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Biomedical subjects

Haibo Liu

Publications and source records attributed to Haibo Liu.

16 recordsLinked to original sources

PPT1 is a negative regulator of STING signaling in cancer cells and its inhibition reactivates immune surveillance in cold tumors.

Immunotherapy modalities have revolutionized cancer treatment for a number of metastatic and treatment-refractory tumor types. Still, many malignancies that lack T cell infiltration and are termed immunologically "cold" fail to respond to these modalities. One approach to increase tumor immunogenicity has been to induce stimulator of interferon gene (STING) and downstream interferon signaling that is often dysregulated in cold tumors. Despite some early success of STING agonists in preclinical cancer models, these approaches have not been successful in the clinic due to poor tumor penetrance and systemic toxicities. Here, we performed a genome-wide CRISPR screen to uncover therapeutic targets to activate STING expression in human tumors. We identified the lysosomal hydrolase Palmitoyl Protein Thioesterase1 (PPT1) as a negative regulator of STING highly expressed in cold ovarian and prostate tumors. Genetic or pharmacological PPT1 suppression increased STING protein stability and its downstream activation of interferon and inflammatory cytokine signaling to enhance T cell migration. Treatment of preclinical prostate and ovarian cancer models expressing low levels of STING with the small molecule PPT1 inhibitor GNS561 enhanced STING expression and activation, leading to infiltration and activation of cytotoxic T cells that turned these tumors "hot" and reduced tumor growth, fibrosis, and dissemination without toxicity. Further analysis demonstrated that PPT1 is associated with reduced STING expression, CD8+ T cell numbers, overall survival, and immunotherapy outcomes in ovarian and prostate cancer patients. Thus, PPT1 inhibition may be a promising approach to activate STING and potentiate the effects of immunotherapy in cold tumors.

Membrane Proteins↗

Toward a designed, functioning genetic system with expanded-size base pairs: solution structure of the eight-base xDNA double helix.

We describe the NMR-derived solution structure of the double-helical form of a designed eight-base genetic pairing system, termed xDNA. The benzo-homologous xDNA design contains base pairs that are wider than natural DNA pairs by ca. 2.4 A (the width of a benzene ring). The eight component bases of this xDNA helix are A, C, G, T, xA, xT, xC, and xG. The structure was solved in aqueous buffer using 1D and 2D NMR methods combined with restrained molecular dynamics. The data show that the decamer duplex is right-handed and antiparallel, and hydrogen-bonded in a way analogous to that of Watson-Crick DNA. The sugar-phosphate backbone adopts a regular conformation similar to that of B-form DNA, with small dihedral adjustments due to the larger circumference of the helix. The grooves are much wider and more shallow than those of B-form DNA, and the helix turn is slower, with ca. 12 base pairs per 360 degrees turn. There is an extensive intra- and interstrand base stacking surface area, providing an explanation for the greater stability of xDNA relative to natural DNA. There is also evidence for greater motion in this structure compared to a previous two-base-expanded helix; possible chemical and structural reasons for this are discussed. The results confirm paired self-assembly of the designed xDNA system. This suggests the possibility that other genetic system structures besides the natural one might be functional in encoding information and transferring it to new complementary strands.

Base Pairing↗

A BAC clone-based physical map of ovine major histocompatibility complex.

An ovine bacterial artificial chromosome (BAC) library containing 190,000 BAC clones was constructed and subsequently screened to construct a BAC-based physical map for the ovine major histocompatibility complex (MHC). Two hundred thirty-three BAC clones were selected by 84 overgo probes designed on human, mouse, and swine MHC sequence homologies. Ninety-four clones were ordered by DNA fingerprinting to form contigs I, II, and III that correspond to ovine MHC class I-class III, class IIa, and class IIb. The minimum tiling paths of contigs I, II, and III are 15, 4, and 4 BAC clones, spanning approximately 1900, 400, and 300 kb, respectively. The order and orientation of most BAC clones in each contig were confirmed by BAC-end sequencing. An open gap exists between class IIa and class III. This work helps to provide a foundation for detailed study of ovine MHC genes and of evolution of MHCs in mammals.

Animals↗

A truncated C-terminal fragment of Mycobacterium tuberculosis HSP70 gene enhanced potency of HBV DNA vaccine.

DNA vaccine represents an attractive approach to therapy of chronic hepatitis B virus (HBV) infection because of its ability to generate antigen-specific immunity; nevertheless, there is still a need to increase the potency of DNA vaccine. Mycobacterium tuberculosis heat shock protein70 (HSP70) has both chaperon and cytokine functions, and has been shown to act as an adjuvant when co-administered with peptide antigens or given as fusion proteins. Here we evaluated the effects of two truncated HSP70 molecules, N-terminal domain (HSP70(1-360), amino acids 1-360) and C-terminal domain (HSP70(359-610), amino acids 359-610) of mycobacterial HSP70, on the potency of antigen-specific immunity generated by a HBV DNA vaccination. We found that only the HSP70(359-610)-fused HBV DNA vaccination resulted in a significant increase in hepatitis B surface antigen (HBsAg)-specific humoral response, while the HSP70(1-360)- or the complete HSP70 molecule-fused vaccine did not. Moreover, HSP70(359-610)-fused DNA vaccine did not induce anti-HSP70 antibody. Interestingly, HSP70(359-610) not only enhanced HBsAg-specific cytotoxic lymphocytes (CTL) responses but also overcame the epitope suppression caused by L(d)-restricted epitope. Meanwhile, HSP70(369-610) mediated T helper (Th) cell balance towards Th1 pathway. In a HBV transgenic mouse model, the HSP70(359-610) fusion vaccine facilitated clearance of circulating HBsAg and down-regulation of HBV replication. These results suggested that the truncated mycobacterial HSP70 molecule, HSP70(359-610), might be a superior candidate to deliver the adjuvant function in HBV DNA vaccination instead of the complete HSP70 molecule.

Adjuvants, Immunologic↗

New designs for DNA bases: expanded DNAs and oligofluorosides.

Properties and applications of two new classes of DNA base replacements are described. The first class is size-expanded DNA bases; these are benzo-homologous versions of A, C, T, G that yield base pairs 2.4 Angstroms larger than natural pairs. New studies have explored the ability of expanded DNA base pairs to be replicated by DNA polymerase enzymes. The second class of DNA-like molecules described here are "oligodeoxyfluorosides" (ODFs), which are deoxyribose-phosphate oligomers in which all nucleobases are replaced by hydrocarbon and heterocyclic fluorophores. These compounds have been prepared in large libraries and have been screened for unusual fluorescence and sensing properties.

Adenine↗

Helix-forming properties of size-expanded DNA, an alternative four-base genetic form.

We describe the chemical and biophysical characterization of a new four-base genetic system, in which all base pairs are larger than the natural pairs. A recent preliminary study showed that three sequences containing size-expanded DNA (xDNA) bases could form stable cooperative complexes. However, many of the standard and essential properties that natural DNA possesses were unexplored for this new class of helical assembly. We therefore undertook a study of several properties of this new genetic complex: strand stoichiometry, preferred strand polarity (i.e., parallel vs antiparallel), mismatch selectivity, base size selectivity, ionic strength dependence, fluorescence behavior, CD spectra, and sequence generality. Results showed that several sequences formed double-stranded helical complexes, and interestingly, a pyrimidine-rich strand of xDNA bases was shown to form a triple helical complex as well. A test of strand polarity showed a preference for antiparallel orientation, as does natural DNA. Mismatch and size selectivity were generally moderate to strong, with one exception. Ionic strength dependence varied by relatively small degrees from that of natural DNA, although a triple helical complex of xDNA showed more marked dependence. Spectral characteristics (fluorescence, CD) were found to be quite different than those of natural DNA, apparently because of large differences in the electronic character of the expanded pi-systems. Finally, several sequence contexts were found to form helices in a sequence-predictable manner. Two exceptions were noted and may be explained by competition from alternative folding structures and/or strong, single-stranded stacking. The viability of xDNA as an alternative genetic system and its possible biotechnological applications are discussed.

Base Pairing↗

Size-expanded analogues of dG and dC: synthesis and pairing properties in DNA.

We describe the completion of the set of four benzo-fused expanded DNA (xDNA) nucleoside analogues. We previously reported the development of benzo-fused analogues of dA and dT and their inclusion in an exceptionally stable new four-base genetic system, termed xDNA, in which the base pairs were expanded in size. Here we describe the preparation and properties of the second half of this nucleotide set: namely, the previously unknown dxC and dxG nucleosides. The dxC analogue was prepared from the previously reported dxT nucleoside in three steps and 57% yield. The large-sized deoxyguanosine analogue was prepared from an intermediate in the synthesis of dxA, yielding dxG in 14 steps overall (2.4%). Suitably protected versions of the deoxynucleosides were prepared for oligonucleotide synthesis following standard procedures, and they were readily incorporated into DNA by automated synthesizer. "Dangling-end" measurements revealed that the benzo-fused homologues stack considerably more strongly on neighboring DNA sequences than do their natural counterparts. Base pairing experiments with xC or xG bases showed that they pair selectively with their Watson-Crick partners, but with mild destabilization, due apparently to their larger size. Overall, the data suggest that the fluorescent xG and xC bases may be useful probes of steric effects in the study of biological nucleotide recognition mechanisms. In addition, the completion of the xDNA nucleoside set makes it possible in the future to construct full four-base xDNA strands that can target any sequence of natural DNA and RNA.

Base Pairing↗

Label-free amplified bioaffinity detection using terahertz wave technology.

A new affinity biosensor based on pulsed terahertz (THz) wave technology has been used to monitor binding between biotin and avidin molecules. Amplified detection of avidin-biotin binding is obtained on supported membranes composed of biotin layers on quartz surface, which is modified with octadecanol. Agarose particles are conjugated with avidin and then applied to biotin, which is already bound to the octadecanol quartz surface, the biotin binds to the conjugate rapidly and causes an enhancement of the THz difference signal between biotin and biotin-avidin complexes by a factor greater than eight fold when compared to the same sample without agarose beads. The technique was able to detect less than 10.3 ng/cm2 avidin, thus, giving the THz system a detection capability of sub-thin solid films better than ellipsometry and reflectometry techniques. Further improvement is underway using highly refractive beads together with appropriate surface chemistry. This newly developed method is being saliently optimized for future application, including the detection of DNA hybridization and ligand-analyte affinity binding.

Affinity Labels↗

Expanded-size bases in naturally sized DNA: evaluation of steric effects in Watson-Crick pairing.

We describe physicochemical properties in DNA of altered-size nucleobases that retain Watson-Crick analogous hydrogen-bonding ability. Size-expanded analogues of adenine and thymine (xA and xT, respectively, which are expanded by benzo-fusion) were incorporated into natural DNA oligonucleotides, and their effects on helix stability were measured. Base stacking studies revealed that the two stretched analogues stack much more strongly than do their naturally sized counterparts. In contrast to this, pairing studies showed that single substitutions of the new bases are destabilizing to the natural helix as compared to A or T in standard A-T pairs in the same context, unless multiple adjacent substitutions are used. Interestingly, the size-expanded bases displayed selective recognition of the hydrogen-bonding complementary partners, suggesting that Watson-Crick analogous pairs were still formed despite local backbone strain. In an attempt to compensate for the added size of the expanded adenine, we tested a formamide deoxynucleoside, which Leonard proposed as a shortened thymine analogue (F(o)). Data showed, however, that this compound adopts a conformation unfavorable for pairing. On the basis of the combined thermodynamic data, we estimate the energetic cost of the 2.4 A stretching of an isolated base pair in DNA at ca. +1 to 2 kcal/mol. Notably, during the pairing studies, the two size-expanded nucleobases were found to display significant changes in fluorescence on formation of stacked versus unstacked structures, suggesting possible applications in probing nucleic acid structures and biochemical mechanisms.

Base Pairing↗

Solution structure of xDNA: a paired genetic helix with increased diameter.

We describe the structure in aqueous solution of an extended-size DNA-like duplex with base pairs that are approximately 2.4 A longer than those of DNA. Deoxy-lin-benzoadenosine (dxA) was employed as a dA analogue to form hydrogen-bonded base pairs with dT. The 10mer self-complementary extended oligodeoxynucleotide 5'-d(xATxAxATxATTxAT) forms a much more thermodynamically stable duplex than the corresponding DNA sequence, 5'-d(ATAATATTAT). NMR studies show that this extended DNA (xDNA) retains many features of natural B-form DNA, but with a few structural alterations due to its increased helical diameter. The results give insight into the structural plasticity of the natural DNA backbone and lend insight into the evolutionary origins of the natural base pairs. Finally, this structural study confirms the hypothesis that extended nucleobase analogues can form stable DNA-like structures, suggesting that alternative genetic systems might be viable for storage and transfer of genetic information.

Base Pairing↗

Obtaining transgenic plants using the bio-active beads method.

Several methods of transformation are currently available for delivering exogenous DNA into animal and plant cells. In this study, a novel and efficient transformation system for DNA delivery/expression with a capacity to transport DNA of high molecular weight was developed. This system can overcome the shortcomings of traditional transformation methods such as Agrobacterium-mediated transformation, particle bombardment, and the electroporation method. The method developed in this study uses calcium alginate micro beads to immobilize DNA molecules in combination with polyethylene glycol treatment. In addition, it is simple and low-cost, and requires limited equipment. Using this method, we have successfully transformed tobacco plants, screening by kanamycin resistance. The transformed genes in the transformants were confirmed by PCR and Southern hybridization.

Alginates↗

Toward a new genetic system with expanded dimensions: size-expanded analogues of deoxyadenosine and thymidine.

We describe the design, preparation, and properties of two key building blocks of a size-expanded genetic system. Nucleoside analogues of the natural nucleosides dA and dT are reported in which the fusion of a benzo ring increases their size by ca. 2.4 A. The expanded dA analogue (dxA), having a tricyclic base, was first reported by Leonard nearly three decades ago. We describe a shortened and more efficient approach to this compound. The expanded dT analogue (dxT), a methylquinazolinedione C-glycoside, was previously unknown; we describe its preparation in eight steps from 5-methylanthranilic acid. The key glycoside bond formation employed Pd-mediated coupling of an aryl iodide precursor with a dihydrofuran derivative of deoxyribose. Both nucleosides are shown to be efficient fluorophores, emitting light in the blue-violet range. The base-protected phosphoramidite derivatives were prepared, and short oligonucleotides containing them were characterized. The two size-expanded nucleosides are key components of a new four-base genetic system designed to form helical paired structures having a diameter greater than that of natural DNA. Elements of the design of this expanded genetic molecule, termed xDNA, are discussed, including the possibility of up to eight base pairs of information storage capability.

DNA↗

A four-base paired genetic helix with expanded size.

We describe a new molecular class of genetic-pairing system that has a native DNA backbone but has all four base pairs replaced by new, larger pairs. The base pairs include size-expanded analogs of thymine and of adenine, both extended by the width of a benzene ring (2.4 A). The expanded-diameter double helices are more thermodynamically stable than the Watson-Crick helix, likely because of enhanced base stacking. Structural data confirm a right-handed, double-stranded, and base-paired helical form. Because of the larger base size, all the pairs of this helical system are fluorescent, which suggests practical applications in detection of natural DNA and RNA. Our findings establish that there is no apparent structural or thermodynamic prohibition against genetic systems having sizes different from the natural one.

Adenine↗

Label-free bioaffinity detection using terahertz technology.

We report the first use of differential terahertz time-domain spectroscopy for bioaffinity sensing. Binding is observed by measuring the transmission of a thin layer of biotin bound to the sensor protein avidin. We demonstrate the THz wave transmission of a sub-micron-thick film and sensitivity to 0.1 microg cm(-2) of biotin. These results point the way for a host of biosensor applications using T-rays, or pulsed far-infrared (FIR) radiation.

Affinity Labels↗