Department of Molecular Medicine

Outreach Core

Students | Workshop | Poster Presentation


The goals of the Core are to enhance the awareness and knowledge of cancer systems biology, recruit next- generation trainees interested in epigenomics, and expand the scope of early-stage and established investigators to engage in omics analysis as part of their research portfolio. Two experienced Core leaders, Dr. Nameer Kirma (UTHSCSA) and Dr. Pearlly Yan (OSU), will coordinate outreach/training activities within the two center sites. In Aim 1, knowledge of advances in cancer systems biology will be disseminated through seminar series and annual symposium. Workshops will provide practical training of novel omics technologies. To maximize exposure and capitalize on our existing expertise, these symposia and workshops will be held every year alternating between the two center sites. In Aim 2, we plan to train new scientists and retool established investigators in systems epigenomics. Postdoctoral fellows and early-stage investigators will have the opportunity to participate in cross-pollination training beyond their current expertise, facilitating a more rounded understanding of systems biology. Early-stage and established investigators will have the opportunity to re-sharpen their research skills in omics analyses through the three proposed projects in our center and the release of annual RFA for supporting two Intra-center Pilot Projects (IPPs). In addition, the Core will organize summer programs for at least six undergraduate students and visiting scientists who will have the opportunity to engage in short-term research projects using omics approaches. Given that both sites have access to a great pool of minority and underserved students in South Texas and Appalachia, we will encourage them to apply for these programs. In Aim 3, we plan to interact with investigators in the RCCSB Consortium and other genomics communities. Working with the leaders of our Administrative Core, we will send a delegation consisting of 10 senior and early-stage investigators and IPP awardees to participate in the annual RCCSB Consortium Steering Committee meeting. Through platform and poster presentations and face-to-face meetings, our investigators will find opportunities and niches for collaboration and data sharing with scientists in the Consortium. Furthermore, we will make contact with members of the NIH-funded 4D nucleome programs and other genomics forums, such as the Cold Spring Harbor Nuclear Organization and Function Symposium, to share our epigenomic findings. To disseminate knowledge on epigenomic advances, we will work with the staff in the Data Analysis and Management Core to set up searchable databases. Ongoing and to-be-developed toolkits will be made available to researchers through our website portal. Collectively, these integrative efforts are expected to nurture next-generation trainees in the area of systems biology and to foster a collaborative spirit with investigators in the RCCSB Consortium and other genomics communities.



UT Health U54 Summer Outreach Program Students

Christian Gonzalez: Christian will worked with Dr. Jason (Zhijie) Liu to analyze available GRO-seq, RNA-seq, and ChIP-seq data sets to find correlation between long non-coding RNAs (lncRNAs), estrogen receptor, and endocrine resistance in breast cancer. This analysis will help us to find function of lncRNA molecules in hormone response and endocrine resistance, and estrogen receptor's regulation function on these functional lncRNAs. We hope to find interactions of lncRNAs with gene regulation mechanisms of breast cancer cells and potentially show reasons for endocrine resistance in breast cancer patients.

Brandon Lieberman: Brandon worked in Dr. Chun-Liang Chen’s lab to focus on castration resistant signaling systems in prostate cancer revealed by single-cell RNA-seq”. Brandon will focus on the Hippo pathway and Epherin pathway in the progression of advanced prostate cancer.

Bianca Gonzalez: Bianca worked with Dr. Nameer Kirma to study endometriosis as a non-malignant gynecologic condition associated with pelvic pain and infertility, and a precursor to the endometrioid ovarian cancer subtype. Our studies revealed the importance of gap junctions, involved in direct cell-cell communication, in the invasiveness of endometriosis. Studies will be conducted for RNA expression of gap junction genes at the bulk and single-cell levels to determine differential expression and cellular heterogeneity of primary eutopic endometrial cells from women with and without endometriosis. The studies are expected to delineate molecular changes associated with endometrial cells prone to endometriosis lesion development.

Logan Alexander Walker: Logan worked with Drs. Raj Muthusamy, Ralf Bundschuh, and Pearlly Yan to objectively screen for transcripts for differentially expressed gene (DEG) analysis in ultralow input RNA seq analysis (defined as input amounts that required global pre-amplification for library generation) for chronic lymphocytic leukemia (CLL) samples. We noted the minute and varying RNA content in rare CLL progenitor cells often lead to unacceptable level of false-positive DEGs. Using a single aliquot of total RNA from two types of sorted cells to build libraries at 3 ultralow levels, we were able to recapitulate distorted transcript coverage profiles observed in single cell- and low cell count transcriptome data. A custom algorithm modeled after read coverage distribution positively impact DEG analysis and PCA separation of two different CLL cell types. Upon further validation, this method will allow us to compare gene expression profiles between cell types of different sizes and transcription activities.

Alexander Pan: Alex worked with Drs. Amal Amer, Ralf Bundschuh, and Pearlly Yan to identify pathways impacted by epigallocatechin-3-gallate (EGCG) treatment in a cystic fibrosis (CF) mouse model. As DNA methylation in most part is reversible, we examined methylation values at single-based resolution between each experiment conditions (CF and control mice; with and without EGCG treatment) to monitor gene promoters and promoter-associated CpG island. Transcription factor binding sites (TFBS) were identified in the differentially methylated cytosines (DMCs) to select functional DMCs (fDMCs) for Ingenuity Pathway Analysis and for visualizing gene interactions in Cytoscape. In summary, CF methylomes were significantly more hypermethylated than WT methylomes and that EGCG had a greater hypomethylating effect in the CF methylomes than the WT methylomes.

Altan Turkoglu: Altan worked with Dr. Huiling He, Ralf Bundschuh, and Pearlly Yan to study papillary thyroid cancer (PTC) – associated SNPs on their neighboring methylomes. Out of 24 PTC – associated SNPs, two met the selection criteria (sufficient read-coverage at SNP loci; presence of DMCs within 100 kb of SNP with 10% methylation differences between PTC samples with SNP and without SNP). Of the two SNPs, one is associated with a long non-coding RNA and the other is with a protein coding gene. STRINGdb was used to identify protein – protein interactive (PPI) network for the protein coding gene. The current study was performed on 12 pairs of PTC tumors and adjacent normal to develop the RRBS-, SNP- and PPI workflows. Data from an additional 24 PTC pairs will be available for complete analyses.

Christopher Merrill Roach: Chris worked with Drs. Qianben Wang, Dayong Wu, Lu Liu, and Pearlly Yan, to compare FoxA1 and GATA2 binding sites (e.g., FoxA1/GATA2 motifs, co-factor motifs, and differences in shared FoxA1/GATA2 binding regions from FoxA1-/GATA2-specific biding regions) in AR- and non-AR regions in LNCaP and C4-2B cells. Being a computer science major with no prior bioinformatics experience, the four-week training enables Chris to amass critical skills (setup account and submit jobs in Marshall’s BigGreen Cluster; download data from GEO; ChIP-seq data preprocessing, data alignment, data QC, peak calling, and peak visualization; project presentation and write-up) to work on the signed project with Dr. Lu Liu (former post-doctoral trainee of Jianhua Ruan, UTSA; new Asst. Prof., Dept. of Computer Science, Marshall University) in Fall, 2017.

Drew Braun: Drew spent 2 days with Dr. Pearlly Yan and the CSBC Summer Trainees. Drew had used ISOC twice in his AP Biology class. The visit bridged the role of next-generation sequencing, personalized medicine and how computation plays a key part in the treatment of cancer for Drew. Due to the recent trend for high school students to take part in the dual enrollment (concurrent HS and college enrollment) program, Drew’s plan to teach AP Biology is now modified to every other year. This insight helps us to identify high school instructors from STEM schools for our subsequent CSBC summer experience.

Marisa Manocchio: Marisa spent 3 days with Dr. Pearlly Yan, the CSBC Summer Trainees, and Darrell Ward (Assoc. Director for Cancer Communication, OSU Wexner Medical Center; Course Instructor of ‘The Introduction to the Science of Cancer’ or ISOC: free via iTUNE App and Marisa had previously integrated a portion of ISOC in her class. Her CSBC visit motivated her to incorporate new activities (genome analysis and visualizing SNPs via IGV) to her class and to bring her students on a school trip early 2018 to visit the new James Cancer Hospital and to visit with our undergraduate trainees to learn about informatics/bioinformatics/biophysics as potential career paths.

Our faculty enjoyed working with these students and enhancing their knowledge and understanding of various methods currently used in our labs to help find more targeted therapies for various cancers.



U54 Education and Outreach Student Workshop

The outreach core hosted a U54 Education and Outreach Student Workshop for our Cancer Systems Biology Program on Wednesday, July 12th, 2017. The workshop was open to students and anyone interested in Cancer Systems Biology across campus. Cancer systems biology focuses on using systems biology approaches to understand cancer genomics, the 4D nucleome, and multiscale cellular profiling, including computational and mathematical modeling, to study cancer as a complex multidimensional biological system.

This workshop created a great introduction into Cancer Systems Biology and the current innovative research happening in our labs today. Attendees included our U54 Summer Students as well as faculty, staff and students from across UT Health.

Below you will find some pictures from the event and the presentation slides that were used.

This was a very successful event with over 50 in attendance!

Topics included:

    • Overview of U54 and the summer program (Dr. Nameer Kirma)
    • Single cell Analysis (Dr. Chun-Liang Chen)
    • Next Generation sequencing (Dr. Zhao Lai)
    • Next generation sequencing applications (Dr. Zhijie Liu)
    • Computational prediction of cancer outcomes (Dr. Jianhua Ruan)

Workshop Presentation Slides, 7/12/2017

    Dr. Chun-Liang Chen – pdf. of slides
    Dr. Zhao Lai – pdf. of slides
    Dr. Jason Liu – pdf. of slides
    Dr. Jianhua Ruan – pdf. of slides



UT Health U54 Summer Research Program Poster Session

The U54 summer students participated in a joint poster session with other students involved in various summer programs throughout the University. This gave them an opportunity to present their research they’ve done while being here.


Over 60 posters were included in this poster session. This gave the students great exposure to this process in a higher education environment.

Posters Presented, 8/09/2017

    Christian Gonzalez – pdf. of poster
    Bianca Gonzalez – pdf. of poster
    Brandon Lieberman – pdf. of poster