Biomedical subjects

Alissa M Weaver

Publications and source records attributed to Alissa M Weaver.

10 recordsLinked to original sources

PubMed2025

A comprehensive analysis of supermere, exomere, and extracellular vesicle isolation and cargo in colorectal cancer.

Biofluids contain a heterogeneous mixture of extracellular vesicles and non-vesicular nanoparticles (including exomeres and supermeres) that transport a diverse array of proteins, RNA, and lipids. Our previous efforts to characterize the contents of these carriers in colorectal cancer relied on 2D culture systems requiring large-scale setups and time-consuming ultracentrifugation-based isolation. To streamline this process, we have combined 3D hollow-fiber bioreactor production and fast-protein liquid chromatography-based size-exclusion chromatography. Here, we compare the impact of culture methods and purification strategies on small extracellular vesicle, exomere, and supermere cargo. Proteomic analyses show consistently distinct profiles for extracellular vesicles, exomeres, and supermeres regardless of culture conditions or isolation method. In contrast, these two variables influence small RNAs, their base modifications, and lipidomic profiles. We present an online tool to query these and future secretome datasets (https://superomics.shinyapps.io/browse).

Humans↗

PubMed2006

Tumor morphology and phenotypic evolution driven by selective pressure from the microenvironment.

Emergence of invasive behavior in cancer is life-threatening, yet ill-defined due to its multifactorial nature. We present a multiscale mathematical model of cancer invasion, which considers cellular and microenvironmental factors simultaneously and interactively. Unexpectedly, the model simulations predict that harsh tumor microenvironment conditions (e.g., hypoxia, heterogenous extracellular matrix) exert a dramatic selective force on the tumor, which grows as an invasive mass with fingering margins, dominated by a few clones with aggressive traits. In contrast, mild microenvironment conditions (e.g., normoxia, homogeneous matrix) allow clones with similar aggressive traits to coexist with less aggressive phenotypes in a heterogeneous tumor mass with smooth, noninvasive margins. Thus, the genetic make-up of a cancer cell may realize its invasive potential through a clonal evolution process driven by definable microenvironmental selective forces. Our mathematical model provides a theoretical/experimental framework to quantitatively characterize this selective pressure for invasion and test ways to eliminate it.

Adaptation, Physiological↗

PubMed2006

Invadopodia: specialized cell structures for cancer invasion.

The spread of cancer cells to distant sites in the body is the major cause of cancer patient death. Growing evidence connects specialized subcellular structures, invadopodia, to cancer invasion and metastasis. Invadopodia, or invasive foot processes, are actin-rich protrusions that localize matrix-degrading activity to cell-substratum contact points and represent sites where cell signaling, proteolytic, adhesive, cytoskeletal, and membrane trafficking pathways physically converge. Understanding how invadopodia form and function should aid in the identification of novel targets for anti-invasive therapy.

Actins↗

PubMed2005

Cortactin promotes cell motility by enhancing lamellipodial persistence.

BACKGROUND: Lamellipodial protrusion, which is the first step in cell movement, is driven by actin assembly and requires activity of the Arp2/3 actin-nucleating complex. However, it is unclear how actin assembly is dynamically regulated to support effective cell migration. RESULTS: Cells deficient in cortactin have impaired cell migration and invasion. Kymography analyses of live-cell imaging studies demonstrate that cortactin-knockdown cells have a selective defect in the persistence of lamellipodial protrusions. The motility and protrusion defects are fully rescued by cortactin molecules, provided both the Arp2/3 complex and F-actin binding sites are intact. Consistent with this requirement for simultaneous contacts with Arp2/3 and F-actin, cortactin is recruited by Arp2/3 complex to lamellipodia and binds with a higher affinity to ATP/ADP-Pi-F-actin than to ADP-F-actin. In situ labeling of lamellipodia revealed that the relative levels of free barbed ends of actin filaments are reduced by over 30% in the cortactin-knockdown cells; however, there is no change in Arp2/3-complex localization to lamellipodia. Cortactin-knockdown cells also have a selective defect in the assembly of new adhesions in protrusions, as assessed by analysis of GFP-paxillin dynamics in living cells. CONCLUSIONS: Cortactin enhances lamellipodial persistence, at least in part through regulation of Arp2/3 complex. The presence of cortactin also enhances the rate of new adhesion formation in lamellipodia. In vivo, these functions may be important during directed cell motility.

Actin-Related Protein 2↗

PubMed2005

Mathematical modeling of cancer: the future of prognosis and treatment.

BACKGROUND: Cancer research has undergone radical changes in the past few years. Producing information both at the basic and clinical levels is no longer the issue. Rather, how to handle this information has become the major obstacle to progress. Intuitive approaches are no longer feasible. The next big step will be to implement mathematical modeling approaches to interrogate the enormous amount of data being produced and extract useful answers (a "top-down" approach to biology and medicine). METHODS: Quantitative simulation of clinically relevant cancer situations-based on experimentally validated mathematical modeling-provides an opportunity for the researcher, and eventually the clinician, to address data and information in the context of well-formulated questions and "what if" scenarios. RESULTS AND CONCLUSIONS: At the Vanderbilt Integrative Cancer Biology Center (VICBC), we are integrating cancer researchers, oncologists, chemical and biological engineers, computational biologists, computer modelers, theoretical and applied mathematicians, and imaging scientists, in order to implement a vision for a combined web site and computational server that will be a home for our mathematical modeling of cancer invasion. The web site (www.vanderbilt.edu/VICBC/) will serve as a portal to our code, which simulates tumor growth by calculating the dynamics of individual cancer cells (an experimental "bottom-up" approach to complement the top-down model). Eventually, cancer researchers outside of Vanderbilt will be able to initiate a simulation based on providing individual cell data through a web page. We envision placing the web site and computer cluster directly in the hands of biological researchers involved in data mining and mathematical modeling. Furthermore, the web site will also contain teaching props for a new generation of biomedical researchers fluent in both mathematics and biology. This is unconventional bioinformatics: We will be incorporating biological data and functional information into a unified community-based mathematical framework. The result will be a tool for cancer modeling that will ultimately have basic research, therapeutic and educational value.

Animals↗

PubMed2005

Cytoskeletal interactions with the outside world.

Cell motility depends on the conversion of extracellular cues into intracellular cytoskeletal responses. A recent Keystone meeting on cell migration and adhesion showcased advances in the field.

Animals↗

PubMed2004

CAS promotes invasiveness of Src-transformed cells.

CAS ('Crk-associated substrate') is an Src substrate found at sites of integrin-mediated cell adhesion and linked to cell motility and survival. In this study, the involvement of CAS in oncogenic transformation was evaluated through analysis of mouse embryo fibroblast populations expressing an activated Src mutant, either in the presence or absence of CAS expression. CAS was not found to be a critical determinant of either Src-mediated morphologic transformation or anchorage-independent growth. However, CAS had a profound effect on other aspects of oncogenic Src function. CAS expression led to a substantial increase in the phosphotyrosine content of FAK and paxillin, supporting a role for CAS as a positive regulator of Src activity at integrin adhesion sites. Importantly, CAS expression resulted in a striking enhancement of the capacity of Src-transformed cells to invade through Matrigel. The increased invasiveness was associated with increased activation of matrix metalloproteinase MMP-2 and formation of large actin-rich podosomal aggregates appearing as ring and belt structures. Thus, elevated CAS-associated tyrosine phosphorylation signaling events occurring at sites of integrin-mediated cell adhesion can have a major role in the development of an invasive cell phenotype.

Animals↗

PubMed2003

Cortactin interacts with WIP in regulating Arp2/3 activation and membrane protrusion.

BACKGROUND: Modulation of actin cytoskeleton assembly is an integral step in many cellular events. A key regulator of actin polymerization is Arp2/3 complex. Cortactin, an F-actin binding protein that localizes to membrane ruffles, is an activator of Arp2/3 complex. RESULTS: A yeast two-hybrid screen revealed the interaction of the cortactin Src homology 3 (SH3) domain with a peptide fragment derived from a cDNA encoding a region of WASp-Interacting Protein (WIP). GST-cortactin interacted with WIP in an SH3-dependent manner. The subcellular localization of cortactin and WIP coincided at the cell periphery. WIP increased the efficiency of cortactin-mediated Arp2/3 complex activation of actin polymerization in a concentration-dependent manner. Lastly, coexpression of cortactin and WIP stimulated membrane protrusions. CONCLUSIONS: WIP, a protein involved in filopodia formation, binds to both actin monomers and cortactin. Thus, recruitment of actin monomers to a cortactin-activated Arp2/3 complex likely leads to the observed increase in cortactin activation of Arp2/3 complex by WIP. These data suggest that a cortactin-WIP complex functions in regulating actin-based structures at the cell periphery.

Actin-Related Protein 2↗

PubMed2003

Integration of signals to the Arp2/3 complex.

The Arp2/3 complex is necessary for nucleating the formation of branched networks of actin filaments at the cell cortex, and an increasing number of proteins able to activate the Arp2/3 complex have been described. The Wiskott-Aldrich syndrome protein (WASP) family and cortactin comprise the large majority of the known activators. WASPs bind to Arp2/3 via an acidic (A) domain, and a WH2 domain appears to bring an actin monomer to Arp2/3, promoting the nucleation of the new filament. Cortactin also binds the Arp2/3 complex via an A domain; however, it also binds to actin filaments, which helps activate the Arp2/3 complex and stabilise the newly created branches between the filaments.

Actin Cytoskeleton↗

PubMed2002

Interaction of cortactin and N-WASp with Arp2/3 complex.

BACKGROUND: Dynamic actin assembly is required for diverse cellular processes and often involves activation of Arp2/3 complex. Cortactin and N-WASp activate Arp2/3 complex, alone or in concert. Both cortactin and N-WASp contain an acidic (A) domain that is required for Arp2/3 complex binding. RESULTS: We investigated how cortactin and the constitutively active VCA domain of N-WASp interact with Arp2/3 complex. Structural studies showed that cortactin is a thin, elongated monomer. Chemical crosslinking studies demonstrated selective interaction of the Arp2/3 binding NTA domain of cortactin (cortactin NTA) with the Arp3 subunit and VCA with Arp3, Arp2, and ARPC1/p40. Cortactin NTA and VCA crosslinking to the Arp3 subunit were mutually exclusive; however, cortactin NTA did not inhibit VCA crosslinking to Arp2 or ARPC1/p40, nor did it inhibit activation of Arp2/3 complex by VCA. We conducted an experiment in which a saturating concentration of cortactin NTA modestly lowered the binding affinity of VCA for Arp2/3; the results of this experiment provided further evidence for ternary complex formation. Consistent with a common binding site on Arp3, a saturating concentration of VCA abolished binding of cortactin to Arp2/3 complex. CONCLUSIONS: Under certain circumstances, cortactin and N-WASp can bind simultaneously to Arp2/3 complex, accounting for their synergy in activation of actin assembly. The interaction of cortactin NTA with Arp2/3 complex does not inhibit Arp2/3 activation by N-WASp, despite competition for a common binding site located on the Arp3 subunit. These results suggest a model in which cortactin may bridge Arp2/3 complex to actin filaments via Arp3 and N-WASp activates Arp2/3 complex by binding Arp2 and/or ARPC1/p40.

Actin-Related Protein 2↗