New Member – Ranjit Pelia
Ranjit Pelia has joined the Haynes lab this summer as a PhD student from the Emory GDBBS Genetics and Molecular Biology graduate program. He earned his Associate Degree at Emory University Oxford College in 2015, his B.S. in Biology from Emory University in 2018, and his M.P.H. from the Emory Rollins School of Public Health in 2022. Ranjit is originally from Mumbai, India but is a native Atlanta resident. His past experience includes working as a clinical research coordinator, lab technician, and data analyst in pediatric Crohn’s disease at the Emory School of Medicine. His research interests include identifying the epigenetic roles of noncoding RNAs in controlling downstream gene regulation using integrative ‘omics. Welcome to the Haynes lab! We look forward to working with you.
Text Book – Epigenetic Cancer Therapy
Chapter 10 – Synthetic biology and cell engineering—deriving new insights into cancer epigenetics.
Franklin KA, Haynes KA. (2023) Translational Epigenetics: Epigenetic Cancer Therapy (Second Edition). Academic Press. pp 195-210
The latest edition of Epigenetic Cancer Therapy includes a chapter that explores how scientists are using synthetic biology and cell engineering techniques, collectively known as epigenetic engineering, to develop powerful tools for understanding and manipulating the regulation of genes in cancer cells. In this chapter, we explain how four general technologies in epigenetic engineering have been used in cancer research. The first two technologies are genetic reporters and protein reporters, which allow us to closely monitor the changes in gene expression inside living cells. The other two technologies are epigenome editing and epigenome actuation. Epigenome editing enables scientists to make precise changes to the chemical modifications on the DNA and proteins that affect gene activity. Epigenome actuation, on the other hand, involves using synthetic molecules to activate or deactivate groups of genes in cancer cells. One exciting aspect of epigenome editing and actuation is that they offer advantages over traditional epigenetic drugs and genetic knockdowns when studying cancer epigenetics. Combining cell engineering with cancer research has the potential to revolutionize our understanding of cancer and may lead to the development of more effective therapies in the future.
Perspective – Trends in Biochem Sci – Adding post-translational modifications and protein-protein interactions to protein schematics
Adding post-translational modifications and protein-protein interactions to protein schematics.
Pandy N, Franklin KA, Haynes KA, Rapé M, Cristea IM. (2023) Trends Biochem Sci. 48: 407–409.
In this “TrendsTalk” of the Special series: Scientific Figure Development, Dr. Karmella Haynes and Kierra Franklin and other recent TiBS authors share their thoughts on aspects to consider when creating figures that depict proteins, post-translational modifications (PTMs), and important protein–protein interactions (PPIs) in protein complexes
Recruiting: Summer 2023 Undergraduate Student – Bioinformatics for Epigenetic Engineering
The Haynes lab at Emory is seeking bright, talented, and motivated undergraduate students from Emory University or Georgia Tech to fill one summer research position with a start date of May or June 2023. This position is a great opportunity to gain hands-on research experience in synthetic biology as it applies to health and medicine. Dr. Haynes has several years of experience mentoring undergraduate research in the classroom, in her research lab (see our publications and posters that include undergraduates), and for the International Genetically Engineered Machines Competition (iGEM).
Undergraduate Researcher, Bioinformatics for Epigenetic Engineering
This opportunity is currently [OPEN]
Type: Volunteer or Course credit
- Processing of raw data from next generation sequencing (NGS) experiments (e.g. RNA-seq, ATAC-seq, ChIP-seq) that involve epigenetically engineered cells
- Downstream gene function and network analyses, with guidance from the PI or other supervisor
- Creation of NGS data figures for posters and publications
- Course: Genomics & Applied Bioinformatics (BIOS 4150); minimum grade of B
- Course: Biological Networks & Genomics (BMED 4477); desired but not required
- Proficiency in basic RNA-seq data processing tools (e.g. Trimmomatic, STAR, DESeq2, etc.)
- Ability to learn advanced NGS software such as BowTie, Picard Tools, MACS, DeepTools, etc.
About the Haynes Lab at Emory: The Haynes lab is part of the joint Emory/ GA Tech W.H. Coulter Department of Biomedical Engineering. We are located in a new state-of-the-art facility in the Health Sciences Research Building. The space is furnished with benches, a dedicated tissue culture room, shared autoclaves and a cold room, and office desks located in a food-friendly area adjacent to the lab. Core facilities for mouse models, next-generation sequencing, flow cytometry, are located on the same campus. A state-of-the-art and microscopy core (including wide-field and confocal) is located in the same building one level below the Haynes lab.
How to Apply: Send a letter of interest as an e-mail with your resume or c.v. as an attachement to kahayne at emory dot edu. In your letter of interest be sure to include your current year, expected graduation year, your major, your GPA, your current or previous (most recent) lab affiliation (if applicable), and explain how you expect the associated Responsibilities (listed above) to support your career development, and summarize how your background fits the Requirements outlined above.
Hiring: Postdoctoral Researcher or Staff Scientist
The Haynes lab for Chromatin Epigenetic Engineering is seeking bright and talented scientists to fill a full-time Postdoc or Staff Scientist position of up to 3 years with a start date as early as April 2023 (negotiable). This position is an exciting opportunity to work at the cutting edge of biomedical synthetic biology. This position involves a project focused on the design and use of noncoding RNA to control chromatin and gene regulation.
Postdoctoral Researcher, Biomedical Engineering & Synthetic Biology:
This opportunity is currently [OPEN]
Emory Job ID: 109933
Emory Application URL: https://staff-emory.icims.com/jobs/109933/job
Other Application URL: https://www.indeed.com/job/postdoctoral-fellow-or-staff-scientist-aa774a29a0b799fa
- Completion of cell culture and molecular biology assays assigned by the PI
- Analysis of data using modern software
- Training new and junior personnel in the lab
- Assisting the PI with project management
- Deep understanding of theoretical frameworks and empirical evidence that support their scientific interests must be demonstrated.
- Participate in developing new research with colleagues.
- Participate in community service activities that support their scientific community.
- Participate in professional development activities (e.g., presenting research at conferences).
- PhD in molecular biology or a related field
- Publication track record that shows strong evidence of data analysis experience/ capability
- Strong proficiency in mammalian tissue culture, molecular cloning, chromatin analysis, and gene expression analysis
- Outstanding proficiency in modern data analysis software (e.g. GraphPad Prism, R, etc.)
- Strong evidence of scientific writing in English (desired)
- Two references (contact information or letters)
Environment: The Haynes lab is part of the joint Emory/ Georgia Tech W.H. Coulter Department of Biomedical Engineering. We are located in a new state-of-the-art facility in the Health Sciences Research Building. The space is furnished with benches, a dedicated tissue culture room, shared autoclaves and a cold room, and office desks located in a food-friendly area adjacent to the lab. Core facilities for mouse models, next-generation sequencing, flow cytometry, are located on the same campus. A state-of-the-art and microscopy core (including wide-field and confocal) is located in the same building one level below the Haynes lab.
How to Apply: Please send as a single PDF document:
- a cover letter identifying which position you are interested in (postdoc or staff scientist) and how you expect the associated Responsibilities (listed above) to support your career development, and summarize how your background fits the Requirements outlined above;
- your c.v. (in academic format, no page limit);
- contact information for up to three references (one page)
Research – bioRxiv – PIC recruitment by synthetic reader-actuators to polycomb-silenced genes blocks triple-negative breast cancer invasion
PIC recruitment by synthetic reader-actuators to polycomb-silenced genes blocks triple-negative breast cancer invasion
Williams NL, Hong L, Jaffe M, Shields CE, Haynes KA. (2023) bioRxiv. https://www.biorxiv.org/content/10.1101/2023.01.23.525196v1
An exciting new approach for cancer therapy is to turn on genes within the cancer cells that can stop them from growing and spreading. This approach, called epigenetic therapy, uses small molecules (inhibitors) to block chromatin-modifying proteins that play a role in silencing anti-cancer genes. However, this approach has shown disappointing results in clinical trials for solid cancers, perhaps due to biological limitations. For example, inhibitors can accidentally activate the proteins they are supposed to block (e.g. EZH inhibitors promote EZH2/FOXM1 complexes, Mahara et al 2016), and inhibitors can’t turn on important gene-regulating proteins that are damaged in many cancers. To overcome these limitations we have developed a new tool, synthetic reader-actuators (SRAs), that directly targets chromatin-silenced regions, activates the pre-initiation complex (PIC), and turns on gene transcription. In this report we tested SRAs in triple negative breast cancer cells (BT-549) and identified 122 activated genes. SRA-expressing BT-549 cells showed reduced spheroid size over time, loss of invasion, and activation of apoptosis. While epigenetic drugs have not been successful in many clinical trials, by using synthetic proteins we showed that robust epigenetic reprogramming is possible in cells from solid cancers.
Methods – Rapid Single-Pot Assembly of Modular Chromatin Proteins for Epigenetic Engineering
Rapid Single-Pot Assembly of Modular Chromatin Proteins for Epigenetic Engineering
Haynes KA, Priode JH. (2023) Methods Mol Biol. 2599:191-214.
Much of epigenetic engineering relies on the assembly of multifunctional fusion proteins. We developed a set of cloning vectors and a protocol for one-step “Golden Gate” construction of recombinant protein-encoding DNA. Standard 2-amino acid linkers allow flexible assembly of any combination of up to four protein modules, eliminating the need to design different compatible Golden Gate overhangs to ligate different modules. The five cloning vectors described in this protocol are available at Addgene: Karmella Haynes Lab Plasmids.
- Addgene. Hot Plasmids and Viral Preps – March 2021. https://blog.addgene.org/hot-plasmids-and-viral-preps-march-2021
- Rapid Single-Pot Assembly of Modular Chromatin Proteins for Epigenetic Engineering
Priode JH, Haynes KA. (2021) Protocols.io. https://dx.doi.org/10.17504/protocols.io.brgcm3sw
Haynes lab presenting research at the 2022 Mid-Atlantic Synthetic Biology Symposium
PhD student Kierra Franklin will present her latest research as a poster at the 3rd annual Mid-Atlantic Synthetic Biology Research Symposium (MASBS) which is taking place December 1 – 2, 2022 at the Georgia Institute of Technology. This will be the first year that this annual event will be hosted in Atlanta, GA. Karmella Haynes is serving as Co-Chair with Mark Styczynski (GA Tech). The MASBS is organized by the Mid-Atlantic Synthetic Biology Network (MASBN), a community of researchers, educators, entrepreneurs (academia, government, and the private sector) from Delaware, Maryland, District of Columbia, Virginia, North Carolina, South Carolina, and Georgia who share a common interest in synthetic biology and its supporting technologies.
Rick Kim – QE Passed!
Congratulations to Seong Hu “Rick” Kim, first-year PhD student in the Wallace H. Coulter Biomedical Engineering graduate program! He passed his qualifying exam on November 8, 2022 and is now ready to start his thesis work on the mapping and engineering of chromatin in human cells for biomedical applications.
Haynes lab presents research at the 2022 EpiBio Conference
PhD student Rick Kim and undergraduate researcher Maya Jaffe are presenting their latest research at the 6th International Conference on Epigenetics and Bioengineering (EpiBio 2022) which is taking place October 27 – 29, 2022 at the Rice University Bioscience Research Collaborative in Houston, Texas. EpiBio brings together interdisciplinary expertise to foster the development of new technologies and tools to answer biological questions in epigenetics. Dr. Karmella Haynes is serving as an organizing committee member. The poster presentations from the Haynes lab include:
- Maya Jaffe (undergraduate researcher), “Pre-Initiation Complex Recruitment By Synthetic Reader-Actuators Triggers an Anti-Cancer Expression Profile in Breast Cancer”
- Rick Kim (PhD student), “Investigating Promoters and Enhancers Targeted By a Synthetic Reader-Actuator in H3K27me3-Enriched Chromatin”