2021 May 28;478(10):1943-1958.
Chen LM, Chai JC, Liu B, Strutt TM, McKinstry KK, Chai KX. Prostasin regulates PD-L1 expression in human lung cancer cells. Biosci Rep. 2021 Jul 30;41(7):BSR20211370.
Cheng T, Kiser K, Grasse L, Iles L, Bartholomeusz G, Samaniego F, Orlowski RZ, Chandra J. Expression of histone deacetylase (HDAC) family members in bortezomib-refractory multiple myeloma and modulation by panobinostat. Cancer Drug Resist. 2021;4(4):888-902.
Chen YC, Dent SYR. Conservation and diversity of the eukaryotic SAGA coactivator complex across kingdoms. Epigenetics Chromatin. 2021 Jun 10;14(1):26.
Dejima H, Hu X, Chen R, Zhang J, Fujimoto J, Parra ER, Haymaker C, Hubert SM, Duose D, Solis LM, Su D, Fukuoka J, Tabata K, Pham HHN, Mcgranahan N, Zhang B, Ye J, Ying L, Little L, Gumbs C, Chow CW, Estecio MR, Godoy MCB, Antonoff MB, Sepesi B, Pass HI, Behrens C, Zhang J, Vaporciyan AA, Heymach JV, Scheet P, Lee JJ, Wu J, Futreal PA, Reuben A, Kadara H, Wistuba II, Zhang J. Immune evolution from preneoplasia to invasive lung adenocarcinomas and underlying molecular features. Nat Commun. 2021 May 11;12(1):2722.
DiNardo CD, Beird HC, Estecio M, Hardikar S, Takahashi K, Bannon SA, Borthakur G, Jabbour E, Gumbs C, Khoury JD, Routbort M, Gong T, Kondo K, Kantarjian H, Garcia-Manero G, Chen T, Futreal PA. Germline DNMT3A mutation in familial acute myeloid leukaemia. Epigenetics. 2021 May;16(5):567-576.
Genois MM, Gagné JP, Yasuhara T, Jackson J, Saxena S, Langelier MF, Ahel I, Bedford MT, Pascal JM, Vindigni A, Poirier GG, Zou L. CARM1 regulates replication fork speed and stress response by stimulating PARP1. Mol Cell. 2021 Feb 18;81(4):784-800.e8
Guo L, Li Y, Cirillo KM, Marick RA, Su Z, Yin X, Hua X, Mills GB, Sahni N*, Yi SS*. mi-IsoNet: systems-scale microRNA landscape reveals rampant isoform-mediated gain of target interaction diversity and signaling specificity. Brief Bioinform. 2021 Sep 2;22(5):bbab091. (*co-corresponding authors)
Hahn WC, Bader JS, Braun TP, Califano A, Clemons PA, Druker BJ, Ewald AJ, Fu H, Jagu S, Kemp CJ, Kim W, Kuo CJ, McManus M, B Mills G, Mo X, Sahni N, Schreiber SL, Talamas JA, Tamayo P, Tyner JW, Wagner BK, Weiss WA, Gerhard DS; Cancer Target Discovery and Development Network. An expanded universe of cancer targets. Cell. 2021 Mar 4;184(5):1142-1155.
He W, Wang H, Wei Y, Jiang Z, Tang Y, Chen Y, Xu H. GuidePro: A multi-source ensemble predictor for prioritizing sgRNAs in CRISPR/Cas9 protein knockouts. Bioinformatics. 2021 Jan 4:btaa1068.
Hu X, Estecio MR, Chen R, Reuben A, Wang L, Fujimoto J, Carrot-Zhang J, McGranahan N, Ying L, Fukuoka J, Chow CW, Pham HHN, Godoy MCB, Carter BW, Behrens C, Zhang J, Antonoff MB, Sepesi B, Lu Y, Pass HI, Kadara H, Scheet P, Vaporciyan AA, Heymach JV, Wistuba II, Lee JJ, Futreal PA, Su D, Issa JJ, Zhang J. Evolution of DNA methylome from precancerous lesions to invasive lung adenocarcinomas. Nat Commun. 2021 Jan 29;12(1):687.
Jung YS, Stratton SA, Lee SH, Kim MJ, Jun S, Zhang J, Zheng B, Cervantes CL, Cha JH, Barton MC, Park JI. TMEM9-v-ATPase Activates Wnt/β-Catenin Signaling via APC Lysosomal Degradation for Liver Regeneration and Tumorigenesis. Hepatology. 2021 Feb;73(2):776-794.
Koutelou E, Farria AT, Dent SYR. Complex functions of Gcn5 and Pcaf in development and disease. Biochim Biophys Acta Gene Regul Mech. 2021 Feb;1864(2):194609.
Kuang X, McAndrew MJ, Mustachio LM, Chen YC, Atanassov BS, Lin K, Lu Y, Shen J, Salinger A, Macatee T, Dent SYR*, Koutelou E*. Usp22 Overexpression Leads to Aberrant Signal Transduction of Cancer-Related Pathways but Is Not Sufficient to Drive Tumor Formation in Mice. Cancers (Basel). 2021 Aug 25;13(17):4276. (*co-corresponding authors)
Lan X, Ren R, Feng R, Ly LC, Lan Y, Zhang Z, Aboreden N, Qin K, Horton JR, Grevet JD, Mayuranathan T, Abdulmalik O, Keller CA, Giardine B, Hardison RC, Crossley M, Weiss MJ, Cheng X, Shi J, Blobel GA. ZNF410 Uniquely Activates the NuRD Component CHD4 to Silence Fetal Hemoglobin Expression. Mol Cell. 2021 Jan 21;81(2):239-254.e8.
Li Y, Burgman B, Khatri IS, Pentaparthi SR, Su Z, McGrail DJ, Li Y, Wu E, Eckhardt SG, Sahni N*, Yi SS. e-MutPath: computational modeling reveals the functional landscape of genetic mutations rewiring interactome networks. Nucleic Acids Res. 2021 Jan 11;49(1):e2 (*co-corresponding author)
Llorens-Agost M, Ensminger M, Le HP, Gawai A, Liu J, Cruz-García A, Bhetawal S, Wood RD, Heyer WD, Löbrich M. POLθ-mediated end joining is restricted by RAD52 and BRCA2 until the onset of mitosis. Nat Cell Biol. 2021 Oct;23(10):1095-1104.
Manickavinayaham S, Dennehey BK, Johnson DG. Direct Regulation of DNA Repair by E2F and RB in Mammals and Plants: Core Function or Convergent Evolution? Cancers (Basel). 2021 Feb 24;13(5):934.
Martin SK, Tomida J, Wood RD. Disruption of DNA polymerase ζ engages an innate immune response. Cell Rep. 2021 Feb 23;34(8):108775.
Morales F, Corrales E, Zhang B, Vásquez M, Santamaría-Ulloa C, Quesada H, Sirito M, Estecio MR, Monckton DG, Krahe R. Myotonic dystrophy type 1 (DM1) clinical subtypes and CTCF site methylation status flanking the CTG expansion are mutant allele length-dependent. Hum Mol Genet. 2021 Dec 27;31(2):262-274.
Muradova E, Patel N, Sell B, Bittencourt BB, Ojeda SS, Adelmann CH, Cen L, Cheng CH, Shen J, Davis CM, Ehli EA, Newberg JY, Cherpelis B, Black MA, Mann MB, Mitragotri S, Tsai KY. Noninvasive Assessment of Epidermal Genomic Markers of UV Exposure in Skin. J Invest Dermatol. 2021 Jan;141(1):124-131.e2.
Pappalardi MB, Keenan K, Cockerill M, Kellner WA, Stowell A, Sherk C, Wong K, Pathuri S, Briand J, Steidel M, Chapman P, Groy A, Wiseman AK, McHugh CF, Campobasso N, Graves AP, Fairweather E, Werner T, Raoof A, Butlin RJ, Rueda L, Horton JR, Fosbenner DT, Zhang C, Handler JL, Muliaditan M, Mebrahtu M, Jaworski JP, McNulty DE, Burt C, Eberl HC, Taylor AN, Ho T, Merrihew S, Foley SW, Rutkowska A, Li M, Romeril SP, Goldberg K, Zhang X, Kershaw CS, Bantscheff M, Jurewicz AJ, Minthorn E, Grandi P, Patel M, Benowitz AB, Mohammad HP, Gilmartin AG, Prinjha RK, Ogilvie D, Carpenter C, Heerding D, Baylin SB, Jones PA, Cheng X, King BW, Luengo JI, Jordan AM, Waddell I, Kruger RG, McCabe MT. Discovery of a first-in-class reversible DNMT1-selective inhibitor with improved tolerability and efficacy in acute myeloid leukemia. Nat Cancer. 2021 Oct;2(10):1002-1017.
Park D, Gharghabi M, Schrock MS, Plow R, Druck T, Yungvirt C, Aldaz CM, Huebner K. Interaction of Wwox with Brca1 and associated complex proteins prevents premature resection at double-strand breaks and aberrant homologous recombination. DNA Repair (Amst). 2022 Feb;110:103264.
Shah VV*, Duncan AD*, Jiang S*, Stratton SA, Allton KL, Yam C, Jain A, Krause PM, Lu Y, Cai S, Tu Y, Zhou X, Zhang X, Jiang Y, Carroll CL, Kang Z, Liu B, Shen J, Gagea M, Manu SM, Huo L, Gilcrease M, Powell RT, Guo L, Stephan C, Davies PJ, Parker-Thornburg J, Lozano G, Behringer RR, Piwnica-Worms H, Chang JT, Moulder SL, Barton MC. Mammary-specific expression of Trim24 establishes a mouse model of human metaplastic breast cancer. Nat Commun. 2021 Sep 10;12(1):5389. (*co-first authors)
Srinivasan J, Lancaster JN, Singarapu N, Hale LP, Ehrlich LIR, Richie ER. Age-Related Changes in Thymic Central Tolerance. Front Immunol. 2021 Apr 22;12:676236. (Review)
Sun M#, Wang Y#, Zheng C#, Wei Y, Hou J, Zhang P, He W, Lv X, Ding Y, Liang H, Hon CC, Chen X, Xu H*, Chen Y*. Systematic functional interrogation of human pseudogenes using CRISPRi. Genome Biol. 2021 Aug 23;22(1):240. (#equal contribution, *co-corresponding authors)
Toraason E, Horacek A, Clark C, Glover ML, Adler VL, Premkumar T, Salagean A, Cole F, Libuda DE. Meiotic DNA break repair can utilize homolog-independent chromatid templates in C. elegans. Curr Biol. 2021 Apr 12;31(7):1508-1514.e5.
Trinh A, Gil Del Alcazar CR, Shukla SA, Chin K, Chang YH, Thibault G, Eng J, Jovanović B, Aldaz CM, Park SY, Jeong J, Wu C, Gray J, Polyak K. Genomic Alterations during the In Situ to Invasive Ductal Breast Carcinoma Transition Shaped by the Immune System. Mol Cancer Res. 2021 Apr;19(4):623-635.
Wright T, Wang Y, Bedford MT. The Role of the PRMT5-SND1 Axis in Hepatocellular Carcinoma. Epigenomes. 2021 Mar;5(1):2. (Review)
Yang F, Chen J, Liu B, Gao G, Sebastian M, Jeter C, Shen J, Person MD, Bedford MT. SPINDOC binds PARP1 to facilitate PARylation. Nat Commun. 2021 Nov 4;12(1):6362.
Yang J, Horton JR, Akdemir KC, Li J, Huang Y, Kumar J, Blumenthal RM, Zhang X, Cheng X. Preferential CEBP binding to T:G mismatches and increased C-to-T human somatic mutations. Nucleic Acids Res. 2021 May 21;49(9):5084-5094.
Yang Y, Ren R, Ly LC, Horton JR, Li F, Quinlan KGR, Crossley M, Shi Y, Cheng X. Structural basis for human ZBTB7A action at the fetal globin promoter. Cell Rep. 2021 Sep 28;36(13):109759.
Yu D#, Horton JR#, Yang J, Hajian T, Vedadi M, Sagum CA, Bedford MT, Blumenthal RM, Zhang X, Cheng X. Human MettL3-MettL14 RNA adenine methyltransferase complex is active on double-stranded DNA containing lesions. Nucleic Acids Res. 2021 Nov 18;49(20):11629-11642. (#equal contribution)
Zahn KE, Jensen RB, Wood RD, Doublié S. Human DNA polymerase θ harbors DNA end-trimming activity critical for DNA repair. Mol Cell. 2021 Apr 1;81(7):1534-1547.e4.
Zhou J#, Horton JR#, Blumenthal RM, Zhang X, Cheng X. Clostridioides difficile specific DNA adenine methyltransferase CamA squeezes and flips adenine out of DNA helix. Nat Commun. 2021 Jun 8;12(1):3436. (#equal contribution)
2020
Abba MC, Canzoneri R, Gurruchaga A, Lee J, Tatineni P, Kil H, Lacunza E, Aldaz CM. LINC00885 a Novel Oncogenic Long Non-Coding RNA Associated with Early Stage Breast Cancer Progression. Int J Mol Sci. 2020 Oct 8;21(19):7407.
Benavides F, Rülicke T, Prins JB, Bussell J, Scavizzi F, Cinelli P, Herault Y, Wedekind D. Genetic quality assurance and genetic monitoring of laboratory mice and rats: FELASA Working Group Report. Lab Anim. 2020 Apr;54(2):135-148.
Bhardwaj SK, Hailu SG, Olufemi L, Brahma S, Kundu S, Hota SK, Persinger J, Bartholomew B. Dinucleosome specificity and allosteric switch of the ISW1a ATP-dependent chromatin remodeler in transcription regulation. Nat Commun. 2020 Nov 20;11(1):5913.
Farria AT, Plummer JB, Salinger AP, Shen J, Lin K, Lu Y, McBride KM, Koutelou E, Dent SYR. Transcriptional Activation of MYC-Induced Genes by GCN5 Promotes B-cell Lymphomagenesis. Cancer Res. 2020 Dec 15;80(24):5543-5553.
Hardikar S, Ying Z, Zeng Y, Zhao H, Liu B, Veland N, McBride K, Cheng X, Chen T. The ZBTB24-CDCA7 axis regulates HELLS enrichment at centromeric satellite repeats to facilitate DNA methylation. Protein Cell. 2020 Mar;11(3):214-218.
Helmink BA, Reddy SM, Gao J, Zhang S, Basar R, Thakur R, Yizhak K, Sade-Feldman M, Blando J, Han G, Gopalakrishnan V, Xi Y, Zhao H, Amaria RN, Tawbi HA, Cogdill AP, Liu W, LeBleu VS, Kugeratski FG, Patel S, Davies MA, Hwu P, Lee JE, Gershenwald JE, Lucci A, Arora R, Woodman S, Keung EZ, Gaudreau PO, Reuben A, Spencer CN, Burton EM, Haydu LE, Lazar AJ, Zapassodi R, Hudgens CW, Ledesma DA, Ong S, Bailey M, Warren S, Rao D, Krijgsman O, Rozeman EA, Peeper D, Blank CU, Schumacher TN, Butterfield LH, Zelazowska MA, McBride KM, Kalluri R, Allison J, Petitprez F, Fridman WH, Sautès-Fridman C, Hacohen N, Rezvani K, Sharma P, Tetzlaff MT, Wang L, Wargo JA. B cells and tertiary lymphoid structures promote immunotherapy response. Nature. 2020 Jan;577(7791):549-555.
Hwang T, Reh S, Dunbayev Y, Zhong Y, Takata Y, Shen J, McBride KM, Murnane JP, Bhak J, Lee S, Wood RD, Takata KI. Defining the mutation signatures of DNA polymerase θ in cancer genomes. NAR Cancer. 2020 Sep;2(3):zcaa017.
Jain K, Fraser CS, Marunde MR, Parker MM, Sagum C, Burg JM, Hall N, Popova IK, Rodriguez KL, Vaidya A, Krajewski K, Keogh MC, Bedford MT*, Strahl BD.* Characterization of the plant homeodomain (PHD) reader family for their histone tail interactions. Epigenetics Chromatin. 2020 Jan 24;13(1):3 (*Co-corresponding authors)
Kumar A, Zhong Y, Albrecht A, Sang PB, Maples A, Liu Z, Vinayachandran V, Reja R, Lee CF, Kumar A, Chen J, Xiao J, Park B, Shen J, Liu B, Person MD, Trybus KM, Zhang KYJ, Pugh BF, Kamm KE, Milewicz DM, Shen X*, Kapoor P*. Actin R256 Mono-methylation Is a Conserved Post-translational Modification Involved in Transcription. Cell Rep. 2020 Sep 29;32(13):108172. (*co-corresponding authors)
Kumar J, Kaur G, Ren R, Lu Y, Lin K, Li J, Huang Y, Patel A, Barton MC, Macfarlan T, Zhang X, Cheng X. KRAB domain of ZFP568 disrupts TRIM28-mediated abnormal interactions in cancer cells. NAR Cancer. 2020 Jun;2(2):zcaa007.
McGrail DJ, Garnett J, Yin J, Dai H, Shih DJH, Lam TNA, Li Y, Sun C, Li Y, Schmandt R, Wu JY, Hu L, Liang Y, Peng G, Jonasch E, Menter D, Yates MS, Kopetz S, Lu KH, Broaddus R, Mills GB, Sahni N,* Lin SY.* Proteome Instability Is a Therapeutic Vulnerability in Mismatch Repair-Deficient Cancer. Cancer Cell. 2020 Mar 16;37(3):371-386.e12. (*Co-corresponding authors)
Shen Y, Gao G, Yu X, Kim H, Wang L, Xie L, Schwarz M, Chen X, Guccione E, Liu J*, Bedford MT*, Jin J*. Discovery of First-in-Class Protein Arginine Methyltransferase 5 (PRMT5) Degraders. J Med Chem. 2020 Sep 10;63(17):9977-9989. (*Co-corresponding authors)
Turner OC, Aeffner F, Bangari DS, High W, Knight B, Forest T, Cossic B, Himmel LE, Rudmann DG, Bawa B, Muthuswamy A, Aina OH, Edmondson EF, Saravanan C, Brown DL, Sing T, Sebastian MM. Society of Toxicologic Pathology Digital Pathology and Image Analysis Special Interest Group Article*: Opinion on the Application of Artificial Intelligence and Machine Learning to Digital Toxicologic Pathology. Toxicol Pathol. 2020 Feb;48(2):277-294.
Veazey KJ, Cheng D, Lin K, Villarreal OD, Gao G, Perez-Oquendo M, Van HT, Stratton SA, Green M, Xu H, Lu Y, Bedford MT, Santos MA. CARM1 inhibition reduces histone acetyltransferase activity causing synthetic lethality in CREBBP/EP300-mutated lymphomas. Leukemia. 2020 Jun 24. doi: 10.1038/s41375-020-0908-8.
Woodcock CB, Horton JR, Zhou J, Bedford MT, Blumenthal RM, Zhang X, Cheng X. Biochemical and structural basis for YTH domain of human YTHDC1 binding to methylated adenine in DNA. Nucleic Acids Res. 2020 Oct 9;48(18):10329-10341.
Zelazowska MA, Dong Q, Plummer JB, Zhong Y, Liu B, Krug LT, McBride KM. Gammaherpesvirus-infected germinal center cells express a distinct immunoglobulin repertoire. Life Sci Alliance. 2020 Feb 6;3(3):e201900526.
Zeng Y*, Ren R*, Kaur G, Hardikar S, Ying Z, Babcock L, Gupta E, Zhang X, Chen T#, Cheng X#. The inactive Dnmt3b3 isoform preferentially enhances Dnmt3b-mediated DNA methylation. Genes Dev. 2020 Oct 1;34(21-22):1546-58. (*co-first authors, #co-corresponding authors)
2019
Bao J, Di Lorenzo A, Lin K, Lu Y, Zhong Y, Sebastian MM, Muller WJ, Yang Y, Bedford MT. (2019) Mouse models of overexpression reveal distinct oncogenic roles for different type I protein arginine methyltransferases. Cancer Res. 79(1):21-32.
Gao G, Zhang L, Villarreal OD, He W, Su D, Bedford E, Moh P, Shen J, Shi X, Bedford MT, Xu H. (2019) PRMT1 loss sensitizes cells to PRMT5 inhibition. Nucleic Acids Res. 47(10):5038-5048.
He W, Zhang L, Villarreal OD, Fu R, Bedford E, Dou J, Patel AY, Bedford MT, Shi X, Chen T, Bartholomew B, Xu H. (2019) De novo identification of essential protein domains from CRISPR-Cas9 tiling-sgRNA knockout screens. Nat Commun. 10(1):4541.
Hussain T, Kil H, Hattiangady B, Lee J, Kodali M, Shuai B, Attaluri S, Takata Y, Shen J, Abba MC, Shetty AK, Aldaz CM. (2019) Wwox deletion leads to reduced GABA-ergic inhibitory interneuron numbers and activation of microglia and astrocytes in mouse hippocampus. Neurobiol Dis. 121:163-176.
Koutelou E, Wang L, Schibler A, Chao HP, Kuang X, Lin K, Lu Y, Shen J, Jeter CR, Salinger A, Wilson M, Chen YC, Atanassov BS, Tang DG, Dent SY. (2019) Usp22 controls multiple signaling pathways that are essential for vasculature formation in the mouse placenta. Development. Feb 22;146(4). pii: dev174037. ]
Manickavinayaham S, Vélez-Cruz R, Biswas AK, Bedford E, Klein BJ, Kutateladze TG, Liu B, Bedford MT, Johnson DG. (2019) E2F1 acetylation directs p300/CBP-mediated histone acetylation at DNA double-strand breaks to facilitate repair. Nat Commun. 10(1):4951.
McBride KM, Kil H, Mu Y, Plummer JB, Lee J, Zelazowski MJ, Sebastian M, Abba MC, Aldaz CM. (2019) Wwox Deletion in Mouse B Cells Leads to Genomic Instability, Neoplastic Transformation, and Monoclonal Gammopathies. Front Oncol. 9:517.
Patel L, Kang R, Rosenberg SC, Qiu Y, Raviram R, Chee S, Hu R, Ren B, Cole F,* Corbett KD*. (2019) Dynamic reorganization of the genome shapes the recombination landscape in meiotic prophase. Nat Struct Mol Biol. 26(3):164-174. (*co-corresponding authors)
Ren R, Hardikar S, Horton JR, Lu Y, Zeng Y, Singh AK, Lin K, Coletta LD, Shen J, Lin Kong CS, Hashimoto H, Zhang X, Chen T, Cheng X. (2019) Structural basis of specific DNA binding by the transcription factor ZBTB24. Nucleic Acids Res. 47(16):8388-8398.
Wible DJ, Chao HP, Tang DG, Bratton SB. (2019) ATG5 cancer mutations and alternative mRNA splicing reveal a conjugation switch that regulates ATG12-ATG5-ATG16L1 complex assembly and autophagy. Cell Discov. 5:42.
Veland N, Lu Y, Hardikar S, Gaddis S, Zeng Y, Liu B, Estecio MR, Takata Y, Lin K, Tomida MW, Shen J, Saha D, Gowher H, Zhao H, Chen T. (2019) DNMT3L facilitates DNA methylation partly by maintaining DNMT3A stability in mouse embryonic stem cells. Nucleic Acids Res. 47(1):152-167.
2018
Appikonda S, Thakkar KN, Shah PK, Dent SYR, Andersen JN, Barton MC. (2018) Cross-talk between chromatin acetylation and SUMOylation of tripartite motif-containing protein 24 (TRIM24) impacts cell adhesion. J Biol Chem. 293(19):7476-7485.
Bao J, Perez CJ, Kim J, Zhang H, Murphy CJ, Hamidi T, Jaubert J, Platt CD, Chou J, Deng M, Zhou MH, Huang Y, Gaitán-Peñas H, Guénet JL, Lin K, Lu Y, Chen T, Bedford MT, Dent SY, Richburg JH, Estévez R, Pan HL, Geha RS, Shi Q, Benavides F. (2018) Deficient LRRC8A-dependent volume-regulated anion channel activity is associated with male infertility in mice. JCI Insight. 3(16):e99767.
Bao J, Rousseaux S, Shen J, Lin K, Lu Y, Bedford MT. The arginine methyltransferase CARM1 represses p300•ACT•CREMτ activity and is required for spermiogenesis. (2018) Nucleic Acids Res. 46(9):4327-4343.
Brahma S, Ngubo M, Paul S, Udugama M, Bartholomew B. (2018) The Arp8 and Arp4 module acts as a DNA sensor controlling INO80 chromatin remodeling. Nat Commun. 90(1):3309
Cheng D, Vemulapalli V, Lu Y, Shen J, Aoyagi S, Fry CJ, Yang Y, Foulds CE, Stossi F, Treviño LS, Mancini MA, O’Malley BW, Walker CL, Boyer TG, Bedford MT. (2018) CARM1 methylates MED12 to regulate its RNA binding ability. Life Sci Alliance. 1(5):e201800117.
Das P, Veazey KJ, Van HT, Kaushik S, Lin K, Lu Y, Ishii M, Kikuta J, Ge K, Nussenzweig A, Santos MA. (2018) Histone methylation regulator PTIP is required to maintain normal and leukemic bone marrow niches. Proc Natl Acad Sci U S A. 2018 Oct 23;115(43):E10137-E10146. pii: 201806019.
Franco HL, Nagari A, Malladi V, Li W, Xi Y, Richardson D, Allton KL, Tanaka K, Li J, Murakami S, Keyomarsi K, Bedford MT, Shi X, Li W, Barton MC, Dent SYR, Kraus WL. (2018) Enhancer transcription reveals subtype-specific gene expression programs controlling breast cancer pathogenesis. Genome Res. 28(2):159-170.
Hamidi T, Singh AK, Veland N, Vemulapalli V, Chen J, Hardikar S, Bao J, Fry CJ, Yang V, Lee KA, Guo A, Arrowsmith CH, Bedford MT, Chen T. (2018) Identification of Rpl29 as a major substrate of the lysine methyltransferase Set7/9. J Biol Chem. 293(33):12770-12780.
Jain AK, Barton MC. (2018) p53: emerging roles in stem cells, development and beyond. Development. 145(8): dev158360.
Kaushik S, Liu F, Veazey KJ, Gao G, Das P, Neves LF, Lin K, Zhong Y, Lu Y, Giuliani V, Bedford MT, Nimer SD, Santos MA. (2018) Genetic deletion or small-molecule inhibition of the arginine methyltransferase PRMT5 exhibit anti-tumoral activity in mouse models of MLL-rearranged AML. Leukemia. 32(2):499-509.
Kang R, Zelazowski MJ, Cole F. (2018) Missing the Mark: PRDM9-dependent methylation is required for meiotic DSB targeting. Mol Cell. 69(5):725-727.
Singarapu N, Ma K, Reeh KAG, Shen J, Lancaster JN, Yi S, Xie H, Orkin SH, Manley NR, Ehrlich LIR, Jiang N, Richie ER. (2018) Polycomb repressive complex 2 is essential for development and maintenance of a functional TEC compartment. Sci Rep. 8(1):14335.
Wang L, Koutelou E, Hirsch C, McCarthy R, Schibler A, Lin K, Lu Y, Jeter C, Shen J, Barton MC, Dent SYR. (2018) GCN5 regulates FGF signaling and activates selective MYC target tenes during early embryoid body differentiation. Stem Cell Reports. 10(1):287-299
Wible DJ, Bratton SB. (2018) Reciprocity in ROS and autophagic signaling. Curr Opin Toxicol. 7:28-36.
2017
Bae N, Viviano M, Su X, Lv J, Cheng D, Sagum C, Castellano S, Bai X, Johnson C, Khalil MI, Shen J, Chen K, Li H, Sbardella G, Bedford MT. (2017) Developing Spindlin1 small-molecule inhibitors by using protein microarrays. Nat Chem Biol. 13(7):750-756.
Brahma S, Udugama MI, Kim J, Hada A, Bhardwaj SK, Hailu SG, Lee TH, Bartholomew B. (2017) INO80 exchanges H2A.Z for H2A by translocating on DNA proximal to histone dimers. Nat Commun. 8:15616.
Carr SM, Munro S, Sagum CA, Fedorov O, Bedford MT, La Thangue NB. (2017) Tudor-domain protein PHF20L1 reads lysine methylated retinoblastoma tumour suppressor protein. Cell Death Differ. 24(12):2139-2149.
Dan J, Rousseau P, Hardikar S, Veland N, Wong J, Autexier C, Chen T. (2017) Zscan4 inhibits maintenance DNA methylation to facilitate telomere Eeongation in mouse embryonic stem cells. Cell Rep. 20(8):1936-1949.
Espejo AB, Gao G, Black K, Gayatri S, Veland N, Kim J, Chen T, Sudol M, Walker C, Bedford MT. (2017) PRMT5 C-terminal phosphorylation modulates a 14-3-3/PDZ interaction switch. J Biol Chem. 292(6):2255-2265.
Li J, Xi Y, Li W, McCarthy RL, Stratton SA, Zou W, Li W, Dent SY, Jain AK, Barton MC. (2017) TRIM28 interacts with EZH2 and SWI/SNF to activate genes that promote mammosphere formation. Oncogene. 36(21):2991-3001.
Manandhar M, Lowery MG, Boulware KS, Lin KH, Lu Y, Wood RD. (2017) Transcriptional consequences of XPA disruption in human cell lines. DNA Repair (Amst). 57:76-90.
Mi W, Guan H, Lyu J, Zhao D, Xi Y, Jiang S, Andrews FH, Wang X, Gagea M, Wen H, Tora L, Dent SYR, Kutateladze TG, Li W, Li H, Shi X. (2017) YEATS2 links histone acetylation to tumorigenesis of non-small cell lung cancer. Nat Commun. 8(1):1088
Mu Y, Zelazowska MA, McBride KM. (2017) Phosphorylation promotes activation-induced cytidine deaminase activity at the Myc oncogene. J Exp Med. 214(12):3543-3552.
Ortiz GJ, Li Y, Post SM, Pant V, Xiong S, Larsson CA, El-Naggar AK, Johnson DG, Lozano G. (2017) Contrasting effects of an Mdm2 functional polymorphism on tumor phenotypes. Oncogene. 37(3):332-340.
Takata KI, Reh S, Yousefzadeh MJ, Zelazowski MJ, Bhetawal S, Trono D, Lowery MG, Sandoval M, Takata Y, Lu Y, Lin K, Shen J, Kusewitt DF, McBride KM, Cole F, Wood RD. (2017) Analysis of DNA polymerase ν function in meiotic recombination, immunoglobulin class-switching, and DNA damage tolerance. PLoS Genet. 13(6):e1006818.
Schrock MS, Batar B, Lee J, Druck T, Ferguson B, Cho JH, Akakpo K, Hagrass H, Heerema NA, Xia F, Parvin JD, Aldaz CM, Huebner K. (2017) Wwox-Brca1 interaction: role in DNA repair pathway choice. Oncogene. 2017 Apr 20;36(16):2215-2227.
Veland N, Hardikar S, Zhong Y, Gayatri S, Dan J, Strahl BD, Rothbart SB, Bedford MT, Chen T. (2017) The arginine methyltransferase PRMT6 regulates DNA methylation and contributes to global DNA hypomethylation in cancer. Cell Rep. 21(12):3390-3397
Wan L*, Wen H*, Li Y, Lyu J, Xi Y, Hoshii T, Joseph JK, Wang X, Loh YE, Erb MA, Souza AL, Bradner JE, Shen L, Li W, Allis CD, Armstrong SA, Shi X. (2017) ENL links histone acetylation to oncogeneic gene expression in acute myeloid leukaemia. Nature. 543(7644):265-269 (*equal contribution)
Zelazowski MJ, Sandoval M, Paniker L, Hamilton HM, Han J, Gribbell MA, Kang R, Cole F. (2017) Age-dependent alterations in meiotic recombination cause chromosome segregation errors in spermatocytes. Cell. 171(3):601-614.e13.
Zhu F, Willette-Brown J, Song NY, Lomada D, Song Y, Xue L, Gray Z, Zhao Z, Davis SR, Sun Z, Zhang P, Wu X, Zhan Q, Richie ER, Hu Y. (2017) Autoreactive T cells and chronic fungal infection drive esophageal carcinogenesis. Cell Host Microbe. 21(4):478-493.
2009-2016
2016
Atanassov BS, Mohan RD, Lan X, Kuang X, Lu Y, Lin K, McIvor E, Li W, Zhang Y, Florens L, Byrum SD, Mackintosh SG, Calhoun-Davis T, Koutelou E, Wang L, Tang DG, Tackett AJ, Washburn MP, Workman JL, Dent SY. (2016) ATXN7L3 and ENY2 coordinate activity of multiple H2B deubiquitinases important for cellular proliferation and tumor growth. Mol Cell. 62(4):558-71.
Bain VE, Gordon J, O’Neil JD, Ramos I, Richie ER, Manley NR. (2016) Tissue-specific roles for sonic hedgehog signaling in establishing thymus and parathyroid organ fate. Development. 143(21):4027-4037.
Jain AK, Xi Y, McCarthy R, Allton K, Akdemir KC, Patel LR, Aronow B, Lin C, Li W, Yang L, Barton MC. (2016) LncPRESS1 is a p53-regulated LncRNA that safeguards pluripotency by disrupting SIRT6-mediated de-acetylation of histone H3K56. Mol Cell. 64(5):967-981
Lange SS, Tomida J, Boulware KS, Bhetawal S, Wood RD. (2016) The polymerase activity of mammalian DNA Pol ζ Is specifically required for cell and embryonic viability. PLoS Genet. 12(1):e1005759.
Li Y, Sabari BR, Panchenko T, Wen H, Zhao D, Guan H, Wan L, Huang H, Tang Z, Zhao Y, Roeder RG, Shi X, Allis CD, Li H. (2016) Molecular coupling of histone crotonylation and active transcription by AF9 YEATS domain. Mol Cell. 62(2):181-93.
Stuckey JI, Dickson BM, Cheng N, Liu Y, Norris JL, Cholensky SH, Tempel W, Qin S, Huber KG, Sagum C, Black K, Li F, Huang XP, Roth BL, Baughman BM, Senisterra G, Pattenden SG, Vedadi M, Brown PJ, Bedford MT, Min J, Arrowsmith CH, James LI, Frye SV. (2016) A cellular chemical probe targeting the chromodomains of Polycomb repressive complex 1. Nat Chem Biol. 12(3):180-7.
Vélez-Cruz R, Manickavinayaham S, Biswas AK, Clary RW, Premkumar T, Cole F, Johnson DG. (2016) RB localizes to DNA double-strand breaks and promotes DNA end resection and homologous recombination through the recruitment of BRG1. Genes Dev. 2016 Nov 15;30(22):2500-2512.
Wu CC, Lee S, Malladi S, Chen MD, Mastrandrea NJ, Zhang Z, Bratton SB. (2016) The Apaf-1 apoptosome induces formation of caspase-9 homo- and heterodimers with distinct activities. Nat Commun. 2016 Nov 24;7:13565
Zhang D, Park D, Zhong Y, Lu Y, Rycaj K, Gong S, Chen X, Liu X, Chao HP, Whitney P, Calhoun-Davis T, Takata Y, Shen J, Iyer VR, Tang DG. (2016) Stem cell and neurogenic gene-expression profiles link prostate basal cells to aggressive prostate cancer. Nat Commun. 7:10798.
Zhang X, Peng D, Xi Y, Yuan C, Sagum CA, Klein BJ, Tanaka K, Wen H, Kutateladze TG, Li W, Bedford MT, Shi X. (2016) G9a-mediated methylation of ERα links the PHF20/MOF histone acetyltransferase complex to hormonal gene expression. Nat Commun. 7:10810.
2015
Hirsch CL, Coban Akdemir Z, Wang L, Jayakumaran G, Trcka D, Weiss A, Hernandez JJ, Pan Q, Han H, Xu X, Xia Z, Salinger AP, Wilson M, Vizeacoumar F, Datti A, Li W, Cooney AJ, Barton MC, Blencowe BJ, Wrana JL, Dent SY. (2015) Myc and SAGA rewire an alternative splicing network during early somatic cell reprogramming. Genes Dev.29(8):803-16.
Hu SB, Xiang JF, Li X, Xu Y, Xue W, Huang M, Wong CC, Sagum CA, Bedford MT, Yang L, Cheng D, Chen LL. (2015) Protein arginine methyltransferase CARM1 attenuates the paraspeckle-mediated nuclear retention of mRNAs containing inverted repeat Alus. Genes Dev. 29(6):630-45.
Kapoor P, Bao Y, Xiao J, Espejo A, Yang L, Bedford MT, Peng G, Shen X. (2015) Phosphorylation-Dependent Enhancement of Rad53 Kinase Activity through the INO80 Chromatin Remodeling Complex. Mol Cell. 58(5):863-9.
Kapoor P, Bao Y, Xiao J, Luo J, Shen J, Persinger J, Peng G, Ranish J, Bartholomew B, Shen X. (2015) Regulation of Mec1 kinase activity by the SWI/SNF chromatin remodeling complex. Genes Dev. 29(6):591-602.
Li M, Hada A, Sen P, Olufemi L, Hall MA, Smith BY, Forth S, McKnight JN, Patel A, Bowman GD, Bartholomew B, Wang MD. (2015) Dynamic regulation of transcription factors by nucleosome remodeling. Elife. 4. doi: 10.7554/eLife.06249.
Pathiraja TN, Thakkar KN, Jiang S, Stratton S, Liu Z, Gagea M, Shi X, Shah PK, Phan L, Lee MH, Andersen J, Stampfer M, Barton MC. (2015) TRIM24 links glucose metabolism with transformation of human mammary epithelial cells. Oncogene. 34(22):2836-45.
Yang Y, Hadjikyriacou A, Xia Z, Gayatri S, Kim D, Zurita-Lopez C, Kelly R, Guo A, Li W, Clarke SG, Bedford MT. (2015) PRMT9 is a type II methyltransferase that methylates the splicing factor SAP145. Nat Commun. 6:6428.
2014
Biswas AK, Mitchell DL, Johnson DG (2014) E2F1 responds to ultraviolet radiation by directly stimulating DNA repair and suppressing carcinogenesis. Cancer Res. 74(12):3369-77.
Cole F, Baudat F, Grey C, Keeney S, de Massy B, Jasin M (2014) Mouse tetrad analysis provides insights into recombination mechanisms and hotspot evolutionary dynamics. Nat Genet. 46(10):1072-80.
Jin M, Zhang T, Liu C, Badeaux MA, Liu B, Liu R, Jeter C, Chen X, Vlassov AV, Tang DG (2014) miRNA-128 suppresses prostate cancer by inhibiting BMI-1 to inhibit tumor-initiating cells. Cancer Res. 74(15):4183-95.
Li Y, Wen H, Xi Y, Tanaka K, Wang H, Peng D, Ren Y, Jin Q, Dent SYR., Li W, Li H, Shi X (2014) AF9 YEATS Domain Links Histone Acetylation to DOT1L-Mediated H3K79 Methylation. Cell.159(3):558-71.
Reeh KA, Cardenas KT, Bain VE, Liu Z, Laurent M, Manley NR, Richie, ER (2014) Ectopic TBX1 suppresses thymic epithelial cell differentiation and proliferation during thymus organogenesis. Development. 141(15):2950-8.
Wen H, Li Y, Xi Y, Jiang S, Stratton S, Peng D, Tanaka K, Ren Y, Xia Z, Wu J, Li B, Barton MC, Li W, Li H, Shi X (2014) ZMYND11 links histone H3.3K36me3 to transcription elongation and tumour suppression. Nature. 508(7495):263-8.
Yang Y, McBride KM, Hensley S, Lu Y, Chedin F, Bedford MT (2014) Arginine methylation facilitates the recruitment of TOP3B to chromatin to prevent R loop accumulation. Mol Cell. 53(3):484-97.
Yousefzadeh MJ, Wyatt DW, Takata K, Mu Y, Hensley SC, Tomida J, Bylund, GO, Doublie S, Johansson E, Ramsden DA, McBride KM and Wood, RD (2014) Mechanism of Suppression of Chromosomal Instability by DNA Polymerase POLQ. PLoS Genet. 10(10):e1004654.
2013
Badeaux MA, Jeter CR, Gong S, Liu B, Suraneni MV, Rundhaug J, Fischer SM, Yang T, Kusewitt D, Tang DG. (2013) In vivo functional studies of tumor-specific retrogene NanogP8 in transgenic animals. Cell Cycle. 12(15):2395-408.
Chen K, Wilson MA, Hirsch C, Watson A, Liang S, Lu Y, Li W, Dent SY (2013) Stabilization of the promoter nucleosomes in nucleosome-free regions by the yeast Cyc8-Tup1 corepressor. Genome Res. 23:312-22.
Johnson DG, Dent SY (2013) Chromatin: receiver and quarterback for cellular signals. Cell. 152(4):685-9.
Kapoor P, Chen M, Winkler DD, Luger K, Shen X (2013) Evidence for monomeric actin function in INO80 chromatin remodeling. Nat Struct Mol Biol. 20(4):426-32.
Kim SJ, Wong PK. (2013) ROS upregulation during the early phase of retroviral infection plays an important role in viral establishment in the host cell. J Gen Virol. 94(Pt 10):2309-17.
Kim SJ, Zhao H, Hardikar S, Singh AK, Goodell MA, Chen T. (2013) A DNMT3A mutation common in AML exhibits dominant-negative effects in murine ES cells. Blood. 2013 Dec 12;122(25):4086-9.
Lange SS, Bedford E, Reh S, Wittschieben JP, Carbajal S, Kusewitt DF, DiGiovanni J, Wood RD (2013) Dual role for mammalian DNA polymerase zeta in maintaining genome stability and proliferative responses. Proc Natl Acad Sci U S A. 110(8):E687-96.
Li J, Zhao Z, Carter C, Ehrlich LI, Bedford MT, Richie ER (2013) Coactivator-associated arginine methyltransferase 1 regulates fetal hematopoiesis and thymocyte development. J Immunol. 190(2):597-604.
Mikulec CD, Rundhaug JE, Simper MS, Lubet RA, Fischer SM. (2013) The chemopreventive efficacies of nonsteroidal anti-inflammatory drugs: the relationship of short-term biomarkers to long-term skin tumor outcome. Cancer Prev Res (Phila). 6(7):675-85.
Perez CJ, Dumas A, Vallières L, Guénet JL, Benavides F. (2013) Several classical mouse inbred strains, including DBA/2, NOD/Lt, FVB/N, and SJL/J, carry a putative loss-of-function allele of Gpr84. J Hered. 2013 Jul-Aug;104(4):565-71.
Takata K, Reh S, Tomida J, Person MD, Wood RD. (2013) Human DNA helicase HELQ participates in DNA interstrand crosslink tolerance with ATR and RAD51 paralogs. Nat Commun. 2013;4:2338.
Yeh TC, Bratton SB (2013) Caspase-dependent regulation of the ubiquitin-proteasome system through direct substrate targeting. Proc Natl Acad Sci U S A. 110(35):14284-9.
Zhao H, Chen T. (2013) Tet family of 5-methylcytosine dioxygenases in mammalian development. J Hum Genet. 58(7):421-7.
2012
Badeaux AI, Yang Y, Cardenas K, Vemulapalli V, Chen K, Kusewitt D, Richie E, Li W, Bedford MT (2012). Loss of the methyl lysine effector protein PHF20 impacts the expression of genes regulated by the lysine acetyltransferase MOF. J Biol Chem. 287(1):429-37.
Biswas AK, Johnson DG. (2012) Transcriptional and nontranscriptional functions of E2F1 in response to DNA damage. Cancer Res. 72(1):13-7.
Chen YC, Gatchel JR, Lewis RW, Mao CA, Grant PA, Zoghbi HY, Dent SY (2012) Gcn5 loss-of-function accelerates cerebellar and retinal degeneration in a SCA7 mouse model. Hum Mol Genet. 21(2):394-405.
Ferguson BW, Gao X, Kil H, Lee J, Benavides F, Abba MC, Aldaz CM (2012) Conditional Wwox deletion in mouse mammary gland by means of two Cre recombinase approaches. PLoS One. 7(5):e36618.
Lange SS, Wittschieben JP, Wood RD (2012) DNA polymerase zeta is required for proliferation of normal mammalian cells. Nucleic Acids Res. 40 (10):4473-82.
Lu M, Liu Z, Yu H, Wang LE, Li G, Sturgis EM, Johnson DG, Wei Q (2012) Combined effects of E2F1 and E2F2 polymorphisms on risk and early onset of squamous cell carcinoma of the head and neck. Mol Carcinog. 51 Suppl 1:E132-41.
Mitchell D, Paniker L, Godar D (2012) Nucleotide excision repair is reduced in oral epithelial tissues compared with skin. Photochem Photobiol. 88(4):1027-32.
Qin J, Liu X, Laffin B, Chen X, Choy G, Jeter CR, Calhoun-Davis T, Li H, Palapattu GS, Pang S, Lin K, Huang J, Ivanov I, Li W, Suraneni MV, Tang DG (2012) The PSA(-/lo) prostate cancer cell population harbors self-renewing long-term tumor-propagating cells that resist castration. Cell Stem Cell. 10(5):556-69.
Regunathan R, Woo J, Pierce MC, Polydorides AD, Raoufi M, Roayaie S, Schwartz M, Labow D, Shin D, Suzuki R, Bhutani MS, Coghlan LG, Richards-Kortum R, Anandasabapathy S, Kim MK. (2012) Feasibility and preliminary accuracy of high-resolution imaging of the liver and pancreas using FNA compatible microendoscopy (with video). Gastrointest Endosc. 76(2):293-300.
2011
Atanassov BS, Dent SY. (2011) USP22 regulates cell proliferation by deubiquitinating the transcriptional regulator FBP1. EMBO Rep. 12(9):924-30.
Atanassov BS, Koutelou E, Dent SY. (2011) The role of deubiquitinating enzymes in chromatin regulation. FEBS Lett. 585(13):2016-23.
Benavides F, Perez C, Blando J, Contreras O, Shen J, Coussens LM, Fischer SM, Kusewitt DF, DiGiovanni J, Conti CJ. (2011) Protective role of cathepsin L in mouse skin carcinogenesis. Mol Carcinog. 51(4):352-61.
Butler JS, Zurita-Lopez CI, Clarke SG, Bedford MT, Dent SY. (2011) Protein-arginine methyltransferase 1 (PRMT1) methylates Ash2L, a shared component of mammalian histone H3K4 methyltransferase complexes. J Biol Chem. 286(14):12234-44.
Chen J, Zhu F, Weaks RL, Biswas AK, Guo R, Li Y, Johnson DG. (2011) E2F1 promotes the recruitment of DNA repair factors to sites of DNA double-strand breaks. Cell Cycle. 10(8):1287-94.
Fernandez AA, Garcia R, Paniker L, Trono D, Mitchell DL. (2011) An experimental population study of nucleotide excision repair as a risk factor for UVB-induced melanoma. Photochem Photobiol. 87(2):335-41.
Fischer SM, Hawk ET, Lubet RA. (2011) Coxibs and other nonsteroidal anti-inflammatory drugs in animal models of cancer chemoprevention. Cancer Prev Res (Phila). 4(11):1728-35.
Guo R, Chen J, Mitchell DL, Johnson DG (2011) GCN5 and E2F1 stimulate nucleotide excision repair by promoting H3K9 acetylation at sites of damage. Nucleic Acids Res. 39(4):1390-7.
Jeter CR, Liu B, Liu X, Chen X, Liu C, Calhoun-Davis T, Repass J, Zaehres H, Shen JJ, Tang DG. (2011) NANOG promotes cancer stem cell characteristics and prostate cancer resistance to androgen deprivation. Oncogene. 30(36):3833-45.
Kim J, Hwangbo J, Wong PK. (2011) p38 MAPK-Mediated Bmi-1 down-regulation and defective proliferation in ATM-deficient neural stem cells can be restored by Akt activation. PLoS One. 2011 Jan 28;6(1):e16615
Lashinger LM, Malone LM, Brown GW, Daniels EA, Goldberg JA, Otto G, Fischer SM, Hursting SD. (2011) Rapamycin partially mimics the anticancer effects of calorie restriction in a murine model of pancreatic cancer. Cancer Prev Res (Phila). 4(7):1041-51.
Latham JA, Chosed RJ, Wang S, Dent SY (2011) Chromatin signaling to kinetochores: transregulation of Dam1 methylation by histone H2B ubiquitination. Cell. 146(5):709-19.
Li H, Tang DG. (2011) Prostate cancer stem cells and their potential roles in metastasis. J Surg Oncol. 103(6):558-62.
Liu C, Kelnar K, Liu B, Chen X, Calhoun-Davis T, Li H, Patrawala L, Yan H, Jeter C, Honorio S, Wiggins JF, Bader AG, Fagin R, Brown D, Tang DG (2011) The microRNA miR-34a inhibits prostate cancer stem cells and metastasis by directly repressing CD44. Nat Med. 17(2):211-5.
Perez C, Parker-Thornburg J, Mikulec C, Kusewitt DF, Fischer SM, Digiovanni J, Conti CJ, Benavides F. (2011) SKHIN/Sprd, a new genetically defined inbred hairless mouse strain for UV-induced skin carcinogenesis studies. Exp Dermatol. 21(3):217-20.
Rahn JJ, Rowley B, Lowery MP, Coletta LD, Limanni T, Nairn RS, Adair GM. (2011) Effects of varying gene targeting parameters on processing of recombination intermediates by ERCC1-XPF. DNA Repair (Amst). 10(2):188-98.
Spannhoff A, Kim YK, Raynal NJ, Gharibyan V, Su MB, Zhou YY, Li J, Castellano S, Sbardella G, Issa JP, Bedford MT (2011) Histone deacetylase inhibitor activity in royal jelly might facilitate caste switching in bees. EMBO Reports. 12(3):238-43.
Surh I, Rundhaug J, Pavone A, Mikulec C, Abel E, Fischer SM. (2011) Upregulation of the EP1 receptor for prostaglandin E2 promotes skin tumor progression. Mol Carcinog. 50(6):458-68.
Yan L, Della Coletta L, Powell KL, Shen J, Thames H, Aldaz CM, MacLeod MC. (2011) Activation of the canonical Wnt/beta-catenin pathway in ATF3-induced mammary tumors. PLoS One. 6(1):e16515.
2010
Alexander A, Cai SL, Kim J, Nanez A, Sahin M, MacLean KH, Inoki K, Guan KL, Shen J, Person MD, Kusewitt D, Mills GB, Kastan MB, Walker CL (2010) ATM signals to TSC2 in the cytoplasm to regulate mTORC1 in response to ROS. Proc Natl Acad Sci U S A.107:4153-8.
Bredfeldt TG, Greathouse KL, Safe SH, Hung MC, Bedford MT, Walker CL. (2010) Xenoestrogen-induced regulation of EZH2 and histone methylation via estrogen receptor signaling to PI3K/AKT. Mol Endocrinol. 24(5):993-1006
Jain A, Bacolla A, Chakraborty P, Grosse F, Vasquez KM. (2010) Human DHX9 helicase unwinds triple-helical DNA structures. Biochemistry. 49(33):6992-9
Kha DT, Wang G, Natrajan N, Harrison L, Vasquez KM. Pathways for double-strand break repair in genetically unstable Z-DNA-forming sequences. J Mol Biol. 2010 398(4):471-80.
Kim D, Lee J, Cheng D, Li J, Carter C, Richie E, Bedford MT. (2010) Enzymatic activity is required for the in vivo functions of CARM1. J Biol Chem. 285(2):1147-52
Guo R, Chen J, Zhu F, Biswas AK, Berton TR, Mitchell DL, Johnson DG (2010) E2F1 localizes to sites of UV-induced DNA damage to enhance nucleotide excision repair. J Biol Chem. 285:19308-15.
Mitchell DL, Fernandez AA, Nairn RS, Garcia R, Paniker L, Trono D, Thames HD, Gimenez-Conti I (2010) Ultraviolet A does not induce melanomas in a Xiphophorus hybrid fish model. Proc Natl Acad Sci U S A. 107(20):9329-34.
Perez CJ, Jaubert J, Guénet JL, Barnhart KF, Ross-Inta CM, Quintanilla VC, Aubin I, Brandon JL, Otto NW, DiGiovanni J, Gimenez-Conti I, Giulivi C, Kusewitt DF, Conti CJ, Benavides F. (2010) Two hypomorphic alleles of mouse argininosuccinate synthetase as a new animal model of citrullinemia type I and other hyperammonemic syndromes. Am J Pathol. 177(4):1958-68.
Pusapati RV, Weaks RL, Rounbehler RJ, McArthur MJ, Johnson DG. (2010) E2F2 suppresses Myc-induced proliferation and tumorigenesis. Mol Carcinog. 49(2):152-6.
Rundhaug JE, Fischer SM. (2010) Molecular mechanisms of mouse skin tumor promotion. Cancers (Basel). 2(2):436-82
Short JD, Dere R, Houston KD, Cai SL, Kim J, Bergeron JM, Shen J, Liang J, Bedford MT, Mills GB, Walker CL. (2010) AMPK-mediated phosphorylation of murine p27 at T197 promotes binding of 14-3-3 proteins and increases p27 stability. Mol Carcinog. 49(5):429-39.
Yang Y, Lu Y, Espejo A, Wu J, Xu W, Liang S, Bedford MT (2010) TDRD3 is an effector molecule for arginine-methylated histone marks. Mol Cell. 40(6):1016-23.
Zhu F, Dollé ME, Berton TR, Kuiper RV, Capps C, Espejo A, McArthur MJ, Bedford MT, van Steeg H, de Vries A, Johnson DG (2010) Mouse models for the p53 R72P polymorphism mimic human phenotypes. Cancer Res. 70(14):5851-9.
2009
Abba MC, Hu Y, Levy CC, Gaddis S, Kittrell FS, Hill J, Bissonnette RP, Brown PH, Medina D, Aldaz CM. (2009) Identification of modulated genes by three classes of chemopreventive agents at preneoplastic stages in a p53-null mouse mammary tumor model. Cancer Prev Res (Phila). 2(2):175-84.
Blando J, Portis M, Benavides F, Alexander A, Mills G, Dave B, Conti CJ, Kim J, Walker CL. (2009) PTEN deficiency is fully penetrant for prostate adenocarcinoma in C57BL/6 mice via mTOR-dependent growth. Am J Pathol. 174(5):1869-79.
Bua DJ, Kuo AJ, Cheung P, Liu CL, Migliori V, Espejo A, Casadio F, Bassi C, Amati B, Bedford MT, Guccione E, Gozani O. Epigenome microarray platform for proteome-wide dissection of chromatin-signaling networks. (2009) PLoS One. 4(8):e6789.
Chen X, Schneider-Broussard R, Hollowell D, McArthur M, Jeter CR, Benavides F, DiGiovanni J, Tang DG. (2009) Abnormal differentiation, hyperplasia and embryonic/perinatal lethality in BK5-T/t transgenic mice. Differentiation. 77(3):324-34.
Falbo KB, Alabert C, Katou Y, Wu S, Han J, Wehr T, Xiao J, He X, Zhang Z, Shi Y, Shirahige K, Pasero P, and Shen X (2009) Involvement of a chromatin remodeling complex in damage tolerance during DNA replication. Nat Struct Mol Biol. 16(11):1167-72.
Griffith AV, Cardenas K, Carter C, Gordon J, Iberg A, Engleka K, Epstein JA, Manley NR, Richie ER (2009) Increased thymus- and decreased parathyroid-fated organ domains in Splotch mutant embryos. Dev Biol. 327(1):216-27.
Jeter CR, Badeaux M, Choy G, Chandra D, Patrawala L, Liu C, Calhoun-Davis T, Zaehres H, Daley GQ, Tang DG. (2009) Functional evidence that the self-renewal gene NANOG regulates human tumor development. Stem Cells. 2009 May;27(5):993-1005.
Kim DJ, Kataoka K, Sano S, Connolly K, Kiguchi K, DiGiovanni J. (2009) Targeted disruption of Bcl-xL in mouse keratinocytes inhibits both UVB- and chemically induced skin carcinogenesis. Mol Carcinog. 48(10):873-85.
Kuang X, Scofield VL, Yan M, Stoica G, Liu N, Wong PK. (2009) Attenuation of oxidative stress, inflammation and apoptosis by minocycline prevents retrovirus-induced neurodegeneration in mice. Brain Res. 1286:174-84.
Liu B, Zhu F, Xia X, Park E, Hu Y. (2009) A tale of terminal differentiation: IKKalpha, the master keratinocyte regulator. Cell Cycle. 8(4):527-31.
Liu Y, Nairn RS, Vasquez KM. (2009) Targeted gene conversion induced by triplex-directed psoralen interstrand crosslinks in mammalian cells. Nucleic Acids Res. 37(19):6378-88.
Ludes-Meyers JH, Kil H, Parker-Thornburg J, Kusewitt DF, Bedford MT, Aldaz CM. (2009) Generation and characterization of mice carrying a conditional allele of the Wwox tumor suppressor gene. PLoS One. 4(11):e7775.
Repass JF, Laurent MN, Carter C, Reizis B, Bedford MT, Cardenas K, Narang P, Coles M, Richie ER. (2009) IL7-hCD25 and IL7-Cre BAC transgenic mouse lines: new tools for analysis of IL-7 expressing cells. Genesis. 47(4):281-7.
Scofield VL, Yan M, Kuang X, Kim SJ, Crunk D, Wong PK. (2009) The drug monosodium luminol (GVT) preserves thymic epithelial cell cytoarchitecture and allows thymocyte survival in mice infected with the T cell-tropic, cytopathic retrovirus ts1. Immunol Lett. 122(2):159-69.
Shirley SH, Rundhaug JE, Tian J, Cullinan-Ammann N, Lambertz I, Conti CJ, Fuchs-Young R. (2009) Transcriptional regulation of estrogen receptor-alpha by p53 in human breast cancer cells. Cancer Res. 69(8):3405-14.
Zhao J, Jain A, Iyer RR, Modrich PL, Vasquez KM. (2009) Human HMGB1 directly facilitates interactions between nucleotide excision repair proteins on triplex-directed psoralen interstrand crosslinks. DNA Repair (Amst). ;8(7):865-72.