Automatic classification of prostate cancer Gleason scores from multiparametric magnetic resonance images
Duc Fehr, Harini Veeraraghavan, Andreas Wibmer, Tatsuo Gondo, Kazuhiro Matsumoto, Herbert Alberto Vargas, Evis Sala, Hedvig Hricak, and Joseph O. Deasy
Gleason scores and ultimately the aggressiveness of prostate cancers determined using transrectal ultrasound (TRUS)-guided biopsy procedures could result in incorrect diagnosis in addition to patient discomfort. The Gleason scores determined from TRUS-guided biopsies often differ from immediate repeat biopsies and the biopsies determined following whole excision of the prostate. Our approach presents a highly accurate and automated method for differentiating between the high ≥7 and low Gleason score 6(3+3), as well as between 7(3+4) and 7(4+3) Gleason score cancers through multiparametric MRI combined with texture features computed on the same images. Noninvasive and accurate techniques such as ours can benefit patient care without subjecting them to unnecessary interventions. (See pp. E6265–E6273.)
Stochastic electrotransport selectively enhances the transport of highly electromobile molecules
Sung-Yon Kim, Jae Hun Cho, Evan Murray, Naveed Bakh, Heejin Choi, Kimberly Ohn, Luzdary Ruelas, Austin Hubbert, Meg McCue, Sara L. Vassallo, Philipp J. Keller, and Kwanghun Chung
Many chemical and biomedical techniques rely on slow diffusive transport because existing pressure-based methods or electrokinetic methods can incidentally damage the sample. This study introduces a novel transport concept termed stochastic electrotransport that can selectively and nondestructively expedite transport of electromobile molecules into a porous sample, such as fixed biological tissues. We use the method to rapidly transport several classes of molecules into whole mouse brains and other organs and achieve rapid clearing and staining of the entire tissue in record time without damaging the sample. Our new method may facilitate the application of various molecular techniques to large and dense tissues. (See pp. E6274–E6283.)
Temperature compensation and temperature sensation in the circadian clock
Philip B. Kidd, Michael W. Young, and Eric D. Siggia
Circadian clocks in animals, plants, and fungi possess the remarkable property of temperature compensation: the clock has a temperature-insensitive period, while retaining the ability to synchronize to temperature cycles. The conservation of temperature compensation across clades means it is likely critical to the function of circadian clocks. Temperature compensation also places the circadian clock in contrast to other biological pathways, which generally have temperature-sensitive time scales. However, the mechanism of temperature compensation remains unknown. We present a general scheme by which a circadian oscillator can be temperature-compensated while still synchronizing to environmental temperature cycles. In particular, we give experimental evidence that the circadian clock consists of a temperature-insensitive core oscillator coupled to a specific adaptive temperature signaling pathway. (See pp. E6284–E6292.)
Telomeric repeat-containing RNA (TERRA) constitutes a nucleoprotein component of extracellular inflammatory exosomes
Zhuo Wang, Zhong Deng, Nadia Dahmane, Kevin Tsai, Pu Wang, Dewight R. Williams, Andrew V. Kossenkov, Louise C. Showe, Rugang Zhang, Qihong Huang, José R. Conejo-Garcia, and Paul M. Lieberman
Loss of telomere repeats leads to cellular senescence and the secretion of inflammatory cytokines. How telomere dysfunction is linked to this inflammatory phenotype and its role in aging and cancer is not yet understood. We show here that noncoding telomere RNA transcripts [telomeric repeat-containing RNA (TERRA)] are secreted into the extracellular environment in exosome vesicle fractions. This cell-free TERRA (cfTERRA) is shorter and more stable than intracellular TERRA, is associated with histone proteins, and can induce inflammatory cytokines in responsive cells. These findings suggest that TERRA can have a cell extrinsic function and provide a mechanism through which telomere dysfunction can lead to the activation of inflammatory cytokine signals in the tissue microenvironment through the signaling capacity of cfTERRA. (See pp. E6293–E6300.)
JAK inhibition alleviates the cellular senescence-associated secretory phenotype and frailty in old age
Ming Xu, Tamara Tchkonia, Husheng Ding, Mikolaj Ogrodnik, Ellen R. Lubbers, Tamar Pirtskhalava, Thomas A. White, Kurt O. Johnson, Michael B. Stout, Vojtech Mezera, Nino Giorgadze, Michael D. Jensen, Nathan K. LeBrasseur, and James L. Kirkland
A hallmark of aging is chronic sterile inflammation, which is closely associated with frailty and age-related diseases. We found that senescent fat progenitor cells accumulate in adipose tissue with aging and acquire a senescence-associated secretory phenotype (SASP), with increased production of proinflammatory cytokines compared with nonsenescent cells. These cells provoked inflammation in adipose tissue and induced macrophage migration. The JAK pathway is activated in adipose tissue with aging, and the SASP can be suppressed by inhibiting the JAK pathway in senescent cells. JAK1/2 inhibitors reduced inflammation and alleviated frailty in aged mice. One possible mechanism contributing to reduced frailty is SASP inhibition. Our study points to the JAK pathway as a potential target for countering age-related dysfunction. (See pp. E6301–E6310.)
Epidermal development, growth control, and homeostasis in the face of centrosome amplification
Anita Kulukian, Andrew J. Holland, Benjamin Vitre, Shruti Naik, Don W. Cleveland, and Elaine Fuchs
The full extent to which centrosome amplification might directly contribute to human disease is poorly understood. We generated a mouse model for the induction of centrosome amplification in the skin, a tissue that remains proliferative even after its development. We uncover defects in stratification of the epidermis during development, which can be attributed to mitotic errors. The skin exhibits remarkable resiliency by clearing out these defective cells via a cell death program, however. Despite sustained centrosome amplification, adult animals are healthy and do not develop tumors or skin abnormalities. Our findings challenge the role for centrosome amplification in the initiation of skin tumorigenesis and demonstrate that certain tissues are better able to cope with its burden. (See pp. E6311–E6320.)
Chronic centrosome amplification without tumorigenesis
Benjamin Vitre, Andrew J. Holland, Anita Kulukian, Ofer Shoshani, Maretoshi Hirai, Yin Wang, Marcus Maldonado, Thomas Cho, Jihane Boubaker, Deborah A. Swing, Lino Tessarollo, Sylvia M. Evans, Elaine Fuchs, and Don W. Cleveland
Centrosomes organize the microtubule cytoskeleton in interphase and mitosis. During mitosis, the centrosomes are important for the formation and positioning of the bipolar mitotic spindle on which chromosomes are segregated. The presence of more than two centrosomes can drive mitotic chromosome segregation errors and the formation of aneuploid cells. Centrosome amplification is a common feature of aneuploid cancer cells, but a long-standing question is whether this is a cause or a consequence of tumor development. To assess this question, we generated mice in which centrosome amplification can be induced widely. Despite chronic centrosome amplification, tumorigenesis was not enhanced, demonstrating that an excess of centrosomes is not sufficient to drive tumor development. (See pp. E6321–E6330.)
Fat, weather, and date affect migratory songbirds’ departure decisions, routes, and time it takes to cross the Gulf of Mexico
Jill L. Deppe, Michael P. Ward, Rachel T. Bolus, Robert H. Diehl, Antonio Celis-Murillo, Theodore J. Zenzal Jr., Frank R. Moore, Thomas J. Benson, Jaclyn A. Smolinsky, Lynn N. Schofield, David A. Enstrom, Eben H. Paxton, Gil Bohrer, Tara A. Beveroth, Arlo Raim, Renee L. Obringer, David Delaney, and William W. Cochran
Bird migration has captivated the attention of scientists and lay people for centuries, but many unanswered questions remain about how birds negotiate large geographic features during migration. We tracked songbirds across the Gulf of Mexico to investigate the factors associated with birds’ departure decisions, arrival at the Yucatan Peninsula (YP), and crossing times. Our findings suggest that a bird’s fat reserves and low humidity, indicative of favorable synoptic weather patterns, shape departure decisions. Fat, date, and wind conditions predict birds’ detection in the YP. This study highlights the complex decision-making process involved in crossing the Gulf and its effects on migratory routes and speeds. A better understanding of the factors influencing migration across these features will inform conservation of migratory animals. (See pp. E6331–E6338.)
Genome-wide redistribution of H3K27me3 is linked to genotoxic stress and defective growth
Evelina Y. Basenko, Takahiko Sasaki, Lexiang Ji, Cameron J. Prybol, Rachel M. Burckhardt, Robert J. Schmitz, and Zachary A. Lewis
Regulators of chromatin structure play critical roles in DNA-based processes. Lysine (K) Methyltransferase 1 (KMT1) homologs perform methylation of H3 lysine-9 and are best known for their essential role in heterochromatin formation and transcriptional silencing. Heterochromatin formation is also important for maintenance of genome stability, although the mechanisms are not well understood. We report that altered activity of Polycomb repressive complex-2 (PRC2), a histone lysine-27 methyltransferase complex, is responsible for genotoxic stress, poor growth, and defective development in KMT1-deficient mutants of Neurospora crassa. Mammalian KMT1 and PRC2 are required for development and are frequently mutated in cancer. This work provides information about the cellular consequences of KMT1 and PRC2 deficiency and provides insights into the regulatory and functional relationships of these conserved enzymes. (See pp. E6339–E6348.)
Amino-terminal p53 mutations lead to expression of apoptosis proficient p47 and prognosticate better survival, but predispose to tumorigenesis
Beng Hooi Phang, Rashidah Othman, Gaelle Bougeard, Ren Hui Chia, Thierry Frebourg, Choong Leong Tang, Peh Yean Cheah, and Kanaga Sabapathy
Mutations in the amino-terminal transactivation domain of the tumor-suppressor p53 are mostly insertions or deletions, and result in loss of full-length p53 expression. However, these changes concomitantly result in the expression of a truncated p47 isoform, which retains the ability to selectively transactivate some apoptotic target genes. The selectivity appears to be due to a default feature, stemming from the lack of acetylation on K382 at the carboxyl terminus, which requires the amino terminus. Consistently, expression of p47 could prognosticate better survival in sporadic cancer patients, corroborating with its ability to induce apoptosis. However, apoptosis proficiency appears to be insufficient for tumor suppression, because these amino-terminal mutations are found in the germ line, leading to the Li–Fraumeni syndrome. (See pp. E6349–E6358.)
Reduced DOCK4 expression leads to erythroid dysplasia in myelodysplastic syndromes
Sriram Sundaravel, Ryan Duggan, Tushar Bhagat, David L. Ebenezer, Hui Liu, Yiting Yu, Matthias Bartenstein, Madhu Unnikrishnan, Subhradip Karmakar, Ting-Chun Liu, Ingrid Torregroza, Thomas Quenon, John Anastasi, Kathy L. McGraw, Andrea Pellagatti, Jacqueline Boultwood, Vijay Yajnik, Andrew Artz, Michelle M. Le Beau, Ulrich Steidl, Alan F. List, Todd Evans, Amit Verma, and Amittha Wickrema
Anemia is the predominant clinical manifestation of myelodysplastic syndromes (MDS). Genes that are aberrantly expressed and/or mutated that lead to the dysplastic erythroid morphology seen in −7/del(7q) MDS have not been identified. In this study, we show that reduced expression of dedicator of cytokinesis 4 (DOCK4) causes dysplasia by disrupting the actin cytoskeleton in developing red blood cells. In addition, our identification of the molecular pathway that leads to morphological defects in this type of MDS provides potential therapeutic targets downstream of DOCK4 that can be exploited to reverse the dysplasia in the erythroid lineage. Furthermore, we developed a novel single-cell multispectral flow cytometry assay for evaluation of disrupted F-actin filaments, which can be used for potential early detection of dysplastic cells in MDS. (See pp. E6359–E6368.)
Deciphering tissue-induced Klebsiella pneumoniae lipid A structure
Enrique Llobet, Verónica Martínez-Moliner, David Moranta, Käthe M. Dahlström, Verónica Regueiro, Anna Tomás, Victoria Cano, Camino Pérez-Gutiérrez, Christian G. Frank, Helena Fernández-Carrasco, José Luis Insua, Tiina A. Salminen, Junkal Garmendia, and José A. Bengoechea
The host launches an antimicrobial defense program upon infection. A long-held belief is that pathogens prevent host recognition by remodeling their surface in response to different host microenvironments. Yet direct evidence that this happens in vivo is lacking. Here we report that the pathogen Klebsiella pneumoniae modifies one of its surface molecules, the lipopolysaccharide, in the lungs of mice to evade immune surveillance. These in vivo-induced changes are lost in bacteria grown after isolation from the tissues. These lipopolysaccharide modifications contribute to survival in vivo and mediate resistance to colistin, one of the last options to treat multidrug-resistant Klebsiella. This work opens the possibility of designing novel therapeutics targeting the enzymes responsible for the in vivo lipid A pattern. (See pp. E6369–E6378.)
Diversity of sharp-wave–ripple LFP signatures reveals differentiated brain-wide dynamical events
Juan F. Ramirez-Villegas, Nikos K. Logothetis, and Michel Besserve
Sharp-wave–ripple (SPW-R) episodes observed in the electrical activity of mammalian hippocampus are traditionally associated to memory consolidation during sleep but have been recently observed during active behavior. Their involvement in various cognitive functions suggests the existence of SPW-R subtypes engaged in distinct neuronal activity patterns at multiple scales. We use concurrent electrophysiological and functional MRI (fMRI) recordings in macaque monkeys to investigate this hypothesis. We discover several subtypes of SPW-R with distinct electrophysiological properties. Importantly, fMRI recordings reveal differences between the large-scale signatures of SPW-R subtypes, indicating differentiated interactions with neocortex, and contributions of neuromodulatory pathways to the SPW-R phenomenon. Understanding the detailed properties of hippocampal SPW-Rs at multiple scales will provide new insights on the function of memory systems. (See pp. E6379–E6387.)
Plant Raf-like kinase integrates abscisic acid and hyperosmotic stress signaling upstream of SNF1-related protein kinase2
Masashi Saruhashi, Totan Kumar Ghosh, Kenta Arai, Yumiko Ishizaki, Kazuya Hagiwara, Kenji Komatsu, Yuh Shiwa, Keiichi Izumikawa, Harunori Yoshikawa, Taishi Umezawa, Yoichi Sakata, and Daisuke Takezawa
Plants can sense loss of water caused by drought and stimulate internal mechanisms for protecting cells from damage with the aid of the stress hormone abscisic acid (ABA). Analysis of a mutant of the basal land plant, the moss Physcomitrella patens, revealed that an impairment of a protooncogene Raf-like protein kinase, designated “ARK” (for “ABA and abiotic stress-responsive Raf-like kinase”), causes a loss of both ABA sensitivity and osmotic stress tolerance. We show evidence that ARK has a role in integrating ABA and osmotic signals upstream of the sucrose nonfermenting 1-related protein kinase2, known to be a central regulator of stress signaling in plants. (See pp. E6388–E6396.)
Hormone-regulated defense and stress response networks contribute to heterosis in Arabidopsis F1 hybrids
Michael Groszmann, Rebeca Gonzalez-Bayon, Rebecca L. Lyons, Ian K. Greaves, Kemal Kazan, W. James Peacock, and Elizabeth S. Dennis
Hybrids are extensively used in agriculture to deliver increases in crop yields, yet the molecular basis of their superior performance (heterosis) is not well understood. We report that some Arabidopsis F1 hybrids show changes to salicylic acid- and auxin-regulated defense and stress response gene expression. These changes could be important for generating the greater growth of some hybrids given the antagonistic relationship between plant growth and defense responses. Hybrids showing different levels of heterosis have changes in the salicylic acid- and auxin-regulated pathways that correlate with differences in the enhanced leaf growth. The larger leaves, and thus greater capacity for energy production, support the increased growth vigor and seed yields of the hybrids. (See pp. E6397–E6406.)