tbuckley/cabot-search huggingface dataset:
Differential timing and patterns of recurrence among breast cancer subtypes
Authors: K. V. Scruggs, S. M. Pradhan, C. Mfalila, D. Moore, E. Burrows, A. Drobish, L. Carey
Journal: Journal of Clinical Oncology (2009)

1076 Background: At present, effects of heterogeneity among breast cancer subtypes on timing and patterns of relapse are not fully understood. We characterized timing and patterns of distant recurrence among subtypes in women followed from initial diagnosis of breast cancer. Methods: 345 pts with newly diagnosed predominantly stage II-III breast cancer were treated with multiagent neoadjuvant therapy and subtyped by IHC: LumA (ER/PR+, HER2-); LumB (-ER/PR+, HER2+); Basal (triple neg); HER2 (HER2+,ER/PR-). Site-specific patterns of distant metastasis (DM) were examined among pts with single site of first DM. Sites of relapse were bone, CNS, viscera, lymph node, and soft tissue. Time to progression (TTP) was from date of initial diagnosis. Results: 108 patients developed metastatic disease; 65 demonstrated a single site of first DM. Basal subtype was associated with greater CNS and visceral metastases and fewer bone metastases than other subtypes. LumA subtype was associated with fewer CNS and greater bone metastases than other subtypes. [See table]. Dichotomizing as Basal v. non-Basal, bone v. no bone and CNS v. no CNS revealed identical trends with increased significance (p=0.01–0.03). TTP trended toward Basals demonstrating earliest DM and LumA latest. Excluding pts with DM at diagnosis, TTP differed between Basals and non-Basals within viscera (p=0.002, n=14/21, median TTP=10/21); CNS (p=0.047, n=8/7, median TTP=11/27); and bone (p=0.002, n=8/31, median TTP=9/21). Conclusions: Subtypes exhibit distinct timing and patterns of relapse within this largely homogeneous cohort of pts with predominantly locally advanced breast cancer, despite modern multiagent neoadjuvant therapy. Specifically, Basal cancers exhibit earlier recurrence and greater involvement of sites more difficult to treat than non-Basals. Within individual sites TTP differences between Basal and non-Basal tumors persist and are even more pronounced, suggesting that tumor microenvironment does not appear to be driving these differences. [Table: see text] No significant financial relationships to disclose.
Donor Lymphocyte Infusion after Haploidentical Transplantation with Post-Transplant Cyclophosphamide
Authors: Clemence Roux, Samia Harbi, Raynier Devillier, Faezeh Legrand, Sabine Fürst, Angela Granata, Stefania Bramanti, Catherine Faucher, Jean ElCheikh, Djamel Mokart, Christian Chabannon, Boris Calmels, Pierre-Jean Weiller, Luca Castagna, Didier Blaise
Journal: Blood (2016)
Abstract 2408: Epigenomic characterization of MSC from myeloid malignancies
Authors: Manuel Rodríguez-Paredes, Stefanie Geyh, Mahshid Gazorpak, Julian Gutekunst, Felix Bormann, Rainer Haas, Thomas Schröder, Frank Lyko
Journal: Cancer Research (2017)

Abstract Ineffective hematopoiesis is a hallmark of myeloid malignancies such as Myelodysplastic Syndromes (MDS) or Acute Myeloid Leukemia (AML). Our previous research has shown that mesenchymal stromal cells (MSC), one of the main cellular regulatory components of the bone marrow niche and essential for the differentiation of new blood cells from Hematopoietic Stem Cells (HSC), are molecularly and functionally impaired in MDS and AML patients. More specifically, these cells display reduced proliferative and differentiation capacities, an increased cellular senescence, or the altered expression of key hematopoietic factors, defects that can provide an explanation for the cytopenia associated with these diseases. But most interestingly, we have also discovered that MDS- and AML-derived MSC present aberrant methylomes. Our data, based on 450k DNA methylation microarrays, show that these abnormalities are shared by the MSC from both malignancies and affect key transcription factors like TBX15, PITX2 or HOXB6, formerly linked to differentiation and development. This results can account for some of the defects observed in the disease-related MSC and represent an important paradigm for cancer-induced epigenetic changes in normal cells. Aiming to further explore the importance of this epigenetic deregulation, we performed RNAseq experiments using MSC from healthy donors as well as from MDS and AML patients. This approach not only suggests a profound impact of the epigenetic aberrancies on gene expression, but also allowed us to identify TGFβ as the soluble factor that, released by the malignant cells in the bone marrow, appears to trigger the above-mentioned defects in the MDS- and AML-derived MSC. Indeed, our results show that, when treated with TGFβ, healthy MSC undergo the deregulation of TBX15, PITX2 or HOXB6 and develop some of the observed aberrant phenotypes. Conversely, the treatment of MDS- and AML-derived MSC with a TGFβ antagonist like SD208 can abrogate these effects. Finally, our preliminary DNA methylation data reveal a very similar deregulation in the methylome of MSC from Multiple Myeloma (MM) patients, strongly suggesting that the same scenario could also be common to other hematological malignancies from the lymphoid branch. Citation Format: Manuel Rodríguez-Paredes, Stefanie Geyh, Mahshid Gazorpak, Julian Gutekunst, Felix Bormann, Rainer Haas, Thomas Schröder, Frank Lyko. Epigenomic characterization of MSC from myeloid malignancies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2408. doi:10.1158/1538-7445.AM2017-2408
Abstract 181: Discovery of novel targeted therapeutics for metastatic breast cancer
Authors: Cristina Del Valle, Eliud Hernández, Cornelis P. Vlaar, Luis A. Cubano, Suranganie Dharmawardhane, Linette Castillo-Pichardo
Journal: Cancer Research (2017)

Abstract Metastatic disease is the primary cause of breast cancer mortality, due to the lack of effective therapy. The Rho GTPase Rac is integral for the promotion of cancer cell migration/invasion, proliferation, and survival. Since metastatic breast cancers often overexpress or exhibit high Rac activity, inhibition of Rac is a viable strategy against metastatic cancer. Recently, we characterized EHop-016, a small molecule that inhibits Rac activity of metastatic breast cancer cells with an IC50 of 1 µM. EHop-016 is 10-100 times more active than previously available Rac inhibitors, and is the first compound shown to inhibit the activation of Rac by the oncogenic GEF Vav. EHop-016 inhibits the activity of the Rac downstream effector p21 activated kinase (PAK), lamellipodia extension, and cell migration of metastatic breast cancer cells. We also reported that EHop-016 at ≥ 25 mg/kg Body Weight (BW) significantly reduced tumor growth, metastasis, and angiogenesis in a mouse model. However, our recent pharmacokinetic study of EHop-016 in a mouse model demonstrated that the bioavailability of Ehop-016 needs to be improved for further pharmacological development. Therefore our hypothesis is that improvement of the EHop-016 structure will provide probes with increased potency against Rac and, therefore, increased bioavailability. Herein we have tested several Ehop-016 derivatives for their effects on breast cancer cell viability and Rac activation. Using MTT assays we found that the Ehop-016 derivatives, HV-107 and HV-118, significantly inhibit the viability of metastatic breast cancer cell lines MDA-MB-231 and MDA-MB-435. The effects of HV-107 and HV-118 on the inhibition of Rac activation were tested by ELISA-based Rac activity assays and pulldown assays. Results show that at 250nM, HV-107 inhibits Rac activation by 55%, whereas HV-118 has a similar effect at 100nM in MDA-MB-231 and MDA-MB-435 cells. Taken together, our findings suggest HV-107 and HV-118 as promising Ehop-016 derivatives with potential as anti-metastatic agents, which should be further characterized. This study was supported by awards from the Susan Komen for the Cure, NIH/NIMHHD U54MD008149, and the Puerto Rico Science and Technology Trust to SD; NIH/NCRR R25GM061838 to UPR MSC; NIH/NIMHHD RCMI 8G12MD007583RCMI, Title V PPOHA 031M10505 and Title V Cooperative P031S130068 from U.S. Department of Education to UCC; and PRINBRE (NIH/NIGMS P20GM103475-13) Pilot Project to LCP. Citation Format: Cristina Del Valle, Eliud Hernández, Cornelis P. Vlaar, Luis A. Cubano, Suranganie Dharmawardhane, Linette Castillo-Pichardo. Discovery of novel targeted therapeutics for metastatic breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 181. doi:10.1158/1538-7445.AM2017-181
Abstract 1282: Analysis of missense variants in <i>BRCA1</i> BRCT domains
Authors: Giuliano Di Pietro, Vanessa Camara Fernandes, Kwabena Amankwah, Cara Shields, Volha A. Golubeva, Carly Harro, Marcelo Alex Carvalho, Alvaro N. Monteiro
Journal: Cancer Research (2017)

Abstract Currently, only ~¼ (133/600) of documented single nucleotide variation leading to missense changes in the BRCA1 gene have been characterized as pathogenic or non-pathogenic (IARC Classes 4 &amp; 5 and 1 &amp; 2, respectively) posing a challenge for carriers of these variants. A detailed understanding of structure-function relationships is critical for the assessment of these variants in the interpretation of data from functional assay and for the development of functional impact predictors. Thus, we have systematically probed the C-terminus of BRCA1 including the N-terminal border of the BRCT domains (M1650, S1651), the BRCT linker region (G1738, D1739, V1740, G1743, H1746, G1748, P1749, R1753, and D1757), and the alpha 1 and alpha’1 helices in BRCT[N] and [C], respectively. We assessed the functional impact of 47 missense variants using a validated transcriptional assay by a protein fusion of the GAL4 DNA-binding domain to BRCA1 C-terminus (aa 1,396-1,863) in HEK 293FT cells. Analysis of functional data redefined the BRCT border (previously thought to be at S1651) at residue M1650. Overall, mutations in the BRCT linker had severe impact on the function. Mutations in the alpha1 and alpha’1 helices also tended to display impaired function despite the lack of functional impact of 16 out of the 17 variants previously analyzed. In summary, our study provides increased granularity in our understanding of BRCA1 regions less tolerant to changes and therefore more likely to contain pathogenic variants. This knowledge will be critical for the assignment of different prior probabilities of pathogenicity given the variant location, improving risk assessment and clinical management of carriers of BRCA1 missense alleles Note: This abstract was not presented at the meeting. Citation Format: Giuliano Di Pietro, Vanessa Camara Fernandes, Kwabena Amankwah, Cara Shields, Volha A. Golubeva, Carly Harro, Marcelo Alex Carvalho, Alvaro N. Monteiro. Analysis of missense variants in BRCA1 BRCT domains [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1282. doi:10.1158/1538-7445.AM2017-1282
Interplay of physiology, social, familial and behavioural adaptation in the long-term outcome of ARDS
Authors: Theodore J Iwashyna, Timothy S Walsh
Journal: Thorax (2017)

Discharge from a hospital after the intensive care unit (ICU) is challenging. Please do not mistake us—we agree many patients are happy to go home. In fact, most critical care survivors are desperate to leave the hospital, typically after a prolonged frightening hospital stay lasting weeks or longer. Unfortunately, most patients have not returned to their preillness physical status when they go home, and many face new cognitive or psychological disabilities that may just be emerging. Yet, constrained budgets, limited acute hospital beds and wide variation in formal rehabilitation mean many patients enter posthospital survivorship without coordinated support. No matter which health system cares for them, many survivors experience an unplanned rehospitalisation within a few months.1–4

Hospital discharge prior to full recovery may be inevitable, as recovery after many illnesses simply takes a really long time (or might never be complete). Data from the Women’s Health and Aging Study (all aged 65+) noted 33% of patients hospitalised for any reason had activity of daily living (ADL) recovery during the 6 months after hospitalisation, and another 14% in the 6 to 12-month interval.5 (See figure 1) A more acutely ill, younger cohort of critical care patients who required at least 7 days of mechanical ventilation experienced improvement in mean function over the first 6 months, but limited change thereafter.6 However, close inspection of these data reveals very wide variation between individuals between 6 and 12 months that are not apparent in population mean estimates. In light of these and related data, our community is rightly expending energy trying to treat this ‘post-intensive care syndrome (PICS),’7 or at least improve the health problems that our patients describe months or years after we discharge them from our ICUs.



Figure 1 
Duration of recovery of function. (Left) Women’s Health and Aging …
Abstract 5430: GAPDH loss in a tumorigenic human glioblastoma cell line
Authors: Zachary Gaertner, Yi Lu, Jinsuh Kim, Gayatry Mohapatra, Ankit Mehta, Sanjani Lakka, Herbert Engelhard
Journal: Cancer Research (2017)

Abstract Background: Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) is a ubiquitous, multifunctional 37 kDa enzyme best known for catalyzing the sixth step in glycolysis. GAPDH expression is so consistent that it has been granted “housekeeping” status, and is used as a standard (along with β-actin) for normalizing Western blots. While increased GAPDH expression has been described in hypoxia, diabetes, and some cancers, decreased expression is rare. Here we describe a new human glioblastoma cell line that exhibits GAPDH loss, while maintaining a high degree of malignancy. Methods: Primary cultures of human glioblastoma cells were initiated and maintained in DMEM with 10% FBS. This particular cell line (designated E297) grew readily, and was passaged more than 40 times. E297 cells were confirmed to be negative for HIV, HTLV, hepatitis B and C, CMV, and mycoplasma contamination. Cells in exponential growth were stained for routine markers, and studied by DNA flow cytometry. GAPDH expression was studied by Western blot analysis using polyclonal rabbit anti-human GAPDH IgG (Abcam, Rosemont, IL), with HeLa, U138, U87 and U251 cells (as well as β-actin staining) as positive controls. For intracranial implantation into Wistar-Furth rats (male, 10-11 weeks), cells were suspended at 20 x 106 cells/ml. Using aseptic technique, rats were anesthetized, and placed into a stereotactic frame. A burr hole was drilled 3 mm right of the bregma and 25 µl of suspension injected (5 mm depth) over 10 min. by Hamilton syringe. Rats were studied by MRI and euthanized when symptomatic. Results: E297 cells have glial/epithelioid morphology, with a doubling time of 24 + 2 hours in logarithmic growth phase, with a single DNA subpopulation with 28% S phase. They stain positively for GFAP, vimentin, bFGF, c-myc and p53, but fail to express GAPDH. 10/10 animals implanted intracerebrally developed tumors, becoming symptomatic and requiring sacrifice at 25 days (mean). Loss of GAPDH expression was confirmed by Western blot analysis. Conclusions: The E297 human glioblastoma cell line is highly aggressive and proliferates rapidly. It is tumorigenic in nonimmunosuppressed rats but lacks GAPDH protein. We conclude that GAPDH expression is not essential for glioblastoma cell proliferation under routine culture conditions, and care needs to be taken when using GAPDH as a normalization standard for Western blots of cancer cells. Citation Format: Zachary Gaertner, Yi Lu, Jinsuh Kim, Gayatry Mohapatra, Ankit Mehta, Sanjani Lakka, Herbert Engelhard. GAPDH loss in a tumorigenic human glioblastoma cell line [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5430. doi:10.1158/1538-7445.AM2017-5430
Abstract 2486: Tumor hypoxia induces DNA repair vulnerabilities through contextual loss of heterozygosity
Authors: Osman Mahamud, Melvin Chua, Winnie Lo, Gaetano Zafarana, Robert Bristow
Journal: Cancer Research (2017)

Abstract Introduction: Intratumoural hypoxia leads to decreased expression in DNA damage response (DDR) and repair pathways. Given the ‘two-hit’ model for loss of gene function, we hypothesize that hypoxia-mediated down-regulation of gene expression and function, coupled with an already inactive allele contributes to an exploitable contextual ‘loss-of- heterozygosity’ phenotype. Method: To interrogate this relationship, isogenic DLD-1 cells heterozygous and homozygous null for BRCA2, were placed under normoxic (21%) or hypoxic (0.2%) conditions for 72 hours. Hypoxia-mediated changes in DDR response and DNA repair were evaluated by cell proliferation, cell cycle analysis, western blots, qPCR, immunofluorescence, clonogenic assays and functional repair assays. Results: No differences in proliferation and cell survival were observed between oxic and hypoxic cells (72 hours - 0.2% O2). Under chronic hypoxic conditions, confirmed by the up-regulation of VEGF and HIF1a, mRNA and protein expression of key homologous recombination (HR) genes (BRCA1, BRCA2, RAD51) were down-regulated. Functionally, BRCA2-/- null cells proved unable to recruit Rad51 foci and were profoundly sensitivity to PARP inhibition. Conversely, heterozygote BRCA2+/- cells retained the ability to recruit Rad51 foci under both oxic and hypoxic conditions. However, exposure to chronic hypoxia resulted in a reduction of foci formation. Chronically hypoxic BRCA2+/- cells exhibited a 30-40% increase in sensitivity to PARP inhibition compared to their oxic counterparts. Preliminary data shows a similar synthetically lethal relationship in genetic (BRCA2-/- ) and tumor microenvironment induced (BRCA2+/-) HR deficient cells, when challenged with DNA damage response (DDR) kinase inhibitors ATRi and DNAPKi. Conclusions: Herein, we demonstrate a novel mechanism of contextual ‘loss-of heterozygosity’, which marries the tumour microenvironment and innate genetic alterations. The resultant increased sensitivity to DDR kinase inhibitors and PARPi highlights the therapeutic significance of this phenomenon. Citation Format: Osman Mahamud, Melvin Chua, Winnie Lo, Gaetano Zafarana, Robert Bristow. Tumor hypoxia induces DNA repair vulnerabilities through contextual loss of heterozygosity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2486. doi:10.1158/1538-7445.AM2017-2486
Abstract 5611: Use of ecto-domain vimentin to target brain cancers
Authors: Ivan Babic, Rajesh Mukthavaram, Pengfei Jiang, Eric Glassy, Natsuko Nomura, Sandeep Pingle, Mark C. Glassy, Santosh Kesari
Journal: Cancer Research (2017)

Abstract Pritumumab is a natural human IgG1 kappa antibody derived from a regional draining lymph node of a patient with cervical carcinoma. The recognized antigen is an altered form of vimentin, called ecto-domain vimentin (EDV), that is expressed on the cell surface of epithelial tumor cells. For brain cancers, immunohistological analysis showed the binding of pritumumab to EDV to be restricted to tumor cells and not normal cells and tissues suggesting EDV may be a useful biomarker. A recombinant version of the mAb was made using the GPEx® system in CHO cells that showed comparable binding activity by flow cytometry, immunohistochemical analysis, Western blot analysis, and Antibody-Dependent Cell-Mediated Cytotoxicity (ADCC; EC50 of 39.6ng/ml) activity. Further studies include establishing xenograft models with both SCID and athymic nude mice in which pritumumab was effective in preventing tumor growth of both brain cancer stem cells as well as pancreatic cancer in nude mice but not in SCID mice suggesting an active immune response is necessary for optimal treatment. Analysis of a blood brain barrier model suggests pritumumab shows minimal distribution in normal brain tissues and significant binding in tumor areas of brain tissues indicating the mAb crosses the tumor brain barrier. Overall, these data together suggest that EDV is a suitable target and biomarker for brain cancers. Citation Format: Ivan Babic, Rajesh Mukthavaram, Pengfei Jiang, Eric Glassy, Natsuko Nomura, Sandeep Pingle, Mark C. Glassy, Santosh Kesari. Use of ecto-domain vimentin to target brain cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5611. doi:10.1158/1538-7445.AM2017-5611