Identifying Key Genes Involved in Axillary Lymph Node Metastasis in Breast Cancer Using Advanced RNA-Seq Analysis: A Methodological Approach with GLMQL and MAS.

Our study aims to address the methodological challenges frequently encountered in RNA-Seq data analysis within cancer studies. Specifically, it enhances the identification of key genes involved in axillary lymph node metastasis (ALNM) in breast cancer. We employ Generalized Linear Models with Quasi-Likelihood (GLMQLs) to manage the inherently discrete and overdispersed nature of RNA-Seq data, marking a significant improvement over conventional methods such as the t-test, which assumes a normal distribution and equal variances across samples. We utilize the Trimmed Mean of M-values (TMMs) method for normalization to address library-specific compositional differences effectively. Our study focuses on a distinct cohort of 104 untreated patients from the TCGA Breast Invasive Carcinoma (BRCA) dataset to maintain an untainted genetic profile, thereby providing more accurate insights into the genetic underpinnings of lymph node metastasis. This strategic selection paves the way for developing early intervention strategies and targeted therapies. Our analysis is exclusively dedicated to protein-coding genes, enriched by the Magnitude Altitude Scoring (MAS) system, which rigorously identifies key genes that could serve as predictors in developing an ALNM predictive model. Our novel approach has pinpointed several genes significantly linked to ALNM in breast cancer, offering vital insights into the molecular dynamics of cancer development and metastasis. These genes, including ERBB2, CCNA1, FOXC2, LEFTY2, VTN, ACKR3, and PTGS2, are involved in key processes like apoptosis, epithelial-mesenchymal transition, angiogenesis, response to hypoxia, and KRAS signaling pathways, which are crucial for tumor virulence and the spread of metastases. Moreover, the approach has also emphasized the importance of the small proline-rich protein family (SPRR), including SPRR2B, SPRR2E, and SPRR2D, recognized for their significant involvement in cancer-related pathways and their potential as therapeutic targets. Important transcripts such as H3C10, H1-2, PADI4, and others have been highlighted as critical in modulating the chromatin structure and gene expression, fundamental for the progression and spread of cancer.

Ultrasonic features of automated breast volume scanner (ABVS) and handheld ultrasound (HHUS) combined with molecular biomarkers in predicting axillary lymph node metastasis of clinical T1-T2 breast cancer.

Background: In the post-American College of Surgeons Oncology Group Z0011 trial era, clinicians are attempting to preoperatively evaluate axillary lymph node (ALN) status using ultrasound. However, the value of preoperative ultrasound examination remains uncertain. The study aimed to investigate the ultrasonic features of automated breast volume scanner (ABVS) and handheld ultrasound (HHUS), in combination with molecular biomarkers, to predict the risk of ALN metastasis (ALNM) in clinical T1-T2 breast cancer. Methods: A retrospective case-control analysis was conducted on 168 patients with clinical T1-T2 breast cancer at Peking University First Hospital between January 2013 and August 2021. Preoperative ABVS and HHUS examinations were performed. According to the pathology results of the ALN, patients were divided into metastatic and nonmetastatic groups. Logistic regression analyses were used to analyze the ultrasonic characteristics of ABVS and HHUS on clinical T1-T2 breast cancer, and molecular biomarkers were incorporated to predict the risk of ALNM. Results: Of the 168 patients, 88 (52.4%) had ipsilateral ALNM while 80 (47.6%) had no ipsilateral ALNM. The univariate analysis showed that shorter tumor-skin distance (P=0.011), the Adler blood flow grade of II-III (P=0.014), and larger tumor size on ABVS (P<0.001) were associated with ALNM. The multivariate logistic analysis showed that these three risk factors, including the tumor-skin distance [odds ratio (OR) =0.279; P=0.024], the Adler blood flow grade (OR =2.164; P=0.046), and the tumor size on ABVS (OR =1.033; P=0.002), were independent predictive parameters. Conclusions: The tumor-skin distance, tumor size on ABVS, and Adler blood flow grade have diagnostic value for ALNM in clinical T1-T2 breast cancer.

The value of microvascular Doppler ultrasound technique, qualitative or quantitative shear-wave elastography of breast lesions for predicting axillary nodal burden in patients with breast cancer.

Background: The status of the axillary lymph node (ALN) in patients with breast cancer can critically inform clinical decision-making and prognosis. Preoperative evaluation of limited nodal burden (0-2 metastatic ALNs) and high nodal burden (≥3 metastatic ALNs) is vital for individual treatment in patients with breast cancer. Thus, this study aimed to evaluate the value of Angio-PLUS (AP; Aixplorer, SuperSonic Imagine) and the qualitative and quantitative shear-wave elastography (SWE) of breast lesions to predict limited or high axillary nodal burden and to develop a model for predicting limited or high axillary nodal burden. Methods: From March 2020 to November 2022, a total of 232 consecutive patients with breast cancer comprising 232 breast lesions were enrolled retrospectively from Yueyang Central Hospital. The sensitivity, specificity, negative predictive value (NPV), positive predictive value (PPV), accuracy, and area under the receiver operating characteristic curve (AUC) of AP, qualitative SWE, quantitative SWE, and the predictive model for evaluating limited or high axillary nodal burden were compared. Results: There was no significant difference in AP patterns between the limited nodal burden group and high nodal burden group. The best cutoff values of Emin (the minimal value of the first Q-box), Emean (the mean value of the first Q-box), Emax (the maximum value of the first Q-box), Eratio (ratio of the first Q-Box and the second Q-Box) and standard deviation for predicting limited or high nodal burden were 80.85 KPa, 133.45 KPa, 153.40 KPa, 9.95, and 19.25 KPa, respectively. The Emax had the highest AUC, and its sensitivity, specificity, PPV, NPV, accuracy, and AUC were 71.64%, 56.36%, 40.00%, 83.04%, 60.78%, and 0.640 [95% confidence interval (CI): 0.575-0.702], respectively. The sensitivity, specificity, PPV, NPV, accuracy, and AUC of seven color patterns for qualitative SWE were 71.64%, 74.55%, 53.33%, 86.62%, 73.71%, and 0.731 (95% CI: 0.669-0.787), respectively, which was significantly higher than all the other quantitative SWE parameters. ALN evaluation in ultrasound and qualitative SWE were independent risk factors for predicting limited or high nodal burden according to a binary logistics regression analysis. The AUC of the predictive model based on independent risk factors was 0.820 (95% CI: 0.765-0.867), which was significantly higher than that of the other independent risk factors. Conclusions: The seven color patterns in the qualitative SWE of breast lesions were valuable for predicting limited or high nodal burden for patients with breast cancer. Compared with quantitative SWE, qualitative SWE exhibited a better diagnostic performance. Breast lesions present no findings, vertical stripes, and spot patterns were important indicators for limited nodal burden. The predictive model developed in this study could be a simple, noninvasive, and convenient method for predicting limited or high nodal burden, which would be beneficial for clinical decision-making and individual treatment to improve prognosis.

Deep learning radiomics for prediction of axillary lymph node metastasis in patients with clinical stage T1-2 breast cancer.

Background: This study investigates whether deep learning radiomics of conventional ultrasound images can predict preoperative axillary lymph node (ALN) status in patients with clinical stages T1-2 breast cancer (BC). Methods: This study retrospectively analyzed the preoperative ultrasound data of 892 patients with BC, who were classified into training (n=535), validation (n=178), and test (n=179) cohorts. Linear combinations of the selected features were weighted by their coefficients to obtain the predicted score. Then, deep learning radiomic features were extracted from the ultrasound images to evaluate the ALN status. Receiver-operating characteristic curves were drawn, followed by the calculation of the area under the curve (AUC) to assess the accuracy of the prediction model in predicting axillary lymph node metastasis (ALNM) in the three cohorts. Results: Deep learning radiomics combined with radiomics and clinical parameters was the optimal diagnostic predictor of the ALN status in the absence and presence of ALNM, with the AUC of 0.920 (95% confidence interval: 0.872 and 0.968, respectively). Additionally, this combination could also differentiate low-load ALNM [N + (1-2)] from heavy-load ALNM with ≥3 positive nodes [N + (≥3)] in the test cohort, with the AUC of 0.819 (95% confidence interval: 0.568 and 1.00, respectively). Conclusions: Conclusively, deep learning radiomics of ultrasound images is a non-invasive approach to predicting preoperative ALNM in BC.

Ultrasonography and clinicopathological features of breast cancer in predicting axillary lymph node metastases.

BACKGROUND: Early identification of axillary lymph node metastasis (ALNM) in breast cancer (BC) is still a clinical difficulty. There is still no good method to replace sentinel lymph node biopsy (SLNB). The purpose of our study was to develop and validate a nomogram to predict the probability of ALNM preoperatively based on ultrasonography (US) and clinicopathological features of primary tumors. METHODS: From September 2019 to April 2022, the preoperative US) and clinicopathological data of 1076 T1-T2 BC patients underwent surgical treatment were collected. Patients were divided into a training set (875 patients from September 2019 to October 2021) and a validation set (201 patients from November 2021 to April 2022). Patients were divided into positive and negative axillary lymph node (ALN) group according pathology of axillary surgery. Compared the US and clinicopathological features between the two groups. The risk factors for ALNM were determined using multivariate logistic regression analysis, and a nomogram was constructed. AUC and calibration were used to assess its performance. RESULTS: By univariate and multivariate logistic regression analysis, age (p = 0.009), histologic grades (p = 0.000), molecular subtypes (p = 0.000), tumor location (p = 0.000), maximum diameter (p = 0.000), spiculated margin (p = 0.000) and distance from the skin (p = 0.000) were independent risk factors of ALNM. Then a nomogram was developed. The model was good discriminating with an AUC of 0.705 and 0.745 for the training and validation set, respectively. And the calibration curves demonstrated high agreement. However, in further predicting a heavy nodal disease burden (> 2 nodes), none of the variables were significant. CONCLUSION: This nomogram based on the US and clinicopathological data can predict the presence of ALNM good in T1-T2 BC patients. But it cannot effectively predict a heavy nodal disease burden (> 2 nodes).

Axillary lymph node metastasis from papillary thyroid carcinoma with elevated CA 19-9 and CA 242 levels: a case report and literature review.

Axillary lymph node metastasis is a rare event in thyroid carcinoma. The simultaneous expression of carbohydrate antigens 19-9 (CA 19-9) and 242 (CA 242) in thyroid tumors is also extremely rare. Herein, we report a case of axillary lymph node metastasis with elevated serum CA 19-9 and CA 242 in papillary thyroid carcinoma. In a 47-year-old woman with thyroid carcinoma, masses developed in the neck and axilla over a two-month period, which were surgically treated using total thyroidectomy, with neck and axillary lymph node dissection. Histopathological examination confirmed a diffuse sclerosing variant-papillary thyroid carcinoma, with 52 of 63 axillary lymph node metastases. Notably, serum CA 19-9 and CA 242 levels decreased from the initial values of 1,110 and 50 kU/L, respectively, to normal levels one month postoperatively and have remained stable for two years since. The aggressive biological behavior of diffuse sclerosing variant-papillary thyroid carcinoma and the abnormal anatomical distortion caused by tumors in this case most likely reflect the mechanisms underlying retrograde dissemination in lymphatic tubes. However, the mechanism leading to a simultaneous elevation of CA 19-9 and CA 242 secreted by the diffuse sclerosing variant-papillary thyroid carcinoma has not been elucidated. The patient has survived for two years suggesting that timely surgery can help such patients achieve a better prognosis.