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Mechanogenomic Control of DNA Exposure and Sequestration

  • Gary S. Stein
    Correspondence
    Address reprint requests to Gary Stein, Department of Cell Biology, University of Massachusetts Medical School, 55 Lake Ave. North, Worcester, MA 01655
    Affiliations
    University of Massachusetts Medical School, Worcester, Massachusetts
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      There is longstanding recognition and appreciation for striking differences in the structure, assembly and organization of regulatory machinery in normal and cancer cells. Drawings from 100 years ago of Galeotti's comparisons of cancer cell and normal cell chromosomes illustrated gross differences in chromatin structure and chromosome numbers in human tissue harboring a tumor.
      • Wilson EB
      Pathological mitosis in cancer cells.
      Tumor-related perturbations in nuclear structure-function interrelationships are well documented by prominent perturbations in the size and number of nucleoli, indicating the reconfiguration of the nuclear infrastructure that supports ribosomal gene expression and consequently protein biosynthesis. However, how higher order chromatin structure is controlled and maintained by the cancer cell and its microenvironment, compared to normal cells, has remained beyond our reach. The work presented by Maniotis et al
      • Maniotis AJ
      • Valyi-Nagy K
      • Karavitis J
      • Moses J
      • Boddipali V
      • Wang Y
      • Nuñez R
      • Setty S
      • Arbieva Z
      • Bissell MJ
      • Folberg R
      Chromatin organization measured by Alu I restriction enzyme changes with malignancy and is regulated by the extracellular matrix and the cytoskeleton.
      in this issue of The American Journal of Pathology shows there are striking differences in restriction enzyme sensitivity between tumor cell and normal cell genomes. Furthermore, Maniotis et al propose that the mechanical contiguity and coordination of nuclear proteins bound to DNA, the cytoskeleton, and the extracellular matrix (ECM) may work in concert to provide a cytoarchitectural resistance mechanism deep within the cell. When verified in other laboratories, these findings may constitute the basis for a paradigm shift in the way we view how the genomes of higher eukaryotic cells, and malignant cells in particular, are regulated.
      By using DNase digestions and nick-end labeling techniques, a previous generation of tumor biologists had established that in order for a gene to become expressed, it had to be “exposed.” Moreover, Puck et al
      • Puck TT
      • Krystosek A
      • Chan DC
      Genome regulation in mammalian cells.
      had shown that transformed and tumor cells that were “reverse transformed” to a normal phenotype with various chemical compounds exhibited a shift in their nuclei's sensitivity to DNase I, and exhibited profound changes in their cytoskeletons and overall morphology.
      Maniotis et al
      • Maniotis AJ
      • Valyi-Nagy K
      • Karavitis J
      • Moses J
      • Boddipali V
      • Wang Y
      • Nuñez R
      • Setty S
      • Arbieva Z
      • Bissell MJ
      • Folberg R
      Chromatin organization measured by Alu I restriction enzyme changes with malignancy and is regulated by the extracellular matrix and the cytoskeleton.
      have compared the extent of exposure or sequestration of a well-characterized collection of highly invasive, poorly invasive, and normal human cell genomes to digestion by specific restriction enzymes. Restriction enzyme digests performed on intact nuclei, not treated with any other chemical agents, showed that AluI and MspI both distinguished normal cell genomes from tumor cell genomes. For example, highly invasive cell nuclei always resisted digestion with AluI and MspI compared to poorly invasive or normal cells in permeabilized cell models, in cell smear preparations, in suspended cells using flow cytometry, and in touch preps of human tissue. Specificity is suggested because other restriction enzymes did not discriminate among normal or tumor cell genomes.
      Differences in Alu site exposure were shown to be independent of the cell cycle, as shown by comparing digestions of complete sets of mitotic chromosomes
      • Maniotis AJ
      • Bojanowski K
      • Ingber DE
      Mechanical continuity and reversible chromosome disassembly within intact genomes removed from living cells.
      • Bojanowski K
      • Maniotis AJ
      • Plisov S
      • Larsen AK
      • Ingber DE
      DNA topoisomerase II can drive changes in higher order chromosome architecture without enzymatically modifying DNA.
      with digestions of interphase nuclei from the same cell types. Taken together with other restriction sites that exhibit cell cycle-stage specific accessibility
      • Chrysogelos S
      • Riley DE
      • Stein G
      • Stein J
      A human histone H4 gene exhibits cell cycle-dependent changes in chromatin structure that correlate with its expression.
      • Chrysogelos S
      • Pauli U
      • Stein G
      • Stein J
      Fine mapping of the chromatin structure of a cell cycle-regulated human H4 histone gene.
      • Stein G
      • Park W
      • Thrall C
      • Mans R
      • Stein J
      Regulation of cell cycle stage-specific transcription of histone genes from chromatin by non-histone chromosomal proteins.
      it appears that there are both conserved and transient components of chromatin organization that must be accommodated during the cell cycle period. It is necessary to mechanistically explain parameters of mitotic chromosome condensation that are independent from the sequestration of restriction sites along the DNA, and the observation that nuclear matrix-associated AML
      • Zaidi SK
      • Young DW
      • Pockwinse SH
      • Javed A
      • Lian JB
      • Stein JL
      • van Wijnen AJ
      • Stein GS
      Mitotic partitioning and selective reorganization of tissue specific transcription factors in progeny cells.
      • Young DW
      • Zaidi SK
      • Furcinitti PS
      • Javed A
      • van Wijnen AJ
      • Stein JL
      • Lian JB
      • Stein GS
      Quantitative signature for architectural organization of regulatory factors using intranuclear informatics.
      • Zeng C
      • van Wijnen AJ
      • Stein JL
      • Meyers S
      • Sun W
      • Shopland L
      • Lawrence JB
      • Penman S
      • Lian JB
      • Stein GS
      • Hiebert SW
      Identification of a nuclear matrix targeting signal in the leukemia and bone-related AML/CBFα transcription factors.
      and ALL
      • Ennas MG
      • Sorio C
      • Greim R
      • Nieddu M
      • Scarpa A
      • Orlandini S
      • Croce CM
      • Fey GH
      • Marschalek R
      The human ALL-1/MLL/HRX antigen is predominantly localized in the nucleus of resting and proliferating peripheral blood mononuclear cells.
      • Nakamura T
      • Mori T
      • Tada S
      • Krajewski W
      • Rozovskaia T
      • Wassell R
      • Dubois G
      • Mazo A
      • Croce CM
      • Canaani E
      ALL-1 is a histone methyltransferase that assembles a supercomplex of proteins involved in transcriptional regulation.
      phenotype-restricted transcription factors, as well as UBF-1
      • Gebrane-Younes J
      • Fomproix N
      • Hernandez-Verdun D
      When rDNA transcription is arrested during mitosis, UBF is still associated with non-condensed rDNA.
      remain on target gene loci during mitosis. New models are required to explain higher order chromatin structure more comprehensively. Such models should account for components of cell cycle-driven chromatin condensation that are operative independent of how specific restriction enzyme sites are cryptic or exposed in highly invasive, poorly invasive, and normal cells.
      Experiments were also presented in the study that showed exposure of chromatin or chromosomes to DTT or β-mercaptoethanol rendered highly invasive and sequestered cell genomes sensitive to AluI. This suggests that proteins rich in disulfide bonds are involved in the sequestration phenomenon in highly invasive cell nuclei. Enzymes or reagents that remove histones or topoisomerases
      • Bojanowski K
      • Maniotis AJ
      • Plisov S
      • Larsen AK
      • Ingber DE
      DNA topoisomerase II can drive changes in higher order chromosome architecture without enzymatically modifying DNA.
      did not discriminate among genomes tested from different cell types. These observations are consistent with the idea that alterations in higher order chromatin structure and may, in part, be controlled by disulfide-rich nuclear matrix proteins,
      • Berezney R
      • Coffey DS
      Nuclear protein matrix: association with newly synthesized DNA.
      • Capco DG
      • Wan KM
      • Penman S
      The nuclear matrix: three-dimensional architecture and protein composition.
      • Pienta KJ
      • Coffey DS
      A structural analysis of the role of the nuclear matrix and DNA loops in the organization of the nucleus and chromosome.
      • Nickerson JA
      • Krockmalnic G
      • Wan KM
      • Turner CD
      • Penman S
      A normally masked nuclear matrix antigen that appears at mitosis on cytoskeleton filaments adjoining chromosomes, centrioles and midbodies.
      • Mancini MA
      • He D
      • Ouspenski II
      • Brinkley BR
      Dynamic continuity of nuclear and mitotic matrix proteins in the cell cycle.
      • Roti Roti JL
      • Wright WD
      • VanderWaal R
      The nuclear matrix: a target for heat shock effects and a determinant for stress response.
      • Stein GS
      • Roberts RM
      • Davis JL
      • Head WJ
      • Stein JL
      • Thrall CL
      • Van Veen J
      • Welch DW
      Are glycoproteins and glycosaminoglycans components of the eukaryotic genome?.
      which orchestrate widespread changes in restriction enzyme site exposure and sequestration. However, these digestion experiments also suggest that the disulfide-rich nuclear matrix cannot be a static or fixed structure, which is consistent with current models of chromatin structure and higher order nuclear organization of gene regulatory machinery in nuclear matrix-associated microenvironments that support combinatorial control of gene expression by dynamic, physiologically responsive targeting and retention mechanisms.
      • Stein GS
      • Montecino M
      • van Wijnen AJ
      • Stein JL
      • Lian JB
      Nuclear structure - gene expression interrelationships: implications for aberrant gene expression in cancer.
      • Zaidi SK
      • Young DW
      • Choi JY
      • Pratap J
      • Javed A
      • Montecino M
      • Stein JL
      • Lian JB
      • van Wijnen AJ
      • Stein GS
      Intranuclear trafficking: organization and assembly of regulatory machinery for combinatorial biological control.
      • Stein GS
      • Zaidi SK
      • Braastad CD
      • Montecino M
      • van Wijnen AJ
      • Choi J-Y
      • Stein JL
      • Lian JB
      • Javed A
      Functional architecture of the nucleus: organizing the regulatory machinery for gene expression, replication and repair.
      • Zink D
      • Fischer AH
      • Nickerson JA
      Nuclear structure in cancer cells.
      • Misteli T
      The concept of self-organization in cellular architecture.
      • Olson MO
      • Hingorani K
      • Szebeni A
      Conventional and nonconventional roles of the nucleolus.
      • Spencer VA
      • Davie JR
      Signal transduction pathways and chromatin structure in cancer cells.
      • Stachowiak MK
      • Fang X
      • Myers JM
      • Dunham SM
      • Berezney R
      • Maher PA
      • Stachowiak EK
      Integrative nuclear FGFR1 signaling (INFS) as a part of a universal “feed-forward-and-gate” signaling module that controls cell growth and differentiation.
      • Taatjes DJ
      • Marr MT
      • Tjian R
      Regulatory diversity among metazoan co-activator complexes.
      • Kosak ST
      • Groudine M
      Gene order and dynamic domains.
      • DeFranco DB
      Navigating steroid hormone receptors through the nuclear compartment.
      • Nagaich AK
      • Rayasam GV
      • Martinez ED
      • Becker M
      • Qiu Y
      • Johnson TA
      • Elbi C
      • Fletcher TM
      • John S
      • Hager GL
      Subnuclear trafficking and gene targeting by steroid receptors.
      • Phair RD
      • Scaffidi P
      • Elbi C
      • Vecerova J
      • Dey A
      • Ozato K
      • Brown DT
      • Hager G
      • Bustin M
      • Misteli T
      Global nature of dynamic protein-chromatin interactions in vivo: three-dimensional genome scanning and dynamic interaction networks of chromatin proteins.
      Because digestions of DNA in nuclei of normal cells with AluI and MspI appear to additionally separate nucleoli from structural components of the nucleus, it appears that the DNA within normal cell chromatin, when it is not digested, may impose constraints that contribute to the architectural organization of intranuclear structure. Maniotis’ case
      • Maniotis AJ
      • Valyi-Nagy K
      • Karavitis J
      • Moses J
      • Boddipali V
      • Wang Y
      • Nuñez R
      • Setty S
      • Arbieva Z
      • Bissell MJ
      • Folberg R
      Chromatin organization measured by Alu I restriction enzyme changes with malignancy and is regulated by the extracellular matrix and the cytoskeleton.
      for DNA as a principal scaffolding on which nuclear proteins are bound, and not vice versa, is consistent with his previous observations of nuclease digestions of microsurgically isolated mitotic chromosomes derived from normal endothelial cells and fibroblasts,
      • Maniotis AJ
      • Bojanowski K
      • Ingber DE
      Mechanical continuity and reversible chromosome disassembly within intact genomes removed from living cells.
      and is supported by his observation that complete chromosome sets are produced as intact genomes from both normal mitotic cells and mitotic tumor cells via microsurgical removal of any single chromosome.
      • Maniotis AJ
      • Bojanowski K
      • Ingber DE
      Mechanical continuity and reversible chromosome disassembly within intact genomes removed from living cells.
      • Bojanowski K
      • Maniotis AJ
      • Plisov S
      • Larsen AK
      • Ingber DE
      DNA topoisomerase II can drive changes in higher order chromosome architecture without enzymatically modifying DNA.
      Reversal of the relative insensitivity of chromatin of highly invasive cells to AluI by disulfide-disrupting agents suggests that the sensitivity of invasive nuclei to AluI and disulfide-rich protein disruption may be due to increased representation of these disulfide-rich proteins, or may suggest that there is a higher affinity of these proteins for the DNA of highly invasive cells. Further work is needed to determine whether nicking the DNA with AluI leads to discontinuities along the DNA, which in turn permits DNA supercoiling to unravel sufficiently to dissociate the disulfide-rich proteins from the DNA throughout the genome, and allow complete digestion to occur.
      There is a requirement to characterize the nuclear matrix disulfide-rich proteins that may be facilitating architecturally linked control of gene expression. Equally important is the necessity to relate the involvement of DNA as a scaffold for control of gene expression that differs in normal and cancer cells with the growing evidence for autologous intranuclear trafficking of regulatory proteins
      • Zeng C
      • van Wijnen AJ
      • Stein JL
      • Meyers S
      • Sun W
      • Shopland L
      • Lawrence JB
      • Penman S
      • Lian JB
      • Stein GS
      • Hiebert SW
      Identification of a nuclear matrix targeting signal in the leukemia and bone-related AML/CBFα transcription factors.
      • DeFranco DB
      Navigating steroid hormone receptors through the nuclear compartment.
      • Nagaich AK
      • Rayasam GV
      • Martinez ED
      • Becker M
      • Qiu Y
      • Johnson TA
      • Elbi C
      • Fletcher TM
      • John S
      • Hager GL
      Subnuclear trafficking and gene targeting by steroid receptors.
      • Phair RD
      • Scaffidi P
      • Elbi C
      • Vecerova J
      • Dey A
      • Ozato K
      • Brown DT
      • Hager G
      • Bustin M
      • Misteli T
      Global nature of dynamic protein-chromatin interactions in vivo: three-dimensional genome scanning and dynamic interaction networks of chromatin proteins.
      that are key for organization and assembly of the regulatory machinery for context-dependent, combinatorial control of gene expression in nuclear matrix-associated microenvironments of interphase cells and at chromosomal loci of mitotic cells.
      • Cook PR
      The organization of replication and transcription.
      • Choi J-Y
      • Pratap J
      • Javed A
      • Zaidi SK
      • Xing L
      • Balint E
      • Dalamangas S
      • Boyce B
      • van Wijnen AJ
      • Lian JB
      • Stein JL
      • Jones SN
      • Stein GS
      Subnuclear targeting of Runx/Cbfa/AML factors is essential for tissue-specific differentiation during embryonic development.
      • Brown KE
      • Baxter J
      • Graf D
      • Merkenschlager M
      • Fisher AG
      Dynamic repositioning of genes in the nucleus of lymphocytes preparing for cell division.
      • Ma H
      • Siegel AJ
      • Berezney R
      Association of chromosome territories with the nuclear matrix: disruption of human chromosome territories correlates with the release of a subset of nuclear matrix proteins.
      • Javed A
      • Barnes GL
      • Pratap J
      • Antkowiakm T
      • Gerstenfeld LC
      • van Wijnen AJ
      • Stein JL
      • Lian JB
      • Stein GS
      Impaired intranuclear trafficking of Runx2 (AML3/CBFA1) transcription factors in breast cancer cells inhibits formation of osteolytic lesions in vivo.
      • Misteli T
      • Spector DL
      RNA polymerase II targets pre-mRNA splicing factors to transcription sites in vivo.
      • Scully R
      • Livingston DM
      In search of the tumour-suppressor functions of BRCA1 and BRCA2.
      • Smith KP
      • Moen PT
      • Wydner KL
      • Coleman JR
      • Lawrence JB
      Processing of endogenous pre-mRNAs in association with SC-35 domains is gene specific.
      • Wagner S
      • Chiosea S
      • Nickerson JA
      The spatial targeting and nuclear matrix binding domains of SRm160.
      In the second part of the work presented by Maniotis et al
      • Maniotis AJ
      • Valyi-Nagy K
      • Karavitis J
      • Moses J
      • Boddipali V
      • Wang Y
      • Nuñez R
      • Setty S
      • Arbieva Z
      • Bissell MJ
      • Folberg R
      Chromatin organization measured by Alu I restriction enzyme changes with malignancy and is regulated by the extracellular matrix and the cytoskeleton.
      in this issue, a systematic search was initiated to test if growth factors, or soluble and polymerized ECM molecules, affect the sequestration or exposure of DNA, and to test if there was specificity of different ECM molecule types on Alu site exposure or sequestration. Exposure of living cells to soluble laminin and RGD-C resulted in sequestration of Alu sites from digestion by AluI in all cells tested. However, sequestration induced by Matrigel, laminin, and RGD-C was always more intense in the nuclei of cells of increasing grades of invasiveness. Serum, fibronectin, bFGF, EGF, and type I collagen had no effect on the seqestration of AluI sensitive sites. When cells were grown in or on polymerized Matrigel or laminin platforms, profound sequestration was observed. This was in contrast to cells that were situated on Type I collagen, serum, or fibronectin. In addition, when comparing six repeated microarrays of highly invasive cells situated on Matrigel versus the same highly invasive cells not situated on Matrigel, a consistent differential expression of 990 transcripts was obtained. These results, when taken together with the observed chemical changes in sensitivity underlying the nuclease digestions, provide preliminary evidence that exposure of only one extracellular matrix molecule on the cell surface for 30 minutes can induce global effects on chromatin organization.
      In multicellular organisms, the cytoskeleton and extracellular matrix are known to play a fundamental role in determining cellular behaviors. To test if different cytoskeletal fiber systems influenced the sequestration or exposed the Alu sites, a variety of cytoskeleton-disrupting drugs were used by Maniotis et al
      • Maniotis AJ
      • Valyi-Nagy K
      • Karavitis J
      • Moses J
      • Boddipali V
      • Wang Y
      • Nuñez R
      • Setty S
      • Arbieva Z
      • Bissell MJ
      • Folberg R
      Chromatin organization measured by Alu I restriction enzyme changes with malignancy and is regulated by the extracellular matrix and the cytoskeleton.
      to determine whether the higher order structure of chromatin was controlled by actin, microtubules, or intermediate filaments. Maniotis et al
      • Maniotis AJ
      • Chen CS
      • Ingber DE
      Demonstration of mechanical connections between integrins, cytoskeletal filaments, and nucleoplasm that stabilize nuclear structure.
      had previously shown that a tug to an integrin receptor could alter the molecular alignment of intranuclear molecules in 1 second, and that each cytoskeletal system exerted a different stabilizing effect on both nuclear structure, and force transduction. In this study, each cytoskeletal fiber system profoundly contributed to the sequestration or exposure effect. Actin disruption decreased sequestration, while microtubule or intermediate filament disruption dramatically increased sequestration. In these experiments, the data suggest that nuclear size and cytoplasmic spreading and gene sequestration or exposure are co-events. A similar relationship between cell growth, cell “differentiation,” and nuclear size in endothelial cells was shown long ago by Folkman and Moscona
      • Folkman J
      • Moscona A
      Role of cell shape in growth control.
      on monolayers coated with increasing amounts of a cellular adhesive. The results of the Maniotis et al study
      • Maniotis AJ
      • Valyi-Nagy K
      • Karavitis J
      • Moses J
      • Boddipali V
      • Wang Y
      • Nuñez R
      • Setty S
      • Arbieva Z
      • Bissell MJ
      • Folberg R
      Chromatin organization measured by Alu I restriction enzyme changes with malignancy and is regulated by the extracellular matrix and the cytoskeleton.
      extend these observations to include the sequestration and exposure of specific DNA sites, and a compelling and testable model is advanced that involves cytoskeletal control of nuclear structure and nuclear pore complexes.
      Together, these findings raise, and experimentally address, new questions regarding the fundamental way genetic information is controlled by proteins containing disulfide-rich bonds, by the extracellular matrix microenvironment, and by the cytoskeleton. The work also has contributed several new approaches that can be used as diagnostic tools. Furthermore, the observed differences in the sequestration of DNA among cells of varying invasive behavior can be exploited to distinguish differing degrees of malignancy that do not depend on presently used molecular markers. Therefore, the differential sensitivity of Alu sites in highly invasive tumor cells versus noninvasive tumor cells offers an alternative for dependence on molecular markers, which have been shown to be highly variable in the context of vasculogenic mimicry, and which manifests as molecular mimicry (deregulated protein expression) in tissue sections of the most invasive types of tumors.
      • Maniotis AJ
      • Folberg R
      • Hess A
      • Seftor EA
      • Gardner LM
      • Pe'er J
      • Trent JM
      • Meltzer PS
      • Hendrix MJ
      Vascular channel formation by human melanoma cells in vivo and in vitro: vasculogenic mimicry.
      • Chen X
      • Maniotis AJ
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      • Pe'er J
      • Folberg R
      Uveal melanoma cell staining for CD34 and assessment of tumor vascularity.
      • Seftor EA
      • Meltzer PS
      • Kirschmann DA
      • Pe'er J
      • Maniotis AJ
      • Trent JM
      • Folberg R
      • Hendrix MJ
      Molecular determinants of human uveal melanoma invasion and metastasis.
      For example, the most highly invasive melanoma tumor cells, although they ultimately derive from the neural crest, are able to express protein markers characteristic of a variety of different normal cell types (such as endothelial cells), but also markers specific to epithelial cells, and a wide variety of other cell types, depending on the degree of deregulation. In this context, clinically relevant lessons can be learned about mechanisms for drug resistance that are mediated by microenvironments that are key components of tissue organization.
      • Bissell MJ
      • Rizki A
      • Mian IS
      Tissue architecture: the ultimate regulator of breast epithelial function.
      • Boudreau N
      • Myers C
      • Bissell MJ
      From laminin to lamin: regulation of tissue-specific gene expression by the ECM.
      All considered, it appears that how genes are sequestered, exposed, and expressed in higher eukaryotic cells can be viewed as part of a mechanically coordinated, cell shape-dependent, hierarchical system.
      • Bissell MJ
      • Rizki A
      • Mian IS
      Tissue architecture: the ultimate regulator of breast epithelial function.
      • Itoh M
      • Bissell MJ
      The organization of tight junctions in epithelia: implications for mammary gland biology and breast tumorigenesis.
      • Novaro V
      • Radisky DC
      • Ramos Castro NE
      • Weisz A
      • Bissell MJ
      Malignant mammary cells acquire independence from extracellular context for regulation of estrogen receptor alpha.
      • Schmeichel KL
      • Bissell MJ
      Modeling tissue-specific signaling and organ function in three dimensions.
      • Roskelley CD
      • Srebrow A
      • Bissell MJ
      A hierarchy of ECM-mediated signalling regulates tissue-specific gene expression.
      • Bissell MJ
      • Barcellos-Hoff MH
      The influence of extracellular matrix on gene expression: is structure the message?.
      • Bissell MJ
      • Hall HG
      • Parry G
      How does the extracellular matrix direct gene expression?.
      • Sood AK
      • Coffin JE
      • Schneider GB
      • Fletcher MS
      • DeYoung BR
      • Gruman LM
      • Gershenson DM
      • Schaller MD
      • Hendrix MJ
      Biological significance of focal adhesion kinase in ovarian cancer: role in migration and invasion.
      • Chunthapong J
      • Seftor EA
      • Khalkhali-Ellis Z
      • Seftor RE
      • Amir S
      • Lubaroff DM
      • Heidger Jr, PM
      • Hendrix MJ
      Dual roles of E-cadherin in prostate cancer invasion.
      • Sood AK
      • Hendrix MJ
      The complexity of tumor vascularity.
      • Hendrix MJ
      • Seftor EA
      • Kirschmann DA
      • Quaranta V
      • Seftor RE
      Remodeling of the microenvironment by aggressive melanoma tumor cells.
      • Hendrix MJ
      • Seftor EA
      • Kirschmann DA
      • Seftor RE
      Molecular biology of breast cancer metastasis: molecular expression of vascular markers by aggressive breast cancer cells.
      In this regard, it has been proposed that the principles of tensional integrity (tensegrity) may be a useful conceptual framework to explore and predict how molecules can function collectively as components of integrated, hierarchical systems, in the physical context of normal living cells, and tissues.
      • Ingber DE
      Tensegrity II: how structural networks influence cellular information processing networks.
      If the information directing these processes are indeed “mechanogenomic” in nature, as described by Maniotis et al
      • Maniotis AJ
      • Valyi-Nagy K
      • Karavitis J
      • Moses J
      • Boddipali V
      • Wang Y
      • Nuñez R
      • Setty S
      • Arbieva Z
      • Bissell MJ
      • Folberg R
      Chromatin organization measured by Alu I restriction enzyme changes with malignancy and is regulated by the extracellular matrix and the cytoskeleton.
      in this issue of The American Journal of Pathology, the apparent complexity of development and cancer may be better understood by insight into how the genome is part of a larger machine that can interpret different signals only in a limited number of ways that is restricted by the ECM microenvironment, and the type of mechanogenomic architecture that environment erects within the cell and nucleus.
      In a broader context, understanding of cell structure-gene expression interrelationships is in its infancy. However, there is accruing evidence for a central role of cellular microenvironments in the detection, integration, and execution of regulatory signals. Support for focal thresholds of genes, transcripts, receptors, and regulatory factors that optimize informative encounters to support gene expression, replication, and repair at multiple levels has emerged from interrogation of fundamental parameters of biological control. Additional insight into the regulation of gene expression should be forthcoming from further exploration of the mechanisms and underlying parameters that mediate the multistep dynamic positioning and combinatorial association of architecturally organized regulatory macromolecules in the nucleus, cytoplasm, and extracellular matrix. Despite compelling support for the physiological relevance of intracellular regulatory domains, there is a requirement to define rate limiting parameters of mechanisms that mediate the temporal and spatial components of cell structure-gene expression interrelationships. The rules governing organization of the regulatory machinery in the three-dimensional context of cellular architecture are being functionally enhanced by the combined applications of molecular, cellular, and in vivo genetic approaches. A prominent position for mechanogenomic control is an important consideration. It is realistic to expect that mechanistic explanations for the dynamic organization, assembly, and activities of regulatory machinery in cellular microenvironments which are subtly or catastrophically compromised in many diseases, including cancer, can provide a platform for novel approaches to diagnosis and treatment. It is further necessary to incorporate consideration of mechanogenomic control into mechanisms that may be operative in physiological processes that include, but are not restricted to, cell motility that is coupled with development, differentiation, tissue turnover, and remodeling, as well as the common denominators that may link mechanogenomic components of control with tumor progression and metastasis.

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