Study Challenges Long-Held Mechanism of HDAC Inhibitors in Cancer Treatment
核心洞察
Researchers at Baylor College of Medicine found that HDAC (搜索) inhibitors may not rely solely on HDAC enzyme inhibition for their anticancer effects, challenging decades of scientific understanding.
Unbiased bioinformatics analyses revealed no consistent correlation between HDAC (搜索) gene expression or genetic variants and most cancers or patient survival across TCGA data.
In mouse models, chemically modified SAHA (SAA (搜索)) lacking HDAC (搜索)-inhibiting activity retained anticancer effects comparable to the parent drug, reducing tumor weight by approximately 10-fold.
A new study published in Signal Transduction and Targeted Therapy is challenging the traditional understanding of how histone deacetylase (HDAC (搜索)) inhibitors function in cancer treatment. Researchers at Baylor College of Medicine and collaborating institutions present evidence suggesting that these drugs do not necessarily rely solely on HDAC enzyme inhibition but may also affect other pathways, calling for a reconsideration of their mechanism of action.
"For decades, scientists believed that these drugs blocked HDAC (搜索) enzymes, which drive cancer development by altering how genes are turned on and off," said corresponding author Dr. Zheng Sun, associate professor of medicine – endocrinology, diabetes and metabolism, and member of the Dan L Duncan Comprehensive Cancer Center at Baylor. "Yet, some findings do not support this idea. In some contexts, HDACs do not promote cancer, but act as tumor suppressors instead. Sometimes HDAC inhibitors can increase histone acetylation but with only moderate effects on gene expression."
Unbiased Analyses Reveal Lack of Universal HDAC (搜索)-Cancer Correlation
The research team conducted a series of unbiased bioinformatics analyses leveraging public databases, including The Cancer Genome Atlas (TCGA). Their findings showed that none of the HDACs exhibit consistent differential gene expression patterns between tumor and non-tumor tissues across major cancer types. Some HDACs, such as HDAC4, were found to be downregulated in breast cancer (搜索) (BRCA) and thyroid cancer (搜索) (THCA) compared to normal tissues, which contradicts their presumed oncogenic role.
Furthermore, there was no consistent correlation between HDAC (搜索) gene expression levels and cancer patient survival. For example, high HDAC11 expression was associated with a low survival rate in acute myeloid leukemia (搜索) (LAML) but a high survival rate in diffuse large B cell lymphoma (搜索) (DLBC), suggesting that HDAC11 might play opposite roles in different cancer types. HDACs also showed a low mutation rate in cancers compared to canonical oncogenes or tumor suppressor genes such as TP53, PTEN, or EGFR (搜索).
"Our unbiased bioinformatics analyses showed that HDACs are not always associated with cancer growth – different types of HDACs or their levels do not correlate consistently with most cancers or patient survival," said first author Dr. Chaitra Rai, postdoctoral fellow in the Sun lab.
CRISPR Library Screens Fail to Identify HDACs as Modulators of HDI Response
Using a genome-wide CRISPR activation (CRISPRa) library screen, the researchers sought to identify genes that modulate HDI-mediated cytotoxicity. The screen, conducted in Hep3B cells treated with SAHA or MS275, did not consistently enrich HDAC (搜索) genes. Instead, genes involved in apoptosis and proliferation showed robust enrichment. Specifically, anti-apoptotic/pro-proliferation genes BCL2L1 (搜索), MCL1, and EGFR (搜索) were positively enriched in the HDI-treated group, while pro-apoptotic/anti-proliferation genes such as BIK, PMAIP1, and BAK1 were negatively enriched.
Independent validation experiments confirmed that inducible overexpression of anti-apoptotic BCL2L1 (搜索) or BCL2 counteracted the cytotoxicity of SAHA or MS275, while overexpression of pro-apoptotic BIM potentiated HDI-induced cytotoxicity.
HDAC (搜索) Enzyme Activity Is Dispensable for Anticancer Effects
In a critical set of experiments, the team overexpressed dominant-negative, catalytically inactive Class I HDAC (搜索) mutants (HDAC1-Y303F, HDAC2-Y304F, HDAC3-Y298F, and HDAC8-Y306F) in cancer cell lines. While these YF mutants caused global histone H3K27 hyperacetylation comparable to that induced by Class I-specific HDIs (FK228 or MS275), they did not cause similar cytotoxicity.
"We also found that the anti-cancer effects of HDAC (搜索) inhibitor FK228 were independent of its ability to inhibit HDACs in a mouse model," Rai noted. "On HDAC inhibitors that block a family of HDACs, we eliminated their ability to inhibit the enzymes, yet the inhibitors retained most of their anti-cancer effects in a mouse model."
RNA-seq analysis revealed that FK228 treatment upregulated 11-fold more genes (914 vs. 77) than YF overexpression, with only 58 overlapping genes. Only 6.5% of FK228-activated genes were recapitulated by YF overexpression. HDI-unique differentially expressed genes were involved in various cancer-related pathways, while shared DEGs were not enriched in cancer-related pathways.
In Vivo Evidence from Mouse Models
In an in situ liver cancer mouse model using transposon-based oncogenes (β-catenin, c-Met, and c-Myc), FK228 treatment efficiently reduced luciferase activity, liver weight, and liver size, while YF overexpression did not change these parameters or affect FK228 effects. H&E staining revealed extensive tumor cell infiltrate in the control group, which was diminished after HDI treatment, accompanied by necrosis and inflammatory infiltrate.
In a separate subcutaneous allograft model using MC38 colon carcinoma cells, the researchers chemically modified SAHA by removing the hydroxamic zinc-binding group, yielding suberanilic acid (SAA (搜索)). While SAHA had an IC50 of 80 nM for inhibiting HDACs in HeLa nuclear extracts, SAA showed no HDAC (搜索)-inhibiting activity even at concentrations above 10,000 nM. Despite this, both SAHA and SAA reduced tumor weight by about 10-fold compared to vehicle control, without altering body weight. Immunostaining showed a significant decrease in proliferating cell nuclear antigen (PCNA) levels in tumors after both SAHA and SAA treatment.
Implications and Limitations
"We propose that HDAC (搜索) inhibitors may also interfere with other proteins and that targeting such proteins may suppress cancer," Sun said. "Identifying other molecular targets of HDAC inhibitors represents an important step toward improving cancer treatment."
The authors acknowledge several limitations. Whether the conclusions are generalizable to other cell lines, cancer models, or cancer types beyond those tested remains to be determined. The study focused on Class I HDACs, and whether the conclusions extend to other HDACs and HDIs requires further investigation. The true targets of HDIs remain elusive, and identifying authentic molecular targets represents an important next step requiring systematic, unbiased approaches.
The study was supported by multiple funding sources, with a complete list of contributing authors and their affiliations available in the publication.