Editor: John H. Frenster, M.D.

Dedicated to the memory of Peyton Rous, discoverer of a viral cause of cancer in 1911.

Welcome to the Biophysics of Cancer website, designed as a resource for all cancer researchers.

Cancer is a disease of mammalian cells, characterized by a loss of gene controls, and mediated by a progression in the spread of metastatic lesions both locally and throughout the body.

Over 100 distinct types of cancer within humans can be recognized under the microscope, and these can be distinguished and positively identified within a biopsy sample by as few as one abnormal cell.

Meisner LF,  and Frenster JH,
"In Vivo Evolution within Radiation-Induced Clones of Human Lymphocytes".

Microscopes are the key instruments for detecting cancer cells, since cancer cells are as small as 10 microns in diameter. Beams of light and other energy particles are used within a system of  lenses to find, photograph and analyze samples of tissue under the microscope.

Microscopes are of varied types, using focused beams of visible light, polarized light, laser light, electrons,  positrons or x-rays, and viewing target cells either by probes, reflection, absorbance, flourescence, or motion. Photos and videoes can be recorded through the microscope for a permanent record, and living cells can be selected and manipulated by fine needle probes and tweezers  within the microscope.

The human adult body contains over 70 trillion ( 70 x 10 ¹² ) normal cells, but cancer usually begins in a single cell. At the time of death of a patient, more than 1 trillion cancer cells may be present, weighing over 1 lb. of one type of cell.

Frenster JH,  "Ultrastructural Continuity Between Active and Repressed Chromatin".

10 nm extended euchromtin microfibrils continuous with condensed heterochromatin masses.

Cancer biophysics utilizes the basic data from the microscopes to study the physiology and biochemistry of living cancer cells, cancer genes, cancer molecules and cancer systems. New medicines can be tested on the cells during such studies. All such biophysical studies reveal an abnormal control within the cancer cells.

During cancer, mutations of one or more genes may be found, together with gene products of the embryonic type. Such cancer types are referred to as embryomas, since they display embryonic proteins and RNAs, and act as aberrant embryonic cells.

Most recently, large modules of embryonic life are found to exist within metastatic adult cancer cells. These EMT modules are aberrent, and may be controlled by the administration of active microRNA molecules.

Within the cancer cell nucleus, competing biophysical ligands display both hydrophobic and hydrophilic features while reacting at the nanometer level with DNA genes and RNA agents of neoplastic transformation. (RNA and Biological Causality).

We will be following with you many of these interesting developments in cancer research.
Frenster JH, and Hovsepian JA, (2010)
"Reprogramming the human cancer cell nucleus".

Please also see an archive of cancer research papers on the Embryoma Gene Networks website under the Editorship of Jeannette A. Hovsepian, M.D.

Recent Developments in Cancer Research:

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

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

3. Sotelo J, Esposito D, Duhagon MA, Banfield K,  Mehalko J, Liao H, Stephens RM, Harris TJR, Munroe DJ, and Wu X, "Long-range enhancers on 8q24 regulate c-Myc".

4. 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".

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

6. 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".

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

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

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

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

11. 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".

12. Sheehy JP, Davis AR, and Znosko BM,
"Thermodynamic characterization of naturally occurring RNA tetraloops".

13. Schudoma C, May P, Nikiforova V, and Walther D,
"Sequence–structure relationships in RNA loops: establishing the basis for loop homology modeling".

14. 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."

15. Junier I, Martin O, and  Képès F, (2010).
"Spatial and Topological Organization of DNA Chains Induced by Gene Co-localization".

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

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

18. Mills M, Orr B, Holl MMB, and Andricioaei I,
"Microscopic Basis for the Mesoscopic Extensibility of Dendrimer-Compacted DNA".

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

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

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

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

23. 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".

24. 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".

25. Schmidt D, Wilson MD, Ballester B, Schwalie PC, Brown GD, Marshall A, Kutter C, Watt S, Martinez-Jimenez CP, Mackay S, Talianidis I, Flicek P, Odom DT,
"Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding".

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

27. 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".

28. He X, Chen C-C, Hong F, Fang F, Sinha S, Ng H-H, Zhong S,
"A Biophysical Model for Analysis of Transcription Factor Interaction and Binding Site Arrangement from Genome-Wide Binding Data".

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

30. 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".

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

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

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

34. 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".

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

36. 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".

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

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

39. 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".

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

41. 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".

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

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

44. 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".

45. 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".

46. 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".

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

48. 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".

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

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

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

52.  Frenster JH,
 "Causality in Complex Systems: Biology of the Cell Nucleus".

53. 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".

54. 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".

55. Nikolova EN. and Al-Hashimi HM,
"Thermodynamics of RNA melting, one base pair at a time".

56. Ohm JE,  Mali P,  Van Neste L,  Berman DM,  Liang L,  Pandiyan K,  Briggs KJ,  Zhang W,  Argani P,  Simons B,  Yu W,  Matsui W,  Van Criekinge W,  Rassool FV,  Zambidis E,  Schuebel KE,  Cope L,  Yen J,  Mohammad HP,  Cheng L, and  Baylin SB
"Cancer-Related Epigenome Changes Associated with Reprogramming to Induced Pluripotent Stem Cells".

57. Ziosi M, Baena-López LA, Grifoni D, Froldi F, Pession A, Garoia F, Trotta V, Bellosta P, Cavicchi S, and Pession A,
"dMyc Functions Downstream of Yorkie to Promote the Supercompetitive Behavior of Hippo Pathway Mutant Cells".

58. Roussos ET, Keckesova Z, Haley JD, Epstein DM, Weinberg RA, and Condeelis JS,
"AACR Special Conference on Epithelial-Mesenchymal Transition and Cancer Progression and Treatment".

59. Huarte M, and  Rinn JL,
"Large non-coding RNAs: missing links in cancer?"

60. Schmitz K-M,  Mayer C,  Postepska A,  and  Grummt I,
"Interaction of noncoding RNA with the rDNA promoter mediates recruitment of DNMT3b and silencing of rRNA genes".

61. Frenster JH, and Hovsepian JA,
"Reprogramming the human cancer cell nucleus".

62. Vogel G,
"New Technique RiPS Open Stem Cell Field",

63. Warren L, Manos PD, Ahfeldt T, Loh Y-H, Li H, Lau F, Ebina W, Mandal PK, Smith ZD, Meissner A, Daley GQ, Brack AS, Collins JJ, Cowan C, Schlaeger TM, and Rossi DJ.
"Highly Efficient Reprogramming to Pluripotency and Directed Differentiation of Human Cells with Synthetic Modified mRNA" ,

64. Kreiter S, Selmi A, Diken M, Koslowski M, Britten CM, Huber C, Tureci O, and Sahin U.
"Intranodal Vaccination with Naked Antigen-Encoding RNA Elicits Potent Prophylactic and Therapeutic Antitumoral Immunity".

65. Chen M, Zhang J, and Manley JL
"Turning on a Fuel Switch of Cancer : hnRNP Proteins Regulate Alternative Splicing of Pyruvate Kinase mRNA".

66. Mitton-Fry RM, DeGregorio SJ, Wang J, Steitz TA, and Steitz JA,
"Poly(A) Tail Recognition by a Viral RNA Element Through Assembly of a Triple Helix".

67. Pique-Regi R, Degner JF, Pai AA, Gaffney DJ, Gilad Y, Pritchard JK,
"Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data".

68. López-Lago MA, Thodima VJ, Guttapalli A, Chan T, Heguy A,  Molina AM, Reuter VE, Motzer RJ, and Chaganti RSK,
"Genomic Deregulation during Metastasis of Renal Cell Carcinoma Implements a Myofibroblast-Like Program of Gene Expression."

69. Ørom UA ,  Derrien T ,  Beringer M ,  Gumireddy K ,  Gardini A ,  Bussotti G ,  Lai F,  Zytnicki M , Notredame C ,  Huang Q ,  Guigo R , and  Shiekhattar R,
"Long noncoding RNAs with enhancer-like function in human cells."

70. Vitezic M, Lassmann T, Forrest ARR, Suzuki M, Tomaru Y, Kawai J, Carninci P,  Suzuki H, Hayashizaki Y and Daub CO,
"Building promoter aware transcriptional regulatory networks using siRNA perturbation and deepCAGE".

71. Dudley ME, Gross CA, Langhan MM, Garcia MR, Sherry RM, Yang JC, Phan GQ, Kammula US, Hughes MS, Citrin DE, Restifo NP, Wunderlich JR, Prieto PA, Hong JJ, Langan RC, Zlott DA, Morton KE, White DE, Laurencot CM, and Rosenberg SA
"CD8+ Enriched “Young” Tumor Infiltrating Lymphocytes Can Mediate Regression of Metastatic Melanoma".

72. Pennisi E,
"Shining a Light on the Genome's 'Dark Matter'

73. Vermeulen L, Todaro M, de Sousa Mello F, Sprick MR, Kemper K, Perez Alea M, Richel DJ, G. Stassi G, and Medema JP
"Single-cell cloning of colon cancer stem cells reveals a multi-lineage differentiation capacity".

74. Tsai M-C, Spitale RC, and Chang HY,
"Long Intergenic Noncoding RNAs: New Links in Cancer Progression".

75. Janic A, Mendizabal L, Llamazares S, Rossell D, and Gonzalez C,
"Ectopic Expression of Germline Genes Drives Malignant Brain Tumor Growth in Drosophila".

76. Sun H, Wu J, Wickramasinghe P , Pal S, Gupta R, Bhattacharyya A, Agosto-Perez FJ, Showe LC, HuangTH-M, and Davuluri RV,
"Genome-wide mapping of RNA Pol-II promoter usage in mouse tissues by ChIP-seq".

77. Borel C, Deutsch S, Letourneau A, Migliavacca E, Montgomery SE, Dimas AS, Vejnar CE, Attar H, Gagnebin M, Gehrig C, Falconnet E, Dupré Y, Dermitzakis ET, and Antonarakis SE,
"Identification of cis- and trans-regulatory variation modulating microRNA expression levels in human fibroblasts".

78. Zhang L, Flygare J, Wong P, Lim P, and Lodish HF,
"miR-191 regulates mouse erythroblast enucleation by down-regulating Riok3 and Mxi1".

79. Gao Y, Schug J, McKenna LB, Lay JL, Kaestner KH, and Greenbaum LE,
"Tissue-specific regulation of mouse MicroRNA genes in endoderm-derived tissues".

80. Meseguer S, Mudduluru G,  Escamilla JM,  Allgayer H,  and  Barettino D,
"MicroRNAs-10a and -10b Contribute to Retinoic Acid-induced Differentiation of Neuroblastoma Cells and Target the Alternative Splicing Regulatory Factor SFRS1 (SF2/ASF)".

81. Ma P, Lin S, Bartolomei MS, and Schultz RM,
"Metastasis Tumor Antigen 2 (MTA2) Is Involved in Proper Imprinted Expression of H19 and Peg3 During Mouse Preimplantation Development".

82.  Png KJ, Yoshida M, Zhang H-F, Shu W , Lee H, Rimner A, Chan TA, Comen E, Andrade VP, Kim SW, King TA, Hudis CA, Norton L, Hicks J, Massagué J, and Tavazoie SF,
"MicroRNA-335 inhibits tumor reinitiation and is silenced through genetic and epigenetic mechanisms in human breast cancer".

83. Berger MF, Lawrence MS, Demichelis F, Drier Y, Cibulskis K, Sivachenko AY, Sboner A, Esgueva R, Pflueger D, Sougnez C, Onofrio R, Carter SL, Park K, Habegger L, Ambrogio L, Fennell T, Parkin M, Saksena G, Voet D, Ramos AH, Pugh TJ, Wilkinson J, Fisher S,  Winckler W, Mahan S, Ardlie K. Baldwin J, Simons JW, Kitabayashi N, MacDonald TY, Kantoff  PW, Chin L, Gabriel SB, Gerstein MB, Golub TR, Meyerson M, Tewari A, Lander ES, Getz G, Rubin MA,  and Garraway LA,
"The genomic complexity of primary human prostate cancer".

84. Roberts M, Bittner D, Brnich S, Conner B, Cox C, Filiberti J, Grant M, Mansuy M, and Forrester J,
"Genetic re-programming of the acute myeloid leukemia cell line HL-60".

85, Belton AM, Iacobuzio-Donahue C, Colletti EJ, Almeida-Porada GD, Huso DL, and Resar L,
"HMGA1 drives expansion of the intestinal stem cell compartment in transgenic mice and tumor progression in colon cancer cells".

86. Arnold CP, Tan R, Zhou B, Yue S-B, Schaffert S, Biggs JR, Doyonnas R, Lo M-C, Perry JM, Renault VM, Sacco A, Somervaille T, Viatour P, Brunet A, Cleary ML, Li L, Sage J, Zhang D-E, Blau HM, Chen C, Chen C-Z
"MicroRNA programs in normal and aberrant stem and progenitor cells".

87. Eilebrecht S, Brysbaert C, Wegert T,  Urlaub H, Benecke B-J, and  Benecke A,
"7SK small nuclear RNA directly affects HMGA1 function in transcription regulation".

88. Millau J-F, Bandele OJ, Perron J, Bastien N, Bouchard EF, Gaudreau L, Bell DA, and Drouin R,
"Formation of stress-specific p53 binding patterns is influenced by chromatin but not by modulation of p53 binding affinity to response elements".

89. Manuel ER, Blache CA, Paquette R, Kaltcheva TI,  Ishizaki H , Ellenhorn JDI, Hensel M, Metelitsa L, and Diamond DJ,
"Enhancement of Cancer Vaccine Therapy by Systemic Delivery of a Tumor Targeting Salmonella-based STAT3 shRNA Suppresses the Growth of Established Melanoma Tumors".

90. Chaffer CL,  Brueckmann I,  Scheel C,  Kaestli AJ,  Wiggins  PA,  Rodrigues LO,  Brooks M,  Reinhardt F,  Su Y,  Polyak K,  Arendt LM, Kuperwasser C,  Bierie B,  and   Weinberg  RA,
"Normal and neoplastic non-stem cells can spontaneously convert to a stem-like state".

91. van Schooneveld E, Wouters M, Van der Auwera I, Peeters D, Huget P, van Dam PA, Vermeulen PB, Van Laere SJ, and Dirix LY,
"Detection of circulating miRNAs in serum from patients with breast cancer and their association with the presence of metastatic disease".

92. Thomas S, Li  X-Y, Sabo PJ, Sandstrom RB, Thurman RE, Canfield TD, Giste E, Fisher W, Hammonds A, Celniker SE, Biggin MD, Stamatoyannopoulos JA.
"Dynamic reprogramming of chromatin accessibility during Drosophila embryo development".

93. Schnall-Levin M, Rissland OS, Johnston W, Perrimon N, Bartel DP, and Berger B
"Unusually effective microRNA targeting within repeat-rich coding regions of mammalian mRNAs".

94. Pérez-Lluch S, Blanco E, Carbonell A, Raha D, Snyder M, Serras F, and Corominas M,
"Genome-wide chromatin occupancy analysis reveals a role for ASH2 in transcriptional pausing".

95. Kogo R, Mimori K, Tanaka F, Komune S, and Mori M,
"Clinical Significance of miR-146a in Gastric Cancer Cases".

96. Kojima K, Takata A, Vadnais C, Otsuka M, Yoshikawa T, Akanuma M, Kondo Y, Kang YJ,  Kishikawa T, Kato N, Xie Z, Zhang WJ, Yoshida H, Omata M, Nepve A, and Koike K,
"MicroRNA122 is a key regulator of a-fetoprotein expression and influences the aggressiveness of hepatocellular carcinoma".

97.  Frenster JH and Hovsepian JA,
“Heterochromatin to Euchromatin Transition within Human Interphase T- Lymphocytes”.

98. Pole JCM, McCaughan F, Newman S, Howarth KD, Dear PH, and Edwards PAW,
"Single-molecule analysis of genome rearrangements in cancer".

99. Kim C, Shah BJ, Subramaniam P,   and Lee K-B,
"Synergistic Induction of Apoptosis in Brain Cancer Cells by Targeted Co-delivery of siRNA and Anti-cancer drug".

100. Wang D, Garcia-Bassets I, Benner C, Li W,  Su X, Zhou Y, Qiu J, Liu W, Kaikkonen MU, Ohgi KA, Glass CK, Rosenfeld MG, & Fu X-D,
"Re-programming transcription by distinct classes of enhancers functionally defined by eRNA".

101. Song L, Zhang Z, Grasfeder LL, Boyle AP, Paul G. Giresi PG, Lee B-K, Sheffield NC, Gräf S, Huss M, Keefe D, Liu Z, London D, McDaniell RM, Shibata Y, Showers KA, Simon JM, Vales T, Wang T, Winter D, Zhang Z, Clarke ND, Birney E, Iyer VR, Crawford GE, Lieb JD, and Furey TS.
"Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity".

102. Frenster JH, "Biophysics of Cancer".

103. Zuber JH,  Shi J,  Wang E,  Rappaport AR,  Herrmann H,  Sison EA,  Magoon D,  Qi J,  Blatt K,  Wunderlich M,   Taylor MJ, Johns C,  Chicas A,  Mulloy JC,  Kogan SC,  Brown P,  Valent P,  Bradner JE,  Lowe SW, and  Vakoc CR,
"RNAi screen identifies Brd4 as a therapeutic target in acute myeloid leukaemia".

104. Ball  P,
"Biophysics: More Than a Bystander".

105. Kreiter S,  Diken M,  Selmi A,  Diekmann J,  Attig S,  Hüsemann Y,  Koslowski M,  Huber C,  Türeci O,  and Sahin U,
"FLT3 Ligand Enhances the Cancer Therapeutic Potency of Naked RNA Vaccines".

106. Ngiow SF, Teng MWL, and Smyth MJ,
"Prospects for TIM3-Targeted Antitumor Immunotherapy".

107. Porter DL, Levine BL, Kalos M, Bagg A, and June CH,
"Chimeric Antigen Receptor–Modified T Cells in Chronic Lymphoid Leukemia".

108. Caskey M, Lefebvre F, Filali-Mouhim A, Cameron MJ, Goulet JP, Haddad EK, Breton G, Trumpfheller C, Pollak SP, Shimeliovich I, Duque-Alarcon A, Pan L, Nelkenbaum A, Salazar AM, Schlesinger SJ, Steinman RM, and Sékaly RP,
"Synthetic double-stranded RNA induces innate immune responses similar to a live viral vaccine in humans".

109. Garde S and Patel AJ,
"Unraveling the hydrophobic effect, one molecule at a time".

110. Patel AJ, Varilly P, Jamadagni SN, Hagan MF, Chandler D, and Garde S.
"Sitting at the edge: How biomolecules use hydrophobicity to tune their interactions and function".

111. Cartellieri M, Michalk I, von Bonin M, Krüger T, Stamova S, Koristka S, Arndt C, Feldmann A, Schmitz M, Wermke M, Lindemann D, Bornhäuser M, Ehninger G, and Bachmann M,
"Chimeric Antigen Receptor-Engineered T Cells for Immunotherapy of Acute Myeloid Leukemia".

112. Frenster JH, and Hovsepian JA,
"Ultrastructural Probes of Clusters of Open Regulatory Elements (CORE) within Chromatin".
 
 

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.cancerbiophysics.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