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Tang, X.-Y.

Publications and source records attributed to Tang, X.-Y..

3 recordsLinked to original sources
bioRxiv2025

When splicing is not all or none: Implications for variant classification

Variants with intermediate functional effects--those that neither eliminate nor fully maintain normal gene function--represent an underrecognized source of genetic complexity and constitute a grey zone that challenges variant classification. Here, we address this issue using GT>GC (+2T>C) 5' splice-site variants as a tractable model, as approximately 15% of such substitutions retain variable amounts of wild-type (WT) transcript. Using residual WT transcript as a quantitative readout, we first show that disease-associated GT>GC variants known to generate substantial WT transcript (for example, SPINK1 c.194+2T>C, HBB c.315+2T>C, and BRCA2 c.8331+2T>C) consistently complicate classification efforts. We then carried out a locus-wide assessment of all 26 GT>GC substitutions in CFTR, applying SpliceAI delta donor-loss scores as an initial screen and cross-checking classifications in expert-curated database. This evaluation indicated that three variants with low or intermediate SpliceAI scores are likely to retain WT transcript. Minigene analyses of four selected CFTR variants, together with additional examination of a BAP1 GT>GC variant with conflicting clinical interpretations, illustrate the methodological challenges in predicting and experimentally quantifying residual WT transcript. These results emphasize that (i) in silico predictors cannot reliably discriminate between complete and partial splice disruption and (ii) experimental systems differ in their ability to detect subtle splicing outcomes. Overall, our integrative analysis shows that GT>GC variants generating appreciable WT transcript exemplify a broader class of intermediate-effect alleles that complicate both computational prediction and experimental assessment, underscoring the need for classification frameworks that incorporate quantitative functional data and better capture the continuum of variant effects.

genetics↗
bioRxiv2023

Transcription regulation of SARS-CoV-2 receptor ACE2 by Sp1: a potential therapeutic target

Angiotensin-converting enzyme 2 (ACE2) is a major cell entry receptor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Induction of ACE2 expression may represent an effective tactic employed by SARS-CoV-2 to facilitate its own propagation. However, the regulatory mechanisms of ACE2 expression after viral infection remain largely unknown. By employing an array of 45 different luciferase reporters, we identify that the transcription factor Sp1 positively and HNF4 negatively regulate the expression of ACE2 at the transcriptional levels in HPAEpiC cells, a human lung epithelial cell line. SARS-CoV-2 infection promotes and inhibits the transcription activity of Sp1 and HNF4, respectively. The PI3K/AKT signaling pathway, which is activated by SARS-CoV-2 infection, is a crucial node for induction of ACE2 expression by increasing Sp1 phosphorylation, an indicator of its activity, and reducing HNF4 nuclear location. Furthermore, we show that colchicine could inhibit the PI3K/AKT signaling pathway, thereby suppressing ACE2 expression. Inhibition of Sp1 by either its inhibitor mithramycin A or colchicine reduces viral replication and tissue injury in Syrian hamsters infected with SARS-CoV-2. In summary, our study uncovers a novel function of Sp1 in regulating ACE2 expression and suggests that Sp1 is a potential target to reduce SARS-CoV-2 infection.

microbiology↗
bioRxiv2018

First estimation of the scale of canonical 5’ splice site GT>GC mutations generating wild-type transcripts and their medical genetic implications

It has long been known that canonical 5 splice site (5SS) GT>GC mutations may be compatible with normal splicing. However, to date, the true scale of canonical 5SS GT>GC mutations generating wild-type transcripts, both in the context of the frequency of such mutations and the level of wild-type transcripts generated from the mutation alleles, remain unknown. Herein, combining data derived from a meta-analysis of 45 informative disease-causing 5SS GT>GC mutations (from 42 genes) and a cell culture-based full-length gene splicing assay of 103 5SS GT>GC mutations (from 30 genes), we estimate that [~]15-18% of the canonical GT 5SSs are capable of generating between 1 and 84% normal transcripts as a consequence of the substitution of GT by GC. We further demonstrate that the canonical 5SSs whose substitutions of GT by GC generated normal transcripts show stronger complementarity to the 5 end of U1 snRNA than those sites whose substitutions of GT by GC did not lead to the generation of normal transcripts. We also observed a correlation between the generation of wild-type transcripts and a milder than expected clinical phenotype but found that none of the available splicing prediction tools were able to accurately predict the functional impact of 5SS GT>GC mutations. Our findings imply that 5SS GT>GC mutations may not invariably cause human disease but should also help to improve our understanding of the evolutionary processes that accompanied GT>GC subtype switching of U2-type introns in mammals.

genetics↗