tbuckley/cabot-search huggingface dataset:
Abstract 4803: Mitochondrial response to temozolomide treatment in glioma cells
Authors: Luana S. Lenz, Mardja M. Silva, Ivi J. Bristot, Fabio Klamt, Guido Lenz
Journal: Cancer Research (2020)

Abstract Mitochondria are a central organelle to metabolism and apoptosis control, it means that their functionality is essential to cellular homeostasis. We investigated the mitochondrial alterations in respose to the chemotherapeutic Temozolomide (TMZ) in glioma cells.We transduced A172 and U87 cells with a fluorescent protein targeted to mitochondria (Addgene #50057), treated these cell with TMZ 100 uM during 3 hours and analyzed them by cytometry, microscopy and high resolution respirometry at days 3, 5 and 7 after treatment.Once tolerance is a dynamic process that can lead to different responses even between related cells, we first asked how related cells respond to TMZ in terms of mitochondria amount. Closely related sisters and cousins cells were not different to random pairs, indicating that mitochondria amount is not inherited and that this feature is very dynamics. Population analysis reveal that five days after TMZ the cells showed an increase in mitochondrial mass and mitochondrial swelling. The PGC-1 expression was reduced by half on day 3, suggesting that increase in mitochondrial mass must be due to accumulation of mitochondria instead of biogenesis. Five days after treatment we observed an increase in mitochondrial membrane potential measure by JC1 and an increase in mitochondria ATP linked respiration. To test if increased mitochondria respiration is a therapeutically targetable adaptation of these cells treated with TMZ, we treated the cells that survived five days after TMZ with KCN, a cytochrome c oxidase inhibitor. As expected, the TMZ-treated cells were more sensitive to the blockage of mitochondrial respiration than untreated cells. On the other hand, cells treated at day five after TMZ with 2-DG, a glycolysis inhibitor, were less affected, indicating that the oxidative phosphorylation is important to tolerance to TMZ.Our results indicate that treatment induce a metabolic reprogramming with increase in oxidative state, and strategies to overcome this tolerance mechanism could be explored. Citation Format: Luana S. Lenz, Mardja M. Silva, Ivi J. Bristot, Fabio Klamt, Guido Lenz. Mitochondrial response to temozolomide treatment in glioma cells [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4803.
Abstract 3513: Genome-wide scan for novel prostate cancer susceptibility loci with clinical consequence utilizing increased genetic drift of the Finnish population
Authors: Csilla Sipeky, Teuvo L. Tammela, Anssi Auvinen, Johanna Schleutker
Journal: Cancer Research (2020)

Abstract Background: Prostate cancer (PC) is the second most common cancer in men worldwide with a rising prevalence. However, only limited number of clinically actionable variants are known. The objective of this study is to identify novel PC susceptibility loci with potential clinical relevance utilizing the increased genetic drift and reduced selective pressure of the recently bottlenecked powerful resource of the Finnish population. Methods: We meta-analysed &amp;gt;185.000 germline single nucleotide polymorphisms (SNPs) in 2738 PC cases and 2401 controls of Finnish origin in the Collaborative Oncological Gene-Environment Study (COGS) using Illumina iSelect custom SNP genotyping platform. Results: Altogether 160 variants remain significant on GWAS level (p&amp;lt;5 × 10−8) in 18 different gene regions. Out of the 160 identified PC susceptibility hits 78 (49%) are novel variants not reported earlier in association with PC. PC associated signals are in close proximity to one another forming genetic hot-spots on chromosomes 8, 7, 11, 17 and 19. The strength of association varies for 101 PC risk variants (OR 1.24-1.86) and 59 protective SNPs (OR 0.59-0.80). The strongest risk gene is CASC8 (OR=1.86; p=1.214 × 10−11). The most significant signals were found at the 8p21.2 chromosomal region (p&amp;lt;7.6 × 10−16). Functional annotation identified a missense coding SNP at KLK3 gene to be a candidate causal variant. We showed evidence for association both with early-onset PC (OR 1.73; P=0.02), high serum PSA level at diagnosis (OR 1.36; P=0.024) and with aggressive PC (Gleason score ≥8; OR 1.44; P=0.02) at 17q21. Conclusion: The results facilitate risk stratification for screening, clinical studies, treatment choices and functional research of PC Citation Format: Csilla Sipeky, Teuvo L. Tammela, Anssi Auvinen, Johanna Schleutker. Genome-wide scan for novel prostate cancer susceptibility loci with clinical consequence utilizing increased genetic drift of the Finnish population [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3513.
Abstract 326: Differences of drug sensitivities between 2-dimensional and 3-dimensional culture systems in triple negative breast cancer cell lines
Authors: Masako Muguruma, Saeko Teraoka, Kana Miyahara, Ai Ueda, Takahiko Kawate, Takashi Ishikawa
Journal: Cancer Research (2020)

Abstract [BACKGROUND] In vitro chemosensitivity tests are not always consistent to clinical results (Hutchinston L et al., Nat Rev Clin Oncol. 2011), partly because of lacking extracellular matrix-cell interactions in 2-dimensional (2D) cell culture system (Antoni D et al., Int J Mol Sci. 2015). Three-dimensional cell culture (3D) system maintains cells with a higher degree of structural complexity and homeostasis, analogous to tissues and organs compared with 2D cell culture system. Thus, 3D cell culture system will be expected for alteration of the animal experiment in chemosensitivity test (Bokhari M et al., J Anat. 2007). Cytotoxic agents are crucial for treating triple negative breast cancer (TNBC).[AIM] To clarify differences of drug sensitivities between 2D and 3D culture in TNBC cell lines, we compared IC50s for Cisplatin (CDDP), Docetaxel (DTX), Epirubicin (EPI) and Bromodomain inhibitor (JQ1). [METHODS] Thirteen TNBC cell lines were examined; HCC1599, HCC1937, HCC38, MDA-MB-468, HCC1806, HCC70, MDA-MB-436, MDA-MB-231, Hs578T, BT549, MDA-MB-453, BT20, and HCC1395. For 2D culture, cells were plated on general 96 well cell culture plate for 24 hours. For 3D culture, cells were plated on the PrimeSurface® 96 well plate (SUMITOMO BAKELITE) for 72 hours. Then, those were incubated in media including CDDP, DTX, EPI or JQ1 for 72 hours. The cell viability was quantified using CellTiter-Glo 2.0 and CellTiter-Glo 3D cell viability Assay (Promega), respectively. [RESULTS] For CDDP, IC50s were highly correlated between 2D and 3D culture (r=0.928) . The mean of IC50 value showed higher in 3D culture (27.67±8.40μM) than 2D culture (12.86 ± 17.23μM). For EPI, the correlation was r=0.593. The mean value showed higher in 3D culture (1.41±1.30μM) than 2D culture (0.62±0.72μM). For DTX and JQ1, the mean values were 1.78 ± 2.05nM and 4.31 ±4.72μM in 2D culture, respectively. However, IC50 failed to be obtained in several TNBC cell lines (HCC1937, HCC38, HCC1806, Hs578T and HCC1395 for JQ1 and MDA-MB-436, MDA-MB-453 and BT20 for DTX) in 3D culture. [CONCLUSION] IC50 value was higher in 3D culture than in 2D culture for CDDP and EPI. The correlation of IC50s between 2D and 3D depended on drugs with the highest in CDDP. We are under investigation on reasons why sensitivity tests for DTX and JQ1 failed in 3D culture system. Citation Format: Masako Muguruma, Saeko Teraoka, Kana Miyahara, Ai Ueda, Takahiko Kawate, Takashi Ishikawa. Differences of drug sensitivities between 2-dimensional and 3-dimensional culture systems in triple negative breast cancer cell lines [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 326.
Abstract 569: Rational combination approaches with CRM-1 inhibitor in ovarian cancer
Authors: Katelyn F. Handley, Cristian Rodriguez-Aguayo, Shaolin Ma, Mark S. Kim, Prahlad T. Ram, Anil K. Sood
Journal: Cancer Research (2020)

Abstract Background: After the frontline treatment, the majority of patients diagnosed with ovarian cancer at an advanced stage will develop recurrence (80%); thus, there is an urgent need for novel therapeutic approaches. Purpose: Selinexor is a CRM1 inhibitor, which is a selective inhibitor of nuclear export and has demonstrated antitumor effects in ovarian cancer. Here, we examined the efficacy of selinexor alone and in combination with PARP inhibitors in ovarian cancer. As Selinexor reduces the expression of DNA damage repair proteins, we hypothesized that this combination should reduce the number of DNA damage repair proteins, resulting in synergistic tumor cell death. Methods: Western blot was performed to assess baseline CRM1 expression in eleven ovarian cancer cell lines. We tested the efficacy of selinexor alone and in combination with olaparib in ovarian cancer cells (A2780ip2, OVCAR5). Combination Indices (CI) were calculated with CompuSyn and were considered synergistic when CI less than 1 for classic MTT arrays. We used the annexin V-FITC/PI assay to assess apoptosis as a result of selinexor and olaparib alone or in combination. Results: Baseline CRM1 expression was positive in eight of eleven ovarian cancer cell lines tested. The average IC50 in A2780ip2 for selinexor and olaparib was 0.09uM and 0.97uM, respectively. The median combination index was 0.81 in A2780ip2 and 0.92 in OVCAR5 cells. Flow cytometry demonstrated an additive effect of selinexor and olaparib in A2780ip2 cell apoptosis (7.34% and 7.93%, respectively, v. 17.86%). Conclusions: Selinexor demonstrates synergistic activity with olaparib, and this combination warrants further investigation. Citation Format: Katelyn F. Handley, Cristian Rodriguez-Aguayo, Shaolin Ma, Mark S. Kim, Prahlad T. Ram, Anil K. Sood. Rational combination approaches with CRM-1 inhibitor in ovarian cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 569.
Abstract LB-326: The role of HER3 in HER2-amplified cancers other than breast cancers
Authors: Avisek Majumder, Veronica Steri, Fernando Salangsang, Mark Moasser
Journal: Cancer Research (2020)

Abstract Introduction: Although recent studies showed that HER3 plays a key role in the pathophysiology of HER2-amplified breast cancers, its role in other cancers driven by HER2 amplification remains unknown. This study aimed to define the importance of HER3 signaling in other types of HER2-amplified cancer. Method: The expression and signaling activity of HER2, HER3, and downstream pathway proteins were studied in cell panels representing HER2-amplified cancers of the breast, bladder, colon and rectal, stomach, esophagus, lung, tongue, and endometrium along with controls lacking HER2 amplification. The time-dependent compensatory upregulation of HER3 in response to HER2 inhibitor therapy was assayed by western blotting and the apoptotic effects of HER2 inhibition were assayed by flow cytometry. The functional significance of HER3 in promoting tumorigenic growth in xenograft assays was determined in selected HER2-amplified cancer cell types by shRNA knockdown. Results: Many HER2-amplified cancers of the breast (HCC1569, HCC1954, HCC1419, UACC732, SUM190), bladder (CLS-439), stomach (N87, OE19), esophagus (TE4, KYSE410), lung (Calu3), and endometrium (USPC-ARC1, USPC-ARC2) showed HER3 activation, whereas HER2-nonamplified cancers of the same organs did not. With some exceptions, all HER2-amplified cancer cells undergo apoptosis when HER2 signaling is inhibited by lapatinib. Lapatinib induced apoptosis correlated with HER3 activation. Tumor growth was reduced upon HER3 knockdown in HER2-amplified cancers other than breast cancers, particularly cancers with constitutive HER3 phosphorylation. Significance: These results suggest that HER3 plays a functionally significant role in HER2 amplified cancers other than breast cancers, and may underlie resistance to HER2-targeting in these cancers. Combined HER2-HER3 targeting may be of value across the spectrum of different types of cancers. Citation Format: Avisek Majumder, Veronica Steri, Fernando Salangsang, Mark Moasser. The role of HER3 in HER2-amplified cancers other than breast cancers [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr LB-326.
Abstract LB-171: Assessing the impact of PIK3CA mutation on the three-dimensional organization of chromatin
Authors: Adam X. Miranda, Ben H. Park, Emily Hodges
Journal: Cancer Research (2020)

Abstract Background: Three-dimensional organization of chromatin within the nucleus is an important and dynamic regulator of cellular transcription. Changes in chromatin topology are implicated in processes like cell differentiation and cell fate decisions, but have been largely unstudied with regards to mutations and cancer cell transformation. Our goal is to assess the changes in chromatin topology that occur in response to a single oncogenic mutation and how these changes may influence cancer cell transformation. Methods: Using AAV-mediated homologous recombination, a E545K “hotspot” PIK3CA mutation was incorporated into MCF10A breast epithelial cells and conversely, corrected back to wild-type in MCF7 breast cancer cells that natively harbor a E545K PIK3CA mutation. To interrogate the chromatin topology of these cell lines and the unmodified versions we will use a technique called tethered chromosome conformation capture (TCC). TCC maps chromatin topology by combining the proximity ligation of interacting DNA segments with next generation sequencing to create a matrix of interacting DNA elements. We can analyze and overlay these matrices to look for significant differences in topologically associating domains (TADs). Results: Preliminary results comparing MCF7 parental cells and MCF7 cells with the PIK3CA exon 9 mutation corrected suggest rearrangement of TADs at many key cancer-associated genes. One of these rearrangements is the formation of a de novo TAD on chromosome 10 near PTEN, a tumor suppressor gene that acts antagonistically to PIK3CA. Rearrangement of chromatin topology at this locus could lead to downregulation of a negative actor on this pathway further stimulating downstream elements of the PIK3CA pathway. Conclusions: Oncogenic mutations can cause changes that can have a drastic impact on transcription. Rearrangement of chromatin topology is a key mechanism by which the transcriptional program of a cell can be modified. Our experiments reveal key sites of chromatin rearrangement caused by a single oncogenic mutation that may promote a cancer phenotype in our cells. We plan to investigate the degree to which the expression of PTEN is altered by chromosomal rearrangements as well as perform CRISPR-KO of the interacting loci to determine the transcriptional effect of removing the loop. These assays will also be conducted for other sites of chromatin rearrangement. Results from these experiments will reveal the influence oncogenic mutations may have on chromatin topology and expression. Citation Format: Adam X. Miranda, Ben H. Park, Emily Hodges. Assessing the impact of PIK3CA mutation on the three-dimensional organization of chromatin [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr LB-171.
Abstract LB-008: Patient derived organoids: Bringing the "patient in the lab" for pre-clinical and clinical development
Authors: Jasper Mullenders, Annemarie Buijs, Inge Van Maanen, Carol Piani, Soura Mardpour, Hans Clevers, Rob Vries, Sylvia Boj
Journal: Cancer Research (2020)

Abstract Pre-clinical disease models are essential for the development of novel therapies and help better understand the molecular processes. In recent years, a novel groundbreaking technology to generate patient specific in vitro cultures based on adult stem-cell organoids, has gained widespread interest for the development of new therapies and as a predictive diagnostic tool. ASC-organoids can be generated at high efficiency from both healthy and diseased tissue (resections as well as biopsies) including most carcinomas. These patient derived cultures can be expanded for prolonged periods of time while maintaining many properties of the tissue they were derived from. At HUB, we have created comprehensive ‘living biobanks' from tumors of different origin like colon, lung, breast, pancreas and ovary. These biobanks have been characterized at the genetic and transcriptional level. These analyses have shown that our ‘living biobanks' capture disease heterogeneity at the genetic and molecular level. Because organoids can be expanded long term, drug screening is feasible in these models. HUB has developed procedures for (high-throughput) compound screening in organoids including small molecules and biologics. In this setting, organoids have been used to identify novel targets, identify lead compounds and stratify potential responders based on their genetic or molecular profile. Recent advances in the field of immuno-oncology have revolutionized the treatment for cancer patients. Despite of the improvements and due to the complex and highly regulated nature of the immune system, treatment does not have a similar effect on all tumors. We have created a co-culture model of tumor derived organoids and immune cells. In these co-cultures, the cytotoxic effect of the immune cell on the tumor can be measured in a reproducible and quantitative manner. Currently we are expanding existing co-culture models to incorporate different immune cells and organoid tumor types. In addition, organoids can serve as a patient avatar in clinical development or diagnostics. In this setting, organoids could add a functional test for therapy response in a patient centered setting providing a unique tool for personalized medicine. Citation Format: Jasper Mullenders, Annemarie Buijs, Inge Van Maanen, Carol Piani, Soura Mardpour, Hans Clevers, Rob Vries, Sylvia Boj. Patient derived organoids: Bringing the "patient in the lab" for pre-clinical and clinical development [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr LB-008.
Abstract 330: <i>Reconstructed Bone</i> (r-<i>Bone</i>): A patient-derived 3D culture platform for prediction of clinical outcomes in multiple myeloma
Authors: Julia Kirshner, Amrita Kirshnan, Nitya Nathwani, Myo Htut, Michael Rosenzweig, Chatchada Karanes, Sahebi Firoozeh, Steven Rosen
Journal: Cancer Research (2020)

Abstract Multiple myeloma (MM), an incurable cancer of the bone marrow plasma cells, is a second most common hematological malignancy. While considerable progress has been made towards treatment of MM, the 5-year survival rate continues to hover around 50%. In this study, we aimed to evaluate the capacity of the Reconstructed Bone (r-Bone) model to predict clinical outcomes in patients with multiple myeloma. The r-Bone system incorporates cellular (hematopoietic and stromal) and extracellular (extracellular matrix and secretory factors) components, supports long-term survival (&amp;gt;30 days) and proliferation, and maintains cellular heterogeneity of the primary human bone marrow. The 1-to-1 reconstruction of the bone marrow architecture established by the r-Bone platform provides an ideal in vitro system to evaluate the efficacy of anti-myeloma agents to select those with highest probability of clinical success. Bone marrow aspirates collected from 21 patients with multiple myeloma were processed and set-up in r-Bone cultures. To establish the correct bone marrow architechture, cultures where grown for 5 days, after which the cells were treated according to the clinical regimen selected by the treating physician based on the orginal bone marrow aspirate. Subsequently, cells were isolated from the r-Bone and processed for flow cytometry. Plasma and non-plasma cell populations were evaluated post-treatment and the extent of cell death was correlated with the observed clinical response. r-Bone cultures correctly predicted the outcome of 19 out of 21 cases with 8 true positivies, 11 true negatives, and 2 false positives. This data demonstrate that the r-Bone system could be used for pipeline attrition management to select drug candidates with the highest probability of clinical success and can be developed into a prognostic tool for the selection of treatment regimen for patients with multiple myeloma. Citation Format: Julia Kirshner, Amrita Kirshnan, Nitya Nathwani, Myo Htut, Michael Rosenzweig, Chatchada Karanes, Sahebi Firoozeh, Steven Rosen. Reconstructed Bone (r-Bone): A patient-derived 3D culture platform for prediction of clinical outcomes in multiple myeloma [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 330.