bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stationary-Phase Persisters to Ofloxacin Sustain DNA Damage and Require Repair Systems Only during Recovery
Authors: Völzing Katherine G. , Brynildsen Mark P. 
Published: September 2015

ABSTRACT

Chronic infections are a serious health care problem, and bacterial persisters have been implicated in infection reoccurrence. Progress toward finding antipersister therapies has been slow, in part because of knowledge gaps regarding the physiology of these rare phenotypic variants. Evidence shows that growth status is important for survival, as nongrowing cultures can have 100-fold more persisters than growing populations. However, additional factors are clearly important, as persisters remain rare even in nongrowing populations. What features, beyond growth inhibition, allow persisters to survive antibiotic stress while the majority of their kin succumb to it remains an open question. To investigate this, we used stationary phase as a model nongrowing environment to study
Escherichia coli
persistence to ofloxacin. Given that the prevailing model of persistence attributes survival to transient dormancy and antibiotic target inactivity, we anticipated that persisters would suffer less damage than their dying kin. However, using genetic mutants, flow cytometry, fluorescence-activated cell sorting, and persistence assays, we discovered that nongrowing ofloxacin persisters experience antibiotic-induced damage that is indistinguishable from that of nonpersisters. Consistent with this, we found that these persisters required DNA repair for survival and that repair machinery was unnecessary until the posttreatment recovery period (after ofloxacin removal). These findings suggest that persistence to ofloxacin is not engendered solely by reduced antibiotic target corruption, demonstrate that what happens following antibiotic stress can be critical to the persistence phenotype, and support the notion that inhibition of DNA damage repair systems could be an effective strategy to eliminate fluoroquinolone persisters.

IMPORTANCE
In the absence of resistant mutants, infection reoccurrences can still occur because of persisters, rare bacterial cells that survive antibiotic treatments to repopulate infection sites. Persister survival is attributed to a transient state of dormancy in which a cell's growth and metabolism are significantly reduced and many essential processes are thought to be inactive. Thus, dormancy is believed to protect persisters from antibiotic-induced damage and death. In this work, we show that in nongrowing populations, persisters to ofloxacin experience the same level of antibiotic-induced damage as cells that succumb to the treatment and that their survival critically depends on repair of this damage after the conclusion of treatment. These findings reveal that persistence to ofloxacin is not engendered solely by reduced antibiotic target corruption and highlight that processes following antibiotic stress are important to survival. We hypothesize that effective antipersister therapies may be developed on the basis of this knowledge.
Selective Sweeps and Parallel Pathoadaptation Drive Pseudomonas aeruginosa Evolution in the Cystic Fibrosis Lung
Authors: Diaz Caballero Julio , Clark Shawn T. , Coburn Bryan , Zhang Yu , Wang Pauline W. , Donaldson Sylva L. , Tullis D. Elizabeth , Yau Yvonne C. W. , Waters Valerie J. , Hwang David M. , Guttman David S. 
Published: September 2015

ABSTRACT

Pulmonary infections caused by
Pseudomonas aeruginosa
are a recalcitrant problem in cystic fibrosis (CF) patients. While the clinical implications and long-term evolutionary patterns of these infections are well studied, we know little about the short-term population dynamics that enable this pathogen to persist despite aggressive antimicrobial therapy. Here, we describe a short-term population genomic analysis of 233
P. aeruginosa
isolates collected from 12 sputum specimens obtained over a 1-year period from a single patient. Whole-genome sequencing and antimicrobial susceptibility profiling identified the expansion of two clonal lineages. The first lineage originated from the coalescence of the entire sample less than 3 years before the end of the study and gave rise to a high-diversity ancestral population. The second expansion occurred 2 years later and gave rise to a derived population with a strong signal of positive selection. These events show characteristics consistent with recurrent selective sweeps. While we cannot identify the specific mutations responsible for the origins of the clonal lineages, we find that the majority of mutations occur in loci previously associated with virulence and resistance. Additionally, approximately one-third of all mutations occur in loci that are mutated multiple times, highlighting the importance of parallel pathoadaptation. One such locus is the gene encoding penicillin-binding protein 3, which received three independent mutations. Our functional analysis of these alleles shows that they provide differential fitness benefits dependent on the antibiotic under selection. These data reveal that bacterial populations can undergo extensive and dramatic changes that are not revealed by lower-resolution analyses.

IMPORTANCE
Pseudomonas aeruginosa
is a bacterial opportunistic pathogen responsible for significant morbidity and mortality in cystic fibrosis (CF) patients. Once it has colonized the lung in CF, it is highly resilient and rarely eradicated. This study presents a deep sampling examination of the fine-scale evolutionary dynamics of
P. aeruginosa
in the lungs of a chronically infected CF patient. We show that diversity of
P. aeruginosa
is driven by recurrent clonal emergence and expansion within this patient and identify potential adaptive variants associated with these events. This high-resolution sequencing strategy thus reveals important intraspecies dynamics that explain a clinically important phenomenon not evident at a lower-resolution analysis of community structure.
Function of the CRISPR-Cas System of the Human Pathogen Clostridium difficile
Authors: Boudry Pierre , Semenova Ekaterina , Monot Marc , Datsenko Kirill A. , Lopatina Anna , Sekulovic Ognjen , Ospina-Bedoya Maicol , Fortier Louis-Charles , Severinov Konstantin , Dupuy Bruno , Soutourina Olga 
Published: September 2015

ABSTRACT

Clostridium difficile
is the cause of most frequently occurring nosocomial diarrhea worldwide. As an enteropathogen,
C. difficile
must be exposed to multiple exogenous genetic elements in bacteriophage-rich gut communities. CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) systems allow bacteria to adapt to foreign genetic invaders. Our recent data revealed active expression and processing of CRISPR RNAs from multiple type I-B CRISPR arrays in
C. difficile
reference strain 630. Here, we demonstrate active expression of CRISPR arrays in strain R20291, an epidemic
C. difficile
strain. Through genome sequencing and host range analysis of several new
C. difficile
phages and plasmid conjugation experiments, we provide evidence of defensive function of the CRISPR-Cas system in both
C. difficile
strains. We further demonstrate that
C. difficile
Cas proteins are capable of interference in a heterologous host,
Escherichia coli
. These data set the stage for mechanistic and physiological analyses of CRISPR-Cas-mediated interactions of important global human pathogen with its genetic parasites.

IMPORTANCE
Clostridium difficile
is the major cause of nosocomial infections associated with antibiotic therapy worldwide. To survive in bacteriophage-rich gut communities, enteropathogens must develop efficient systems for defense against foreign DNA elements. CRISPR-Cas systems have recently taken center stage among various anti-invader bacterial defense systems. We provide experimental evidence for the function of the
C. difficile
CRISPR system against plasmid DNA and bacteriophages. These data demonstrate the original features of active
C. difficile
CRISPR system and bring important insights into the interactions of this major enteropathogen with foreign DNA invaders during its infection cycle.
Development of Delirium in the Intensive Care Unit in Patients after Endovascular Aortic Repair: A Retrospective Evaluation of the Prevalence and Risk Factors
Authors: Kawatani Yohei , Nakamura Yoshitsugu , Hayashi Yujiro , Taneichi Tetsuyoshi , Ito Yujiro , Kurobe Hirotsugu , Suda Yuji , Hori Takaki 
Published: September 2015

Delirium is an acute form of nervous system dysfunction often observed in patients in the intensive care unit. Endovascular aortic repair (EVAR) is considered a minimally invasive surgical treatment for abdominal aortic aneurysm. Although the operation method is widely used, there are few investigations of the rate and risk factors of delirium development after the operation. In this study, we retrospectively examined the rate of delirium development in the intensive care unit (ICU) after EVAR, as well as the associated preoperative risk factors and effects on the lengths of ICU and hospital stays. We examined the 81 consecutive patients who underwent elective EVAR between November 2013 and August 2014. The Intensive Care Delirium Screening Checklist was used to diagnose delirium. Twenty patients (24.7%) were diagnosed with delirium in this study. The ICU and hospital length of stays of patients with delirium were 3.3 ± 2.4 days and 14.5 ± 11.9 days, respectively, the latter of which was significantly longer than that of patients without delirium (p= 0.019). Additionally, renal dysfunction, preoperative benzodiazepine use, and intraoperative transfusion were found to be risk factors for the development of delirium after elective EVAR.
Predicting the Response of Breast Cancer to Neoadjuvant Therapy Using a Mechanically Coupled Reaction–Diffusion Model
Authors: Weis Jared A. , Miga Michael I. , Arlinghaus Lori R. , Li Xia , Abramson Vandana , Chakravarthy A. Bapsi , Pendyala Praveen , Yankeelov Thomas E. 
Published: September 2015

Abstract
Although there are considerable data on the use of mathematical modeling to describe tumor growth and response to therapy, previous approaches are often not of the form that can be easily applied to clinical data to generate testable predictions in individual patients. Thus, there is a clear need to develop and apply clinically relevant oncologic models that are amenable to available patient data and yet retain the most salient features of response prediction. In this study we show how a biomechanical model of tumor growth can be initialized and constrained by serial patient-specific magnetic resonance imaging data, obtained at two time points early in the course of therapy (before initiation and following one cycle of therapy), to predict the response for individual patients with breast cancer undergoing neoadjuvant therapy. Using our mechanics coupled modeling approach, we are able to predict, after the first cycle of therapy, breast cancer patients that would eventually achieve a complete pathologic response and those who would not, with receiver operating characteristic area under the curve (AUC) of 0.87, sensitivity of 92%, and specificity of 84%. Our approach significantly outperformed the AUCs achieved by standard (i.e., not mechanically coupled) reaction–diffusion predictive modeling (0.75), simple analysis of the tumor cellularity estimated from imaging data (0.73), and the Response Evaluation Criteria in Solid Tumors (0.71). Thus, we show the potential for mathematical model prediction for use as a prognostic indicator of response to therapy. The work indicates the considerable promise of image-driven biophysical modeling for predictive frameworks within therapeutic applications. Cancer Res; 75(22); 4697–707. ©2015 AACR.
Cell-of-Origin of Cancer versus Cancer Stem Cells: Assays and Interpretations
Authors: Rycaj Kiera , Tang Dean G. 
Published: September 2015

Abstract
A tumor originates from a normal cell that has undergone tumorigenic transformation as a result of genetic mutations. This transformed cell is the cell-of-origin for the tumor. In contrast, an established clinical tumor is sustained by subpopulations of self-renewing cancer cells operationally called cancer stem cells (CSC) that can generate, intraclonally, both tumorigenic and nontumorigenic cells. Identifying and characterizing tumor cell-of-origin and CSCs should help elucidate tumor cell heterogeneity, which, in turn, should help understand tumor cell responses to clinical treatments, drug resistance, tumor relapse, and metastatic spread. Both tumor transplantation and lineage-tracing assays have been helpful in characterizing these cancer cell populations, although each system has its strengths and caveats. In this article, we briefly review and summarize advantages and limitations of both assays in support of a combinatorial approach to accurately define the roles of both cancer-initiating and cancer-propagating cells. As an aside, we also wish to clarify the definitions of cancer cell-of-origin and CSCs, which are often interchangeably used by mistake. Cancer Res; 75(19); 4003–11. ©2015 AACR.
Tetraspanin CD81 Promotes Tumor Growth and Metastasis by Modulating the Functions of T Regulatory and Myeloid-Derived Suppressor Cells
Authors: Vences-Catalán Felipe , Rajapaksa Ranjani , Srivastava Minu K. , Marabelle Aurelien , Kuo Chiung-Chi , Levy Ronald , Levy Shoshana 
Published: September 2015

AbstractTumor cells counteract innate and adaptive antitumor immune responses by recruiting regulatory T cells (Treg) and innate myeloid-derived suppressor cells (MDSC), which facilitate immune escape and metastatic dissemination. Here we report a role in these recruitment processes for CD81, a member of the tetraspanin family of proteins that have been implicated previously in cancer progression. We found that genetic deficiency in CD81 reduced tumor growth and metastasis in two genetic mouse backgrounds and multiple tumor models. Mechanistic investigations revealed that CD81 was not required for normal development of Treg and MDSC but was essential for immunosuppressive functions. Notably, adoptive transfer of wild-type Treg into CD81-deficient mice was sufficient to promote tumor growth and metastasis. Our findings suggested that CD81 modulates adaptive and innate immune responses, warranting further investigation of CD81 in immunomodulation in cancer and its progression. Cancer Res; 75(21); 4517–26. ©2015 AACR.
New Strategies in Sarcoma: Linking Genomic and Immunotherapy Approaches to Molecular Subtype
Authors: Lim Jamie , Poulin Neal M. , Nielsen Torsten O. 
Published: September 2015

Abstract
There are more than 100 sarcoma subtypes, each uncommon and diagnostically challenging. Conventional chemotherapy has little benefit for most soft-tissue sarcomas; new treatment strategies are needed. Multiple recent genomic studies have provided detailed insights into sarcoma biology, including more accurate classification by molecular subtype, identification of recurrent mutations in oncogenic pathways, and evidence of epigenetic dysregulation. Advances in immunotherapy (adoptive immune cell transfer, tumor vaccine strategies, and immune checkpoint inhibition) have also provided a better understanding of how immuno-oncology might best be applied to sarcoma treatment, including connections to oncogenic pathways that may support combination strategies with conventional and targeted therapies. In this article, we review the latest sarcoma genomic studies and immuno-oncology developments and discuss how the findings suggest potential strategies to improve diagnosis and treatment across multiple sarcoma subtypes. Clin Cancer Res; 21(21); 4753–9. ©2015 AACR.
Tumor MET Expression and Gene Amplification in Chinese Patients with Locally Advanced or Metastatic Gastric or Gastroesophageal Junction Cancer
Authors: Peng Zhi , Li Zhongwu , Gao Jing , Lu Ming , Gong Jifang , Tang En-Tzu , Oliner Kelly S. , Hei Yong-Jiang , Zhou Hui , Shen Lin 
Published: September 2015

AbstractMET and its sole ligand, hepatocyte growth factor (HGF), are promising targets in gastric and gastroesophageal junction cancer. We evaluated whether MET protein expression or MET gene amplification is prognostic for overall survival (OS) in Chinese patients with advanced gastric or gastroesophageal junction cancer. Archival formalin-fixed, paraffin-embedded tumor samples from patients with unresectable locally advanced or metastatic gastric or gastroesophageal junction cancer enrolled in clinical trials at Peking University Cancer Hospital from 2008 to 2010 were assessed for MET and phospho-MET (p-MET) expression by immunohistochemistry and MET amplification by FISH. MET-positive expression was defined as membrane protein staining in ≥25% of tumor cells. MET amplification was defined as MET:centromere 7 ratio &gt;2.0. We tested the association of MET status with clinical characteristics and OS, and also evaluated the association between expression and amplification. One hundred sixty-eight patients were eligible. Of the evaluable samples, 53 of 137 (39%) were MET positive, eight of 134 (6%) were p-MET positive, and eight of 113 (7%) were MET amplified. Neither MET expression nor MET amplification were associated with clinical characteristics, except Lauren classification (P = 0.04); MET amplification was associated with diffuse type. No significant OS difference was observed between MET-positive and MET-negative populations, regardless of first-line chemotherapy received. In 95 evaluable patients, MET expression was significantly associated with MET amplification (P &lt; 0.001); all MET-amplified tumor samples showed some MET expression. In 96 evaluable patients, p-MET positivity was significantly associated with MET amplification (P &lt; 0.001). Further evaluation in larger and independent sample sets is warranted to confirm our findings. Mol Cancer Ther; 14(11); 2634–41. ©2015 AACR.
A Novel Fully Humanized 3D Skin Equivalent to Model Early Melanoma Invasion
Authors: Hill David S. , Robinson Neil D.P. , Caley Matthew P. , Chen Mei , O'Toole Edel A. , Armstrong Jane L. , Przyborski Stefan , Lovat Penny E. 
Published: September 2015

AbstractMetastatic melanoma remains incurable, emphasizing the acute need for improved research models to investigate the underlying biologic mechanisms mediating tumor invasion and metastasis, and to develop more effective targeted therapies to improve clinical outcome. Available animal models of melanoma do not accurately reflect human disease and current in vitro human skin equivalent models incorporating melanoma cells are not fully representative of the human skin microenvironment. We have developed a robust and reproducible, fully humanized three-dimensional (3D) skin equivalent comprising a stratified, terminally differentiated epidermis and a dermal compartment consisting of fibroblast-generated extracellular matrix. Melanoma cells incorporated into the epidermis were able to invade through the basement membrane and into the dermis, mirroring early tumor invasion in vivo. Comparison of our novel 3D melanoma skin equivalent with melanoma in situ and metastatic melanoma indicates that this model accurately recreates features of disease pathology, making it a physiologically representative model of early radial and vertical growth-phase melanoma invasion. Mol Cancer Ther; 14(11); 2665–73. ©2015 AACR.
Cancer Metastasis: Perivascular Macrophages Under Watch
Authors: Kadioglu Ece , De Palma Michele 
Published: September 2015

Abstract
Summary: TIE2-expressing macrophages cluster around blood vessels and sustain tumor angiogenesis. Harney and colleagues now use live imaging of mouse mammary tumors to show that these perivascular macrophages also promote the transient opening of tumor blood vessels to facilitate hematogenous cancer cell dissemination and metastasis. Cancer Discov; 5(9); 906–8. ©2015 AACR.
See related article by Harney et al., p. 932.
Coordinated Membrane Ballooning and Procoagulant Spreading in Human Platelets
Authors: Agbani Ejaife O. , van den Bosch Marion T.J. , Brown Ed , Williams Christopher M. , Mattheij Nadine J.A. , Cosemans Judith M.E.M , Collins Peter W. , Heemskerk Johan W.M. , Hers Ingeborg , Poole Alastair W. 
Published: September 2015

Background—
Platelets are central to the process of hemostasis, rapidly aggregating at sites of blood vessel injury and acting as coagulation nidus sites. On interaction with the subendothelial matrix, platelets are transformed into balloonlike structures as part of the hemostatic response. It remains unclear, however, how and why platelets generate these structures. We set out to determine the physiological relevance and cellular and molecular mechanisms underlying platelet membrane ballooning.

Methods and Results—

Using 4-dimensional live-cell imaging and electron microscopy, we show that human platelets adherent to collagen are transformed into phosphatidylserine-exposing balloonlike structures with expansive macro/microvesiculate contact surfaces, by a process that we termed procoagulant spreading. We reveal that ballooning is mechanistically and structurally distinct from membrane blebbing and involves disruption to the platelet microtubule cytoskeleton and inflation through fluid entry. Unlike blebbing, procoagulant ballooning is irreversible and a consequence of Na
+
, Cl
–
, and water entry. Furthermore, membrane ballooning correlated with microparticle generation. Inhibition of Na
+
, Cl
–
, or water entry impaired ballooning, procoagulant spreading, and microparticle generation, and it also diminished local thrombin generation. Human Scott syndrome platelets, which lack expression of Ano-6, also showed a marked reduction in membrane ballooning, consistent with a role for chloride entry in the process. Finally, the blockade of water entry by acetazolamide attenuated ballooning in vitro and markedly suppressed thrombus formation in vivo in a mouse model of thrombosis.

Conclusions—
Ballooning and procoagulant spreading of platelets are driven by fluid entry into the cells, and are important for the amplification of localized coagulation in thrombosis.