Other Publications

Text Book – Epigenetic Cancer Therapy

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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

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TIBS_2022_reviewAdding 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.
PMID: 37059055

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

Methods – Rapid Single-Pot Assembly of Modular Chromatin Proteins for Epigenetic Engineering

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Abstract_v1Rapid Single-Pot Assembly of Modular Chromatin Proteins for Epigenetic Engineering
Haynes KA, Priode JH. (2023) Methods Mol Biol. 2599:191-214.
PMID: 36427151

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.


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.
PMID: 35361951

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.

Commentary – Cell – Fund Black scientists

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Fund Black scientists
Stevens KR, Masters KS, Imoukhuede PI, Haynes KA, Setton LA, Cosgriff-Hernandez E, Bell MAL, Rangamani P, Sakiyama-Elbert SE, Finley SD, Willits RK, Koppes AN, Chesler NC, Christman KL, Allen JB, Wong JY, El-Samad H, Desai TA, Eniola-Adefeso O. (2021) Cell. 184: 561-565.
PMID: 33503447

Many excellent papers have reported quantitative disparities in NIH funding awarded to Black scientists. Disparities persist even after controlling for an applicant’s education and training, country of origin, award track record, publication record, and institutional environment. The NIH would need to appropriate only ∼0.07% of its annual budget to achieve racial R01-equivalent level funding equity. In this commentary we, a nationwide group of women faculty in biomedical engineering, share actionable recommendations to dismantle funding barriers.

Commentary – Nature SMB – Chromatin engineering offers an opportunity to advance epigenetic cancer therapy

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Chromatin engineering offers an opportunity to advance epigenetic cancer therapy
Baskin NL, Haynes KA. (2019) Nature Struct Mol Biol. 26: 842-845.
PMID: 31582843

After scientists had discovered that DNA damage is linked to cancer, further research revealed an additional culprit: the misregulation of normal, undamaged genes. DNA folding is a highly regulated process in which a DNA-RNA-protein network called chromatin ensures that genes are switched on and off in the appropriate time and place. In cancer, this process often becomes misregulated to the advantage of the cancer cell, allowing cancer cells to grow unchecked, evade anti-cancer drugs, and generate new tumors. This discovery has enabled scientists to develop a new class of cancer treatment called epigenetic therapy, which targets misregulated chromatin and therefore works differently at the molecular level compared to more traditional chemotherapies (e.g. cisplatin). In our commentary we discuss how protein engineering could be used to further advance epigenetic therapy so that it is more effective against difficult-to-treat cancers.

Review – Current Opinion – Chromatin Research and Biological Engineering: An evolving relationship poised for new biomedical impacts

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Chromatin Research and Biological Engineering: An evolving relationship poised for new biomedical impacts
Haynes KA. (2019) Curr Opin Sys Biol. 14: 73-81.

Recent work at the interface of biomedical engineering and chromatin research indicates that cell engineers are approaching the biochemically complex, protein-packaged eukaryotic genome with less trepidation and greater enthusiasm. In this review article, I describe landmark discoveries (i.e., the link between cell phenotype and chromatin features, and how these features are generated and maintained) that have paved the way toward the rational design of artificial chromatin states. Synthetic systems have been used for basic research to produce mechanistic data. These data, plus information from descriptive profiling and associative studies are converging upon a new research paradigm to solve long-standing puzzles of causality. This work will enable biomedical innovations that use chromatin as a drug target and as a substrate for engineered systems.

Review – CEP – Unlocking access to DNA in chromatin

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Unlocking access to DNA in chromatin
Barrett C and Haynes KA (2018) Chemical Engineering Progress. https://www.aiche.org/resources/publications/cep/2018/september/unlocking-access-dna-chromatin

Since the early 1970’s when scientists first began using bacterial enzymes to cut purified “naked” DNA, scientists have further developed bacterial enzyme-based systems to target and edit specific DNA sequences in eukaryotic hosts, including human cells. However, DNA within eukaryotic cells is not always fully exposed. Instead, it is packed into DNA/protein complexes that form a structure called chromatin. This review highlights new technologies that have enabled scientists to better understand and manipulate the chromosomal structures that impede or enhance access to the underlying DNA.

Review – NAR – Molecular structures guide the engineering of chromatin

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Molecular structures guide the engineering of chromatin
Tekel SJ and Haynes KA (2017) Nucleic Acids Res. 45: 7555-7570.
PMID: 28609787 | PMCID: PMC5570049

Specialized proteins within the nuclei of human and other eukaryotic cells wrap DNA into a structure called chromatin. For decades, scientists have used biochemistry, genetics, and comparative evolutionary biology to understand the specific interactions and processes that guide the highly-regulated packaging of DNA into chromatin, as well as chromatin features that act to switch gene expression on and off. Basic research has enabled chromatin engineering by rational design for building new tools to further understand chromatin, and for applications such as molecular interventions of cellular disease states. This review highlights key discoveries in chromatin research and engineering efforts that have been supported by this knowledge.