bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pomalidomide, bortezomib, and dexamethasone (PVd) in lenalidomide (LEN)-pretreated relapsed refractory multiple myeloma: Subanalysis of patients with renal impairment in OPTIMISMM.
Authors: Schjesvold Fredrik , Dimopoulos Meletios A. , Beksac Meral , Oriol Albert , Lindsay Jindriska , Liberati Anna Marina , Galli Monica , Robak Pawel , Weisel Katja , Larocca Alessandra , Yagci Münci , Vural Filiz , Anderson, Jr Larry D. , Kanate Abraham Sebastian , Casal Mendez Eva , Jiang Ruiyun , Srinivasan Shankar , Grote Lara , Biyukov Tsvetan Nikolov , Richardson Paul G. 
Published: May 2020

e20562 Background: Upfront LEN until disease progression is a standard treatment (Tx) in multiple myeloma (MM). Data are limited on optimal Tx after first-line LEN, especially in LEN-refractory patients (pts), a growing population. In OPTIMISMM (phase 3, NCT01734928), PVd significantly improved median PFS at first relapse in relapsed refractory MM (RRMM) pts, of whom 100% were LEN pretreated and 57% were LEN refractory (median, 20.7 vs 11.6 mos; HR = 0.54 [95% CI, 0.36-0.82]; P = .0027) vs Vd (Richardson, 2019). Pd has shown efficacy and safety in RRMM pts with moderate or severe renal impairment (RI), including those on dialysis (Dimopoulos, 2018). However, outcomes with second-line PVd in RRMM pts with RI have not been assessed. Here we report efficacy and safety of PVd vs Vd at first relapse by renal status (CrCl < 60 vs ≥ 60 mL/min). Methods: Pts received PVd or Vd (1:1) in 21-day (D) cycles (C); POM 4 mg/D on D1-14 (PVd arm only); BORT 1.3 mg/m2 on D1, 4, 8, 11 of C1-8 and on D1, 8 of C9+; and DEX 20 mg/D (10 mg/D for pts aged > 75 yrs) on days of and after BORT. Pts on dialysis were excluded. Results: Of 559 pts enrolled, 226 (40%) had 1 prior line of therapy; of whom 28% had CrCl < 60 mL/min and 4% had severe RI (CrCl < 30 mL/min). In pts with CrCl < 60 mL/min (PVd vs Vd), median age was 74 vs 73 yrs. In pts with CrCl ≥ 60 mL/min (PVd vs Vd), median age was 62 vs 64 yrs. A higher proportion of pts with baseline CrCl < 60 (23% vs 43%) than ≥ 60 mL/min (7% vs 8%) had ISS stage III at study entry. Data cutoff was Oct 26, 2017. Median PFS was improved with PVd in both renal groups (Table). ORR significantly improved regardless of renal status. Depth of response also improved with PVd vs Vd; ≥ VGPR occurred in 54% vs 21% in the CrCl < 60 mL/min group and 64% vs 23% in the CrCl ≥ 60 mL/min group. Myelosuppression was the most common grade 3/4 TEAE (Table). Conclusions: Second-line PVd led to improved vs Vd in pts with RRMM and RI; however, the PFS difference was not statistically significant. Safety was consistent for PVd with no new signals in pts with RI. These findings further support the earlier use of POM-based Tx in RRMM pts, including those with mild to moderate RI. Clinical trial information: NCT01734928. [Table: see text]
HealthTree Patient Portal mediated myeloma patient reported diagnostic imaging and pathology testing.
Authors: Sweeney Nathan W. , Ahlstrom Jenny , Thompson Michael A. 
Published: May 2020

e20565 Background: Multiple myeloma (MM) prognostic risk factors include cancer genetics as well as imaging characteristics. In order to engage the patient (pt) community regarding genetic testing and diagnostic imaging we utilized a patient-centered platform, HealthTree (www.healthtree.org), to evaluate the patient understanding of cancer genetic characteristics as well as evaluation of radiology methods used to evaluate their disease. Methods: An investigator-submitted online survey asking pts about myeloma genetic testing and imaging was fielded via HealthTree to 4,944 pts from May 10, 2019, to January 9, 2020. De-identified responses were aggregated and reviewed. The study was determined to be exempt by the Western Institutional Review Board. Results: 558 MM pts participated in the surveys. Pts who received more than one imaging or genetic test were able to indicate by selecting more than one option, this total response is indicated in the tables. Abbreviated questions and simplified responses are noted in the Table including: 1. At your diagnosis (or any time), did you receive any of the following tests to better understand the genetic profile of your disease? 2. At diagnosis (or any time), what imaging (radiology) tests were performed? Conclusions: Patient self-reported data registries are limited by patient perception or recall; however, these engaged and online MM pts may also be more biased toward knowing more about their medical history than the average pt. There are certainly real or perceived gaps in optimized genetic and imaging testing, which may reflect a communication or education gap. Pt reported interventions via an online portal can help investigators survey the pt community and result in hypothesis generating research questions including the actual use of testing, communication and education about testing and testing options, and MD trends in testing. [Table: see text][Table: see text]
Front-line daratumumab in newly diagnosed AL amyloidosis patients.
Authors: Kennedy Vanessa Elaine , Shah Nina , Wolf Jeffrey Lee , Martin Thomas G. , Wong Sandy Wai Kuan 
Published: May 2020

e20569 Background: Light chain amyloidosis (AL) is a plasma cell dyscrasia characterized by organ dysfunction, morbidity, and early mortality. Treatment focuses on suppressing monoclonal light chain production as measured by hematologic response criteria (Comenzo et al., 2012). Daratumumab (DARA), a monoclonal CD38 antibody, has demonstrated efficacy in heavily pretreated AL patients (Kaufman et al., 2017). We report the outcomes of newly diagnosed AL patients treated with a DARA-based regimen. Methods: A single-center retrospective chart review with an IRB-approved protocol was performed on newly diagnosed AL patients treated with first line DARA-based regimens between 1/2018 – 12/2019. Results: Fourteen patients were evaluated. The median age was 69 years (45 – 87), 50% were male, and 50% produced monoclonal lambda light chains. All patients had cardiac and renal involvement. Per the 2004 Mayo staging system, 1/14 (7%) patients had stage I cardiac disease, 2/14 (14%) had stage II, and 11/14 (79%) had stage III, of which two were stage IIIb. Regarding renal staging (Palladini et al., 2014), 10/14 (71%) patients were stage I, 3/14 (21%) stage II, and 1/4 (7%) stage III. Most patients (11/14) received DARA in combination with bortezomib and dexamethasone, while one patient received DARA and dexamethasone (DEX). Two patients received DARA in combination with bortezomib, cyclophosphamide, and DEX. Patients received a median of 5 cycles of DARA (1 – 14). After a median follow-up of 4.4 months (1 – 19), all patients were still receiving DARA. DARA was well tolerated, with 4 patients (29%) experiencing grade 1 infusion reactions and no additional toxicities observed. Responses were rapid, with a median time of 11 days (7 – 61) to first response and 46 days (9 8– 168) to best response. First response was classified as partial response (PR) in 8/14 patients (57%), very good PR (VGPR) in 3/14 (21%), and complete response (CR) in 1/14 (7%). Best response included a PR in 3/14 (21%), VGPR in 7/14 (50%), and CR in 2/14 (14%). In most patients, responses deepened over time. Cardiac response was seen in 5/7 (71%) evaluable patients with median time to response of 39 days (21 – 263). Renal response was seen in 2/4 (50%) evaluable patients with median time to response of 152 days (94 – 194). Conclusions: First line use of DARA in AL amyloidosis produced rapid and deep hematologic and organ response, resulting in a 93% objective hematologic response rate. DARA was well-tolerated and efficacious even among patients with extensive organ involvement and cardiac dysfunction. Prospective studies of first line DARA are warranted.
The association of CD8+ T-cell infiltration and PD-L1 expression with prognosis of Chinese pulmonary large cell neuroendocrine carcinoma.
Authors: Li Ye , Shi Xinying , Wang Jinliang , Mao Beibei , Li Jie , Hu Yukai , Qu Baolin , Zhang Henghui , Jiao Shun Chang 
Published: May 2020

e21003 Background: Pulmonary large cell neuroendocrine carcinoma (LCNCE) is a high-grade neuroendocrine tumor with poor prognosis. The genomic profile and immune feature of LCNEC have been reported in many studies. However, the relationship between immune microenvironment and the prognosis of LCNEC patients is poorly understood. Our study was aimed to examine the infiltration of CD8+ T cell and PD-L1+ cells in LCNEC patients, and explore whether CD8+T cell and PD-L1+ cells are related to LCNEC patients’ prognosis. Methods: 37 eligible LCNEC patients (stage I-III) with received the treatment of surgical operation (27 among 37 patients underwent adjuvant radiochemotherapy) were included, tumor tissues were collected from the first medical center of Chinese PLA General Hospital. Multiplex immunohistochemistry (Multi IHC) was performed using the antibodies of CD8 and PD-L1. The univariate and multivariate cox proportional hazards analyses were used to assess the association between the abundance of CD8+T cell and PD-L1+ cells with the clinical outcome of LCNEC patients. Results: Patients were divided into high and low group using the median positive percentage of CD8 or PD-L1 as cutoff. The univariate analysis showed that patients with stromal high CD8+ T cell infiltration or stage I had significantly longer disease free survival (DFS) (CD8, p = 0.03; stage I, p = 0.036), and patients with high PD-L1 expression in stroma region, I stage, adjvant radiochemotherapy had notably increased overall survival (OS) (p = 0.049, p = 0.031, p = 0.023, respectively). However, the infiltration of CD8+ T cell or PD-L1 expression in total or tumor region had no correlation with survival of LCNEC patients. Furthermore, multivariate analysis demonstrated that low CD8+ T cell density in stroma region was an independent risk factor for PFS (p = 0.03), advanced TNM stage (II-III stage, p = 0.0009) and low stromal PD-L1 expression were independent risk factors for OS (p = 0.013). Conclusions: High infiltration of CD8+ T cell or PD-L1+ cell in stroma region were independent good prognosis factors of LCNEC patients. However, these findings need a larger LCNEC cohort to validate.
Post-PACIFIC trial era: Patterns of outcomes and toxicities from a single private institution in a developing country.
Authors: Przybysz Daniel 
Published: May 2020

e21005 Background: Despite the twenty-first century, NSCLC remains the leading cause of cancer related deaths in a great variety of nations around the globe. However, the scenario has changed dramatically in the past 5 years. Immunotherapy features have opened a gigantic range of combinations now possible towards a better suited treatment for these patients. And we have seen results as we have never before - even in developing countries. Therefore, the goal of this study was to retrospectively analyze the patterns of outcomes, toxicities and safeness in the post-PACIFIC trial era, reporting results on patients that underwent chemoradiation followed by immunotherapy. Methods: We retrospectively collected and analyzed data on patients diagnosed with locally-advanced NSCLC treated in a single private institution in Rio de Janeiro, Brazil, between January 2017 and May 2019. All electronic medical records were accessed in order to obtain demographics, treatment and follow-up pattern data. Patients that received full chemoradiation treatment were included. Patients that did not meet the inclusion criteria were excluded from the study. Results: 121 patients were analyzed. 38 did not meet the inclusion criteria, and were excluded. The median age was 73.5y (50-95). 55% (46) were females. 59% (49) patients were smokers, 12% non-smokers. 29% of them did not have that info on their EMR. Adenocarcinoma was the most common histologic subtype (67%). All patients received chemotherapy regimen according to the best suited to patient, being carbo-taxol the most commonly used one (73%). All patients received radiation therapy, and the mostly used scheme was 60Gy in 30 fractions (38.5%). During a medium follow-up of 1.2 years on Durvalumab, 8 patients died (9.6%), none of them being a treatment-related death. Most toxicities presented during treatment and follow-up were mucositis (62.5%), cough (52%), cutaneous rash (48.8%). Other minor toxicities were nauseas (22.9%) and hematologic (14.5%). No grade 5 toxicity was reported. Conclusions: This study carries limitations inherent to retrospective analysis. Yet, we found the utmost importance on understanding how our patient population is responding to this new era of NSCLC-oncology. Despite all issues related within a developing nation, we showed that our results are compatible with the current data published. The treatment of locally advanced NSCLC brings exciting results and a big hope for these patients.
Interferon gamma resistance in setting of LKB1 loss: Phenotypic characterization and investigation of mechanism.
Authors: Kaufman Jacob 
Published: May 2020

e21015 Background: NSCLC Patients with LKB1 loss respond poorly to immune checkpoint inhibitors (ICI). Determining mechanisms of the underlying immune resistance and strategies to overcome it are urgent and unmet clinical needs. Methods: We re-expressed WT LKB1 into LKB1 mutant NSCLC cell lines and measured effects on immune associated phenotypes in vitro. Specifically, we evaluated response to exogenous interferon gamma (IFNG), as well T-cell mediated cytotoxicity using a T-cell co-culture assay. To identify IFNG signaling changes influenced by LKB1, we evaluated the differential effects of LKB1 on IFNG induced gene expression using RNAseq. Finally, we performed a whole genome loss of function screen using CRISPR-Cas9 library (TKOv3) to identify genes and pathways that modify susceptibility to IFNG in the LKB1 mutant and LKB1 WT state in the A549 cell line. Results: Across multiple LKB1 mutant cell lines, restoration of WT LKB1 enhanced anti-proliferative effects of IFNG in vitro. Furthermore, WT LKB1 enhanced T-cell mediated cytotoxicity in T-cell co-culture assays using anti-NY-ESO TCR and expression of NY-ESO antigen into an HLA matched NSCLC cell line, H2023 (17% vs 40% cell death; P < 0.01). IFNG treatment induced expression of a core set of interferon-driven genes in both the mutant and LKB1 WT state. However, differentially expressed gene classes included downregulation of proliferation-associated genes in the LKB1 WT state, as well as upregulation of ferroptosis genes, and enhanced IFNG-driven expression of immune evasion genes including PDL1, PDL2, TRAF1, and IDO1 in the LKB1 WT state. PDL1 expression was assessed by flow cytometry and found to be upregulated upon expression of LKB1. Our functional genomics screen identified genes whose inhibition enhanced IFNG susceptibility in the A549 mutant state, and genes whose inhibition restored IFNG resistance in the A549 LKB1 WT state. Preliminary analysis identifies candidate signaling and metabolic pathways that appear to confer IFNG sensitivity in the mutant state without significant effect on IFNG sensitivity after LKB1 add-back. These include modifiers of the Hippo/YAP pathway as well as modifiers of ferroptosis, which will form the basis for further mechanistic experiments. Conclusions: ICI resistance caused by LKB1 loss is associated with insensitivity to IFNG, and can be modified in vitro by re-expression of WT LKB1. An integrated approach to evaluate modifiers of IFNG effects identifies resistance mechanisms that may be potential therapeutic targets.
Causal inferencing of -omics data from The Cancer Genome Atlas: Lung adenocarcinoma tumors for mechanistic disease characterization and feature engineering.
Authors: Schneider Nimisha , Korkhov Sergey , Foroozan Alexis , Marshall Scott , Deehan Renee 
Published: May 2020

e21016 Background: Advances in high throughput measurement technologies (-omics data) have made it possible to generate high complexity, high volume data for oncology research. Researchers are often confronted many more measurements than samples (p > > > n), which poses challenges for both modeling the complexity of disease at the molecular mechanism level, and overfitting when generating predictive models with complex data. Here, we applied a prior knowledge-driven approach to characterize and classify heavy versus light smokers with lung cancer from The Cancer Genome Atlas, an open source repository that catalogs, harmonizes and hosts -omics data collected from samples generously donated from cancer patients. Methods: We applied a reverse inferencing approach to systematically interrogate RNAseq measurements from tumor and control biopsies against a knowledgebase of directed gene networks curated from published experiments. If patterns observed in the data are significantly similar to those in a network, an inference about the directional activity of that network can be made; e.g., the increased transcriptional activity of NFKB. Our library was nucleated through an open sourced knowledge graph and enhanced with updated and relevant knowledge using the open sourced Biological Expression Language framework. Directed networks were either qualitatively scored and used to build disease models, or semi-quantitatively scored and used as classification features. Results: In LUAD tumors, we detected a pattern of gene signatures which indicated a tumor stem cell-like phenotype characterized by predicted decreases in the activity of pro-differentiation factors and an increased response to hypoxia. Analysis of patients with heavy ( > 40) versus light ( < 10) pack-year burden suggested an augmented dedifferentiation profile in heavy smokers. In this example, improved classification was observed through features compression through directed network scoring compared to using individual RNA measurements selected by filtration methods. Conclusions: In-silico analysis of lung cancer patient biopsies generated hypotheses implicating stem cell signaling in tumors, and a further stratification of this signal based on patient pack year burden. Mechanistic modeling may be a useful application to the overfitting problem often encountered with -omics data in translational studies. Data from other TCGA indications can be used to evaluate the consistency of this type of approach
Low TWEAK expression indicates poor survival and is correlated with sparse TIICs in lung adenocarcinoma (LUAD).
Authors: Wu Jinchun , Liu Xianyu , Mou Yanhua , Zeng Shan , Zhang Jin , Zhou RongRong , Lu Jingchen , Yang Gao , Zhang Chunfang , Duan Chaojun , Li Bin 
Published: May 2020

e21017 Background: Lung adenocarcinoma (LUAD) occupies the most of non-small cell lung cancer (NSCLC) and shows promising response to PD-1 immunotherapy, but immune escape will cause treatment failure indicating poor prognosis. TWEAK (Tumor necrosis factor-related weak inducer of apoptosis, also known as TNFSF12) combining with its receptor FN14 (fibroblast growth factor–inducible 14) mediates crucial innate and adaptive immune pathways to promote the progression of multiple autoimmune diseases. So we assumed that TWEAK is a prognostic predictor and related with tumor-infiltrating immune cells (TIICs) in LUAD. Methods: TWEAK expression of LUAD was primarily investigated in The Cancer Immunome Atlas (TCIA) and then validated in Tumor Immune Estimation Resource (TIMER) databases. We assessed the effect of TWEAK on the survival via the Kaplan-Meier plotter, GEPIA2 (gene expression profiling interactive analysis) and PrognoScan databases. The relation between TWEAK and TIICs was explored in TIMER and TCIA, as well as the correlation of TWEAK and FN14 was analyzed in TIMER and GEPIA2. Results: Low TWEAK expression was significantly associated with poor relapse-free survival (RFS) (HR = 0.62, 95% CI = 0.4~0.97, logrank P = 0.035) and overall survival (OS) (HR = 0.61, 95% CI = 0.46~0.83, logrank P = 0.0012) in LUAD from Kaplan-Meier plotter. Similar impacts of TWEAK on the survival were validated in GEPIA2 and four independent cohorts from PrognoScan (jacob-00182-CANDF, GSE13213, jacob-00182-MSK and GSE31210). Moreover, reduced TWEAK expression was closely related with the paucity of TIICs which contributed to poor OS, including central memory CD8 T cells, plasmacytoid dendritic cells, activated CD8 T cells, monocytes, T follicular helper cells, immature B cells and eosinophils. In addition, TWEAK expression was positively related with the expression level of FN14 in both GEPIA2(R = 0.13, P= 0.0031) and TIMER (partial.cor = 0.212, P= 2.04e-06). Conclusions: Low TWEAK expression maybe indicate poor prognosis in LUAD, and correlated with the impaired infiltration of immune cells in the tumor region. The defective TWEAK/FN14 pathway possibly accounts for these observations, but the underlying mechanism needs to be further explored.
Non-small cell lung cancer: Analysis using mass cytometry and next generation sequencing reveals new opportunities for the development of personalized therapies.
Authors: Raju Paul Susan , Bagaev Alexander , Valiev Ivan , Zyrin Vladimir , Zaitsev Aleksandr , Dyykanov Daniyar , Nuzhdina Katerina , Kotlov Nikita , Frenkel Felix , Korek Skylar , Reeves Patrick , Davies Diane L. , Wright Cameron D , Ott Harald , Muniappan Ashok , Tsiper Maria , Fowler Nathan , Lanuti Michael , Ataullakhanov Ravshan , Poznansky Mark C 
Published: May 2020

e21026 Background: Comprehensive molecular profiling and the use of biomarkers as companion diagnostics have transformed precision medicine for cancer patients. To identify patient-specific tumor microenvironment and biomarker profiles, we assessed the accuracy of our deconvolution algorithm in identifying cellular compositions from whole exome (WES) and whole transcriptome (RNA-seq) sequencing of solid tumors compared with cell populations identified by Mass Cytometry by Time of Flight (CyTOF) in surgically resected tissue from non-small cell lung cancer (NSCLC) patients. Methods: Resected NSCLC tissue was divided for RNA-seq and WES of whole tissue (n = 9) and for generating tissue single cell suspensions through mechanical dissociation and enzymatic digestion (n = 11). Bulk RNA-seq and CyTOF were performed on all cell suspensions. Cellular phenotypes were identified using clustering algorithms in CyTOF and predicted from bulk RNA-seq using our proprietary computational method. Results: Cellular composition reconstructed from RNA-seq correlated with the composition detected by CyTOF (R2= 0.922, n = 7) from cell suspensions. To recover the cell percentage from bulk RNA-seq, a machine learning framework was trained on the cell compendia comprising 7,117 unique cell type RNA-seq profiles. A two-stage hierarchical learning procedure generated a gradient boosting Light GBM model that included training on artificial RNA-seq mixtures of different cell types. With this method, we found that stromal and malignant cells were depleted during single cell suspension preparation, resulting in statistically significant differences in the tumor cell composition reconstructed from solid tissue and single cell suspensions. Immune cell types namely T cells and macrophages were similarly represented in both the bulk tumor tissue and matched single cell suspensions. Transcriptomics revealed a subgroup of patients whose tumors were B-cell-enriched, which was validated in other NSCLC cohorts and was associated with greater CD4+ and CD8+ T cell infiltration and improved clinical outcomes. Conclusions: Since preparation of single cell suspensions leads to the loss of several cellular components, RNA-seq of tumor bulk tissue better describes the molecular and cellular properties of the tumor microenvironment. The combination of RNA-seq and WES of tumor tissue provides a comprehensive profile of cellular composition, suggesting that this combination is ideal for precision medicine applications.