Department Head | Canadian Research Chair in Interfacial Biotechnology (Tier 1)
Office: CHBE 261
Biotechnology, Genomics, Biophysics, Bioengineering and Biomolecular Engineering Applied to Biologic Drug Discovery and Manufacturing, Therapeutics Design, Cancer Diagnostics, and Affinity Ligand Discovery
University of California, Berkeley, 1991, Ph.D.
University of Texas, Austin, 1986, B.Sc.
Research interests + projects
Dr. Charles Haynes is a Professor and Tier I Canada Research Chair in Interfacial Biotechnology within the Michael Smith Laboratories, and is currently serving as Head of the Department of Chemical and Biological Engineering of the University of British Columbia.
The Haynes Lab seeks to improve understanding of the interfacial, thermodynamic and binding behavior of biomolecular and cellular systems, and to use this fundamental knowledge to invent commercial technologies, methodologies and molecules.
Research in the lab involves collaborations with engineers, pathologists, chemists, and microbiologists. This collaborative research environment mirrors the multidisciplinary nature of industrial biotechnology and provides a sound foundation for understanding the complex structures and functions of proteins and thus, promising pathways for their purification.
Current Research Projects being conducted in the Haynes Lab include:
Novel Reagents and Methods for Digital-PCR-based Cancer Diagnostics
The relatively recent commercial availability of digital PCR (dPCR) instruments and supporting technologies has led to their growing application in clinical settings, including clinical oncology, where dPCR is finding use in plasma genotyping in cancer patients undergoing treatment. As part of that larger effort, we have shown that dPCR enables accurate measurement of copy number by partitioning a PCR reaction into thousands of nanoliter-scale droplets, so that a genomic sequence of interest—whose presence or absence in a droplet is determined by end-point fluorescence—can be digitally counted. Our work includes development of dPCR methods to analyze copy number variants and somatic point mutations in genomic DNA isolated from tissue biopsy or circulation, including the design of effective assays, the optimization of reactions and unnatural priming chemistries offering greatly improved selectivity, and the interpretation of data. Representative publications from this work include:
CB Hughesman, XJD Lu, KYP Liu, Y Zhu, RM Towle, C Haynes, CF Poh. Detection of clinically relevant copy number alterations in oral cancer progression using multiplexed droplet digital PCR. Scientific reports 7 (1), 1-11.
CB Hughesman, XJD Lu, KYP Liu, Y Zhu, CF Poh, C Haynes. A robust protocol for using multiplexed droplet digital PCR to quantify somatic copy number alterations in clinical tissue specimens. PloS One. 2016; 11 (8).
R Bidshahri, D Attali, K Fakhfakh, K McNeil, A Karsan, JR Won, R Wolber, C Haynes. Quantitative detection and resolution of BRAF V600 status in colorectal cancer using droplet digital PCR and a novel wild-type negative assay. The Journal of Molecular Diagnostics 18 (2), 190-204.
Lund HL, Hughesman CB, McNeil K, Clemens S, Hocken K, Pettersson R, Karsan A, Foster LJ, Haynes C. Initial diagnosis of chronic myelogenous leukemia based on quantification of M-BCR status using droplet digital PCR. Anal Bioanal Chem. 2016; 408(4):1079-94.
Hughesman C, Fakhfakh K, Bidshahri R, Lund HL, Haynes C. A new general model for predicting melting thermodynamics of complementary and mismatched B-form DNA duplexes containing locked nucleic acids: application to probe design for digital PCR detection of somatic mutations. Biochemistry. 2015 Feb 17;54(6):1338-52.
Hi-Fi SELEX Technology – Rapid Selection of High-Affinity DNA Aptamers:
In addition to its growing use in detecting and quantifying genes and larger genomic events, the partitioning used in digital PCR can serve as a powerful tool for high-fidelity amplification of synthetic combinatorial libraries of single-stranded DNA. Sequence-diverse libraries of this type are used as a basis for selecting tight-binding aptamers against a specific target, typically by employing a directed panning procedure known as SELEX (Systematic Evolution of Ligand by Exponential Enrichment). That process suffers from a number of known limitations that can lead to its failure to discover useful high-affinity aptamers. To address this, we developed a new method, Hi-Fi SELEX, for rapid and efficient DNA aptamer selection that offers significant advantages over other aptamer selection methods in part through the use of the massive partitioning capability of digital PCR. Hi-Fi SELEX begins with the incubation of ~1014 competent aptamer library members with a target displayed on the surface of a micro-titre plate that has been neutralized and passivated against non-specific adsorption. Upon equilibration, the bound members are eluted from the target and then amplified using droplet digital PCR to restore the total quantity of library members back to ~1014. The improved ddPCR protocol can amplify any amount of retained library up to a limit of 109 unique sequences. After regenerating the ssDNA from dsDNA amplification product using λ-exonuclease catalyzed digestion, phenol/chloroform extraction is combined with membrane-assisted buffer exchange to remove enzyme and digested nucleotides to recover the desired pure ssDNA library. Representative publications from this work include:
A Ang, E Ouellet, KC Cheung, C Haynes. Highly efficient and reliable DNA aptamer selection using the partitioning capabilities of ddPCR: the Hi-Fi SELEX method. Digital PCR, Methods in Molecular Biology Series, 531-554.
Ouellet E, Foley JH, Conway EM, Haynes C. Hi-Fi SELEX: a high-fidelity digital PCR based therapeutic aptamer discovery platform. Biotechnol Bioeng. 2015 Aug;112(8):1506-22.
Ouellet E, Lagally ET, Cheung KC, Haynes CA. A simple method for eliminating fixed-region interference of aptamer binding during SELEX. Biotechnol Bioeng. 2014 Nov;111(11):2265-79.
Novel Technologies for Purifying Biologics at Analytical and Preparative Scales:
A key problem limiting the growth of biotechnology is the difficulty associated with separating these novel biomaterials from the complex aqueous solutions in which they are produced. The diversity of products in biotechnology has led to a rich pool of bioseparation processes. The common link among all bioseparation processes is that each is controlled by the physical and chemical interactions biomolecules have with each other and with their surroundings. In this context, understanding the physico-chemical properties of biomaterials and the intra- and intermolecular forces which govern their behavior in liquid solution is crucial to tailoring processes for isolating target biomolecules. One current area of research in my laboratory is concerned with the development of a new more rational approach for designing and optimizing bioseparation processes, biomaterials and diagnostic systems based on quantitatively assessing the differences in the physico-chemical properties of biomolecules and in the intermolecular forces between biomolecules, ligands and separation media. This approach has led to our development of a number of novel biopurification technologies and better methods for optimizing existing processes, our advancing of fundamental understanding of protein and oligonucleotide interactions with solid-liquid interfaces, and our development of new technologies for high-throughput functional genomics and proteomics. Representative publications from this work include:
J Coffman, B Marques, R Orozco, M Aswath, H Mohammad, …, C Haynes, RC Willson. Highland games: a benchmarking exercise in predicting biophysical and drug properties of monoclonal antibodies from amino acid sequences. Biotechnology and Bioengineering. 2020; in press, https://doi.org/10.1002/bit.27349
P Vázquez-Villegas, E Ouellet, C González, F Ruiz-Ruiz, C Haynes. A micro-device assisted approach to the preparation, characterization and selection of continuous two-phase extraction systems: from micro- to bench scale. 2017; Lab on a Chip 16 (14), 2662-2672.
DYC Choy, AL Creagh, C Haynes. Improved isoelectric focusing chromatography on strong anion exchange media via a new model that custom designs mobile phases using simple buffers. Biotechnology and Bioengineering. 2016; 111 (3), 552-564.
DYC Choy, AL Creagh, E von Lieres, C Haynes. A new mixed-mode model for interpreting and predicting protein elution during isoelectric chromatofocusing. Biotechnology and Bioengineering. 2016; 111 (5), 925-936.
Design and Characterization of Functionalized Hyper-Branched Poly-glycols for Treatment of Blood Disorders:
Hyper-branched polyglyclycerols (HPGs) are complex macromolecules comprised of about 50 – 60% dendritic structure that can be made to exhibit globular nano-forms conferring unique properties, such as low viscosity, exceptionally high solubility, and a large number of terminal functional groups that can be used to attach drug payloads, affinity ligands, etc. Due to their versatility in terms of functionalization and superb biocompatibility profiles, HPGs are proving to be a promising class of materials suitable for numerous applications in nano-medicine and biomedical technologies. Our collaboration with Dr. Kizhakkedathu (and more recently Dr. Jim Morrissey; U.Michigan) have focused on designing and characterizing complex nano-structures utilizing these chemistries to create therapeutics addressing unmet clinical needs, including universal antidotes against all heparin-based anticoagulants, a new macromolecular iron chelator for treatment of iron-overload disorders (e.g., dysmetabolic iron overload syndrome), and effective inhibitors of polyphosphates and other known poly-anionic prothrombotic agents present or shed into the cardiovasculature. My role in this has largely focused on experimental and molecular modeling studies of HPG-target interactions (binding thermodynamics and kinetics, stoichiometry, the role of participating ligands and their presentation, etc.), work that has helped to enable optimization of HPG size, ligand chemistry and spacing, etc. to realize higher affinity and selectivity toward the intended poly-anionic target. Representative publications from this work include:
MT Kalathottukaren, AL Creagh, S Abbina, G Lu, MJ Karbarz, A Pandey, PB Conley, JN Kizhakkedathu, C Haynes. Comparison of reversal activity and mechanism of action of UHRA, andexanet and PER977 on heparin and oral FXa inhibitors. Blood advances 2 (16), 2104-2114
MT Kalathottukaren, S Abbina, K Yu, RA Shenoi, AL Creagh, C Haynes, JN Kizhakkedathu. A polymer therapeutic having universal heparin reversal activity: molecular design and functional mechanism. Biomacromolecules 18 (10), 3343-3358.
A Mafi, S Abbina, MT Kalathottukaren, JH Morrissey, C Haynes, JN Kizhakkedathu, J Pfaendtner, KC Chou. Design of polyphosphate inhibitors: a molecular dynamics investigation on polyethylene glycol-linked cationic binding groups. Biomacromolecules 19 (4), 1358-1367
Shenoi RA, Kalathottukaren MT, Travers RJ, Lai BF, Creagh AL, Lange D, Yu K, Weinhart M, Chew BH, Du C, Brooks DE, Carter CJ, Morrissey JH, Haynes CA, Kizhakkedathu JN. Affinity-based design of a synthetic universal reversal agent for heparin anticoagulants. Sci Transl Med. 2014 Oct 29;6(260):260ra150.
Yu K, Creagh AL, Haynes CA, Kizhakkedathu JN. Lectin interactions on surface-grafted glycostructures: influence of the spatial distribution of carbohydrates on the binding kinetics and rupture forces. Anal Chem. 2013 Aug 20;85(16):7786-93.
Scholarly and professional activities + affiliations
Royal Society of Canada, Fellow
Canadian Academy of Engineering, Fellow