bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 616: Blood-based molecular landscapes of resistance to EGFR blockade in colorectal cancer patients
Authors: Siravegna Giulia , Mussolin Benedetta , Buscarino Michela , Corti Giorgio , Cassingena Andrea , Crisafulli Giovanni , Corcoran Ryan B. , Ponzetti Agostino , Budillon Alfredo , Racca Patrizia , Marsoni Silvia , Di Nicolantonio Federica , Loupakis Fotios , Siena Salvatore , Sartore Bianchi Andrea , Bardelli Alberto 
Published: August 2015

Abstract
The molecular landscape of colorectal cancers (CRC) is presently assessed by genotyping neoplastic tissue obtained through surgical or bioptic procedures. We evaluated whether blood-based molecular profiles could be used to perform diagnostic determinations and monitor resistance to therapy in colorectal cancer patients. We find that RAS pathway mutations, which are commonly evaluated prior to administration of anti-EGFR antibodies, can be ascertained directly in the blood. Sequencing of circulating DNA identified genomic alterations in KRAS, NRAS, MET, ERBB2, FLT3, and MEK1 in patients with primary or acquired resistance to cetuximab or panitumumab. Secondary resistance to EGFR blockade is frequently accompanied by emergence of mutant RAS clones, which can be tracked in blood. We find that upon withdrawal of anti-EGFR antibodies, KRAS alleles decline in circulating DNA indicating that clonal evolution continues beyond clinical progression. Functional analysis of CRC cell populations, which had acquired resistance to cetuximab, revealed that KRAS mutant clones can decay when EGFR blockade is suspended. These results establish proof of principle that genotyping colorectal cancers using circulating DNA can inform therapeutic decisions, identify mechanisms of drug resistance and provide insights for further lines of therapy.
Citation Format: Giulia Siravegna, Benedetta Mussolin, Michela Buscarino, Giorgio Corti, Andrea Cassingena, Giovanni Crisafulli, Ryan B. Corcoran, Agostino Ponzetti, Alfredo Budillon, Patrizia Racca, Silvia Marsoni, Federica Di Nicolantonio, Fotios Loupakis, Salvatore Siena, Andrea Sartore Bianchi, Alberto Bardelli. Blood-based molecular landscapes of resistance to EGFR blockade in colorectal cancer patients. [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 616. doi:10.1158/1538-7445.AM2015-616
Abstract 620: Monitoring leptomeningeal metastasis treatment response using tumor cell free DNA from cerebral spinal fluid
Authors: Hayden Gephart Melanie 
Published: August 2015

Abstract
Background:
Cerebral Spinal Fluid (CSF) from brain tumor patients contains tumor cell free DNA (cfDNA), which may provide a non-invasive and routinely accessible method to obtain tumor genomic information. This “liquid biopsy” method would prove considerably less morbid compared to an open removal of tumor tissue from the brain. The opportunities of cfDNA in CSF have not been systematically studied in CSF, particularly in relation to how metastatic brain tumor cfDNA may respond to intrathecal therapy.
Methods:
A patient who presented with elevated intracranial pressure from metastatic melanoma to the leptomeninges underwent serial therapuetic lumbar punctures, approximately every two weeks over a period of three months. CSF was obtained through an informed consent, IRB approved protocol. The primary melanoma tumor was known to have a BRAF mutation 1799T&gt;A (V600E). cfDNA was isolated from the CSF, and sequenced to confirm the presence of this same tumor-specific BRAF mutation. Droplet Digital PCR (ddPCR) quantified the mutant DNA amount and fraction in CSF. These results were compared to the clinical cytology results from the same sample.
Results:
Six time points were collected in 61 days. Tumor cfDNA was detectable in the first five time points. Mutant DNA fraction decreased from 53% to almost zero. The total amount of mutant DNA decreased from 220 copies per ml of CSF to 4 copies per ml of CSF. This result was concordant with the patient's clinical response to therapy.
Conclusion:
Tumor cfDNA was found in CSF from a cancer patient with leptomeningeal metastases. Both the mutant fraction and total copies of mutant DNA corresponded with the patient's response to systemic therapy. This non-invasive method may provide a powerful tool for identifying and monitoring the genetic fingerprint of brain metastases.
Citation Format: Melanie Hayden Gephart. Monitoring leptomeningeal metastasis treatment response using tumor cell free DNA from cerebral spinal fluid. [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 620. doi:10.1158/1538-7445.AM2015-620
Abstract 621: Serum circulating DNA and nucleosomes increase in response to neoadjuvant chemoradiation and surgical resection for pancreatic cancer
Authors: Naqvi Ibtehaj A. , Gunaratne Ruwan , Pisetsky David , White Rebekah 
Published: August 2015

Abstract
Introduction: Pancreatic cancer (PC) is the deadliest of the major cancers, and response rates to standard therapies are low. Tumor cells release circulating extracellular DNA (exDNA) and nucleosomes (short segments of DNA in complex with histone proteins). These factors have been evaluated as markers of disease burden for prognosis and response to therapy. We hypothesized that exDNA and nucleosome (NUC) levels would correlate with each other and decrease in patients (pts) undergoing neoadjuvant chemoradiation (CRT) and surgical resection for localized PC.
Methods: Blood was collected from pts with radiographically localized PC before and 4-6 weeks after CRT (N = 8), intraop and 1 week postop in pts with resectable tumors (N = 4), as well as from pts with advanced disease (N = 3) and normal volunteers (N = 6) to create a spectrum of data for disease burden. ExDNA and NUC were isolated from serum samples and quantified using a fluorescent DNA-specific stain (Picogreen) and ELISA, respectively.
Results: Normal volunteers had the lowest exDNA/NUC levels while patients with advanced disease had the highest levels. Overall, exDNA/NUC levels increased ∼3-fold in patients who underwent CRT to levels similar to those of patients with advanced disease, regardless of whether they had radiographic partial response (N = 4), stable disease (N = 4), or progressive disease (N = 2) on restaging nor whether they were subsequently able to undergo resection. ExDNA and NUC levels correlated well except in pts who underwent resection, when exDNA but not NUC levels peaked intraop at &gt;5-fold post-CRT levels. Both exDNA and NUC levels remained elevated at least one week postop.
Discussion: Contrary to our hypothesis, exDNA and NUC levels increased following neoadjuvant CRT regardless of radiographic response to therapy. ExDNA and NUC levels correlated well except during the intraop period, when exDNA but not NUC levels were dramatically elevated. These data suggest that exDNA and NUC are not simply markers of disease burden. We postulate that exDNA and NUC are released by tumor cells and also by host immune cells in response to CRT and surgical trauma. In order to put this into a broader context, we are expanding our dataset to include more patients and time points. We are evaluating other specific forms of exDNA as well as DNA-associated proteins as markers of cell death that may be more useful for monitoring response to therapy.
Citation Format: Ibtehaj A. Naqvi, Ruwan Gunaratne, David Pisetsky, Rebekah White. Serum circulating DNA and nucleosomes increase in response to neoadjuvant chemoradiation and surgical resection for pancreatic cancer. [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 621. doi:10.1158/1538-7445.AM2015-621
Abstract 634: Novel antibody-drug conjugates targeting Axl show anti-tumor activity in solid cancer xenograft models
Authors: Breij Esther C.W. , Verploegen Sandra , Lingnau Andreas , van den Brink Edward N. , Janmaat Maarten , Houtkamp Mischa , Bleeker Wim K. , Satijn David , Parren Paul W.H.I. 
Published: August 2015

Abstract
Axl is a receptor tyrosine kinase of the TAM family, which is structurally characterized by the presence of two extracellular immunoglobulin-like domains and two fibronectin type III domains, a single-pass transmembrane region and an intracellular tyrosine kinase domain. Axl is aberrantly expressed and activated in both solid and hematological malignancies and has been associated with poor clinical prognosis in a number of cancers, including non-small cell lung cancer, breast cancer, pancreatic cancer and acute myeloid lymphoma. Functionally, Axl has been implicated in multiple pathological processes, such as tumor cell motility, adherence and migration, epithelial-to-mesenchymal transition, metastasis, angiogenesis and resistance to tyrosine kinase inhibitors.
With the aim to target Axl expressing cancers, a panel of Axl-specific antibody-drug conjugates (ADC) was generated. First, high affinity human Axl antibodies were generated in HuMAb mice. Binding studies using Axl mutants, in which specific human Axl domains had been replaced with their murine analogs, demonstrated that the Axl antibody panel consisted of antibodies against different Axl extracellular domains. Second, the Axl antibodies were conjugated with the microtubule disrupting agent monomethyl auristatin E (MMAE) using the protease cleavable valine citrulline linker.
Axl ADCs showed cytotoxic activity in vitro, which was dependent on target expression and on conjugation with cytotoxic payload. The anti-tumor activity of Axl ADCs was confirmed in vivo. Axl ADCs induced tumor regression in cell line derived xenograft models for lung cancer and epidermoid carcinoma. Anti-tumor activity was especially efficient in the lung cancer xenograft model, in which inhibition of tumor growth was observed upon treatment with a single dose of 0.5 mg/kg Axl ADC. In the same model, 1 mg/kg Axl ADC was sufficient to induce complete tumor regression. Importantly, Axl ADCs also showed efficient anti-tumor activity in patient-derived xenograft (PDX) models that showed heterogeneous target expression.
In summary, Axl is a novel target for antibody-mediated delivery of cytotoxic agents into tumor cells. The promising results obtained in preclinical tumor models support further development of Axl-specific ADCs.
Citation Format: Esther C.W. Breij, Sandra Verploegen, Andreas Lingnau, Edward N. van den Brink, Maarten Janmaat, Mischa Houtkamp, Wim K. Bleeker, David Satijn, Paul W.H.I. Parren. Novel antibody-drug conjugates targeting Axl show anti-tumor activity in solid cancer xenograft models. [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 634. doi:10.1158/1538-7445.AM2015-634
Abstract 639: Site specific conjugation of ARX-788, an antibody drug conjugate (ADC) targeting HER2, generates a potent and stable targeted therapeutic for multiple cancers
Authors: Humphreys Robin C. , Kirtely Jessica , Hewit Amha , Biroc Sandra , Knudsen Nick , Skidmore Lillian , Wahl Alan 
Published: August 2015

Abstract
Creation of ADCs by conjugating drug linkers and toxin payloads to available native lysines or cysteines generates ADCs with highly variable drug to antibody loading and linker stability profiles. Variable drug loading, amino acid position, conjugation chemistry and linker design affect the pharmacokinetic characteristics, potency and toxicity of the ADC. We describe here the synthesis and pharmacology of an ADC comprising a site-specifically conjugated dolastatin analog to an antibody targeting the EGF family receptor, HER2. To specify the site of conjugation and drug loading, a non-natural amino acid, para acetyl phenylalanine (pAcF), was incorporated at defined sites within the antibody primary sequence. This non-natural amino acid provides a linkable platform for covalent conjugation of a diverse array of payloads through a stable oxime bond. The dolastatin analog, MMAF, was coupled via a non-cleavable linker to the HER2 antibody at two specific sites to generate the ADC; ARX-788. In vitro cytotoxicity assays of ARX-788 generated picomolar IC50's across a spectrum of HER2 + cell lines from breast, ovarian, lung and gastric cancer. Multiple in vivo murine xenograft studies demonstrated a potent increase in anti-tumor activity when compared to T-DM1. A single injection of ARX-788 in established xenograft models of HER2 positive ovarian, gastric and breast cancer cell lines (SKOV3, BT474, N-87, and HCC1954) induced rapid regression in all models. ARX-788 induced regression in a Herceptin-resistant derived breast xenograft (JIMT-1) and was significantly more effective than T-DM1 at equivalent doses. Pharmacokinetic evaluation of ARX-788 in rodent and non-human primates (NHP) revealed long term stability of 12 and 8 days respectively. Importantly, the conjugated form of ARX-788 remained intact over the course of the 3 week study in NHP. Precise payload stability and effective half-life of ARX-788 due to site-specific conjugation provides an improved therapeutic window for this HER2-targeting ADC. ARX-788 is currently completing non-human safety and PK studies in anticipation of clinical trial evaluation in 2015.
Citation Format: Robin C. Humphreys, Jessica Kirtely, Amha Hewit, Sandra Biroc, Nick Knudsen, Lillian Skidmore, Alan Wahl. Site specific conjugation of ARX-788, an antibody drug conjugate (ADC) targeting HER2, generates a potent and stable targeted therapeutic for multiple cancers. [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 639. doi:10.1158/1538-7445.AM2015-639
Abstract 646: Structurally guided development of meditope-based antibody-drug conjugates
Authors: Matho Michael M. , Gardiner Elisabeth M. , Dumitru Calin D. 
Published: August 2015

Abstract
Meditopes are cyclic peptides that bind the Fab fragment noncovalently, in a novel and unique site, outside the paratope. This property can be utilized to harness cytotoxic payloads to an antibody in a site-specific and consistent manner. One of the originally described peptides, named cQFD, presents a moderate affinity for the humanized antibody cetuximab (KD = 0.43 uM). The binding site involves residues from the heavy as well as the light chain of the antibody, and from both sides of the variable-to-constant hinge of the Fab domain, with a predominance for residues of the variable region. A similar affinity of cQFD to trastuzumab was achieved by mutating thirteen specific residues of the antibody, all located in the variable (Fv) region of the Fab domain; Nine of which are located in the light chain (LC: V9, I10, R39, T40, N41, G42, S43, R45, I83, D85, A100), two in the heavy chain (HC: S40 and I89). We refer to those mutations as to the “meditope enabling”. Via a combined approach, we (i) looked into peptide modifications to increase meditope's affinity for the antibody, and (ii) evaluated the transferability of this approach onto a panel of human antibodies of therapeutic relevance. Based on X-ray crystallography analysis, antibody modeling—in the case of antibodies for which no structure is available—and guided docking, we suggested a number of modifications (point mutations and/or peptide extension) that were subsequently tested via surface plasmon resonance. The top meditope leads were conjugated to MMAE and DM1 and their binding was reassessed to a number of humanized/IgG1 antibodies-confirming that payload conjugation does not interfere with meditope binding and also that meditope enabling and binding does not interfere with antigen binding. Finally, the complexes between antibodies and meditope-drug conjugates were tested in vitro in a panel of tumor cell lines, to measure and rank the efficacy of those leads in our ADC pipeline for further development as novel oncology therapeutics.
Citation Format: Michael M. Matho, Elisabeth M. Gardiner, Calin D. Dumitru. Structurally guided development of meditope-based antibody-drug conjugates. [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 646. doi:10.1158/1538-7445.AM2015-646
Abstract 648: Optimization of a PEGylated glucuronide-auristatin linker for antibody-drug conjugates
Authors: Burke Patrick J. , Hamilton Joseph Z. , Jeffrey Scott C. , Hunter Joshua H. , Doronina Svetlana O. , Okeley Nicole M. , Anderson Martha E. , Senter Peter D. , Lyon Robert P. 
Published: August 2015

Abstract
The clinical success of antibody-drug conjugates (ADCs) brentuximab vedotin and ado-trastuzumab emtansine has led to an increased effort to identify new antibody payloads and develop improved linker technologies. Most antibody payloads impart significant hydrophobicity to the ADC resulting in accelerated plasma clearance and diminished in vivo activity, particularly for conjugates with high drug to antibody ratios (DAR). Consequently, drug-linkers have been designed to minimize or mask hydrophobicity, enabling a higher DAR and improved pharmacokinetic properties, translating to enhanced in vivo potency. We recently reported on the incorporation of a discrete PEG polymer as a side chain in the β-glucuronide-monomethylauristatin E (MMAE) linker to provide homogeneous DAR 8 conjugates with decreased plasma clearance and increased antitumor activity in xenograft models relative to a non-PEGylated control. The PEG-glucuronide-MMAE lead has now been optimized by minimizing the size of the PEG side chain and incorporating a self-stabilizing maleimide to prevent payload de-conjugation in vivo. Multiple PEG-glucuronide-MMAE linker constructs were prepared with PEG size varying from 0 to 24 ethylene oxide units, and uniform DAR 8 ADCs were evaluated. PEG size had small but variable effects in vitro, with diminished activity observed in some cell lines. In contrast, a clear relationship was observed between PEG length and plasma pharmacokinetics. Longer PEG chains resulted in slower clearance, with a ‘threshold’ length beyond which clearance was not impacted. Conjugates bearing PEG of sufficient length to minimize ADC plasma clearance provided a wider therapeutic window relative to conjugates bearing shorter PEGs. Thus, sufficient masking of drug hydrophobicity is a viable strategy to provide uniform DAR 8 ADCs that preserve ADC pharmacokinetics and increase potency through higher drug loading.
Citation Format: Patrick J. Burke, Joseph Z. Hamilton, Scott C. Jeffrey, Joshua H. Hunter, Svetlana O. Doronina, Nicole M. Okeley, Martha E. Anderson, Peter D. Senter, Robert P. Lyon. Optimization of a PEGylated glucuronide-auristatin linker for antibody-drug conjugates. [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 648. doi:10.1158/1538-7445.AM2015-648
Abstract 652: Antibody-drug conjugates (ADCs) of indolino-benzodiazepine DNA-alkylating agents
Authors: Miller Michael L. , Shizuka Manami , Fishkin Nathan , Reid Emily , Archer Katie , Maloney Erin , Bai Chen , Ab Olga , Yoder Nick C. , Wu Rui , Hong Erica , Bogalhas Megan , Wilhelm Alan , Whiteman Kathleen , Chari Ravi 
Published: August 2015

Abstract
There are over thirty ADCs in the clinic today, reflecting the interest in ADCs for the treatment of cancer. Most of these ADCs utilize a tubulin-interacting small molecule as their cytotoxic payload. In order to continue to extend the utility of ADCs to more types of cancers, there is a strong interest in developing cytotoxic payloads with other mechanisms of action. Previously we have described the development of a class of indolino-benzodiazepine dimers (IGNs) with high potency and specificity. ADCs made with a mono-imine containing IGN, which only alkylate DNA, were found to display improved tolerability, along with the absence of delayed toxicity, compared to their DNA-cross-linking di-imine counterparts.
Additional structure-activity relationship studies with mono-imine containing IGNs have resulted in two promising new leads, IGN-D1 and IGN-P1, which are conjugated to an antibody via either a disulfide or peptide linker, respectively. ADCs of IGN-D1 and IGN-P1 were prepared for evaluation using a folate receptor α (FRα)-binding antibody, anti-FRα, and EGFR-binding antibody, anti-EGFR.
Anti-FRα-IGN-D1 and anti-FRα-IGN-P1 were found to be highly potent against the FRα-expressing KB cell line (IC50 values of 8 pM and 4 pM, respectively) and also demonstrated strong activity against nearby target-negative cancer cells. The addition of excess unconjugated antibody blocked the cytotoxic effect of these conjugates, thus demonstrating that their activity is antigen specific. In addition, both anti-FRα-IGN conjugates were found to be highly potent (IC50 values of 100 pM and 30 pM, respectively) against the breast ductal carcinoma cell line, T47D, despite only a moderate level of antigen expression on the target cells. Similarly, anti-EGFR-IGN-D1 and anti-EGFR-IGN-P1 were found to have IC50 values in the picomolar range against a panel of EGFR-expressing cell lines. In vivo, anti-FRα-IGN-D1 and anti-FRα-IGN-P1 were found to be effective against NCI-H2110 non-small cell lung cancer xenografts, with anti-tumor activity observed at single doses as low as 3 μg/kg (payload dose, equivalent to 0.15 mg/kg Ab dose).
These data support evaluation of new ADC therapies with these two new IGNs for solid tumor indications as well as tumors with low antigen expression.
Citation Format: Michael L. Miller, Manami Shizuka, Nathan Fishkin, Emily Reid, Katie Archer, Erin Maloney, Chen Bai, Olga Ab, Nick C. Yoder, Rui Wu, Erica Hong, Megan Bogalhas, Alan Wilhelm, Kathleen Whiteman, Ravi Chari. Antibody-drug conjugates (ADCs) of indolino-benzodiazepine DNA-alkylating agents. [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 652. doi:10.1158/1538-7445.AM2015-652