tbuckley/cabot-search huggingface dataset:
331. Development of Neisseria meningitidis CRISPR/Cas9 Systems for Efficient and Specific Genome Editing
Authors: Ciaran M. Lee, Thomas J. Cradick, Gang Bao
Journal: Molecular Therapy (2015)

Targeted genome modification using the CRISPR/Cas9 system has been extensively embraced by the research community as a powerful tool in biotechnology and life sciences, and it holds promise for the future of personalized medicine. The CRISPR/Cas9 system consists of an RNA guide strand (gRNA) for target site recognition and the CRISPR associated protein Cas9 for DNA cleavage. Cleavage of a site requires a protospacer adjacent motif (PAM) sequence. CRISPR induced DNA double-strand breaks (DSBs) stimulate cellular DNA repair via non-homologous end joining or homologous recombination, which allows specific genome modification. However, previous studies have demonstrated high levels of off-target cleavage with CRISPR/Cas9 that may lead to unwanted or deleterious genomic modifications. Therefore, developing strategies to reduce nuclease off-target effects is essential for therapeutic applications of genome editing. The widely used Streptococcus pyogenes (Sp) CRISPR/Cas9 system recognizes a total of 22 bases, twenty via the gRNA and two via the PAM NGG. Here we describe further development of the Neisseria meningitidis (Nm) orthologous CRISPR/Cas9 system for efficient and specific genome editing in mammalian cells. The Nm Cas9 recognizes a longer PAM sequence than that of Sp Cas9, which has the potential to result in fewer off-target sites genome-wide. The Nm CRISPR/Cas9 systems preferentially recognize longer target sites than the Sp system, and a longer PAM as previously identified, NNNNGATT. The Nm cleavage activity level is as high as 70%, similar to that of Sp Cas9. We tested the ability of Nm Cas9 to cleave targets with other PAM sequences and found that other PAM allowed cleavage, such that the PAM preference can be represented as NNNNGHTT. Interestingly, there was a difference between the one guide strand and two guide strand systems. The single guide strand system (sgRNA) displayed greater stringency in PAM recognition than the innate system (with separate tracrRNA and crRNA). Nm gRNAs were able to tolerate 1 base mismatches and 1 base DNA and RNA bulges to some extent when tested in a single-strand annealing assay. To further investigate the specificity of Nm CRISPR/Cas9 at the genomic level we used deep sequencing of potential off-target sites after CRISPR transfection. To directly compare the specificity of both Sp and Nm CRISPR/Cas9 systems, overlapping Nm and Sp target sites were identified in seven different genes. For the three targets where there was comparable on-target activity, potential Nm and Sp off-target sites were identified and subjected to deep sequencing using the Illumina MiSeq platform. We found that Sp CRISPR/Cas9 displayed greater levels of genome-wide off-target activity. In conclusion, our results demonstrate that the Nm CRISPR/Cas9 systems have better targeting specificity and thus provide an alternative to the widely used Sp CRISPR/Cas9.
Abstract 420: The role of tumor microenvironment in therapy resistance and melanoma progression
Authors: Rajasekharan Somasundaram, Gao Zhang, Stephan N. Wagner, Mizuho Fukunaga-Kalabis1, Meenhard Herlyn
Journal: Cancer Research (2015)

Abstract Melanoma patients develop resistance to both chemo- and targeted-therapy drugs. Promising pre-clinical and clinical results with immune checkpoint inhibitors using antibodies directed against CTLA4 and PD1 have re-energized the field of immune-based therapies in melanoma. However, similar to chemo- or targeted-therapies only subsets of melanoma patients respond to immune checkpoint blockade. Studies from our laboratory have indicated that the tumor microenvironment (TME) might play a role in the emergence of therapy resistant tumor subpopulations. The TME actively recruits a number of immune and non-immune cells. A recent study describes immune cells as an important component of TME. About 33% of the infiltrating immune cells are of ‘B-cell’ lineage and yet, there is very little information on the role of these cells in melanoma cell biology. Our results suggest that B cells isolated from the tumor tissues of melanoma patients show higher inflammatory cytokine expressions (IGF-1, IL-1, PDGF and VEGF) when compared to circulating B cells. Presence of inflammatory cytokines in the TME results in the induction of heterogeneous melanoma subpopulation, down modulation of melanoma associated antigens (MAA), and thus, therapy resistance of melanoma. Here, we report a novel mechanism of acquired drug resistance in melanoma induced by tumor-associated B cells involving FGF-2/FGFR-3 and IGF-1 signaling. B-cell derived IGF-1 modulates the emergence of therapy resistant heterogeneous melanoma subpopulations. Neutralization of IGF-1 reverses the induction of heterogeneous melanoma subpopulations. We are currently evaluating the mechanism of down modulation of MAA in presence of inflammatory cytokines. Our studies confirm the important role of the TME in the induction of therapy resistant tumor subpopulations and offer a new combination treatment approach of targeting melanoma (Supported by AMRF and NIH grant CA114046). Citation Format: Rajasekharan Somasundaram, Gao Zhang, Stephan N. Wagner, Mizuho Fukunaga-Kalabis1, Meenhard Herlyn. The role of tumor microenvironment in therapy resistance and melanoma progression. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 420. doi:10.1158/1538-7445.AM2015-420
The Roles of RUNX1 in Human Hematopoiesis and Megakaryopoiesis Revealed By Genome-Targeted Human iPSCs and an Improved Hematopoietic Differentiation Model
Authors: Bin-Kuan Chou, Hao Bai, Yongxing Gao, Ying Wang, Zhaohui Ye, Erika Mijin Kwon, Pu Paul Liu, Alan D. Friedman, Zack Z. Wang, Linzhao Cheng
Journal: Blood (2015)
Phase IA/II Study of Oral LBH589, a Novel Deacetylase Inhibitor (DACi), Administered on 2 Schedules, in Patients with Advanced Hematologic Malignancies.
Authors: Andrew Spencer, Miles Prince, Daniel J. DeAngelo, Thomas Fischer, Kapil N. Bhalla, Francis J. Giles, Angela Liu, Kathryn Parker, Glen Laird, Eric Masson, John Rediske, Jeffrey W. Scott, Oliver G. Ottmann
Journal: Blood (2007)
Does L-arginine/Korean ginseng/gingko biloba/damiana-based supplement improve the sexual function and quality of life of female cancer survivors: A randomized trial.
Authors: K. Greven, L. D. Case, L. R. Nycum, P. J. Zekan, D. D. Hurd, E. P. Balcueva, G. M. Mills, R. Zon, P. J. Flynn, D. Biggs, E. G. Shaw
Journal: Journal of Clinical Oncology (2011)

9016 Background: There is a lack of research to support interventions that may be effective in improving quality of life and sexual function disorders in female cancer survivors. L-arginine/Korean ginseng/gingko biloba/damiana-based supplement (ArginMax) contains L-arginine, which enhances systemic nitric oxide synthesis, resulting in vasodilation that may improve sexual function. Methods: This was a 12 week, randomized, placebo controlled trial. Eligible patients were females at least 6 months from active treatment and without current evidence of cancer. All patients took 3 capsules two times daily (6 total/day) and kept pill diaries. The primary outcome measure was the Female Sexual Function Inventory (FSFI) while the secondary outcome measure was the FACT-G quality of life instrument. Assessments including toxicities were made at baseline, 4, 8, and 12 weeks. Results: 186 patients were accrued to this trial between 5/10/07 and 3/24/10. Ages ranged from 23 to 79 with a median of 50 years. 76% of the participants were White, 21% were Black, and 3% were Hispanic. Patients were survivors of breast (78%), gynecological (12%) or other (10%) primaries. There was a high rate of sexual dysfunction at baseline: 58% <1 intercourse per month, 67% moderate to extreme dissatisfaction, and 64% moderate to extreme disinterest. Overall sexual function, as measured by the FSFI, improved by 3 points in the control group and 3.7 points in the ArginMax arm over the 12 week study period, a difference that was not statistically significant (p = .610). FACT-G total quality of life scores, however, were significantly better at 12 weeks among participants receiving ArginMax compared to those receiving placebo (LS means of 87.5 vs 82.9, p = .009). The physical (24.6 vs 22.9, p = .001) and functional (21.6 vs 19.8, p = .007) subscale scores were most impacted. Toxicities were similar on both arms, although more hot flashes were reported on the ArginMax versus placebo arm (73% vs 59%, p = .065). Conclusions: This trial documented a high rate of sexual dysfunction in female cancer survivors. While ArginMax had no significant impact on sexual function, quality of life was significantly better at 12 weeks for the participants receiving ArginMax. Supported by NCI/DCP CCOP Research Base Grant 5 U10 CA081851-11.
The BCR-ABL1-Regulated hnRNP A1, hnRNP E2, and hnRNP K Are Differentially Expressed Between CD34+ and CD34+/CD38- Ph+ Cells, and After Blastic Transformation of CML.
Authors: Jason G Harb, Paolo Neviani, Joshua J Oaks, Guido Marcucci, Peter Hokland, Denis-Claude Roy, Danilo Perrotti
Journal: Blood (2010)
Utility of Interphase FISH To Stratify Patients into Cytogenetic Risk Categories at Diagnosis of AML in an ECOG Clinical Trial (E1900).
Authors: Gail H. Vance, Haesook Kim, Gary Hicks, Athena Cherry, Rodney Higgins, Martin S. Tallman, Hugo F. Fernandez, Gordon Dewald
Journal: Blood (2005)
Abstract 3602: Cross-resistance to 1st, 2nd, and 3rd generation EGFR tyrosine kinase inhibitors <i>in vitro</i> is characterized by MET amplification and PTEN loss
Authors: Sarah M. Paul, Dorothee Nickles, Xioafen Ye, Robert L. Yauch, David S. Shames
Journal: Cancer Research (2015)

Abstract Reversible EGFR tyrosine kinase inhibitors (TKIs) such as erlotinib and gefitinib offer significant clinical benefit to patients with EGFR mutation positive non-small cell lung cancer (NSCLC) compared to chemotherapy alone, but high rates of resistance especially at EGFR T790M (50-60% of resistant cases) underscore the need for better targeted treatments for NSCLC patients. Third generation irreversible TKIs–AZD9291 and CO-1686–were developed for efficacy in the T790M setting. However, resistance to the new class of EGFR TKIs is inevitable, prompting us to investigate the relationship between erlotinib and AZD9291 resistance mechanisms and explore novel ones. NSCLC cell lines harboring activating EGFR mutations with (NCI-H1975) or without T790M (HCC4006, HCC827, and PC-9) were exposed to erlotinib, dacomitnib, or AZD9291 at IC 75 or greater for three months to generate resistance. We observed cross-resistance to other EGFR TKIs in nearly all resistant lines, suggesting that T790M was not the main driver of resistance in the erlotinib-treated lines and that a common mechanism might account for resistance in each cell line set. An epithelial to mesenchymal transition (EMT) was observed and a corresponding increase in vimentin staining was seen in resistant lines, consistent with cross-resistance. Previous studies showed that MET amplification caused erlotinib resistance in HCC827; our data suggest MET amplification also accounted for the AZD9291 and dacomitnib resistance in HCC827. In AZD9291-resistant HCC4006 and H1975 lines, PTEN levels were substantially reduced compared to the parental line, with a corresponding increase in PIK3 pathway markers. Whole exome sequencing data support homozygous deletion of PTEN loss as a mechanism of acquired resistance to AZD9291 in NCI-H1975. The PTEN null line NCI-H1650 was found to be resistant to all three TKIs without long-term drug exposure, implicating PTEN loss as a mechanism of de novo resistance. An analysis of EGFR mutation status, PTEN status, MET expression, and the kinetics of acquired resistance will be presented and clinical implications will be discussed. Citation Format: Sarah M. Paul, Dorothee Nickles, Xioafen Ye, Robert L. Yauch, David S. Shames. Cross-resistance to 1st, 2nd, and 3rd generation EGFR tyrosine kinase inhibitors in vitro is characterized by MET amplification and PTEN loss. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3602. doi:10.1158/1538-7445.AM2015-3602
Abstract IA18: Probing tumor heterogeneity with mouse models
Authors: Ben Z. Stanger
Journal: Cancer Research (2016)

Abstract Although the majority of pancreatic cancers harbor mutations in a small set of cancer genes, individual tumors vary widely with respect to histology, gene expression patterns, and response to therapy. This inter-tumoral heterogeneity is likely due to mutations or epigenetic events affecting less commonly-mutated cancer genes, resulting in tumors that can be broadly grouped into three or four categories based upon transcriptional profiling. To determine the extent to which the KPC model captures the inter-tumoral heterogeneity of pancreatic cancer, we performed RNA-sequencing on isolated tumor cells from 11 murine pancreatic tumors. Using unsupervised clustering, tumors fell into two broad categories: cluster 1 tumors, which were poorly-differentiated and well-vascularized, and cluster 2 tumors, which were moderately- to well-differentiated and poorly-vascularized. Differences in gene expression could account for some of these differences; for example, cluster 1 tumor cells exhibited low levels of Shh expression, consistent with the paucity of stroma. Moreover, mechanisms of EMT differed between the two classes of tumors. Gene set variation analysis with whole transcriptome data from human PDA revealed a correlation between cluster 1 tumors and the squamous or quasi-mesenchymal subtype. Likewise, cluster 2 tumors were correlated with the classical, ADEX, and pancreatic progenitor subtypes of human PDA. These data suggest that the KPC mouse model, despite its foundation on Kras and p53 mutations alone, captures the heterogeneity of human PDA and may therefore be useful for understanding heterogeneous responses to therapy. Citation Format: Ben Z. Stanger.{Authors}. Probing tumor heterogeneity with mouse models. [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Advances in Science and Clinical Care; 2016 May 12-15; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2016;76(24 Suppl):Abstract nr IA18.
Abstract 4660: Association of longer telomere length with increased risk of chronic hepatitis B and hepatocelluar carcinoma
Authors: Qiang Ma, Jiajing Cai, Yan Cai, Yuan Xu, Fan Chang, Lei Xu, Xiaolan Guo
Journal: Cancer Research (2015)

Abstract Telomere, which consists of small tandem nucleotide repeats (5′-TTAGGG-3′ in human), plays a critical role in the maintenance of genomic stability in eukaryotic chromosomes. More and more findings have shown that alteration in telomere length was involved in some diseases, however whether the telomere length is associated with the development and/or progression of disease remains poorly understood. Here a case-control study was employed to illustrate the correlation of relative telomere length(RTL) with chronic hepatitis B(CHB) and hepatocellular carcinoma(HCC). In this study, 115 cases of HCC patients, 212 patients with chronic hepatitis B and 184 healthy controls well matched with age and gender were recruited. Genomic DNA was extracted from the peripheral blood leukocytes and fluorescence quantitative polymerase chain reaction(FQ-PCR) was used to detect the telomere repeated numbers. We found that the RTL in HCC group was the longest, followed by CHB patients group and healthy control group was the shortest, showing significant statistical differences. When compared with age, the RTLs of individuals who aged more than 50 years old were obvious shorter than those younger ones in the control group, but not in the HCC and CHB group. Moreover, individuals who had longer RTLs indicated a significant increased risk of chronic hepatitis B (OR: 1.83, 95%CI: 1.22-2.73), and the longest RTLs showed higher incidence of HCC (OR: 3.22, 95%CI: 2.01-5.17) when the healthy control was used as the reference group. Most importantly, when the chronic hepatitis B group was used as the reference group, individuals who had longer RTL also suffered a significant increased risk of HCC(OR: 1.58, 95%CI: 1.03-2.41). Our results suggest that longer RTL is associated with the increased risk of chronic hepatitis B and HCC, which indicates that telomere length might be involved in the development or progression of HCC, also RTL might be used as a potential predicator of HBV relative chronic liver disease and HCC. Citation Format: Qiang Ma, Jiajing Cai, Yan Cai, Yuan Xu, Fan Chang, Lei Xu, Xiaolan Guo. Association of longer telomere length with increased risk of chronic hepatitis B and hepatocelluar carcinoma. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4660. doi:10.1158/1538-7445.AM2015-4660
A Multicenter Phase II Trial of Etoposide, Methylprednisolone, High-Dose Cytarabine, and Oxaliplatin (ESHAOx) for Patients with Refractory/Relapsed Aggressive Non-Hodgkin’s Lymphoma.
Authors: Sun Jin Sym, Hye Jin Kang, Seung-Hyun Nam, Hoyoung Kim, Seok Jin Kim, Hyeon Seok Eom, Won Seog Kim, Cheolwon Suh
Journal: Blood (2007)
Treatment with Pegylated Interferon α (PegIntron) for High-Risk Essential Thrombocythemia: Results of a Phase II Study.
Authors: Christian Langer, Eva Lengfelder, Jurgen Thiele, Hans M. Kvasnika, Heike Pahl, Axel Matzdorff, Barbara Stade, Stefanie Schauer, Heinz Gisslinger, Hartmut Dohner, Martin Griesshammer
Journal: Blood (2004)
296. Pre-Selection of Anti-HIV Lentiviral Vector Gene Modified Hematopoietic Stem Cells Significantly Improves Protection from HIV Infection: The Basis for a Future Clinical Trial
Authors: Sharlie L. Barclay, Yimin Yang, Sirou Zhang, Ryan Fong, Alfonso Barraza, Jan A. Nolta, Mehrdad Abedi, Joseph S. Anderson
Journal: Molecular Therapy (2015)

The successful treatment and cure of HIV in the Berlin Patient has highlighted the utility of HIV-resistant hematopoietic stem cells (HSC) to offer a potential functional cure for HIV infected individuals. Stem cell gene therapy for HIV can mimic this result by genetically engineering a patient's own HSC with lentiviral vectors encoding HIV resistance genes. Clinical trials of HIV stem cell gene therapy have been unsuccessful at demonstrating complete efficacy due to the transplantation of a low percentage of anti-HIV gene expressing cells. Therefore, to bridge the gap between these previous approaches and the Berlin patient, we have developed a pre-selection process which allows for the purification of vector transduced cells prior to transplantation into patients. This pre-selective lentiviral vector (1TAX) encodes a triple combination of anti-HIV genes (a human/rhesus macaque TRIM5alpha, a CCR5 shRNA, and a TAR decoy) in addition to a truncated/mutated form of human CD25 which is expressed on the cell surface of transduced HSC and is used to enrich for the HIV-resistant cell population. Purity levels of 1TAX transduced human HSC obtained after selection for CD25+ were >94% as determined by flow cytometry. Safety of the 1TAX vector transduced/purified human HSC was demonstrated in vivo in NOD-SCID-Rag-/-IL2rgamma-/-(NRG) mice with the detection of engraftment and multi-lineage hematopoiesis into human T cells, B cells, and macrophages in the peripheral blood and lymphoid organs. Upon infection of 1TAX mice with a CCR5-tropic BaL-1 or a CXCR4-tropic NL43 strain of HIV-1, maintenance of normal human CD4+ cell levels were observed in the peripheral blood. A significant decrease (>4 logs) in HIV-1 plasma viremia was also demonstrated in 1TAX mice as compared to mice transplanted with nontransduced human HSC. Together, this work has demonstrated the safety and efficacy of this 1TAX pre-selective lentiviral vector in HSC and is the basis for a future human clinical trial of HIV stem cell gene therapy.
Abstract 1622: The AKT inhibitor reverses protein trafficking and inhibits tumor cell motility of p27-mislocalized osteosarcoma cells
Authors: Xiang Chen, Yiting Li, Manjula Nakka, Tsz Kwong Man
Journal: Cancer Research (2015)

Abstract Osteosarcoma is the most common malignant bone tumor in children. The development of metastasis remains to be the leading cause of death in osteosarcoma. This clinical challenge urges the development of a novel therapeutic strategy to improve the survival of the metastatic patients. mTOR has recently been regarded as a potential target for metastatic osteosarcoma. However, because of its feedback loop in the pathway, it has become clear that inhibition of mTOR alone would not yield effective therapeutics. More importantly, it is still not clear if the mTOR upstream kinases phosphorylate other important molecules that can also promote metastasis. Our lab has recently demonstrated that a vast majority of osteosarcoma cases harbor cytoplasmic mislocalization of p27. p27 is a tumor suppressor gene that regulates normal cell cycle progression when it is localized in the nucleus. We and others have indicated that p27 acquires a new pro-metastatic function in the cytoplasm of osteosarcoma and other tumors. To evaluate if this observation has any therapeutic significance, our lab has created a set of p27 phosphomutants and found that specific phosphorylations (S10 and T198) are important for the pro-metastatic function in the cytoplasm. Furthermore, shRNA-mediated gene silencing experiments showed that knocking down the expression of p27 decreased the motility of metastatic LM7 cells. Since AKT, the upstream kinase of mTOR, has shown to phosphorylate p27, we tested if AKT inhibitors have any effect on the migration/invasion ability of three osteosarcoma cell lines (LM7, MG63 and G292) that harbor the p27 mislocalization. The results showed that both the AKT1/2 inhibitor and the PI3K/mTOR dual inhibitor PP242, but not mTORC1 inhibitor rapamycin, reduced the tumor cell migration/invasion ability. Interestingly, the inhibitors could also reverse the protein trafficking of p27 into the nucleus. These results suggest that the inhibitors may be able to inhibit the pro-metastatic function and restore the cell cycle inhibitory function of p27. Our long-term goal is to develop a precision medicine approach that will ultimately improve the outcome of metastatic osteosarcoma. By targeting the p27 mislocalization, we believe that we will develop a novel and clinically applicable therapeutic strategy that would eradicate metastatic osteosarcoma and improve the outcome of children affected by this tumor. Citation Format: Xiang Chen, Yiting Li, Manjula Nakka, Tsz Kwong Man. The AKT inhibitor reverses protein trafficking and inhibits tumor cell motility of p27-mislocalized osteosarcoma cells. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1622. doi:10.1158/1538-7445.AM2015-1622
Influence of N-Acetyl Cysteine on Early Graft Outcome of Recipient in Live Donor Liver Transplantation: A Double Blind Randomised Controlled Trial
Authors: Akshay P. Bavikatte, None Abdulatheef, Puneet Dhar, B. Dinesh, G. Unnikrishnan, S. Ramachandran, S. Sudhindran
Journal: Clinical Gastroenterology and Hepatology (2016)
Angio-Phenotype of Pediatric Acute Lymphoblastic Leukemia and Pharmacodynamic Evaluation of the Antiangiogenic Activity of Corticosteroids.
Authors: Sylvain Baruchel, Patricia Mancuso, Marco Marinoni, Valentina Raia, Cristina Rabascio, Angelica Calleri, Luca Saronni, Diana Stempak, Jessica Quarna, Pierluigi Antoiotti, Andrea Biondi, Francesco Bertolini, Alessandra Sala
Journal: Blood (2006)