bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of the epigenetic mechanism for colorectal cancer stem cell regulation through the comprehensive microRNA expression profiling of human colorectal cancer tissues.
Authors: Mukohyama Junko , Shinoda Masahiro , Itano Osamu , Kakeji Yoshihiro , Shimono Yohei 
Published: August 2023

42 Background: MicroRNAs (miRNAs) are key regulators of cancer stem cell (CSC) functions, including self-renewal and differentiation. However, little is known about miRNAs that regulate such properties in human colorectal cancer. Methods: We compared the expression levels of 754 miRNAs between paired samples of EpCAM+/CD44+ cancer cells (enriched in CSCs) and EpCAM+/CD44neg cancer cells (non-tumorigenic cancer cells (NTCs)) sorted in parallel from human primary colorectal cancers by multiplex semi-quantitative PCR. Results: Comparison of the expression levels of miRNAs in the CSCs and NTCs resulted in the identification of 10 miRNAs upregulated (miR-221, miR-218, miR-500 and miR-195) or downregulated (miR-185, miR-19a, miR-337, miR-10a, miR-21 and miR-24) in CSCs compared to NTCs. Among them, miR-221 was most highly expressed in CSCs; and its expression level was very low in NTCs and normal colon epithelial cells (n=6, p<0.05). Kaplan-Myer estimates and univariate and multivariate analyses showed that higher miR-221 expression was an independent prognosis factor for poorer outcome. Constitutive overexpression of miR-221 enhanced organoid-forming capacity of both conventional colorectal carcinoma cell lines and patient-derived xenografts (PDX) in vitro. Importantly, constitutive downregulation of miR-221 suppressed organoid-forming capacity in vitro and substantially reduced the tumorigenic capacity of CSC populations from PDX lines in vivo. miR-221 directly targeted Quaking (QKI) 5, the most abundant splicing isoform of the human QKI gene, and suppressed its protein level. Knockdown of miR-221 suppressed the clonogenicity of colorectal CSCs in vitro in a QKI-expression dependent manner and ability to form tumors in vivo. Conclusions: Our study reveals a mechanistic link between miR-221 and QKI and highlights their key role in regulating CSC properties in human colorectal cancer and proposes that miR-221 will be a promising marker and a specific therapeutic target for human colorectal CSCs.
i-Biomarker CaDx: A circulating miRNA-based multi-cancer detection tool with explainable AI for breast cancer.
Authors: Floares Alexandru George , Zety Adrian Vasile , Floares Carmen , Calin George , Kreutz Carvalho Eduardo , Radi Khaoula 
Published: August 2023

5 Background: Breast cancer is requires early and accurate detection for effective treatment and improved patient outcomes. Current methods, such as mammography and biopsy, have limitations in accuracy, invasiveness, and accessibility. Circulating microRNAs (miRNAs) are promising non-invasive biomarkers for cancer detection, including breast cancer. i-Biomarker CaDx is a technology-agnostic, multi-cancer early detection and diagnosis test, covering 13 cancer types with 99-100% accuracy. This study evaluates i-Biomarker CaDx performance for breast cancer using a publicly available dataset and assesses explainable artificial intelligence (XAI) interpretations. Methods: The dataset (GEO: GSE73002) contains 1,280 breast cancer patients and an equal number of age-matched healthy individuals. Circulating miRNA profiles were measured using microarray technology. Multiple classification algorithms, including an ensemble of decision trees, neural networks, and support vector machines, were employed for feature selection, classification, and XAI. Hyperparameter optimization was performed, and the best classifiers were integrated with weights proportional to their performance into a final model. The performance of i-Biomarker CaDx was evaluated using cross-validation and independent test sets, while the XAI component provided cohort-level and individual-level explanations of the miRNA alterations associated with the diagnostic outcome. Results: i-Biomarker CaDx demonstrated remarkable diagnostic performance in detecting breast cancer, achieving 100% accuracy in the studied dataset. The sensitivity, specificity, positive predictive value, and negative predictive value of i-Biomarker CaDx surpassed those of traditional diagnostic methods such as mammography and biopsy. The ensemble classifier, consisting of decision trees, neural networks, and support vector machines, effectively captured the complex interactions among miRNAs. The XAI component of i-Biomarker CaDx provided valuable insights into the biological relevance of miRNA alterations in breast cancer diagnosis. Cohort-level and individual-level explanations elucidated the miRNA patterns and their associations with breast cancer, enhancing the understanding of the underlying molecular mechanisms. Conclusions: i-Biomarker CaDx, a technology-agnostic multi-cancer early detection and diagnosis tool, has shown exceptional accuracy in breast cancer detection, outperforming traditional diagnostic methods. The integration of explainable artificial intelligence (XAI) facilitates a deeper understanding of miRNA alterations and their associations with breast cancer, contributing to improved interpretation at both the cohort and individual levels. The results of this study demonstrate the potential of i-Biomarker CaDx as a powerful, non-invasive diagnostic tool for breast cancer.
Unraveling the heterogeneity of intercellular crosstalk in intrahepatic and extrahepatic cholangiocarcinoma using single-cell and spatial transcriptome profiling.
Authors: Chen Xingyu , Song Yinghui , Tan Zhiguo , Yang Ranzhiqiang , Mao Xianhai , Peng Chuang , Chen Haotian , Liu Sulai 
Published: August 2023

50 Background: Extrahepatic cholangiocarcinoma (ECC) and intrahepatic cholangiocarcinoma (ICC) are two types of malignant tumors that arise from the bile duct epithelium at different locations. Currently, effective treatment options for these tumors are limited, and their microenvironmental differences remain poorly understood. Methods: We collected retrospective clinicopathological data of ECC (N=64) and ICC (N=153) patients from our hospital and integrated public database information to analyze the clinical characteristics, survival, and prognosis of ECC and ICC. We performed single-cell sequencing (scRNA-seq) and spatial transcriptomic techniques on three ECC and three ICC tumor tissues. Verification of scRNA-seq results was done using immunohistochemistry, flow cytometry, and polychromatic immunofluorescence. Additionally, we analyzed RNA and ATAC sequencing data for exhausted CD8+ T cells TEX obtained from ICC and ECC tissue samples. We used InferCNV to infer copy number variations (CNVs) of epithelial cells from ICC and ECC. Results: Our results showed that ECC and ICC differ in their clinical characteristics such as age, gender, bilirubin, CEA, and outcome. ECC had higher copy number amplification variation and exhibited inflammatory signaling and ongoing immunoediting, reflected in higher immune checkpoint expression such as PDCD1, CTLA4, and LAG3, and tumor infiltration with highly differentiated dysfunctional PDCD1+ LAG3+ CXCL13+ exhausted CD8+ T cells (TEX) and precursors of exhausted T (TPEX). RNA velocity analysis revealed different developmental trajectories of T cells in ECC and ICC, predominantly in naive/stem-like and memory T cells. We also identified a trefoil factor 3 (TFF3)-positive epithelial subpopulation in ECC. TFF3+ epithelial cells had closer interaction with CTHRC1+ fibroblasts, which induced more CD8+ T cells to TEX and TPEX. TFF3+ cells exhibited higher CNV scores and higher PD-L1 and PD-L2 expression, and co-localized with TEX and TPEX, providing one explanation for the immunosuppressive environment in ECC and suggesting a potential response to immune checkpoint therapy (ICT). Conclusions: Our study provides a comprehensive characterization of the cellular heterogeneity landscape of ECC and ICC, which can guide the optimization of personalized cancer immunotherapy. We identified potential biomarkers and targets for immunotherapies, and our findings shed light on the underlying mechanisms of tumor immune evasion and provide a foundation for further research in this area.
Single cell profiling of tumour biopsies and heterogeneity in response of dedifferentiated melanoma.
Authors: Lim Esther , Lin Yingxin , Pedersen Bernadette , Stewart Ashleigh , Scolyer Richard A. , Long Georgina V. , Yang Jean , Rizos Helen 
Published: August 2023

64 Background: Patients with advanced BRAFV600-mutant melanoma can be treated with immune checkpoint inhibitors or combination BRAF/MEK inhibitors. The sequence of these therapies can influence response to second-line treatment. Patients who progress on first-line PD1 blockade have poorer outcomes on BRAF/MEK inhibitors compared to patients who are treatment-naïve. Thus, defining the molecular features that are modified by therapy and that influence subsequent treatment responses require thorough characterization. Methods: In this study, tumor biopsies from five BRAF-mutant melanoma patients progressing on anti-PD1 (PROG) and five BRAF-mutant treatment-naïve (NAÏVE) patients were dissociated and treated ex vivo with BRAF/MEK inhibitors (dabrafenib+trametinib (DT)) before flow cytometry profiling and single cell transcriptome sequencing. Results: DT treatment did not alter tumor or immune cell proportions but effectively inhibited MAPK signaling by decreasing phosphorylated S6 levels in tumor cells within 8/10 melanoma samples. Single cell RNA-sequencing of the tumor dissociates identified four distinct melanoma differentiation states (e.g. melanocytic, transitory, neural crest-like and undifferentiated). The proportions of these cell states differed between tumor specimens, and were not affected by DT treatment. The neural crest-like and undifferentiated melanoma cells were enriched in PROG compared to NAIVE tumor samples and all differentiation states responded, albeit variably. For instance, MAPK inhibition after DT treatment was less pronounced in undifferentiated melanoma cells. Importantly, within the undifferentiated cell state, we identified a proportion of melanoma cells capable of responding to DT, and comparison of responding vs non-responding undifferentiated cells showed enrichment of pro-inflammatory IL-6 and TNFα signaling in the non-responding population. Elevated IL-6 and TNFα pathway activity correlated with decreased potency to MAPK inhibition, indicating that increased IL-6 and TNFα signaling in undifferentiated melanoma may contribute to resistance to MAPK inhibition. Conclusions: Ex vivo treatment of tumor dissociates coupled with single cell transcriptome sequencing identified cell state-specific responses to MAPK inhibition. Resistance to MAPK inhibition may be driven, in part, by tumor-intrinsic pro-inflammatory IL-6 and TNFα signalling.
Her-2 promoting tumor progression and cisplatin resistance as a novel therapeutic target in penile squamous cell carcinoma.
Authors: Tan Xingliang , Yao Kai 
Published: August 2023

67 Background: Cisplatin-based chemotherapy has been the first choice for advanced penile squamous cell carcinoma (PSCC) in the last decade, but remains challenging owing the unsatisfied response rates, frustrating systemic toxicity and chemoresistance leading to poor prognosis. There is no standard second-line therapy for advanced PSCC. Antibody-drug conjugates (ADC) were novel targeted and low-toxicity agents, of which Her-2 targeted ADCs widely used and have greatly improved clinical outcomes in breast, gastric and bladder cancers. We aimed to explore the expression pattern, clinical significance, oncogenic roles of Her-2 and the therapeutic potentiality of Her-2 target ADCs in PSCC. Methods: The immunohistochemical expression of Her-2 was detected in the largest single center cohort of 367 PSCC patients up to date. PSCC cell lines, cisplatin-resistant cell lines and animal models were established to investigated the biological roles of Her-2 in PSCC progression and cisplatin chemoresistance. Disitamab vedotin (RC48), an Her-2 targeted ADC drug, was used to evaluate the efficiency in PSCC. Results: Her-2 was an unfavourable prognostic indicator with around 47.7% immunohistochemical expression rate (1+, 23.2%; 2+, 18.0%; 3+, 6.5%) in PSCC. Her-2 positive immunohistochemical expression (2+/3+) was associated with advanced pT, pN stages, metastasis and poor overall survival (positive vs. negative, HR (95%Cl): 3.133 (2.120-4.631), p=0.000). Cellular and animal experiments confirmed that Her-2 promoted tumor progression, inhibited cisplatin-induced cell apoptosis via Akt pathways and increased cisplatin resistance in PSCC. Meanwhile, cisplatin-resistant PSCC cells up-regulated Her-2 expression. More importantly, Her-2 targeted ADCs Disitamab Vedotin displayed remarkable anti-tumor activities both in Her2-positive and cisplatin-resistant PSCC tumors. Conclusions: Our study suggested that Her-2 was an available therapeutic biomarker in PSCC. Targeting Her-2 ADCs might be a prospective option to improve clinical outcomes in high-risk Her-2 positive advanced PSCC patients and provided precious opportunity for cisplatin-based chemoresistance patients.
Risk factors and predictors of tumor recurrence among breast cancer patients in a tertiary government hospital in the Philippines.
Authors: Maaño Omar Paningbatan , Soliman Mary Claire V. 
Published: August 2023

7 Background: This study aims to identify the risk factors and predictors of tumor recurrence of breast cancer patients using the local data available in the Breast Care Center in East Avenue Medical Center, Quezon City, Philippines. Methods: A chart review of 529 charts was done at the Breast Care Center between 2011–2017, and 474 charts were included. Demographics and Clinicopathologic features were gathered from the chart. Cox-proportional hazard regression was used to compute hazard ratios [95% confidence interval] of the different variables to compare the recurrence rates. Results: Breast cancer subtypes are as follows: 246 (52%) patients were HR+/Her2-, 52 (11%) were HR-/Her2+, 81 (17%) were HR+/Her2+, and 95 (20%) were HR-/Her2-. The mean age at diagnosis was 50 years old. The median BMI was 25 kg/m2. Most have hypertension (HTN) (21.7%) and diabetes mellitus (DM) (7%). The most common histology was invasive carcinoma NOS (92.6%), and 42.5% had a lymphovascular invasion. Only 6.7% received neoadjuvant systemic therapy, the rest had adjuvant systemic therapy. Mostly underwent modified radical mastectomy (92.8%). The most common cytotoxic agent used were cyclophosphamide (96.14%), doxorubicin (87.13%), docetaxel (53.37%), and 5-fluorouracil (37.87%). In the her2+ subtype, only 19.54% received trastuzumab. Among breast cancer subtypes, HR-/Her2+ has the highest tumor recurrence (15.38%), and HR+/Her2-, HR+/Her2+, and HR-/Her2- had 8.54%, 7.41%, and 11.96% had tumor recurrence, respectively. The median time to recurrence was 47, 24, 39.5, and 47 months with HR+/Her2-, HR-/Her2+, HR+/Her2+, and HR-/Her2-, respectively. The most common site of recurrence were bone (39%) and local recurrence (32.37%). Contralateral breast recurrence occurred in 2 patients with HR-/Her2+. In univariate analysis, HTN (HR 0.34 [0.13, 0.85], p=0.022), DM (HR 2.55 [1.19, 5.48], p=0.016), stage IIIA (HR 3.78 [1.04, 13.73], p=0.044), IIIB (HR 9.11 [2.46, 33.68] p=0.001), IIIC (HR 12.59 [3.50, 45.22], p<0.001), positive lymph nodes (HR 1.07 [1.02, 1.12] p=0.002), and patients who received doxorubicin (HR 0.44[0.23, 0.86], p=0.015) were statistically significant for tumor recurrence. In multivariate analysis, HTN (HR 0.32 [0.11, 0.94], p=0.038) and doxorubicin (HR 0.30 [0.13, 0.70], p=0.005) have the strongest effect for decreasing recurrence rate and DM (HR 7.45 [2.85, 19.46] p<0.001) and locally advanced stage (IIIB) (HR 10.97 [2.51, 48.06], p=0.001) were associated with greater risk of recurrence. Conclusions: In this study, we determined the risk factors and predictors of breast cancer tumor recurrence in a tertiary government hospital in a third-world country like the Philippines. Certain co-morbidities (HTN and DM), locally advanced stage at diagnosis, and systemic treatment received (doxorubicin) significantly affected tumor recurrences with breast cancer in our setting.
Using sacituzumab govitecan for metastatic urothelial carcinoma after prior treatment with enfortumab vedotin: A single institution experience.
Authors: Maroli Kimberly , Wee Christopher Eing , Nizam Amanda , Ornstein Moshe Chaim , Gilligan Timothy D. , Martin Allison , Bonham Amanda , Lynn David , Vyas Neil , Gupta Shilpa 
Published: August 2023

78 Background: The Trop-2-directed antibody drug conjugate sacituzumab govitecan (SG) has demonstrated efficacy in metastatic urothelial cancer (mUC) previously treated with checkpoint inhibitors +/- prior chemotherapy based on the results from the TROPHY U-01 study. However, only 10/118 and 7/38 patients in the reported Cohorts 1 and 2 respectively had received prior enfortumab vedotin (EV). Given that EV is preferred prior to SG given proven overall survival (OS) benefit vs chemotherapy, we analyzed our institution’s experience to determine real-world outcomes when SG is used after prior EV treatment. Methods: We identified patients who had received EV for mUC at our institution and identified a subset of patients who had received SG after prior treatment with EV. Patient characteristics (e.g. age, sex, primary site of disease) were noted, as well as the number of lines of prior systemic therapy for mUC. Best response to SG was recorded, as well as time to progression, reason for discontinuation, and time to death. Progression free survival (PFS) was calculated from time of SG treatment initiation until progression or death, and overall survival (OS) was calculated from time of SG treatment initiation until death. Results: Ten patients were identified having been treated with SG for mUC after prior EV treatment. Seven out of ten were male and the median age at time of initial EV treatment was 68 years. Half of the patients had the primary upper tract urothelial carcinoma. There were no responses to treatment with SG; the best response to SG treatment was stable disease (SD) in 3/10 patients, progressive disease in 4/10 patients, and three patients’ responses were not assessed due to death or transition to hospice at time of last follow-up. The median PFS was 2.5 months and median OS was 3.2 months. Only two patients survived more than six months (7.1 months and 10.8 months). Conclusions: In this small retrospective series at a single institution, real-world outcomes (response to treatment, PFS, OS) using SG for mUC after prior EV treatment appear to be worse than the reported outcomes in TROPHY-U01 trial. The lack of prior EV treatment in the majority of the SG clinical trial patients could contribute to these disparate results.
Deep learning based quantitative models to distinguish tumoral and stromal tumor-infiltrating lymphocytes and the prognosis patients with high-grade serous ovarian cancer.
Authors: Hamada Kohei , Murakami Ryusuke , Ueda Akihiko , Taki Mana , Yamanoi Koji , Yamaguchi Ken , Hamanishi Junzo , Mandai Masaki 
Published: August 2023

84 Background: The better prognostic value of tumor-infiltrating lymphocytes (TILs) has been reported in high-grade serous ovarian cancer (HGSOC). However, the TILs evaluation of previous reports largely depends on manual quantification based on a visual assessment within limited section of pathological slides or tissue microarrays, which is subject to inter-observer variability. Since tumor immune microenvironment (TIME) of HGSOC is highly heterogeneous, there is a need to quantify TILs in large areas of pathological slides in an objective and time-saving manner. Here we present an AI-powered quantification method to distinguish tumoral TILs and stromal TILs using hematoxylin and eosin (H&E)-stained whole-slide images (WSIs) of HGSOC. Methods: 161 H&E stained WSIs of HGSOC patients treated at our hospital between 1998 and 2021 were prepared, and by using these WSIs we generated two AI-powered models. Initially, a TILs detection model (TIL-model) was created using a publicly available dataset of 86104 pan-cancer TILs images of 100 × 100 pixels at magnification of x200 (Saltz et al., 2018, Cell Reports). Secondary, a tumor and stroma segmentation model (T/S seg-model) was developed using 136962 patches of 224 × 224 pixels at magnification of x50 which were manually annotated with tumoral regions and stromal regions in 102 H&E stained WSIs of HGSOC from The Cancer Genome Atlas (TCGA). Deep convolutional neural networks of NASNet-Large for the TIL-model and TransUNet for the T/S seg-model were used. TILs density score (number of TILs positive tiles per tumor area) of each sample was calculated, and association between TILs density score and the prognosis was investigated. Results: The established models achieved high accuracy: the TIL-model showed an area under the curve (AUC) value of 0.896, and the T/S seg-model showed an intersection over union value of 0.967. By combining the two models, we successfully distinguished tumoral TILs and stromal TILs. Using our dataset of 161 WSIs, we split the patients by TILs density score at top quartile into high tumoral TILs subgroup (n=40) and low tumoral TILs subgroup (n=121). High tumoral TILs subgroup showed significantly longer overall survival (OS) and progression free survival (PFS) (OS: median 70 months vs not reached, p < 0.005. PFS: median 34 months vs 21 months, p = 0.02). Conclusions: We developed deep learning based pathological AI models to detect TILs and tumors using H&E stained WSIs, which achieved to quantify tumoral and stromal TILs. The objective assessment of TILs using these models will lead to the development of clinically applicable tools for the evaluation of the immune status in HGSOC.