Burden and trend of dietary risk-related colorectal cancer in China and its provinces: findings from the Global Burden of Disease Study 2019

OBJECTIVES

The objective of this experiment was to evaluate the spatial pattern and temporal trend of colorectal cancer (CRC) burden attributed to dietary risk factors in China from 1990 to 2019 using data from the Global Burden of Diseases, Injuries, and Risk Factors study (GBD) 2019.

METHODS

Numbers and age-standardised rates of deaths, disability-adjusted life years (DALYs) and corresponding average annual percentage change (AAPC) were determined. The joinpoint regression analysis was used to assess the temporal trends of CRC deaths and DALYs from 1990 to 2019.

RESULTS

In China, the number of diet-attributable CRC deaths and DALYs in 2019 were 90.41 (95% uncertainty interval: 65.69, 114.67) and 2234.06 (1609.96, 2831.24) per-1000 population, marking 2.05% and 1.68% annual increases since 1990, respectively. The region with the highest increase in age-standardised rates (ASRs) of diet-related CRC deaths and DALYs was in Taiwan with an AAPC of 2.00% (1.51, 2.48), whereas the highest decline in ASRs of CRC deaths and DALYs was observed in Hong Kong with an AAPC of -0.63% (-0.90, -0.35) (all P < 0.05). Nationally, men suffered higher CRC deaths and DALY burdens attributable to dietary risks than did women. Regarding the specific diet group, diets low in calcium, milk, and whole grains contributed to CRC deaths and DALYs the most.

CONCLUSIONS

Diet is an important contributor to increasing CRC burden in China. Necessary measures should be taken to kerb the growing burden attributed to dietary factors, particularly in males and in regions with middle Socio-demographic Index or lower.

[The 504th case: Multiple lymph node enlargement, renal insufficiency, blindness, and white matter lesions of the brain]

A 65-year-old male patient was admitted for recurrent lymph node enlargement for 5 years and elevated creatinine for 6 months. This patient was diagnosed with angioimmunoblastic T-cell lymphoma 5 years ago and underwent multiple lines of anti-tumor therapy, including cytotoxic chemotherapy; epigenetic modifying drugs such as chidamide and azacitidine; the immunomodulator lenalidomide; and targeted therapy such as rituximab, a CD20-targeting antibody, and brentuximab vedotin, which targets CD30. Although the tumor was considered stable, multiple virus activation (including BK virus, JC virus, and cytomegalovirus) accompanied by the corresponding organ damage (polyomavirus nephropathy, cytomegalovirus retinitis, and progressive multifocal leukoencephalopathy) occurred during anti-tumor treatment. Anti-tumor therapy was suspended and ganciclovir was used. The serum viral load decreased and organ functions were stabilized. The purpose of this report was to raise clinicians' awareness of opportunistic virus reactivation during anti-tumor treatment.

CloudDenseNet: Lightweight Ground-Based Cloud Classification Method for Large-Scale Datasets Based on Reconstructed DenseNet

Cloud observation serves as the fundamental bedrock for acquiring comprehensive cloud-related information. The categorization of distinct ground-based clouds holds profound implications within the meteorological domain, boasting significant applications. Deep learning has substantially improved ground-based cloud classification, with automated feature extraction being simpler and far more accurate than using traditional methods. A reengineering of the DenseNet architecture has given rise to an innovative cloud classification method denoted as CloudDenseNet. A novel CloudDense Block has been meticulously crafted to amplify channel attention and elevate the salient features pertinent to cloud classification endeavors. The lightweight CloudDenseNet structure is designed meticulously according to the distinctive characteristics of ground-based clouds and the intricacies of large-scale diverse datasets, which amplifies the generalization ability and elevates the recognition accuracy of the network. The optimal parameter is obtained by combining transfer learning with designed numerous experiments, which significantly enhances the network training efficiency and expedites the process. The methodology achieves an impressive 93.43% accuracy on the large-scale diverse dataset, surpassing numerous published methods. This attests to the substantial potential of the CloudDenseNet architecture for integration into ground-based cloud classification tasks.

Tissue Distribution of mtDNA Copy Number And Expression Pattern of An mtDNA-Related Gene in Three Teleost Fish Species

Teleosts are the most speciose vertebrates and have diverse swimming performance. Based on swimming duration and speed, teleosts are broadly divided into sustained, prolonged, and burst swimming fish. Teleosts with different swimming performance have different energy requirements. In addition, energy requirement also varies among different tissues. As mitochondrial DNA (mtDNA) copy number is correlated with ATP production, we speculated that mtDNA copy number varies among fish with different swimming performance, as well as among different tissues. In other species, mtDNA copy number is regulated by tfam (mitochondrial transcription factor A) through mtDNA compaction and mito-genome replication initiation. In order to clarify the tissue distribution of mtDNA copy number and expression pattern of tfam in teleosts with disparate swimming performance, we selected representative fish with sustained swimming (Pseudocaranx dentex), prolonged swimming (Takifugu rubripes), and burst swimming (Paralichthys olivaceus). We measured mtDNA copy number and tfam gene expression in 10 tissues of these three fish. The results showed the mtDNA content pattern of various tissues was broadly consistent among three fish, and high-energy demanding tissues contain higher mtDNA copy number. Slow-twitch muscles with higher oxidative metabolism possess a greater content of mtDNA than fast-twitch muscles. In addition, relatively higher mtDNA content in fast-twitch muscle of P. olivaceus compared to the other two fish could be an adaptation to their frequent burst swimming demands. And the higher mtDNA copy number in heart of P. dentex could meet their oxygen transport demands of long-distance swimming. However, tfam expression was not significantly correlated with mtDNA copy number in these teleosts, suggesting tfam may be not the only factor regulating mtDNA content among various tissues. This study can lay a foundation for studying the role of mtDNA in the adaptive evolution of various swimming ability in teleost fish.

Development of an Efficient, Effective, and Economical Technology for Proteome Analysis

Proteomics experiments have typically high economic and technical barriers to broad biomedical scientists, which not only result in costly supplies and accessories for sample preparation but also the reluctance to adapt new techniques. In the present study, we present an effective and efficient, yet economical technology, which we call E3technology, for proteomics sample preparation. By immobilizing silica microparticles into a polytetrafluoroethylene (PTFE) matrix, we developed a novel medium, which could be used as a robust and reliable proteomics platform to generate LCMS-friendly samples in a rapid and low-cost fashion. Using different formats of E3technology, including E3tip, E3filter, E3cartridge, and E3plate, we explored a variety of sample types in varied complexity, quantity, volume, and size, including bacterial, fungi, mammalian cells, mouse tissue, and human body fluids. We benchmark their performance against several established approaches. Our data suggest that E3technology outperforms many of the currently available techniques in terms of proteome identification and quantitation. It is widely applicable, highly reproducible, readily scalable and automatable, and is user-friendly and stress-free to non-expert proteomics laboratories. It does not require specialized expertise and equipment, and significantly lowers the technical and economical barrier to proteomics experiments. An enhanced version, E4technology, also opens new avenues to sample preparation for low input and/or low-cell proteomics analysis. The presented technologies by our study represent a breakthrough innovation in biomedical science, and we anticipate widespread adoption by the proteomics community.

Triubiquitin Probes for Identification of Reader and Eraser Proteins of Branched Polyubiquitin Chains

The important roles played by branched polyubiquitin chains were recently uncovered in proteasomal protein degradation, mitotic regulation, and NF-κB signaling. With the new realization of a wide presence of branched ubiquitin chains in mammalian cells, there is an urgent need of identifying the reader and eraser proteins of the various branched ubiquitin chains. In this work, we report the generation of noncleavable branched triubiquitin probes with combinations of K11-, K48-, and K63-linkages. Through a pulldown approach using the branched triUb probes, we identified human proteins that recognize branched triubiquitin structures including ubiquitin-binding proteins and deubiquitinases (DUBs). Proteomics analysis of the identified proteins enriched by the branched triubiquitin probes points to possible roles of branched ubiquitin chains in cellular processes including DNA damage response, autophagy, and receptor endocytosis. In vitro characterization of several identified UIM-containing proteins demonstrated their binding to branch triubiquitin chains with moderate to high affinities. Availability of this new class of branched triubiquitin probes will enable future investigation into the roles of branched polyubiquitin chains through identification of specific reader and eraser proteins, and the modes of branched ubiquitin chain recognition and processing using biochemical and biophysical methods.

Cross-Corpus Speech Emotion Recognition Based on Multi-Task Learning and Subdomain Adaptation

To solve the problem of feature distribution discrepancy in cross-corpus speech emotion recognition tasks, this paper proposed an emotion recognition model based on multi-task learning and subdomain adaptation, which alleviates the impact on emotion recognition. Existing methods have shortcomings in speech feature representation and cross-corpus feature distribution alignment. The proposed model uses a deep denoising auto-encoder as a shared feature extraction network for multi-task learning, and the fully connected layer and softmax layer are added before each recognition task as task-specific layers. Subsequently, the subdomain adaptation algorithm of emotion and gender features is added to the shared network to obtain the shared emotion features and gender features of the source domain and target domain, respectively. Multi-task learning effectively enhances the representation ability of features, a subdomain adaptive algorithm promotes the migrating ability of features and effectively alleviates the impact of feature distribution differences in emotional features. The average results of six cross-corpus speech emotion recognition experiments show that, compared with other models, the weighted average recall rate is increased by 1.89~10.07%, the experimental results verify the validity of the proposed model.

Photo-activatable Ub-PCNA probes reveal new structural features of the Saccharomyces cerevisiae Polη/PCNA complex

The Y-family DNA polymerase η (Polη) is critical for the synthesis past damaged DNA nucleotides in yeast through translesion DNA synthesis (TLS). TLS is initiated by monoubiquitination of proliferating cell nuclear antigen (PCNA) and the subsequent recruitment of TLS polymerases. Although individual structures of the Polη catalytic core and PCNA have been solved, a high-resolution structure of the complex of Polη/PCNA or Polη/monoubiquitinated PCNA (Ub-PCNA) still remains elusive, partly due to the disordered Polη C-terminal region and the flexibility of ubiquitin on PCNA. To circumvent these obstacles and obtain structural insights into this important TLS polymerase complex, we developed photo-activatable PCNA and Ub-PCNA probes containing a p-benzoyl-L-phenylalanine (pBpa) crosslinker at selected positions on PCNA. By photo-crosslinking the probes with full-length Polη, specific crosslinking sites were identified following tryptic digestion and tandem mass spectrometry analysis. We discovered direct interactions of the Polη catalytic core and its C-terminal region with both sides of the PCNA ring. Model building using the crosslinking site information as a restraint revealed multiple conformations of Polη in the polymerase complex. Availability of the photo-activatable PCNA and Ub-PCNA probes will also facilitate investigations into other PCNA-containing complexes important for DNA replication, repair and damage tolerance.

A large-scale genome-wide association analysis reveals QTL and candidate genes for intramuscular fat content in Duroc pigs

This study aimed at identifying genomic regions and genes associated with intramuscular fat content (IMF) in Duroc pigs using a weighted single-step GWAS. Data from 3912 pigs, of which 3770 animals were genotyped with GeneSeek Porcine 50K Bead chip, were used for the association analysis. We identified 19 genomic regions that each explained >1% of the additive genetic variance associated with IMF. Notably, a consistent QTL on SSC7 (117.42-117.92 Mb) was confirmed, explaining 3.70% of the additive genetic variance, and two genes, BDKRB2 and ATG2B, were highlighted as promising candidates for IMF. Two QTL (SSC7, 94.19-94.64 Mb; SSC14, 123.25-123.75 Mb), which harbored MED6 and MAP3K9 genes and TCF7L2 gene respectively, were newly identified as associated with IMF. In conclusion, we identified a consistent QTL and additional genomic regions and genes that contributed to the genetic variance of IMF using a large-scale sample size of genotyped pigs and genealogical information.

Translating Fecobionics Into a Technique That Addresses Clinical Needs for Objective Perineal Descent Measurements

INTRODUCTION

Perineal descent is a phenomenon associated with anorectal dysfunction. It is diagnosed by defecography but subjected to manual measurements on the images/videos and interobserver bias. Fecobionics is a simulated feces for assessing important physiological parameters during defecation. Here, we translate Fecobionics into a new method for estimation of perineal descent based on electronic signals from the embedded inertial measurement units (IMUs).

METHODS

A displacement measurement method by a combined zero-velocity update and gravity compensation algorithm from IMUs was developed. The method was verified in a robot model, which mimicked perineal descent motion.

RESULTS

The method correlated well with the reference (R = 0.9789) and had a deviation from the peak displacement (range 0.25-2.5 cm) of -0.04 ± 0.498 cm. The method was further validated in 5 human experiments with comparison to the benchmark defecography technology (R = 0.79).

DISCUSSION

The proposed technology is objective, i.e., electronic measurements rather than by fluoroscopy or MRI. The development may impact clinical practice by providing a resource-saving and objective technology for diagnosing perineal descent in the many patients suffering from anorectal disorders. The technology may also be used in colon experiments with Fecobionics and for other gastrointestinal devices containing IMUs such as ingestible capsules like the Smartpill.

Chemical methods for protein site-specific ubiquitination

Ubiquitination is an important protein post-translational modification regulating many cellular processes in eukaryotes. Ubiquitination is catalyzed by a three-enzyme cascade resulting in the conjugation of the C-terminal carboxylate of ubiquitin (Ub) to the ε-amino group of a lysine residue in the acceptor protein via an isopeptide bond. In vitro enzymatic ubiquitination utilizing Ub ligases has been successfully employed to generate Ub dimers and polymers. However, limitations of the enzymatic approach exist, particularly due to the requirement of specific Ub ligase for any given target protein and the low catalytic efficiency of the Ub ligase. To achieve an in-depth understanding of the molecular mechanism of Ub signaling, new methods are needed to generate mono- and poly-ubiquitinated proteins at a specific site with defined polyubiquitin chain linkage and length. Chemical methods offer an attractive solution to the above-described challenges. In this review, we summarize the recently developed chemical methods for generating ubiquitinated proteins using synthetic and semisynthetic approaches. These new tools and approaches, as an important part of the Ub toolbox, are crucial to our understanding and exploitation of the Ub system for novel therapeutics.

Photocaged Cell-Permeable Ubiquitin Probe for Temporal Profiling of Deubiquitinating Enzymes

Photocaged cell-permeable ubiquitin probe holds promise in profiling the activity of cellular deubiquitinating enzymes (DUBs) with the much needed temporal control. Here we report a new photocaged cell-permeable ubiquitin probe that undergoes photoactivation upon 365 nm UV treatment and enables intracellular deubiquitinating enzyme profiling. We used a semisynthetic approach to generate modular ubiquitin-based probe containing a tetrazole-derived warhead at the C-terminus of ubiquitin and employed a cyclic polyarginine cell-penetrating peptide (cR₁₀) conjugated to the N-terminus of ubiquitin via a disulfide linkage to deliver the probe into live cells. Upon 365 nm UV irradiation, the tetrazole group is converted to a nitrilimine intermediate in situ, which reacts with nearby nucleophilic cysteine residue from the DUB active site. The new photocaged cell-permeable probe showed good reactivity toward purified DUBs, including USP2, UCHL1, and UCHL3, upon photoirradiation. The Ub-tetrazole probe was also assessed in HeLa cell lysate and showed robust labeling only upon photoactivation. We further carried out protein profiling in intact HeLa cells using the new photocaged cell-permeable ubiquitin probe and identified DUBs captured by the probe using label-free quantitative (LFQ) mass spectrometry. Importantly, the photocaged cell-permeable ubiquitin probe captured DUBs specifically in respective G1/S and G2/M phases in synchronized HeLa cells. Moreover, using this probe DUBs were profiled at different time points following the release of HeLa cells from G1/S phase. Our results showed that photocaged cell-permeable probe represents a valuable new tool for achieving a better understanding of the cellular functions of DUBs.

An analysis of the variations and clinical applications of the lateral circumflex femoral artery

BACKGROUND

Identifying the arterial variation of the lateral circumflex femoral artery (LCFA) is a vital step in planning surgical and radiological approach. The aim of the study was to evaluate the variations and discuss the clinical correlates of the LCFA.

MATERIALS AND METHODS

Fifty eight adult cadavers (male 45, female 13) with 115 usable sides were used to assess and classify the origin and branches of the LCFA. Also its external diameter, distance from mid-inguinal ligament to sites of origin from the profunda femoris artery or femoral arteries.

RESULTS

There were seven types of LCFA variations in this sample. We classified them as types A to G, of which type A was normal, that is, the one showing a single LCFA arising from the profunda femoris artery. Nearly 50.43% of the sample had type B-G variations, each having 13, 10, 23, 4, 4, and 3 cases, accounting for 11.30%, 8.70%, 20.00%, 3.48%, 3.48%, and 2.61%, respectively.

CONCLUSIONS

There are many variant types in the LCFA. To avoid iatrogenic injuries, clinicians must have a sound understanding of the variation types of this important blood vessel.

Activity-Based Ubiquitin Probes for Investigation of Deubiquitinases

Ubiquitination is emerging as an important post-translational modification (PTM) for numerous cellular functions including protein degradation, DNA damage repair and tolerance, and cell cycle progression. Compared with other small-molecule modifiers found in phosphorylation, acetylation and glycosylation, ubiquitin is a small protein modifier that exists as either a single ubiquitin or a polyubiquitin chain. Furthermore, the polyubiquitin chains are formed via various linkages imparting an additional layer of specificity in cellular signaling. In order to adequately study ubiquitin signaling and particularly deubiquitination, a number of ubiquitin activity-based probes (ABPs) were developed and utilized in understanding the deubiquitinase (DUBs) function. Here, we focus on the current state of the DUB ABP development and their application in understanding DUB function and specificity for polyubiquitin chains and ubiquitinated proteins.

The applied anatomy and clinical significance of the proximal, V1 segment of vertebral artery

BACKGROUND

The aim of the study was to probe the morphological features of the proximal segment (V1) of vertebral artery (VA) in a sample of Chinese cadavers.

MATERIALS AND METHODS

The origin, course and outer diameter at origin of the pre-vertebral part of the VAs were evaluated in 119 adult cadavers.

RESULTS

It was found that 94.12% of the VAs originated from the subclavian arteries, bilaterally. The variant origins were present in 5.88% of the cadavers and all originated directly from the arch of the aorta. All the variations were observed on the left side of male cadavers. The average outer diameters at origin of the normal and variation groups were 4.35 ± 1.00 mm and 4.82 ± ± 1.42 mm, respectively, p = 0.035. In the normal group, but not in the variation group, the average diameter in the males was significantly larger than that in the females (4.50 ± 0.99 mm, 3.92 ± 0.92 mm, respectively, p = 0.000). In addition, only 5 cadavers in the normal group had hypoplastic VAs (4.20%, 4 males, 3 right-sided). Vertebral artery dominance (VAD) was present in 91 (69 males) out of 112 cadavers and more common on the left (n = 48). In addition, 3 cadavers satisfied conditions for coexistence of VAD and vertebral artery hypoplasia. All 7 cadavers in the variation group exhibited VAD, which was more common on the right side (n = 5).

CONCLUSIONS

The morphologic variations and frequencies described above have implications for the early prevention, abnormal anatomy detection, accurate diagnosis, safe surgery and endovascular treatment of cardiovascular and neurological disease.

Induction of M2 Macrophages Prevents Bone Loss in Murine Periodontitis Models

Periodontitis is characterized by the progressive destruction of tooth-supporting alveolar bone, which is mainly caused by chronic inflammation in response to persistent bacterial insult. It has recently become clear that the pathogenesis of periodontitis is associated with a high ratio of proinflammatory M1 (classically activated) macrophages to anti-inflammatory M2 (alternatively activated). To decrease the inflammatory activity, we locally delivered the C-C motif chemokine ligand 2 (CCL2) using controlled-release microparticles (MPs). CCL2 is known to promote chemotaxis of M0 or M2 phenotype macrophages to the inflamed site and induce M2 phenotype polarization locally. Our in vitro data showed that CCL2 increased the number of M2 phenotype macrophages, decreased TNF-α secretion, and enhanced chemotaxis of RAW264.7 cells toward CCL2 MPs. Moreover, we induced periodontal disease in 2 animal models through inoculation of Porphyromonas gingivalis and ligature around the murine molar. Micro-computed tomography analysis showed significant reduction of alveolar bone loss in the CCL2 MP treatment group when compared with a blank MP group and a no-treatment periodontitis group in both models. Immunohistologic analysis showed a significant increase in the M2 phenotype subset and a decrease in the M1 phenotype subset in the CCL2 MP group of the P. gingivalis-induced model. Also, in both models, tartrate-resistant acidic phosphatase staining showed significantly fewer numbers of osteoclasts in the CCL2 MP group in alveolar bone area. Moreover, quantitative polymerase chain reaction results showed a significant increase in IL-1RA (interleukin 1 receptor antagonist) mRNA expression and a decrease in RANKL (receptor activator of nuclear factor kappa-Β ligand) mRNA expression in the CCL2 MP group in the ligature model. In summary, manipulation of endogenous M2 phenotype macrophages with CCL2 MPs decreased the M1 phenotype:M2 phenotype ratio and prevented alveolar bone loss in mouse periodontitis models. The delivery of CCL2 MPs provides a novel approach to treat periodontal disease.

Activity-based ubiquitin-protein probes reveal target protein specificity of deubiquitinating enzymes

Ubiquitination is an essential eukaryotic post-translational modification that regulates various cellular processes. The removal of ubiquitin from its target protein is catalyzed by deubiquitinating enzymes (DUBs). Although it was proposed that many DUBs specifically interact and recognize ubiquitinated proteins as substrates, more direct evidence is needed to support this notion. Here we report protein-targeting activity-based DUB probes that allowed the identification of DUBs recognizing monoubiquitinated proliferating cell nuclear antigen (PCNA) in Saccharomyces cerevisiae. This new class of DUB probes contain a Michael acceptor as a warhead between ubiquitin and the target protein PCNA through a linkage that mimics the native isopeptide bond. We selected two known and biologically relevant ubiquitination sites on PCNA to generate the DUB probes. This allowed us to interrogate the site-specific deubiquitination of a target protein by DUBs. DUBs were profiled in yeast cell lysates using the two Ub-PCNA DUB probes in conjunction with two control probes that contain a noncleavable linkage but no warhead. We identified yeast DUBs through pulldown coupled with quantitative mass spectrometry analysis of the pulled down proteins. Our results showed that specific yeast DUBs recognize monoubiquitinated PCNA and corroborated previous genetic study. We also identified DUBs as potential new deubiquitinase of PCNA. Remarkably, identified DUBs clearly distinguish the different modification sites on PCNA, thus supporting a high level of DUB specificity beyond the target protein identity.

Cell-Permeable Activity-Based Ubiquitin Probes Enable Intracellular Profiling of Human Deubiquitinases

Advancement in our knowledge of deubiquitinases (DUBs) and their biological functions requires biochemical tools permitting interrogation of DUB activities under physiologically relevant conditions. Activity-based DUB probes (DUB ABPs) have been widely used in investigating the function and activity of DUBs. However, most ubiquitin (Ub)-based DUB ABPs are not cell-permeable, limiting their utility to purified proteins and cell lysates. Lysis of cells usually leads to dilution of the cytoplasm and disruption of the normal cellular organization, which may alter the activity of many DUBs and DUB complexes. Here, we report a new class of cell-permeable DUB ABPs that enable intracellular DUB profiling. We used a semisynthetic approach to generate modular ubiquitin-based DUB probes containing a reactive warhead for covalent trapping of DUBs with a catalytic cysteine. We employed cell-penetrating peptides (CPPs), particualrly cyclic polyarginine (cR₁₀), to deliver the DUB ABPs into cells, as confirmed using live-cell fluorescence microscopy and DUB ABPs containing a fluorophore at the C-terminus of Ub. In comparison to TAT, enhanced intacellular delivery was observed through conjugation of a cyclic polyarginine (cR₁₀) to the N-terminus of ubiquitin via a disulfide linkage. Using the new cell-permeable DUB ABPs, we carried out DUB profiling in intact HeLa cells, and identified active DUBs using immunocapture and label-free quantitative mass spectrometry. Additionally, we demonstrated that the cell-permeable DUB ABPs can be used in assessing the inhibition of DUBs by small-molecule inhibitors in intact cells. Our results indicate that cell-permeable DUB ABPs hold great promise in providing a better understanding of the cellular functions of DUBs and advancing drug discovery efforts targeting human DUBs.

Apparent diffusion coefficient measurement in luminal breast cancer: will tumour shrinkage patterns affect its efficacy of evaluating the pathological response?

AIM

To determine which region of interest (ROI) placement method of apparent diffusion coefficient (ADC) measurement has the best performance for predicting pathological complete response (PCR) at two cycles of neoadjuvant chemotherapy (NAC) according to different tumour shrinkage patterns of luminal breast cancer and to assess the evaluative accuracy of ADC value combined with other clinicopathological indicators.

MATERIALS AND METHODS

Sixty-one patients who underwent NAC for histopathologically confirmed breast cancer were enrolled in this retrospective study. The ADC values of different shrinkage patterns (concentric shrinkage, nest or dendritic shrinkage, and mixed shrinkage) for tumours shown by diffusion-weighted imaging (DWI) were measured independently using three ROI placement methods (single-round, three-round, and freehand). Intraclass correlation coefficients (ICCs) were used to assess the interobserver variability in the ADC values. Multivariate logistic regression analysis was performed to identify the independent predictors of PCR.

RESULTS

The best placement method found was single-round ROI in all the patients (AUC=0.863). When analysed separately, the effectiveness results differed: the single-round method was optimal for concentrically shrinking tumours (AUC=0.970); the freehand method was optimal for nest or dendritically shrinking tumours (AUC=0.714); and the three-round method was optimal for mixed shrinking tumours (AUC=0.975). Multivariate logistic analysis showed that oestrogen receptor (ER), ΔADC% and tumour diameter reduction (ΔD%) were independent factors in evaluating the PCR.

CONCLUSION

The methods for measuring ADC values vary across different shrinkage patterns of luminal tumours. ΔADC%, ER and ΔD% were independent factors for evaluating the PCR.

Utility of apparent diffusion coefficient as an imaging biomarker for assessing the proliferative potential of invasive ductal breast cancer

AIM

To determine the clinical utility of apparent diffusion coefficient (ADC) metrics for the non-invasive assessment of tumour proliferation indicated by Ki-67 labelling index (LI) in invasive ductal breast cancer.

MATERIALS AND METHODS

Eighty patients with 80 histopathologically proven invasive ductal breast cancers underwent diffusion-weighted imaging with b-values of 0 and 800 s/mm² at a 3-T system. ADC metrics including ADC_mean, ADC_median, ADC_min, ADC_max, and ΔADC (ADC_max-ADC_min) were recorded from the entire tumour volume on ADC maps, and correlated with the Ki-67 LI. Ki-67 staining of ≥14% was considered to indicate high proliferation and <14% was considered to indicate low proliferation.

RESULTS

ADC_min, ADC_max, and ΔADC showed significant correlations with the Ki-67 LI (for all tumours, r=-0.311, 0.436, and 0.551, respectively; for luminal/human epidermal growth factor receptor 2 (HER2)-negative group, r=-0.437, 0.512, and 0.639, respectively; all p<0.01), whereas ADC_mean and ADC_median showed no significant correlation (both p>0.05). Receiver operating characteristic (ROC) curve analysis for the differentiation of high- from low-proliferation groups showed that ΔADC yielded the highest area under the ROC curve for the whole tumour population (0.825; 95% confidence interval [CI]: 0.724, 0.901), as well as for the luminal/HER2-negative group (0.844; 95% CI: 0.692, 0.940).

CONCLUSION

ΔADC may serve as a promising imaging biomarker for the prediction of Ki-67 proliferation status in invasive ductal breast cancer.

Cell Lysate-Based AlphaLISA Deubiquitinase Assay Platform for Identification of Small Molecule Inhibitors

The deubiquitinases, or DUBs, are associated with various human diseases, including neurological disorders, cancer, and viral infection, making them excellent candidates for pharmacological intervention. Drug discovery campaigns against DUBs require enzymatic deubiquitination assays amenable for high-throughput screening (HTS). Although several DUB substrates and assays have been developed in recent years, they are largely limited to recombinantly purified DUBs. Many DUBs are large multidomain proteins that are difficult to obtain recombinantly in sufficient quantities for HTS. Therefore, an assay that obviates the need of recombinant protein generation and also recapitulates a physiologically relevant environment is highly desirable. Such an assay will open doors for drug discovery against many therapeutically relevant, but currently inaccessible, DUBs. Here, we report a cell lysate DUB assay based on AlphaLISA technology for high throughput screening. This assay platform uses a biotin-tagged ubiquitin probe and a HA-tagged DUB expressed in human cells. The assay was validated and adapted to a 1536-well format, which enabled a screening against UCHL1 as proof of principle using a library of 15 000 compounds. We expect that the new platform can be readily adapted to other DUBs to allow the identification of more potent and selective small molecule inhibitors and chemical probes.

Chemical Synthesis of Activity-Based Diubiquitin Probes

Activity-based diubiquitin probes are highly useful in probing the deubiquitinase (DUB) activity and ubiquitin chain linkage specificity. Here we describe a detailed protocol to synthesize a new class of diubiquitin DUB probes. In this method, two ubiquitin moieties are connected through a linker resembling the native linkage in size and containing a Michael acceptor for trapping the DUB active-site cysteine. Detailed procedures for generating the linker molecule are also described.

Divergence in Ubiquitin Interaction and Catalysis among the Ubiquitin-Specific Protease Family Deubiquitinating Enzymes

Deubiquitinating enzymes (DUBs) are responsible for reversing mono- and polyubiquitination of proteins and play essential roles in numerous cellular processes. Close to 100 human DUBs have been identified and are classified into five families, with the ubiquitin-specific protease (USP) family being the largest (>50 members). The binding of ubiquitin (Ub) to USP is strikingly different from that observed for the DUBs in the ubiquitin C-terminal hydrolase (UCH) and ovarian tumor domain protease (OTU) families. We generated a panel of mutant ubiquitins and used them to probe the ubiquitin's interaction with a number of USPs. Our results revealed a remarkable divergence of USP-Ub interactions among the USP catalytic domains. Our double-mutant cycle analysis targeting the ubiquitin residues located in the tip, the central body, and the tail of ubiquitin also demonstrated different crosstalk among the USP-Ub interactions. This work uncovered intriguing divergence in the ubiquitin-binding mode in the USP family DUBs and raised the possibility of targeting the ubiquitin-binding hot spots on USPs for selective inhibition of USPs by small molecule antagonists.

Exploring the regulatory role of isocitrate dehydrogenase mutant protein on glioma stem cell proliferation

OBJECTIVE

Glioma is the most lethal form of cancer that originates mostly from the brain and less frequently from the spine. Glioma is characterized by abnormal regulation of glial cell differentiation. The severity of the glioma was found to be relaxed in isocitrate dehydrogenase 1 (IDH1) mutant. The present study focused on histological discrimination and regulation of cancer stem cell between IDH1 mutant and in non-IDH1 mutant glioma tissue.

PATIENTS AND METHODS

Histology, immunohistochemistry and Western blotting techniques are used to analyze the glioma nature and variation in glioma stem cells that differ between IDH1 mutant and in non-IDH1 mutant glioma tissue.

RESULTS

The aggressive form of non-IDH1 mutant glioma shows abnormal cellular histological variation with prominent larger nucleus along with abnormal clustering of cells. The longer survival form of IDH1 mutant glioma has a control over glioma stem cell proliferation. Immunohistochemistry with stem cell markers, CD133 and EGFRvIII are used to demonstrate that the IDH1 mutant glioma shows limited dependence on cancer stem cells and it shows marked apoptotic signals in TUNEL assay to regulate abnormal cells. The non-IDH1 mutant glioma failed to regulate misbehaving cells and it promotes cancer stem cell proliferation.

CONCLUSIONS

Our finding supports that the IDH1 mutant glioma has a regulatory role in glioma stem cells and their survival.

Pretreated baseline neutrophil count and chemotherapy-induced neutropenia may be conveniently available as prognostic biomarkers in advanced gastric cancer

BACKGROUND

Increasing evidence suggests that neutrophils play a critical role in tumorigenesis, tumour cell proliferation and metastasis. The prognostic significance of such inflammation-associated markers has been explored in different cancers.

AIM

To evaluate the prognostic effect of baseline neutrophil counts and nadir neutrophils on advanced gastric cancer (AGC) patients who were treated with two different chemotherapy regimens in our institution.

METHODS

Data were collected retrospectively for 260 AGC patients treated between 1 February 2009 and 31 December 2011. The prognostic effect of baseline neutrophil counts and nadir neutrophils on AGC patients was evaluated.

RESULTS

Approximately 79% of the patients experienced neutropenia during chemotherapy. The median survival was 369 days for patients with neutrophil counts ≤7.5 × 10(9) /L and 326 days for patients with neutrophil counts >7.5 × 10(9) /L (P < 0.001).The median survival was 340 days for patients with no neutropenia (grade 0), 422 days for patients with mild neutropenia (grade 1-2) and 339 days for patients with severe neutropenia (grade 3-4) (P < 0.001).The adjusted hazard ratios (HR) for mild and severe neutropenia compared with absent neutropenia were 0.572 (P = 0.002) and 1.246 (P = 0.219) respectively. Furthermore, it was suggested that pretreatment baseline neutrophil counts ≤7.5 × 10(9) /L may be an independent predictor (HR = 0.683; P = 0.005). We also observed that other factors were independently associated with worse survival, such as higher performance status, stage IV and the presence of ascites.

CONCLUSION

Our findings suggest that baseline neutrophil count and chemotherapy-induced neutropenia can be conveniently available as clinical biomarkers in AGC. Mild myelosuppression in patients with AGC most likely leads to better overall survival, whereas a high baseline neutrophil count may be associated with a worse prognosis.

Chemical Protein Ubiquitylation with Preservation of the Native Cysteine Residues

We report a cysteine-based ligation strategy for generating a monoubiquitylated protein while preserving the native cysteine residues on the acceptor protein. In monoubiquitylation of proliferating cell nuclear antigen (PCNA) this method circumvents the need to mutate the native cysteine residues on PCNA. The chemically ubiquitylated PCNA contains a noncleavable linkage of the same length as the native isopeptide linkage. It also retains the normal function of the native Ub-PCNA in stimulating the ATPase activity of replication factor C (RFC) and lesion bypass synthesis by Polη. This method may be adapted for chemical ubiquitylation of other proteins and for site-specific modification of a target protein at a specific site through sulfhydryl chemistry.

Comparison of Simulated Workplace Protection Factors Offered by N95 and P100 Filtering Facepiece and Elastomeric Half-Mask Respirators against Particles of 10 to 400 nm

This study compared the simulated workplace protection factors (SWPFs) between NIOSH-approved N95 respirators and P100 respirators, including two models of filtering facepiece respirator (FFR) and two models of elastomeric half-mask respirator (EHR), against sodium chloride particles (NaCl) in a range of 10 to 400 nm. Twenty-five human test subjects performed modified OSHA fit test exercises in a controlled laboratory environment with the N95 respirators (two FFR models and two EHR models) and the P100 respirators (two FFRs and two EHRs). Two Scanning Mobility Particle Sizers (SMPS) were used to measure aerosol concentrations (in the 10-400 nm size range) inside (Cin) and outside (Cout) of the respirator, simultaneously. SWPF was calculated as the ratio of Cout to Cin. The SWPF values obtained from the N95 respirators were then compared to those of the P100 respirators. SWPFs were found to be significantly different (P<0.05) between N95 and P100 class respirators. The 10th, 25th, 50th, 75th and 90th percentiles of the SWPFs for the N95 respirators were much lower than those for the P100 models. The N95 respirators had 5th percentiles of the SWPFs > 10. In contrast, the P100 class was able to generate 5th percentiles SWPFs > 100. No significant difference was found in the SWPFs when tested against nano-size (10 to 100 nm) and large-size (100 to 400 nm) particles. Overall, the findings suggest that the two FFRs and two EHRs with P100 class filters provide better performance than those with N95 filters against particles from 10 to 400 nm, supporting current OSHA and NIOSH recommendations.

Structurally distinct ubiquitin- and sumo-modified PCNA: implications for their distinct roles in the DNA damage response

Proliferating cell nuclear antigen (PCNA) is a pivotal replication protein, which also controls cellular responses to DNA damage. Posttranslational modification of PCNA by SUMO and ubiquitin modulate these responses. How the modifiers alter PCNA-dependent DNA repair and damage tolerance pathways is largely unknown. We used hybrid methods to identify atomic models of PCNAK107-Ub and PCNAK164-SUMO consistent with small-angle X-ray scattering data of these complexes in solution. We show that SUMO and ubiquitin have distinct modes of association to PCNA. Ubiquitin adopts discrete docked binding positions. By contrast, SUMO associates by simple tethering and adopts extended flexible conformations. These structural differences are the result of the opposite electrostatic potentials of SUMO and Ub. The unexpected contrast in conformational behavior of Ub-PCNA and SUMO-PCNA has implications for interactions with partner proteins, interacting surfaces accessibility, and access points for pathway regulation.

Abstract LB-11: Discovery, synthesis, and structure-activity relationship of N-benzyl-2-phenylpyrimidin-4-amine derivatives as potent USP1/UAF1 deubiquitinase inhibitors with anticancer activity against non-small cell lung cancer

Protein ubiquitination is a dynamic and reversible post-translational modification that has been linked to many essential cellular processes in eukaryotes. In addition, deregulation of ubiquitin conjugation or deconjugation has been implicated in the pathogenesis of many human diseases, including cancer. For example, the deubiquitinating enzyme USP1 (ubiquitin-specific protease 1) in association with its WD40-repeat protein binding partner, UAF1 (USP1-associated factor 1), is a known regulator of DNA damage tolerance and repair and has been proposed as a promising target for anticancer therapy. To further evaluate the USP1/UAF1 complex as a therapeutic target, we conducted a quantitative high throughput screen of &gt;400,000 compounds and subsequent medicinal chemistry optimization in pursuit of small molecules that inhibit the deubiquitinating activity of USP1/UAF1. These efforts lead to the identification of ML323 and a series of N-benzyl-2-phenylpyrimidin-4-amine derivatives, which possess nanomolar USP1/UAF1 inhibition and exhibit excellent selectivity over related proteases. Moreover, we demonstrate a strong correlation between compound IC50 values for USP1/UAF1 inhibition in vitro and activity in non-small cell lung cancer cells, specifically increasing the level of ubiquitinated-PCNA and decreasing cell survival. Taken together, our results establish the druggability of the USP1/UAF1 deubiquitinase complex and its potential as molecular target for anticancer therapies.

Citation Format: Thomas S. Dexheimer, Andrew S. Rosenthal, Diane Luci, Qin Liang, Mark A. Villamil, Ajit Jadhav, Anton Simeonov, Zhihao Zhuang, David J. Maloney. Discovery, synthesis, and structure-activity relationship of N-benzyl-2-phenylpyrimidin-4-amine derivatives as potent USP1/UAF1 deubiquitinase inhibitors with anticancer activity against non-small cell lung cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr LB-11. doi:10.1158/1538-7445.AM2014-LB-11

Entrenchment-Based Horn Contraction

The AGM framework is the benchmark approach in belief change. Since the framework assumes an underlying logic containing classical Propositional Logic, it can not be applied to systems with a logic weaker than Propositional Logic. To remedy this limitation, several researchers have studied AGM-style contraction and revision under the Horn fragment of Propositional Logic (i.e., Horn logic). In this paper, we contribute to this line of research by investigating the Horn version of the AGM entrenchment-based contraction. The study is challenging as the construction of entrenchment-based contraction refers to arbitrary disjunctions which are not expressible under Horn logic. In order to adapt the construction to Horn logic, we make use of a Horn approximation technique called Horn strengthening. We provide a representation theorem for the newly constructed contraction which we refer to as entrenchment-based Horn contraction. Ideally, contractions defined under Horn logic (i.e., Horn contractions) should be as rational as AGM contraction. We propose the notion of Horn equivalence which intuitively captures the equivalence between Horn contraction and AGM contraction. We show that, under this notion, entrenchment-based Horn contraction is equivalent to a restricted form of entrenchment-based contraction.

Synthesis and structure-activity relationship studies of N-benzyl-2-phenylpyrimidin-4-amine derivatives as potent USP1/UAF1 deubiquitinase inhibitors with anticancer activity against nonsmall cell lung cancer

Deregulation of ubiquitin conjugation or deconjugation has been implicated in the pathogenesis of many human diseases including cancer. The deubiquitinating enzyme USP1 (ubiquitin-specific protease 1), in association with UAF1 (USP1-associated factor 1), is a known regulator of DNA damage response and has been shown as a promising anticancer target. To further evaluate USP1/UAF1 as a therapeutic target, we conducted a quantitative high throughput screen of >400000 compounds and subsequent medicinal chemistry optimization of small molecules that inhibit the deubiquitinating activity of USP1/UAF1. Ultimately, these efforts led to the identification of ML323 (70) and related N-benzyl-2-phenylpyrimidin-4-amine derivatives, which possess nanomolar USP1/UAF1 inhibitory potency. Moreover, we demonstrate a strong correlation between compound IC₅₀ values for USP1/UAF1 inhibition and activity in nonsmall cell lung cancer cells, specifically increased monoubiquitinated PCNA (Ub-PCNA) levels and decreased cell survival. Our results establish the druggability of the USP1/UAF1 deubiquitinase complex and its potential as a molecular target for anticancer therapies.

Chemical protein polyubiquitination reveals the role of a noncanonical polyubiquitin chain in DNA damage tolerance

Polyubiquitination of proteins regulates a variety of cellular processes, including protein degradation, NF-κB pathway activation, apoptosis, and DNA damage tolerance. Methods for generating polyubiquitinated protein with defined ubiquitin chain linkage and length are needed for an in-depth molecular understanding of protein polyubiquitination. However, enzymatic protein polyubiquitination usually generates polyubiquitinated proteins with mixed chain lengths in a low yield. We report herein a new chemical approach for protein polyubiquitination with a defined ubiquitin chain length and linkage under a mild condition that preserves the native fold of the target protein. In DNA damage tolerance, K63-polyubiquitinated proliferating cell nuclear antigen (PCNA) plays an important yet unclear role in regulating the selection of the error-free over error-prone lesion bypass pathways. Using the chemically polyubiquitinated PCNA, we revealed a mechanism of the K63 polyubiquitin chain on PCNA in promoting the error-free lesion bypass by suppressing the DNA translesion synthesis (TLS).

Activity-based diubiquitin probes for elucidating the linkage specificity of deubiquitinating enzymes

We report a new class of deubiquitinating enzyme (DUB) probes that resemble the native diubiquitin with a same linkage size and contain a Michael addition acceptor for trapping the DUB active-site cysteine. Both K63- and K48-linked diubiquitin probes were generated using a facile chemical ligation method. The diUb probes were demonstrated to label DUBs from different families and revealed intrinsic linkage specificities of DUBs.

Axl-altered microRNAs regulate tumorigenicity and gefitinib resistance in lung cancer

The involvement of Axl kinase in non-small cell lung cancer's (NSCLC) acquired resistance to tyrosine kinase inhibitors (TKIs) gefitinib or erlotinib has been identified recently, but the mechanism by which Axl contributes to TKI resistance is largely unknown. MicroRNAs (miRNAs) repress gene expression and their critical role in tumorigenesis has been implicated. To investigate the role of miRNAs in the Axl-mediated acquired gefitinib resistance, we examined the Axl-mediated miRNA changes in gefitinib-resistant lung cancers. A panel of Axl kinase-altered miRNAs was identified. In this study, we validate and report that miR-374a and miR-548b modulated by Axl have essential roles in cell cycle arrest, gefitinib-induced apoptosis, epithelial-to-mesenchymal transition, migration and tumorigenesis of gefitinib-resistant lung cancer cells in vitro and in vivo by targeting Wnt5a and CCNB1 genes, respectively. Of clinical significance, high expression of Axl and miR-374a and low expression of miR-548b are associated with poor disease-free survival postoperatively. These findings indicate that the modulation of specific miRNAs may provide a therapeutic target to treat or reverse gefitinib resistance in NSCLC with high expression of Axl in the future.