In a recent poster presentation, Rory Staunton of Arizona State University and his colleagues compare the physiology of normal and cancerous cells, observing intriguing distinctions that may be used to improve diagnosis and treatment of deadly disease.

The poster was presented on April 5th, for the Physical Sciences-Oncology Center’s Network Investigators Meeting, held in National Harbor, Maryland. Staunton’s effort was subsequently rewarded by judges at the conference and selected as one of three outstanding poster presentations from the 70 entrants displayed at the meeting.

Staunton, a first year graduate student studying experimental nanobiophysics in professor Robert Ros’ lab at the Center for Biological Physics, explores the mechanical properties of cells. He explains that such properties offer valuable clues to cellular physiology, behavior and critically, the potential for the cells to metastasize. By examining cells with a physicist’s eye, researchers like Staunton hope to better understand the behavior and trajectory of these cells in ways not possible through a purely biology-based approach.

The work is part of an ambitious, multi-institute consortium devoted to a fresh approach to cancer study, using materials and techniques common to the physical sciences. The Physical Sciences-Oncology Center (PSOC) initiative involves Arizona State University, in conjunction with 11 other institutions, receiving $22.7 million in initial funding from the National Institutes of Health’s National Cancer Institute.

To investigate the mechanical properties of cancer cells, Staunton measures these cells using a combined atomic force microscope and confocal laser scanning microscope (AFM/CLSM), with fluorescence lifetime imaging (FLIM).  The AFM is used to indent the cells in order to determine the Young’s modulus, a quantitative measure of a material’s stiffness. The CLSM is used to optically image the cells in order to see how stiffness varies in regions near different subcellular structures like the nucleus.  FLIM is a technique that exploits differences that arise in the decay rates of fluorescent dyes in differing conditions (such as pH or ion concentration) to learn more about the local environment inside the cells.  Future experiments will take advantage of fluorescence for detailed study of specific proteins involved in cell mechanics.

Results of Staunton’s research confirm earlier findings indicating that the nuclei of cancer cells are softer in texture than normal cells and display greater elasticity. Staunton stresses the importance of examining cells in an environment that better approximates their normal conditions in the body than in traditional microscopy studies. Rather than existing as isolated entities, cells are enmeshed in a network of fibers and proteins known as the extracellular matrix or ECM. “Not only do cells push and pull against the ECM and their neighbors within it, but they use it as a ‘telephone’ to send signals to other cells and as a ‘refrigerator’ to store nutrients for later,” Staunton said.

The subtle relationships between cells and the ECM they inhabit were examined in the current study by means of specialized techniques known as force spectroscopy and time-resolved fluorescence microscopy. Distinctions were observed in the response to indentation of the cancerous cells, compared with their normal counterparts. Staunton’s poster shows raw AFM data of force-distance plots. A tell-tale “scimitar” shape observed in cancer cells is not seen in normal cells, a point meriting further investigation.  Staunton hopes continued research will explore these findings in greater detail. “Everyone working in this field that we’ve talked to about our project has been enthusiastic about the potential of our techniques to shine light on some unanswered questions in cancer biology. Moving from 2D to 3D environments is definitely the way to go.”

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Source: http://www.biodesign.asu.edu/news/soft-cell-new-research-into-the-physics-of-cancer

Written by Richard Harth
Biodesign Institute Science Writer
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Atomic Force Microscopy(ATM) Workshop April 15-16 2010.

Facilitators: Stuart Lindsay and Robert Ros

Location: Agilent, Chandler and ASU campus, Tempe.
This workshop welcomed 10 scientists from Northwestern PSOC, Oregon Health Sciences Center, University of Texas and Arizona State University to be trained in scanning probe theory and practice.

Day 1:
Morning lectures in AFM theory and applications at Agilent Technologies in Chandler, Arizona http://www.home.agilent.com/
Afternoon: Hands-on training at Agilent

Day 2:
All day in lab receiving hands-on experience in the labs of Dr Robert Ros in physics and Dr Stuart Lindsay in Biodesign, Arizona State University.

Agenda | Attendees

Out of 70 posters at the conference, Jack ‘Rory’ Staunton’s poster entitled ‘Development of a Method for Quantitative Mechanical Nanotomography of Cells Embedded in 3D Matrixes’ was one of 3 to receive an award. In his poster, Rory presented some preliminary results that confirm previous indications that cancer cells are softer than their normal counterparts, and also provided some new observations about the raw AFM data (i.e., the different shapes of the force distance curves). The observations demonstrate the need for the development of new data analysis methods, and hopefully their subsequent adoption by others in the field. As part of the award, Rory received a 405 nm laser pointer that is already being put to good use in the lab while installing some new optical equipment.

Rory is a first year graduate student studying Experimental Nanobiophysics in Dr Robert Ros’ lab in the Center for Biological Physics. He is investigating the mechanical properties of cancer cells using a combined atomic force microscope and confocal laser scanning microscope (AFM/CLSM) with fluorescence lifetime imaging (FLIM). Congratulations Rory!

Rory Annual Meeting Poster (54×40) (png)

Rory Annual Meeting Poster (54×40) (pdf)

(click slide to view video)

NOTE: This excellent seminar talk is approximately 1 hour. We were unable to record audio between the start of the talk 0” -4’42” and again between 10’48” – 13’28”. For completeness, we have kept in the slides where the audio is lacking. We recommend that you start to watch at 4’42” and skip the later break in the audio.

Speaker: Michael Barrett, Ph.D., Unit Head, Oncogenomics Laboratory at TGen

Date & Time: April 8th, 2010 12:00 p.m.

Title: Clonal Analyses and Clinical Behaviors of Human Cancer

Abstract:

Clonal Analyses and Clinical Behaviors of Human Cancer

Cancer, in general, is thought to evolve from natural selection of cells within a neoplasm. While this hypothesis is still being refined, it is widely accepted that competition amongst neoplastic clones, coupled with genetic changes and environment, are integral to cancer. Genomic instability appears to cooperate with Darwinian selection to promote cancer formation through a process in which genomic aberrations occur at accelerated rates, and those alterations that provide a selective growth advantage lead to clonal evolution and expansion. The fundamental hypothesis of our studies is that cancers consist of heterogeneous populations that can rapidly respond to stress (e.g. cytotoxic therapies) by exploiting fundamental principles of evolution. These behaviors are of major clinical significance for both primary and metastatic cancers where distinct clonal populations of tumor cells with variable evolutionary fitness are dispersed to multiple sites within a patient. Our long-range objective is to develop new therapeutic options for patients with cancer including advanced metastatic pancreatic ductal adenocarcinoma (PDA).Towards this goal we are using flow cytometric sorting strategies to identify and purify diploid and aneuploid cell populations in each sample of interest. These then are comprehensively profiled with high resolution genomic tools to define clinical contexts in each patient. Genes associated with pathways disrupted by selected clonal aberrations in neoplastic genomes in vivo can then be functionally interrogated in RNAi-based assays to evaluate their potential as therapeutic targets. Validated “hits” that target genes essential for the evolution, maintenance, or persistence of neoplastic cell lineages represent highly favorable candidates for improved therapeutic strategies. I will discuss some of our recent findings in PDA genomes and the role of clonal behaviors in mediating therapeutic responses.

Authors: Sebastian A Sandersius1 and Timothy J Newman1,2

Abstract:
Recently, the Subcellular Element Model (SEM) has been introduced, primarily to compute the dynamics of large numbers of three-dimensional deformable cells in multicellular systems. Within this model framework, each cell is represented by a collection of elastically coupled elements, interacting with one another via short-range potentials, and dynamically updated using over-damped Langevin dynamics. The SEM can also be used to represent a single cell in more detail, by using a larger number of subcellular elements exclusively identified with that cell. We have tested whether, in this context, the SEM yields viscoelastic properties consistent with those measured on single living cells. Employing virtual methods of bulk rheology and microrheology we find that the SEM successfully captures many cellular rheological properties at intermediate time scales and moderate strains, including weak power law rheology. In its simplest guise, the SEM cannot describe long-time/large-strain cell responses. Capturing these cellular properties requires extensions of the SEM which incorporate active cytoskeletal rearrangement. Such extensions will be the subject of a future publication.

Modeling cell rheology with the Subcellular Element Model (pdf)

Author: T. J. Newman

Abstract:
We introduce a model for describing the dynamics of large numbers of interacting cells. The fundamental dynamical variables in the model are sub-cellular elements, which interact with each other through phenomenological intra- and intercellular potentials. Advantages of the model include: i) adaptive cell-shape dynamics, ii) flexible accommodation of additional intracellular biology, and iii) the absence of an underlying grid. We present here a detailed description of the model, and use successive mean-¯eld approximations to connect it to more coarse-grained approaches, such as discrete cell-based algorithms and coupled partial differential equations. We also discuss efficient algorithms for encoding the model, and give an example of a simulation of an epithelial sheet. Given the biological flexibility of the model, we propose that it can be used effectively for modeling a range of multicellular processes, such as tumor dynamics and embryogenesis.

Modeling Multicellular systems using sub-cellular elements (pdf)

Speaker: Carlo Maley, Ph.D., Assistant Professor, Molecular and Cellular Oncogenesis Program, Systems Biology Division, The Wistar Institute

Location: Biodesign Auditorium

Date & Time: March 31, 2010 7:30 p.m.

Title: Why we get cancer and why it has been so hard to cure.

Abstract: The story of cancer begins approximately 1 billion years ago, with the rise of multicellular organisms. Before that point, there was no cancer. Afterwards, cancer was the central problem threatening the integrity of the body. Cancer has become a particular problem in developed countries. In the U.S., men have a 45% and women a 38% lifetime risk of developing cancer. Despite the enormous progress we have made in technology and medicine in the last 50 years, we have made almost no progress reducing deaths from cancer, even when we take into account changes in lifespan.

Why is cancer such a difficult problem to solve? Because cells in tumors evolve. Tumor cells mutate a high rates and compete for space and resources like oxygen. Mutant cells that can reproduce or survive better than their competitors tend to spread in a tumor. Thus, tumors are microcosms of natural selection. By the time we detect a tumor in the clinic, it contains billions of cells carrying tens of thousands of mutations. By chance, some of those mutant cells are often resistant to the anti-cancer drugs we use. The result is temporary remission followed by relapse with a resistant tumor. Therapeutic resistance is so common that attention has recently switched to detecting cancer early in its development when it is still easy to cut out, or preventing cancer altogether.

Carlo’s Biosketch: Carlo Maley is an assistant professor in the systems biology division of the molecular and cellular oncogenesis program at the Wistar Institute and part of the Seattle Barrett’s Esophagus Research Program. He is a member of the University of Pennsylvania genomics and computational biology graduate program as well as the cellular and molecular biology graduate program. He received an M.Sc. degree from the University of Oxford, studying evolutionary biology with W.D. Hamilton. He earned his Ph.D. in computational biology from MIT, working with Rodney Brooks and Michael Donoghue, and then moved into cancer biology as a postdoc with Stephanie Forrest at the University of New Mexico and as a staff scientist with Brian Reid at the Fred Hutchinson Cancer Research Center. His research lies at the intersection of evolutionary biology, computational biology and cancer biology and includes both dry lab (computational) and wet lab (genetics of tumors and evolutionary tissue culture experiments) projects. He is interested in how cells evolve in neoplastic progression and in response to therapy with the goal of controlling that evolution to prevent cancer and therapeutic resistance.

(click slide to view video)

25th March 2010

Speaker: Kimberly J. Bussey, Ph.D., Associate Investigator in the Clinical Translational Research Division, Lead Investigator of the Adrenocortical Carcinoma (ACC) Research Program at TGen

Title: The role of Bioinformatics in teasing apart epigenetics in cancer

Abstract:
The epigenome refers to heritable and reversible marks in the genome that do not result from changes in DNA sequence. These include modifications of DNA and/or histones such as methylation, acetylation, sumolation, and ubiquitination, as well as the region-specific incorporation of variant histone proteins. Recent work has highlighted the importance of the epigenome in regulating gene expression and contributing to phenotypic heterogeneity. The number and types of data being generated to look at various aspects of the epigenome is rapidly expanding and requires the adaptation of existing bioinformatics approaches or more commonly the development of new approaches. We will discuss where the field of epigenomics is currently, both experimentally and bioinformatically, and what questions need to be addressed, particularly as they relate to cancer.

Kim’s Biosketch: Dr. Bussey received her B.S. in general biology from the University of Arizona. She received her Ph.D. in Molecular and Medical Genetics from Oregon Health Sciences University where her dissertation research focused on the cytogenetic and molecular characterization of pediatric germ cell tumors, a group of rare tumors in children. Prior to coming to TGen as an Associate Investigator and Lead Investigator for the ACC Research Program, she did a post-doctoral fellowship and worked as a contract scientist with John Weinstein, M.D., Ph.D. and the Genomics and Bioinformatics lab in the Laboratory of Molecular Pharmacology at the NCI. Her work there focused on integrative analysis of array CGH data and expression data in the NCI60 and development of computational tools to facilitate such analyses.

• Interview with Scott McRae

  Matthew Wilson, a student in the Hugh Downs School of Human Communication interviews fellow undergraduate Scott McRae, who makes videos about the physical sciences and cancer projects at ASU.

  Audio clip: Adobe Flash Player (version 9 or above) is required to play this audio clip. Download the latest version here. You also need to have JavaScript enabled in your browser.

Automated Selection and Placement of Single Cells Using Vision-Based Feedback Control

We present a robotic manipulation system for automated selection and transfer of individual living cells to analysis locations. We begin with a commonly used cell transfer technique using glass capillary micropipettes to aspirate and release living cells suspended in liquid growth media. Using vision-based feedback and closed-loop process control, two individual three-axis robotic stages position the micropipette tip in proximity to the cell of interest. The cell is aspirated and the tip is moved to a target location where the cell is dispensed. Computer vision is used to monitor and inspect the success of the dispensing process. In our initial application, the target cell destination is a microwell etched in a fused silica substrate. The system offers a robust and flexible technology for cell selection and manipulation. Applications for this technology include embryonic stem cells transfer, blastomere biopsy, cell patterning, and cell surgery.