tbuckley/cabot-search huggingface dataset:
Biomarkers in cancer: Survey of diagnostic needs
Authors: T. Holzman, W. Gibbons
Journal: Journal of Clinical Oncology (2009)

e22222 Background: Much ongoing work in the field of diagnostics is related to identifying novel and clinically useful tumor markers. However, it is not clear that this discovery is focused on the clinical uses that are most important to physicians. Methods: Consequently, we conducted a survey to assess these needs. Our survey of oncologists, specialists and primary care physicians received 236 responses. Of these, 214 doctors provided their view, ranking with an 8 point Likert scale, for which of eight aspects of cancer that they would like to better differentially diagnose. Of the respondents, 45% were oncologists, 17% primary care, 16% urology and 15% OB/Gyn. Of the physicians surveyed, 57% were in private practice and 32% were in academic medicine, with the remaining 11% in a variety of other settings. Results: As may be unexpected, respondents believed that they still could benefit most from diagnosis itself (indexed score 6.1), followed closely by improving earlier diagnosis or identifying latent disease (5.6), as opposed to simple screening (4.82). The aspects that they believed required the least improvement were prognosis for metastasis (3.6) and prognosis for progression (4.0). Surprisingly, desire for the ability for better treatment planning was unremarkable as well (4.3). We also gauged the respondents familiarity with tumor markers using a 5 point Likert scale. 29% considered themselves very familiar, and only 13% considered themselves with less than average familiarity. Conclusions: The results of the survey suggest it may be useful to consider evaluation of biomarkers which aid early diagnosis rather than disease prognosis. [Table: see text]
Activity of trastuzumab-based therapy beyond disease progression in heavily pretreated metastatic breast cancer patients—Single institution experience
Authors: P. Tokajuk, B. Czartoryska-Arlukowicz, M. Z. Wojtukiewicz
Journal: Journal of Clinical Oncology (2006)

13159 Background: Benefits from continuing trastuzumab-based (TZB) therapy beyond disease progression in HER-2-overexpressing metastatic breast cancer (MBC) patients (pts) remain obscure. Methods: A retrospective analysis was undertaken to assess activity of TZB therapy for MBC pts treated in our institution from 2002 to 2005 outside clinical trials. Results: 27 pts were evaluated. Median age: 52 years (range, 33–62). 9 pts (33.3%) were premenopausal. Hormonal receptors status: 9 pts ER(+), 4 pts PgR (+), 2 unknown. HER-2 overexpression was determined by IHC staining (3+ score) in all pts. Metastases location: 18 pts soft tissues/bone, 18 pts visceral disease. Median number of metastatic sites: 2 (range: 1–4). 9 pts (33.3%) had metastases in &lt; 2 locations. 16 pts (59.2%) received neo/adjuvant chemotherapy: 11 pts doxorubicin, 8 pts CMF, 2 pts docetaxel, 4 pts other. Median previous chemotherapy lines for advanced disease: 2 (range: 0–6). 16 pts received doxorubicin/epirubicin, 14 pts docetaxel, 13 pts vinorelbine as a part of advanced disease chemotherapy regimen. Trastuzumab was administered at standard doses and combined with docetaxel, vinorelbine, cisplatin, capecitabine, etoposide, gemcitabine or administered as monotherapy. Response for the first-line TZB therapy was as follows: CR 5/27 pts (18.5%); PR 10/27 pts (37%). Median TTP was 5.8 months (range: 0–22). 14/27 pts (51.8%) received a second-line TZB therapy beyond disease progression. Response for the second-line therapy: CR 2/14 pts (14.3%); PR 5/14 pts (35.7%). Median TTP was 5.1 months (range: 0–24). 6/14 pts received a third-line and subsequent lines (up to five lines) of TZB therapy. PR for subsequent lines of therapy was observed in 4 pts. Median survival has not been reached. Pts who received ≥2 of TZB regimens survived significantly longer than pts who had received only 1 regimen (P = 0,02 logrank). Pts with metastasis in 1 location survived significantly longer than pts with metastasis in ≥2 sites (P = 0,01 logrank). Conclusions: Trastuzumab-based therapy seems to be active in MBC pts beyond disease progression even in heavily pretreated population. Durable responses were observed in some cases. No significant financial relationships to disclose.
Specific changes in faecal microbiota are associated with familial Mediterranean fever
Authors: Samuel Deshayes, Soraya Fellahi, Jean-Philippe Bastard, Jean-Marie Launay, Jacques Callebert, Thibault Fraisse, David Buob, Jean-Jacques Boffa, Irina Giurgea, Charlotte Dupont, Sarah Jegou, Marjolène Straube, Alexandre Karras, Achille Aouba, Gilles Grateau, Harry Sokol, Sophie Georgin-Lavialle
Journal: Annals of the Rheumatic Diseases (2019)

Objectives Familial Mediterranean fever (FMF) can be complicated by AA amyloidosis (AAA), though it remains unclear why only some patients develop amyloidosis. We examined the gut microbiota composition and inflammatory markers in patients with FMF complicated or not by AAA. Methods We analysed the gut microbiota of 34 patients with FMF without AAA, 7 patients with FMF with AAA, 19 patients with AAA of another origin, and 26 controls using 16S ribosomal RNA gene sequencing with the Illumina MiSeq platform. Associations between bacterial taxa and clinical phenotypes were evaluated using multivariate association with linear models statistical method. Blood levels of interleukin (IL)−1β, IL-6, tumour necrosis factor-α and adipokines were assessed by ELISA; indoleamine 2,3-dioxygenase (IDO) activity was determined by high-performance liquid chromatography. Results Compared with healthy subjects, specific changes in faecal microbiota were observed in FMF and AAA groups. Several operational taxonomic units (OTUs) were associated with FMF. Moreover, two OTUs were over-represented in FMF-related AAA compared with FMF without AAA. Additionally, higher adiponectin levels and IDO activity were observed in FMF-related AAA compared with FMF without AAA (p&lt;0.05). Conclusion The presence of specific changes in faecal microbiota in FMF and in FMF-related AAA suggests that intestinal microorganisms may play a role in the pathogenesis of these diseases. These findings may offer an opportunity to use techniques for gut microbiota manipulation.
Evidence-based recommendations for energy intake in pregnant women with obesity
Authors: Jasper Most, Marshall St Amant, Daniel S. Hsia, Abby D. Altazan, Diana M. Thomas, L. Anne Gilmore, Porsha M. Vallo, Robbie A. Beyl, Eric Ravussin, Leanne M. Redman
Journal: Journal of Clinical Investigation (2019)

BACKGROUND. In women with obesity, excess gestational weight gain (≥270 g/week) occurs in 2 out of 3 pregnancies and contributes to metabolic impairments in both mother and baby. To improve obstetrical care, objectively assessed information on energy balance is urgently needed. The objective of this study was to characterize determinants of gestational weight gain in women with obesity.
Use of Von-Hippel Lindau (VHL) mutation status to predict objective response to vascular endothelial growth factor (VEGF) -targeted therapy in metastatic renal cell carcinoma (RCC)
Authors: T. K. Choueiri, S. A. Vaziri, B. I. Rini, P. Elson, I. Bhalla, E. Jaeger, V. Weinberg, F. M. Waldman, M. Zhou, R. M. Bukowski, R. Ganapathi
Journal: Journal of Clinical Oncology (2007)

5012 Background: The clinical response to VEGF-targeted therapy in metastatic RCC is robust, yet variability in outcome exists. VHL is often mutated in RCC, but the relation to therapeutic outcome is unclear. Identification of tumor molecular characteristics associated with outcome would aid in patient selection and interpretation of clinical trials. Materials and Methods: Patients with metastatic, clear-cell RCC with available baseline frozen or paraffin-embedded tumor samples who received VEGF-targeted monotherapy with sunitinb, sorafenib, axitinib or bevacizumab at Cleveland Clinic or University of California San Francisco, were included. Patient characteristics, VHL gene status (mutated or not mutated) and objective response rate (ORR) were documented. ORR was investigator-assessed per RECIST criteria. Fisher’s exact test and logistic regression models were used to assess ORR in univariate and multivariate analyses, respectively. Results: One-hundred twenty-three patients were evaluable. The ORR was 36.5% for the entire cohort. VHL mutation was found in 48% of patients and was seen across all three exons. Patients with VHL mutation had an ORR of 46% versus 28% for pts without a mutated VHL gene (p=0.06). In multivariate analysis, presence of a VHL mutation remained an independent prognostic factor associated with improved ORR (p=.02) when multiple clinical prognostic factors (ECOG PS, hemoglobin, corrected calcium, LDH, prior radiation, prior therapy and number of metastatic sites) were also considered. Conclusion: This is the first large study testing the impact of VHL mutation on response to VEGF-targeted agents in metastatic RCC. Although objective responses were more likely among patients with mutated VHL gene, lack of VHL mutation did not preclude a response. Additional tissue analysis and identification of biomarkers relevant to response to VEGF-targeted agents in metastatic RCC are warranted. [Table: see text]
Gastrointestinal stromal tumor associated with neurofibromatosis type I.
Authors: Toshirou Nishida, Tsuyoshi Takahashi, Mari Kaneda, Maiko Ako, Takeshi Omori, Toru Masuzawa, Satoshi Serada, Tetsuji Naka, Masahiko Tsujimoto, Seiichi Hirota
Journal: Journal of Clinical Oncology (2013)

10539 Background: Most gastrointestinal stromal tumors (GIST) have either KIT or PDGFRA mutations. Neurofibromatosis type 1 pts caused by mutations in the NF1 gene have increased risk of GIST development, which may have no mutation in both genes. In this study, we analyzed clinical and pathological features of NF-1 associated GISTs. Methods: Study 1: We have screened 95 adults NF1 pts (age 31-66, 35 male and 60 female) by enhanced MDCT between 2003 and 2012. Study 2: We collected 1,184 sporadic GISTs from community hospitals in Japan between 2001 and 2010 retrospectively, and found 24 primary NF1-GISTs (1.7% of sporadic) and 2 recurrent NF1-GISTs, of whom clinicopathological features were analyzed. Results: Study1: By MDCT screening, we have found histologically confirmed 6 GISTs (4 males and 2 female; 6/1,000 NF1-persons/year) in the small intestine. Median age of NF1-GIST was 45, and five pts had multiple tumors, ICC hyperplasia in the normal intestine and no mutation in the KIT and PDGFRA genes. Study 2: Median age of 26 NF1-GIST (12 male and 14 female) was 58. 25 GISTs were located in the small bowel and one in the stomach. 17 pts had multiple GISTs and 9 pts single lesion. Pathologically, KIT was positive for all NF1-GISTs. 24 pts had spindle cell tumors and 2 had mixed or epithelioid. No mutation was found in the KIT and PDGFRA genes of 11 pts examined. Median values of mitosis (0/50HPF) and Ki67 (0.5%) were lower than those of sporadic GIST (3/50HPF and 2.5%). With media follow-up of 3.6 years, 8 pts had recurrences and 4 pts died of the disease. By western blotting, KIT was faintly phosphorylated but its downstream kinases including MEK, p44/22, AKT, mTOR, p38 and STAT3, were activated. Six pts received imatinib and had no response and, subsequently, 5 pts received sunitinib with 4 PD and 1 short-term SD. Conclusions: NF1-associated GIST is a rare entity of GIST and has distinctive features from conventional sporadic GISTs. KIT-targeted TKI appeared to be ineffective to recurrent and advanced NF1-GISTs.
<i>KRAS</i> mutation analysis in patients (pts) with locally advanced pancreatic cancer (LAPC) treated with gefitinib and chemoradiation therapy (CT-RT) in a phase I trial
Authors: H. Chen, D. Raben, T. Schefter, M. Kane, M. McCarter, C. Olsen, K. McCoy, S. G. Eckhardt, P. H. Gumerlock
Journal: Journal of Clinical Oncology (2006)

4106 Background: Correlative studies that incorporate biomarkers to rapidly analyze response to new agents are needed. Unique to pancreatic cancer is the high incidence of KRAS mutations (over 90%). This pilot study evaluated plasma KRAS mutations for disease monitoring in LAPC pts treated on a Phase I trial combining CT-RT with the EGFR inhibitor, gefitinib. Methods: DNA was extracted from plasma of 11 pts collected at 3 timepoints: pre-gefitinib, pre-CT-RT, and post-gefitinib+CT-RT. Matched tissue DNA was obtained from 4 pts with available paraffin blocks. KRAS codon 12 mutations were detected using a two-stage RFLP-PCR assay. Cell line controls: Calu-1 (mutant KRAS) and LNCaP (wild-type KRAS). Mutations were confirmed by direct DNA sequencing. Results were related to pt clinical data. Results: KRAS mutations were detected in the pre-gefitinib plasma of 5/11 pts, and in the matched tumor tissue of 3/4 pts. Of the 5 pts with plasma KRAS mutations, 2 pts with no detectable mutant KRAS in the plasma post-gefitinib+CT-RT had overall survival of 8 and 21 months, whereas 2 pts who retained mutant KRAS had overall survival of only 2 and 5 months, and one pt withdrew early. Of the 3 tumor tissues containing mutant KRAS, the mutations were also detectable in the matched plasma in 2 pts (67%). KRAS codon 12 mutations spectrum: 4 GGT→GAT, 2 GGT→GTT and 1 GGT→AGT. Conclusions: Plasma KRAS mutations are readily detectable in LAPC pts, and the clearance or persistence of plasma KRAS mutations after treatments reflected the clinical course in some cases. The use of plasma KRAS mutation as a marker of survival and response will be further assessed in a recently approved phase I trial using a proteasome inhibitor with chemoradiation at the University of Colorado. No significant financial relationships to disclose.
Combination of quadruplex qPCR and next-generation sequencing for qualitative and quantitative analysis of the HIV-1 latent reservoir
Authors: Christian Gaebler, Julio C.C. Lorenzi, Thiago Y. Oliveira, Lilian Nogueira, Victor Ramos, Ching-Lan Lu, Joy A. Pai, Pilar Mendoza, Mila Jankovic, Marina Caskey, Michel C. Nussenzweig
Journal: The Journal of Experimental Medicine (2019)

HIV-1 infection requires lifelong therapy with antiretroviral drugs due to the existence of a latent reservoir of transcriptionally inactive integrated proviruses. The goal of HIV-1 cure research is to eliminate or functionally silence this reservoir. To this end, there are numerous ongoing studies to evaluate immunological approaches, including monoclonal antibody therapies. Evaluating the results of these studies requires sensitive and specific measures of the reservoir. Here, we describe a relatively high-throughput combined quantitative PCR (qPCR) and next-generation sequencing method. Four different qPCR probes covering the packaging signal (PS), group-specific antigen (gag), polymerase (pol), and envelope (env) are combined in a single multiplex reaction to detect the HIV-1 genome in limiting dilution samples followed by sequence verification of individual reactions that are positive for combinations of any two of the four probes (Q4PCR). This sensitive and specific approach allows for an unbiased characterization of the HIV-1 latent reservoir.
Randomized phase III trial of standard D2 versus D2 + para-aortic lymph node (PAN) dissection (D) for clinically M0 advanced gastric cancer: JCOG9501
Authors: M. Sasako, T. Sano, S. Yamamoto, A. Nashimoto, A. Kurita, H. Furukawa, T. Tsujinaka, T. Kinoshita, K. Arai
Journal: Journal of Clinical Oncology (2006)

LBA4015 Background: The INT-0116 study proved the efficacy of radiochemotherapy after R0 resection for gastric cancer and thus the importance of the local control and the insufficiency of D0/1 surgery. Recently D2 surgery was for the first time proven to improve the survival compared with D1 in a Taiwanese RCT (Lancet Oncol 2006). In our study, D2+PAND was compared with D2 in a RCT. Low operative mortality has been reported (Sano et al. J Clin Oncol 2004) and we now present the survival results. Methods: Eligibility criteria included; histologically proven adenocarcinoma, cT2b-T4, cM0, no macroscopic metastasis to the PAN, negative lavage cytology, adequate organ function, and age &lt;76. Linitis plastica was excluded. Eligible pts were randomly assigned to D2 with or without PAND during surgery. All patients were followed without adjuvant therapy until recurrence. The primary endpoint was overall survival (OS) to be compared by stratified log-rank test. Assuming 256 eligible pts in each arm, the study had 75% power to detect 0.73 hazard ratio for D2+PAND to D2 in OS at 0.05 one-sided alpha. Results: Between 07/1995 and 04/2001, 523 pts were randomized (263 to D2 and 260 to D2+PAND). Baseline characteristics were well balanced between the arms. At the time of the final analysis on 23/03/06, 191 (96 and 95, in D2 and D2+PAND, respectively) had died. The 3- and 5-year OS were 76% and 69% in D2 and 76% and 70% in D2+PAND, respectively (p = 0.57, Hazard ratio was 1.03 (95% CI: 0.77–1.37)). Disease free survival did not show any difference between the groups as well. Median operation time was 63 minutes longer and median blood loss was 230 ml larger in D2+PAND than in D2. There was no difference in the incidence of major surgical complications and hospital mortality (0.8% in both arms). Conclusions: D2 or D2+PAND could be carried out safely and showed excellent survival for advanced gastric cancer treated with curative intent. PAND could not improve the survival achieved by D2. General use of PAND should be avoided. No significant financial relationships to disclose.
Immediate Transfusion and Transfusion Volume in African Children with Severe Anemia
Authors: Julie R. Ingelfinger
Journal: New England Journal of Medicine (2019)

Severe anemia is common among children in sub-Saharan Africa and presents a unique challenge, given the high prevalence of malaria, infectious diarrhea, and malnutrition in underresourced regions.1-4 The guidelines of the World Health Organization (WHO)5 suggest transfusing a volume of 20 ml of whole-blood equivalent per kilogram of body weight, but it is unclear whether that volume is appropriate, as is the timing of transfusion in a child with severe anemia, irrespective of the location.6 In this issue of the Journal, two articles by Maitland and colleagues7,8 report the results from the Transfusion and Treatment of Severe Anemia in African . . .
Does the Association of Diabetes With Stroke Risk Differ by Age, Race, and Sex? Results From the REasons for Geographic and Racial Differences in Stroke (REGARDS) Study
Authors: Gargya Malla, D. Leann Long, Suzanne E. Judd, Marguerite R. Irvin, Brett M. Kissela, Daniel T. Lackland, Monika M. Safford, Deborah A. Levine, Virginia J. Howard, George Howard, J. David Rhodes, Jenifer H. Voeks, Dawn O. Kleindorfer, Aaron Anderson, James F. Meschia, April P. Carson
Journal: Diabetes Care (2019)

OBJECTIVE Given temporal changes in diabetes prevalence and stroke incidence, this study investigated age, race, and sex differences in the diabetes–stroke association in a contemporary prospective cohort, the REasons for Geographic and Racial Differences in Stroke (REGARDS) Study. RESEARCH DESIGN AND METHODS We included 23,002 non-Hispanic black and white U.S. adults aged ≥45 years without prevalent stroke at baseline (2003–2007). Diabetes was defined as fasting glucose ≥126 mg/dL, random glucose ≥200 mg/dL, or use of glucose-lowering medication. Incident stroke events were expert adjudicated and available through September 2017. RESULTS The prevalence of diabetes was 19.1% at baseline. During follow-up, 1,018 stroke events occurred. Among adults aged &amp;lt;65 years, comparing those with diabetes to those without diabetes, the risk of stroke was increased for white women (hazard ratio [HR] 3.72 [95% CI 2.10–6.57]), black women (HR 1.88 [95% CI 1.22–2.90]), and white men (HR 2.01 [95% CI 1.27–3.27]) but not black men (HR 1.27 [95% CI 0.77–2.10]) after multivariable adjustment. Among those aged ≥65 years, diabetes increased the risk of stroke for white women and black men, but not black women (HR 1.05 [95% CI 0.74–1.48]) or white men (HR 0.86 [95% CI 0.62–1.21]). CONCLUSIONS In this contemporary cohort, the diabetes–stroke association varied by age, race, and sex together, with a more pronounced effect observed among adults aged &amp;lt;65 years. With the recent increase in the burden of diabetes complications at younger ages in the U.S., additional efforts are needed earlier in life for stroke prevention among adults with diabetes.
Anti-OX40 Antibody Directly Enhances The Function of Tumor-Reactive CD8+ T Cells and Synergizes with PI3Kβ Inhibition in PTEN Loss Melanoma
Authors: Weiyi Peng, Leila J. Williams, Chunyu Xu, Brenda Melendez, Jodi A. McKenzie, Yuan Chen, Heather L. Jackson, Kui S. Voo, Rina M. Mbofung, Sara Elizabeth Leahey, Jian Wang, Gregory Lizee, Hussein A. Tawbi, Michael A. Davies, Axel Hoos, James Smothers, Roopa Srinivasan, Elaine M. Paul, Niranjan Yanamandra, Patrick Hwu
Journal: Clinical Cancer Research (2019)

OX40 agonist-based combinations are emerging as a novel avenue to improve the effectiveness of cancer immunotherapy. To better guide its clinical development, we characterized the role of the OX40 pathway in tumor-reactive immune cells. We also evaluated combining OX40 agonists with targeted therapy to combat resistance to cancer immunotherapy.Experimental Design: We utilized patient-derived tumor-infiltrating lymphocytes (TILs) and multiple preclinical models to determine the direct effect of anti-OX40 agonistic antibodies on tumor-reactive CD8+ T cells. We also evaluated the antitumor activity of an anti-OX40 antibody plus PI3Kβ inhibition in a transgenic murine melanoma model (Braf mutant, PTEN null), which spontaneously develops immunotherapy-resistant melanomas.We observed elevated expression of OX40 in tumor-reactive CD8+ TILs upon encountering tumors; activation of OX40 signaling enhanced their cytotoxic function. OX40 agonist antibody improved the antitumor activity of CD8+ T cells and the generation of tumor-specific T-cell memory in vivo. Furthermore, combining anti-OX40 with GSK2636771, a PI3Kβ-selective inhibitor, delayed tumor growth and extended the survival of mice with PTEN-null melanomas. This combination treatment did not increase the number of TILs, but it instead significantly enhanced proliferation of CD8+ TILs and elevated the serum levels of CCL4, CXCL10, and IFNγ, which are mainly produced by memory and/or effector T cells.These results highlight a critical role of OX40 activation in potentiating the effector function of tumor-reactive CD8+ T cells and suggest further evaluation of OX40 agonist-based combinations in patients with immune-resistant tumors.