A pan-cancer interrogation of intronic polyadenylation and its association with cancer characteristics.

3'UTR-APAs have been extensively studied, but intronic polyadenylations (IPAs) remain largely unexplored. We characterized the profiles of 22 260 IPAs in 9679 patient samples across 32 cancer types from the Cancer Genome Atlas cohort. By comparing tumor and paired normal tissues, we identified 180 ~ 4645 dysregulated IPAs in 132 ~ 2249 genes in each of 690 patient tumors from 22 cancer types that showed consistent patterns within individual cancer types. We selected 2741 genes that showed consistently patterns across cancer types, including 1834 pan-cancer tumor-enriched and 907 tumor-depleted IPA genes; the former were amply represented in the functional pathways such as deoxyribonucleic acid damage repair. Expression of IPA isoforms was associated with tumor mutation burden and patient characteristics (e.g. sex, race, cancer stages, and subtypes) in cancer-specific and feature-specific manners, and could be a more accurate prognostic marker than gene expression (summary of all isoforms). In summary, our study reveals the roles and the clinical relevance of tumor-associated IPAs.

Pathologic characteristics, patterns of care, and outcomes of Asian-Americans and Pacific islanders with uterine cancer.

OBJECTIVES: To compare the patterns of care and outcomes of Asian-Americans/Pacific Islanders (AAPI) to non-Hispanic White (NHW) women with uterine cancer, and examine differences across Asian country of origin. METHODS: National Cancer Database was used to identify AAPI and NHW women with uterine cancer diagnosed from 2004 to 2017. Marginal multivariable log-linear regression models and Cox proportional-hazards models were developed to estimate differences in quality-of-care and all-cause mortality between AAPI and NHW women and across AAPI ethnic groups. RESULTS: We identified 13,454 AAPI and 354,693 NHW women. Compared to NHW women, AAPI patients were younger at diagnosis (median age 57 vs. 62 years), had fewer comorbidities, more often had serous or sarcoma histologic subtypes and stage III/IV cancer. AAPI women had a slightly higher rate of receiving pelvic lymphadenectomy for deeply invasive or high-grade tumors (77.6% vs. 74.3%), and a lower rate of undergoing minimally invasive surgery (70.4% vs. 74.8%) for stage I-IIIC tumors. Among patients undergoing hysterectomy, AAPI women had a lower mortality compared with NHW women for cancer stage I/II/III, and a 28% reduction for type I (grade 1 or 2 endometrioid cancers) disease (aHR = 0.72; 95% CI, 0.64-0.81). Among AAPI subgroups, Pacific Islanders had the worst survival across different cancer stage and disease type. CONCLUSION: AAPI women are diagnosed with uterine cancer at a younger age and have more aggressive histologic subtypes and advanced stage than their White counterparts. They have a similar level of quality-of-care as NHW women, and an improved survival for early stage and type I disease.

Presence of secondary bladder cancer following radical nephroureterectomy for upper tract urothelial carcinoma: characteristics, risk factors, and predictive value.

BACKGROUND: To assess the characteristics, predictive risk factors, and prognostic effect of secondary bladder cancer (SBCa) following radical nephroureterectomy (RNU) in upper tract urothelial carcinoma (UTUC). METHODS: Using the Surveillance, Epidemiology, and End Results database, the authors analyzed clinicopathologic characteristics and survival data from 472 UTUC patients with SBCa after RNU, between 2004 and 2017. Cox's proportional hazard regression model was implemented to identify independent predictors associated with post-recurrence outcomes. The threshold for statistical significance was p < 0.05. RESULTS: In total, 200 Ta-3N0M0 localized UTUC patients with complete data were finally included. With a median follow-up of 71.0 months (interquartile ranges [IQR] 36.0 -103.8 months), 52.5% (n = 105) had died, with 30.5% (n = 61) dying of UTUC. The median time interval from UTUC to SBCa was 13.5 months (IQR 6.0-40.8 months). According to multivariable Cox regression analysis, patients with SBCa located at multiple sites, advanced SBCa stage, higher SBCa grade, elderly age and a shorter recurrence time, encountered worse cancer-specific survival (CSS), all p < 0.05. CONCLUSION: For primary UTUC patients with SBCa after radical surgery, advanced age, multiple SBCa sites, shorter recurrence time, higher SBCa stage, and grade proved to be significant independent prognostic factors of CSS. We ought to pay more attention to SBCa prevention as well as to earlier signs which may increase the likelihood of early detection. Having the ability to manage what may be seen as the superficial SBCa signs may enable us to improve survival but further research is required.

Comparison of breast cancers detected in the Verona screening program following transition to digital breast tomosynthesis screening with cancers detected at digital mammography screening.

BACKGROUND: The Verona population-based breast cancer (BC) screening program provides biennial mammography to women aged 50-69 years. Based on emerging evidence of enhanced detection, the program transitioned to digital breast tomosynthesis (DBT) screening. METHODS: This is a prospective pilot evaluation of DBT with synthesised 2D mammography screening implemented during April 2015-March 2017; the rate and characteristics of cancers detected at DBT screening were compared with those detected at the preceding digital mammography (DM) screening round (April 2013-March 2015) in the same screening program. Distribution of imaging and tumour characteristics were compared. RESULTS: Amongst 34,071 women screened in the Verona DBT pilot, 315 BCs were detected; 153 BCs were detected amongst 29,360 women in the DM screening round. Estimated CDRs were 9.2/1000 (95% CI 8.3-10.3) DBT screens versus 5.2/1000 (95% CI 4.4-6.1) DM screens, P < 0.001. Statistically significant differences were found in the distribution of whether recall by one/both screen readers (more BCs recalled by both readers at DBT than DM); whether detected on one/two views (higher proportion detected on only one view at DBT than DM); type of radiological lesions; tumour stage, pT and histological categories (lower proportion of DCIS/pTis, higher proportions of pT1a and pT1b, and higher proportion of invasive cancers of special types, at DBT than DM); and tumour grade (higher proportion of grade I at DBT than DM). There were no differences in distributions of nodal and hormone receptor (ER/PR) status. CONCLUSIONS: Our findings provide early insights into the extent that transitioning to DBT screening may modify the characteristics of screen-detected breast cancer to inform discussion regarding pros and cons of DBT screening; although our data provide some reassurance that DBT does not increase the proportion of screen-detected DCIS, they highlight mixed findings on comparative tumour characteristics, suggesting a potential for enhancing screening benefit and possibly also over-diagnosis from DBT screening.

Explainable DCNN Decision Framework for Breast Lesion Classification from Ultrasound Images Based on Cancer Characteristics.

In recent years, deep convolutional neural networks (DCNNs) have shown promising performance in medical image analysis, including breast lesion classification in 2D ultrasound (US) images. Despite the outstanding performance of DCNN solutions, explaining their decisions remains an open investigation. Yet, the explainability of DCNN models has become essential for healthcare systems to accept and trust the models. This paper presents a novel framework for explaining DCNN classification decisions of lesions in ultrasound images using the saliency maps linking the DCNN decisions to known cancer characteristics in the medical domain. The proposed framework consists of three main phases. First, DCNN models for classification in ultrasound images are built. Next, selected methods for visualization are applied to obtain saliency maps on the input images of the DCNN models. In the final phase, the visualization outputs and domain-known cancer characteristics are mapped. The paper then demonstrates the use of the framework for breast lesion classification from ultrasound images. We first follow the transfer learning approach and build two DCNN models. We then analyze the visualization outputs of the trained DCNN models using the EGrad-CAM and Ablation-CAM methods. We map the DCNN model decisions of benign and malignant lesions through the visualization outputs to the characteristics such as echogenicity, calcification, shape, and margin. A retrospective dataset of 1298 US images collected from different hospitals is used to evaluate the effectiveness of the framework. The test results show that these characteristics contribute differently to the benign and malignant lesions' decisions. Our study provides the foundation for other researchers to explain the DCNN classification decisions of other cancer types.

Characteristics of Cancers in Community Members Exposed to the World Trade Center Disaster at a Young Age.

The destruction of the World Trade Center (WTC) towers on 11 September 2001 (9/11) released tons of dust and smoke into the atmosphere, exposing hundreds of thousands of community members (survivors) and responders to carcinogens. The WTC Environmental Health Center (WTC EHC) is a federally designated surveillance and treatment program for community members who were present in the New York City disaster area on 9/11 or during the months that followed. WTC EHC enrollment requires exposure to the WTC dust and fumes and a federally certifiable medical condition, which includes most solid and blood cancers. Several studies have described the prevalence and characteristics of cancers in responders and survivors exposed to the WTC dust and fumes as adults. Cancers in those exposed at a young age warrant specific investigation since environmental toxin exposure at a younger age may change cancer risk. We describe the characteristics of 269 cancer patients with 278 cancer diagnoses among WTC EHC enrollees who were young in age (aged 0 to 30) on 9/11. These include 215 patients with a solid tumor (79.9%) and 54 with a lymphoid and/or hematopoietic cancer (20.1%). Among them, 9 patients had a known second primary cancer. A total of 23 different types of cancer were identified, including cancer types rare for this age group. Many were diagnosed in individuals lacking traditional cancer-specific risk factors such as tobacco use. The current study is the first to report specifically on cancer characteristics of younger enrollees in the WTC EHC program.

Mammographic breast density and characteristics of invasive breast cancer.

INTRODUCTION: Inconclusive data exist on the association between breast density and breast cancer characteristics. MATERIALS AND METHODS: We conducted a case-only study on 667 invasive breast cancers, using data from the Piedmont Cancer Registry. We applied a multivariate logistic regression model to estimate odds ratios (ORs) and the corresponding 95% confidence intervals (CIs) of high breast density (Breast Imaging Reporting and Data System, BI-RADS 3-4) versus low (BI-RADS 1-2) in relation to histologic grade, pathological tumour size and lymph node status, histotype, estrogen and progesterone receptor, HER2 and Ki67 status. Histopathological data were assessed according to the American Joint Committee on Cancer (AJCC) Staging Manual guidelines. The model includes terms for age at diagnosis, education level, body mass index, reproductive factors, family history of breast cancer, smoking and diabetes. RESULTS: As regards histologic grade, compared to well differentiated tumours, the OR of high (versus low) breast density cases was 0.61 (95% CI 0.38-0.98) for moderately-poorly differentiated tumours. No other associations with hormonal and histopathological characteristics were observed. DISCUSSION: Our results indicate that low breast density is associated with moderately-poorly differentiated breast tumours.

Lung Cancer Characteristics in the World Trade Center Environmental Health Center.

The destruction of the World Trade Center (WTC) towers on 11 September 2001 resulted in acute and chronic dust and fume exposures to community members, including local workers and residents, with well-described aerodigestive adverse health effects. This study aimed to characterize lung cancer in the WTC Environmental Health Center (WTC EHC) focusing on gender and smoking history. WTC EHC patients undergo an initial evaluation that includes WTC exposure information, demographics, and tobacco use. Detailed cancer characteristics are recorded from pathology reports. As of 31 December 2019, 248 WTC EHC patients had a diagnosis of lung cancer. More patients with lung cancer were women (57%) compared to men (43%). Many cases (47% women, 51% men) reported acute dust cloud exposure. Thirty-seven percent of lung cancer cases with available smoking history were never-smokers (≤1 pack-years) and 42% had a ≤5 pack-year history. The median age of cancer diagnosis in never-smoking women was 61 years compared to 66 years in men. Adenocarcinoma was more common in never-smokers compared to ever-smokers (72% vs. 65%) and in women compared to men (70% vs. 65%). We provide an initial description of lung cancers in local community members with documented exposure to the WTC dust and fumes.

Characteristics of Cancer Patients in the World Trade Center Environmental Health Center.

The destruction of the World Trade Center (WTC) towers on 11 September 2001 released many tons of aerosolized dust and smoke with potential for carcinogenic exposures to community members as well as responders. The WTC Environmental Health Center (WTC EHC) is a surveillance and treatment program for a diverse population of community members ("Survivors"), including local residents and workers, present in the NYC disaster area on 9/11 or in the days or weeks following. We report a case series of cancers identified in the WTC EHC as of 31 December 2019. Descriptive characteristics are presented for 2561 cancer patients (excluding non-melanoma skin cancer) and 5377 non-cancer WTC-EHC participants who signed informed consent. We identified a total of 2999 cancer diagnoses in 2561 patients: 2534 solid tumors (84.5%) and 465 lymphoid and hematopoietic tissue cancers (15.5%) with forty-one different cancer types. We describe the distribution, frequency, median age of cancer diagnosis and median latency from 9/11 by cancer site. In addition to common cancer types, rare cancers, including male breast cancers and mesotheliomas have been identified. The current study is the first report on cancer characteristics of enrollees at WTC EHC, a federally designated treatment and surveillance program for local community members affected by the 9/11 terrorist attack on the WTC.

Challenges and Opportunities from Basic Cancer Biology for Nanomedicine for Targeted Drug Delivery.

BACKGROUND: Effective cancer therapy is still a great challenge for modern medical research due to the complex underlying mechanisms of tumorigenesis and tumor metastasis, and the limitations commonly associated with currently used cancer therapeutic options. Nanotechnology has been implemented in cancer therapeutics with immense potential for improving cancer treatment. OBJECTIVE: Through information about the recent advances regarding cancer hallmarks, we could comprehensively understand the pharmacological effects and explore the mechanisms of the interaction between the nanomaterials, which could provide opportunities to develop mechanism-based nanomedicine to treat human cancers. METHODS: We collected related information and data from articles. RESULTS: In this review, we discussed the characteristics of cancer including tumor angiogenesis, abnormalities in tumor blood vessels, uncontrolled cell proliferation markers, multidrug resistance, tumor metastasis, cancer cell metabolism, and tumor immune system that provide opportunities and challenges for nanomedicine to be directed to specific cancer cells and portray the progress that has been accomplished in application of nanotechnology for cancer treatment. CONCLUSION: The information presented in this review can provide useful references for further studies on developing effective nanomedicine for the treatment of cancer.

Determinants of acquired activated protein C resistance and D-dimer in breast cancer.

BACKGROUND: We have previously reported acquired activated protein C (APC) resistance and elevated plasma D-dimer levels in breast cancer patients. Here, we aimed to identify phenotypic and genetic determinants that contribute to the acquired APC resistance and increased D-dimer levels in breast cancer. Healthy controls served as reference. We also addressed whether higher APC resistance or D-dimer levels could be potential markers of clinicopathological breast cancer characteristics. MATERIALS AND METHODS: 358 breast cancer patients and 273 healthy controls were enrolled and hemostatic plasma parameters were determined; factor (F) V, FVIII, FIX, FX, fibrinogen, von Willebrand factor (VWF), normalized APC sensitivity ratio (n-APC-sr), protein C, protein S, antithrombin, tissue factor pathway inhibitor (TFPI), and D-dimer. Common single nucleotide polymorphisms were genotyped in coagulation-related genes in the breast cancer patients. RESULTS: The phenotypic hemostatic factors explained 25% and 31% of the variability in acquired APC resistance and D-dimer levels, respectively, in the breast cancer patients. Fibrinogen (ß=-0.35, P<0.001), protein C (ß=0.28, P<0.001), and FIX (ß=0.22, P=0.026) were identified as determinants of n-APC-sr (in FV Leiden non-carriers), whereas TFPI (ß=0.28, P<0.001), antithrombin (ß=-0.25, P<0.001), and FX (ß=0.15, P=0.040) were the major determinants of D-dimer. Moreover, borderline higher APC resistance (>75th percentile) was found in patients with triple negative tumors (odds ratio (OR) 1.97, 95% CI 0.99-3.90). CONCLUSIONS: This study reports phenotypic hemostatic parameters that determine acquired APC resistance and D-dimer levels in breast cancer patients. The explanatory power was modest, however, our findings are hypothesis generating and may contribute to further understand the background for cancer associated-coagulopathy and thrombosis.