tbuckley/cabot-search huggingface dataset:
Predictability of B cell clonal persistence and immunosurveillance in breast cancer
Authors: Stephen-John Sammut, Jacob D. Galson, Ralph Minter, Bo Sun, Suet-Feung Chin, Leticia De Mattos-Arruda, Donna K. Finch, Sebastian Schätzle, Jorge Dias, Oscar M. Rueda, Joan Seoane, Jane Osbourn, Carlos Caldas, Rachael J. M. Bashford-Rogers
Journal: Nature Immunology (2024)

Abstract B cells and T cells are important components of the adaptive immune system and mediate anticancer immunity. The T cell landscape in cancer is well characterized, but the contribution of B cells to anticancer immunosurveillance is less well explored. Here we show an integrative analysis of the B cell and T cell receptor repertoire from individuals with metastatic breast cancer and individuals with early breast cancer during neoadjuvant therapy. Using immune receptor, RNA and whole-exome sequencing, we show that both B cell and T cell responses seem to coevolve with the metastatic cancer genomes and mirror tumor mutational and neoantigen architecture. B cell clones associated with metastatic immunosurveillance and temporal persistence were more expanded and distinct from site-specific clones. B cell clonal immunosurveillance and temporal persistence are predictable from the clonal structure, with higher-centrality B cell antigen receptors more likely to be detected across multiple metastases or across time. This predictability was generalizable across other immune-mediated disorders. This work lays a foundation for prioritizing antibody sequences for therapeutic targeting in cancer.
Comparison of CAR T-cell vs. bispecific antibody as third- or later-line large B-cell lymphoma therapy: A Meta-analysis
Authors: Jinchul Kim, Jinhyun Cho, Moon Hee Lee, Sang Eun Yoon, Won Seog Kim, Seok Jin Kim
Journal: Blood (2024)

Abstract This meta-analysis evaluates the efficacy and safety of chimeric antigen receptor (CAR) T-cell therapy and bispecific antibodies for relapsed/refractory diffuse large B-cell lymphoma (R/R DLBCL). We searched MEDLINE, Embase, and Cochrane databases until July 2023 for trials assessing CAR T-cell therapies and CD20×CD3 bispecific antibodies as third or subsequent lines in R/R DLBCL. Random-effects models estimated the complete response (CR) rate and secondary outcomes, with meta-regressions adjusting for relevant covariates. Sixteen studies comprising 1347 patients were included in the pooled analysis. The pooled CR rate for bispecific antibodies was 0.36 (95% confidence interval [CI], 0.29-0.43), compared with 0.51 (95% CI, 0.46-0.56) for CAR T-cell therapy (P &amp;lt; .01). This superiority persisted when comparing the CAR T-cell–naive patients within the bispecific antibody group, with a CR rate of 0.37 (95% CI, 0.32-0.43). Multivariable meta-regression also revealed better efficacy of CAR T cells with adjustment for the proportion of double-hit lymphoma. The pooled 1-year progression-free survival rate mirrored these findings (0.32 [95% CI, 0.26-0.38] vs 0.44 [95% CI, 0.41-0.48]; P &amp;lt; .01). For adverse events of grade ≥3, the bispecific antibody had incidences of 0.02 (95% CI, 0.01-0.04) for cytokine release syndrome, 0.01 (95% CI, 0.00-0.01) for neurotoxicity, and 0.10 (95% CI, 0.03-0.16) for infections. The CAR T cell had rates of 0.08 (95% CI, 0.03-0.12), 0.11 (95% CI, 0.06-0.17), and 0.17 (95% CI, 0.11-0.22), respectively, with significant differences observed in the first 2 categories. In summary, CAR T-cell therapy outperformed bispecific antibody in achieving higher CR rates, although with an increase in severe adverse events.
Similar non-vertebral antifracture efficacy demonstrated with monthly ibandronate versus weekly bisphosphonate therapy: A retrospective cohort study
Authors: Jean-Yves Reginster, C. E. Barr, W. A. Blumentals, S. T. Harris
Journal: Annals of the Rheumatic Diseases (2008)

commencement and remained in the database for ≥3 months following enrolment. Only new or incident fractures were included in the analysis. Persistent (remaining on therapy for ≥90 days) patients were included in the primary analysis population. Patients were followed for 12 months until the first fracture, nonpersistence (refill gap of 45 days for monthly ibandronate, 30 days for weekly bisphosphonates) or they switched therapy. Patients who were diagnosed with malignant neoplasm or Paget's disease of bone were excluded from the analysis. A Cox regression model was used to calculate relative risk (RR) for fracture, comparing ibandronate with weekly bisphosphonates (adjusting for potential confounding variables). Secondary analyses including all patients (nonadherent and adherent) were performed. Results: At 12 months, a similar risk of nonvertebral and hip fractures was observed with monthly ibandronate and the weekly bisphosphonates (RR=0.88, p=0.26; RR=1.06, p=0.84, respectively). Comparing monthly ibandronate with alendronate and risedronate individually found the same results. Similar results were seen in the secondary analyses, thus confirming results for hip and nonvertebral fractures in the primary anal ysis population. Conclusion: These results suggest that the nonvertebral and h ip antifracture efficacy of monthly oral ibandronate (150mg) is consistent with that for weekly alendronate and risedronate.
Abstract PO1-25-09: A new generation of breast cancer modeling has been achieved through somatic precision gene editing, offering high flexibility and efficiency
Authors: Wen Bu, Yi li
Journal: Cancer Research (2024)

Abstract Breast cancer, along with many other cancers, is primarily caused by genetic mutations, typically involving the alteration of nucleotides (A, G, C, T) within genes (with a total of 12 possible mutations). Gene sequencing advancements have facilitated the identification of numerous gene mutations in tumor samples. However, comprehending the precise mechanisms through which these gene mutations contribute to tumor initiation, development, and their impact on tumor characteristics cannot be solely determined from these findings. Therefore, it is crucial to observe the influence of mutations on tumor initiation and development from the moment they occur. Since conducting such observations in human subjects is impractical, animal models with simulated gene mutations have become essential for studying tumor initiation and development. Mice, with a genome comprising approximately 2.7 billion nucleotides, are commonly used as animal models in cancer research due to their cost-effectiveness and high similarity to humans. About 90% of their genes share similar functions, particularly those associated with cancer development. However, achieving precise alterations to specific nucleotides among the 2.7 billion nucleotides within live mouse cells (with a total of 12 possible changes) has presented significant technical challenges. In this study, we present modifications to the CRISPR/Cas9 vector system, enabling homology-directed repair-mediated precise editing of any proto-oncogene in murine somatic mammary epithelial cells, thereby generating mammary tumor models with exceptional flexibility and efficiency. The resulting tumors exhibit significant advantages over traditional mouse models. This technological breakthrough bridges the gap between the potential of CRISPR technology and the accuracy of mouse models, facilitating the study of human tumor evolution and preclinical drug testing. Citation Format: Wen Bu, Yi li. A new generation of breast cancer modeling has been achieved through somatic precision gene editing, offering high flexibility and efficiency [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO1-25-09.
Abstract PO2-08-05: ERBB2 mutated breast cancer detected by next generation sequencing: integrated analysis based on real-world data and The Cancer Genome Atlas
Authors: Junghyun Kim, Yoonwon Kook, Seung Ho Baek, Min Ji Kim, Sohyun Moon, Seung Eun Lee, Jee Hung Kim, Soong June Bae, Joon Jeong, Sung Gwe Ahn
Journal: Cancer Research (2024)

Abstract Background ERBB2 mutation has been recognized as an actionable target for pan-HER tyrosine kinase inhibitors in the era of precision medicine for solid tumors. In our real-world cohort utilizing next-generation sequencing (NGS), we successfully identified cases of ERBB2-mutated breast cancer. Furthermore, we investigated the clinical and pathological characteristics of these cases by integrating our data with The Cancer Genome Atlas (TCGA). Methods Our real-world cohort with NGS included 423 breast cancer patients treated at Gangnam Severance Hospital in Seoul, Republic of Korea, between April 2017 and January 2023. Among these patients, 13 were confirmed to have ERBB2 mutation through NGS analysis. We also incorporated data from TCGA database, which included 818 cases with ERBB2 sequencing. We compared the clinical characteristics (age, sex, stage, and ER, PR, and HER2 status) between the two groups. Furthermore, we examined the frequency of two of the most common mutations, PIK3CA and TP53, in both groups. Additionally, we investigated the distribution of PAM50 subtypes in the TCGA cohort. Results This study analyzed a total of 1,244 cases with NGS data. Among these cases, 31 (2.5%) exhibited ERBB2 mutation, with 13 patients identified in our dataset and 18 in the TCGA data. Among the 31 cases with ERBB2 mutation, 21 (67.7%) had HER2-negative disease. No significant differences were observed in other clinical characteristics based on ERBB2 status. Within the group of 31 ERBB2-mutated cases, TP53 mutations were found in 12 cases (38.7%), while PIK3CA mutations were found in 12 cases (38.7%). In the TCGA dataset, 4 cases (22.2%) with ERBB2 mutation were classified as HER2-E subtype, and the rate of HER2-E subtype was significantly higher in the ERBB2-mutated group compared to the ERBB2-wild group (22.2% vs. 7.6%, p=0.024). Conversely, 14 cases (77.8%) with ERBB2 mutation exhibited a non-HER2 enriched subtype. Conclusions Consistent with previous knowledge, ERBB2 mutations can be detected in HER2-negative breast cancer, despite their rarity. Furthermore, a considerable proportion of ERBB2-mutated breast cancer may depend on various oncogenic signaling pathways other than the HER2 pathway. Further studies are warranted to optimize therapeutic strategies for ERBB2-mutated breast cancer. Citation Format: Junghyun Kim, Yoonwon Kook, Seung Ho Baek, Min Ji Kim, Sohyun Moon, Seung Eun Lee, Jee Hung Kim, Soong June Bae, Joon Jeong, Sung Gwe Ahn. ERBB2 mutated breast cancer detected by next generation sequencing: integrated analysis based on real-world data and The Cancer Genome Atlas [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO2-08-05.
Abstract PO1-24-10: B cell–mediated immunity predicts survival of patients with ER-positive breast cancer
Authors: Seungbok Lee, Byung-Hee Kang, Han-Byoel Lee, Wonshik Han, In Ah Kim
Journal: Cancer Research (2024)

Abstract Background: The estrogen receptor-positive (ER+) breast cancer (BC), which constitutes the majority of BC cases, exhibits highly heterogeneous clinical behavior. To aid precision treatments, we aimed to find molecular subtypes of ER+ BC representing the tumor microenvironment. Methods: We analyzed RNA-seq data of 113 BC patients and classified them according to the PAM50 intrinsic subtypes using gene expression profiles. Among them, we further focused on 48 patients with luminal-type (ER+) BC for subclassification. The Cancer Genome Atlas (TCGA) data of BC patients were utilized as a validation dataset to verify the new classification. Results: Principal component analysis clearly divided the patients into two subgroups separately from the luminal A and B classification. The top differentially expressed genes between the subgroups were distinctly characterized by immunoglobulin and B cell–related genes. We could also cluster a separate cohort of patients with luminal-type BC from TCGA into two subgroups based on the expression of a B cell–specific gene set, and patients with high B cell immune activity had better prognoses than other patients. Conclusions: Our transcriptomic approach defines a novel molecular phenotype of B cell immunity in ER+ BC that may help to predict disease prognosis. Although further researches are required, B cell immunity for ER+ BC patients may be helpful for identifying patients who are good responder to chemotherapy or immunotherapy. Work supported by grants from the National Research Foundation of Korea (NRF-2023R1A2C3003782) Citation Format: Seungbok Lee, Byung-Hee Kang, Han-Byoel Lee, Wonshik Han, In Ah Kim. B cell–mediated immunity predicts survival of patients with ER-positive breast cancer [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO1-24-10.
Abstract PO3-01-08: Interaction of Prior Chemotherapy and Addition of Ovarian Function Suppression on Menopausal Symptoms in Tamoxifen-Treated Breast Cancer Patient: A prospective, Observational study
Authors: Youngwon Lee, Jong Won Lee, Sae Byul Lee, Byung Ho Son, Hee Jeong Kim, Beom Seok Ko, Jisun Kim, Il-Yong Chung, Tae-Kyung Yoo
Journal: Cancer Research (2024)

Abstract Background: Adjuvant endocrine therapy (AET) is commonly used for hormone receptor-positive breast cancer patients. Combining ovarian function suppression (OFS) with tamoxifen improves survival outcomes, but is associated with menopausal symptom-related issues and treatment discontinuation. This study aimed to compare menopausal symptoms between tamoxifen alone and tamoxifen plus OFS over 12 months and identify related factors. Methods: This prospective study included 209 premenopausal breast cancer patients on tamoxifen. Menopausal symptoms were assessed using the Menopausal Rating Scale (MRS) at baseline, 3, 6, and 12 months. Statistical analysis involved linear regression and generalized estimating equations. Results: Of the participants, 27.8% received tamoxifen plus OFS and were younger and more likely to be unmarried. The tamoxifen plus OFS group had lower baseline MRS scores, but higher scores at 6 and 12 months compared to tamoxifen alone. MRS scores increased significantly in both groups, plateauing at 6 months with tamoxifen alone and at 12 months with tamoxifen plus OFS. Factors associated with higher MRS scores at 6 months were baseline MRS scores and addition of OFS. Impact of OFS on MRS scores varied with prior chemotherapy status, being significant in patients without prior chemotherapy. Conclusion: Adding OFS to tamoxifen in premenopausal breast cancer patients was associated with a higher burden of menopausal symptoms compared to tamoxifen alone, particularly in patients who have not undergone prior chemotherapy. Therefore, careful consideration and decision-making regarding this issue are crucial in terms of both treatment outcomes and quality of life. Table 1. Baseline characteristics, Overall and According to adjuvant endocrine therapy, tamoxifen alone versus tamoxifen plus ovarian function suppression (OFS) Table 2. Multivariable linear regression about MRS scores from the baseline to 6 months, and with interaction between addition of OFS and prior chemotherapy effect Table 3. Interaction effect of additional OFS depending on prior chemotherapy; (a) without prior chemotherapy, (b) with prior chemotherapy Citation Format: Youngwon Lee, Jong Won Lee, Sae Byul Lee, Byung Ho Son, Hee Jeong Kim, Beom Seok Ko, Jisun Kim, Il-Yong Chung, Tae-Kyung Yoo. Interaction of Prior Chemotherapy and Addition of Ovarian Function Suppression on Menopausal Symptoms in Tamoxifen-Treated Breast Cancer Patient: A prospective, Observational study [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO3-01-08.
Abstract PO4-17-10: Epidemiological Analysis and Overall Survival of Female Adolescent and Young Adults Breast Cancer in a Developing Middle Eastern Country Over 18 Years
Authors: Ahmed Abdulelah, Zaid Abdulelah, Abdulrahman Alhajahjeh, Ahmad Ghazzawi, Layla El-Amayreh, Hikmat Abdel-Razeq
Journal: Cancer Research (2024)

Abstract Background: Breast cancer is the most common type of cancer among female adolescents and young adults (AYAs) aged 15-39 years at diagnosis. AYAs with breast cancer have worse prognosis and are more likely to present with unfavorable tumor biology. However, breast cancer in AYAs is still poorly reported in middle eastern populations. Methodology: This is a retrospective cohort study which examined female AYAs patients aged 15 to 39 years at the time of diagnosis who were diagnosed with breast cancer between 2000 and 2018, using data from the Jordan Cancer Registry. Kaplan-Meier analysis was performed to assess the 5-year overall survival of the patients over time. Results: A total of 3831 Female AYAs were diagnosed with breast cancer in Jordan between 2000 and 2018 with a median age of 34.2 (IQR 30.9-38.3) years. 43.2% of female AYAs breast cancer cases were right breast cancer, whereas left breast cancer occurred in 47.4% of cases, and only 2.15% of cases were bilateral breast cancer. Meanwhile, 7.31% of cases did not have a reported laterality in the registry records. Most female AYAs patients had high grade breast cancer with grade III breast cancer being the most common (N=1349, 35.2%) followed by grade II breast cancer (N=1093, 28.5%). Among this female AYA cohort, 2208 (59.3%) were treated with surgical intervention, 1621 (43.5%) patients were given chemotherapy, 1220 (32.7%) patients had radiotherapy, 265 (7.15%) patients had hormonal therapy and only 47 (1.27%) were treated with immunotherapy. Among the entire studied cohort, 229 (5.98%) patients died during follow up period. The 5-year overall survival was 94% (95% CI 93.3% to 94.8%) Conclusion: Female AYAs breast cancer tends to have a predilection towards the left breast, but presents at a more advanced grade compared with other age groups in females. Citation Format: Ahmed Abdulelah, Zaid Abdulelah, Abdulrahman Alhajahjeh, Ahmad Ghazzawi, Layla El-Amayreh, Hikmat Abdel-Razeq. Epidemiological Analysis and Overall Survival of Female Adolescent and Young Adults Breast Cancer in a Developing Middle Eastern Country Over 18 Years [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO4-17-10.
Abstract PO4-25-02: Long-range Deployment of Tumor-antigen Specific Cytotoxic T Lymphocytes Inhibits Lung Metastasis of Breast Cancer
Authors: Yue Xing, Shicheng Su, Erwei Song
Journal: Cancer Research (2024)

Abstract Effector Immune Cell Deployment (EICD) refers to systemic deployment of anti-tumor effector immune cells in cancer patients, including the priming, circulation, trafficking, activity and fate of the immunocytes, and is a panorama to reflect the generation, distribution and development of anti-tumor immunity. Tumor antigen-specific T cells are the main component of effector immune cells in anti-tumor immune responses, but their systemic deployment in breast cancer patients and the underlying mechanisms remain largely unknown. Here, we identified a cluster of CD8+ T cell exhibiting tissue-resident memory (TRM) phenotype in the tumor-draining lymph nodes (TDLNs) of 487 breast cancer patients, whose abundancy specifically predicts improved lung, but not other target organ metastasis-free survival. Also, high lung CD8+ TRM infiltration is associated with lower metastatic burden in breast cancer patients. Using single-cell RNA sequencing, we observed that in multiple mouse cancer models, CD8+TRM accumulate at early tumor stages when lung metastasis was not identified. Functionally, the CD8+TRM isolated from pre-metastatic lungs of the animals were tumor antigen specific and cytotoxic to the tumor cells. Nevertheless, the abundancy of CD8+TRM in the lungs were dramatically decreased in the lungs upon metastasis establishment. Moreover, in Cd8cre/+ Itgaeloxp/+-diphtheria toxin receptor conditional knockout mice, we unambiguously demonstrated that specific depletion of the CD8+ TRM subset facilitates lung metastasis in vivo, while adoptive transfer of CD8+ TRM successfully inhibited lung metastasis and prolonged survival of the mice. Mechanistically, using cell-tracing techniques in the photo-convertible Kaede-Tg mice, we found that tumor-specific CD8+ TRM were generated in the TDLNs of the mice and were recruited to the lungs via CCL25/CCR9 signaling axis. However, the circulating exosomes secreted by primary tumor cells were taken up by alveolar macrophages and polarized them to release IDO1 and impaired anti-tumor T cell immunity, facilitating lung metastasis. More importantly, inhibition of IDO1 effectively retrieves TRM-mediated protection against lung metastasis. Collectively, we have revealed a cross-talk between tumor cells and the inflammatory environment of distant organs, which could drive lung metastasis by impairing EICD. Our findings also highlight the therapeutic potential of orchestrating EICD in turning “cold” metastatic tumor foci to “hot” ones. Citation Format: Yue Xing, Shicheng Su, Erwei Song. Long-range Deployment of Tumor-antigen Specific Cytotoxic T Lymphocytes Inhibits Lung Metastasis of Breast Cancer [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO4-25-02.