Publications by authors named "Martín Whittle"

41 Publications

Noninvasive prenatal paternity determination using microhaplotypes: a pilot study.

BMC Med Genomics 2020 10 23;13(1):157. Epub 2020 Oct 23.

Department of Clinical Toxicological Analyzes, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil.

Background: The use of noninvasive techniques to determine paternity prenatally is increasing because it reduces the risks associated with invasive procedures. Current methods, based on SNPs, use the analysis of at least 148 markers, on average.

Methods: To reduce the number of regions, we used microhaplotypes, which are chromosomal segments smaller than 200 bp containing two or more SNPs. Our method employs massively parallel sequencing and analysis of microhaplotypes as genetic markers. We tested 20 microhaplotypes and ascertained that 19 obey Hardy-Weinberg equilibrium and are independent, and data from the 1000 Genomes Project were used for population frequency and simulations.

Results: We performed simulations of true and false paternity, using the 1000 Genomes Project data, to confirm if the microhaplotypes could be used as genetic markers. We observed that at least 13 microhaplotypes should be used to decrease the chances of false positives. Then, we applied the method in 31 trios, and it was able to correctly assign the fatherhood in cases where the alleged father was the real father, excluding the inconclusive results. We also cross evaluated the mother-plasma duos with the alleged fathers for false inclusions within our data, and we observed that the use of at least 15 microhaplotypes in real data also decreases the false inclusions.

Conclusions: In this work, we demonstrated that microhaplotypes can be used to determine prenatal paternity by using only 15 regions and with admixtures of DNA.
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http://dx.doi.org/10.1186/s12920-020-00806-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7584091PMC
October 2020

Fibroblasts in Pancreatic Ductal Adenocarcinoma: Biological Mechanisms and Therapeutic Targets.

Gastroenterology 2019 05 2;156(7):2085-2096. Epub 2019 Feb 2.

Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Division of Medical Oncology, University of Washington School of Medicine, Seattle, Washington. Electronic address:

The desmoplastic reaction of pancreas cancer may begin as a wound healing response to the nascent neoplasm, but it soon creates an insidious shelter that can sustain the growing tumor and rebuff therapy. Among the many cell types subverted by transformed epithelial cells, fibroblasts are recruited and activated to lay a foundation of extracellular matrix proteins and glycosaminoglycans that alter tumor biophysics and signaling. Their near-universal presence in pancreas cancer and ostensible support of disease progression make fibroblasts attractive therapeutic targets. More recently, however, it has also become apparent that diverse subpopulations of fibroblasts with distinct phenotypes and secretomes inhabit the stroma, and that targeted depletion of particular fibroblast subsets could either provide substantial therapeutic benefit or accelerate disease progression. An improved characterization of these fibroblast subtypes, along with their potential relationships to tumor subtypes and mutational repertoires, is needed in order to make anti-fibroblast therapies clinically viable.
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http://dx.doi.org/10.1053/j.gastro.2018.12.044DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6486863PMC
May 2019

Understanding Disease Biology and Informing the Management of Pancreas Cancer With Preclinical Model Systems.

Cancer J 2017 Nov/Dec;23(6):326-332

Recent advances in cytotoxic therapies for pancreatic ductal adenocarcinoma (PDA) are overshadowed by stalled clinical progress of more targeted strategies, the vast majority of which have failed in clinical trials. Inability to translate preclinical promise into clinical efficacy derives, in part, from imperfect disease modeling and mismatches between preclinical and clinical study design and execution. Into these gaps fall our patients who enter the clinical trial landscape expectantly and bear the brunt of its inadequacies. If improving patient survival is paramount, then it must be acknowledged that the failure of a phase III trial represents a larger failure of all of the work that preceded it. Repeated failures suggest a need to reappraise the current preclinical-to-clinical apparatus. Exceptional models of PDA are now available to researchers, and the first steps toward a new era of success can begin with improved selection and application of these systems. We discuss the key features of the major preclinical platforms for PDA and propose a paradigm for rigorous interrogation of prospective therapies.
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http://dx.doi.org/10.1097/PPO.0000000000000289DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5726424PMC
July 2018

Runx3 and Cell Fate Decisions in Pancreas Cancer.

Adv Exp Med Biol 2017 ;962:333-352

Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, M5-C800, Seattle, WA, 98109-1024, USA.

The RUNX family transcription factors are critical regulators of development and frequently dysregulated in cancer. RUNX3, the least well characterized of the three family members, has been variously described as a tumor promoter or suppressor, sometimes with conflicting results and opinions in the same cancer and likely reflecting a complex role in oncogenesis. We recently identified RUNX3 expression as a crucial determinant of the predilection for pancreatic ductal adenocarcinoma (PDA) cells to proliferate locally or promulgate throughout the body. High RUNX3 expression induces the production and secretion of soluble factors that support metastatic niche construction and stimulates PDA cells to migrate and invade, while simultaneously suppressing proliferation through increased expression of cell cycle regulators such as CDKN1A/p21 . RUNX3 expression and function are coordinated by numerous transcriptional and post-translational inputs, and interactions with diverse cofactors influence whether the resulting RUNX3 complexes enact tumor suppressive or tumor promoting programs. Understanding these exquisitely context-dependent tumor cell behaviors has the potential to inform clinical decision-making including the most appropriate timing and sequencing of local vs. systemic therapies.
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http://dx.doi.org/10.1007/978-981-10-3233-2_21DOI Listing
September 2017

Enhancer Remodeling during Adaptive Bypass to MEK Inhibition Is Attenuated by Pharmacologic Targeting of the P-TEFb Complex.

Cancer Discov 2017 03 20;7(3):302-321. Epub 2017 Jan 20.

Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina.

Targeting the dysregulated BRAF-MEK-ERK pathway in cancer has increasingly emerged in clinical trial design. Despite clinical responses in specific cancers using inhibitors targeting BRAF and MEK, resistance develops often involving nongenomic adaptive bypass mechanisms. Inhibition of MEK1/2 by trametinib in patients with triple-negative breast cancer (TNBC) induced dramatic transcriptional responses, including upregulation of receptor tyrosine kinases (RTK) comparing tumor samples before and after one week of treatment. In preclinical models, MEK inhibition induced genome-wide enhancer formation involving the seeding of BRD4, MED1, H3K27 acetylation, and p300 that drives transcriptional adaptation. Inhibition of the P-TEFb-associated proteins BRD4 and CBP/p300 arrested enhancer seeding and RTK upregulation. BRD4 bromodomain inhibitors overcame trametinib resistance, producing sustained growth inhibition in cells, xenografts, and syngeneic mouse TNBC models. Pharmacologic targeting of P-TEFb members in conjunction with MEK inhibition by trametinib is an effective strategy to durably inhibit epigenomic remodeling required for adaptive resistance. Widespread transcriptional adaptation to pharmacologic MEK inhibition was observed in TNBC patient tumors. In preclinical models, MEK inhibition induces dramatic genome-wide modulation of chromatin, in the form of enhancer formation and enhancer remodeling. Pharmacologic targeting of P-TEFb complex members at enhancers is an effective strategy to durably inhibit such adaptation. .
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http://dx.doi.org/10.1158/2159-8290.CD-16-0653DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5340640PMC
March 2017

Mutant p53 Together with TGFβ Signaling Influence Organ-Specific Hematogenous Colonization Patterns of Pancreatic Cancer.

Clin Cancer Res 2017 Mar 16;23(6):1607-1620. Epub 2016 Sep 16.

The David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York.

TP53 and the TGFβ pathway are major mediators of pancreatic cancer metastasis. The mechanisms by which they cause hematogenous metastasis have not been fully explored. (;; ) mice were generated, and the frequency and morphology of organ-specific hematogenous metastases compared with that seen in and littermates (). Key findings were validated in primary cells from each genotype and samples of human pancreatic cancer liver metastases. The frequency of hematogenous metastasis in mice was significantly lower than for mice (41% vs. 68%, < 0.05), largely due to a reduction in liver metastases. No differences were found between and lung metastases, whereas liver metastases in mice showed a profound extravasation deficiency characterized by sinusoidal growth and lack of desmoplastic stroma. Analogous findings were confirmed in liver samples from patients indicating their clinical relevance. Portal vein colonization as a direct mode of access to the liver was observed in both mice and humans. Secretome analyses of cells revealed an abundance of secreted prometastatic mediators including Col6A1 and Lcn2 that promoted early steps of metastatic colonization. These mediators were overexpressed in primary tumors but not metastases, suggesting that the ability to colonize is, in part, developed within the primary site, a phenomenon we refer to as the "Cinderella effect." These findings establish a novel paradigm for understanding pancreatic cancer metastasis and the observed clinical latencies of liver versus lung metastases specifically. .
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http://dx.doi.org/10.1158/1078-0432.CCR-15-1615DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5354987PMC
March 2017

RUNX3 defines disease behavior in pancreatic ductal adenocarcinoma.

Mol Cell Oncol 2016 Mar 29;3(2):e1076588. Epub 2015 Jul 29.

Clinical Research Division, Seattle, WA; Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA; Division of Medical Oncology, University of Washington School of Medicine, Seattle, WA.

Runt-related transcription factor 3 (RUNX3) functions downstream of transforming growth factor beta (TGFβ) and plays dual roles in pancreas cancer by both suppressing (by inhibiting proliferation) and promoting (by enhancing migratory and metastatic capacity) disease progression. Consideration of the contextual regulation of RUNX3 together with its myriad downstream effects may help improve clinical outcomes for pancreas cancer patients.
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http://dx.doi.org/10.1080/23723556.2015.1076588DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4905377PMC
March 2016

Disconnect between EMT and metastasis in pancreas cancer.

Oncotarget 2015 Oct;6(31):30445-6

Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.

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http://dx.doi.org/10.18632/oncotarget.5720DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4741540PMC
October 2015

RUNX3 Controls a Metastatic Switch in Pancreatic Ductal Adenocarcinoma.

Cell 2015 Jun 21;161(6):1345-60. Epub 2015 May 21.

Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Division of Medical Oncology, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA. Electronic address:

For the majority of patients with pancreas cancer, the high metastatic proclivity is life limiting. Some patients, however, present with and succumb to locally destructive disease. A molecular understanding of these distinct disease manifestations can critically inform patient management. Using genetically engineered mouse models, we show that heterozygous mutation of Dpc4/Smad4 attenuates the metastatic potential of Kras(G12D/+);Trp53(R172H/+) pancreatic ductal adenocarcinomas while increasing their proliferation. Subsequent loss of heterozygosity of Dpc4 restores metastatic competency while further unleashing proliferation, creating a highly lethal combination. Expression levels of Runx3 respond to and combine with Dpc4 status to coordinately regulate the balance between cancer cell division and dissemination. Thus, Runx3 serves as both a tumor suppressor and promoter in slowing proliferation while orchestrating a metastatic program to stimulate cell migration, invasion, and secretion of proteins that favor distant colonization. These findings suggest a model to anticipate likely disease behaviors in patients and tailor treatment strategies accordingly.
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http://dx.doi.org/10.1016/j.cell.2015.04.048DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4458240PMC
June 2015

Hereditary polycystic kidney disease: genetic diagnosis and counseling.

Rev Assoc Med Bras (1992) 2014 Mar-Apr;60(2):98-102

Sociedade Brasileira de Genética Médica.

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http://dx.doi.org/10.1590/1806-9282.60.01.004DOI Listing
June 2015

A global analysis of Y-chromosomal haplotype diversity for 23 STR loci.

Authors:
Josephine Purps Sabine Siegert Sascha Willuweit Marion Nagy Cíntia Alves Renato Salazar Sheila M T Angustia Lorna H Santos Katja Anslinger Birgit Bayer Qasim Ayub Wei Wei Yali Xue Chris Tyler-Smith Miriam Baeta Bafalluy Begoña Martínez-Jarreta Balazs Egyed Beate Balitzki Sibylle Tschumi David Ballard Denise Syndercombe Court Xinia Barrantes Gerhard Bäßler Tina Wiest Burkhard Berger Harald Niederstätter Walther Parson Carey Davis Bruce Budowle Helen Burri Urs Borer Christoph Koller Elizeu F Carvalho Patricia M Domingues Wafaa Takash Chamoun Michael D Coble Carolyn R Hill Daniel Corach Mariela Caputo Maria E D'Amato Sean Davison Ronny Decorte Maarten H D Larmuseau Claudio Ottoni Olga Rickards Di Lu Chengtao Jiang Tadeusz Dobosz Anna Jonkisz William E Frank Ivana Furac Christian Gehrig Vincent Castella Branka Grskovic Cordula Haas Jana Wobst Gavrilo Hadzic Katja Drobnic Katsuya Honda Yiping Hou Di Zhou Yan Li Shengping Hu Shenglan Chen Uta-Dorothee Immel Rüdiger Lessig Zlatko Jakovski Tanja Ilievska Anja E Klann Cristina Cano García Peter de Knijff Thirsa Kraaijenbrink Aikaterini Kondili Penelope Miniati Maria Vouropoulou Lejla Kovacevic Damir Marjanovic Iris Lindner Issam Mansour Mouayyad Al-Azem Ansar El Andari Miguel Marino Sandra Furfuro Laura Locarno Pablo Martín Gracia M Luque Antonio Alonso Luís Souto Miranda Helena Moreira Natsuko Mizuno Yasuki Iwashima Rodrigo S Moura Neto Tatiana L S Nogueira Rosane Silva Marina Nastainczyk-Wulf Jeanett Edelmann Michael Kohl Shengjie Nie Xianping Wang Baowen Cheng Carolina Núñez Marian Martínez de Pancorbo Jill K Olofsson Niels Morling Valerio Onofri Adriano Tagliabracci Horolma Pamjav Antonia Volgyi Gusztav Barany Ryszard Pawlowski Agnieszka Maciejewska Susi Pelotti Witold Pepinski Monica Abreu-Glowacka Christopher Phillips Jorge Cárdenas Danel Rey-Gonzalez Antonio Salas Francesca Brisighelli Cristian Capelli Ulises Toscanini Andrea Piccinini Marilidia Piglionica Stefania L Baldassarra Rafal Ploski Magdalena Konarzewska Emila Jastrzebska Carlo Robino Antti Sajantila Jukka U Palo Evelyn Guevara Jazelyn Salvador Maria Corazon De Ungria Jae Joseph Russell Rodriguez Ulrike Schmidt Nicola Schlauderer Pekka Saukko Peter M Schneider Miriam Sirker Kyoung-Jin Shin Yu Na Oh Iulia Skitsa Alexandra Ampati Tobi-Gail Smith Lina Solis de Calvit Vlastimil Stenzl Thomas Capal Andreas Tillmar Helena Nilsson Stefania Turrina Domenico De Leo Andrea Verzeletti Venusia Cortellini Jon H Wetton Gareth M Gwynne Mark A Jobling Martin R Whittle Denilce R Sumita Paulina Wolańska-Nowak Rita Y Y Yong Michael Krawczak Michael Nothnagel Lutz Roewer

Forensic Sci Int Genet 2014 Sep 28;12:12-23. Epub 2014 Apr 28.

Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin, Berlin, Germany. Electronic address:

In a worldwide collaborative effort, 19,630 Y-chromosomes were sampled from 129 different populations in 51 countries. These chromosomes were typed for 23 short-tandem repeat (STR) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, GATAH4, DYS481, DYS533, DYS549, DYS570, DYS576, and DYS643) and using the PowerPlex Y23 System (PPY23, Promega Corporation, Madison, WI). Locus-specific allelic spectra of these markers were determined and a consistently high level of allelic diversity was observed. A considerable number of null, duplicate and off-ladder alleles were revealed. Standard single-locus and haplotype-based parameters were calculated and compared between subsets of Y-STR markers established for forensic casework. The PPY23 marker set provides substantially stronger discriminatory power than other available kits but at the same time reveals the same general patterns of population structure as other marker sets. A strong correlation was observed between the number of Y-STRs included in a marker set and some of the forensic parameters under study. Interestingly a weak but consistent trend toward smaller genetic distances resulting from larger numbers of markers became apparent.
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http://dx.doi.org/10.1016/j.fsigen.2014.04.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4127773PMC
September 2014

Application of multiplexed kinase inhibitor beads to study kinome adaptations in drug-resistant leukemia.

PLoS One 2013 24;8(6):e66755. Epub 2013 Jun 24.

Department of Pharmacology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, United States of America.

Protein kinases play key roles in oncogenic signaling and are a major focus in the development of targeted cancer therapies. Imatinib, a BCR-Abl tyrosine kinase inhibitor, is a successful front-line treatment for chronic myelogenous leukemia (CML). However, resistance to imatinib may be acquired by BCR-Abl mutations or hyperactivation of Src family kinases such as Lyn. We have used multiplexed kinase inhibitor beads (MIBs) and quantitative mass spectrometry (MS) to compare kinase expression and activity in an imatinib-resistant (MYL-R) and -sensitive (MYL) cell model of CML. Using MIB/MS, expression and activity changes of over 150 kinases were quantitatively measured from various protein kinase families. Statistical analysis of experimental replicates assigned significance to 35 of these kinases, referred to as the MYL-R kinome profile. MIB/MS and immunoblotting confirmed the over-expression and activation of Lyn in MYL-R cells and identified additional kinases with increased (MEK, ERK, IKKα, PKCβ, NEK9) or decreased (Abl, Kit, JNK, ATM, Yes) abundance or activity. Inhibiting Lyn with dasatinib or by shRNA-mediated knockdown reduced the phosphorylation of MEK and IKKα. Because MYL-R cells showed elevated NF-κB signaling relative to MYL cells, as demonstrated by increased IκBα and IL-6 mRNA expression, we tested the effects of an IKK inhibitor (BAY 65-1942). MIB/MS and immunoblotting revealed that BAY 65-1942 increased MEK/ERK signaling and that this increase was prevented by co-treatment with a MEK inhibitor (AZD6244). Furthermore, the combined inhibition of MEK and IKKα resulted in reduced IL-6 mRNA expression, synergistic loss of cell viability and increased apoptosis. Thus, MIB/MS analysis identified MEK and IKKα as important downstream targets of Lyn, suggesting that co-targeting these kinases may provide a unique strategy to inhibit Lyn-dependent imatinib-resistant CML. These results demonstrate the utility of MIB/MS as a tool to identify dysregulated kinases and to interrogate kinome dynamics as cells respond to targeted kinase inhibition.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0066755PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3691232PMC
January 2014

Comparison of southern Chinese Han and Brazilian Caucasian mutation rates at autosomal short tandem repeat loci used in human forensic genetics.

Int J Legal Med 2014 Jan 3;128(1):1-9. Epub 2013 Apr 3.

Shanghai Key Laboratory of Forensic Medicine, Institute of Forensic Science, Ministry of Justice, Shanghai, People's Republic of China.

The short tandem repeat (STR) loci used in human genetic studies are characterized by having relatively high mutation rates. In particular, to ensure an appropriate evaluation of genetic evidence in parentage and forensic analyses, it is essential to have accurate estimates of the mutation rates associated with the commonly used autosomal and sex chromosome STR loci. Differences in STR mutation rates between different ethnic groups should also be determined. Mutation data from two laboratories working with different ethnic groups were extracted from many meiotic transmissions ascertained for 15 autosomal STR loci currently used in forensic routine. Forty-five thousand and eighty-five trios were checked for the biological consistency of maternity and paternity through the analysis of a minimum of 15 loci. Mutations were scored as paternal, maternal, or ambiguous according to the most parsimonious explanation for the inconsistency, using always the least requiring hypothesis in terms of number of repeat differences. The main findings are: (a) the overall mutation rate across the 15 loci was 9.78 × 10(-4) per gamete per generation (95% CI = 9.30 × 10(-4)-1.03 × 10(-3)), and with just 48 (out of 1,587) exceptions, all of the mutations were single-step; (b) repeat gains were more frequent than losses; (c) longer alleles were found to be more mutable; and (d) the mutation rates differ at some loci between the two ethnic groups. Large worldwide meiotic transmission datasets are still needed to measure allele-specific mutation rates at the STR loci consensually used in forensic genetics.
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http://dx.doi.org/10.1007/s00414-013-0847-2DOI Listing
January 2014

The dynamic nature of the kinome.

Biochem J 2013 Feb;450(1):1-8

The Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.

Recent advances in proteomics have facilitated the analysis of the kinome 'en masse'. What these studies have revealed is a surprisingly dynamic network of kinase responses to highly selective kinase inhibitors, thereby illustrating the complex biological responses to these small molecules. Moreover these studies have identified key transcription factors, such as c-Myc and FOXO (forkhead box O), that play pivotal roles in kinome reprogramming in cancer cells. Since many kinase inhibitors fail despite a high efficacy of blocking their intended targets, elucidating kinome changes at a more global level will be essential to understanding the mechanisms of kinase inhibitor pharmacology. The development of technologies to study the kinome, as well as examples of kinome resilience and reprogramming, will be discussed in the present review.
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http://dx.doi.org/10.1042/BJ20121456DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3808244PMC
February 2013

Combined PI3K/mTOR and MEK inhibition provides broad antitumor activity in faithful murine cancer models.

Clin Cancer Res 2012 Oct 7;18(19):5290-303. Epub 2012 Aug 7.

Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, NC, USA.

Purpose: Anticancer drug development is inefficient, but genetically engineered murine models (GEMM) and orthotopic, syngeneic transplants (OST) of cancer may offer advantages to in vitro and xenograft systems.

Experimental Design: We assessed the activity of 16 treatment regimens in a RAS-driven, Ink4a/Arf-deficient melanoma GEMM. In addition, we tested a subset of treatment regimens in three breast cancer models representing distinct breast cancer subtypes: claudin-low (T11 OST), basal-like (C3-TAg GEMM), and luminal B (MMTV-Neu GEMM).

Results: Like human RAS-mutant melanoma, the melanoma GEMM was refractory to chemotherapy and single-agent small molecule therapies. Combined treatment with AZD6244 [mitogen-activated protein-extracellular signal-regulated kinase kinase (MEK) inhibitor] and BEZ235 [dual phosphoinositide-3 kinase (PI3K)/mammalian target of rapamycin (mTOR) inhibitor] was the only treatment regimen to exhibit significant antitumor activity, showed by marked tumor regression and improved survival. Given the surprising activity of the "AZD/BEZ" combination in the melanoma GEMM, we next tested this regimen in the "claudin-low" breast cancer model that shares gene expression features with melanoma. The AZD/BEZ regimen also exhibited significant activity in this model, leading us to testing in even more diverse GEMMs of basal-like and luminal breast cancer. The AZD/BEZ combination was highly active in these distinct breast cancer models, showing equal or greater efficacy compared with any other regimen tested in studies of over 700 tumor-bearing mice. This regimen even exhibited activity in lapatinib-resistant HER2(+) tumors.

Conclusion: These results show the use of credentialed murine models for large-scale efficacy testing of diverse anticancer regimens and predict that combinations of PI3K/mTOR and MEK inhibitors will show antitumor activity in a wide range of human malignancies.
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http://dx.doi.org/10.1158/1078-0432.CCR-12-0563DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715399PMC
October 2012

Dynamic reprogramming of the kinome in response to targeted MEK inhibition in triple-negative breast cancer.

Cell 2012 Apr;149(2):307-21

Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA.

Kinase inhibitors have limited success in cancer treatment because tumors circumvent their action. Using a quantitative proteomics approach, we assessed kinome activity in response to MEK inhibition in triple-negative breast cancer (TNBC) cells and genetically engineered mice (GEMMs). MEK inhibition caused acute ERK activity loss, resulting in rapid c-Myc degradation that induced expression and activation of several receptor tyrosine kinases (RTKs). RNAi knockdown of ERK or c-Myc mimicked RTK induction by MEK inhibitors, and prevention of proteasomal c-Myc degradation blocked kinome reprogramming. MEK inhibitor-induced RTK stimulation overcame MEK2 inhibition, but not MEK1 inhibition, reactivating ERK and producing drug resistance. The C3Tag GEMM for TNBC similarly induced RTKs in response to MEK inhibition. The inhibitor-induced RTK profile suggested a kinase inhibitor combination therapy that produced GEMM tumor apoptosis and regression where single agents were ineffective. This approach defines mechanisms of drug resistance, allowing rational design of combination therapies for cancer.
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http://dx.doi.org/10.1016/j.cell.2012.02.053DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3328787PMC
April 2012

Defining the expressed breast cancer kinome.

Cell Res 2012 Apr 7;22(4):620-3. Epub 2012 Feb 7.

Biomedical Engineering and Curriculum in Bioinformatics and Computational Biology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA.

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http://dx.doi.org/10.1038/cr.2012.25DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3317564PMC
April 2012

Dynamic simulations of colloids by core-modified dissipative particle dynamics.

J Chem Phys 2010 Mar;132(12):124906

Department of Engineering Materials, University of Sheffield, Sir Robert Hadfield Building, Mappin Street, Sheffield S1 3JD, United Kingdom.

We develop a core-modified dissipative particle dynamics model of colloidal systems which includes an extra term to counteract depletion forces. Results are presented covering the full range of volume fractions. Radial distribution functions for the suspending fluid are shown to change significantly as the volume fraction of colloid increases. Equilibrium results for the long-time diffusion coefficient behave as expected, but the short-time coefficient is anomalous. The form of the equilibrium stress correlation functions is discussed and the derived Green-Kubo viscosities are compared with expected semiempirical forms. For nonequilibrium shear-field simulations we find that the system temperature is not adequately controlled by the dissipative particle dynamics (DPD) thermostat alone. Results using three alternative auxiliary thermostats are compared; a naive choice leading to a string phase at high shear rate. Using a thermostat based on relative particle velocities, the model reproduced the four classical regions of colloid rheology: a first Newtonian plateau, a shear-thinning region, a second Newtonian plateau, and finally a shear-thickening region at high strain rate. The most unexpected result of this exercise is that the core-modified DPD model without auxiliary thermostat almost exactly follows the same curve despite recording a temperature increase of a factor approximately 2.5 over the range.
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http://dx.doi.org/10.1063/1.3364011DOI Listing
March 2010

A GEP-ISFG collaborative study on the optimization of an X-STR decaplex: data on 15 Iberian and Latin American populations.

Int J Legal Med 2009 May 12;123(3):227-34. Epub 2008 Dec 12.

IPATIMUP Institute of Pathology and Molecular Immunology, University of Porto, Porto, Portugal.

In a collaborative work carried out by the Spanish and Portuguese ISFG Working Group (GEP-ISFG), a polymerase chain reaction multiplex was optimized in order to type ten X-chromosome short tandem repeats (STRs) in a single reaction, including: DXS8378, DXS9902, DXS7132, DXS9898, DXS6809, DXS6789, DXS7133, GATA172D05, GATA31E08, and DXS7423. Using this X-decaplex, each 17 of the participating laboratories typed a population sample of approximately 200 unrelated individuals (100 males and 100 females). In this work, we report the allele frequencies for the ten X-STRs in 15 samples from Argentina (Buenos Aires, Córdoba, Río Negro, Entre Ríos, and Misiones), Brazil (São Paulo, Rio de Janeiro, Paraná, and Mato Grosso do Sul), Colombia (Antioquia), Costa Rica, Portugal (Northern and Central regions), and Spain (Galicia and Cantabria). Gene diversities were calculated for the ten markers in each population and all values were above 56%. The average diversity per locus varied between 66%, for DXS7133, and 82%, for DXS6809. For this set of STRs, a high discrimination power was obtained in all populations, both in males (> or =1 in 5 x 10(5)) and females (> or =1 in 3 x 10(9)), as well as high mean exclusion chance in father/daughter duos (> or =99.953%) and in father/mother/daughter trios (> or =99.999%). Genetic distance analysis showed no significant differences between northern and central Portugal or between the two Spanish samples from Galicia and Cantabria. Inside Brazil, significant differences were found between Rio de Janeiro and the other three populations, as well as between São Paulo and Paraná. For the five Argentinean samples, significant distances were only observed when comparing Misiones with Entre Ríos and with Río Negro, the only two samples that do not differ significantly from Costa Rica. Antioquia differed from all other samples, except the one from Río Negro.
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http://dx.doi.org/10.1007/s00414-008-0309-4DOI Listing
May 2009

Prevention and treatment of surgical site infection: summary of NICE guidance.

BMJ 2008 Oct 28;337:a1924. Epub 2008 Oct 28.

Department of Wound Healing, Cardiff University, Cardiff.

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http://dx.doi.org/10.1136/bmj.a1924DOI Listing
October 2008

Population and segregation data on 17 Y-STRs: results of a GEP-ISFG collaborative study.

Int J Legal Med 2008 Nov 24;122(6):529-33. Epub 2008 Jul 24.

University of Santiago de Compostela, C/San Francisco, A Coruña, Spain.

A collaborative work was carried out by the Spanish and Portuguese International Society for Forensic Genetics Working Group in order to extend the existing data on Y-short tandem repeat (STR) mutations at the 17 Y chromosome STR loci included in the AmpFlSTR YFiler kit (Applied Biosystems): DYS19, DYS385, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, and GATA H4.1. In a sample of 701 father/son pairs, 26 mutations were observed among 11,917 allele transfers across the 17 loci. After summing previously reported mutation data with our sample, mutation rates varied between 4.25 x 10(-4) (95% CI 0.05 x 10(-3)-1.53 x 10(-3)) at DYS438 and 6.36 x 10(-3) (95% CI 2.75 x 10(-3)-12.49 x 10(-3)) at DYS458. All mutations were single step, and mutations in the same father/son pair were found twice.
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http://dx.doi.org/10.1007/s00414-008-0265-zDOI Listing
November 2008

A comparison of field-based similarity searching methods: CatShape, FBSS, and ROCS.

J Chem Inf Model 2008 Apr 20;48(4):719-29. Epub 2008 Mar 20.

Department of Information Studies, University of Sheffield, Western Bank, Sheffield, S10 2TN, United Kingdom.

Three field-based similarity methods are compared in retrospective virtual screening experiments. The methods are the CatShape module of CATALYST, ROCS, and an in-house program developed at the University of Sheffield called FBSS. The programs are used in both rigid and flexible searches carried out in the MDL Drug Data Report. UNITY 2D fingerprints are also used to provide a comparison with a more traditional approach to similarity searching, and similarity based on simple whole-molecule properties is used to provide a baseline for the more sophisticated searches. Overall, UNITY 2D fingerprints and ROCS with the chemical force field option gave comparable performance and were superior to the shape-only 3D methods. When the flexible methods were compared with the rigid methods, it was generally found that the flexible methods gave slightly better results than their respective rigid methods; however, the increased performance did not justify the additional computational cost required.
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http://dx.doi.org/10.1021/ci700130jDOI Listing
April 2008

Care of healthy women and their babies during childbirth: summary of NICE guidance.

BMJ 2007 Sep;335(7621):667-8

Reproductive Sciences Section, Department of Cancer Studies and Molecular Medicine, University of Leicester, Leicester LE2 7LX.

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http://dx.doi.org/10.1136/bmj.39322.703380.ADDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1995472PMC
September 2007

Use of X-linked short tandem repeat loci in routine parentage casework.

Transfusion 2007 Jun;47(6):1050-3

Genomic Engenharia Molecular, São Paulo, SP, Brazil.

Background: Dealing with genetic inconsistencies in parentage testing, especially in motherless cases, remains a continual difficulty.

Study Design And Methods: Four difficult cases, comprising two trios and two duos, were selected from routine parentage testing casework. In these, relatively low combined paternity indices were observed as a result of few discrepant loci that were treated as being due to paternal mutations. An additional eight short tandem repeat (STR) loci along the X chromosome were studied in the alleged father and female child to try and help resolve these cases.

Results: In all four cases, the X chromosome haplotypes in the alleged father were different from those in the child, showing decisively that the alleged father could be excluded from being the biologic father of the child.

Conclusion: In recent times the study of X chromosome haplotypes has been shown to be useful in parentage testing where the alleged father is absent and where only his close relatives are available for testing. This work demonstrates that such studies can also prove valuable in the testing of standard trios and duos in cases where there only a few genetic inconsistencies amongst the loci tested, making it difficult to distinguish between paternal mutations and a close relative of the alleged father being the biologic father.
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http://dx.doi.org/10.1111/j.1537-2995.2007.01238.xDOI Listing
June 2007

Analysis of data fusion methods in virtual screening: similarity and group fusion.

J Chem Inf Model 2006 Nov-Dec;46(6):2206-19

Department of Information Studies, University of Sheffield, 211 Portobello Street, Sheffield S1 4DP, UK.

In a recent companion paper we have related the operation of simple data fusion rules used in virtual screening to a multiple integral formalism. In this paper we extend these ideas to the analysis of data fusion methods applied to real data. We examine several cases of similarity fusion using different coefficients and different representations and consider the reasons for positive or negative results in terms of the similarity distributions. Results are obtained using the SUM-, MAX- MIN-, and CombMNZ-fusion rules. We also develop a customized fusion rule, which provides an estimate of the optimal possible result for fusing multiple searches of a specific database; this shows that similarity fusion can, in principle, achieve retrieval enhancements even if this is not achieved in practice with current fusion rules. The methods are extended to analyze the comparatively successful results of group fusion with multiple actives, and we provide a rationale for the observed superiority of the MAX-rule over the SUM-rule in this context.
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http://dx.doi.org/10.1021/ci0496144DOI Listing
February 2007

Analysis of data fusion methods in virtual screening: theoretical model.

J Chem Inf Model 2006 Nov-Dec;46(6):2193-205

Department of Information Studies, University of Sheffield, 211 Portobello Street, Sheffield S1 4DP, UK.

This paper presents a theoretical model of how data fusion can be used to combine the results of multiple similarity searches of chemical databases. The model is based on frequency distributions of similarity values that are fused using a multiple integration over regions defined by the particular fusion rule that is being applied. For pairwise fusion, the resulting double integrals are straightforward to evaluate for simple model distributions. Similarity values for recovered-active and recovered-nonactive frequency distributions are independently modeled using a constant background, linearly biased terms, and a first-order correlated term. The model shows that two standard fusion rules can give performance enhancements in some cases but that the results of fusion are dependent on many factors that, taken together, can lead to seemingly inconsistent levels of enhancement.
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http://dx.doi.org/10.1021/ci049615wDOI Listing
February 2007

An audit of outcome in intravascular transfusions using the intrahepatic portion of the fetal umbilical vein compared to cordocentesis.

Fetal Diagn Ther 2006 ;21(3):272-6

Department of Fetal Medicine, Division of Reproduction and Child Health, Birmingham Women's Hospital, University of Birmingham, UK.

Introduction: Maternal red cell alloimmunization is a potential cause of perinatal morbidity and mortality. The outcome of severe disease has been transformed by the use of in-utero and particularly, fetal intravascular transfusion. In the majority of instances this is performed by cordocentesis. However, this cohort study represents the experience in a large tertiary referral centre in performing fetal intravascular transfusions via the intrahepatic vein (IHV).

Methods: Over an 8-year period, 1997-2004, 221 in-utero transfusions (IUT) were performed for rhesus disease in 66 pregnancies. 86% had severe fetal anaemia caused by anti-D, 10.6% by anti-Kell and 3.4% by anti-c. The median maternal age of the cohort was 31 years (range 19-43). The median gestation at initial IUT was 25 weeks (interquartile range (IQR) 23-29 weeks).

Results: A median number of three IUT were performed in each fetus (IQR 2-5) with a median haemoglobin at first fetal blood sampling of 7.3 g% (IQR 4.6-8.8 g%) (73% < or =5 SD and 27% < or =2 SD). Of the total intravascular transfusions, 170 were performed via the IHV (71.7%), 33 via cordocentesis (13.9%) and 1 by intracardiac puncture (0.5%). There were 'transient' bradycardias complicating 4.1% of all transfusions and amniorrhexis following 1.4%. 92% of babies were live born at a median gestation of 34 weeks (range 21-38) with a birth weight centile of 50 (range 3-90). There was no significant difference in intravascular transfusion complication rate when the procedure was performed via the IHV (7.6%) as compared to cord root puncture (3.0%) (Fisher's exact test, p < 0.47).

Conclusion: IUT performed by fetal IHV puncture is safe and carries no excess morbidity when performed for severe rhesus disease.
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http://dx.doi.org/10.1159/000091355DOI Listing
August 2006

Results of the 2003-2004 GEP-ISFG collaborative study on mitochondrial DNA: focus on the mtDNA profile of a mixed semen-saliva stain.

Forensic Sci Int 2006 Jul 21;160(2-3):157-67. Epub 2005 Oct 21.

Instituto Nacional de Toxicología y Ciencias Forenses, Servicio de Biología, Barcelona, Spain.

We report here a review of the seventh mitochondrial DNA (mtDNA) exercise undertaken by the Spanish and Portuguese working group (GEP) of the International Society for Forensic Genetics (ISFG) corresponding to the period 2003-2004. Five reference bloodstains from five donors (M1-M5), a mixed stain of saliva and semen (M6), and a hair sample (M7) were submitted to each participating laboratory for nuclear DNA (nDNA; autosomal STR and Y-STR) and mtDNA analysis. Laboratories were asked to investigate the contributors of samples M6 and M7 among the reference donors (M1-M5). A total of 34 laboratories reported total or partial mtDNA sequence data from both, the reference bloodstains (M1-M5) and the hair sample (M7) concluding a match between mtDNA profiles of M5 and M7. Autosomal STR and Y-STR profiling was the preferred strategy to investigate the contributors of the semen/saliva mixture (M6). Nuclear DNA profiles were consistent with a mixture of saliva from the donor (female) of M4 and semen from donor M5, being the semen (XY) profile the dominant component of the mixture. Strikingly, and in contradiction to the nuclear DNA analysis, mtDNA sequencing results yield a more simple result: only the saliva contribution (M4) was detected, either after preferential lysis or after complete DNA digestion. Some labs provided with several explanations for this finding and carried out additional experiments to explain this apparent contradictory result. The results pointed to the existence of different relative amounts of nuclear and mtDNAs in saliva and semen. We conclude that this circumstance could strongly influence the interpretation of the mtDNA evidence in unbalanced mixtures and in consequence lead to false exclusions. During the GEP-ISFG annual conference a validation study was planned to progress in the interpretation of mtDNA from different mixtures.
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http://dx.doi.org/10.1016/j.forsciint.2005.09.005DOI Listing
July 2006

Mitochondrial DNA error prophylaxis: assessing the causes of errors in the GEP'02-03 proficiency testing trial.

Forensic Sci Int 2005 Mar;148(2-3):191-8

Unidad de Genética, Facultad de Medicina de la Universidad de Santiago de Compostela, Instituto de Medicina Legal, A Coruña, Galicia-Spain.

We report the results of the Spanish and Portuguese working group (GEP) of the International Society for Forensic Genetics (ISFG) Collaborative Exercise 2002-2003 on mitochondrial DNA (mtDNA) analysis. Six different samples were submitted to the participating laboratories: four blood stains (M1-M2-M3-M4), one mixture blood sample (M5), and two hair shaft fragments (M6). Most of the labs reported consensus results for the blood stains, slightly improving the results of previous collaborative exercises. Although hair shaft analysis is still carried out by a small number of laboratories, this analysis yielded a high rate of success. On the contrary, the analysis of the mixture blood stain (M5) yielded a lower rate of success; in spite of this, the whole results on M5 typing demonstrated the suitability of mtDNA analysis in mixture samples. We have found that edition errors are among the most common mistakes reported by the different labs. In addition, we have detected contamination events as well as other minor problems, i.e. lack of standarization in nomenclature for punctual and length heteroplasmies, and indels. In the present edition of the GEP-ISFG exercise we have paid special attention to the visual phylogenetic inspection for detecting common sequencing errors.
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http://dx.doi.org/10.1016/j.forsciint.2004.06.008DOI Listing
March 2005

Enhancing the effectiveness of virtual screening by fusing nearest neighbor lists: a comparison of similarity coefficients.

J Chem Inf Comput Sci 2004 Sep-Oct;44(5):1840-8

Krebs Institute for Biomolecular Research and Department of Information Studies, University of Sheffield, Western Bank, Sheffield S10 2TN, U.K.

This paper evaluates the effectiveness of various similarity coefficients for 2D similarity searching when multiple bioactive target structures are available. Similarity searches using several different activity classes within the MDL Drug Data Report and the Dictionary of Natural Products databases are performed using BCI 2D fingerprints. Using data fusion techniques to combine the resulting nearest neighbor lists we obtain group recall results which, in many cases, are a considerable improvement on standard average recall values obtained for individual structures. It is shown that the degree of improvement can be related to the structural diversity of the activity class that is searched for, the best results being found for the most diverse groups. The group recall of active compounds using subsets of the class is also investigated: for highly self-similar activity classes, the group recall improvement saturates well before the full activity class size is reached. A rough correlation is found between the relative improvement using the group recall and the square of the number of unique compounds available in all of the merged lists. The Tanimoto coefficient is found unambiguously to be the best coefficient to use for the recovery of active compounds using multiple targets. Furthermore, when using the Tanimoto coefficient, the "MAX" fusion rule is found to be more effective than the "SUM" rule for the combination of similarity searches from multiple targets. The use of group recall can lead to improved enrichment in database searches and virtual screening.
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http://dx.doi.org/10.1021/ci049867xDOI Listing
November 2005