Mechanisms governing initiation steps of the assembly of endogenous multi-protein complexes (EMC) remain incompletely understood. Here, multiple lines of observations are reported describing the function-aligned initiation sequence of hybrid assembly pathways (HAP) of EMC. The first step of HAP-guided chain reactions of protein-protein interactions (PPI) of EMC assemblies constitutes the creation of cell type-specific pools of hetero and homo dimers. The molecular anatomy of HAP was elucidated by defining qualitative and quantitative characteristics of protein binding to a compendium of 200,393 distinct genomic regulatory elements (GRE), including 49,667 sequences representing control sets of genomic loci as well as 150,726 GRE of different evolutionary origins. The consensus sequence of HAP actions consists of: a) Initiation on genomic DNA of the formation of metastable hetero- and homodimers of EMCs’ protein constituents; b) Release of dimers from DNA templates for delivery to the EMC assembly compartments; c) Assembly of defined EMC by sequential on demand addition of proteins to preformed dimers serving as attractors of EMC-specific ensembles of monomers. Chromosome-naïve DNA scaffolds facilitating creation of intracellular dimer pools engage networks of ~700 transcription factors (TFs), 534 of which manifest region-specific patterns of significantly enriched expression in 1358 brain regions. HAP initiators appear to operate within nucleosome-depleted islands of transposable elements (TE) – derived sequences within heterochromatin. PPI assembly lines of EMCs operate in 2 concurrent modes: TF-TF PPI cascade and PPI HUB protein cascade. Regardless of the number of DNA-bound initiator TFs (ranging from one to 716 TFs), both modes of operations reached the equilibrium at the PPI constituents saturation levels of ~245 proteins for TF-TF PPI modes and of ~351 proteins for PPI HUB protein modes. Distinct panels of DNA-bound initiator TFs and proteins of PPI cascade ensembles are enriched in either defined sets of neuroanatomical structures (TF-TF mode) or among structural-functional constituents of synapses (HUB proteins mode). Thus, these bifurcated cascades appear biologically congruent: TF–TF constituents map to transcriptional signatures of hundreds of brain regions, whereas HUB constituents map to synaptogenesis and synaptic structures, suggesting the unified logic of genomic functions coordinating region identity and connectivity. Evidence-supported examples of default operations of PPI-guided assemblies of hetero- and homodimers of Yamanaka factors, neurogenesis constituents, and protein components of postsynaptic density of excitatory and inhibitory synaptogenesis are reported with detailed analytical focus on human Claustrum. The foundational set of observations reported in this contribution should facilitate experimental and theoretical explorations of TE-seeded genomic codes for initiators of PPI chain reactions of protein dimerization creating pools of attractors to guide and accelerate the EMC assemblies.

At inception, eukaryotes solved the conflict of the physical dimensions of meter-sized linear chromatin fibers placed into micron-sized nuclei by employing two mechanisms: (i) fragmenting genomic DNA into sets of shorter segments, called chromosomes; (ii) compacting each chromosome by folding it into 3D chromatin arrays. Despite this physical segregation, eukaryotic genomes possess an intrinsic regulatory connectivity that facilitates remarkable chromosome-naive function-aligned integration and striking developmental precision in conveying genetic information from conception and embryogenesis to adulthood. In this contribution, gene ontology-guided proximity placement analyses of 8839 highly conserved retroviral Long Terminal Repeat (LTR) elements fixed in human genomes and linked to 5444 down-stream target genes revealed chromosome-naive compartmentalization and function-aligned integration along major developmental networks of the global genomic regulatory dominion (GRD), components of which operate during human embryogenesis, development, and adulthood. Evolution forged the GRD into a functionally consonant constellation of 26 genome-wide multimodular genomic regulatory networks (GRNs), each of which is defined by significant enrichment of numerous single gene ontology (GO)-specific traits. GRN coordinates appear scattered across chromosomes, occupying 5.5–15.09% of the human genome. Each GRN harbors 529–1486 regulatory LTRs derived from LTR7, MLT2A1, and MLT2A2 sequences, which appear quantitatively balanced according to their genome-wide abundance. GRNs govern the activities of between 199 and 805 down-stream target genes, including transcription factors, chromatin-state remodelers, signal-sensing and signal transduction mediators, enzymatic and receptor-binding effectors, intracellular complexes and extracellular matrix elements, and cell–cell adhesion molecules. GRNs consist of several hundred to thousands of smaller, GO enrichment-defined genomic regulatory modules (GRMs), which include from a dozen to hundreds of LTRs and down-stream target genes. GRMs appear to operate along specific phenotypic avenues on the timescale of an individual’s life-span, exerting profound effects on patterns of transcription, protein–protein interaction, developmental phenotypes, physiological traits, and pathological conditions in Modern Humans. Overall, this study identifies 69,573 statistically significant regulatory LTR-linked GRMs (binominal FDR q-value threshold of 0.001), including 27,601 GRMs validated by single GO-specific directed acyclic graph (DAG) analyses across six GO annotations. Collectively, the reported observations support the hypothesis that pan-primate endogenous retroviruses have made significant impacts on the evolution of the global regulatory connectivity of GRNs affecting the physiological traits and pathological conditions of Modern Humans, including phenotypes whose manifestations are considered human-specific.

The journal retracts the article “Triazole Modified Tetraiodothyroacetic Acid Conjugated to Polyethylene Glycol, a Thyrointegrin αvβ3 Antagonist as a Radio- and Chemo-Sensitizer in Pancreatic Cancer” [...]

Radioresistance is a substantial barrier to success in cancer management. A number of molecular mechanisms support radioresistance. We have shown experimentally that the thyroid hormone analogue receptor on the extracellular domain of integrin αvβ3 may modulate the state of radiosensitivity of tumor cells. Specifically, tetraiodothyroacetic acid (tetrac), a derivative of L-thyroxine (T4), can reduce radioresistance in cancer cells. In this review, we list a number of intrinsic signal transduction molecules and other host factors that have been reported to support/induce radioresistance in cancer cells and that are also subject to control by T4 through actions primarily initiated at integrin αvβ3. Additional preclinical evidence is needed to support these radioresistance-relevant actions of thyroid hormone.

Two distinct families of pan-primate endogenous retroviruses, namely HERVL and HERVH, infected primates germline, colonized host genomes, and evolved into the global genomic regulatory dominion (GRD) operating during human embryogenesis (HE). Analyzed in this contribution GRD derived from HERV sequences constitutes 8839 highly conserved fixed LTR elements linked to 5444 down-stream target genes forged by evolution into a functionally-consonant constellation of 26 genome-wide multimodular genomic regulatory networks (GRNs), each of which is defined by significant enrichment of numerous single gene ontology (GO)-specific traits. Locations of GRNs appear scattered across chromosomes to occupy from 5.5%-15.09% of human genome. Each GRN harbors from 529-1486 regulatory LTRs derived from LTR7, MLT2A1, and MLT2A2 sequences that appear quantitatively balanced according to their genome-wide abundance. GRNs integrate activities from 199-805 down-stream target genes, including transcription factors, chromatin-state remodelers, signal-sensing and signal-transduction mediators, enzymatic and receptor binding effectors, intracellular complexes and extracellular matrix elements, and cell-cell adhesion molecules. GRNs compositions consist of several hundred to thousands smaller GO enrichment-defined genomic regulatory modules (GRMs) combining from a dozen to hundreds LTRs and down-stream target genes, which appear to operate on individuals life-span timescale along specific phenotypic avenues to exert profound effects on patterns of transcription, protein-protein interactions, developmental phenotypes, physiological traits, and pathological conditions of Modern Humans. Overall, this study identifies 69,573 statistically significant regulatory LTR-linked GRMs (Binominal FDR q-value threshold of 0.001), including 27,601 GRMs validated by the single GO-specific directed acyclic graph (DAG) analyses across six GO annotations. Collectively, reported herein observations support the hypothesis that pan-primate ERVs have made significant impacts on evolution of GRNs affecting physiological traits and pathological conditions of Modern Humans, including phenotypes manifestation of which considered human-specific.

Emergence during mammalian evolution of common and divergent traits of genomic regulatory networks (GRNs) encompassing ubiquitous, compositionally nearly identical yet quantitatively distinct panels of DNA sequences of transcription factor binding sites (TFBS) for 716 proteins is reported. The evolutionary-conserved foundation of these GRNs appears assembled from arrays of DNA codes for ~770 TFBS, including 65 instances of immediately adjacent TFBS for two distinct TFs. A majority of protein constituents of these GRNs (770 of 716; 98%) is defined by Gene Ontology (GO) features of sequence-specific double-stranded DNA binding (GO: 1990837). Genome-wide and individual chromosome-level analyses of 17,935 ATAC-seq-defined brain development regulatory regions (BDRRs) revealed nearly universal representations of TFBS for TF-constituents of these networks, TFBS densities of which appear consistently higher within thousands BDRRs of Modern Humans compare to Chimpanzee. Transposable elements (TE), including LTR/HERV, SINE/Alu, SVA, and LINE families, appear to harbor consensus regulatory nodes of identified herein highly conserved sequence-specific double-stranded DNA binding networks. Notably, selections of quantitative features of TFBS panels of these GRNs manifest individual chromosome-specific profiles and species-specific divergence patterns. Collectively, this contribution highlights a previously unrecognized essential function of genomic DNA sequences derived from multiple TE families in providing genome-wide regulatory seed templates of sequence-specific double-stranded DNA binding GRNs. Since DNA sequences of TFBS panels for 716 proteins are encoded by transposons that remain active in genomes of present day humans, namely SVA and LINE families, retrotransposition-mediated spread of seeds for these GRNs may contribute to continuing divergent genomic evolution of human and chimpanzee brain development.

Two distinct families of pan-primate endogenous retroviruses, namely HERVL and HERVH, infected primates germline, colonized host genomes, and evolved into the global retroviral genomic regulatory dominion (GRD) operating during human embryogenesis (HE). HE retroviral GRD constitutes 8839 highly conserved fixed LTR elements linked to 5444 down-stream target genes forged by evolution into a functionally-consonant constellation of 26 genome-wide multimodular genomic regulatory networks (GRNs), each of which is defined by significant enrichment of numerous single gene ontology (GO)-specific traits. Locations of GRNs appear scattered across chromosomes to occupy from 5.5%-15.09% of human genome. Each GRN harbors from 529-1486 retroviral LTRs derived from LTR7, MLT2A1, and MLT2A2 sequences that are quantitatively balanced according to their genome-wide abundance. GRNs integrate activities from 199-805 down-stream target genes, including transcription factors, chromatin-state remodelers, signal-sensing and signal-transduction mediators, enzymatic and receptor binding effectors, intracellular complexes and extracellular matrix elements, and cell-cell adhesion molecules. GRNs compositions consist of several hundred to thousands smaller GO enrichment-defined genomic regulatory modules (GRMs) combining from a dozen to hundreds LTRs and down-stream target genes, which appear to operate on individuals life-span timescale along specific phenotypic avenues to exert profound effects on patterns of transcription, protein-protein interactions, developmental phenotypes, physiological traits, and pathological conditions of Modern Humans. Overall, this study identifies 69,573 statistically significant retroviral LTR-linked GRMs (Binominal FDR q-value threshold of 0.001), including 27,601 GRMs validated by the single GO-specific directed acyclic graph (DAG) analyses across six GO annotations.

During millions years of primate evolution, two distinct families of pan-primate endogenous retroviruses, namely HERVL and HERVH, infected primates’ germline, colonized host genomes and evolved to contribute to creation of the global retroviral genomic regulatory dominion (GRD) operating during human embryogenesis. Retroviral GRD constitutes of 8839 highly conserved LTR elements linked to 5444 down-stream target genes forged by evolution into a functionally-consonant constellation of 26 genome-wide multimodular genomic regulatory networks (GRNs) each of which is defined by significant enrichment of numerous single gene ontology-specific traits. Locations of GRNs appear scattered across chromosomes to occupy from 5.5% to 15.09% of the human genome. Each GRN harbors from 529 to 1486 human embryo retroviral LTR elements derived from LTR7, MLT2A1, and MLT2A2 sequences that are quantitatively balanced according to their genome-wide abundance. GRNs integrate activities from 199 to 805 down-stream target genes, including transcription factors, chromatin-state remodelers, signal sensing and signal transduction mediators, enzymatic and receptor binding effectors, intracellular complexes and extracellular matrix elements, and cell-cell adhesion molecules. GRN’s compositions consist of several hundred to thousands smaller gene ontology enrichment analysis-defined genomic regulatory modules (GRMs), each of which combines from a dozen to hundreds LTRs and down-stream target genes. Overall, this study identifies 69,573 statistically significant retroviral LTR-linked GRMs (Binominal FDR q-value < 0.001), including 27,601 GRMs validated by the single ontology-specific directed acyclic graph (DAG) analyses across 6 gene ontology annotations databases. These observations were corroborated and extended by execution of a comprehensive series of Gene Set Enrichment Analyses (GSEA) of retroviral LTRs down-stream target genes employing more than 70 genomics and proteomics databases, including a large panel of databases developed from single-cell resolution studies of healthy and diseased human’s organs and tissues. Genes assigned to distinct GRNs and GRMs appear to operate on individuals’ life-span timescale along specific phenotypic avenues selected from a multitude of down-stream gene ontology-defined and signaling pathways-guided frameworks to exert profound effects on patterns of transcription, protein-protein interactions, developmental phenotypes, physiological traits, and pathological conditions of Modern Humans. GO analyses of Mouse phenotype databases and GSEA of the MGI Mammalian Phenotype Level 4 2021 database revealed that down-stream regulatory targets of human embryo retroviral LTRs are enriched for genes making essential contributions to development and functions of all major tissues, organs, and organ systems, that were documented by numerous developmental defects in a single gene KO models. Genes comprising candidate down-stream regulatory targets of human embryo retroviral LTRs are engaged in protein-protein interaction (PPI) networks that have been implicated in pathogenesis of human common and rare disorders (3298 and 2071 significantly enriched records, respectively), in part, by impacting PPIs that are significantly enriched in 1783 multiprotein complexes recorded in the NURSA Human Endogenous Complexome database and 6584 records of virus-host PPIs documented in Virus-Host PPI P-HIPSTer 2020 database. GSEA-guided analytical inference of the preferred cellular targets of human embryo retroviral LTR elements supported by analyses of genes with species-specific expression mapping bias in Human-Chimpanzee hybrids identified Neuronal epithelium, Radial Glia, and Dentate Granule Cells as cell-type-specific marks within a Holy Grail sequence of embryonic and adult neurogenesis. Observations reported in this contribution support the hypothesis that evolution of human embryo retroviral LTR elements created the global GRD consisting of 26 gene ontology enrichment-defined genome-wide GRNs. Decoded herein the hierarchical super-structure of retroviral LTR-associated GRD and GRNs represents an intrinsically integrated developmental compendium of thousands GRMs congregated on specific genotype-phenotypic trait associations. Many highlighted in this contribution GRMs may represent the evolutionary selection units driven by inherent genotype-phenotype associations affecting primate species’ fitness and survival by exerting control over mammalian offspring survival genes implicated in reduced fertility and infertility phenotypes. Mechanistically, programmed activation during embryogenesis and ontogenesis of genomic constituents of human embryo retroviral GRD coupled with targeted epigenetic silencing may guide genome-wide heterochromatin patterning within nanodomains and topologically-associated domains during differentiation, thus affecting 3D folding dynamics of linear chromatin fibers and active transcription compartmentalization within interphase chromatin of human cells.

Abstract Evolution created two distinct families of pan-primate endogenous retroviruses, namely HERVL and HERVH, which infected primates’ germline, colonized host genomes, and evolved into the global retroviral genomic regulatory dominion (GRD) operating during human embryogenesis. Retroviral GRD constitutes 8839 highly conserved fixed LTR elements linked to 5444 down-stream target genes forged by evolution into a functionally-consonant constellation of 26 genome-wide multimodular genomic regulatory networks (GRNs), each of which is defined by significant enrichment of numerous single gene ontology (GO)-specific traits. Locations of GRNs appear scattered across chromosomes to occupy from 5.5%-15.09% of the human genome. Each GRN harbors from 529–1486 human embryo retroviral LTRs derived from LTR7, MLT2A1, and MLT2A2 sequences that are quantitatively balanced according to their genome-wide abundance. GRNs integrate activities from 199–805 down-stream target genes, including transcription factors, chromatin-state remodelers, signal-sensing and signal-transduction mediators, enzymatic and receptor binding effectors, intracellular complexes and extracellular matrix elements, and cell-cell adhesion molecules. GRN’s compositions consist of several hundred to thousands smaller GO enrichment-defined genomic regulatory modules (GRMs), each of which combines from a dozen to hundreds LTRs and down-stream target genes. Overall, this study identifies 69,573 statistically significant retroviral LTR-linked GRMs (Binominal FDR q-value < 0.001), including 27,601 GRMs validated by the single GO-specific directed acyclic graph (DAG) analyses across 6 GO annotations. Gene Set Enrichment Analyses (GSEA) of retroviral LTRs down-stream targets employing > 70 genomics and proteomics databases (DB), including a large panel of DB developed from single-cell resolution studies of healthy and diseased human’s organs and tissues, demonstrate that genes assigned to distinct GRNs and GRMs appear to operate on individuals’ life-span timescale along specific phenotypic avenues selected from a multitude of GO-defined and signaling pathways-guided frameworks to exert profound effects on patterns of transcription, protein-protein interactions (PPI), developmental phenotypes, physiological traits, and pathological conditions of Modern Humans. GO analyses of Mouse phenotype DB and GSEA of the MGI Mammalian Phenotype Level 4 2021 DB revealed that down-stream regulatory targets of human embryo retroviral LTRs are enriched for genes making essential contributions to development and functions of all major tissues, organs, and organ systems, that were corroborated by documented numerous developmental defects in a single gene KO models. Genes comprising candidate down-stream regulatory targets of human embryo retroviral LTRs are engaged in PPI networks that have been implicated in pathogenesis of human common and rare disorders (3298 and 2071 significantly enriched records, respectively), in part, by impacting PPIs that are significantly enriched in 1783 multiprotein complexes recorded in the NURSA Human Endogenous Complexome DB and 6584 records of virus-host PPIs documented in Virus-Host PPI P-HIPSTer 2020 DB. GSEA-guided analytical inference of the preferred cellular targets of human embryo retroviral LTR elements supported by analyses of genes with species-specific expression mapping bias in Human-Chimpanzee hybrids identified Neuronal epithelium, Radial Glia, and Dentate Granule Cells as cell-type-specific marks within a Holy Grail sequence of embryonic and adult neurogenesis. Decoded herein the hierarchical super-structure of retroviral LTR-associated GRD and GRNs represents an intrinsically integrated developmental compendium of thousands GRMs congregated on specific genotype-phenotype associations. Highlighted specific GRMs may represent the evolutionary selection units which are driven by inherent genotype-phenotype associations affecting primate species’ fitness and survival by exerting control over mammalian offspring survival genes implicated in reduced fertility and infertility phenotypes. Mechanistically, programmed activation during embryogenesis and ontogenesis of genomic constituents of human embryo retroviral GRD coupled with targeted epigenetic silencing may guide genome-wide heterochromatin patterning within nanodomains and topologically-associated domains during differentiation, thus affecting 3D folding dynamics of linear chromatin fibers and active transcription compartmentalization within interphase chromatin of human cells.

Apoptosis is induced in cancer cells and tumor xenografts by the thyroid hormone analogue tetraiodothyroacetic acid (tetrac) or chemically modified forms of tetrac. The effect is initiated at a hormone receptor on the extracellular domain of plasma membrane integrin αvβ3. The tumor response to tetrac includes 80% reduction in size of glioblastoma xenograft in two weeks of treatment, with absence of residual apoptotic cancer cell debris; this is consistent with efferocytosis. The molecular basis for efferocytosis linked to tetrac is incompletely understood, but several factors are proposed to play roles. Tetrac-based anticancer agents are pro-apoptotic by multiple intrinsic and extrinsic pathways and differential effects on specific gene expression, e.g., downregulation of the X-linked inhibitor of apoptosis (XIAP) gene and upregulation of pro-apoptotic chemokine gene, CXCL10. Tetrac also enhances transcription of chemokine CXCR4, which is relevant to macrophage function. Tetrac may locally control the conformation of phagocyte plasma membrane integrin αvβ3; this is a cell surface recognition system for apoptotic debris that contains phagocytosis signals. How tetrac may facilitate the catabolism of the engulfed apoptotic cell debris requires additional investigation.

Background: In neuroendocrine tumors, the norepinephrine transporter (NET) is very active and has been exploited for diagnostic imaging purposes and/or therapy with localized radiotherapy. Integrin αvβ3 is generously expressed by and/or activated on cancer cells, but not by nonmalignant cells. Purpose: In the present investigation, the anticancer efficacy of the dual targeting of norepinephrine transporter (NET), benzylguanidine (BG), and thyrointegrin αvβ3 receptors antagonist triazole tetraiodothyroacetic acid (TAT) conjugated via the non-cleavable linker polyethylene glycol (P, PEG400) in the treatment of human neuroblastoma was evaluated. Experimental approach: The synthesized dual targeting compound, a novel new chemical entity named BG-P400-TAT, has purity > 98% and was formulated and tested in neuroblastoma models using neuroblastoma cell lines (SK-N-FI, SMS-KCN and SMS-KANR) implanted in SCID and NSG mice models. Key Results: BG-P400-TAT demonstrated significant (**P<0.01, ***P< 0.001) suppression of neuroblastoma tumor progression, growth, and viability in both mice models implanted with the neuroblastoma. The pharmacokinetic and biodistribution profile of BG-P400-TAT showed a significant increase in BG-P400-TAT levels in plasma and xenografts of NSG compared to SCID mice. Further our RNAseq genome-wide expression profiling experiments in neuroblastoma cell line SKNAS results showed that BG-P400-TAT treatment altered the signal transduction pathways, intracellular multiprotein complexes and Independent GSEA. Conclusion & Implications: BG-P400-TAT represents a potential lead candidate for the treatment of neuroblastoma and other neuroendocrine tumors.

Targeted DNA sequences conservation analyses of 17 primate species demonstrated that human endogenous retroviruses (HERV) LTR7/HERVH and LTR5_Hs/HERVK appear to have distinct evolutionary histories charted by evidence of the earliest presence and expansion of highly-conserved (HC) LTR sequences. HC-LTR7 loci were mapped to genomes of Old World Monkeys (18% of all HC-LTR7 loci), suggesting that LTR7/HERVH have entered germlines of primates in Africa after the separation of the New World Monkey lineage. HC-LTR5_Hs loci have been identified in the Gibbon’s genome (24% of all HC-LTR5_Hs loci), suggesting that LTR5_Hs/HERVK successfully colonized primates’ germlines after the segregation of Gibbons’ species. Subsequently, both LTR7 and LTR5_Hs undergo a marked ∼4-5-fold expansion in genomes of Great Apes. Timelines of quantitative expansion of both LTR7 and LTR5_Hs loci during evolution of Great Apes appear to replicate the consensus evolutionary sequence of increasing cognitive and behavioral complexities of non-human primates, which seems particularly striking for LTR7 loci and 11 distinct LTR7 subfamilies. Consistent with previous reports, identified in this study 351 human-specific (HS) insertions of LTR7 (175 loci) and LTR5_Hs (176 loci) regulatory sequences have been linked to genes implicated in establishment and maintenance of naïve and primed pluripotent states and preimplantation embryogenesis phenotypes. Unexpectedly, HS regulatory LTRs appear linked with genes encoding markers of 12 distinct cells’ populations of fetal gonads, as well as genes implicated in physiology and pathology of human spermatogenesis, including Y-linked spermatogenic failure, oligo- and azoospermia. Granular investigations of genes linked with eleven LTR7 subfamilies revealed that mammalian offspring survival (MOS) genes seem to remain one of consistent regulatory targets throughout ∼30 MYA of the divergent evolution of LTR7 loci. Differential GSEA of MOS versus non-MOS genes identified clearly discernable dominant enrichment patterns of phenotypic traits affected by MOS genes linked with LTR7 (562 MOS genes) and LTR5_Hs (126 MOS genes) regulatory loci across the large panel of genomics and proteomics databases reflecting a broad spectrum of human physiological and pathological traits. GSEA of LTR7-linked MOS genes identified more than 2200 significantly enriched records of human common and rare diseases and gene signatures of 466 significantly enriched records of Human Phenotype Ontology traits, including 92 genes of Autosomal Dominant Inheritance and 93 genes of Autosomal Recessive Inheritance. One of the most informative categories of genes linked with LTR7 elements were genes implicated in functional and morphological features of central nervous system, including genes regulating synaptic transmission and protein-protein interactions at synapses, as well as gene signatures differentially regulated in cells of distinct neurodevelopmental stages and morphologically diverse cell types residing and functioning in human brain. These include Neural Stem/Precursor cells, Radial Glia cells, Bergman Glia cells, Pyramidal cells, Tanycytes, Immature neurons, Interneurons, Trigeminal neurons, GABAergic neurons, and Glutamatergic neurons. GSEA of LTR7-linked regulatory targets identified significantly enriched sets of genes encoding markers of more than 80 specialized types of neurons and markers of 521 human brain regions, most prominently, subiculum and dentate gyrus amongst top significantly enriched records. These observations were validated and extended by identification and characterization of 1944 genes comprising high-fidelity down-steam regulatory targets of LTR7 and/or LTR5_Hs loci, which are markedly enriched for genes implicated in neoplasm metastasis, intellectual disability, autism, multiple cancer types, Alzheimer’s, schizophrenia, and other brain disorders. Despite distinct evolutionary histories of retroviral LTRs, genes representing down-stream regulatory targets of LTR7 and LTR5_Hs elements exert the apparently cooperative and exceedingly broad phenotypic impacts on human physiology and pathology. Observations reported in this contribution highlight the need to accelerate the in-depth experimental and translational explorations of these important genomic determinants of Modern Humans’ health and disease states.

Background Acute myeloid leukemia (AML) is associated with poor long-term survival, even with newer therapeutic agents. Here, we show the results of our preclinical study, in which we evaluated the efficacy of a new thyrointegrin αvβ3 antagonist, named fluorobenzyl polyethylene glycol conjugated tetraiodothyroacetic acid (fb-PMT). Methods and Results fb-PMT (NP751) is a potent αvβ3 antagonist of molecular weight of 2,478.9 Da. it represents a conjugate of tetraiodothyroacetic acid (tetrac) and monodisperse polyethylene glycol (PEG36), with a 4-fluorobenzyl group capping the other end of the PEG. fb-PMT effectively suppresses the malignant growth of human acute myeloid leukemia (AML) after successful engraftment in transgenic NSG-S xenograft mouse models of either established human AML cell line or primary AML cells. Daily treatment with fb-PMT (1–10 mg/kg body weight) subcutaneously (s.c.) for 3–4 weeks was associated with marked regression of leukemogenesis and extended survival in both models. The efficiency of the fb-PMT therapy was verified using in vivo imaging system (IVIS) imaging, flow cytometry, and histopathological examination to monitor the engraftment of leukemic cells in the bone marrow and other organs. fb-PMT therapy for 3–4 weeks at 3 and 10 mg/kg daily doses exhibited significant reduction (p < 0.0001) of leukemic cell burden of 74% and >95%, respectively. All fb-PMT-treated mice in the 10 mg/kg treatment arm successfully maintained remission after discontinuing the daily treatment. Comprehensive fb-PMT safety assessments demonstrated excellent safety and tolerability at multiple folds above the anticipated human therapeutic doses. Lastly, our genome-wide microarray screens demonstrated that fb-PMT works through the molecular interference mechanism with multiple signaling pathways contributing to growth and survival of leukemic cells. Conclusion Our preclinical findings of the potent anticancer activities of fb-PMT and its favorable safety profiles warrant its clinical investigation for the effective and safe management of AML.

Thyroid hormone L thyroxine stimulates pancreatic carcinoma cell proliferation via thyrointegrin αvβ3 receptors, and antagonist tetraiodothyroacetic acid (tetrac) inhibits cancer cell growth. Chemically modified bis-triazole-tetrac conjugated with polyethylene glycol (P-bi-TAT) has higher binding affinity to αvβ3 receptors compared to tetrac. We investigated the antiproliferation effect of P-bi-TAT in pancreatic cancer cells (SUIT2) and its radio- and chemo-sensitizing roles in a mouse model of pancreatic cancer. P-bi-TAT treatment increased tumor-targeted radiation-induced cell death and decreased tumor size. P-bi-TAT acted as a chemo-sensitizer and enhanced the 5-fluorouracil (5FU) effect in decreasing pancreatic tumor weight compared to 5FU monotherapy. Withdrawal of treatment continued the tumor regression; however, the 5FU group showed tumor regrowth. The mechanisms of the anti-cancer activity of P-bi-TAT on SUIT2 cells were assessed by microarray experiments, and genome-wide profiling identified significant alterations of 1348 genes' expression. Both down-regulated and up-regulated transcripts suggest that a molecular interference at the signaling pathway-associated gene expression is the prevalent mode of P-bi-TAT anti-cancer activity. Our data indicate that non-cytotoxic P-bi-TAT is not only an anti-cancer agent but also a radio-sensitizer and chemo-sensitizer that acts on the extracellular domain of the cell surface αvβ3 receptor.

Abstract Background Thyrointegrin αvβ3 receptors are unique molecular cancer therapeutic targets because of their overexpression on cancer and rapidly dividing blood vessel cells compared and quiescent on normal cells. A macromolecule, TriAzole Tetraiodothyroacetic acid (TAT) conjugated to polyethylene glycol with a lipophilic 4-fluorobenyl group (fb-PMT and NP751), interacts with high affinity (0.21 nM) and specificity with the thyrointegrin αvβ3 receptors on the cell surface without nuclear translocation in contrast to the non-polymer conjugated TAT. Methods The following in vitro assays were carried out to evaluate NP751 including binding affinity to different integrins, transthyretin (TTR)-binding affinity, glioblastoma multiforme (GBM) cell adhesion, proliferation assays, nuclear translocations, chorioallantoic membrane model of angiogenesis, and microarray for molecular mechanisms. Additionally, in vivo studies were carried out to evaluate the anticancer efficacy of NP751, its biodistribution, and brain GBM tumor versus plasma levels kinetics. Results NP751 demonstrated a broad spectrum of antiangiogenesis and anticancer efficacy in experimental models of angiogenesis and xenografts of human GBM cells. Tumor growth and cancer cells’ viability were markedly decreased (by > 90%; P < .001) in fb-PMT-treated U87-luc or 3 different primary human GBM xenograft-bearing mice based on tumor in vivo imaging system (IVIS) imaging and histopathological examination, without relapse upon treatment discontinuation. Additionally, it effectively transports across the blood-brain barrier via its high-affinity binding to plasma TTR with high retention in brain tumors. NP751-induced effects on gene expression support the model of molecular interference at multiple key pathways essential for GBM tumor progression and vascularization. Conclusions fb-PMT is a potent thyrointegrin αvβ3 antagonist with potential impact on GBM tumor progression.

Chemically modified forms of tetraiodothyroacetic acid (tetrac), an L-thyroxine derivative, have been shown to exert their anticancer activity at plasma membrane integrin αvβ3 of tumor cells. Via a specific hormone receptor on the integrin, tetrac-based therapeutic agents modulate expression of genes relevant to cancer cell proliferation, survival and energy metabolism. P-bi-TAT, a novel bivalent tetrac-containing synthetic compound has anticancer activity in vitro and in vivo against glioblastoma multiforme (GBM) and other types of human cancers. In the current study, microarray analysis was carried out on a primary culture of human GBM cells exposed to P-bi-TAT (10−6 tetrac equivalent) for 24 h. P-bi-TAT significantly affected expression of a large panel of genes implicated in cancer cell stemness, growth, survival and angiogenesis. Recent interest elsewhere in ATP synthase as a target in GBM cells caused us to focus attention on expression of genes involved in energy metabolism. Significantly downregulated transcripts included multiple energy-metabolism-related genes: electron transport chain genes ATP5A1 (ATP synthase 1), ATP51, ATP5G2, COX6B1 (cytochrome c oxidase subunit 6B1), NDUFA8 (NADH dehydrogenase (ubiquinone) FA8), NDUFV2I and other NDUF genes. The NDUF and ATP genes are also relevant to control of oxidative phosphorylation and transcription. Qualitatively similar actions of P-bi-TAT on expression of subsets of energy-metabolism-linked genes were also detected in established human GBM and pancreatic cancer cell lines. In conclusion, acting at αvβ3 integrin, P-bi-TAT caused downregulation in human cancer cells of expression of a large number of genes involved in electron transport and oxidative phosphorylation. These observations suggest that cell surface thyroid hormone receptors on αvβ3 regulate expression of genes relevant to tumor cell stemness and energy metabolism.

We have developed a DNA aptamer-conjugated graphene field-effect transistor (GFET) biosensor platform to detect receptor-binding domain (RBD), nucleocapsid (N), and spike (S) proteins, as well as viral particles of original Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) coronavirus and its variants in saliva samples. The GFET biosensor is a label-free, rapid (≤20 min), ultrasensitive handheld wireless readout device. The limit of detection (LoD) and the limit of quantitation (LoQ) of the sensor are 1.28 and 3.89 plaque-forming units (PFU)/mL for S protein and 1.45 and 4.39 PFU/mL for N protein, respectively. Cognate spike proteins of major variants of concern (N501Y, D614G, Y453F, Omicron-B1.1.529) showed sensor response ≥40 mV from the control (aptamer alone) for fM to nM concentration range. The sensor response was significantly lower for viral particles and cognate proteins of Middle East Respiratory Syndrome (MERS) compared to SARS-CoV-2, indicating the specificity of the diagnostic platform for SARS-CoV-2 vs. MERS viral proteins. During the early phase of the pandemic, the GFET sensor response agreed with RT-PCR data for oral human samples, as determined by the negative percent agreement (NPA) and positive percent agreement (PPA). During the recent Delta/Omicron wave, the GFET sensor also reliably distinguished positive and negative clinical saliva samples. Although the sensitivity is lower during the later pandemic phase, the GFET-defined positivity rate is in statistically close alignment with the epidemiological population-scale data. Thus, the aptamer-based GFET biosensor has a high level of precision in clinically and epidemiologically significant SARS-CoV-2 variant detection. This universal pathogen-sensing platform is amenable for a broad range of public health applications and real-time environmental monitoring.

Repetitive DNA sequences (repeats) colonized two-third of human genome and a majority of repeats comprised of transposable genetic elements (TE). Evolutionary distinct categories of TE represent nucleic acid sequences that are repeatedly copied from and pasted into chromosomes at multiple genomic locations and acquired a multitude of regulatory functions. Here, genomics-guided maps of stemness regulatory signatures were drawn to dissect the contribution of TE to clinical manifestations of malignant phenotypes of human cancers. From patients’ and physicians’ perspectives, the clinical definition of a tumor’s malignant phenotype could be restricted to the early diagnosis of sub-types of malignancies with the increased risk of existing therapy failure and high likelihood of death from cancer. It is the viewpoint from which the understanding of stemness and malignant regulatory signatures is considered in this contribution. Genomics-guided analyses of experimental and clinical observations revealed the pivotal role of human stem cell-associated retroviral sequences (SCARS) in the origin and pathophysiology of clinically-lethal malignancies. SCARS were defined as the evolutionary- and biologically-related family of genomic regulatory sequences, the principal physiological function of which is to create and maintain the stemness phenotype during human preimplantation embryogenesis. For cell differentiation to occur, SCARS expression must be silenced and SCARS activity remains repressed in most terminally-differentiated human cells which are destined to perform specialized functions in the human body. Epigenetic reprogramming, de-repression, and sustained activity of SCARS results in various differentiation-defective phenotypes. One of the most prominent tissue- and organ-specific clinical manifestations of sustained SCARS activities is diagnosed as a pathological condition defined by a consensus of morphological, molecular, and genetic examinations as the malignant growth. Here, contemporary evidence are acquired, analyzed, and reported defining both novel diagnostic tools and druggable molecular targets readily amenable for diagnosis and efficient therapeutic management of clinically-lethal malignancies. These diagnostic and therapeutic approaches are based on monitoring of high-fidelity molecular signals of continuing SCARS activities in conjunction with genomic regulatory networks of thousands’ functionally-active embryonic enhancers affecting down-stream phenotype-altering genetic loci. Collectively, reported herein observations support a model of SCARS-activation triggered singular source code facilitating the intracellular propagation and intercellular (systemic) dissemination of disease states in the human body.

Background: Acute myeloid leukemia (AML) is associated with poor long-term survival, even with newer therapeutic agents. Here we show the results of our pre-clinical study, in which we evaluate the efficacy of a new thyrointegrin αvβ3 antagonist, named f luoro b enzyl P olyethylene glycol conjucated tetraiodothyroacetic acid (fb-PMT). Methods and Results: fb-PMT effectively suppresses the malignant growth of human acute myeloid leukemia (AML) after successful engraftment in transgenic NSG-S xenograft mouse models of either established human AML cell line or primary AML cells. Daily treatment with fb-PMT (1-10 mg/kg body weight) subcutaneously (s.c.) for 3-4 weeks was associated with marked regression of leukemogenesis and extended survival in both models. The efficiency of the fb-PMT therapy was verified using IVIS imaging, flowcytometry and histopathological examination to monitor the engraftment of leukemic cells in the bone marrow and other organs. fb-PMT therapy for 3-4 weeks at 3 and 10 mg/kg daily doses exhibited significant reduction ( P <0.0001) of leukemic cell burden of 74% and >95%, respectively. All fb-PMT-treated mice in the 10 mg/kg treatment arm successfully maintained remission after discontinuing the daily treatment. Comprehensive fb-PMT safety assessments demonstrated excellent safety and tolerability at multiple folds above the anticipated human therapeutic doses. Lastly, our genome-wide microarray screens demonstrated that fb-PMT works through the molecular interference mechanism with multiple signaling pathways contributing to growth and survival of leukemic cells . Conclusion: our preclinical findings of the potent anticancer activities of fb-PMT and its favorable safety profiles warrant its clinical investigation for the effective and safe management of AML.

Leukemic cells are able to receive and send several signals within bone marrow niche that play an important role in their survival. One of the important crosstalk is the interaction between the bone marrow microenvironment proteins (vitronectin, fibronectin, fibrinogen, and ostepontin) and thyrointegrin αVβ3 on leukemic cells, generating ligand-specific outside-in signals that are relevant to a variety of cell functions, including gene transcription, cell division, cell attachment, and motility