Valine can inhibit tumor growth

Amino acids are the basic components of proteins and important components of human tissues, playing the role of cell signal transduction, enzyme activity regulation, immune function and other physiological functions.

The abundances of amino acids in cells often change in different physiological and pathological states. Therefore, how the body senses the change of amino acid level and makes an adaptive response is an important scientific problem of metabolic stress and cell fate.

Abnormal amino acid sensing is closely related to cancer, diabetes, neurodegenerative diseases and aging process. Therefore, exploring the molecular mechanism of abnormal amino acid induction may provide a new target for the prevention or treatment of metabolic diseases and cancer. Valine, as an essential branched-chain amino acid, plays an important role in protein synthesis, neurobehavior, and leukemia progression. However, the mechanism and function of cellular sensing of valine remain unclear.

On November 20, 2024, Wang Ping's team from Tongji University School of Medicine / 10th Affiliated People's Hospital published a research paper entitled "Human HDAC6 senses valine abundancy to regulate DNA damage" in the journal Nature.

This study identified a novel valine-specific sensor, human deacetylase HDAC6, and revealed the specific mechanism by which valine restriction leads to nuclear translocation of HDAC6, thereby enhancing TET2 activity and inducing DNA damage.

Interestingly, this sensing mechanism is unique to primates, and further mechanism analysis revealed that primate HDAC6 contains a specific serine-rich glutamate-tetranectide (SE14) repeat domain and senses valine abundance through this domain. In terms of tumor treatment, moderate valine restriction or combination of PARP inhibitors can effectively inhibit tumor growth.

This study reveals a novel mechanism by which nutritional stress regulates DNA damage through epigenetic modification, and proposes a novel strategy for tumor treatment with valine-restricted diet combined with PARP inhibitors.

Amino acid sensors usually need to combine amino acids in order to recognize and respond to changes in amino acid concentration inside and outside the cell, so as to perform their sensing function.

In order to systematically identify valine-binding proteins, biotinylated valine probes were used for immunocoprecipitate experiments combined with mass spectrometry, and unbiased screening of valine-binding proteins was performed by chemical biology.

The authors found that in addition to the known valyl tRNA synthetases (VARS), the deacetylase HDAC6 showed a stronger D-valine binding capacity compared to VARS. The authors further confirmed that HDAC6 can directly bind valine with an affinity of Kd ≈ 2μM through isotope binding experiments, isothermal titration calorimetry (ITC) experiments and thermal drift experiments. The analysis of the structural characteristics of amino acids recognized by sensing proteins is helpful to further understand the molecular mechanism of the change of amino acid abundance induced by cells. By analyzing the binding experiments of valine analogues, the authors found that HDAC6 recognizes the carboxyl terminal and side chain of valine and can tolerate the amino terminal modification. In addition, in HDAC6 knockout cells, the regulation of mTOR signaling pathway by valine restriction was not significantly different from that of the control group, suggesting that this binding was different from the traditional amino acid sensing signaling pathway.

In order to explore the important domain and function of HDAC6 sensing valine. The authors further determined that HDAC6 binds valine through its SE14 domain through the HDAC6 truncated body binding experiment. Surprisingly, the authors found by homology comparison that the SE14 domain is only present in HDAC6 in primates. Unlike primate (human and monkey) HDAC6, mouse HDAC6 does not bind to valine. This finding reveals the differences between different species in valine induction, suggesting that species evolution plays an important role in amino acid induction.

Based on the conclusion that HDAC6 directly binds valine through its SE14 domain, the authors speculated that changes in the binding strength of HDAC6 and valine may affect its structure and function when the abundance of valine in cells changes. Through a series of experiments and combined with the literature on the important role of the SE14 domain in the cytoplasmic retention of HDAC6, the authors found that intracellular valine deficiency can induce HDAC6 translocation to the nucleus. The enzyme active region (DAC1 and DAC2) binds to the active region (CD domain) of the DNA hydroxymethylase TET2, promoting the deacetylation of TET2, and then activating its enzyme activity. Using methylomics techniques such as WGBS, ACE-Seq and MAB-Seq, we further confirmed that intracellular valine starvation can promote active DNA demethylation through the HDAC6-TET2 signal axis. Previously, Andre Nussenzweig's team found that thymine DNA glycosylase (TDG) -dependent active DNA demethylation resulted in DNA single-strand damage on neuronal enhancer. By combining TET2 ChIP-Seq with high-throughput sequencing technology END-Seq and ddC S1 END-Seq, we determined that valine deficiency promotes DNA damage. The DNA damage induced by valine deficiency is also dependent on the single strand damage caused by TDG excision of oxymethylcytosine (5fC/5caC).

Taken together, the authors discovered novel valine sensors and for the first time elucidated the molecular mechanism by which valine limits the induction of DNA damage via the HDAC6-TET2-TDG signaling axis, adding a new dimension to the understanding of the function of amino acid stress in cell fate determination.

Dietary restriction or targeting of amino acid metabolism and sensing has become an adjunctive strategy for life extension and treatment of many diseases, including cancer. Given that valine deprivation can induce DNA damage, the authors further investigated whether valine restriction plays a role in cancer treatment. In a colorectal cancer xenograft tumor model, an appropriate valine-restricted diet (0.41% valine, w/w) significantly inhibited tumor growth with fewer side effects. In both the prevention and treatment groups, the authors further demonstrated that a valine-restricted diet inhibited tumorigenesis and progression using a colorectal cancer PDX model. In tumor samples, decreased valine levels were positively correlated with increased HDAC6 nuclear translocations, 5hmC levels, and DNA damage. Since inducing DNA damage is an anticancer therapy, it is clinically possible to block DNA repair by using PARP inhibitors. The authors found that the combination of valine-restricted diet and PARP inhibitor talazoparib significantly enhanced the antitumor effect, providing strong evidence for the therapy to treat cancer by inducing DNA damage.

In conclusion, the study found that HDAC6 in primates is a novel valine sensing protein independent of traditional sensors, revealing differences in valine sensing among different species, indicating the important role of biological evolution in amino acid sensing.

In addition, this study elucidates a new mechanism of the interactive regulation of nutritional metabolic stress, epigenetic regulation and DNA damage, broadens the importance of nutritional metabolic stress in stress biology, and finds that the combination of valine-restricted diet and PARP inhibitors can be used as a new strategy for cancer treatment.