Single-cell analysis of treatment-resistant prostate cancer: Implications of cell state changes for cell surface antigen-targeted therapies.

Targeting cell surface molecules using radioligand and antibody-based therapies has yielded considerable success across cancers. However, it remains unclear how the expression of putative lineage markers, particularly cell surface molecules, varies in the process of lineage plasticity, wherein tumor cells alter their identity and acquire new oncogenic properties. A notable example of lineage plasticity is the transformation of prostate adenocarcinoma (PRAD) to neuroendocrine prostate cancer (NEPC)-a growing resistance mechanism that results in the loss of responsiveness to androgen blockade and portends dismal patient survival. To understand how lineage markers vary across the evolution of lineage plasticity in prostate cancer, we applied single-cell analyses to 21 human prostate tumor biopsies and two genetically engineered mouse models, together with tissue microarray analysis on 131 tumor samples. Not only did we observe a higher degree of phenotypic heterogeneity in castrate-resistant PRAD and NEPC than previously anticipated but also found that the expression of molecules targeted therapeutically, namely PSMA, STEAP1, STEAP2, TROP2, CEACAM5, and DLL3, varied within a subset of gene-regulatory networks (GRNs). We also noted that NEPC and small cell lung cancer subtypes shared a set of GRNs, indicative of conserved biologic pathways that may be exploited therapeutically across tumor types. While this extreme level of transcriptional heterogeneity, particularly in cell surface marker expression, may mitigate the durability of clinical responses to current and future antigen-directed therapies, its delineation may yield signatures for patient selection in clinical trials, potentially across distinct cancer types.

Characterization of HOXB13 expression patterns in localized and metastatic castration-resistant prostate cancer.

HOXB13 is a key lineage homeobox transcription factor that plays a critical role in the differentiation of the prostate gland. Several studies have suggested that HOXB13 alterations may be involved in prostate cancer development and progression. Despite its potential biological relevance, little is known about the expression of HOXB13 across the disease spectrum of prostate cancer. To this end, we validated a HOXB13 antibody using genetic controls and investigated HOXB13 protein expression in murine and human developing prostates, localized prostate cancers, and metastatic castration-resistant prostate cancers. We observed that HOXB13 expression increases during later stages of murine prostate development. All localized prostate cancers showed HOXB13 protein expression. Interestingly, lower HOXB13 expression levels were observed in higher-grade tumors, although no significant association between HOXB13 expression and recurrence or disease-specific survival was found. In advanced metastatic prostate cancers, HOXB13 expression was retained in the majority of tumors. While we observed lower levels of HOXB13 protein and mRNA levels in tumors with evidence of lineage plasticity, 84% of androgen receptor-negative castration-resistant prostate cancers and neuroendocrine prostate cancers (NEPCs) retained detectable levels of HOXB13. Notably, the reduced expression observed in NEPCs was associated with a gain of HOXB13 gene body CpG methylation. In comparison to the commonly used prostate lineage marker NKX3.1, HOXB13 showed greater sensitivity in detecting advanced metastatic prostate cancers. Additionally, in a cohort of 837 patients, 383 with prostatic and 454 with non-prostatic tumors, we found that HOXB13 immunohistochemistry had a 97% sensitivity and 99% specificity for prostatic origin. Taken together, our studies provide valuable insight into the expression pattern of HOXB13 during prostate development and cancer progression. Furthermore, our findings support the utility of HOXB13 as a diagnostic biomarker for prostate cancer, particularly to confirm the prostatic origin of advanced metastatic castration-resistant tumors. © 2023 The Pathological Society of Great Britain and Ireland.

Genomic Characterization of Prostatic Basal Cell Carcinoma.

Basal cell carcinoma (BCC) of the prostate is a rare tumor. Compared with the more common acinar adenocarcinoma (AAC) of the prostate, BCCs show features of basal cell differentiation and are thought to be biologically distinct from AAC. The spectrum of molecular alterations of BCC has not been comprehensively described, and genomic studies are lacking. Herein, whole genome sequencing was performed on archival formalin-fixed, paraffin-embedded specimens of two cases with BCC. Prostatic BCCs were characterized by an overall low copy number and mutational burden. Recurrent copy number loss of chromosome 16 was observed. In addition, putative driver gene alterations in KIT, DENND3, PTPRU, MGA, and CYLD were identified. Mechanistically, depletion of the CYLD protein resulted in increased proliferation of prostatic basal cells in vitro. Collectively, these studies show that prostatic BCC displays distinct genomic alterations from AAC and highlight a potential role for loss of chromosome 16 in the pathogenesis of this rare tumor type.

Assessing Knowledge, Usage, and Perceptions of the Frazier Free Water Protocol: A Pilot Study.

INTRODUCTION: Dysphagia is very common among hospitalized patients and is associated with increased length of hospital stay, morbidity, and mortality. Diet restrictions for dysphagia cause dehydration and discontent. The Frazier Free Water Protocol (FFWP) was developed to improve hydration and quality of life in dysphagia patients by establishing the safety of allowing sips of water between meals. Despite these potential benefits, we hypothesized that the FFWP is not widely utilized. We sought to determine barriers to utilization by assessing the familiarity, usage, and perceptions of the FFWP among health-care providers at our institution. METHODS: We distributed an anonymous questionnaire to a convenience sample of nurses in the hospital during daily huddles. The questionnaire was adapted from a validated framework to assess provider acceptability of health-care interventions. RESULTS: Of the 66 surveys distributed, we had 58 completed (88%). Only 10 nurses (17%) had heard of the "FFWP" by name. For those that were familiar with the indications, benefits, and risks of giving free water to patients with dysphagia (n = 18), less than half (39%) reported doing so. No nurses that had less than 10 y of patient care experience gave water to dysphagia patients, even if they knew the indications, benefits, and risks. Similarly, less than a fifth (19%) of all nurses surveyed were comfortable giving water to dysphagia patients, but comfort increased for some if the protocol was recommended by a speech-language pathologist (33%) or physician (13%). Nursing experience of >10 y or in intensive care settings did not yield significant differences in knowledge, usage, or comfort level than those with less years or nonintensive care experience, respectively. CONCLUSIONS: Nurses are essential to the implementation of the FFWP, yet many are unfamiliar and uncomfortable with utilizing it. Education about the protocol is necessary to improve patient outcomes and quality of life. We plan to provide targeted education about the FFWP as well as assess other members of the health-care team, in an attempt to increase utilization of the protocol and improve dysphagia management.

Transepithelial phototherapeutic keratectomy for treatment-resistant recurrent corneal erosion syndrome.

BACKGROUND: To evaluate the efficacy and safety of trans-epithelial phototherapeutic keratectomy (TE-PTK) as a treatment for recurrent corneal erosion syndrome (RCES) in patients with symptoms refractory to conventional treatments. METHODS: All patients who received TE-PTK treatment for RCES had failed 3 or more conventional treatments and were reviewed, and if met criteria, approved by healthcare workers of the British Columbia public health authority (Medical Services Plan (MSP). A retrospective chart review and telephone survey were conducted at the Pacific Laser Eye Centre (PLEC). Exclusion criteria were ocular co-morbidities potentially affecting treatment efficacy. RESULTS: This study included 593 eyes of 555 patients (46.2% male; 50.9 ± 14.2 years old) who underwent TE-PTK. The leading identified causes of RCES were trauma (45.7%) and anterior basement membrane dystrophy (44.2%). The most common pre-PTK interventions were ocular lubricants (90.9%), hypertonic solutions (77.9%), and bandage contact lenses (50.9%). Thirty-six eyes had undergone surgical interventions such as stromal puncture, epithelial debridement, or diamond burr polishing. Post-PTK, 78% of patients did not require any subsequent therapies and 20% required ongoing drops. Six patients (1.1%) reported no symptom improvement and required repeat TE-PTK for ongoing RCES symptoms after initial TE-PTK. All 6 eyes were successfully retreated with TE-PTK (average time to retreatment was 11.3 ± 14.9 months). There was no significant difference in best corrected visual acuity pre- vs. post-operatively. The mean post-operative follow-up was 60.5 months (range: 5-127 months). CONCLUSION: TE-PTK has a good efficacy and safety profile for treatment-resistant RCES. The third-party public health-reviewed nature of this study, the low recurrence rate of RCES, and the low PTK retreatment rate suggest that TE-PTK might be considered for wider use in the management of RCES.

Structure-Activity relationships of replacements for the triazolopyridazine of Anti-Cryptosporidium lead SLU-2633.

Cryptosporidiosis is a diarrheal disease particularly harmful to children and immunocompromised people. Infection is caused by the parasite Cryptosporidium and leads to dehydration, malnutrition, and death in severe cases. Nitazoxanide is the only FDA approved drug but is only modestly effective in children and ineffective in immunocompromised patients. To address this unmet medical need, we previously identified triazolopyridazine SLU-2633 as potent against Cryptosporidium parvum, with an EC50 of 0.17 µM. In the present study, we develop structure-activity relationships (SAR) for the replacement of the triazolopyridazine head group by exploring different heteroaryl groups with the aim of maintaining potency while reducing affinity for the hERG channel. 64 new analogs of SLU-2633 were synthesized and assayed for potency versus C. parvum. The most potent compound, 7,8-dihydro-[1,2,4]triazolo[4,3-b]pyridazine 17a, was found to have a Cp EC50 of 1.2 µM, 7-fold less potent than SLU-2633 but has an improved lipophilic efficiency (LipE) score. 17a was found to decrease inhibition in an hERG patch-clamp assay by about two-fold relative to SLU-2633 at 10 µM despite having similar inhibition in a [3H]-dofetilide competitive binding assay. While most other heterocycles were significantly less potent than the lead, some analogs such as azabenzothiazole 31b, have promising potency in the low micromolar range, similar to the drug nitazoxanide, and represent potential new leads for optimization. Overall, this work highlights the important role of the terminal heterocyclic head group and represents a significant extension of the understanding of the SAR for this class of anti-Cryptosporidium compounds.

DBGC: Dimension-Based Generic Convolution Block for Object Recognition.

The object recognition concept is being widely used a result of increasing CCTV surveillance and the need for automatic object or activity detection from images or video. Increases in the use of various sensor networks have also raised the need of lightweight process frameworks. Much research has been carried out in this area, but the research scope is colossal as it deals with open-ended problems such as being able to achieve high accuracy in little time using lightweight process frameworks. Convolution Neural Networks and their variants are widely used in various computer vision activities, but most of the architectures of CNN are application-specific. There is always a need for generic architectures with better performance. This paper introduces the Dimension-Based Generic Convolution Block (DBGC), which can be used with any CNN to make the architecture generic and provide a dimension-wise selection of various height, width, and depth kernels. This single unit which uses the separable convolution concept provides multiple combinations using various dimension-based kernels. This single unit can be used for height-based, width-based, or depth-based dimensions; the same unit can even be used for height and width, width and depth, and depth and height dimensions. It can also be used for combinations involving all three dimensions of height, width, and depth. The main novelty of DBGC lies in the dimension selector block included in the proposed architecture. Proposed unoptimized kernel dimensions reduce FLOPs by around one third and also reduce the accuracy by around one half; semi-optimized kernel dimensions yield almost the same or higher accuracy with half the FLOPs of the original architecture, while optimized kernel dimensions provide 5 to 6% higher accuracy with around a 10 M reduction in FLOPs.

Phenotypic characterization of two novel cell line models of castration-resistant prostate cancer.

BACKGROUND: Resistance to androgen deprivation therapies is a major driver of mortality in advanced prostate cancer. Therefore, there is a need to develop new preclinical models that allow the investigation of resistance mechanisms and the assessment of drugs for the treatment of castration-resistant prostate cancer. METHODS: We generated two novel cell line models (LAPC4-CR and VCaP-CR) which were derived by passaging LAPC4 and VCaP cells in vivo and in vitro under castrate conditions. We performed detailed transcriptomic (RNA-seq) and proteomic analyses (SWATH-MS) to delineate expression differences between castration-sensitive and castration-resistant cell lines. Furthermore, we characterized the in vivo and in vitro growth characteristics of these novel cell line models. RESULTS: The two cell line derivatives LAPC4-CR and VCaP-CR showed castration-resistant growth in vitro and in vivo which was only minimally inhibited by AR antagonists, enzalutamide, and bicalutamide. High-dose androgen treatment resulted in significant growth arrest of VCaP-CR but not in LAPC4-CR cells. Both cell lines maintained AR expression, but exhibited distinct expression changes on the mRNA and protein level. Integrated analyses including data from LNCaP and the previously described castration-resistant LNCaP-abl cells revealed an expression signature of castration resistance. CONCLUSIONS: The two novel cell line models LAPC4-CR and VCaP-CR and their comprehensive characterization on the RNA and protein level represent important resources to study the molecular mechanisms of castration resistance.

Shared Resource Laboratory Operations: Changes Made During Initial Global COVID-19 Lockdown of 2020.

Undoubtedly, the global pandemic caused by the SARS-CoV-2 virus has had a significant impact on Shared Resource Laboratories (SRL) operations worldwide. Unlike other crises (e.g., natural disasters, acts of war, or terrorism) which often result in a sudden and sustained cessation of scientific research usually affecting one or two cities at a time, this impact is being seen simultaneously in every SRL worldwide albeit to a varying degree. The alterations to SRL operations caused by the COVID-19 pandemic can generally be divided into three categories: (1) complete shutdown, (2) partial shutdown, and (3) uninterrupted operations. In many cases, SRLs that remained partially or fully operational during the initial wave of global infections saw a concurrent increase in COVID-19-related research coming through their facilities. This forced SRLs to make rapid adjustments to core operations at the same time as infectious disease experts were still developing recommendations for the safety of frontline medical workers. Although many SRLs already had contingency plans in place, this pandemic has highlighted the importance of having such plans for continuity of service, if possible, during a crisis. Immediate changes have occurred in the way SRLs operate due to potential virus transmission and in line with this new "Best Practices" have been established, that is,social distancing, remote working, and technology-based meetings and training. Many of these changes are likely to be in place for some time with the threat of further waves of infections toward the end of 2020 and into 2021. Some of these best practices, such as having many training resources recorded and available online, are likely to remain long-term. Although many changes have been made in haste, these will alter the future operations of SRLs. In addition, we have learnt how to deal with future crises that may be encountered in the workplace. © 2020 The Authors. Cytometry Part A published by Wiley Periodicals LLC. on behalf of International Society for Advancement of Cytometry.

Type 2 Diabetes as a Determinant of Parkinson's Disease Risk and Progression.

BACKGROUND: Type 2 diabetes (T2DM) and Parkinson's disease (PD) are prevalent diseases that affect an aging population. Previous systematic reviews and meta-analyses have explored the relationship between diabetes and the risk of PD, but the results have been conflicting. OBJECTIVE: The objective was to investigate T2DM as a determinant of PD through a meta-analysis of observational and genetic summary data. METHODS: A systematic review and meta-analysis of observational studies was undertaken by searching 6 databases. We selected the highest-quality studies investigating the association of T2DM with PD risk and progression. We then used Mendelian randomization (MR) to investigate the causal effects of genetic liability toward T2DM on PD risk and progression, using summary data derived from genome-wide association studies. RESULTS: In the observational part of the study, pooled effect estimates showed that T2DM was associated with an increased risk of PD (odds ratio [OR] 1.21, 95% confidence interval [CI] 1.07-1.36), and there was some evidence that T2DM was associated with faster progression of motor symptoms (standardized mean difference [SMD] 0.55, 95% CI 0.39-0.72) and cognitive decline (SMD -0.92, 95% CI -1.50 to -0.34). Using MR, we found supportive evidence for a causal effect of diabetes on PD risk (inverse-variance weighted method [IVW] OR 1.08, 95% CI 1.02-1.14; P = 0.010) and some evidence of an effect on motor progression (IVW OR 1.10, 95% CI 1.01-1.20; P = 0.032) but not on cognitive progression. CONCLUSIONS: Using meta-analyses of traditional observational studies and genetic data, we observed convincing evidence for an effect of T2DM on PD risk and new evidence to support a role in PD progression. © 2021 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.

Draft Genome Analysis of Acinetobacter indicus Strain UBT1, an Efficient Lipase and Biosurfactant Producer.

Acinetobacter indicus strain UBT1 has shown efficient lipase (243 U ml-1) and biosurfactant (61.1% E24% emulsification and surface tension reduction to 37.7 mN m-1) production capabilities using agro-industrial waste as sole carbon source. We report here the draft genome sequence of A. indicus strain UBT1 having genome size of 2.97 Mb with 45.90% GC content. Total 2721 coding genes were predicted using National Center for Biotechnology Information-Prokaryotic Genome Annotation Pipeline (NCBI-PGAP). The whole genome shotgun project sequence data are accessible through NCBI Gene Bank under accession no. JABFOI000000000. PGAP annotation revealed the presence of the triacylglycerol lipase, phospholipase etc., that circuitously confers the oil consumption competency to the strain UBT1. Rapid Annotation using the Subsystem Technology (RAST) server used for mapping the genes to the subsystem resulted in 278 subsystem with 30% subsystem coverage. The draft genome data can be used to exploit the A. indicus strain UBT1 for its advance biotechnological application and also for further comparative genomic studies.

hnRNPC regulates cancer-specific alternative cleavage and polyadenylation profiles.

Alternative cleavage and polyadenylation (APA) can occur at more than half of all human genes, greatly enhancing the cellular repertoire of mRNA isoforms. As these isoforms can have altered stability, localisation and coding potential, deregulation of APA can disrupt gene expression and this has been linked to many diseases including cancer progression. How APA generates cancer-specific isoform profiles and what their physiological consequences are, however, is largely unclear. Here we use a subcellular fractionation approach to determine the nuclear and cytoplasmic APA profiles of successive stages of colon cancer using a cell line-based model. Using this approach, we show that during cancer progression specific APA profiles are established. We identify that overexpression of hnRNPC has a critical role in the establishment of APA profiles characteristic for metastatic colon cancer cells, by regulating poly(A) site selection in a subset of genes that have been implicated in cancer progression including MTHFD1L.

Anterior Lamellar Repositioning in the Management of Meibomian Gland Inversion Secondary to Meibomian Gland Dysfunction.

PURPOSE: To describe a simple alternative surgical approach to treat patients with Meibomian gland inversion (MGI; posterior migration of the Meibomian gland orifices) in the upper eyelid, secondary to cicatricial Meibomian gland dysfunction (MGD) not responding to maximal medical management. METHODS: This was a retrospective, noncomparative, interventional case series of all patients with MGI not responding to conservative MGD treatment who underwent anterior lamellar repositioning through a skin crease incision with or without Blepharoplasty, between July 2017 and July 2019. RESULTS: Eleven eyes of 7 patients were included in the study. All patients had a diagnosis of MGD with MGI and had been treated on average for 32 months with intensive medical therapy. Treatment included lubricants, topical ciclosporin 0.1%, topical steroids, and doxycycline. Despite intensive treatment, these patients remained symptomatic with persistent superior ocular surface staining. Following surgery, on average, the patients were followed for 23 months. Ten eyes (91%) had improvement of symptoms and superior ocular surface staining. All patients (100%) demonstrated improvement in the anatomical eversion of the eyelid margin and Meibomian gland orifice. CONCLUSION: A simple upper eyelid everting surgery with anterior lamellar repositioning can be effective in managing patients with MGI giving them symptomatic relief when all medical treatment fail. To the best of the authors' knowledge, this is the first case series describing this simple surgical technique in the management of this subgroup of patients.

Nurse-led service for children with gastrostomies: a 2-year review.

BACKGROUND: Percutaneous endoscopic gastrostomy (PEG) feeding can provide long-term nutritional support for patients with a functional gastrointestinal system but insufficient oral intake. Some patients, however, may require jejunal feeding, which can be achieved using a PEG tube with jejunal extension (PEG-J). A previous review at a tertiary paediatric hospital revealed poor documentation and a high incidence of buried bumper syndrome (BBS) in children with gastrostomies. Subsequently, a nurse-led service for gastrostomy care was introduced. AIM: To determine the impact of the nurse-led service. METHODS: Prospective review, at 1 year and 2 years, following either a PEG or PEG-J insertion. Patient records were reviewed and a telephone survey was conducted. Statistical analysis was performed using Fisher's exact test. FINDINGS: 32 PEG and 6 PEG-J patients were included in this study. There was 100% documentation of provision of care instructions. Average satisfaction with the service was over 8/10. Incidence of BBS was 0% in the PEG group and 17% in the PEG-J group. Of those parents/carers surveyed, 74% wanted additional tube care support via SMS text message. CONCLUSION: Introduction of a nurse-led service resulted in complete documentation of provision of care and sustained high levels of parental satisfaction. Future care should focus on utilising technological platforms.

Myeloid-Derived Lymphatic Endothelial Cell Progenitors Significantly Contribute to Lymphatic Metastasis in Clinical Breast Cancer.

Lymphatic metastasis is a high-impact prognostic factor for mortality of breast cancer (BC) patients, and it directly depends on tumor-associated lymphatic vessels. We previously reported that lipopolysaccharide-induced inflammatory lymphangiogenesis is strongly promoted by myeloid-derived lymphatic endothelial cell progenitors (M-LECPs) derived from the bone marrow (BM). As BC recruits massive numbers of provascular myeloid cells, we hypothesized that M-LECPs, within this recruited population, are specifically programmed to promote tumor lymphatics that increase lymph node metastasis. In support of this hypothesis, high levels of M-LECPs were found in peripheral blood and tumor tissues of BC patients. Moreover, the density of M-LECPs and lymphatic vessels positive for myeloid marker proteins strongly correlated with patient node status. It was also established that tumor M-LECPs coexpress lymphatic-specific, stem/progenitor and M2-type macrophage markers that indicate their BM hematopoietic-myeloid origin and distinguish them from mature lymphatic endothelial cells, tumor-infiltrating lymphoid cells, and tissue-resident macrophages. Using four orthotopic BC models, we show that mouse M-LECPs are similarly recruited to tumors and integrate into preexisting lymphatics. Finally, we demonstrate that adoptive transfer of in vitro differentiated M-LECPs, but not naïve or nondifferentiated BM cells, significantly increased metastatic burden in ipsilateral lymph nodes. These data support a causative role of BC-induced lymphatic progenitors in tumor lymphangiogenesis and suggest molecular targets for their inhibition.

Ancient role of vasopressin/oxytocin-type neuropeptides as regulators of feeding revealed in an echinoderm.

BACKGROUND: Vasopressin/oxytocin (VP/OT)-type neuropeptides are well known for their roles as regulators of diuresis, reproductive physiology and social behaviour. However, our knowledge of their functions is largely based on findings from studies on vertebrates and selected protostomian invertebrates. Little is known about the roles of VP/OT-type neuropeptides in deuterostomian invertebrates, which are more closely related to vertebrates than protostomes. RESULTS: Here, we have identified and functionally characterised a VP/OT-type signalling system comprising the neuropeptide asterotocin and its cognate G-protein coupled receptor in the starfish (sea star) Asterias rubens, a deuterostomian invertebrate belonging to the phylum Echinodermata. Analysis of the distribution of asterotocin and the asterotocin receptor in A. rubens using mRNA in situ hybridisation and immunohistochemistry revealed expression in the central nervous system (radial nerve cords and circumoral nerve ring), the digestive system (including the cardiac stomach) and the body wall and associated appendages. Informed by the anatomy of asterotocin signalling, in vitro pharmacological experiments revealed that asterotocin acts as a muscle relaxant in starfish, contrasting with the myotropic actions of VP/OT-type neuropeptides in vertebrates. Furthermore, in vivo injection of asterotocin had a striking effect on starfish behaviour-triggering fictive feeding where eversion of the cardiac stomach and changes in body posture resemble the unusual extra-oral feeding behaviour of starfish. CONCLUSIONS: We provide a comprehensive characterisation of VP/OT-type signalling in an echinoderm, including a detailed anatomical analysis of the expression of both the VP/OT-type neuropeptide asterotocin and its cognate receptor. Our discovery that asterotocin triggers fictive feeding in starfish provides important new evidence of an evolutionarily ancient role of VP/OT-type neuropeptides as regulators of feeding in animals.

Subcellular RNA profiling links splicing and nuclear DICER1 to alternative cleavage and polyadenylation.

Alternative cleavage and polyadenylation (APA) plays a crucial role in the regulation of gene expression across eukaryotes. Although APA is extensively studied, its regulation within cellular compartments and its physiological impact remains largely enigmatic. Here, we used a rigorous subcellular fractionation approach to compare APA profiles of cytoplasmic and nuclear RNA fractions from human cell lines. This approach allowed us to extract APA isoforms that are subjected to differential regulation and provided us with a platform to interrogate the molecular regulatory pathways that shape APA profiles in different subcellular locations. Here, we show that APA isoforms with shorter 3' UTRs tend to be overrepresented in the cytoplasm and appear to be cell-type-specific events. Nuclear retention of longer APA isoforms occurs and is partly a result of incomplete splicing contributing to the observed cytoplasmic bias of transcripts with shorter 3' UTRs. We demonstrate that the endoribonuclease III, DICER1, contributes to the establishment of subcellular APA profiles not only by expected cytoplasmic miRNA-mediated destabilization of APA mRNA isoforms, but also by affecting polyadenylation site choice.

TIM-1 Mediates Dystroglycan-Independent Entry of Lassa Virus.

Lassa virus (LASV) is an Old World arenavirus responsible for hundreds of thousands of infections in West Africa every year. LASV entry into a variety of cell types is mediated by interactions with glycosyltransferase LARGE-modified O-linked glycans present on the ubiquitous receptor α-dystroglycan (αDG). However, cells lacking αDG are permissive to LASV infection, suggesting that alternative receptors exist. Previous studies demonstrated that the phosphatidylserine (PtdSer)-binding receptors Axl and Tyro3 along with C-type lectin receptors mediate αDG-independent entry. Here, we demonstrate that another PtdSer receptor, TIM-1, mediates LASV glycoprotein (GP)-pseudotyped virion entry into αDG-knocked-out HEK 293T and wild-type (WT) Vero cells, which express αDG lacking appropriate glycosylation. To investigate the mechanism by which TIM-1 mediates enhancement of entry, we demonstrate that mutagenesis of the TIM-1 IgV domain PtdSer-binding pocket abrogated transduction. Furthermore, the human TIM-1 IgV domain-binding monoclonal antibody ARD5 blocked transduction of pseudovirions bearing LASV GP in a dose-dependent manner. Finally, as we showed previously for other viruses that use TIM-1 for entry, a chimeric TIM-1 protein that substitutes the proline-rich region (PRR) from murine leukemia virus envelope (Env) for the mucin-like domain served as a competent receptor. These studies provide evidence that, in the absence of a functional αDG, TIM-1 mediates the entry of LASV pseudoviral particles through interactions of virions with the IgV PtdSer-binding pocket of TIM-1.IMPORTANCE PtdSer receptors, such as TIM-1, are emerging as critical entry factors for many enveloped viruses. Most recently, hepatitis C virus and Zika virus have been added to a growing list. PtdSer receptors engage with enveloped viruses through the binding of PtdSer embedded in the viral envelope, defining them as GP-independent receptors. This GP-independent entry mechanism should effectively mediate the entry of all enveloped viruses, yet LASV GP-pseudotyped viruses were previously found to be unresponsive to PtdSer receptor enhancement in HEK 293T cells. Here, we demonstrate that LASV pseudovirions can utilize the PtdSer receptor TIM-1 but only in the absence of appropriately glycosylated α-dystroglycan (αDG), the high-affinity cell surface receptor for LASV. Our studies shed light on LASV receptor utilization and explain why previous studies performed with α-DG-expressing cells did not find that LASV pseudovirions utilize PtdSer receptors for virus uptake.

HSP90 inhibition sensitizes head and neck cancer to platin-based chemoradiotherapy by modulation of the DNA damage response resulting in chromosomal fragmentation.

BACKGROUND: Concurrent cisplatin radiotherapy (CCRT) is a current standard-of-care for locally advanced head and neck squamous cell carcinoma (HNSCC). However, CCRT is frequently ineffective in patients with advanced disease. It has previously been shown that HSP90 inhibitors act as radiosensitizers, but these studies have not focused on CCRT in HNSCC. Here, we evaluated the HSP90 inhibitor, AUY922, combined with CCRT. METHODS: The ability of AUY922 to sensitize to CCRT was assessed in p53 mutant head and neck cell lines by clonogenic assay. Modulation of the CCRT induced DNA damage response (DDR) by AUY922 was characterized by confocal image analysis of RAD51, BRCA1, 53BP1, ATM and mutant p53 signaling. The role of FANCA depletion by AUY922 was examined using shRNA. Cell cycle checkpoint abrogation and chromosomal fragmentation was assessed by western blot, FACS and confocal. The role of ATM was also assessed by shRNA. AUY922 in combination with CCRT was assessed in vivo. RESULTS: The combination of AUY922 with cisplatin, radiation and CCRT was found to be synergistic in p53 mutant HNSCC. AUY922 leads to significant alterations to the DDR induced by CCRT. This comprises inhibition of homologous recombination through decreased RAD51 and pS1524 BRCA1 with a corresponding increase in 53BP1 foci, activation of ATM and signaling into mutant p53. A shift to more error prone repair combined with a loss of checkpoint function leads to fragmentation of chromosomal material. The degree of disruption to DDR signalling correlated to chromosomal fragmentation and loss of clonogenicity. ATM shRNA indicated a possible rationale for the combination of AUY922 and CCRT in cells lacking ATM function. CONCLUSIONS: This study supports future clinical studies combining AUY922 and CCRT in p53 mutant HNSCC. Modulation of the DDR and chromosomal fragmentation are likely to be analytical points of interest in such trials.

Cleavage and polyadenylation: Ending the message expands gene regulation.

Cleavage and polyadenylation (pA) is a fundamental step that is required for the maturation of primary protein encoding transcripts into functional mRNAs that can be exported from the nucleus and translated in the cytoplasm. 3'end processing is dependent on the assembly of a multiprotein processing complex on the pA signals that reside in the pre-mRNAs. Most eukaryotic genes have multiple pA signals, resulting in alternative cleavage and polyadenylation (APA), a widespread phenomenon that is important to establish cell state and cell type specific transcriptomes. Here, we review how pA sites are recognized and comprehensively summarize how APA is regulated and creates mRNA isoform profiles that are characteristic for cell types, tissues, cellular states and disease.