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Han Ma

Publications and source records attributed to Han Ma.

7 recordsLinked to original sources
PubMed2026

CAGNet: a structure-aware clustering-alternated graph network for cell-cell interaction inference in spatial transcriptomics.

MOTIVATION: Understanding cell-cell interactions (CCIs) in spatial transcriptomics is crucial for uncovering the spatial organization and functional heterogeneity of tissues. However, existing graph-based models typically rely on static clustering or fixed adjacency structures, which limits their ability to capture dynamic cellular relationships. RESULTS: We propose CAGNet, a two-stage framework for CCI inference from spatial transcriptomics data. In Stage 1, a Graph Attention Network encoder with joint feature and graph reconstruction learns structure-aware node embeddings from spatial gene expression profiles. In Stage 2, an alternating optimization mechanism iteratively updates cluster centers via KL-guided soft assignment and refines node embeddings through spatial graph reconstruction, establishing a closed-loop between representation learning and clustering. Experiments on three 10x Genomics Visium datasets demonstrate that CAGNet consistently outperforms six CCI inference baselines across ACC, AUC, AP, Precision, Recall, and F1. CAGNet also achieves the highest Adjusted Rand Index on all three datasets against six spatial domain identification methods, confirming that the learned embeddings capture biologically relevant spatial organization. Information-theoretic analysis further shows that CAGNet retains the highest mutual information between input features and learned embeddings among all compared methods. Ablation studies and 5-fold cross-validation confirm the contribution of each component and the reproducibility of the results. AVAILABILITY: The proposed method is implemented in the CAGNet package available at http://github.com/mahan1233333-maker/CAGNet .

Spatial Transcriptomics↗
PubMed2006

In vitro selected Con1 subgenomic replicons resistant to 2'-C-methyl-cytidine or to R1479 show lack of cross resistance.

The HCV polymerase is an attractive target for the development of new and specific anti-HCV drugs. Herein, the characterization of the inhibitory effect of 2'-C-Methyl-Cytidine shows that it is a potent inhibitor of both genotype 1b and 1a HCV replicon replication, both of laboratory-optimized as well as of NS5B clinical isolates-chimera replicons. The corresponding 5'-triphosphate derivative is a potent inhibitor of native HCV replicase isolated from replicon cells and of the recombinant genotype 1b and 1a HCV polymerase-mediated RNA synthesis. Resistance to 2'-C-Methyl-Cytidine was mapped to amino acid substitution S282T in the NS5B coding region. Cross-resistance was observed to 2'-C-Methyl-Adenosine but not to interferon alpha-2a, to non-nucleoside HCV polymerase inhibitors or to R1479, a new and potent nucleoside inhibitor of NS5B polymerase. In vitro studies mapped resistance to R1479 to amino acid substitutions S96T and S96T/N142T of the NS5B polymerase. These mutations did not confer resistance to 2-C-Methyl-Cytidine, thus confirming the lack of cross-resistance between these two HCV inhibitors. These data will allow the optimization of new polymerase inhibitors and their use in combination therapy.

Antiviral Agents↗
PubMed2005

The novel nucleoside analog R1479 (4'-azidocytidine) is a potent inhibitor of NS5B-dependent RNA synthesis and hepatitis C virus replication in cell culture.

Hepatitis C virus (HCV) polymerase activity is essential for HCV replication. Targeted screening of nucleoside analogs identified R1479 (4'-azidocytidine) as a specific inhibitor of HCV replication in the HCV subgenomic replicon system (IC(50) = 1.28 microM) with similar potency compared with 2'-C-methylcytidine (IC(50) = 1.13 microM). R1479 showed no effect on cell viability or proliferation of HCV replicon or Huh-7 cells at concentrations up to 2 mM. HCV replicon RNA could be fully cleared from replicon cells after prolonged incubation with R1479. The corresponding 5'-triphosphate derivative (R1479-TP) is a potent inhibitor of native HCV replicase isolated from replicon cells and of recombinant HCV polymerase (NS5B)-mediated RNA synthesis activity. R1479-TP inhibited RNA synthesis as a CTP-competitive inhibitor with a K(i) of 40 nM. On an HCV RNA-derived template substrate (complementary internal ribosome entry site), R1479-TP showed similar potency of NS5B inhibition compared with 3'-dCTP. R1479-TP was incorporated into nascent RNA by HCV polymerase and reduced further elongation with similar efficiency compared with 3'-dCTP under the reaction conditions. The S282T point mutation in the coding sequence of NS5B confers resistance to inhibition by 2'-C-MeATP and other 2'-methyl-nucleotides. In contrast, the S282T mutation did not confer cross-resistance to R1479.

Antiviral Agents↗
PubMed2005

Activation of nuclear receptor coactivator PGC-1alpha by arginine methylation.

Peroxisome proliferator-activated receptor gamma coactivator 1alpha (PGC-1alpha), a tissue-specific and inducible transcriptional coactivator for several nuclear receptors, plays a key role in energy metabolism. We report here that PGC-1alpha coactivator activity is potentiated by arginine methylation by protein arginine methyltransferase 1 (PRMT1), another nuclear receptor coactivator. Mutation of three substrate arginines in the C-terminal region of PGC-1alpha abolished the cooperative coactivator function of PGC-1alpha and PRMT1, and compromised the ability of PGC-1alpha to induce endogenous target genes. Finally, endogenous PRMT1 contributes to PGC-1alpha coactivator activity, and to the induction of genes important for mitochondrial biogenesis.

Animals↗
PubMed2005

Inhibition of native hepatitis C virus replicase by nucleotide and non-nucleoside inhibitors.

A number of nucleotide and non-nucleoside inhibitors of HCV polymerase are currently under investigation as potential antiviral agents to treat HCV-infected patients. HCV polymerase is part of a replicase complex including the polymerase subunit NS5B together with other viral and host proteins and viral RNA. The RNA synthesis activity of the native replicase complex was inhibited by 3'-deoxy-CTP, a chain-terminating nucleotide analog, but not inhibited by non-nucleoside NS5B polymerase inhibitors of three different structural classes. The HCV replicase was also resistant to heparin, a broad-spectrum, RNA-competitive polymerase inhibitor. Prebinding of the recombinant NS5B protein with a RNA template rendered the polymerase largely resistant to the inhibition by heparin and the non-nucleoside inhibitors, but did not affect the inhibitory potency of 3'-deoxy-CTP. Therefore, the HCV replicase showed a similar pattern of inhibitor sensitivity as compared to RNA-bound NS5B. These results suggest that the native HCV replicase complex represents a stable and productive polymerase-RNA complex. The allosteric non-nucleoside NS5B polymerase inhibitors are inactive against established HCV replicase but may function antagonistically with the formation of a productive enzyme-template complex.

Allosteric Regulation↗
PubMed2003

The roles of protein-protein interactions and protein methylation in transcriptional activation by nuclear receptors and their coactivators.

Hormone-activated nuclear receptors (NR) bind to the promoters of their target genes and recruit coactivator proteins to help activate transcription. The p160 coactivators bind directly to activated NRs and recruit secondary coactivators CBP/p300 with protein acetyltransferase activity and CARM1 with protein methyltransferase activity. To further investigate the components of the p160 coactivator complex and their mechanisms of action, we have used two guiding assumptions. First, the coactivators constitute a signal transduction pathway that convey the signal from DNA-bound NRs to the transcription machinery. Second, each coactivator has signal input and signal output domains that facilitate signal transduction. These assumptions were used to address the mechanism by which CARM1 and the N-terminal region of p160 coactivators transmit activating signals to the transcription machinery. The p160-binding activity of CARM1 is in the same centrally located structural domain as the methyltransferase activity; the p160-binding domain anchors CARM1 to the target gene promoter and thereby serves as its signal input domain. CARM1 has two signal output mechanisms: the protein methyltransferase activity, which methylates histones and other proteins in the transcription initiation complex; and a strong autonomous activation function in the C-terminal region. We identified a protein, CCCP, which binds to the C-terminal region of CARM1 and cooperates synergistically with CARM1 to enhance NR function. We also defined the N-terminal region of p160 coactivators as another signal output domain, which binds a novel coactivator called coiled-coil coactivator (CoCoA). CoCoA acts synergistically with p160 coactivators to enhance NR function.

Acetyltransferases↗