scholarly journals Prognostic Ferroptosis-Related lncRNA Signatures Associated With Immunotherapy and Chemotherapy Responses in Patients With Stomach Cancer

2022 ◽  
Vol 12 ◽  
Author(s):  
Donlin Lai ◽  
Lin Tan ◽  
Xiaojia Zuo ◽  
DingSheng Liu ◽  
Deyi Jiao ◽  
...  

Ferroptosis is associated with the prognosis and therapeutic responses of patients with various cancers. LncRNAs are reported to exhibit antitumor or oncogenic functions. Currently, few studies have assessed the combined effects of ferroptosis and lncRNAs on the prognosis and therapy of stomach cancer. In this study, transcriptomic and clinical data were downloaded from TCGA database, and ferroptosis-related genes were obtained from the FerrDb database. Through correlation analysis, Cox analysis, and the Lasso algorithm, 10 prognostic ferroptosis-related lncRNAs (AC009299.2, AC012020.1, AC092723.2, AC093642.1, AC243829.4, AL121748.1, FLNB-AS1, LINC01614, LINC02485, LINC02728) were screened to construct a prognostic model, which was verified in two test cohorts. Risk scores for patients with stomach cancer were calculated, and patients were divided into two risk groups. The low-risk group, based on the median value, had a longer overall survival time in the KM curve, and a lower proportion of dead patients in the survival distribution curve. Potential mechanisms and possible functions were revealed using GSEA and the ceRNA network. By integrating clinical information, the association between lncRNAs and clinical features was analyzed and several features affecting prognosis were identified. Then, a nomogram was developed to predict survival rates, and its good predictive performance was indicated by a relatively high C-index (0.67118161) and a good match in calibration curves. Next, the association between these lncRNAs and therapy was explored. Patients in the low-risk group had an immune-activating environment, higher immune scores, higher TMB, lower TIDE scores, and higher expression of immune checkpoints, suggesting they might receive a greater benefit from immune checkpoint inhibitor therapy. In addition, a significant difference in the sensitivity to mitomycin. C, cisplatin, and docetaxel, but not etoposide and paclitaxel, was observed. In summary, this model had guiding significance for prognosis and personalized therapy. It helped screen patients with stomach cancer who might benefit from immunotherapy and guided the selection of personalized chemotherapeutic drugs.

Author(s):  
Jianglin Zheng ◽  
Zijie Zhou ◽  
Yue Qiu ◽  
Minjie Wang ◽  
Hao Yu ◽  
...  

Recent studies have demonstrated that long non-coding RNAs (lncRNAs) are implicated in the regulation of tumor cell ferroptosis. However, the prognostic value of ferroptosis-related lncRNAs has never been comprehensively explored in glioma. In this study, the transcriptomic data and clinical information of glioma patients were downloaded from TCGA, CGGA and Rembrandt databases. We identified 24 prognostic ferroptosis-related lncRNAs, 15 of which (SNAI3-AS1, GDNF-AS1, WDFY3-AS2, CPB2-AS1, WAC-AS1, SLC25A21-AS1, ARHGEF26-AS1, LINC00641, LINC00844, MIR155HG, MIR22HG, PVT1, SNHG18, PAXIP1-AS2, and SBF2-AS1) were used to construct a ferroptosis-related lncRNAs signature (FRLS) according to the least absolute shrinkage and selection operator (LASSO) regression. The validity of this FRLS was verified in training (TCGA) and validation (CGGA and Rembrandt) cohorts, respectively. The Kaplan-Meier curves revealed a significant distinction of overall survival (OS) between the high- and low-risk groups. The receiver operating characteristic (ROC) curves exhibited robust prognostic capacity of this FRLS. A nomogram with improved accuracy for predicting OS was established based on independent prognostic factors (FRLS, age, and WHO grade). Besides, patients in the high-risk group had higher immune, stroma, and ESTIMATE scores, lower tumor purity, higher infiltration of immunosuppressive cells, and higher expression of immune checkpoints. Patients in the low-risk group benefited significantly from radiotherapy, while no survival benefit of radiotherapy was observed for those in the high-risk group. In conclusion, we identified the prognostic ferroptosis-related lncRNAs in glioma, and constructed a prognostic signature which was associated with the immune landscape of glioma microenvironment and radiotherapy response.


2019 ◽  
Vol 21 (5) ◽  
pp. 1742-1755 ◽  
Author(s):  
Siqi Bao ◽  
Hengqiang Zhao ◽  
Jian Yuan ◽  
Dandan Fan ◽  
Zicheng Zhang ◽  
...  

Abstract Emerging evidence revealed the critical roles of long non-coding RNAs (lncRNAs) in maintaining genomic instability. However, identification of genome instability-associated lncRNAs and their clinical significance in cancers remain largely unexplored. Here, we developed a mutator hypothesis-derived computational frame combining lncRNA expression profiles and somatic mutation profiles in a tumor genome and identified 128 novel genomic instability-associated lncRNAs in breast cancer as a case study. We then identified a genome instability-derived two lncRNA-based gene signature (GILncSig) that stratified patients into high- and low-risk groups with significantly different outcome and was further validated in multiple independent patient cohorts. Furthermore, the GILncSig correlated with genomic mutation rate in both ovarian cancer and breast cancer, indicating its potential as a measurement of the degree of genome instability. The GILncSig was able to divide TP53 wide-type patients into two risk groups, with the low-risk group showing significantly improved outcome and the high-risk group showing no significant difference compared with those with TP53 mutation. In summary, this study provided a critical approach and resource for further studies examining the role of lncRNAs in genome instability and introduced a potential new avenue for identifying genomic instability-associated cancer biomarkers.


Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 4128-4128
Author(s):  
Christiane E Dobbelstein ◽  
Jochen Metzger ◽  
Elke Dammann ◽  
Uwe Borchert ◽  
Stefanie Buchholz ◽  
...  

Abstract Abstract 4128 Objectives: Allogeneic stem cell transplantation (SCT) is an established treatment for many severe disorders of hematopoiesis. Although SCT has considerable curative potential, its application is limited by transplant-related complications such as infections and graft-versus host disease (GvHD) which could lead to high mortality rates especially in older or less fit patients. Therefore, a careful pre-SCT assessment of risk and benefit is mandatory and different scores have recently emerged as helpful tools. We have previously applied proteomics to identify a specific urinary polypeptide patterns (PP) predictive for developing acute GvHD (aGvHD) (Weissinger EM et al, Blood 2007;109:5511–5519). The aim of this study was to investigate whether the PPs can predict overall outcome after allo-SCT and to compare these findings to those of the hematopoietic cell transplantation comorbidity index (HCT-CI) (Sorror M et al, Blood 2005;106:2912–2919). Methods: In this retrospective analysis from Hannover Medical School, the datasets from all patients (pts) with acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS), who were allo-transplanted from a fully matched donor (matched related/unrelated donor (MRD/MUD)) between 2003–2008 and for whom relevant PP data were available, were included. Pts with a pt-donor HLA-mismatch constellation were excluded from this study. PP data from urine samples which were prospectively collected by day ≥ +7 after allo-SCT were correlated with overall survival (OS), aGvHD, non-relapse mortality (NRM), relapse rate and mortality (RM), and compared to the predictive value of the HCT-CI. Results: PP data were available from 111 pts (97 pts with AML, 14 with MDS; median age 52y; median EBMT score 4; 59 male/52 female; 69 MUD/42 MRD). They were grouped in high (PP-HRG), low (PP-LRG) or intermediate risk groups (PP-IRG). Forty-three pts (39%) belonged to the PP-LRG for aGvHD compared to 47 pts (42%) who were classified PP-HRG. Patient characteristics of PP-LRG and PP-HRG were similar in terms of age, sex and EBMT score (median 4 in both groups). OS compared favorably for the PP-LRG with an OS of 72% vs. 49% for the PP-HRG (p=0.03), also if only reduced intensity conditioning (RIC) was considered (73% vs 42%; p=0.01), respectively. There was a trend for higher incidence of NRM in the PP-HRG compared to PP-LRG (30% vs 14%, p=0.07) for the whole cohort, and a significant higher NRM rate, if only RIC was evaluated (35% vs 11%, p=0.01). However, if risk stratification was based on the HCT-CI, there was no significant difference between high risk (S-HRG) and low risk group (S-LRG) in terms of OS and NRM regardless of intensity of conditioning (OS for whole cohort: 57% vs 45%, p=0.4; OS for RIC: 56% vs 36%, p=0.2; NRM for whole cohort: 20% vs 23%, p=0.8; NRM for RIC: 18% vs 29%, p=0.4). Concerning the PP-IRG, there was a difference in OS between PP-IRG and PP-LRG (38% vs 73%, p=0.02). However, there was no significant difference in OS of the PP-IRG compared to the other PP-based risk groups nor between the HCT-CI based risk groups. Further, NRM did not show a significant difference neither for PP-based nor HCT-CI-based intermediate risk group compared to the other risk groups. Thirty vs 15 pts developed aGvHD in PP-HRG and PP-LRG (64% vs 35%, p<0.01) compared to 48% vs 64% (p=0.2) for S-HRG and S-LRG of the whole cohort, respectively. Incidence of aGvHD differed also significantly in the RIC cohort for PP-HRG and PP-LRG (65% vs 32%, p=0.01), but not for HCT-CI-based risk groups (47% vs 64%, p=0.1). Relapse rates and RM were not significantly different between high and low risk groups, neither for PP-based nor HCT-CI based (whole cohort and RIC subgroup), respectively. Conclusion: Risk stratification according to GvHD-match based PP, which has previously been shown to predict aGvHD, now also allows the identification of patient groups with significantly different OS and NRM. In comparison to the HCT-CI, PP-based prediction shows significantly higher accuracy in this rather homogeneous cohort of patients. Since proteomics is a new method which has been available only at a few centers, further multicenter analyses are essential to determinate the value of PP-based prediction of complications and outcome in SCT. Disclosures: Metzger: Mosaiques Diagnostics GmbH: Employment.


Author(s):  
Xinshuang Yu ◽  
Peng Dong ◽  
Yu Yan ◽  
Fengjun Liu ◽  
Hui Wang ◽  
...  

Pancreatic cancer is a highly aggressive disease with poor prognosis. N6-methyladenosine (m6A) is critical for post-transcriptional modification of messenger RNA (mRNA) and long non-coding RNA (lncRNA). However, the m6A-associated lncRNAs (m6A-lncRNA) and their values in predicting clinical outcomes and immune microenvironmental status in pancreatic cancer patients remain largely unexplored. This study aimed to evaluate the importance of m6A-lncRNA and established a m6A-lncRNA signature for predicting immunotherapeutic response and prognosis of pancreatic cancer. The m6A-lncRNA co-expression networks were constructed using data from the TCGA and GTEx database. Based on the least absolute shrinkage and selection operator (LASSO) analysis, we constructed an 8 m6A-lncRNA signature risk model, and selection operator (LASSO) analysis, and stratified patients into the high- and low-risk groups with significant difference in overall survival (OS) (HR = 2.68, 95% CI = 1.74–4.14, P &lt; 0.0001). Patients in the high-risk group showed significantly reduced OS compared to patients in the low-risk group (P &lt; 0.001). The clinical characteristics and m6A-lncRNA risk scores were used to construct a nomogram which accurately predicted the OS in pancreatic cancer. TIMER 2.0 were used to investigate tumor immune infiltrating cells and its relationship with pancreatic cancer. CIBERSORT analysis revealed increased higher infiltration proportions of M0 and M2 macrophages, and lower infiltration of naive B cell, CD8+ T cell and Treg cells in the high-risk group. Compared to the low-risk group, functional annotation using ssGSEA showed that T cell infiltration and the differential immune-related check-point genes are expressed at low level in the high-risk group (P &lt; 0.05). In summary, our study constructed a novel m6A-associated lncRNAs signature to predict immunotherapeutic responses and provided a novel nomogram for the prognosis prediction of pancreatic cancer.


2020 ◽  
Author(s):  
zhiyong zeng ◽  
Chaohui Wu ◽  
Zhenlv Lin ◽  
Yong Ye ◽  
Shaodan Feng ◽  
...  

Abstract Background No therapeutics have demonstrated specific efficacy for patients with COVID-19. Methods We retrospectively evaluated 351 patients with COVID-19 admitted to the Third People's Hospital of Yichang from 9 January to 25 March, 2020.Univariate logistic regression and least absolute shrinkage and selection operator (LASSO) regression were employed to identify risk factors associated with progression, which were then incorporated into the nomogram. Survival of patients between high-risk and low-risk groups was compared by kaplan-Meier analysis. Moreover, we assessed the effects of existing common drugs on survival of patients with high-risk. Results Based on the LASSO, four variables (white blood cell, C-reactive protein, whether lymphocyte ≥ 0.8 × 109/L, and whether lactate dehydrogenase ≥ 400 U/L) were selected for construction of the nomogram. Patients in the total cohort were stratified into low-risk group (total point < 160) and high-risk group (total point ≥ 160). Kaplan-Meier analysis demonstrated that there was significant difference in survival of patients between high-risk and low-risk groups (8-week survival rate: 71.41% vs 100%, P < 0.0001). Among the common drugs, we found that patients with high-risk received oseltamivir, lopinavir/ritonavir or Reduning injection exhibited better survival. The combination of these three drugs showed the effect of improving survival, although single drug may have no effect in different grouping analysis. Conclusions The combination of oseltamivir, lopinavir/ritonavir and Reduning injection may improve survival of COVID-19 patients with high-risk identified by our simple-to-use nomogram.


2021 ◽  
Vol 2021 ◽  
pp. 1-20
Author(s):  
Zhicheng Zhuang ◽  
Huajun Cai ◽  
Hexin Lin ◽  
Bingjie Guan ◽  
Yong Wu ◽  
...  

Background. Pyroptosis has been confirmed as a type of inflammatory programmed cell death in recent years. However, the prognostic role of pyroptosis in colon cancer (CC) remains unclear. Methods. Dataset TCGA-COAD which came from the TCGA portal was taken as the training cohort. GSE17538 from the GEO database was treated as validation cohorts. Differential expression genes (DEGs) between normal and tumor tissues were confirmed. Patients were classified into two subgroups according to the expression characteristics of pyroptosis-related DEGs. The LASSO regression analysis was used to build the best prognostic signature, and its reliability was validated using Kaplan–Meier, ROC, PCA, and t-SNE analyses. And a nomogram based on the multivariate Cox analysis was developed. The enrichment analysis was performed in the GO and KEGG to investigate the potential mechanism. In addition, we explored the difference in the abundance of infiltrating immune cells and immune microenvironment between high- and low-risk groups. And we also predicted the association of common immune checkpoints with risk scores. Finally, we verified the expression of the pyroptosis-related hub gene at the protein level by immunohistochemistry. Results. A total of 23 pyroptosis-related DEGs were identified in the TCGA cohort. Patients were classified into two molecular clusters (MC) based on DEGs. Kaplan–Meier survival analysis indicated that patients with MC1 represented significantly poorer OS than patients with MC2. 13 overall survival- (OS-) related DEGs in MCs were used to construct the prognostic signature. Patients in the high-risk group exhibited poorer OS compared to those in the low-risk group. Combined with the clinical features, the risk score was found to be an independent prognostic factor of CC patients. The above results are verified in the external dataset GSE17538. A nomogram was established and showed excellent performance. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses indicated that the varied prognostic performance between high- and low-risk groups may be related to the immune response mediated by local inflammation. Further analysis showed that the high-risk group has stronger immune cell infiltration and lower tumor purity than the low-risk group. Through the correlation between risk score and immune checkpoint expression, T-cell immunoglobulin and mucin domain-containing protein 3 (TIM-3) was predicted as a potential therapeutic target for the high-risk group. Conclusion. The 13-gene signature was associated with OS, immune cells, tumor purity, and immune checkpoints in CC patients, and it could provide the basis for immunotherapy and predicting prognosis and help clinicians make decisions for individualized treatment.


Cancers ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1730
Author(s):  
Ruotong Tian ◽  
Yimin Li ◽  
Qian Liu ◽  
Minfeng Shu

The prognosis of patients with glioma is largely related to both the tumor-infiltrating immune cells and the expression of RNA-binding proteins (RBPs) that are able to regulate various pro-inflammatory and oncogenic mediators. However, immune-associated RBPs in glioma remain unexplored. In this study, we captured patient data from The Cancer Genome Atlas (TCGA) and divided them into two immune subtype groups according to the difference in infiltration of immune cells. After differential expression and co-expression analysis, we identified 216 RBPs defined as immune-associated RBPs. After narrowing down processes, eight RBPs were selected out to construct a risk signature that proven to be a novel and independent prognostic factor. The patients were divided into high- and low-risk groups on the basis of risk score. Higher risk scores meant worse overall survival and higher expression of human leukocyte antigen and immune checkpoints such as PD1 and CTLA4. In addition, analyses of pathway enrichment, somatic mutation, copy number variations and immuno-/chemotherapeutic response prediction were performed in high- and low-risk groups and compared with each other. For the first time, we demonstrated a novel signature composed of eight immune-associated RBPs that was valuable in predicting the survival of glioma patients and directing immunotherapy and chemotherapy.


2019 ◽  
Vol 44 (2) ◽  
pp. 127-137
Author(s):  
E Achilleos ◽  
C Rahiotis ◽  
K Kavvadia ◽  
G Vougiouklakis

SUMMARYThe aim of this study was to investigate the management of incipient caries lesions in adults with two preventive protocols. A total of 44 adult patients with high, moderate and low caries risk with 516 incipient caries took part in the study. These patients were assessed for caries with International Caries Detection and Assessment System (ICDAS) criteria and were then divided into three groups depending on their caries risk profile: a high-risk group (group A), a moderate-risk group (group B), and a low-risk group (group C). Participants in each group were further divided randomly into two subgroups. In subgroups A1, B1, and C1, an intensive preventive protocol was applied, while in subgroups A2, B2, and C2, the protocol consisted only of instructions in oral hygiene. The invasive-intensive protocol included the topical application of fluoride, brushing with 5000-ppm fluoride toothpaste, use of amorphous calcium phosphate-casein phosphopeptide, applications of sealants for occlusal lesions (ICDAS code 2), and minimal resin restorations for occlusal lesions (ICDAS code 3). There was no statistically significant difference in the number of lesions (baseline and after one year) in the high-risk and moderate-risk groups that received the intensive protocol (groups A1 and B1), while the control groups were statistically significant different (groups A2 and B2). In the low-risk group, there was no statistically significant difference in the number of lesions (groups C1 and C2). The two different preventive protocols in the high- and moderate-risk groups presented differences in effectiveness, while in the low-risk group, no significant difference was demonstrated.


2008 ◽  
Vol 18 (5) ◽  
pp. 1097-1101 ◽  
Author(s):  
Y. Ma ◽  
Y. Xiang ◽  
X. R. Wan ◽  
Y. Chen ◽  
F. Z. Feng ◽  
...  

A retrospective analysis of 123 postpartum choriocarcinoma cases treated at the Peking Union Medical College Hospital between December 1985 and December 2006 was performed. All the patients with postpartum choriocarcinoma received chemotherapy, combined with comprehensive therapy. The total number of chemotherapy cycles was 1041 (8.5 for every patient on average). The complete remission (CR) was achieved in 108 patients (87.8%), whereas five patients had partial remission and ten died. Of the 26 patients who became resistant to 5-fluorouracil combined chemotherapy, 18 achieved CR. Of the four cases who had recurrence, three achieved CR. The patients were divided into high- and low-risk groups, based on the new FIGO 2000 risk factor scoring system. Seventy-five patients were in high-risk group, with a score of 7 or more. Among them, 62 achieved CR (82.7%). The remaining 48 patients were in the low-risk group, with a score of 6 or less, among whom 46 patients achieved CR (95.8%). There is a significant difference in CR rate between the two groups. Based on the FIGO staging and scoring system, 24 patients were diagnosed as FIGO stage I, 9 stage II, 66 stage III, and 24 stage IV. The rate of CR was 100%, 100%, 91%, and 62.5%, respectively. Our experience shows that prognosis of postpartum choriocarcinoma is good when multiagent systemic chemotherapy is applied. Shortened time interval between the antecedent pregnancy and the treatment will lead to better prognosis


2021 ◽  
Author(s):  
Rongchang Zhao ◽  
Dan Ding ◽  
Yan Ding ◽  
Rongbo Han ◽  
Xiujuan Wang ◽  
...  

Abstract Background Multiple factors affect the survival time of patients with lung adenocarcinoma (LUAD). Specifically, the therapeutic effect of medicines and the disease recurrence probability differs among patients with the same stage of LUAD. Thus, effective prognostic predictors need to be identified. Methods Based on the tumor mutation burden (TMB) data obtained by TCGA, LUAD was divided into high and low groups, and the differentially expressed glycolysis-related genes between the two groups were screened out. Cox regression was used to obtain a prognostic model. A receiver operating characteristic (ROC) curve and calibration curve were generated to evaluate the nomogram that was constructed based on clinicopathological characteristics and the risk score. Two datasets (GSE68465 and GSE11969) from Gene Expression Omnibus (GEO) were used to verify the prognostic performance of the gene. Furthermore, differences in immune cell distribution, immune-related molecules and drug susceptibility were assessed for their relationship with the risk score. Results We confirmed a 5-gene signature (FKBP4, HMMR, B4GALT1, ERO1L, ENO1) capable of dividing patients into two risk groups. There was a significant difference in overall survival (OS) times between the high-risk group and the low-risk group (P = 1.085e-4), with the low-risk group having a better survival outcome. Through multivariate Cox analysis, the risk score was confirmed to be an independent prognostic factor (HR = 1.289, 95% CI = 1.202-1.383, P < 0.001), and the ROC curve and nomogram exhibited accurate prediction performance. Validation of the data obtained in the GEO database yielded similar results. Additionally, there were significant differences in cisplatin, paclitaxel, gemcitabine, docetaxel, gefitiniband erlotinib sensitivity between the low-risk and high-risk groups. Conclusions Our results reveal that glycolysis-related gene are feasible predictors of LUAD patient survival and response to therapeutics.


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