Understand how machine learning impact lung cancer research from 2010 to 2021: A bibliometric analysis.

Advances in lung cancer research applying machine learning (ML) technology have generated many relevant literature. However, there is absence of bibliometric analysis review that aids a comprehensive understanding of this field and its progress. Present article for the first time performed a bibliometric analysis to clarify research status and focus from 2010 to 2021. In the analysis, a total of 2,312 relevant literature were searched and retrieved from the Web of Science Core Collection database. We conducted a bibliometric analysis and further visualization. During that time, exponentially growing annual publication and our model have shown a flourishing research prospect. Annual citation reached the peak in 2017. Researchers from United States and China have produced most of the relevant literature and strongest partnership between them. Medical image analysis and Nature appeared to bring more attention to the public. The computer-aided diagnosis, precision medicine, and survival prediction were the focus of research, reflecting the development trend at that period. ML did make a big difference in lung cancer research in the past decade.

Alveolar macrophage modulation via the gut-lung axis in lung diseases.

Several studies have demonstrated great potential implications for the gut-lung axis in lung disease etiology and treatment. The gut environment can be influenced by diet, metabolites, microbiotal composition, primary diseases, and medical interventions. These changes modulate the functions of alveolar macrophages (AMs) to shape the pulmonary immune response, which greatly impacts lung health. The immune modulation of AMs is implicated in the pathogenesis of various lung diseases. However, the mechanism of the gut-lung axis in lung diseases has not yet been determined. This mini-review aimed to shed light on the critical nature of communication between the gut and AMs during the development of pulmonary infection, injury, allergy, and malignancy. A better understanding of their crosstalk may provide new insights into future therapeutic strategies targeting the gut-AM interaction.

cGAS-STING pathway in ischemia-reperfusion injury: a potential target to improve transplantation outcomes.

Transplantation is an important life-saving therapeutic choice for patients with organ or tissue failure once all other treatment options are exhausted. However, most allografts become damaged over an extended period, and post-transplantation survival is limited. Ischemia reperfusion injury (IRI) tends to be associated with a poor prognosis; resultant severe primary graft dysfunction is the main cause of transplant failure. Targeting the cGAS-STING pathway has recently been shown to be an effective approach for improving transplantation outcomes, when activated or inhibited cGAS-STING pathway, IRI can be alleviated by regulating inflammatory response and programmed cell death. Thus, continuing efforts to develop selective agonists and antagonists may bring great hopes to post-transplant patient. In this mini-review, we reviewed the role of the cGAS-STING pathway in transplantation, and summarized the crosstalk between this pathway and inflammatory response and programmed cell death during IRI, aiming to provide novel insights into the development of therapies to improve patient outcome after transplantation.

Integrative learning in developing an immunologic lncRNA signature as a consensus risk-stratification tool for lung adenocarcinoma.

Background: In the tumor immune microenvironment, the contribution of innate and adaptive immune cells to tumor progression has been consistently demonstrated. However, reliable prognostic biomarkers for lung adenocarcinoma (LUAD) have not yet been identified. We thus developed and validated an immunologic long noncoding RNA (lncRNA) signature (ILLS) to facilitate the classification of patients with high and low risk and provide potential "made-to-measure" treatment choices. Methods: The LUAD data sets were obtained and processed from public databases of The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). The abundance of immune infiltration and its related pathways were calculated through consensus clustering, weighted gene coexpression network analysis (WGCNA), and an integrated ImmLnc to identify immune-related lncRNAs and extract immune-related prognostic lncRNAs. Based on the integrative procedure, the best algorithm composition was least absolute shrinkage and selection operator (LASSO) and stepwise Cox regression in both directions to develop the ILLS in the TCGA-LUAD data set and validate the predictive power of 4 independent data sets, GSE31210, GSE37745, GSE30219, and GSE50081 through survival analysis, receiver operating characteristic (ROC) analysis, and multivariate Cox regression. The concordance index (C-index) analysis was transversely compared with 49 published signatures in the above 5 data sets to further confirm its stability and superiority. Finally, drug sensitivity analysis was conducted to explore potential therapeutic agents. Results: Patients from the high-risk groups consistently had worse overall survival (OS) compared to the low-risk groups. ILLS proved to be an independent prognostic factor with favorable sensitivity and specificity. Among the 4 GEO data sets, compared to those reported in the other literature, ILLS maintained stable prediction ability and was more suitable as a consensus risk-stratification tool. However, The Cancer Immunome Atlas and IMvigor210 data sets demonstrated practical utility in recognizing target populations with effective immunotherapy, while the high-risk group exhibited potential targets for certain chemotherapy drugs, such as carmustine, etoposide, arsenic trioxide, and alectinib. Conclusions: ILLS demonstrated superior and stable prognostic prediction ability and thus has potential as a tool for assisting in risk classification and clinical decision-making in patients with LUAD.

Identification and transfer of a new Pm21 haplotype with high genetic diversity and a special molecular resistance mechanism.

KEY MESSAGE: A new functional Pm21 haplotype, Pm21(8#), was cloned from the new wheat-H. villosa translocation line T6VS(8#)·6DL, which confers the same strong resistance to powdery mildew through a different resistance mechanism. Broad-spectrum disease resistance genes are desirable in crop breeding for conferring stable, durable resistance in field production. Pm21(4#) is a gene introduced from wild Haynaldia villosa into wheat that confers broad-spectrum resistance to wheat powdery mildew and has been widely used in wheat production for approximately 30 years. The discovery and transfer of new functional haplotypes of Pm21 into wheat will expand its genetic diversity in production and avoid the breakdown of resistance conferred by a single gene on a large scale. Pm21(4#) previously found from T6VS(4#)·6AL has been cloned. In this study, a new wheat-H. villosa translocation, T6VS(8#)·6DL, was identified. A new functional Pm21 haplotype, designated Pm21(8#), was cloned and characterized. The genomic structures and the splicing patterns of Pm21(4#) and Pm21(8#) were different, and widespread sequence diversity was observed in the gene coding region and the promoter region. In the field, Pm21(8#) conferred resistance to Blumeria graminis f. sp. tritici (Bgt), similar to Pm21(4#), indicating that Pm21(8#) was also a resistance gene. However, Bgt development during the infection stage was obviously different between Pm21(4#)- and Pm21(8#)-containing materials under the microscopic observation. Pm21(4#) inhibited the formation of haustoria and the development of hyphae in the initial infection stage, while Pm21(8#) limited the growth of hyphae and inhibited the formation of conidiophores in the late infection stage. Therefore, Pm21(8#) is a new functional Pm21 haplotype that provides a new gene resource for wheat breeding.

miR-144 inhibits the IGF1R-ERK1/2 signaling pathway via NUDCD1 to suppress the proliferation and metastasis of colorectal cancer cells: a study based on bioinformatics and in vitro and in vivo verification.

PURPOSE: Colorectal cancer (CRC) is a severe health condition characterized by high mortalities. NudC domain containing 1 (NUDCD1) is abnormally upregulated in multiple tumors and is recognized as a cancer antigen. In CRC, NUDCD1 upregulation accelerates tumor progression by activating the IGF1R-ERK1/2 signaling pathway. Its specific regulatory mechanisms, however, remain unclear. METHODS: In the present study, we predicted the regulators of NUDCD1 and analyzed the expression profile of NUDCD1 in CRC tissues using the gene chip dataset. We also determined the regulation between miR-144, NUDCD1 and IGF1R-ERK1/2 signaling in vitro and in vivo. Then, the expression of miR-144 in CRC tissues was detected and its cell functions were verified in vitro. RESULTS: As predicted by bioinformatics, we found that NUDCD1 is a predicted target of miR-144 and confirmed that miR-144 directly binds to NUDCD1. In vitro and in vivo, miR-144 was determined to specifically regulate NUDCD1 expression and as such, can reduce the activity of the IGF1R-ERK1/2 signaling pathway. Moreover, miR-144 was significantly downregulated in CRC tissues; its levels were significantly negatively correlated with CRC primary range and lymph node metastasis. Cell function studies verified that miR-144 acts as a tumor suppressor, because it significantly inhibits the proliferation, metastasis, and invasion of CRC cells as well as inducing cell cycle arrest and apoptosis. CONCLUSIONS: Our study demonstrates that miR-144 regulates IGF1R-ERK1/2 signaling via NUDCD1 to inhibit CRC cell proliferation and metastasis. The miR-144/NUDCD1/IGF1R-ERK1/2 signaling axis may be crucial in the progression of CRC.

Genome-wide identification of the NLR gene family in Haynaldia villosa by SMRT-RenSeq.

BACKGROUND: Nucleotide-binding and leucine-rich repeat (NLR) genes have attracted wide attention due to their crucial role in protecting plants from pathogens. SMRT-RenSeq, combining PacBio sequencing after resistance gene enrichment sequencing (RenSeq), is a powerful method for selectively capturing and sequencing full-length NLRs. Haynaldia villosa, a wild grass species with a proven potential for wheat improvement, confers resistance to multiple diseases. So, genome-wide identification of the NLR gene family in Haynaldia villosa by SMRT-RenSeq can facilitate disease resistance genes exploration. RESULTS: In this study, SMRT-RenSeq was performed to identify the genome-wide NLR complement of H. villosa. In total, 1320 NLRs were annotated in 1169 contigs, including 772 complete NLRs. All the complete NLRs were phylogenetically analyzed and 11 main clades with special characteristics were derived. NLRs could be captured with high efficiency when aligned with cloned R genes, and cluster expansion in some specific gene loci was observed. The physical location of NLRs to individual chromosomes in H. villosa showed a perfect homoeologous relationship with group 1, 2, 3, 5 and 6 of other Triticeae species, however, NLRs physically located on 4VL were largely in silico predicted to be located on the homoeologous group 7. Fifteen types of integrated domains (IDs) were integrated in 52 NLRs, and Kelch and B3 NLR-IDs were found to have expanded in H. villosa, while DUF948, NAM-associated and PRT_C were detected as unique integrated domains implying the new emergence of NLR-IDs after H. villosa diverged from other species. CONCLUSION: SMRT-RenSeq is a powerful tool to identify NLR genes from wild species using the baits of the evolutionary related species with reference sequences. The availability of the NLRs from H. villosa provide a valuable library for R gene mining and transfer of disease resistance into wheat.

Association of pre-pregnancy body mass index with adverse pregnancy outcome among first-time mothers.

BACKGROUND: Studies have reported an increased risk of adverse pregnancy outcome associated with pre-pregnancy body mass index (BMI). However, the data on such associations in urban areas of southern Chinese women is limited, which drive us to clarify the associations of pre-pregnancy BMI and the risks of adverse pregnancy outcomes (preterm birth (PTB) and low birth weight (LBW)) and maternal health outcomes (gestational hypertension and cesarean delivery). METHODS: We performed a hospital-based case-control study including 3,864 Southern Chinese women who gave first birth to a live singleton infant from January 2015 to December 2015. PTB was stratified into three subgroups according to gestational age (extremely PTB, very PTB and moderate PTB). Besides, we combined birth weight and gestational age to dichotomise as being small for gestational age (SGA, less than the tenth percentile of weight for gestation) and non-small for gestational age (NSGA, large than the tenth percentile of weight for gestation), gestational week was also classified into categories of term, 34-36 week and below 34 week.. We then divided newborns into six groups: (1) term and NSGA; (2) 34-36 week gestation and NSGA; (3) below 34 week gestation and NSGA; (4) term and SAG; (5) 34-36 week gestation and SAG; (6) below 34 week gestation and SAG. Adjusted logistic regression models was used to estimate the odds ratios of adverse outcomes. RESULTS: Underweight women were more likely to give LBW (AOR = 1.44, 95% CI [1.11-1.89]), the similar result was seen in term and SAG as compared with term and NSAG (AOR = 1.78, 95% CI [1.45-2.17]), whereas underweight was significantly associated with a lower risk of gestational hypertension (AOR = 0.45, 95% CI [0.25-0.82) and caesarean delivery (AOR = 0.74, 95% CI [0.62-0.90]). The risk of extremely PTB is relatively higher among overweight and obese mothers in a subgroup analysis of PTB (AOR = 8.12, 95% CI [1.11-59.44]; AOR = 15.06, 95% CI [1.32-172.13], respectively). Both maternal overweight and obesity were associated with a greater risk of gestational hypertension (AOR = 1.71, 95% CI [1.06-2.77]; AOR = 5.54, 95% CI [3.02-10.17], respectively) and caesarean delivery (AOR = 1.91, 95% CI [1.53-2.38]; AOR = 1.85, 95% CI [1.21-2.82], respectively). CONCLUSIONS: Our study suggested that maternal overweight and obesity were associated with a significantly higher risk of gestational hypertension, caesarean delivery and extremely PTB. Underweight was correlated with an increased risk of LBW and conferred a protective effect regarding the risk for gestational hypertension and caesarean delivery for the first-time mothers among Southern Chinese.

Association of induced abortion with preterm birth risk in first-time mothers.

Women who have previously had an induced abortion (IA) before their first birth have been associated with preterm birth (PTB). However, previous studies on the PTB are inconsistent. Therefore, the aim of this study was to clarify the association between IA and PTB and low birth weight (LBW) for first-time mothers. A total of 3,684 Southern Chinese women who gave birth for the first time to a live singleton infants were recruited between January 2015 and December 2015 in the province of Guangdong, China. Univariable and multivariable analyses were conducted to determine whether IA was associated with PTB and LBW. Previous IA was not associated with increased risks of PTB or LBW, adjusted odds ratios were 0.80 (95% CI = 0.53 to 1.20) and 0.86 (95% CI = 0.57 to 1.31), respectively. Additionally, no significant associations were observed for infants born at before 37, before 32, and before 28 gestational weeks. And no significant associations were also observed for LBW measuring lower than 2500 grams and also measuring lower than 1500 grams. Our study suggested that a previous IA, as compared with women who reported no previous IA, does not increase the risk of PTB or LBW in subsequent pregnancy for the first-time mothers among Southern Chinese women.

Association between glutathione S-transferases M1 and T1 gene polymorphisms and esophageal cancer prognosi.

OBJECTIVE: To investigate the independent factors affecting the prognosis of patients after resection of esophageal cancer, and to inquire into the relationship between GSTM1, GSTT1 gene polymorphisms and esophageal cancer prognosis. METHODS: The clinical data of 273 patients with esophageal cancer were retrospectively analyzed. The patients were followed-up after their surgery, and the gene polymorphisms of GSTM1 and GSTT1 in each individual were detected by polymerase chain reaction (PCR). The clinical features along with the gene polymorphisms of GSTM1 and GSTT1 associated with the prognosis of patients were analyzed by using the method of univariate analysis and Cox proportional hazard model. The cumulative survival rate was estimated by Kaplan-Meier methods, and the survival curves were compared by using the log-rank test. RESULTS: The overall cumulative survival rate of first year, third year and fifth year is 94.6%, 58.5% and 17.8%, respectively. The median survival time (MST) is 38.7 months. The results of univariate analysis showed that: infiltration depth, length of tumor, the number of lymph node metastasis, the region of lymph node metastasis and the genetic polymorphism of GSTM1 and GSTT1 gene loci were associated with the survival of postoperative patients. Cox multivariate analysis further indicated that the length of tumor, the number of lymph node metastasis and the combined genotype (1) [GSTM1 (+/+) or (+/-) & GSTT1 (-/-)] were the independent prognostic factors. The length of tumor, the number of lymph node metastasis were the risk factors for the prognosis, and the combined genotype (1) had protective effect on survival when compared with reference [GSTM1 (+/+) or (+/-) & GSTT1 (+/+) or (+/-)]. CONCLUSION: The length of tumor, the number of lymph node metastasis were confirmed as the independent prognostic factors of esophageal carcinoma, and the null genotypes for GSTT1 (-/-) might be a protective factor for survival and GSTM1 (-/-) might be a potential negative prognostic factor in patients with esophageal cancer.

Effects of α-enolase (ENO1) over-expression on malignant biological behaviors of AGS cells.

OBJECTIVE: To investigate the effects of α-Enolase (ENO1) over-expression on the proliferative and migratory abilities of AGS cells. METHODS: The target gene was cloned and mounted to the eukaryotic expression vector pcDNA3.1(+), then was transfected into gastric cancer cell lines AGS. mRNA and protein level of ENO1 in AGS cells were verified by real-time quantitative RT-PCR and Western Blot, respectively. The effects of over-expression of ENO1 on proliferative and migratory abilities of AGS cells were detected by the experiments of CCK-8, colony formation and wound healing assays. RESULTS: The eukaryotic expression vector pcDNA3.1(+)/eno1 was successfully constructed, and verified by sequencing. It was shown from the cell proliferation curves that the proliferative ability of AGS-ENO1 transfected group was higher than that of the control group after 72 hours (t = 3.44, P = 0.04), meanwhile, the number of the cell-colonies of the AGS-ENO1 group were significantly greater than that of the control group (t = 5.26, P = 0.01). For the ability of migration, it was significantly enhanced in the over-expression ENO1 cells than in the negative cells (t = 7.35, P < 0.001). CONCLUSION: The over-expression of ENO1 protein can enhance the abilities of proliferation and migration in gastric cancer cells of AGS, which indicates that ENO1 may be an important potential tumor-marker associated with the development of gastric cancer.