Construction of an immune-related genes nomogram for the preoperative prediction of axillary lymph node metastasis in triple-negative breast cancer

Axillary lymph node metastasis in breast cancer: from historical axillary surgery to updated advances in the preoperative diagnosis and axillary management

Axillary lymph node status, which was routinely assessed by axillary lymph node dissection (ALND) until the 1990s, is a crucial factor in determining the stage, prognosis, and therapeutic strategy used for breast cancer patients. Axillary surgery for breast cancer patients has evolved from ALND to minimally invasive approaches. Over the decades, the application of noninvasive imaging techniques, machine learning approaches and emerging clinical prediction models for the detection of axillary lymph node metastasis greatly improves clinical diagnostic efficacy and provides optimal surgical selection. In this work, we summarize the historical axillary surgery and updated perspectives of axillary management for breast cancer patients.

Noninvasive Staging of Lymph Node Status in Breast Cancer Using Machine Learning: External Validation and Further Model Development

BACKGROUND

Most patients diagnosed with breast cancer present with a node-negative disease. Sentinel lymph node biopsy (SLNB) is routinely used for axillary staging, leaving patients with healthy axillary lymph nodes without therapeutic effects but at risk of morbidities from the intervention. Numerous studies have developed nodal status prediction models for noninvasive axillary staging using postoperative data or imaging features that are not part of the diagnostic workup. Lymphovascular invasion (LVI) is a top-ranked predictor of nodal metastasis; however, its preoperative assessment is challenging.

OBJECTIVE

This paper aimed to externally validate a multilayer perceptron (MLP) model for noninvasive lymph node staging (NILS) in a large population-based cohort (n=18,633) and develop a new MLP in the same cohort. Data were extracted from the Swedish National Quality Register for Breast Cancer (NKBC, 2014-2017), comprising only routinely and preoperatively available documented clinicopathological variables. A secondary aim was to develop and validate an LVI MLP for imputation of missing LVI status to increase the preoperative feasibility of the original NILS model.

METHODS

Three nonoverlapping cohorts were used for model development and validation. A total of 4 MLPs for nodal status and 1 LVI MLP were developed using 11 to 12 routinely available predictors. Three nodal status models were used to account for the different availabilities of LVI status in the cohorts and external validation in NKBC. The fourth nodal status model was developed for 80% (14,906/18,663) of NKBC cases and validated in the remaining 20% (3727/18,663). Three alternatives for imputation of LVI status were compared. The discriminatory capacity was evaluated using the validation area under the receiver operating characteristics curve (AUC) in 3 of the nodal status models. The clinical feasibility of the models was evaluated using calibration and decision curve analyses.

RESULTS

External validation of the original NILS model was performed in NKBC (AUC 0.699, 95% CI 0.690-0.708) with good calibration and the potential of sparing 16% of patients with node-negative disease from SLNB. The LVI model was externally validated (AUC 0.747, 95% CI 0.694-0.799) with good calibration but did not improve the discriminatory performance of the nodal status models. A new nodal status model was developed in NKBC without information on LVI (AUC 0.709, 95% CI: 0.688-0.729), with excellent calibration in the holdout internal validation cohort, resulting in the potential omission of 24% of patients from unnecessary SLNBs.

CONCLUSIONS

The NILS model was externally validated in NKBC, where the imputation of LVI status did not improve the model's discriminatory performance. A new nodal status model demonstrated the feasibility of using register data comprising only the variables available in the preoperative setting for NILS using machine learning. Future steps include ongoing preoperative validation of the NILS model and extending the model with, for example, mammography images.

Development, assessment and validation of a novel prediction nomogram model for risk identification of tracheobronchial tuberculosis in patients with pulmonary tuberculosis

OBJECTIVE

Tracheobronchial tuberculosis (TBTB), a specific subtype of pulmonary tuberculosis (PTB), can lead to bronchial stenosis or bronchial occlusion if not identified early. However, there is currently no available means for predicting the risk of associated TBTB in PTB patients. The objective of this study was to establish a risk prediction nomogram model for estimating the associated TBTB risk in every PTB patient.

METHODS

A retrospective cohort study was conducted with 2153 PTB patients. Optimised characteristics were selected using least absolute shrinkage and selection operator regression. Multivariate logistic regression was applied to build a predictive nomogram model. Discrimination, calibration and clinical usefulness of the prediction model were assessed using C-statistics, receiver operator characteristic curves, calibration plots and decision analysis. The developed model was validated both internally and externally.

RESULTS

Among all PTB patients who underwent bronchoscopies (n=2153), 40.36% (n=869) were diagnosed with TBTB. A nomogram model incorporating 11 predictors was developed and displayed good discrimination with a C-statistics of 0.782, a sensitivity of 0.661 and a specificity of 0.762 and good calibration with a calibration-in-the-large of 0.052 and a calibration slope of 0.957. Model's discrimination was favourable in both internal (C-statistics, 0.782) and external (C-statistics, 0.806) validation. External validation showed satisfactory accuracy (sensitivity, 0.690; specificity, 0.804) in independent cohort. Decision curve analysis showed that the model was clinically useful when intervention was decided on at the exacerbation possibility threshold of 2.3%-99.2%. A clinical impact curve demonstrated that our model predicted high-risk estimates and true positives.

CONCLUSION

We developed a novel and convenient risk prediction nomogram model that enhances the risk assessment of associated TBTB in PTB patients. This nomogram can help identify high-risk PTB patients who may benefit from early bronchoscopy and aggressive treatment to prevent disease progression.

A novel immune score model predicting the prognosis and immunotherapy response of breast cancer

Breast cancer (BC) is one of the most common malignancies. However, the existing pathological grading system cannot accurately and effectively predict the survival rate and immune checkpoint treatment response of BC patients. In this study, based on The Cancer Genome Atlas (TCGA) database, a total of 7 immune-related genes (IRGs) were screened out to construct a prognostic model. Subsequently, the clinical prognosis, pathological characteristics, cancer-immunity cycle, tumour immune dysfunction and exclusion (TIDE) score, and immune checkpoint inhibitor (ICI) response were compared between the high- and low-risk groups. In addition, we determined the potential regulatory effect of NPR3 on BC cell proliferation, migration, and apoptosis. The model consisting of 7 IRGs was an independent prognostic factor. Patients with lower risk scores exhibited longer survival times. Moreover, the expression of NPR3 was increased but the expression of PD-1, PD-L1, and CTLA-4 was decreased in the high-risk group compared to the low-risk group. In addition, compared with si-NC, si-NPR3 suppressed proliferation and migration but promoted apoptosis in both MDA-MB-231 and MCF-7 cells. This study presents a model for predicting survival outcomes and provides a strategy to guide effective personalized immunotherapy in BC patients.

Development and Validation of a Nomogram for Predicting Axillary Lymph Node Metastasis in Breast Cancer

BACKGROUND

Axillary lymph node (ALN) status is a key prognosis indicator for breast cancer patients. To develop an effective tool for predicting axillary lymph node metastasis in breast cancer, a nomogram was established based on mRNA expression data and clinicopathological characteristics.

MATERIALS AND METHODS

A 1062 breast cancer patients with mRNA data and clinical information were obtained from The Cancer Genome Atlas (TCGA). We first analyzed the differentially expression genes (DEGs) between ALN positive and ALN negative patients. Then, logistic regression, least absolute shrinkage and selection operator (Lasso) regression, and backward stepwise regression were performed to select candidate mRNA biomarkers. The mRNA signature was constructed by the mRNA biomarkers and corresponding Lasso coefficients. The key clinical factors were obtained by Wilcoxon-Mann-Whitney U test or Pearson's χ² test. Finally, the nomogram for predicting axillary lymph node metastasis was developed and evaluated by concordance index (C-index), calibration curve, decision curve analysis (DCA), and receptor operating characteristic (ROC) curve. Furthermore, the nomogram was externally validated using Gene Expression Omnibus (GEO) dataset.

RESULTS

The nomogram for predicting ALN metastasis yielded a C-index of 0.728 (95% CI: 0.698-0.758) and an AUC of 0.728 (95% CI: 0.697-0.758) in the TCGA cohort. In the independent validation cohort, the C-index and AUC of the nomogram were up to 0.825 (95% CI: 0.695-0.955) and 0.810 (95% CI: 0.666-0.953), respectively.

CONCLUSION

This nomogram could predict the risk of axillary lymph node metastasis in breast cancer and may provide a reference for clinicians to design individualized axillary lymph node management strategies.

Prognostic Characteristics of Immune-Related Genes and the Related Regulatory Axis in Patients With Stage N+M0 Breast Cancer

Breast cancer (BRCA) has the highest incidence rate among female tumours. The function of the immune system affects treatment efficacy and prognosis in patients with BRCA. However, the exact role of immune-related genes (IRGs) in stage N+M0 BRCA is unknown. We constructed a predictive risk scoring model with five IRGs (CDH1, FGFR3, INHBA, S100B, and SCG2) based on the clinical, mutation, and RNA sequencing data of individuals with stage N+M0 BRCA sourced from The Cancer Genome Atlas. Results from the Shandong Cancer Hospital and Institute validation cohort suggested that regardless of clinical stage, tumour size, or the number of lymph node metastases, this model was able to reliably discriminate low-risk patients from high-risk ones and assess the prognosis of patients with stage N+M0 BRCA, and low-risk patients could benefit more from immunotherapy than high-risk patients. In addition, significant inter-group variations in immunocyte infiltration and the tumour microenvironment were observed. Moreover, risk score and age were found to be independent factors in multivariate COX regression analysis, which influenced the outcome of patients with stage N+M0 BRCA. Based on the above findings, we plotted a prognostic nomogram. Finally, we constructed a lncRNA KCNQ1OT1-LINC00665-TUG1/miR-9-5p/CDH1 regulatory axis of the ceRNA network to explore the mechanism of BRCA progression. In summary, we conducted a systemic and extensive bioinformatics investigation and established an IRG-based prognostic scoring model. Finally, we constructed a ceRNA regulatory axis that might play a significant role in BRCA development. More research is required to confirm this result. Scoring system-based patient grouping can help predict the outcome of patients with stage N+M0 BRCA more effectively and determine their sensitivity to immunotherapies, which will aid the development of personalised therapeutic strategies and inspire the research and development of novel medications.

Nomogram to predict 3-month unfavorable outcome after thrombectomy for stroke

Background

Mechanical thrombectomy (MT) is an effective treatment for large-vessel occlusion in acute ischemic stroke, however, only some revascularized patients have a good prognosis. For stroke patients undergoing MT, predicting the risk of unfavorable outcomes and adjusting the treatment strategies accordingly can greatly improve prognosis. Therefore, we aimed to develop and validate a nomogram that can predict 3-month unfavorable outcomes for individual stroke patient treated with MT.

Methods

We analyzed 258 patients with acute ischemic stroke who underwent MT from January 2018 to February 2021. The primary outcome was a 3-month unfavorable outcome, assessed using the modified Rankin Scale (mRS), 3–6. A nomogram was generated based on a multivariable logistic model. We used the area under the receiver-operating characteristic curve to evaluate the discriminative performance and used the calibration curve and Spiegelhalter’s Z-test to assess the calibration performance of the risk prediction model.

Results

In our visual nomogram, gender (odds ratio [OR], 3.40; 95%CI, 1.54–7.54), collateral circulation (OR, 0.46; 95%CI, 0.28–0.76), postoperative mTICI (OR, 0.06; 95%CI, 0.01–0.50), stroke-associated pneumonia (OR, 5.76; 95%CI, 2.79–11.87), preoperative Na (OR, 0.82; 95%CI, 0.72–0.92) and creatinine (OR, 1.02; 95%CI, 1.01–1.03) remained independent predictors of 3-month unfavorable outcomes in stroke patients treated with MT. The area under the nomogram curve was 0.8791 with good calibration performance (P = 0.873 for the Spiegelhalter’s Z-test).

Conclusions

A novel nomogram consisting of gender, collateral circulation, postoperative mTICI, stroke-associated pneumonia, preoperative Na and creatinine can predict the 3-month unfavorable outcomes in stroke patients treated with MT.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12883-022-02633-1.

Transcriptomic Analysis of Breast Cancer Patients Sensitive and Resistant to Chemotherapy: Looking for Overall Survival and Drug Resistance Biomarkers

Worldwide breast cancer ranks first in mortality and incidence rates in women over 20 years old. Rather than one disease, breast cancer is a heterogeneous group of diseases that express distinct molecular profiles. Neoadjuvant chemotherapy is an important therapeutic strategy for breast cancer patients independently of their molecular subtype, with the drawback of resistance development. In addition, chemotherapy has adverse effects that combined with resistance could contribute to lower overall survival. Although great efforts have been made to find diagnostic and prognostic biomarkers for breast cancer and for response to targeted and immune therapy for this pathology, little has been explored regarding biomarkers of response to anthracyclines and taxanes based neoadjuvant chemotherapy. This work aimed to evaluate the molecular profile of patients who received neoadjuvant chemotherapy to identify differentially expressed genes (DEGs) that could be used as biomarkers of chemotherapy response and overall survival. Breast cancer patients who were candidates for neoadjuvant chemotherapy were enrolled in this study. After treatment and according to their pathological response, they were assigned as sensitive or resistant. To evaluate DEGs, Gene Ontology, Kyoto Encyclopedia Gene and Genome (KEGG), and protein–protein interactions, RNA-seq information from all patients was obtained by next-generation sequencing. A total of 1985 DEGs were found, and KEGG analysis indicated a great number of DEGs in metabolic pathways, pathways in cancer, cytokine–cytokine receptor interactions, and neuroactive ligand-receptor interactions. A selection of 73 DEGs was used further for an analysis of overall survival using the METABRIC study and the ductal carcinoma dataset of The Cancer Genome Atlas (TCGA) database. Nine DEGs correlated with overall survival, of which the subexpression of C1QTNF3, CTF1, OLFML3, PLA2R1, PODN, KRT15, HLA-A, and the overexpression of TUBB and TCP1 were found in resistant patients and related to patients with lower overall survival.

Nomogram for predicting preoperative regional lymph nodes metastasis in patients with metaplastic breast cancer: a SEER population-based study

Background

Metaplastic breast cancer (MBC) is a rare subtype of breast cancer, and generally associated with poor outcomes. Lymph nodes metastasis (LNM) is confirmed as a critical independent prognostic factor and determine the optimal treatment strategies in MBC patients. We aimed to develop and validate a nomogram to predict the possibility of preoperative regional LNM in MBC patients.

Methods

MBC patients diagnosed between 1990 and 2016 in the Surveillance, Epidemiology, and End Results (SEER) database were included and stochastically divided into a training set and validation set at a ratio of 7:3. The risk variables of regional LNM in the training set were determined by univariate and multivariate logistic regression analyses. And then we integrated those risk factors to construct the nomogram. The prediction nomogram was further verified in the verification set. The discrimination, calibration and clinical utility of the nomogram were evaluated by the area under the receiver operating characteristic (ROC) curve (AUC), calibration plots and decision curve analysis (DCA), respectively.

Results

A total of 2205 female MBC patients were included in the study. Among the 2205 patients, 24.8% (546/2205) had positive regional lymph nodes. The nomogram for predicting the risk of regional LNM contained predictors of grade, estrogen receptor (ER) status and tumor size, with AUC of 0.683 (95% confidence interval (CI): 0.653–0.713) and 0.667 (95% CI: 0.621–0.712) in the training and validation sets, respectively. Calibration plots showed perfect agreement between actual and predicted regional LNM risks. At the same time, DCA of the nomogram demonstrated good clinical utilities.

Conclusions

The nomogram established in this study showed excellent prediction ability, and could be used to preoperatively estimate the regional LNM risk in MBC.

Identification of a prognostic signature based on immune-related genes in bladder cancer

Bladder cancer (BLCA) has a high incidence and recurrence rate, and the effect of immunotherapy varies from person to person. Immune-related genes (IRGs) have been shown to be associated with immunotherapy and prognosis in many other cancers, but their role in immunogenic BLCA is less well defined. In this study, we constructed an eight-IRG risk model, which demonstrated strong prognostic and immunotherapeutic predictive power. The signature was significantly related to tumor clinicopathological characteristics, tumor class, immune cell infiltration and mutation status. Additionally, a nomogram containing the risk score and other potential risk factors could effectively predict the long-term overall survival probability of BLCA patients. The enriched mechanisms identified by gene set enrichment analysis suggested that the reason why this signature can accurately distinguish high- and low-risk populations may be closely related to the different degrees of innate immune response and T cell activation in different patients.

Construction of an immune-related gene signature to predict survival and treatment outcome in gastric cancer

Immune cells have emerged as key regulators in the occurrence and development of multiple tumor types. However, it is unclear whether immune-related genes (IRGs) and the tumor immune microenvironment can predict prognosis for patients with gastric cancer (GC). The mRNA expression data in GC tissues (n = 368) were obtained from The Cancer Genome Atlas (TCGA) database. Differentially expressed IRGs in patients with GC were determined using a computational difference algorithm. A prognostic signature was constructed using COX regression and random survival forest (RSF) analyses. In addition, datasets related to "gemcitabine resistance" and "trastuzumab resistance" (GSE58118 and GSE77346) were obtained for GEO database, and DEGs associated with drug-resistance were screened. Then, we analyzed correlations between gene expression and cancer immune infiltrates via Tumor Immune Estimation Resource (TIMER) site. The cBioportal database was used to analyze drug-resistant gene mutation status and survival. One hundred and fifty-five differentially expressed IRGs were screened between GC and normal tissues, and a prognostic signature consisting of four IRGs (NRP1, PPP3R1, IL17RA, and FGF16) was closely related to the overall survival (OS). According to cutoff value of risk score, patients were divided into high-risk and low-risk group. Patients in the high-risk group had shorter OS compared to the low-risk group in both the training (p < 0.0001) and testing sets (p = 0.0021). In addition, we developed a 5-IRGs (LGR6, DKK1, TNFRSF1B, NRP1, and CXCR4) signature which may participate in drug resistance processes in GC. Survival analysis showed that patients with drug-resistant gene mutations had shorter OS (p = 0.0459) and DFS (p < 0.001). We constructed four survival-related IRGs and five IRGs related to drug resistance which may contribute to predict the prognosis of GC.

Nomogram for Predicting Lymph Node Involvement in Triple-Negative Breast Cancer

Background

Lymph node metastasis of triple-negative breast cancer (TNBC) is essential in treatment strategy formulation. This study aimed to build a nomogram that predicts lymph node metastasis in patients with TNBC.

Materials and Methods

A total of 28,966 TNBC patients diagnosed from 2010 to 2017 in the Surveillance, Epidemiology and End Results (SEER) database were enrolled, and randomized 1:1 into the training and validation sets, respectively. Univariate and multivariate logistic regression analysis were applied to identify the predictive factors, which composed the nomogram. The receiver operating characteristic curves showed the efficacy of the nomogram.

Result

Multivariate logistic regression analyses revealed that age, race, tumor size, tumor primary site, and pathological grade were independent predictive factors of lymph node status. Integrating these independent predictive factors, a nomogram was successfully developed for predicting lymph node status, and further validated in the validation set. The areas under the receiver operating characteristic curves of the nomogram in the training and validation sets were 0.684 and 0.689 respectively, showing a satisfactory performance.

Conclusion

We constructed a nomogram to predict the lymph node status in TNBC patients. After further validation in additional large cohorts, the nomogram developed here would do better in predicting, providing more information for staging and treatment, and enabling tailored treatment in TNBC patients.

Development of a novel immune-related genes prognostic signature for osteosarcoma

Immune-related genes (IRGs) are responsible for osteosarcoma (OS) initiation and development. We aimed to develop an optimal IRGs-based signature to assess of OS prognosis. Sample gene expression profiles and clinical information were downloaded from the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) and Genotype-Tissue Expression (GTEx) databases. IRGs were obtained from the ImmPort database. R software was used to screen differentially expressed IRGs (DEIRGs) and functional correlation analysis. DEIRGs were analyzed by univariate Cox regression and iterative LASSO Cox regression analysis to develop an optimal prognostic signature, and the signature was further verified by independent cohort (GSE39055) and clinical correlation analysis. The analyses yielded 604 DEIRGs and 10 hub IRGs. A prognostic signature consisting of 13 IRGs was constructed, which strikingly correlated with OS overall survival and distant metastasis (p < 0.05, p < 0.01), and clinical subgroup showed that the signature's prognostic ability was independent of clinicopathological factors. Univariate and multivariate Cox regression analyses also supported its prognostic value. In conclusion, we developed an IRGs signature that is a prognostic indicator in OS patients, and the signature might serve as potential prognostic indicator to identify outcome of OS and facilitate personalized management of the high-risk patients.

Radiotherapy Versus Surgery-Which Is Better for Patients With T1-2N0M0 Glottic Laryngeal Squamous Cell Carcinoma? Individualized Survival Prediction Based on Web-Based Nomograms

Background

Both radiotherapy and surgery are now recommended for early stage glottic laryngeal squamous cell carcinoma (LSCC), and both have their own advantages in patients with different characteristics. For each patient, it is hard to determine whether radiotherapy or surgery is more appropriate.

Methods

Patients with T1-2N0M0 glottic LSCC who received radiotherapy or surgery in the 2004–2016 SEER database were reviewed, then randomly divided into training and validation cohorts. Propensity score matching was used to eliminate the baseline variations, and competing risk analyses helped to exclude the effects of other causes of death. Based on univariate and multivariate analyses, we built two nomograms to visually predict the survival of each patient with different characteristics who received radiotherapy or surgery, then validated the accuracy in both training and validation cohorts. Using nomogramEx, we quantified the algorithms of the nomograms and put the nomograms on the websites.

Results

A total of 6538 patients in the SEER database were included. We found that therapy (p = 0.004), T stage (p < 0.001), age (p < 0.001), race (p < 0.044), grade (p = 0.001), and marital status (p < 0.001) were independent prognostic factors. Two nomograms were built to calculate the survival for each patient who received radiotherapy (C-index = 0.668 ± 0.050 in the training cohort and 0.578 ± 0.028 in the validation cohort) or underwent surgery (C-index = 0.772 ± 0.045 in the training cohort and 0.658 ± 0.090 in the validation cohort). Calibration plots showed the accuracy of the nomograms. Using the nomograms, we found that 3872 patients (59.22%) had no difference between the two therapies, 706 patients (10.80%) who received radiotherapy had better survival outcomes, and 1960 patients (29.98%) who underwent surgery had better survival outcome.

Conclusion

Nomograms were used to comprehensively calculate independent factors to determine which treatment (radiotherapy or surgery) is better for each patient. A website was used to offer guidance regarding surgery or radiation for patients and physicians.

Pathology of triple negative breast cancer

Triple negative breast cancer (TNBC) is a subtype of breast tumor lacking hormone receptors expression and HER2 gene amplification and represents 24 % of newly diagnosed breast neoplasms. In this review, pathological aspects of triple-negative breast cancer are illustrated, with particular attention to the seminal studies that defined this subtype of breast cancer by a molecular point of view. This paper also focuses on practical issues raised in clinical routine by the introduction of genetic expression breast cancer profiling and the innovative prognostic and predictive impact on triple-negative breast cancer pathology. Moreover, histopathological aspects of triple-negative neoplasms are also mentioned, underlying the importance of histologic diagnosis of particular cancer subtypes with decisive impact on clinical outcome. Importantly, focus on new therapeutic frontier represented by immunotherapy is illustrated, with particular mention of immune checkpoint inhibitors introduction in TNBC therapy and their impact on future treatments.

Synthesis of heteronanostructures for multimodality molecular imaging-guided photothermal therapy

Here, a heteronanostructure (Au-Fe₃O₄@PDA-PEG-DTPA-Gd) has been constructed for multimodality molecular imaging (T₁-/T₂-weighted MRI and CT imaging)-guided PTT of cancer by combination of Au-Fe₃O₄, PDA shell and DTPA-Gd into one nanoplatform.