The Ljungman lab

Ljungman lab, Summer 2015:  Front row: Mithun Saha, Emily Ljungman, Brian Magnuson, Ishwarya Venkata Narayanan. Back row: Mats Ljungman, Killeen Kirkconnell, Michelle Paulsen and Karan Bedi. 

Projects 2015

Novel Approaches to Explore Mechanisms of Gene Expression
We have developed four new techniques based on bromouridine labeling of nascent RNA that allows us to estimate both the rate of transcription (Bru-seq) and the rate of degradation (BruChase-seq) of any mRNA. In addition, the use of UV light to introduce random transcription-blocking lesions allowing us to map transcription start sites and active enhancer elements genome-wide (BruUV-seq). Finally, BruDRB-seq allows for the assessment of transcription elongation rates genome-wide. We have gotten funding from NIHGR and we participate in the ENCODE consortium to further develop these new technologies. We are currently collaborating with more than 50 labs in 10 countries to run and analyze various Bru-seq experiments.
Mechanisms of DNA damage-induced gene expression
Exposure of cells to DNA-damaging agents is known to alter gene expression as part of a DNA damage response pathway. However, whether gene expression alterations occur at the level of transcription, splicing and/or RNA stability is not well understood. Using our new Bru-seq techniques we have found that cells modify their gene expression both at the level of synthesis and stability and we have been able to map a number of enhancer elements responding to the DNA damage insult.  We are currently exploring the underlying mechanisms of mRNA stabilization and enhancer element regulation and these studies may lead to the identification of new potential therapeutic targets for cancer treatment. 
Mechanisms of gene expression alterations in cancer
A major component of the carcinogenesis process is the reprogramming of gene expression. Extensive studies have documented gene expression reprogramming in cancer cells but it cannot be determined from these studies whether such changes are due to alterations in the synthesis or degradation of mRNAs. We are currently exploring whether cancer cells have altered their gene expression of mRNAs and ncRNAs at the level of transcription and/or RNA stability. We are exploring splicing efficiencies and the regulation of alternative splicing.  Furthermore, we are mapping the cancer-specific utilization of promoter and enhancer elements genome-wide. 
Mechanisms of splicing and nuclear quality control by the RNA exosome
Our Bru-seq data suggest that splicing is a rather inefficient process where lots of “mistakes” are occurring during co-transcriptional splicing. Although such “mistakes” are wasteful in terms of energy expenditure, they increase the diversity of gene products that the cell can use for protein synthesis. However, most of the produced transcripts appear to be degraded in a time-dependent way in a RNA exosome-dependent process. We are collaborating with Dr. Nouri Neamati to generate specific exosome inhibitors and we have discovered a “first-in-class” compound and are in the process to further develop this lead compound. Since many cancers have alterations in function or expression of splicing factors, and thus would be expected to produce more aberrant transcripts, our hypothesis is that cancer cells would be preferentially susceptible to exosome inactivation.
Exploration of regulation of gene expression during the cell cycle
It is thought that the progression of cells through the cell cycle depends on timely regulation of gene expression. We are currently using our BrU-labeling techniques to explore gene expression alterations at the level of transcription and RNA stability as well as mapping the cell cycle-specific activity of enhancer elements and transcription elongation rates on a genome-wide scale. 
Transcription in single cells
Most of our accumulated knowledge regarding mechanisms of transcription regulation has been obtained from cell population studies where average assessments of gene expression have been performed.  We are developing techniques to assess nascent RNA synthesis in single cells for a dynamic assessment of transcription in the 4D nucleome.
Novel Therapeutics in Pancreatic Cancer.
Pancreatic cancer has the worst survival rate of any human cancer. There is currently no useful therapy for pancreatic cancer. We have ongoing projects focused on exploring novel therapeutic approaches to treat pancreatic cancer.  In a collaboration with the Simeone lab, we recently reported that ATDC is highly expressed in pancreatic cancers and exhibits oncogenic properties by promoting cell proliferation via the WNT/b-catenin pathway have also shown that ATDC protects pancreatic cancer cells against radiation and chemotherapy suggesting it plays a role in the DNA damage response.