Ubiquitination of proteins modifies protein function by either altering their activities, promoting their degradation, or altering their subcellular localization. Deubiquitinating enzymes are proteases that reverse this ubiquitination. Previous studies demonstrate that proteins that contain an ovarian tumor (OTU) domain possess deubiquitinating activity. This domain of ϳ130 amino acids is weakly similar to the papain family of proteases and is highly conserved from yeast to mammals. Here we report structural and functional studies on the OTU domain-containing protein from yeast, Otu1. We show that Otu1 binds polyubiquitin chain analogs more tightly than monoubiquitin and preferentially hydrolyzes longer polyubiquitin chains with Lys 48 linkages, having little or no activity on Lys 63 -and Lys 29 -linked chains. We also show that Otu1 interacts with Cdc48, a regulator of the ER-associated degradation pathway. We also report the x-ray crystal structure of the OTU domain of Otu1 covalently complexed with ubiquitin and carry out structure-guided mutagenesis revealing a novel mode of ubiquitin recognition and a variation on the papain protease catalytic site configuration that appears to be conserved within the OTU family of ubiquitin hydrolases. Together, these studies provide new insights into ubiquitin binding and hydrolysis by yeast Otu1 and other OTU domain-containing proteins.
In the light of novel cancer immune therapies, the status of antitumor inflammatory response and its regulation has gained much attention in patients with lung cancer. Ample datasets exist for non-small-cell lung cancer, but those for pulmonary neuroendocrine tumors are scarce and controversial. Here, tumor-associated inflammation, CD8+ cell infiltration and PD-L1 status were evaluated in a cohort of 57 resected carcinoids and 185 resected neuroendocrine carcinomas of the lung (58 large cell carcinomas and 127 small cell carcinomas). Data were correlated with clinicopathological factors and survival. Moderate or high tumor-associated inflammation was detected in 4 carcinoids (7%) and in 37 neuroendocrine carcinomas (20%). PD-L1 immunoreactivity was seen in immune cells of 73 (39%) neuroendocrine carcinomas, while tumor cells were labeled in 21 (11%) cases. Inflammatory cells and tumor cells in carcinoids lacked any PD-L1 expression. In neuroendocrine carcinomas, PD-L1 positivity in immune cells, but not in tumor cells, was associated with intratumoral CD8+ cell infiltration ( < 0.001), as well as with the severity of tumor-associated inflammation ( < 0.001). In neuroendocrine carcinomas, tumor-associated inflammation and PD-L1 positivity in immune cells correlated with prolonged survival and the latter factor was also an independent prognosticator ( < 0.01, hazard ratio 0.4 for overall survival, < 0.001 hazard ratio 0.4 for disease-free survival). Taken together, in neuroendocrine tumors, antitumor inflammatory response and PD-L1 expression are largely restricted to neuroendocrine carcinomas, and in this tumor entity, PD-L1 expression in inflammatory cells is positively correlated to patient survival.
This article describes the benefits of patient‐driven research in the field of head and neck oncology, reviews lessons learned from establishing partnerships with patients and caregivers, and serves as a model for further patient‐driven research endeavors.
Head and neck cancer survivors underwent training including that of effective communication and the basics of research methodology. They then drove the agendas for monthly meetings that included a multidisciplinary team of providers, facilitated by a physician champion (S.S.C.).
The advisors reported concrete areas for improvement of the clinical flow, including the formation of a dental oncology clinic and a post‐treatment survivorship clinic. They also refined research topics of interest, such as treatment regret. The advisors have also driven efforts to increase public awareness and have participated in cancer symposiums and local presentations.
Patient‐driven research improves the relevance and implementation of head and neck oncology research and clinical processes.
The Sulfolobus solfataricus protein acetyltransferase (PAT) acetylates ALBA, an abundant nonspecific DNA-binding protein, on Lys 16 to reduce its DNA affinity, and the Sir2 deacetylase reverses the modification to cause transcriptional repression. This represents a "primitive" model for chromatin regulation analogous to histone modification in eukaryotes. We report the 1.84-Å crystal structure of PAT in complex with coenzyme A. The structure reveals homology to both prokaryotic GNAT acetyltransferases and eukaryotic histone acetyltransferases (HATs), with an additional "bent helix" proximal to the substrate binding site that might play an autoregulatory function. Investigation of active site mutants suggests that PAT does not use a single general base or acid residue for substrate deprotonation and product reprotonation, respectively, and that a diffusional step, such as substrate binding, may be rate-limiting. The catalytic efficiency of PAT toward ALBA is low relative to other acetyltransferases, suggesting that there may be better, unidentified substrates for PAT. The structural similarity of PAT to eukaryotic HATs combined with its conserved role in chromatin regulation suggests that PAT is evolutionarily related to the eukaryotic HATs.Sulfolobus solfataricus, a thermoacidophile, is a member of the archaeal domain of life, and is likely to have diverged from bacteria and eukaryotes early during evolution. Despite its lack of a nucleus or other organelles, archaeal DNA replication and chromatin regulation seem to more closely resemble eukaryotes than bacteria (1, 2). Sulfolobus belongs to the phylum Crenarchaeota, which lacks histones, and instead uses two analogous chromatin proteins: Sul7d and ALBA 3 (acetylation lowers binding affinity). Both proteins have been shown to undergo post-translational modification in Sulfolobus. Sul7d is monomethylated (3) and ALBA is acetylated (4, 5). The acetylation of ALBA by protein acetyltransferase (PAT) on Lys 16 has been shown to reduce DNA-binding affinity, and deacetylation of ALBA by archaeal Sir2 deacetylase has been shown to repress transcription in what appears to be a primitive form of chromatin regulation by reversible post-translational modification (4, 5). PAT is also likely to regulate other proteins in Sulfolobus. Based on its homology to PAT from Salmonella enterica, PAT from Sulfolobus may also play a role in metabolism by regulating the activity of acetyl-coenzyme A synthetase (6).There are at least four families of histone acetyltransferases (HATs) in eukaryotes: the Gcn5/PCAF family that also shows sequence and structural homology to the GNAT (Gcn5-related acetyltransferase) superfamily, which includes many small molecule acetyltransferases such as antibiotic acetyltransferases (aminoglycoside N-acetyltransferases) and serotonin N-acetyltransferase; the MYST family, named from the founding members of MOZ, Ybf2/Sas3, Sas2, and Tip60; the metazoan-specific transcriptional coactivators p300 and CREB-binding protein; and the recently characterized fungal-s...
Thyroid nodules discovered incidentally are increasing the diagnosis of subclinical thyroid cancers. Not investigated previously, our study found that the mode of detection was not related to malignancy or surgery.
There is a significant association between BCNC stenosis and impaired speech discrimination, independent of degree of hearing loss. Further investigation is needed to determine whether BCNC stenosis is a poor prognostic factor for auditory rehabilitation.
Noise-induced hearing loss (NIHL) is a prevalent health risk. Inbred mouse strains 129S6/SvEvTac (129S6) and MOLF/EiJ (MOLF) show strong NIHL resistance (NR) relative to CBA/CaJ (CBACa). In this study, we developed quantitative trait locus (QTL) maps for NR. We generated F1 animals by intercrossing (129S6×CBACa) and (MOLF×CBACa). In each intercross, NR was recessive. N2 animals were produced by backcrossing F1s to their respective parental strain. The 232 N2-129S6 and 225 N2-MOLF progenies were evaluated for NR using auditory brainstem response. In 129S6, five QTL were identified on chromosomes (Chr) 17, 18, 14, 11, and 4, referred to as loci nr1, nr2, nr3, nr4, and nr5, respectively. In MOLF, four QTL were found on Chr 4, 17, 6, and 12, referred to as nr7, nr8, nr9, and nr10, respectively. Given that NR QTL were discovered on Chr 4 and 17 in both the N2-129S6 and N2-MOLF cross, we generated two consomic strains by separately transferring 129S6-derived Chr 4 and 17 into an otherwise CBACa background and a double-consomic strain by crossing the two strains. Phenotypic analysis of the consomic strains indicated that whole 129S6 Chr 4 contributes strongly to mid-frequency NR, while whole 129S6 Chr 17 contributes markedly to high-frequency NR. Therefore, we anticipated that the double-consomic strain containing Chr 4 and 17 would demonstrate NR across the mid-and high-frequency range. However, whole 129S6 Chr 17 masks the expression of mid-frequency NR from whole 129S6 Chr 4. To further dissect NR on 129S6 Chr 4 and 17, CBACa.129S6 congenic strains were generated for each chromosome. Phenotypic analysis of the Chr 17 CBACa.129S6 congenic strains further defined the NR region on proximal Chr 17, uncovered another NR locus (nr6) on distal Chr 17, and revealed an epistatic interaction between proximal and distal 129S6 Chr 17.
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