Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs

Only a small proportion of the mouse genome is transcribed into mature messenger RNA transcripts. There is an international collaborative effort to identify all full-length mRNA transcripts from the mouse, and to ensure that each is represented in a physical collection of clones. Here we report the manual annotation of 60,770 full-length mouse complementary DNA sequences. These are clustered into 33,409 'transcriptional units', contributing 90.1% of a newly established mouse transcriptome database. Of these transcriptional units, 4,258 are new protein-coding and 11,665 are new non-coding messages, indicating that non-coding RNA is a major component of the transcriptome. 41% of all transcriptional units showed evidence of alternative splicing. In protein-coding transcripts, 79% of splice variations altered the protein product. Whole-transcriptome analyses resulted in the identification of 2,431 sense-antisense pairs. The present work, completely supported by physical clones, provides the most comprehensive survey of a mammalian transcriptome so far, and is a valuable resource for functional genomics.

Prediction of the hip joint centre in adults, children, and patients with cerebral palsy based on magnetic resonance imaging

The location of the hip joint centre (HJC) is required for calculations of hip moments, the location and orientation of the femur, and muscle lengths and lever arms. In clinical gait analysis, the HJC is normally estimated using regression equations based on normative data obtained from adult populations. There is limited relevant anthropometric data available for children, despite the fact that clinical gait analysis is predominantly used for the assessment of children with cerebral palsy. In this study, pelvic MRI scans were taken of eight adults (ages 23-40), 14 healthy children (ages 5-13) and 10 children with spastic diplegic cerebral palsy (ages 6-13). Relevant anatomical landmarks were located in the scans, and the HJC location in pelvic coordinates was found by fitting a sphere to points identified on the femoral head. The predictions of three common regression equations for HJC location were compared to those found directly from MRI. Maximum absolute errors of 31 mm were found in adults, 26 mm in children, and 31 mm in the cerebral palsy group. Results from regression analysis and leave-one-out cross-validation techniques on the MRI data suggested that the best predictors of HJC location were: pelvic depth for the antero-posterior direction; pelvic width and leg length for the supero-inferior direction; and pelvic depth and pelvic width for the medio-lateral direction. For single-variable regression, the exclusion of leg length and pelvic depth from the latter two regression equations is proposed. Regression equations could be generalised across adults, children and the cerebral palsy group.

miR-424(322) reverses chemoresistance via T-cell immune response activation by blocking the PD-L1 immune checkpoint

Immune checkpoint blockade of the inhibitory immune receptors PD-L1, PD-1 and CTLA-4 has emerged as a successful treatment strategy for several advanced cancers. Here we demonstrate that miR-424(322) regulates the PD-L1/PD-1 and CD80/CTLA-4 pathways in chemoresistant ovarian cancer. miR-424(322) is inversely correlated with PD-L1, PD-1, CD80 and CTLA-4 expression. High levels of miR-424(322) in the tumours are positively correlated with the progression-free survival of ovarian cancer patients. Mechanistic investigations demonstrated that miR-424(322) inhibited PD-L1 and CD80 expression through direct binding to the 3'-untranslated region. Restoration of miR-424(322) expression reverses chemoresistance, which is accompanied by blockage of the PD-L1 immune checkpoint. The synergistic effect of chemotherapy and immunotherapy is associated with the proliferation of functional cytotoxic CD8+ T cells and the inhibition of myeloid-derived suppressive cells and regulatory T cells. Collectively, our data suggest a biological and functional interaction between PD-L1 and chemoresistance through the microRNA regulatory cascade.

Actinonin, a naturally occurring antibacterial agent, is a potent deformylase inhibitor

Peptide deformylase (PDF) is essential in prokaryotes and absent in mammalian cells, thus making it an attractive target for the discovery of novel antibiotics. We have identified actinonin, a naturally occurring antibacterial agent, as a potent PDF inhibitor. The dissociation constant for this compound was 0.3 x 10(-)(9) M against Ni-PDF from Escherichia coli; the PDF from Staphylococcus aureus gave a similar value. Microbiological evaluation revealed that actinonin is a bacteriostatic agent with activity against Gram-positive and fastidious Gram-negative microorganisms. The PDF gene, def, was placed under control of P(BAD) in E. coli tolC, permitting regulation of PDF expression levels in the cell by varying the external arabinose concentration. The susceptibility of this strain to actinonin increases with decreased levels of PDF expression, indicating that actinonin inhibits bacterial growth by targeting this enzyme. Actinonin provides an excellent starting point from which to derive a more potent PDF inhibitor that has a broader spectrum of antibacterial activity.

The fasciated ear2 gene encodes a leucine-rich repeat receptor-like protein that regulates shoot meristem proliferation in maize

The ability to initiate organs throughout the lifecycle is a unique feature of plant development that is executed by groups of stem cells called meristems. The balance between stem cell proliferation and organ initiation is carefully regulated and ensures that organs can be initiated in regular geometric patterns. To understand how this regulation is achieved, we isolated a novel mutant of maize, fasciated ear2 (fea2), which causes a massive overproliferation of the ear inflorescence meristem and a more modest effect on floral meristem size and organ number. We cloned the fea2 gene using transposon tagging, and it encodes a membrane localized leucine-rich repeat receptor-like protein that is most closely related to CLAVATA2 from Arabidopsis. These findings provide evidence that the CLAVATA pathway for regulation of meristem size is functionally conserved throughout the angiosperms. A possible connection of fea2 to the control of crop yields is discussed.

The indeterminate gene encodes a zinc finger protein and regulates a leaf-generated signal required for the transition to flowering in maize

Flowering in plants is a consequence of the transition of the shoot apex from vegetative to reproductive growth in response to environmental and internal signals. The indeterminate1 gene (id1) controls the transition to flowering in maize. We show by cloning the id1 gene that it encodes a protein with zinc finger motifs, suggesting that the id1 gene product functions as a transcriptional regulator of the floral transition. id1 mRNA expression studies and analyses of transposon-induced chimeric plants indicate that id1 acts non-cell-autonomously to regulate the production of a transmissible signal in the leaf that elicits the transformation of the shoot apex to reproductive development. These results provide molecular and genetic data consistent with the florigen hypothesis derived from classical plant physiology studies.

Prediction of protein subcellular locations using Markov chain models

A novel method was introduced to predict protein subcellular locations from sequences. Using sequence data, this method achieved a prediction accuracy higher than previous methods based on the amino acid composition. For three subcellular locations in a prokaryotic organism, the overall prediction accuracy reached 89.1%. For eukaryotic proteins, prediction accuracies of 73.0% and 78.7% were attained within four and three location categories, respectively. These results demonstrate the applicability of this relative simple method and possible improvement of prediction for the protein subcellular location.

Cerebral arterial aneurysm formation and rupture in 20,767 elderly patients: hypertension and other risk factors

Cerebral arterial aneurysms are common in the general population and their rupture is a catastrophic event. Considerable uncertainty remains concerning the conditions that predispose individuals to aneurysm formation or rupture. The role of systemic hypertension in aneurysm formation and rupture has been especially controversial. Demographic variables have rarely been addressed because of the small sample sizes in previous studies. The authors describe the demographics and prevalence of hypertension in 20,767 Medicare patients with an unruptured aneurysm and compared these to a random sample of the hospitalized Medicare population. The prevalence of hypertension in patients with unruptured aneurysms was 43.2% compared with 34.4% in the random sample. Patients who survived their initial hospitalization were separated into two groups: those with an unruptured cerebral aneurysm as the primary diagnosis and those with an unruptured cerebral aneurysm as a secondary diagnosis. Follow-up data for 18,119 patients were examined to determine the risk of subarachnoid hemorrhage (SAH) associated with age, gender, race, hypertension, insulin-dependent diabetes mellitus, and surgical treatment. For patients with an unruptured cerebral aneurysm as the primary diagnosis, hypertension was found to be a significant risk factor for future SAH (risk ratio: 1.46, 95% confidence interval (CI): 1.01-2.11), whereas surgical treatment (risk ratio: 0.29, 95% CI: 0.09-0.97) had a significant protective effect. Advancing age had a small but significant protective effect in both groups. Elderly patients identified with unruptured aneurysms are more likely to have coexisting hypertension than the general hospitalized population. In elderly patients hospitalized with an unruptured cerebral aneurysm as their primary diagnosis, hypertension is a risk factor for subsequent SAH, whereas surgical treatment is a protective factor against SAH.

Frequent requirement of hedgehog signaling in non-small cell lung carcinoma

Although it had previously been suggested that the hedgehog (HH) pathway might be activated in some lung tumors, the dependence of non-small cell lung carcinomas (NSCLC) for HH activity had not been comprehensively studied. During a screen of a panel of 60 human tumor cell lines with an HH antagonist, we observed that the proliferation of a subset of NSCLC cell lines was inhibited. These NSCLC cell lines express HH, as well as key HH target genes, consistent with them being activated through an autocrine mechanism. Interestingly, we also identified a number of NSCLC cell lines that express high levels of the downstream transcription factor GLI1 and harbor enhanced levels of HH activity, but appear insensitive to known HH antagonists. We hypothesized that the high levels of GLI1 in these cells would function downstream of the HH antagonist target, allowing them to bypass the antagonist-mediated block in proliferation. Consistent with this hypothesis, when the levels of GLI1 are knocked down in such cells, they become sensitive to these inhibitors. We go on to show that a large percentage of primary NSCLC samples express GLI1, consistent with constitutive activation of the HH pathway in these samples. Taken together, these results establish the involvement of the HH signaling pathway in a subset of NSCLCs.

Surgery for colorectal cancer: Race-related differences in rates and survival among Medicare beneficiaries

This study examined surgery for colorectal cancer among Medicare beneficiaries 65 years of age or older with an initial diagnosis in 1987 (n = 81 579). Black patients were less likely than White to undergo surgical resection (68% vs 78%), even after age, comorbidity, and location and extent of tumor were controlled for. Among those who underwent resection, Black patients were more likely to die (a 2-year mortality rate of 40.0% vs 33.5% in White patients); this disparity also remained after confounders had been controlled. The disparities were similar in teaching and nonteaching hospitals and in private and public hospitals. These data may indicate racially based differences among Medicare beneficiaries in access to and quality of care for colorectal cancer.

Ongoing declines for the world's amphibians in the face of emerging threats

Systematic assessments of species extinction risk at regular intervals are necessary for informing conservation action1,2. Ongoing developments in taxonomy, threatening processes and research further underscore the need for reassessment3,4. Here we report the findings of the second Global Amphibian Assessment, evaluating 8,011 species for the International Union for Conservation of Nature Red List of Threatened Species. We find that amphibians are the most threatened vertebrate class (40.7% of species are globally threatened). The updated Red List Index shows that the status of amphibians is deteriorating globally, particularly for salamanders and in the Neotropics. Disease and habitat loss drove 91% of status deteriorations between 1980 and 2004. Ongoing and projected climate change effects are now of increasing concern, driving 39% of status deteriorations since 2004, followed by habitat loss (37%). Although signs of species recoveries incentivize immediate conservation action, scaled-up investment is urgently needed to reverse the current trends.

How good is prediction of protein structural class by the component-coupled method?

Proteins of known structures are usually classified into four structural classes: all-alpha, all-beta, alpha+beta, and alpha/beta type of proteins. A number of methods to predicting the structural class of a protein based on its amino acid composition have been developed during the past few years. Recently, a component-coupled method was developed for predicting protein structural class according to amino acid composition. This method is based on the least Mahalanobis distance principle, and yields much better predicted results in comparison with the previous methods. However, the success rates reported for structural class prediction by different investigators are contradictory. The highest reported accuracies by this method are near 100%, but the lowest one is only about 60%. The goal of this study is to resolve this paradox and to determine the possible upper limit of prediction rate for structural classes. In this paper, based on the normality assumption and the Bayes decision rule for minimum error, a new method is proposed for predicting the structural class of a protein according to its amino acid composition. The detailed theoretical analysis indicates that if the four protein folding classes are governed by the normal distributions, the present method will yield the optimum predictive result in a statistical sense. A non-redundant data set of 1,189 protein domains is used to evaluate the performance of the new method. Our results demonstrate that 60% correctness is the upper limit for a 4-type class prediction from amino acid composition alone for an unknown query protein. The apparent relatively high accuracy level (more than 90%) attained in the previous studies was due to the preselection of test sets, which may not be adequately representative of all unrelated proteins.

The sensitivity of Medicare claims data for case ascertainment of six common cancers

BACKGROUND

Although Medicare claims data have been used to identify cases of cancer in older Americans, there are few data about their relative sensitivity.

OBJECTIVES

To investigate the sensitivity of diagnostic and procedural coding for case ascertainment of breast, colorectal, endometrial, lung, pancreatic, and prostate cancer.

SUBJECTS

Three hundred and eighty nine thousand and two hundred and thirty-six patients diagnosed with cancer between 1984 and 1993 resided in one of nine Surveillance Epidemiology and End Results (SEER) areas.

MEASURES

The sensitivity of inpatient and Part B diagnostic and cancer-specific procedural codes for case finding were compared with SEER.

RESULTS

The sensitivity of inpatient and inpatient plus Part B claims for the corresponding cancer diagnosis was 77.4% and 91.2%, respectively. The sensitivity of inpatient claims alone was highest for colorectal (86.1%) and endometrial (84.1%) cancer and lowest for prostate cancer (63.6%). However, when Part B claims were included, the sensitivity for diagnosis of breast cancer was greater than for other cancers (93.6%). Inpatient claim sensitivity was highest for earlier years of the study, and, because of more complete data and longer follow up, the highest sensitivity of combined inpatient and Part B claims was achieved in the late 1980s or early 1990s.

CONCLUSIONS

Medicare claims provide reasonably high sensitivity for the detection of cancer in the elderly, especially if inpatient and Part B claims are combined. Because the study did not measure other dimensions of accuracy, such as specificity and predictive value, the potential costs of including false positive cases need to be assessed.

Universal COI primers for DNA barcoding amphibians

DNA barcoding is a proven tool for the rapid and unambiguous identification of species, which is essential for many activities including the vouchering tissue samples in the genome 10K initiative, genealogical reconstructions, forensics and biodiversity surveys, among many other applications. A large-scale effort is underway to barcode all amphibian species using the universally sequenced DNA region, a partial fragment of mitochondrial cytochrome oxidase subunit I COI. This fragment is desirable because it appears to be superior to 16S for barcoding, at least for some groups of salamanders. The barcoding of amphibians is essential in part because many species are now endangered. Unfortunately, existing primers for COI often fail to achieve this goal. Herein, we report two new pairs of primers (➀, ➁) that in combination serve to universally amplify and sequence all three orders of Chinese amphibians as represented by 36 genera. This taxonomic diversity, which includes caecilians, salamanders and frogs, suggests that the new primer pairs will universally amplify COI for the vast majority species of amphibians.

Risk of stroke in patients with atrial flutter

Using a Medicare-based retrospective cohort study, the stroke risk in patients with atrial flutter (RR = 1.41) was determined to be greater than that in a control group (RR = 1.00) but less than that in an atrial fibrillation group (RR = 1.64). Furthermore, patients with atrial flutter who subsequently had an episode of atrial fibrillation had a higher risk of stroke (RR = 1.56) than patients with atrial flutter who never had a subsequent episode of atrial fibrillation (RR = 1.11).

Quality of life for children with fecal incontinence after surgically corrected anorectal malformation

PURPOSE

The aim of this study was to investigate influences of fecal incontinence on children's quality of life after surgically corrected anorectal malformation.

METHODS

Seventy-one children with anorectal malformation underwent follow-up for 8 to 16 years postoperatively. They were divided into good, fair, and poor groups by assessment of anal function. The quality of life was investigated by self-structured disease impact questionnaires and Achenbach's Child Behavior Check List (CBCL). A quality-of-life scoring criteria was established to assess quality of life of the 71 children with operated anorectal malformation and controls.

RESULTS

Owing to fecal incontinence, 12 (16.9%) children reported that there were problems in peer relationships; school absences happened in 13 (18.3%) children; 17 (23.9%) children had to restrict themselves to certain food. Based on CBCL, 13 (18.3%) children had behavior problems. The behavior problems in children with poor fecal continence (66.7%) were significantly higher than those of children with good fecal continence (8.6%). According to the quality-of-life scoring criteria, the scores of children with operated anorectal malformation (9.4+/-3.7) were significantly lower than those of the controls (11.2+/-0.9). The scores of children with poor fecal continence (4.8+/-1.4) were significantly lower than those of children with good fecal continence (10.9+/-1.2).

CONCLUSIONS

The children with poor fecal continence have poor quality of life caused by fecal dysfunction. Attention should be paid to the rehabilitation of fecal continence after surgery, such as bowel training and biofeedback therapy. The somatic and psychological care and long-term follow-up are necessary to improve the quality of life.

Agreement of Medicare claims and tumor registry data for assessment of cancer-related treatment

BACKGROUND

Although health claims data are increasingly used in evaluating variations in patterns of cancer care and outcomes, little is known about the comparability of these data with tumor registry information.

OBJECTIVES

To evaluate the agreement between Medicare claims and tumor registry data in measuring patterns of diagnostic and therapeutic procedures for older cancer patients.

RESEARCH DESIGN

Analysis of a database linking Surveillance, Epidemiology and End Results (SEER) registry data and Medicare claims in patients aged > or =65 years with cancer.

SUBJECTS

361,255 Medicare patients with invasive breast, colorectal, endometrial, lung, pancreatic, and prostate cancer diagnosed between 1984 and 1993.

MEASURES

Concordance of SEER files with corresponding Medicare claims.

RESULTS

Medicare claims generally identified patients who underwent resection and radical surgery according to SEER (ie, concordance > or =85%-90%) but less likely biopsy or local excision (ie, concordance < or =50%). In some instances, claims also categorized patients as having more invasive surgery than was listed in SEER and also provided incremental information about the use of surgical treatment after 4 months. SEER files and, to a lesser degree, Medicare claims identified radiation therapy not included in the other data source, and Medicare files also captured a significant number of patients with codes for chemotherapy.

CONCLUSIONS

Medicare files may be appropriate for studies of patterns of use of surgical treatment, but not for diagnostic procedures. The potential benefit of Medicare claims in identifying delayed surgical intervention and chemotherapy deserves further study.

Bevacizumab treatment for radiation brain necrosis: mechanism, efficacy and issues

Vascular damage is followed by vascular endothelial growth factor (VEGF) expression at high levels, which is an important mechanism forradiation brain necrosis development. Bevacizumab alleviates brain edema symptoms caused by radiation brain necrosis through inhibiting VEGF and acting on vascular tissue around the brain necrosis area. Many studies have confirmed that bevacizumab effectively relieves symptoms caused by brain necrosis, improves patients' Karnofsky performance status (KPS) scores and brain necrosis imaging. However, necrosis is irreversible, and hypoxia and ischemia localized in the brain necrosis area may easily lead to radiation brain necrosis recurrence after bevacizumab is discontinued. Further studies are necessary to investigate brain necrosis diagnoses, bevacizumab indications, and the optimal mode of administration, bevacizumab resistance and necrosis with a residual or recurrent tumor.

Gut microbial dysbiosis is associated with development and progression of radiation enteritis during pelvic radiotherapy

Radiation enteritis (RE) is the most common complication of radiotherapy for pelvic irradiation receivers. Herein we investigated the alterations in gut microbial profiles and their association with enteritis in patients undergoing pelvic radiotherapy. Faecal samples were collected from 18 cervical cancer patients during radiotherapy. Microbiota profiles were characterized based on 16S rRNA sequencing using the Illumina HiSeq platform. Epithelial inflammatory response was evaluated using bacterial‐epithelial co‐cultures. Dysbiosis was observed among patients with RE, which was characterized by significantly reduced α‐diversity but increased β‐diversity, relative higher abundance of Proteobacteria and Gammaproteobacteria and lower abundance of Bacteroides.Coprococcus was clearly enriched prior to radiotherapy in patients who later developed RE. Metastat analysis further revealed unique grade‐related microbial features, such as more abundant Virgibacillus and Alcanivorax in patients with mild enteritis. Additionally, using bacterial‐epithelial co‐cultures, RE patient‐derived microbiota induced epithelial inflammation and barrier dysfunction, enhanced TNF‐α and IL‐1β expression compared with control microbiota. Taken together, we define the overall picture of gut microbiota in patients with RE. Our results suggest that dysbiosis of gut microbiota may contribute to development and progression of RE. Gut microbiota can offer a set of biomarkers for prediction, disease activity evaluation and treatment selection in RE.

Bacterial Peptide deformylase inhibitors: a new class of antibacterial agents

Peptide deformylase (PDF) is a prokaryotic metalloenzyme that is essential for bacterial growth but is not required by mammalian cells. Thus, it represents a selective and promising target for the development of new antibacterial agents. Since deformylase inhibitors have yet to be used clinically as antibacterial drugs, compounds targeting this enzyme should avoid cross-resistance with currently used antibacterial agents. The PDF enzyme is a ferrous ion-containing metallohydrolase, but a nickel-containing surrogate is routinely used in the laboratory for testing inhibitors due to its better stability. Enzymes from several bacterial species have been cloned and both their three-dimensional structures and co-crystal structures with bound inhibitor have been determined. As a metallo enzyme, PDF lends itself to the well-precedented mechanism-based rational drug design approach. Using structural and mechanistic information together with high throughput screening, several types of potent PDF inhibitors have been identified. PDF inhibitors identified to date share a common structural feature of a "chelator + peptidomimetic" scaffold. Although compounds with many different chelators inhibit the cell free enzyme, only compounds containing hydroxamic acid or N-formyl hydroxylamine exhibit appreciable antibacterial activity. Several lead inhibitors have demonstrated in vivo efficacy and an excellent safety profile. Two PDF inhibitors, VIC-104959 (LBM415) and BB-83698, have progressed to Phase I clinical trials. In this review, different PDF inhibitors are compared and their biological activities are discussed. Structure-activity relationships have been established and the implications of this work in the design of future PDF inhibitors are considered.

Peptide deformylase in Staphylococcus aureus: resistance to inhibition is mediated by mutations in the formyltransferase gene

Peptide deformylase, a bacterial enzyme, represents a novel target for antibiotic discovery. Two deformylase homologs, defA and defB, were identified in Staphylococcus aureus. The defA homolog, located upstream of the transformylase gene, was identified by genomic analysis and was cloned from chromosomal DNA by PCR. A distinct homolog, defB, was cloned from an S. aureus genomic library by complementation of the arabinose-dependent phenotype of a P(BAD)-def Escherichia coli strain grown under arabinose-limiting conditions. Overexpression in E. coli of defB, but not defA, correlated to increased deformylase activity and decreased susceptibility to actinonin, a deformylase-specific inhibitor. The defB gene could not be disrupted in wild-type S. aureus, suggesting that this gene, which encodes a functional deformylase, is essential. In contrast, the defA gene could be inactivated; the function of this gene is unknown. Actinonin-resistant mutants grew slowly in vitro and did not show cross-resistance to other classes of antibiotics. When compared to the parent, an actinonin-resistant strain produced an attenuated infection in a murine abscess model, indicating that this strain also has a growth disadvantage in vivo. Sequence analysis of the actinonin-resistant mutants revealed that each harbors a loss-of-function mutation in the fmt gene. Susceptibility to actinonin was restored when the wild-type fmt gene was introduced into these mutant strains. An S. aureus Deltafmt strain was also resistant to actinonin, suggesting that a functional deformylase activity is not required in a strain that lacks formyltransferase activity. Accordingly, the defB gene could be disrupted in an fmt mutant.

Deformylase as a novel antibacterial target

Bacterial genomics has revealed a plethora of previously unknown targets of potential use in the discovery of novel antibacterial drugs. However, so far little has emerged from this approach. Peptide deformylase is an interesting target that was discovered more than 30 years ago, but was not exploited until recently. The reawakening of interest in this target resulted from an improved understanding of the enzyme, making it a more tractable and attractive target. Information on the properties of the enzyme, such as its three-dimensional structure, the activity of inhibitors, its resistance and suitability as a target are discussed.

CD4/CD8 + T cells, DC subsets, Foxp3, and IDO expression are predictive indictors of gastric cancer prognosis

BACKGROUND

The tumor microenvironment represents an abnormal niche containing numerous factors, such as T cells, dendritic cells (DCs), regulatory T cells (Tregs), and indoleamine 2,3-dioxygenase (IDO), involved in maintaining immune homeostasis and tolerance. All these factors may influence the choice of therapy and the clinical outcomes.

METHODS

Flow cytometry was performed to identify CD4+/CD8 + T cells and DCs, and immunohistochemistry was used to evaluate IDO and Forkhead Box P3 (Foxp3) expression; these experiments were performed in order to explore the clinical and prognostic significance of CD4/CD8 + T cells, DCs, Tregs, and IDO expression in gastric carcinoma.

RESULTS

Smaller tumor size was correlated with higher expression levels of peripheral CD4 + T cells (P = .003) and CD8 + T cells (P = .002), and lower IDO expression (P = .044) in tumors. Well-differentiated gastric carcinomas displayed higher peripheral (P = .029) and tumor-infiltrating CD4 + T cell (P = .009) populations and a higher tumor-infiltrating DC1/DC2 ratio (P = .048). Gastric cancer in the early T stages exhibited higher populations of peripheral DC2s (P = .044) and a higher tumor-infiltrating DC1/DC2 ratio (P = .012). Gastric cancer at the N0 stage had lower tumor-infiltrating DC2s (P = .032) and a higher DC1/DC2 ratio (P = .037). IDO expression was positively correlated with tumor-infiltrating Foxp3 + Tregs (P < .001) as well as DC2s (P < .001), whereas it was negatively correlated with the tumor-infiltrating CD4/CD8 + T cell ratio (P = .023). Tumor-infiltrating Foxp3 + Treg was positively correlated with tumor-infiltrating DC2s (r²  = 0.772; P < .001). At T, N, and TNM stages, the expression levels of peripheral DC2s, tumor-infiltrating DC1/DC2 ratios, Foxp3 + Tregs, and IDO were significantly correlated with prognosis (P < .05). The T stage and peripheral DC2s were significant risk factors for overall survival.

CONCLUSION

Immunocompetent cells and humoral immune factors, including DC2s, CD4+/CD8 + T cells, Foxp3 + Tregs, and IDO, interact with each other to compose a complex community of tumor immune microenvironment, ultimately affecting tumor progression and survival of gastric cancer.