bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bayesian Framework for Detecting Gene Expression Outliers in Individual Samples
Authors: Vivian John , Eizenga Jordan M. , Beale Holly C. , Vaske Olena M. , Paten Benedict 
Published: February 2020

PURPOSE Many antineoplastics are designed to target upregulated genes, but quantifying upregulation in a single patient sample requires an appropriate set of samples for comparison. In cancer, the most natural comparison set is unaffected samples from the matching tissue, but there are often too few available unaffected samples to overcome high intersample variance. Moreover, some cancer samples have misidentified tissues of origin or even composite-tissue phenotypes. Even if an appropriate comparison set can be identified, most differential expression tools are not designed to accommodate comparisons to a single patient sample. METHODS We propose a Bayesian statistical framework for gene expression outlier detection in single samples. Our method uses all available data to produce a consensus background distribution for each gene of interest without requiring the researcher to manually select a comparison set. The consensus distribution can then be used to quantify over- and underexpression. RESULTS We demonstrate this method on both simulated and real gene expression data. We show that it can robustly quantify overexpression, even when the set of comparison samples lacks ideally matched tissue samples. Furthermore, our results show that the method can identify appropriate comparison sets from samples of mixed lineage and rediscover numerous known gene-cancer expression patterns. CONCLUSION This exploratory method is suitable for identifying expression outliers from comparative RNA sequencing (RNA-seq) analysis for individual samples, and Treehouse, a pediatric precision medicine group that leverages RNA-seq to identify potential therapeutic leads for patients, plans to explore this method for processing its pediatric cohort.
Phase Ib/II Clinical Trial of Pembrolizumab With Bevacizumab for Metastatic Renal Cell Carcinoma: BTCRC-GU14-003
Authors: Dudek Arkadiusz Z. , Liu Li C. , Gupta Shilpa , Logan Theodore F. , Singer Eric A. , Joshi Monika , Zakharia Yousef N. , Lang Joshua M. , Schwarz James K. , Al-Janadi Anas , Alva Ajjai S. 
Published: February 2020

PURPOSE We hypothesized that bevacizumab will potentiate activity of pembrolizumab. We conducted a phase Ib/II, single-arm, multisite clinical trial of the combination in metastatic renal cell carcinoma (RCC). PATIENTS AND METHODS Patients with metastatic clear cell RCC who experienced progression after at least one systemic therapy (phase Ib) or were treatment naïve (phase II) were enrolled. In phase Ib, pembrolizumab (200 mg) and bevacizumab (10 or 15 mg/kg) were given intravenously every 3 weeks. The primary end point for phase II was overall response rate (ORR). With an 80% statistical power and a type I error probability of 0.1, 48 patients were to be accrued to detect an ORR of 42%. RESULTS Thirteen patients (ages 33-68 years; median, 55 years) were enrolled in the phase Ib study. No dose-limiting toxicities were reported. Pembrolizumab 200 mg and bevacizumab 15 mg/kg were chosen for phase II. Forty-eight patients (ages 42-84 years; median age, 61 years; 33 males) were accrued for the phase II study. The primary end point was met, with the ORR reaching 60.9% (95% CI, 45.4% to 74.9%), consisting of 1 complete response (CR), 2 CRs in target lesions, 25 partial responses, 18 responses of stable disease, 2 unevaluable responses. Median progression-free survival was 20.7 months (95% CI, 11.3 to 27.4 months). Median overall survival was not reached at the median follow-up of 28.3 months. The most common treatment-related grade 3 toxicities were hypertension and proteinuria. There were two grade 4 toxicities: duodenal ulcer and hyponatremia. Presence of tumor-infiltrating T cells, but not programmed death-ligand 1 expression, in tumor tissue correlated with response. CONCLUSION The combination of 200 mg of pembrolizumab and a 15 mg/kg dose of bevacizumab given every 3 weeks is safe and active in metastatic RCC.
Safety and efficacy of tazemetostat, a first-in-class EZH2 inhibitor, in patients (pts) with epithelioid sarcoma (ES) (NCT02601950).
Authors: Stacchiotti Silvia , Schoffski Patrick , Jones Robin , Agulnik Mark , Villalobos Victor Manuel , Jahan Thierry Marie , Chen Tom Wei-Wu , Italiano Antoine , Demetri George D. , Cote Gregory Michael , Chugh Rashmi , Attia Steven , Gupta Abha A. , Loggers Elizabeth T. , Van Tine Brian , Sierra Laura , Yang Jay , Rajarethinam Anand , Gounder Mrinal M. 
Published: February 2020

11003 Background: ES is a rare soft tissue sarcoma that metastasizes in approximately 30% to 50% of cases. More than 90% of ES tumors lack expression of INI1, an important component of epigenetic regulation. Loss of INI1 function allows another epigenetic modifier, EZH2, to become an oncogenic driver in tumor cells. Tazemetostat, a first-in-class, selective, oral inhibitor of EZH2, has demonstrated tumor regression and favorable safety in phase 1/2 trials. Methods: Data from a phase 2 open-label, multicenter trial of pts with locally advanced or metastatic ES are reported. Efficacy was assessed with primary and secondary endpoints including objective response rate (ORR) by RECIST 1.1, disease control rate (DCR; objective confirmed response of any duration or stable disease [SD] lasting ≥32 weeks), duration of response (DOR), progression-free survival (PFS), overall survival (OS); safety and tolerability were also evaluated. Results: As of September 17, 2018, 62 INI1-negative ES pts were enrolled and treated with tazemetostat 800 mg BID. The median number of prior lines of therapy was 1 (range: 0-9). There were 9/62 (15%) confirmed partial responses (PRs) with an ORR of 15% and DCR of 26%. The DOR ranged from 7.1+ weeks to 103.0+ weeks (median: not reached) with a median OS of 82.4 weeks (95% CI: 47.4, not estimable) for all 62 pts. Tazemetostat was generally well tolerated. Treatment-emergent adverse events (TEAEs) were generally mild to moderate with the most commonly reported adverse events (AEs; ≥10% incidence) regardless of attribution being fatigue (24/62; 39%), nausea (22/62; 35%), and cancer pain (20/62; 32%). Any treatment-related TEAEs of grade ≥3 were reported in 10/62 (16%) pts. TEAEs grade ≥3 reported in ≥2 pts included anemia (6%) and decreased weight (3%). There were no drug-related deaths and a low discontinuation rate (1.7%). Conclusions: In the largest prospective clinical trial of ES to date, tazemetostat achieved disease control in 26% of pts with advanced ES who entered this study. Durable clinical response of the drug was documented. Tazemetostat demonstrated favorable safety with few pts with treatment-related AEs grade ≥3. Clinical trial information: NCT02601950.
ABI-009 (nab-sirolimus) in advanced malignant perivascular epithelioid cell tumors (PEComa): Preliminary efficacy, safety, and mutational status from AMPECT, an open label phase II registration trial.
Authors: Wagner Andrew J. , Ravi Vinod , Ganjoo Kristen N. , Van Tine Brian Andrew , Riedel Richard F. , Chugh Rashmi , Cranmer Lee D. , Gordon Erlinda Maria , Hornick Jason L. , Kwiatkowski David J. , Du Heng , Grigorian Berta , Schmid Anita N. , Hou Shihe , Harris Katherine , Desai Neil , Dickson Mark Andrew 
Published: February 2020

11005 Background: Malignant PEComa is a rare, aggressive sarcoma, with no approved treatment or prior clinical trials. Case reports suggest mTOR activation through mutations or deletions of TSC1 or TSC2 and activity of mTOR inhibitors in this disease. ABI-009 is an albumin-bound mTOR inhibitor with increased tumor uptake. The AMPECT trial is the first prospective study in malignant PEComa. Methods: Eligible patients (pts) with centrally confirmed PEComa receive ABI-009 (100 mg/m2 IV, wkly, 2/3 wks) until progression or unacceptable toxicity. Primary endpoint: ORR by independent review (IR), assessed every 6 wks (RECIST v1.1). Secondary endpoints: duration of response (DOR), PFS6, PFS, and safety. Exploratory endpoints (EE): investigator-assessed (IA) outcomes and mutational status. Sample size: 30 efficacy-evaluable pts based on target ORR of 30% (primary analysis planned when all pts treated ≥6 mo). Results: EE and safety are reported (IR pending). As of Feb 12, 2019, enrollment is complete; 34 pts treated, 31 evaluable for efficacy, 42% (13/31) pts ongoing Rx. IA ORR is 42% PR (13/31, 95% CI: 24.5, 60.9), 35% SD (11/31), and 23% PD (7/31); 69% of PRs were reached at 1st restaging (wk 6); 69% PRs are ongoing, with 5 pts >1yr and 2 pt >2 yrs on Rx (all ongoing). Other IA outcomes: median DOR is not reached; PFS6 is 66%; median PFS is 8.9 mo (95% CI: 5.5, -). The most common (>30%) nonhematologic treatment-related AEs (TRAEs) of any grade: mucositis (65%), fatigue (53%), nausea/weight loss (35% each), diarrhea (32%); the most common (>15%) hematologic TRAEs: anemia (44%) and thrombocytopenia (18%). Pneumonitis (15%) was G1/G2. The most common (>10%) G3 TRAEs: mucositis (18%), anemia (12%); No grade ≥4 TRAEs. TSC1 or TSC2 mutations occurred in 5 and 9 (no overlap) of 25 pts with known mutational status, respectively. PR was seen in 100% (9/9) pts with TSC2 mutation, 20% (1/5) pts with TSC1 mutation, and 9% (1/11) pts without mutation in TSC1 or TSC2, P < 0.0001 (2x3 Fisher exact test). PR was significantly higher in pts with TSC2 mutations vs pts without mutation in TSC1 or TSC2, P = 0.0001 (Fisher exact test). Disease control (PR+SD) was seen in 93% (13/14) pts with TSC1 or TSC2 mutations vs 55% (6/11) pts without mutation in TSC1 or TSC2, P = NS. Conclusions: Preliminary IA outcomes showed that ABI-009 treatment of PEComa resulted in substantial and durable responses with manageable toxicities. TSC2 mutations were associated with IA response. Clinical trial information: NCT02494570.
Does distress screening lead to mental health care in older adult surgical patients?
Authors: Trevino Kelly Marie , Nelson Christian J. , Saracino Rebecca , Korc-Grodzicki Beatriz , Sarraf Saman , Shahrokni Armin 
Published: February 2020

11543 Background: Surgery is a notable stressor for older adults with cancer who are often medically complex and frail. The American College of Surgeons Commission on Cancer requires distress screening in accredited cancer care settings. The degree to which distress screening leads to mental health use is unclear. This study examined rates and predictors of post-surgical mental health care in older adults referred for a preoperative evaluation. Methods: Patients aged 75 years or older (n = 1,008) referred to the Geriatrics Service at a comprehensive cancer center were enrolled. Patients underwent elective surgery with a length of stay of 3 days or longer and were followed for at least 30 days after surgery. A comprehensive geriatric assessment (CGA) was administered as part of routine care. Surgical characteristics and post-surgical encounters with social work, psychology, and psychiatry were abstracted from the electronic medical record. Bivariate relationships between demographic and surgical characteristics and the CGA and post-operative receipt of mental health services were examined. Characteristics with significant (p < .01) bivariate relationships were entered into a multivariable regression predicting post-operative mental health service use. Results: One-quarter of the total sample (n = 246, 24.4%) received post-operative mental health services. In multivariable analyses, high distress (Distress Thermometer score≥4; p = .01), poor social support (p = .01), iADL dependence (p = .04), and longer length of stay (p < .001) were associated with receipt of mental health services after controlling for significant sociodemographic and surgical characteristics and CGA variables. Of patients with high distress, poor social support, or iADL dependence, only one-third (29-33%) received mental health care. Conclusions: Distressed older adults and those with low levels of support pre-operatively were more likely to receive mental health services after surgery, controlling for sociodemographic and surgical characteristics. Yet, only one-third of these patients received mental health care. These findings suggest that barriers to translating distress screening into provision of mental health services remain.
Rapid reduction of peripheral blasts in older patients with refractory acute myeloid leukemia (AML) using reinduction with single agent anti-CD45 targeted iodine (131I) apamistamab [Iomab-B] radioimmunotherapy in the phase III SIERRA trial.
Authors: Tomlinson Ben Kent , Reddy Vijay , Berger Mark S. , Spross Jennifer , Lichtenstein Renee , Gyurkocza Boglarka 
Published: February 2020

7048 Background: The SIERRA trial is a prospective, randomized, phase 3, open-label, ongoing multicenter trial for patients aged ≥55 years with active, relapsed/refractory (R/R) AML evaluating allogeneic hematopoietic cell transplantation (HCT) versus conventional care (CC). Recent preliminary data demonstrated robust donor engraftment in all patients treated with Iomab-B (Blood 2018 132:1017) despite active disease. We hypothesize that successful engraftment was due to rapid disease reduction with Iomab-B. Methods: Patients are randomized to receive Iomab-B and HCT or to a CC therapy including approved targeted agents followed by HCT if in remission. Majority of patients (79%) in the CC arm did not achieve CR and the study allowed crossover to receive Iomab-B. Results: Data were evaluated for the first 25% of patients (N=38). Twenty-nine patients received Iomab-B, either directly (N=19) or via crossover (N=10). Median baseline marrow blasts were 30% (4-74) for Iomab-B and 24% (6-70%) for CC, which increased to 45% (10-70%) at crossover. Peripheral blast data was available in 16 patients (Iomab 7, Crossover 9). By day 3 post-Iomab, blasts were reduced by 98% with 100% reduction by day 8 (assuming 0% blasts due to lack of differential at WBC 0.1; Table). All patients engrafted with ANC at a median of 13 days (9-22 days). Conclusions: Targeted re-induction radioimmunotherapy with single agent Iomab-B rapidly decreases peripheral blasts in chemotherapy refractory AML. This significant reduction of leukemia burden followed by successful engraftment after HCT is encouraging in this underserved population. Clinical trial information: NCT02665065. [Table: see text]
Safety and preliminary efficacy in patients (pts) with relapsed/refractory (R/R) mantle cell lymphoma (MCL) receiving lisocabtagene maraleucel (Liso-cel) in TRANSCEND NHL 001.
Authors: Wang Michael , Gordon Leo I. , Palomba Maria Lia , Abramson Jeremy S. , Andreadis Charalambos , Ghosh Nilanjan , Lunning Matthew Alexander , Maloney David G. , Farazi Thalia Andrea , Garcia Jacob , Xie Benhuai , Newhall Kathryn J. , Dehner Christine , Siddiqi Tanya 
Published: February 2020

7516 Background: Most pts with MCL relapse after first-line immunochemotherapy, with poor responses to salvage therapy. We report initial dose-finding results from pts with R/R MCL treated with liso-cel (JCAR017), an investigational, anti-CD19 CAR T cell product administered as a defined composition of CD4+/CD8+ CAR T cells, in the ongoing phase 1 TRANSCEND study. Methods: Eligible pts had confirmed MCL (cyclin D1 expression, t[11;14]) with R/R disease after ≥1 prior lines of therapy. After lymphodepleting chemotherapy, liso-cel was administered at 1 of 2 dose levels (DL): DL1 = 50 × 106 or DL2 = 100 × 106 total CAR+ T cells. Results: At data cutoff, 9 pts (DL1, n = 6; DL2, n = 3) had received liso-cel. The median (range) age was 66 (58‒78) years; 7 pts were male. Histologies included blastoid (n = 3) and pleiomorphic (n = 1) variants. 8 pts had documented Ki67 > 30% (40%‒80%); 1 pt had TP53 mutation. Pts had received a median of 5 (3‒7) prior therapies; 3 pts had received prior hematopoietic stem cell transplant. All 9 pts had prior ibrutinib; 4 had a best response of progressive disease on ibrutinib. 6/9 pts (67%) received bridging chemotherapy. 4/9 pts (44%) had serious treatment-emergent adverse events (TEAEs). 5/9 pts (56%) had grade (G) 3/4 TEAEs, primarily anemia, neutropenia, and hypophosphatemia (22% each). 3/9 pts (33%) had cytokine release syndrome (CRS); all were G1. Median time to CRS onset was 6 (2‒7) days; median time to resolution was 6 (2‒6) days. 1 pt received tocilizumab and corticosteroids. There were no neurological events. 4 pts died, all in DL1 (3 from disease progression; 1 after receiving new anticancer therapy post liso-cel). Overall response rate was 78% (7/9 pts; 4/6 in DL1, median follow-up 12.4 [95% CI: 9.2–12.4] mo; 3/3 in DL2, median follow-up 1.4 [95% CI: 1.0–1.4] mo). 2 pts in DL1 maintained a durable CR until last follow-up (day 281 and 378, respectively). Median time to peak CAR+ T cell expansion: 9.5 (9–10) days at DL1 and 17.5 (10–27) days at DL2. Conclusions: In this phase 1 study in pts with R/R MCL, liso-cel treatment showed tolerable toxicity and had clinical activity. Updated DL2 data and longer follow-up will be presented. Clinical trial information: NCT02631044.
Patient-reported outcomes (PROs) with ibrutinib-rituximab in Waldenström macroglobulinemia (WM): Results from iNNOVATE.
Authors: Tedeschi Alessandra , Dimopoulos Meletios A. , Trotman Judith , Garcia-Sanz Ramón , MacDonald David , Mahe Beatrice , Herbaux Charles , Heffner Leonard T. , Tam Constantine Si Lun , Varettoni Marzia , Palomba Maria Lia , Matous Jeffrey , Shustik Chaim , Kastritis Efstathios , Treon Steven P. , Li Jianling , Poulsen Erik , Hauns Bernhard , Buske Christian , Leblond Veronique 
Published: February 2020

8018 Background: Anemia and fatigue can impair quality of life in patients (pts) with WM. Ibrutinib (ibr) as single agent or in combination with RTX is FDA-approved for WM. In pts with RTX-refractory WM, single-agent ibr induced meaningful improvements in PROs (Trotman, EHA 2017). In iNNOVATE, ibr-RTX (IR) produced higher rates of sustained hemoglobin improvement and meaningful improvements in PROs versus placebo-RTX (R; Dimopoulos NEJM 2018). Here, we report detailed PRO analyses from iNNOVATE. Methods: Pts with symptomatic WM requiring therapy were randomized to daily 420 mg oral ibr or placebo, both with RTX (375 mg/m2/week IV at weeks 1–4 and 17–20). PRO measures included FACIT-Fatigue (FACIT-F), FACT-An total score (TS) and anemia subscale score (AS), and EQ-5D-5L (EuroQol Research Foundation. EQ-5D is a trade mark of the EuroQol Research Foundation) visual analog scale (VAS), and utility score (US). Results: For 150 randomized pts (n=75/arm), most common reasons for initiating therapy were fatigue (61%), constitutional symptoms (32%), and anemia (32%). Baseline PRO scores were comparable in both arms. At a median follow-up of 26.5 mo, numerically more pts showed clinically meaningful improvement in FACIT-F, TS, and AS with IR than R (Table). Median time to PRO improvement was short (1-2 mo) in both arms. At week 25, the Pearson correlation coefficients were 0.28, 0.29, and 0.26 for changes in hemoglobin levels vs changes in FACIT-F, TS and AS, respectively, in the IR arm; no meaningful correlations were observed on R. The correlation coefficients were -0.32, -0.33, -0.35 and -0.26 for changes in IgM levels vs changes in FACIT-F, TS, AS, and EQ-VAS, respectively, for IR and 0.29 and 0.35 vs FACIT-F and TS for R. Conclusions: Clinical response and improvements in anemia with IR are consistent with more pts showing clinically meaningful improvement in PROs versus R. Changes in IgM correlate with improvements in PROs. Clinical trial information: NCT02165397. [Table: see text]
Unique racial patterns in rare T-cell lymphomas: A National Cancer Registry analysis from 2001 to 2015.
Authors: Shah Nishi , Herrera Diego Adrianzen , Shah Urvi , Kolla Bhaskar Chandu , Kaur Gurbakhash , Sica Roberto Alejandro , Shastri Aditi , Mantzaris Ioannis , Verma Amit , Janakiram Murali 
Published: February 2020

e19070 Background: Peripheral T-cell lymphomas (PTCL) are a rare heterogenous group of lymphomas and modern studies on incidence patterns of PTCL are lacking. Methods: Using the National Program of Cancer registries (NPCR) database, which covers 99% of the US population, we aim to evaluate the incidence of PTCL according to age, race-ethnicity, and gender; and examine trends over time. We identified PTCL using ICD-O-3 codes and evaluated incidence trends from 2001 to 2015. Results: A total of 78722 PTCL cases were identified, the most common were Mycoses fungoides/Sezary syndrome (MF-SS), PTCL Not Otherwise Specified (NOS), and ALK+ Anaplastic Large Cell Lymphoma (ALK+ ALCL). The age-adjusted incidence rate was 2.1 per 100,000. Incidence of PTCL increased with age (6.7/100,000 in 80+years). PTCL was more common in males than females (incidence rate ratio [IRR] of 0.6, p<0.05). Most PTCL were more common in Non-Hispanic Blacks (NHB). Incidence rates of MF-SS, PTCL NOS, Hepatosplenic TCL (HSL) in NHB were 0.8, 0.8, and 0.02 per 100,000 [IRR 1.7, 1.8, 2.2, p<0.05] respectively which is approximately twice that of Non-Hispanic whites (NHW). Viral related PTCL like Adult T-cell Leukemia Lymphoma (HTLV), Angio-Immunoblastic T-cell Lymphoma [AITL] (EBV), Extranodal NK-TCL nasal type [ENK TCL] (EBV), NK cell leukemia (EBV) are higher in groups at highest predisposition such as NHB and Non-Hispanic Asian Pacific Islanders (NHAPI). Primary cutaneous (PC) gamma-delta TCL occurs exclusively in NHW at an incidence rate of 0.03 per 100,000. There was no increase in overall yearly incidence of PTCL over the study period (0.1%, p=NS) but the incidence increased in NHB (Annual Percent Change [APC] 1.4%, p <0.05). Incidence of ENK TCL and AITL increased in NHAPI (2.2% and 3.7%, respectively [p <0.05]). The incidence of ALK + ALCL, PC CD30+ TCL decreased (APC -4.2%, -2% [p≤0.05] respectively). Conclusions: This is the first study to show unique incidence patterns of PTCL namely higher incidence in males, African Americans (esp. MF, PTCL-NOS and HSL unaccounted for viral etiologies) and exclusivity of primary cutaneous gamma delta TCL in NHW. Further research is needed to understand these differences.
Establishment of chromatin accessibility by the conserved transcription factor Grainy head is developmentally regulated
Authors: Nevil Markus , Gibson Tyler J. , Bartolutti Constantine , Iyengar Anusha , Harrison Melissa M. 
Published: February 2020

ABSTRACT
The dramatic changes in gene expression required for development necessitate the establishment of cis-regulatory modules defined by regions of accessible chromatin. Pioneer transcription factors have the unique property of binding closed chromatin and facilitating the establishment of these accessible regions. Nonetheless, much of how pioneer transcription factors coordinate changes in chromatin accessibility during development remains unknown. To determine whether pioneer-factor function is intrinsic to the protein or whether pioneering activity is developmentally modulated, we studied the highly conserved, essential transcription factor Grainy head (Grh). Prior work established that Grh is expressed throughout Drosophila development and is a pioneer factor in the larva. We demonstrated that Grh remains bound to mitotic chromosomes, a property shared with other pioneer factors. By assaying chromatin accessibility in embryos lacking maternal and/or zygotic Grh at three stages of development, we discovered that Grh is not required for chromatin accessibility in early embryogenesis, in contrast to its essential functions later in development. Our data reveal that the pioneering activity of Grh is temporally regulated and likely influenced by additional factors expressed at a given developmental stage.