Symposium – BME Symposium on Health Disparities

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Coulter-BME-5Ltext-4515-540Triple negative breast cancer is highly lethal, is resistant to therapy, and continues to disproportionately affect African-American women (X Du 2022). Some studies suggest that mortality is highest in Black women with obesity (LA Carey et al 2006). To investigate the molecular mechanism of obesity-induced aggressiveness in triple negative breast cancer, we have teamed up with the Henry lab (Dr. Curtis Henry, Emory Pediatrics), the first group to discover an obesity-associated drug target in patients with leukemia.  Results from our new collaboration, “Murine model to identify epigenetic mediators of obesity-associated drug resistance in triple negative breast cancer” will be presented by Dr. Haynes at the BME Symposium on Health Disparities on Monday, April 18, 2022 at the Historic Academy of Medicine in Atlanta, GA.

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Review – Trends in Biochem Sci – Beyond the marks: reader-effectors as drivers of epigenetics and chromatin engineering

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TIBS_2022_reviewBeyond the marks: reader-effectors as drivers of epigenetics and chromatin engineering
Franklin KA, Shields C, Haynes KA. (2022) Trends Biochem Sci. 47: 417–432. Free access (until June 3, 2022)
PMID: 35267540 | PMCID: PMC9074927

Epigenetics is a process where changes in gene expression are inherited through cell divisions and in some cases across familial generations. As more links between epigenetics and human development and disease have emerged, scientists have become more interested in controlling epigenetic states using molecular technologies including protein engineering. In this review, we discuss a relatively new substrate for epigenetic engineering, a class of gene regulators called “reader-effectors.” These are different from DNA-binding transcription factors in that a single reader-effector type can engage at multiple sites through interactions with biochemical marks (“signals”) on chromatin, the protein/DNA structure that organizes the genome. So far, scientists have used “epigenome editing” to generate or erase signals to alter epigenetic states. Relatively little has been done to control how these signals are transduced into outputs, such as gene regulation, to ultimately control cell behavior. We discuss what natural systems have taught us about the mechanism of two basic composable parts, the “reader” and “effector” domains,  and discuss potential of reader-effector engineering, a technique we call “epigenome actuation.”

Perspective – Nature – The living interface between synthetic biology and biomaterial design

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Nature_biomat_rev_2022The living interface between synthetic biology and biomaterial design
Liu AP, Appel EA, Ashby PD, Baker BM, Franco E, Gu L, Haynes K, Joshi NS, Kloxin AM, Kouwer PHJ, Mittal J, Morsut L, Noireaux V, Parekh S, Schulman R, Tang SKY, Valentine MT, Vega SL, Weber W, Stephanopoulos N, Chaudhuri O. (2022) Nature Materials. 21: 390–397.

This Perspective reviews recent key advances in the fields of synthetic biology and biomaterials engineering, and lays out a general strategy for collaboration between the two fields. Potential applications are described, such as bio-inspired building blocks, and ‘living’ materials that sense and respond based on the interactions between materials and embedded cells. Such applications have the potential to address grand challenges in health, biotechnology and sustainability.

New Member – Seong Hu Kim

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SKim1Seong Hu “Rick” Kim has joined the Haynes lab this fall as a PhD student from the GA Tech/ Emory Biomedical Engineering graduate program. He earned his B.S. in Biomedical Engineering with a Mathematics Minor from Georgia Tech. at Stanford University in Stanford, CA in 2017. As an undergraduate student, he gained lab research experience at the Nano System Application Laboratory, University of Seoul (2018) and in the lab of Dr. Susan Margulies (2019 – 2020) at Georgia Tech. Welcome to the Haynes lab! We look forward to working with you.

Research – RETM – Differential epigenetic effects of BMI1 inhibitor PTC-028 on fusion-positive rhabdomyosarcoma cell lines from distinct metastatic sites

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CShields_RETM2021_Abstract_Fig_KAHDifferential epigenetic effects of BMI1 inhibitor PTC-028 on fusion-positive rhabdomyosarcoma cell lines from distinct metastatic sites
Shields C, Schnepp RW, Haynes KA. (2022) Regen Eng Transl Med. https://doi.org/10.1007/s40883-021-00244-9

Previously, we reported in “Epigenetic regulator BMI1 promotes alveolar rhabdomyosarcoma proliferation and constitutes a novel therapeutic target” that genetic and pharmacologic inhibition of BMI1 reduces the viability of alveolar rhabdomyosarcoma (ARMS) cells, suggesting a new treatment option for patients with the rare pediatric cancer fusion-positive rhabdomyosarcoma (FP-RMS). In a follow-on study, we identified gene expression changes that underlie the loss of cell viability and proliferation, and addressed some open questions about the affect of BMI1 inhibition on ARMS. For instance, in our previous study, BMI1 inhibition affected phosphorylation of LATS1/2, but BMI1 is a transcriptional regulator, not a kinase or phosphatase. In the new study, through RNA-sequencing we found that the mRNA levels of two kinases EPHA2 and PDGFRA were affected during BMI1 inhibition, revealing a possible gene regulation link between BMI1 and kinases that target LATS1/2. RNA-seq also revealed transcription profile differences between ARMS cells derived from two different sites (metastases to an axillary lymph node and bone marrow). Despite this heterogeneity, epigenetic intervention (BMI1 inhibition) induces an anti-cancer response.

Research – bioRxiv – Targeted regulation of episomal plasmid DNA expression in eukaryotic cells with a methylated-DNA-binding activator

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Fig_abstract_v1Targeted regulation of episomal plasmid DNA expression in eukaryotic cells with a methylated-DNA-binding activator
Enwerem-Lackland I, Warga E, Dugoni M, Elmer J, Haynes KA. (2021) bioRxiv. https://www.biorxiv.org/content/10.1101/2021.11.01.466616v1

This work was inspired by our team’s interest in making DNA delivery into human cells easier and more more reliable. Currently, synthetic viruses are the most efficient method, but only up to ~1000 bp of DNA can be reliably packaged in these vectors, and current DNA-delivering viruses can cause dangerous and lethal immunogenic reactions. Non-viral plasmid DNA may be a safer alternative, but delivery and expression tends to be poor and unreliable. Our work and research from other labs has implicated epigenetic blockades as one culprit. Therefore, we developed a small protein, inspired by work from the van Steensel lab and Khalil lab, that carries a gene expression activator to newly-delivered methylated plasmid DNA to boost its expression. The “landing pad” for the activator is the smallest of its kind (4 base pair unit, GAmeTC), and therefore should be easy to use in any plasmid DNA. We named this system The Dpn Adaptor Linked Effector (DAL-E) to honor the pioneering biochemist Marie M. Daly, the first scientist to determine that a central epigenetic protein (histone) is lysine-rich, and the first black woman to earn a PhD in Chemistry in the U.S.

Kierra Franklin – QE Passed!

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KFranklin1Congratulations to Kierra Franklin, first-year PhD student in the Wallace H. Coulter Biomedical Engineering graduate program! She passed her qualifying exam on September 9, 2021 and is now ready to start her thesis work on chromatin engineering for cancer research and treatment.

Karmella Haynes Joins NIH Biosecurity Advisory Board

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NIH_logoDr. Karmella Haynes is joining the National Institutes of Health (NIH) National Science Advisory Board for Biosecurity (NSABB), a federal advisory committee chartered to provide advice, guidance, and leadership for dual-use research.  She will serve a three-year term to help the U.S. evaluate research with legitimate and important scientific purpose that could also produce technologies or information that could be harmful if they are misused.

 

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Chavis Ferguson – Summer LGS-SOAR Undergrad Research Fellow

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CFerguson1Congratulations to Chavis Ferguson, recipient of an Emory Laney Graduate School Summer Opportunity for Academic Research (Emory LGS-SOAR) undergraduate fellowship. He completed a hypothesis-driven project in the Haynes lab this summer under the supervision of Dr. Natecia Williams. He gained hands-on experience investigating a mouse triple negative breast cancer cell line (4T1) by using a Boyden chamber transwell assay, designing and running reverse transcription quantitative PCR (RT-qPCR), and exploring public RNA-seq data for 4T1 and non-cancer cells. He presented his work as a poster, “Gene Expression and Migration of Mouse Triple Negative Breast Cancer Cells,” during the 2021 Emory Summer Research Symposium (online) on Thursday, August 5, 2021. Chavis will return to his home institution, the University of Missouri, College of Engineering, to complete his senior year.

Haynes lab members present research at the 2021 SEED conference

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SEED2017Four members from the Haynes lab presented their latest research at the 2021 Synthetic Biology: Engineering, Evolution & Design (SEED) conference that took place June 16 – 18, 2021 on a virtual platform. SEED 2021 focused on advances in science, technology, applications, and related investments in the field of synthetic biology. Dr. Karmella Haynes served as session chair for “Translating Synthetic Biology into the Clinic” and the “Funder’s Panel.” The four poster presentations from the Haynes lab included:

  • Dr. Isioma Enwerem (postdoc), “Time-course expression profiling reveals early and late responders to a synthetic chromatin regulator”
  • Harrison Priode (research specialist), “Synthetic epigenetic reader engineering with an all-in-one cell-free expression and protein interaction microarray”
  • Paige Steppe (undergraduate researcher), “Using newly-identified epigenetic reader-effector BAHCC1 to engineer a H3K27me3-binding transcriptional activator”
  • Dr. Natecia Williams (senior research specialist), “A synthetic chromatin reader-effector activates key silenced tumor suppressor genes in triple negative breast cancer cells”