HDACs are enzymes found in virtually all eukaryotic cells. Their principal job is to remove acetyl chemical groups from histones, the spool-like proteins around which DNA is wound. When histones are heavily acetylated, chromatin is loose and genes can be read; when HDACs strip those acetyl groups away, chromatin condenses and gene transcription is silenced. The enzymes also modify non-histone proteins, influencing protein stability and activity directly. Based on their similarity to yeast proteins, HDACs are sorted into four classes: Classes I, II, and IV are zinc-dependent enzymes, while Class III, the sirtuins, depend on the metabolic cofactor NAD+. Class I members HDAC1, 2, 3, and 8 operate within multiprotein complexes and have been linked to cancer, inflammation, and infection. Class II enzymes shuttle between nucleus and cytoplasm, with HDAC6 in particular targeting non-histone substrates such as alpha-tubulin and molecular chaperones, thereby regulating autophagy and cellular architecture.

What the new review makes clear is that HDAC family members are not uniformly disrupted in endometriosis; instead, each subtype follows its own pattern, and those patterns appear to map onto different stages and features of disease. HDAC1 is broadly upregulated. Studies of endometriotic stromal cell lines show elevated HDAC1 mRNA and protein compared with normal cells, and immunohistochemistry of human lesions reveals strong staining in ovarian, skin, and gastrointestinal implants, with ovarian lesions showing the highest levels. Experiments with exosomes derived from ovarian endometrioma tissue found that the long non-coding RNA HOTAIR upregulates HDAC1 by suppressing microRNA-761, and that these exosomes promote ectopic lesion growth in mice. Genetic work has even linked HDAC1 single nucleotide polymorphisms to endometriosis risk in South Indian women, and in mouse models HDAC1 staining intensity rises as lesions progress. In deep infiltrating endometriosis, the most aggressive form, HDAC1 levels correlate positively with the degree of fibrosis.

HDAC2 tells a more complicated story. Its expression is elevated in some cell models and in skin lesions and eutopic endometrial stroma, yet lower in ovarian and peritoneal implants, and one study found HDAC2 staining actually declines as mouse lesions progress while being significantly lower in deep infiltrating disease than in ovarian endometrioma. Functionally, however, silencing HDAC2 in endometriotic cells activates the HNF4A/ARID1A axis, curbing proliferation and invasion while promoting apoptosis, and reduces lesion size in animals. HDAC3, by contrast, is downregulated, particularly in women with infertility. In baboon models of the disease, HDAC3 expression falls as disease advances, and mice lacking HDAC3 specifically in the uterus show implantation failure and defective decidualization, tied to de-repression of collagen genes and impaired progesterone signaling. HDAC8, meanwhile, is upregulated and strongly linked to fibrosis: a specific HDAC8 activator accelerated lesion growth and scarring in mice, while the inhibitor PCI-34,051 dose-dependently suppressed lesions, eased fibrosis, and reduced pain.

Among the Class II and III enzymes, HDAC6 stands out for its dependence on lesion subtype and cellular context. A tissue microarray analysis of 168 endometriotic lesions confirmed that HDAC6 is significantly elevated in both epithelium and stroma of deep infiltrating disease and positively correlated with fibrosis, but unchanged in ovarian endometrioma. In cases lacking ARID1A expression, epithelial HDAC6 was higher still, suggesting a possible route toward malignant transformation. On the sirtuin side, SIRT1 is persistently expressed throughout the menstrual cycle in patients, whereas in healthy endometrium it appears only during menstruation. Mice engineered to overexpress Sirt1 in the uterus show implantation failure and downregulation of progesterone target genes, and the SIRT1/BCL6 axis has been implicated in the progesterone resistance that characterizes the disease. SIRT3, which governs mitochondrial energy metabolism and antioxidant defense, is reduced in ovarian endometrioma tissue, while SIRT7 is upregulated in ectopic lesions and drives a metabolic shift from mitochondrial respiration toward glycolysis through the TUFM/SIRT7 axis, promoting proliferation and lesion growth in mice.

These expression anomalies feed into five interconnected pathological pathways. HDACs promote transcription of pro-inflammatory cytokines such as TNF-alpha, IL-1 beta, and IL-6, and weaken immune surveillance that would otherwise clear ectopic cells; exosomal miR-22-3p from peritoneal macrophages, for example, suppresses SIRT1 and activates the pro-invasive NF-kappaB pathway. HDAC1 and HDAC2 silence cyclin-dependent kinase inhibitors such as p21 and p57, pushing cells through the G1/S checkpoint, while SIRT1 upregulation is linked to reduced p53-mediated apoptosis. Invasion and migration are enhanced through epithelial-mesenchymal transition: HDAC1 suppresses RHOB, HDAC2 modulates the HNF4A/ARID1A axis, and HDAC6 remodels the cytoskeleton via alpha-tubulin deacetylation. HDAC1 also activates STAT3 to promote angiogenesis, and under hypoxia HDACs bind HIF-1 to drive adhesion, proliferation, and vessel-forming genes. Finally, HDACs regulate aromatase and estrogen receptor alpha, boosting local estrogen, and mediate epigenetic silencing of progesterone receptor B, the molecular basis of progesterone resistance.

The therapeutic logic follows directly. Histone deacetylase inhibitors, already established as anti-cancer drugs, can restore acetylation and reactivate silenced genes, and because epigenetic modifications are reversible, a single inhibitor can theoretically correct multiple pathological programs at once. Preclinical evidence is accumulating rapidly. Vorinostat, or SAHA, upregulated thioredoxin-binding protein-2 in endometrial stromal cells and promoted apoptosis through the TRX/TBP-2 system; in a mouse model of endometriosis-associated ovarian cancer it reduced tumor volume by inhibiting M2 macrophage polarization and lowering IL-10. Romidepsin, a Class I-specific inhibitor, inhibited HDAC activity in endometriotic epithelial cells with an IC50 of 6.5 nanomolar, induced histone acetylation, upregulated p21, and triggered caspase-dependent apoptosis. Trichostatin A reduced lesion area by 54.3 percent and relieved hyperalgesia in mice, suppressed NF-kappaB activation in endometriotic cells, which proved more than ten times more sensitive than normal cells, and induced apoptosis via NAG-1 in primary stromal cells.

Perhaps the most unexpected player is butyrate, a short-chain fatty acid produced by gut bacteria. Mouse studies showed endometriosis depletes butyrate-producing microbiota and colonic butyrate levels; fecal microbiota transfer confirmed that stool from diseased mice promotes lesion growth while normal stool inhibits it. Mechanistically, butyrate suppresses endometrial cell proliferation by activating GPR43 and GPR109A, inhibiting HDAC activity, and upregulating RAP1GAP, and it enhances ferroptosis sensitivity of ectopic cells through the FFAR2/PPAR-gamma/PINK1/Parkin axis. Serum butyrate in patients is reduced and inversely correlated with disease stage. Valproic acid, a widely used antiepileptic, also inhibits HDACs: in rats it dose-dependently shrank lesions and eased pain, and in human cells it silenced the CYP19 aromatase promoter, cutting estrogen synthesis, while reactivating the tumor suppressor C/EBPalpha. Selective HDAC8 inhibition with PCI-34,051 in a deep infiltrating disease model cut lesion weight by nearly two-thirds, reduced fibrosis, and relieved pain, hinting that subtype-selective drugs could avoid the off-target toxicity of pan-inhibitors.

Formidable obstacles remain before any of this reaches the clinic. No HDAC inhibitor is approved for endometriosis, and the known safety profile from oncology, including myelosuppression, thrombocytopenia, gastrointestinal symptoms, fatigue, and QT prolongation, is a serious concern for long-term use in benign disease. Reproductive safety is the thorniest issue: HDACs regulate gametogenesis, follicular development, implantation, and endometrial receptivity. Valproic acid carries a well-documented teratogenic risk of roughly 10 percent congenital malformation rate with pregnancy exposure, and embryonic exposure to butyrate or valproate can impair primordial germ cell development in mice. The review’s authors therefore call for subtype-selective inhibitors guided by single-cell expression maps, lesion-targeted delivery systems such as nanoparticles or exosomes to limit systemic exposure, combination strategies with hormonal, anti-inflammatory, or anti-angiogenic drugs, and biomarkers such as histone H3 acetylation states and circulating exosomal non-coding RNAs to stratify patients. If those pieces come together, epigenetic therapy could open the first genuinely new front against endometriosis in decades.

Subject of Research: The role of histone deacetylases and their inhibitors in the pathogenesis and treatment of endometriosis

Article Title: Research Progress of Histone Deacetylase and Its Inhibitors in Endometriosis

Article References: Xiong, S., Xu, J., Pu, J., Zhao, S., & Jiang, L. (2026). Research Progress of Histone Deacetylase and Its Inhibitors in Endometriosis. Reproductive Sciences. https://doi.org/10.1007/s43032-026-02184-7

Image Credits: AI Generated

DOI: 10.1007/s43032-026-02184-7

Keywords: endometriosis, histone deacetylase, HDAC inhibitors, epigenetics, vorinostat, romidepsin, trichostatin A, butyrate, valproic acid, fibrosis, progesterone resistance, reproductive health

The case began innocuously. The patient developed persistent hoarseness after an upper respiratory infection, and flexible laryngoscopy revealed a tumor arising from the left true vocal fold and extending toward the anterior commissure. Scans showed the mass confined to the glottic and supraglottic regions of the larynx, with no lymph node involvement or spread to distant organs. A biopsy was read as poorly differentiated squamous cell carcinoma, the most common and most familiar cancer of the head and neck. Because the histology looked conventional, and because the patient was initially staged with a potentially curable stage II disease, no test for NUT carcinoma was performed at that time. That decision, the report makes clear, would shape everything that followed.

Given his youth, the clinical team pursued a larynx-preserving strategy. He received induction chemotherapy with docetaxel, cisplatin, and cetuximab, followed by definitive chemoradiotherapy delivering seventy gray of intensity-modulated radiation with concurrent carboplatin and 5-fluorouracil. The primary tumor vanished completely on endoscopy and imaging, and maintenance therapy with the oral agent S-1 followed. For ten months the remission held. Then, in August 20X1, a recurrent lesion appeared at the original site, this time with paralysis of the vocal fold on the same side. Surgeons performed a total laryngectomy, removing the entire voice box, and pathology again showed moderately to poorly differentiated squamous cell carcinoma. The tumor, everyone assumed, had been dealt with.

It had not. Five months after surgery the patient developed painful swallowing, and imaging revealed an ulcerative mass on the posterior pharyngeal wall along with a solitary lesion in the iliac bone of the pelvis. Chemotherapy with cisplatin and docetaxel failed within a single cycle. The immune checkpoint inhibitor nivolumab, which works well in a subset of head and neck cancers, also failed within weeks. Comprehensive genomic profiling using the FoundationOne CDx assay detected no actionable alterations and, crucially, did not detect the BRD4::NUTM1 fusion—a false negative that is well documented for NUTM1 rearrangements, since DNA-based sequencing depends on where the breakpoint falls and how well that region is captured. The tumor’s biomarker profile, with a low tumor mutational burden of four mutations per megabase and a microsatellite-stable genome, offered no foothold for immunotherapy.

The definitive answer came only after a third salvage operation. Radical surgery at Aichi Cancer Center involved circumferential pharyngectomy, removal of the cervical esophagus, and reconstruction with a free segment of jejunum. When yet another recurrence appeared around the permanent tracheostoma five months later, additional immunohistochemistry on the resected tissue revealed diffuse nuclear staining for the NUT protein with a characteristic speckled pattern, alongside expression of the squamous markers p63 and p40. That single stain established the true diagnosis: NUT carcinoma. Retrospective testing of archived specimens using fluorescence in situ hybridization and RNA-based reverse transcription polymerase chain reaction confirmed a BRD4::NUTM1 fusion and proved the tumor had been NUT carcinoma from the very beginning, hidden behind a costume of ordinary squamous cancer.

The biology explains both the disguise and the ferocity. NUT carcinoma is driven by fusion proteins that typically join the tandem bromodomains of BRD4, which latch onto acetylated histones, to the NUT moiety, which recruits the p300/CBP acetyltransferases. The result is enormous hyperacetylated chromatin domains that force MYC expression and lock immature epithelial cells into a perpetual, proliferating, non-differentiating state. Because the cells still express squamous markers such as p63 and p40, pathologists see a plausible squamous cell carcinoma under the microscope. Only diffuse NUT immunostaining or molecular detection of the NUTM1 rearrangement separates the two diseases, and the report argues forcefully that young, non-smoking patients with aggressive, poorly differentiated tumors at midline or head and neck sites should trigger NUT-specific testing early.

With the diagnosis finally in hand, the team tried what mechanistic logic suggested should work. A bromodomain and extra-terminal, or BET, inhibitor—the class of drugs designed precisely to displace BRD4 from acetylated chromatin—was given through a clinical trial. The response was swift and dramatic: imaging at three months showed a marked partial regression. But after roughly six months, new lesions emerged and treatment stopped after eight cycles. Resistance to BET inhibition is thought to arise not through target mutations but through adaptive rewiring, in which tumor cells restore MYC-centered transcriptional programs using compensatory co-regulators such as p300/CBP and histone deacetylases, or bypass signaling through the MAPK/ERK pathway. A trial of the histone deacetylase inhibitor vorinostat, intended to attack that same acetylation circuitry from the opposite direction, produced no control whatsoever, consistent with functional redundancy between HDAC1 and HDAC2.

Even intensive cytotoxic chemotherapy delivered only borrowed time. Alternating cycles of vincristine, doxorubicin, and cyclophosphamide with ifosfamide and etoposide—a regimen borrowed from pediatric sarcoma practice—shrank the tumor markedly after two cycles, a reminder that this highly proliferative cancer retains some sensitivity to DNA-damaging agents. Yet regrowth appeared during the third cycle. Paclitaxel with cetuximab failed twice, and pembrolizumab combined with cisplatin and 5-fluorouracil achieved nothing. By June 20X4 the disease had replaced much of the anterior neck, and care shifted to palliation. Weekly applications of Mohs paste, a zinc chloride-based preparation rarely discussed in modern oncology, were used to harden the tumor surface and control malodorous exudate and bleeding, while morphine managed pain. The patient died in late July with his family present, having lost more than thirty kilograms from his baseline weight.

The autopsy delivered the report’s most consequential insight. Although the lungs were studded with innumerable metastatic nodules, each only a few millimeters across, the immediate cause of death was not disseminated cancer. It was overwhelming infection driven by uncontrolled locoregional disease—a massive twenty-three by twenty centimeter infiltrative tumor occupying the neck, invading the reconstructed jejunum, and compromising the airway, complicated by bilateral cavitary lung abscesses. This distribution matters therapeutically: fatal outcomes in NUT carcinoma may hinge less on distant metastasis than on relentless local progression along the aerodigestive tract, reinforcing evidence from prior series that durable locoregional control with surgery and radiotherapy underpins the only long-term survivals recorded.

The authors place their experience against the eighteen previously documented laryngeal cases, most of which arose in the supraglottis and claimed their victims within a year. Their patient’s glottic origin, four-year course, and autopsy characterization are all firsts for this site, and his survival of more than two years beyond the detection of an iliac bone metastasis stands against registry data showing zero percent two-year survival for metastatic head and neck NUT carcinoma. The broader lesson is uncomfortable but clear: despite its microscopic resemblance to squamous cell carcinoma, this is a transcription-addicted malignancy that standard head and neck regimens—induction chemotherapy, platinum-taxane combinations, and checkpoint inhibitors—all failed to hold in check. Some researchers now argue NUT carcinoma should be regarded as a molecularly defined subtype of squamous carcinoma rather than a separate entity, a framing that would push NUT testing into routine practice. Whether future patients benefit will likely depend on diagnosing the fusion early and combining epigenetic drugs with cytotoxic debulking and definitive local therapy, rather than adding agents one at a time to a network evolution too easily circumvents.

Subject of Research: Diagnosis and treatment resistance in BRD4::NUTM1 fusion laryngeal NUT carcinoma

Article Title: Laryngeal NUT Carcinoma With BRD4::NUTM1 Fusion: A 4‐Year Clinical Course Highlighting the Limitations of Current Multimodal Therapy

Article References: Kanno, M., Sasaki, C., Kato, E., Terada, H., Hanai, N., Sasaki, E., Fukushima, M., Masuishi, T., Takanari, K., Fukada, Y., Miyazaki, Y., Sonoda, Y., Kato, Y., Morikawa, T., Takabayashi, T., & Fujieda, S. (2026). Laryngeal NUT Carcinoma With BRD4 :: NUTM1 Fusion: A 4‐Year Clinical Course Highlighting the Limitations of Current Multimodal Therapy. Cancer Reports, 9(9), Article e70679. https://doi.org/10.1002/cnr2.70679

Image Credits: AI Generated

DOI: 10.1002/cnr2.70679

Keywords: NUT carcinoma, BRD4::NUTM1 fusion, laryngeal cancer, BET inhibitor, vorinostat, squamous cell carcinoma, NUTM1 rearrangement, chemoradiotherapy, immune checkpoint inhibitor, autopsy findings, epigenetic therapy, rare cancer