Welcome to Embryoma Gene Networks, designed as an archive of Biomedical Information concerning those adult neoplasms which express one or more embryo-exclusive genes within their adult transcription programs.

Embryo-exclusive genes in vertebrates are those genes which are characteristic of  embryonic and fetal life, and which are not normally expressed  in adult life.

Other embryo-mixed genes are often expressed together with adult genes in normal adult life.

Neoplasms in adults can be initiated by the expression of as little as one embryo-exclusive gene within a normal adult cell.

Such embryo gene-induced adult neoplasms are called embryomas,  and can be reverted by specific embryonic microRNAs added to such neoplastic cells.

Most embryomas are organized as multi-gene networks.

We are entering an era in which embryo-exclusive genes can be observed  as initiators and reverters of specific adult neoplasms.

1. Frenster JH, and Hovsepian JA,  ( 2007 )
    “Models of Embryonic Gene-Induced Initiation and Reversion of Adult Neoplasms”.

2. Frenster JH, and Hovsepian JA,  ( 2008 )
    "Models of  Embryonic RNA Initiating and Reverting Adult Neoplasms".

3. Frenster JH, and Hovsepian JA,  ( 2008 )
     "Micro RNAs and adult neoplasms of embryonic type".

4. Hovsepian JA, and Frenster JH,  ( 2009 )
     "Genomic Models of Functional Embryomas within Adult Neoplastic Cells".

5. Frenster JH, and Hovsepian JA, ( 2009 )
     "Functional Embryomas as a Result of Embryonic Gene Re-Expression".

6. Frenster JH, and Hovsepian JA, ( 2010 )
     "Cellular Dynamics of Embryomas within Adult Neoplasms".

7. Frenster JH, and Hovsepian JA,  ( 2010 )
      "Analysis of Intra-Nuclear Entropy Changes during EMT Activation".

8. Hovsepian JA, and Frenster JH, ( 2010 )
      Heterochromatin -to- Euchromatin Transition ( H-ET ) during Gene Activation.

9. Frenster JH, and Hovsepian JA,  ( 2010 )
      "The Biophysics of the Cancer Cell".

10. Frenster JH, and Hovsepian JA,
       "Reprogramming and Neoplasia".

11. Frenster JH, and Hovsepian JA, (2010)
"Reprogramming the human cancer cell nucleus".

Conclusions:

Further Topics:

1. Tiolo VA, (1965)
"Nineteenth Century Foundations of Cancer Research
Advances in Tumor Pathology, Nomenclature, and Theories of Oncogenesis",
http://cancerres.aacrjournals.org/cgi/content/abstract/25/2_Part_1/75

2. DeCarvalho S, (1963)
"Effect of RNA from Normal Human Marrow on Leukaemic Marrow In-Vivo".

3. Abelev GI, Perova SD,  Khramkova NI, Postnikova ZA, and Irlin IS,  (1963)
"Production of embryonal alpha-globulin by transplantable mouse hepatomas".
Transplantation Apr;1:174-180.

4. Frenster JH, Allfrey VG, and Mirsky AE,  (1963)
"Repressed and Active Chromatin Isolated from Interphase Lymphocytes",
Proc. Natl. Acad. Sci., U.S.A., 50: 1026-1032.

5a. Frenster JH,  (1965a)
"Ultrastructural Continuity Between Active and Repressed Chromatin".
Nature 205: 1341-1342.
10 nm euchromtin microfibrils continuous with heterochromatin.

5b. Frenster JH,  (1965b)
 "Nuclear Polyanions as De-Repressors of Synthesis of Ribonucleic Acid".
 Nature 206: 680-683.

5c. Frenster JH,  (1965c)
"A Model of Specific De-repression within Interphase Chromatin".
Nature 206: 1269-1270.

5d. Frenster JH,  (1965d)
 "Localized Strand Separations within Deoxyribonucleic Acid during Selective Transcription".
Nature 208: 894-896.

5e. Frenster JH,  (1965e)
  "Correlation of the Binding to DNA Loops or to DNA Helices with the Effect on RNA Synthesis".
Nature 208: 1093.
Ligands shift DNA equilibrium from inactive to active state.

5f. Frenster JH  (1965f)
"Mechanisms of Repression and De-repression within Interphase Chromatin".
In-Vitro 1: 78-101.

5g. Rose HG, and Frenster JH,  (1965g)
"Composition and Metabolism of Lipids within Repressed and Active Chromatin of Interphase Lymphocytes".
Biochim. Biophys. Acta 106: 577-591

5h. Frenster JH,  (1965h)
"Analysis of Queueing and Renewal within Human Systems",
Nature, Nature, 207: 1139-1140
Throughput system queues with renewing service channels.

6. Gold P, and Freedman SO,  (1965).
 "Specific Carcinoembryonic Antigens of the Human Digestive System".
 J. Exp. Med. 122: 467-481.

7a. Meisner LF,  and Frenster JH,  (1968)
"In Vivo Evolution within Radiation-Induced Clones of Human Lymphocytes".

7b. Stanley DA, Frenster JH, and Rigas DA (1968)
"Subnuclear Localization of Tritiated Phytohemagglutinin during Gene De-repression within Human Lymphocytes".

8a. Markert CL,  (1968)
"Neoplasia: A Disease of Cell Differetiation".
Cancer Res. 28: 1908-1914.
http://cancerres.aacrjournals.org/cgi/reprint/28/9/1908

8b. Frenster JH,  (1969)
"Electron Microscope Localization of Acridine Orange Binding within Nuclei of Human Leukemic Bone Marrow Cells".

8c. Frenster JH, (1969)
"Ultrastructural Effects of Mercuric Chloride on Nuclear Heterochromatin within Human Lymphocytes".

8d. Frenster JH (1970)
"Correlation Between the Ultrastuctural Binding Site of Nuclear Ligands and the Effect of the Ligand on RNA Synthesis in Human Leukocytes".

9. Abelev GI,  (1971)
 "Alpha-fetoprotein in Ontogenesis and Its Association with Malignant Neoplasms",
 Adv. Cancer Res. 14: 295-358.

10a. Keshgegian AA, Meisner LF, and Frenster JH, (1971)
"Thymidine Reversal of Ribothymidine Inhibition of Lymphocyte Mitosis".

10b. Frenster JH,  (August, 1971)
 "Electron Microscopic Localization of Acridine Orange Binding to DNA within Human Leukemic Bone Marrow Cells".
Cancer Res. 31: 1128-1133.

Probes within Human leukemia cell.

11. Watabe H,  (1971)
 "Early Appearance of Embryonic Alpha-globulin in Rat Serum during Carcinogenesis with 4-dimethylaminoazobenzene",
Cancer Res. 31: 1192-1194.

12. Herstein PR, and Frenster JH,  (1972)
 "Mated Models of Gene Regulation in Eukaryotes".

13. Ballas M,  (1972)
 "Yolk Sac Carcinoma of the Ovary with Alpha-fetoprotein in Serum and Ascitic Fluid Demonstrated by Immunoosmopheresis".
Amer. J. Clin. Path. 57: 511.

14. Frenster JH, and Herstein PR,  (June, 1973)
Review: "Gene De-Repression",
New Eng. J. Med. 288: 1224-1229

Displacement of Histones (Dark Blocks) from DNA.

15. Coggin J, and Anderson N,  (1974)
 "Cancer, Differentiation and Embryonic Antigens: Some Central Problems",
 Adv. Cancer Res. 19: 105-165.

16a. Frenster JH, Nakatsu SL, and Masek, MA  (1974a)
"Ultrastructural Probes of DNA Templates within Human Bone Marrow and Lymph Node Cells",
 Adv.Cell Molec. Biol. 3: 1-19.

Normal Human Bone Marrow Stem Cell.

16b. Nakatsu SL, Masek MA, Landrum S, and Frenster JH  (1974b)
"Activity of DNA Templates During Cell Division and Cell Differentiation".
Nature, 248 : 334-335.

17. Fishman WH, and Sell S, eds. (1976)
 "Onco-Developmental Gene Expression", 1-788, Academic Press, Inc. New York, NY

18. Groudine M, and Weintraub H,  (1976)
 "Rous Sarcoma Virus Activates Embryonic Globin Gene in Chicken Fibroblasts",
 Proc. Natl. Acad. Sci. USA 72: 4464-4468.

19. Frenster JH,  (1976)
"Selective Control of DNA Helix Openings during Gene Regulation".
Cancer Res. 36: 3394-3398.

Interaction of De-repressor RNA with specific DNA gene sites.

20. Frenster JH, Papalian MM, Masek MA and Frenster JA,  (1979)
"Electron Microscopic Analysis of Lymph Node Cellular Activity in Hodgkin's Disease".
 J. Natl. Cancer Inst. 63: 331-335.
Reed-Sternberg cell surrounded by active T-lymphocytes.

21. Frenster JH,  (1980)
"Selective Gene De-Repression by De-Repressor RNA".

22. Frenster JH,  (1983)
"Single-Cell Analysis of DNase I-Sensitive Sites During Neoplastic Cell Differentiation within Hodgkin's Disease Lymph Nodes".

23. Frenster JH,  (1989)
"Single-Cell Analysis of DNase I-Sensitive Sites during Neoplastic and Normal Cell Differentiation within Human Bone Marrow".

Comparison of viral oncogenesis to cell differentiation.

24a. Gold MO, and Rice AP, (1999a)
"Targeting of CDK8 to a promoter-proximal RNA element demonstrates catalysis-dependent activation of gene expression".

24b. Frenster JH,  (1999b)
 "Oncogenes as Molecular Targets within Active Chromatin".
  Clinical Cancer Research, vol. 5, suppl. l, p. 3855s, (624), (November, 1999).

24c. Frenster JH,  (1999c)
"Nuclear RNA Species Activate DNA Transcription within Chromatin".

25. Frenster JH,  (2000)
"Nuclear Ribosomes and RNA-RNA Duplexes".

26a. Frenster JH,  (2001a)
"Activation of DNA Transcription within Repressed Chromatin by Nuclear RNA Species".

26b. Frenster JH,  (2001b)
"Activation of DNA Transcription within Repressed Chromatin".

27. Frenster JH,  (2001)
 "Ultrastructural Probes of Active DNA Sites, and the RNA Activators of DNA".

28. Thiery JP,  (June, 2002)
"Epithelial–mesenchymal transitions in tumour progression",
Nat. Rev. Cancer 2: 442-454, 2002).

29a. Frenster JH,  (2002a)
"Uni-Polar Clustering of Lymphocyte DNA Templates Toward Neoplastic Target Cells Within Hodgkin's Disease Lymph Nodes".

29b. Frenster JH,  (2002b)
"Yeast RNA Re-Programming of Already-Active Mammalian Chromatin".

29c. Frenster JH, and Hovsepian JA,  (2002c)
"RNA Feedback Mechanisms during Eukaryotic Gene Regulation".

29d. Hovsepian JA, and Frenster JH,  (2002d)
"RNA-Induced Melting of DNA during Selective Gene Transcription".

30a. Frenster JH, and Hovsepian JA,  (2003a)
"Overshoot in Late Telophase for RNA Re-Programming of Mitotic Chromatin".

30b. Hovsepian JA, and Frenster JH,  (2003b)
"Euchromatin as an Extensile Force within Mammalian Cell Nuclei".

30c. Hovsepian JA, and Frenster JH,  (2003c)
"Bioassays of Isolated Nuclear RNA Species as Activators of DNA Transcription".

31a. Frenster JH, and Hovsepian JA,  (2004a)
"Activator RNA Exchange during Interphase Chromatin Reprogramming".

31b. Frenster JH, and Hovsepian JA,  (2004b)
"Ultrastructure  of Closed Loops within Euchromatin of Isolated Lymphocyte Nuclei".

31c. Hovsepian JA, and Frenster JH,  (2004c)
"Reprogramming as an Approach to Neoplasms".

32a. Hovsepian JA, and Frenster JH,  (2005a)
"Sense and Antisense during RNA Initiation of the DNA Transcription Bubble".

32b. Frenster JH, and Hovsepian JA,  (2005b)
"Ultrastructure of Euchromatin Contact Points between the Closed Loops of Adjacent Interphase Chromosomes".

33a. Frenster JH, and Hovsepian JA,  (2006a)
"Kissing Chromosomes and Paired Sense-Antisense RNA Synthesis".

Tetraplex formation between kissing chromosomes.

33b. Frenster JH, and Hovsepian JA,  (2006b)
"Activator RNA Initiation of the DNA Transcription Bubble".

33c. Hovsepian JA, and Frenster JH,  (2006c)
"Chromosome-Chromosome Contact Points and Paired Sense-Antisense RNA Synthesis".

33d. Frenster JH, and Hovsepian JA,  (2006d)
"DNase-I Ultrastructural Probe Sites and Kissing Chromosomes".

DNase-I sensitive sites,  leukemia.

34. Weinberg RA,   (2007)
"EMTs are Programmed by Transcription Factors that Orchestrate Key Steps of Embryogenesis", Chapter 14.5, pp. 615-621, "The Biology of Cancer",  Garland Science, New York, NY. (http://www.garlandscience.com)

Fig. 14.30: Similarities between EMT-signalling  during embryogenesis and tumor progression.
The signal transcription cascades that are responsible for activating the epithelial-mesenchymal transition (EMT) in a rat bladder carcinoma model (left) and during gastrulation early in mouse embryogenesis (right) have striking parallels. These similarities provide further support for the notion that the EMT program expressed by invasive carcinoma cells represents a reactivation of latent cell-biological programs, many of which are normally active in early mammalian embryonic development.
(From J.P. Thiery, Nat. Rev. Cancer 2: 442-454, 2002).
"Epithelial–mesenchymal transitions in tumour progression", (June 2002)

35. Rossi JJ,  (2007)
"Transcriptional activation by small RNA duplexes".

36a. Frenster JH, and Hovsepian JA,  (2007a)
"DNA-DNA Tetraplex Model of Paired Sense-Antisense RNA Synthesis".

36b. Frenster JH, and Hovsepian JA,  (2007b)
"Embryonic Gene Re-expression May Initiate Adult Neoplasms".

36c. Okita K, Ichisaka T,  and  Yamanaka S, (2007c)
“Generation of germline-competent induced pluripotent stem cells”.

36d. Frenster JH, and Hovsepian JA,  (October, 2007d)
 “Models of Embryonic Gene-Induced Initiation and Reversion of Adult Neoplasms”.

37a. Koslowski M, Sahin U, Mitnacht-Kraus R, Seitz G, Huber C, and Türeci O, (October, 2007a)
"A Placenta-Specific Gene Ectopically Activated in Many Human Cancers Is Essentially Involved in Malignant Cell Processes".

37b. Berx G, Raspe E, Christfori G, Thiery JP, and Sleeman JP, (November, 2007b)
"Pre-EMTing metastasis? Recapitulation of morphogenetic processes in cancer".
Clin Exp Metastasis, 2007;24(8):587-97, Epub 2007 Nov3.

38. Sarrió D, Rodriguez-Pinilla SM, Hardisson D, Cano A, Moreno-Bueno G, and Palacios J,  (Feb. 2008)
"Epithelial-Mesenchymal Transition in Breast Cancer Relates to the Basal-like Phenotype",
Cancer Research 68, 989-997, February 15, 2008.

39. Kumar MS, Erkeland SJ, Pester RE, Chen CY, Ebert MS, Sharp PA, and  Jacks T., (March, 2008)
"Suppression of non-small cell lung tumor development by the let-7 microRNA family".

40. Haigis KM, Kendall KR, Wang Y, Cheung A, Haigis MC, Glickman JN, Niwa-Kawakita M,  Sweet-Cordero A, Sebolt-Leopold J, Shannon KM, Settleman J, Giovannini M,  and  Jacks T.  (March 30, 2008) "Differential effects of oncogenic K-Ras and N-Ras on proliferation, differentiation and tumor progression in the colon".
Nature Genetics 40, 600 - 608 (2008). Published online: 30 March 2008 | doi:10.1038/ng.115)

41. Boyerinas B, Park S-M, Shomron N, Hedegaard MM, Vinther J, Andersen JS, Feig C, Xu J,  Burge CB, and Peter ME,  (April, 15, 2008)
"Identification of Let-7–Regulated Oncofetal Genes",
Cancer Research vol. 68, no. 8, pp. 2587-2591  (April 15, 2008).

42. Marcucci G, Radmacher MD, Maharry K, Mrózek K, Ruppert AS, Paschka P, Vukosavljevic T, Whitman SP, Baldus CD, Langer C, Liu C-G, Carroll AJ, Powell BL, Garzon R, Croce CM, Kolitz JE, Caligiuri MA, Larson RA, and Bloomfield CD,  (May 1, 2008)
"MicroRNA Expression in Cytogenetically Normal Acute Myeloid Leukemia",
New England Journal of Medicine vol. 358: no. 18, pp. 1919-1928 May 1, 2008.)

43. Mani SA, Guo W, Liao M-J, Eaton EN, Ayyanan A, Zhou AY, Brooks M, Reinhard F,  Zhang CC, Shipitsin M, Campbell LL, Polyak K, Brisken C, Yang J, and Weinberg RA,  (May 16, 2008)
"The Epithelial-Mesenchymal Transition Generates Cells with Properties of Stem Cells".
Cell, vol: 133, pp. 704-715 (May 16,  2008).

44. Abelev GI, and Eraiser TL,  (2008)
"Review: On the Path to Understanding the Nature of Cancer."
Biochemistry (Moscow) 2008, May; 73(5): 487-497.

45. Frenster JH, and Hovsepian JA,  (July, 2008)
"Models of  Embryonic RNA Initiating and Reverting Adult Neoplasms".

46. Vermeulen L, Todaro M, de Sousa Mello, Sprick FMR, Kemper K, Perez Alea M, Richel DJ, Stassi G, and Medema JP,  (September 8, 2008)
"Single-cell cloning of colon cancer stem cells reveals a multi-lineage differentiation capacity".
PNAS September 9, 2008 vol. 105 no. 36 13427-13432
http://www.pnas.org/content/105/36/13427.abstract?etoc.

47a. Frenster JH, and Hovsepian JA,  (Dec. 2008a)
"Models of successive levels of resolution during individual gene transcription".

47b. Frenster JH, and Hovsepian JA,  (Dec. 2008b)
 "Micro RNAs and adult neoplasms of embryonic type".

49. Judge AD, Robbins M, Tavakoli I, Levi J, Hu L, Fronda A, Ambegia E, McClintock K, and MacLachlan I,  (February, 2009)
"Confirming the RNAi-mediated mechanism of action of siRNA-based cancer therapeutics in mice",

50a. Guttman M, Amit I, Garber M, French C, Lin MF, Feldser D, Huarte M, Zuk O, Carey BW, Cassady JP, Cabili MN, Jaenisch R, Mikkelsen TS, Jacks T, Hacohen N, Bernstein BE, Kellis M, Regev A, Rinn JL, Lander ES. (March, 2009).
"Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals".

50b. Cantone I, Marucci L, Iorio F, Ricci MA, Belcastro V, Bansal M, Santini S, di Bernardo M, di Bernardo D, and Maria Cosma MP,  (April, 2009)
"A Yeast Synthetic Network for In Vivo Assessment of Reverse-Engineering and Modeling Approaches".

51. Crunkhorn S, (Aug. 2009)
"Therapy: microRNA suppresses liver cancer"

52.  Kota J, Chivukula RR, O'Donnell KA, Wentzel EA, Montgomery CL, Hwang H-W, Chang T-C, Vivekanandan P, Torbenson M, Clark KR, Mendell JR, and Mendel JT    (June, 2009)
"Therapeutic microRNA Delivery Suppresses Tumorigenesis in a Murine Liver Cancer Model",
Cell, Volume 137, Issue 6, 1005-1017, 12 June 2009,

53.  Rossi JJ,   (August, 2009)
"New Hope for a MicroRNA Therapy for Liver Cancer"
http://www.cell.com/abstract/S0092-8674(09)00643-6

54a. Khalil AM, Guttman M, Huarte M, Garber M, Raj A, Rivea Morales D, Thomas K, Presser A, Bernstein BE, van Oudenaarden A, Regev A, Lander ES, Rinn JL. (July 14, 2009).
"Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression".

54b.. Shimono Y, Zabala M, Cho RW, Lobo N, Dalerba P, Qian D, Diehn M, Liu H, Panula SP, Chiao E, Dirbas FM, Somlo G, Reijo Pera RA, Lao K and Clarke MF,
"Downregulation of miRNA-200c Links Breast Cancer Stem Cells with Normal Stem Cells".

55. Creighton CJ, Li X, Landis M, Dixon JM, Neumeister VM, Sjolund A, Rimm DL, Wong H, Rodriguez A, Herschkowitz JI, Fan C, Zhang X, He X, Pavlick A, Gutierrez MC, Renshaw L, Larionov AA, Faratian D, Hilsenbeck SG, Perou CM, Lewis MT, Rosen JM, Chang JC,
"Residual breast cancers after conventional therapy display mesenchymal as well as tumor-initiating features".

56. Chan KS, Espinosa I, Chao M, Wong D, Ailles L, Diehn M, Gill H, Presti J Jr, Chang HY, van de Rijn M, Shortliffe L, Weissman IL.
"Identification, molecular characterization, clinical prognosis, and therapeutic targeting of human bladder tumor-initiating cells".

57. Krizhanovsky V, and Lowe SW,
"The promises and perils of p53".

58. Marión RM, Strati K, Li H, Murga M, Blanco R, Ortega S, Fernandez-Capetillo O, Serrano M, Blasco MA.
"A p53-mediated DNA damage response limits reprogramming to ensure iPS cell genomic integrity".

59. Utikal J, Polo JM, Stadtfeld M, Maherali N, Kulalert W, Walsh RM, Khalil A, Rheinwald JG, and Hochedlinger K.
"Immortalization eliminates a roadblock during cellular reprogramming into iPS cells".

60. Kawamura T, Suzuki J, Wang YV, Menendez S, Morera LB, Raya A, Wahl GM, and Belmonte JC. (Aug. 2009).
"Linking the p53 tumour suppressor pathway to somatic cell reprogramming".

61. Li H, Collado M, Villasante A, Strati K, Ortega S, Cañamero M, Blasco MA, Serrano M.
"The Ink4/Arf locus is a barrier for iPS cell reprogramming".

62. Hong H, Takahashi K, Ichisaka T, Aoi T, Kanagawa O, Nakagawa M, Okita K, Yamanaka S.
"Suppression of induced pluripotent stem cell generation by the p53-p21 pathway".

63. Whitehead J, Pandey GK, Kanduri C., (Sept. 2009).
"Regulation of the mammalian epigenome by long noncoding RNAs".
Biochim Biophys A009 Sep;1790(9):936-47.

64. Eminli S, Foudi A, Stadtfeld M, Maherali N, Ahfeldt T, Mostoslavsky G, Hock H, Hochedlinger K.
"Differentiation stage determines potential of hematopoietic cells for reprogramming into induced pluripotent stem cells".

65. Kirouac DC, Madlambayan GJ, Yu M, Sykes EA, Ito C, and  Zandstra PW,
"Cell–cell interaction networks regulate blood stem and progenitor cell fate".

66. Hermans TM, Broeren MAC, Gomopoulos N, van der Schoot P, van Genderen MHP,  Sommerdijk NAJM, Fytas G, and Meijer EW,
"Self-assembly of soft nanoparticles with tunable patchiness".

67. Katoh M,  and Katoh M,
"Integrative genomic analyses of WNT11: Transcriptional mechanisms based on canonical WNT signals and GATA transcription factors signaling",

68. Scholl C, Fröhling S, Dunn IF, Schinzel AC, Barbie DA, Kim SY, Silver SJ, Tamayo P, Wadlow RC, Ramaswamy S, Döhner K, Bullinger L, Sandy P, Boehm JS, Root DE, Jacks T, William C. Hahn WC ,   and Gilliland DG
"Synthetic Lethal Interaction between Oncogenic KRAS Dependency and STK33 Suppression in Human Cancer Cells".

69. Gordân R, Hartemink AJ, and Bulyk ML
"Distinguishing direct versus indirect transcription factor-DNA interactions".

70. Utikal J, Maherali N, Kulalert W, Hochedlinger K.
"Sox2 is dispensable for the reprogramming of melanocytes and melanoma cells into induced pluripotent stem cells".

71. Von Hoff DD, Lorusso PM, Rudin CM, Reddy JC, Yauch RL, Tibes R, Weiss GJ, Borad MJ, Hann CL, Brahmer JR, Mackey HM, Lum BL, Darbonne WC, Marsters JC Jr, de Sauvage FJ, Low JA.
"Inhibition of the Hedgehog Pathway in Advanced Basal-Cell Carcinoma",

72. Cook PR,  and  Marenduzzo D,
"Entropic organization of interphase chromosomes".

73. Reddy TE, Pauli F, Sprouse RO, Neff NF, Newberry KM, Garabedian MJ, and Myers RM,
"Genomic Determination of the Glucocorticoid Response Reveals Unexpected Mechanisms of Gene Regulation".

74. Strizzi L, Hardy KM, Seftor EA, Costa FF, Kirschmann DA, Seftor RE, Postovit LM, Hendrix MJ.,
"Development and cancer: at the crossroads of Nodal and Notch signaling."

75. Mishra PJ,  and Merlino G,
"MicroRNA reexpression as differentiation therapy in cancer".

76. Taulli R, Bersani F, Foglizzo V, Linari A, Vigna E, Ladanyi M, Tuschl T, and Ponzetto C,
"The muscle-specific microRNA miR-206 blocks human rhabdomyosarcoma growth in xenotransplanted mice by promoting myogenic differentiation".

77. Nayak RR, Kearns M, Spielman RS, and Cheung VG,
  "Coexpression network based on natural variation in human gene expression reveals gene interactions and functions".

78. Ji J, Shi J, Budhu A, Yu Z, Forgues M, Roessler S, , Ambs S, Chen Y, Meltzer PS, Croce CM, Qin L-X, Man K, Lo C-M, Lee J, Ng IOL, Fan J, Tang Z-Y, Sun H-C, and Wang XW.
"MicroRNA Expression, Survival, and Response to Interferon in Liver Cancer".

79. Koslowski M, Türeci  O, Biesterfeld S, Seitz G, Huber C, and Sahin U,
"Selective Activation of Trophoblast-specific PLAC1 in Breast Cancer by CCAAT/Enhancer-binding Protein b (C/EBPb) Isoform 2".

80. Home P, Ray S, Dutta D, Bronshteyn I, Larson M, and Paul S,
"GATA3 Is Selectively Expressed in the Trophectoderm of Peri-implantation Embryo and Directly Regulates Cdx2 Gene Expression".

81. Tchabo NE, Mhawech-Fauceglia P, Caballero OL, Villella J, Beck AF, Miliotto AJ, Liao J, Andrews C, Lele S, Old LJ, and Odunsi K,
"Expression and serum immunoreactivity of developmentally restricted differentiation antigens in epithelial ovarian cancer".

82. Osborne JD, Flatow J, Holko M, Lin SM, Kibbe WA, Zhu LJ, Danila MI, Feng G, and Chisholm RI,
"Annotating the human genome with Disease Ontology".

83. Bernthaler A, Mühlberger I, Fechete R, Perco P, Lukas A, and Mayer B,
"A dependency graph approach for the analysis of differential gene expression profiles".

84a. Bernards R, (2008)
Perspective: "Cancer: Entangled pathways".

84b. Firestein R, Shima K, Nosho K, Irahara N, Baba Y, Bojarski E, Giovannucci EL, Fuchs CS, Ogino S,
"CDK8 expression in 470 colorectal cancers in relation to b-catenin activation, other molecular alterations and patient survival".

85. Firestein R  and Hahn WC, "Revving the Throttle on an Oncogene: CDK8 Takes the Driver Seat", Cancer Research, 69: (20), 7899-7901 (October 15, 2009).
Roles for CDK8 transcriptional activity in normal and colon cancer cells.
CDK8 oncogenes (orange) stimulating  b-catenin (silver) within the cell nucleus.

B, in colon cancer, amplification of CDK8 and/or copy number gain of RB lead to stimulation of b-catenin activity either directly or via suppression of E2F1. (Firestein R and Hahn WC, October, 2009).

86. Ooi CH, Ivanova T, Wu J, Lee M, Tan IB, Tao J, Ward L, Koo JH, Gopalakrishnan V, Zhu Y, Cheng LL, Lee J, Rha SY, Chung HC, Ganesan K, So J, Soo KC, Lim D, Chan WH,  Wong WK, Bowtell D, Yeoh KG, Grabsch H, Boussioutas A, and Tan P, (2009).
"Oncogenic Pathway Combinations Predict Clinical Prognosis in Gastric Cancer".

87. Valastyan S, Benaich N, Chang A, Reinhardt F, and Weinberg RA, (2009).
"Concomitant suppression of three target genes can explain the impact of a microRNA on metastasis".

88. Li L, Feng T, Lian Y, Zhang G, Garen A, and Song X, (2009).
"Role of human noncoding RNAs in the control of tumorigenesis".

89. Kim HH, Kuwano Y, Srikantan S, Lee EK, Martindale JL, and Gorospe M, (2009).
"HuR recruits let-7/RISC to repress c-Myc expression".

90. Kotani A, Ha D, Hsieh J, Rao PK, Schotte D, den Boer ML, Armstrong SA, and Lodish HF, (2009).
"miR-128b is a potent glucocorticoid sensitizer in MLL-AF4 acute lymphocytic leukemia cells and exerts cooperative effects with miR-221".

91. Thiery JP, Acloque H, Huang RYJ, and Nieto MA, (2009).
"Epithelial-Mesenchymal Transitions in Development and Disease".

92. Kessler JD, Hasegawa H, Brun SN, Emmenegger BA, Yang Z-J, Dutton JW, Wang F,  Wechsler-Reya RJ, (2009).
"N-myc alters the fate of preneoplastic cells in a mouse model of medulloblastoma".

93. Short B, (2009)
"Genes make their position clear".

94. Navin N, Krasnitz A, Rodgers L, Cook K, Meth J, Kendal J, Riggs M, Eberling Y, Troge J, Grubor V, Levy D, Lundin P, Månér S, Zetterberg A,  Hicks J,  and Wigler M, (2009).
"Inferring tumor progression from genomic heterogeneity".

95. Hovsepian JA, and  Frenster JH,  (2009).
"Genomic Models of Functional Embryomas within Adult Neoplastic Cells".

96. Frenster JH, and Hovsepian JA,  (2009).
"Functional Embryomas as a Result of Embryonic Gene Re-expression".

97. Besançon R, Valsesia-Wittmann S, Locher C, Delloye-Bourgeois C, Furhman L, Tutrone G, Bertrand C, Jallas A-C, Garin E, and Puisieux A,
"Upstream ORF affects MYCN translation depending on exon 1b alternative splicing".

98. Grinchuk OV, Jenjaroenpun P, Orlov YL, Zhou J, and Kuznetsov VA,
"Integrative analysis of the human cis-antisense gene pairs, miRNAs and their transcription regulation patterns".

99. Hiratani I, Ryba T, Itoh M, Rathjen J, Kulik M, Papp B, Fussner E, Bazett-Jones DP, Plath K, Dalton S,
Rathjen PD,  and Gilbert DM.
"Genome-wide dynamics of replication timing revealed by in vitro models of mouse embryogenesis".

100. Nicodemi M,  and  Prisco A,
"Thermodynamic Pathways to Genome Spatial Organization in the Cell Nucleus".

101. Chen TS, Lai RC , Lee MM, Choo ABH, Lee CN, and Lim SK,
"Mesenchymal stem cell secretes microparticles enriched in pre-microRNAs".

102. Vu TH, Nguyen AH, and Hoffman AR,
"Loss of IGF2 imprinting is associated with abrogation of long-range intrachromosomal interactions in human cancer cells".

103. Mohamed JS, Gaughwin PM, Lim B, Robson P,  and Lipovich L,
"Conserved long noncoding RNAs transcriptionally regulated by Oct4 and Nanog modulate pluripotency in mouse embryonic stem cells".

   Long Non-coding RNAs Modulate Pluripotency in Stem Cells.

105. Resar LMS,
"The High Mobility Group A1 Gene: Transforming Inflammatory Signals into Cancer?"

106. Deng N-J,  and Cieplak P,
"Free Energy Profile of RNA Hairpins: A Molecular Dynamics Simulation Study".

107. Schoenfelder S, Sexton T, Chakalova L, Cope NF, Horton A, Andrews S, Kurukuti S, Mitchell JA, Umlauf D, Dimitrova DS, Eskiw CH, Luo Y, Wei C-L, Ruan Y, Bieker JJ, and Fraser P,
"Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells".

108. Zhang H, Li Y, and Lai M,
"The microRNA network and tumor metastasis".

109. Frenster JH, and Hovsepian JA,
     "Cellular Dynamics of Embryomas within Adult Neoplasms".

110a. Special Conference by American Association for Cancer Research on EMT/MET in Adult Neoplasms.

110b. Frenster JH, and Hovsepian JA,
"Analysis of Intra-Nuclear Entropy Changes during EMT Activation".

111. Inui M, Martello G, and Piccolo S,
"MicroRNA control of signal transduction".

112. Ong KM, Blackford Jr JA , Kagan BI, Simons Jr. SS, and Chow CC,
"A theoretical framework for gene induction and experimental comparisons".

113. Blackburn EH, Tlsty TD, and Lippman SM,
"Unprecedented Opportunities and Promise for Cancer Prevention Research".

114. Steidl C, Lee T, Shah SP, Farinha P, Han G, Nayar T, Delaney A, Jones SJ, Iqbal J, Weisenburger DD, Bast MA, Rosenwald A, Muller-Hermelink H-K, Rimsza LM, Campo E., Delabie J, Braziel RM, Cook JR, Tubbs RR, Jaffe ES, Lenz G, Connors JM, Staudt LM, Chan WC, and Gascoyne RD.
"Tumor-Associated Macrophages and Survival in Classic Hodgkin's Lymphoma".

115. Frenster JH,
"Hodgkin Lymphoma Immuno-Pathology".

116. Koh W, Sheng CT, Tan B, Lee QY, Kuznetsov V , Kiang LS,  and  Tanavde V,
"Analysis of deep sequencing microRNA expression profile from human embryonic stem cells derived mesenchymal stem cells reveals possible role of let-7 microRNA family in downstream targeting of Hepatic Nuclear Factor 4 Alpha".

117. Carninci  P,
"RNA Dust: Where are the Genes?"

118. Nakao H, and  Mikhailov AS,
"Turing patterns in network-organized activator–inhibitor systems".

119. Ryba T, Hiratani I, Lu J, Itoh M, Kulik M, Zhang J, Dalton S, and Gilbert DM,
"Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types".

120. Riester M, Attolini CS-O, Downey RJ, Singer S, and Michor F,
"A Differentiation-Based Phylogeny of Cancer Subtypes".

121. Gupta RA, Shah N, Wang KC, Kim J, Horlings HM, Wong DJ, Tsai M-C, Hung T, Argani P, Rinn JL, Wang Y, Brzoska P, Kong B, Li R, West RB, van de Vijver MJ, Sukumar S,  and Chang HY,
"Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis".

122. Gao JS, Zhang Y, Li M, Tucker LD, Machan JT, Quesenberry P, Rigoutsos I , and Ramratnam B.
"Atypical transcription of microRNA gene fragments".

123. DePaul AJ, Thompson EJ, Patel SS, Haldeman K, and Sorin EJ,
"Equilibrium conformational dynamics in an RNA tetraloop from massively parallel molecular dynamics".

124. Dunoyer P, Schott G, Himber C, Meyer D, Takeda A, Carrington JC, and Voinne O,
"Small RNA Duplexes Function as Mobile Silencing Signals Between Plant Cells".

125. van Berkum NL, Lieberman-Aiden E, Williams L, Imakaev M, Gnirke A, Mirny LA, Dekker J, and Lander ES,    "Hi-C: a method to study the three-dimensional architecture of genomes".

126. Kosaka N, Iguchi H, Yoshioka Y, Takeshita F, Matsuki Y, and Ochiya T,
"Secretory Mechanisms and Intercellular Transfer of MicroRNAs in Living Cells?"

127. Yamanaka S,  and Blau HM,
"Nuclear reprogramming to a pluripotent state by three approaches".

128. Boyerinas B, Park S-M, Hau A, Murmann AE, and Peter ME,
"The role of let-7 in cell differentiation and cancer".

129. Mestdagh P, Fredlund E, Pattyn  F, Rihani  A, Van Maerken T, Vermeulen J, Kumps C, Menten B, De Preter K, Schramm A, Schulte J, Noguera R, Schleiermacher G, Janoueix-Lerosey I, Laureys G, Powel R, Nittner D, Marine J-C , Ringnér M, Speleman F, and Vandesompele J,
"An integrative genomics screen uncovers ncRNA T-UCR functions in neuroblastoma tumours".

130. Moriarty CH, Pursell B, and  Mercurio AM,
"miR-10b Targets Tiam1: Implications for Rac activation and carcinoma migration".

131. van Riggelen J, Müller J, Otto T, Beuger V, Yetil A, Choi PS, Kosan C, Möröy T, Felsher DW,and Eilers M,
"The interaction between Myc and Miz1 is required to antagonize TGFb-dependent autocrine signaling during lymphoma formation and maintenance".

132. Mondal T, Rasmussen M, Pandey GK, Isaksson A ,and Kanduri C,
"Characterization of the RNA content of chromatin".

133. DeVlaminck I, Vidic I, van Loenhout MTJ, Kanaar R, Lebbink JHG, and Dekker C,
"Torsional regulation of hRPA-induced unwinding of double-stranded DNA".

134. Tsai M-C, Manor O, Wan Y, Mosammaparast N, Wang JK, Lan F, Shi Y, Segal E, and Chang HY,
"Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes".

135. Washington JM, Rathjen J, Felquer F, Lonic A, Bettess MD, Hamra N, Semendric L, Tan BSN, Lake J-A, Keough RA, Morris MB, and Rathjen PD,
"L-Proline induces differentiation of ES cells: a novel role for an amino acid in the regulation of pluripotent cells in culture".

136. Green MR, Monti S, Rodig SJ, Juszczynski P, Currie T, O'Donnell E, Chapuy B, Takeyama K, Neuberg D, Golub TR, Kutok JL, and Shipp MA,
"Integrative analysis reveals selective 9p24.1 amplification, increased PD-1 ligand expression, and further induction via JAK2 in nodular sclerosing Hodgkin lymphoma and primary mediastinal large B-cell lymphoma".

137. Rosenberg MI,  and Desplan C,
"Hiding in Plain Sight",

138. Taft RJ,  Simons C,  Nahkuri S,  Oey H,  Korbie DJ,  Mercer TR,  Holst J,  Ritchie W,  Wong JJ-L,   Rasko JEJ,  Rokhsar DS,  Degnan BM and Mattick JS,
"Nuclear-localized tiny RNAs are associated with transcription initiation and splice sites in metazoans".

139. Tsuchiya S, Kobayashi Y, Goto Y, Okumura H, Nakae S, Konno T, and Tada K,
"Induction of Maturation in Cultured Human Monocytic Leukemia Cells by a Phorbol Diester".

140. Hume D, and Hiyashizaki Y,
"The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line".

141. Tanaka Y, Yoshimura I,  and Nakai K,
"Positional variations among heterogeneous nucleosome maps give dynamical information on chromatin".

142. Klusmann J-H, Godinho FJ, Heitmann K, Maroz A, Koch ML, Reinhardt D, Orkin SH, and Li Z,
"Developmental stage-specific interplay of GATA1 and IGF signaling in fetal megakaryopoiesis and leukemogenesis".

143. Liu L, Luo G-Z, Yang W, Zhao X, Zheng Q, Lv Z, Li W, Wu H-J, Wang L, Wang XJ and Zhou Q,
"Activation of the Imprinted Dlk1-Dio3 Region Correlates with Pluripotency Levels of Mouse Stem Cells".
 
 

1. Each cell retains all of its embryonic genes for a lifetime.

2. Controls for embryonic genes are often absent in adults.

3. Uncontrolled embryonic genes can replicate wildly.

4.  Replicating genes participate in  intra-cellular competition.

5.  The basis for gene competition is selective transcription.

6.  MicroRNAs can reprogram embryomic transcription.

7.  Gene reprogramming can produce normal phenotypes.

8.  Normal phenotypes can by-pass chromosomal lesions.

9.  MicroRNA therapy may need to be permanent.

10. Transplantation of microRNAs could be preferred.

http://www.embryomas.net/

1. Pathways within cell genomes involve a flow of information.

2. Information can flow by direct contact or by third parties.

3. Direct contact within whole genomes is difficult to regulate.

4. DNA-DNA direct contects are influenced by agents.

5. Nuclear agents include hydrophilic ionic and hydrophobic conforming ligands.

6. Third parties within genomes involve RNAs and proteins.

7.  RNAs and proteins are easy to regulate or reverse.

8.  Information can be shared, lost, or transformed.

9. System information can be hidden during system isolation.

10.  Local information can be permanently lost during system entropy.

http://www.embryomas.net/

Links to Current Research in Euchromatin:
Links to Euchromatin Activator RNA Reviews:
Links to Euchromatin Activator RNA Research:
Links to Ultrastructural Probes of DNase I-Sensitive Sites:
Links to RNA as a Therapeutic Agent:
Links to Hodgkin Lymphoma Immuno-Pathology:
Links to Activated T-Lymphocyte Immunotherapy:
Links to Medical Systems Biology:
Links to Selective Gene Transcription:
Links to RNA-Induced Epigenetics:
Links to RNA-Induced Embryogenesis:
Links to RNA and Biological Causality:
Links to Reprogramming and Neoplasia:

A Brief History of Activator RNA:

"Ultrastructural Probes of Active DNA Sites, and the RNA Activators of DNA".
(PowerPoint Presentation).

Top of Page - Euchromatin Network -  Euchromatin Research -  Research in Quantitative Radiology

For Further Information and Feedback:

Jeannette A. Hovsepian, M.D.
E-mail: frensasc@ix.netcom.com
Phone:  +1 650 367 6483