A POLR3B-variant reveals a Pol III transcriptome response dependent on La protein/SSB

RNA polymerase III (Pol III, POLR3) synthesizes tRNAs and other small non-coding RNAs. Human POLR3 pathogenic variants cause a range of developmental disorders, recapitulated in part by mouse models, yet some aspects of POLR3 deficiency have not been explored. We characterized a human POLR3B:c.1625A>G;p.(Asn542Ser) disease variant that was found to cause mis-splicing of POLR3B. Genome-edited POLR3B1625A>G HEK293 cells acquired the mis-splicing with decreases in multiple POLR3 subunits and TFIIIB, although display auto-upregulation of the Pol III termination-reinitiation subunit POLR3E. La protein was increased relative to its abundant pre-tRNA ligands which bind via their U(n)U-3'-termini. Assays for cellular transcription revealed greater deficiencies for tRNA genes bearing terminators comprised of 4Ts than of ≥5Ts. La-knockdown decreased Pol III ncRNA expression unlinked to RNA stability. Consistent with these effects, small-RNAseq showed that POLR3B1625A>G and patient fibroblasts express more tRNA fragments (tRFs) derived from pre-tRNA 3'-trailers (tRF-1) than from mature-tRFs, and higher levels of multiple miRNAs, relative to control cells. The data indicate that decreased levels of Pol III transcripts can lead to functional excess of La protein which reshapes small ncRNA profiles revealing new depth in the Pol III system. Finally, patient cell RNA analysis uncovered a strategy for tRF-1/tRF-3 as POLR3-deficiency biomarkers.

Promiscuous splicing-derived hairpins are dominant substrates of tailing-mediated defense of miRNA biogenesis in mammals

Canonical microRNA (miRNA) hairpins are processed by the RNase III enzymes Drosha and Dicer into ∼22 nt RNAs loaded into an Argonaute (Ago) effector. In addition, splicing generates numerous intronic hairpins that bypass Drosha (mirtrons) to yield mature miRNAs. Here, we identify hundreds of previously unannotated, splicing-derived hairpins in intermediate-length (∼50-100 nt) but not small (20-30 nt) RNA data. Since we originally defined mirtrons from small RNA duplexes, we term this larger set as structured splicing-derived RNAs (ssdRNAs). These associate with Dicer and/or Ago complexes, but generally accumulate modestly and are poorly conserved. We propose they contaminate the canonical miRNA pathway, which consequently requires defense against the siege of splicing-derived substrates. Accordingly, ssdRNAs/mirtrons comprise dominant hairpin substrates for 3' tailing by multiple terminal nucleotidyltransferases, notably TUT4/7 and TENT2. Overall, the rampant proliferation of young mammalian mirtrons/ssdRNAs, coupled with an inhibitory molecular defense, comprises a Red Queen's race of intragenomic conflict.

Patients not taking a previously prescribed bone active medication now prescribed medication through Ontario FLS

In an Ontario fracture liaison service (FLS), we compared medication prescription rates among patients not taking a previously prescribed bone active medication to those with no previous prescription. Prescription rates were similar between these two groups of patients. The FLS provided a secondary opportunity for patients to initiate bone active medication.

PURPOSE

We compared bone active medication prescription rates among patients presenting to an Ontario fracture liaison service (FLS) who reported not taking a previously prescribed bone active medication to those with no history of prescription.

METHODS

Eligible patients were those screened in 39 fracture clinics between July 1, 2017, and September 15, 2019, who were not taking bone active medication at the time of screening and classified as high risk for future fracture based on CAROC or FRAX. Sociodemographic and clinical risk factor variables were assessed at screening. Bone active medication prescription rate was assessed within 6 months of screening and defined as having received a prescription for the medication from either a specialist or primary care provider. In cases where a specialist report was not available, patient self-reported data were collected. The chi-square test of independence was used to assess differences in prescription rates.

RESULTS

Of 17,575 patients screened, eligible patients were 350 with a previous prescription and 2644 without a previous prescription. Compared with patients who reported no previous prescription, those who had a previous prescription were older, more likely to be female and to report a previous fracture, and less likely to smoke. There was no statistically significant difference between the medication prescription rate of patients with a previous prescription (73.7%) compared to patients with no previous prescription (70.7%) (p = 0.157).

CONCLUSION

A large jurisdiction-wide FLS approach provided a secondary opportunity to patients who were not taking a previously prescribed bone active medication to initiate that medication.

TENT2, TUT4, and TUT7 selectively regulate miRNA sequence and abundance

TENTs generate miRNA isoforms by 3' tailing. However, little is known about how tailing regulates miRNA function. Here, we generate isogenic HEK293T cell lines in which TENT2, TUT4 and TUT7 are knocked out individually or in combination. Together with rescue experiments, we characterize TENT-specific effects by deep sequencing, Northern blot and in vitro assays. We find that 3' tailing is not random but highly specific. In addition to its known adenylation, TENT2 contributes to guanylation and uridylation on mature miRNAs. TUT4 uridylates most miRNAs whereas TUT7 is dispensable. Removing adenylation has a marginal impact on miRNA levels. By contrast, abolishing uridylation leads to dysregulation of a set of miRNAs. Besides let-7, miR-181b and miR-222 are negatively regulated by TUT4/7 via distinct mechanisms while the miR-888 cluster is upregulated specifically by TUT7. Our results uncover the selective actions of TENTs in generating 3' isomiRs and pave the way to investigate their functions.

Fragility fracture patients with a history of prior fractures more likely to present with multiple risk factors: findings from a province-wide fracture liaison service

We examined the demographic characteristics and risk factors of FLS fragility fracture patients who had sustained prior fragility fracture(s) and found that this is an important high-risk subgroup that warrants further attention within FLS priority pathways in order to disrupt their fragility fracture cycle.

PURPOSE

Our primary objective was to examine whether fragility fracture patients presenting to a provincial fracture liaison service (FLS) having a history of prior fractures, versus those without, differ in demographic characteristics and risk factors for future fracture. A secondary objective was to understand if those who report two or more prior fractures differ from those reporting one prior fracture.

METHODS

This cohort study included fragility fracture patients aged 50 + enrolled in the Ontario FLS between July 2017 and September 2019. Patients with versus those without prior fractures were compared on age, sex, index fracture site, biological parents' history of hip fracture, current fracture due to a fall, history of feeling unsteady when walking, history of falls in the past year, smoking, oral steroid use, and comorbid chronic conditions. Pearson's chi-square, Fischer's exact, and analysis of variance tests were used to assess differences.

RESULTS

Among 14,454 patients, 16.8% (n = 2428) reported a history of one or more prior fractures after the age of 40. They were significantly more likely to be older, female, with a higher number of comorbidities, with greater incidence of falls, and feel unsteady when walking. Compared to those with one prior fracture, patients with greater than one prior fracture were more likely to report falls in the past year and feel unsteady when walking.

CONCLUSION

Findings suggest that FLS fragility fracture patients who had sustained prior fragility fracture are an important high-risk subgroup that warrants further attention within FLS priority pathways in order to disrupt their fragility fracture cycle.

Flexible pri-miRNA structures enable tunable production of 5’ isomiRs

The Drosha cleavage of a pri-miRNA defines mature microRNA sequence. Drosha cleavage at alternative positions generates 5’ isoforms (isomiRs) which have distinctive functions. To understand how pri-miRNA structures influence Drosha cleavage, we performed a systematic analysis of the maturation of endogenous pri-miRNAs and their variants both in vitro and in vivo. We show that in addition to previously known features, the overall structural flexibility of pri-miRNA impact Drosha cleavage fidelity. Internal loops and nearby G · U wobble pairs on the pri-miRNA stem induce the use of non-canonical cleavage sites by Drosha, resulting in 5’ isomiR production. By analysing patient data deposited in the Cancer Genome Atlas, we provide evidence that alternative Drosha cleavage of pri-miRNAs is a tunable process that responds to the level of pri-miRNA-associated RNA-binding proteins. Together, our findings reveal that Drosha cleavage fidelity can be modulated by altering pri-miRNA structure, a potential mechanism underlying 5’ isomiR biogenesis in tumours.

Graphical Abstract

Cytidine acetylation yields a hypoinflammatory synthetic messenger RNA

Synthetic messenger RNA (mRNA) is an emerging therapeutic platform with important applications in oncology and infectious disease. Effective mRNA medicines must be translated by the ribosome but not trigger a strong nucleic acid-mediated immune response. To expand the medicinal chemistry toolbox for these agents, here we report the properties of the naturally occurring nucleobase N⁴-acetylcytidine (ac4C) in synthetic mRNAs. We find that ac4C is compatible with, but does not enhance, protein production in the context of synthetic mRNA reporters. However, replacement of cytidine with ac4C diminishes inflammatory gene expression in immune cells caused by synthetic mRNAs. Chemoproteomic capture indicates that ac4C alters the protein interactome of synthetic mRNAs, reducing binding to cytidine-binding proteins and an immune sensor. Overall, our studies illustrate the unique ability of ac4C to modulate RNA-protein interactions and provide a foundation for using N⁴-cytidine acylation to fine-tune the properties of nucleic acid therapeutics.

Patients 80 + have similar medication initiation rates to those aged 50-79 in Ontario FLS

Among individuals presenting to an Ontario FLS, we compared bone active medication initiation rates of patients 80 years and older with those 50-79 years old. After accounting for fracture risk status, there was no statistically significant difference in medication initiation rates between the two age groups INTRODUCTION: A Fracture Liaison Service (FLS) offers post-fracture services to individuals over the age of 50 years and could potentially address age inequities in pharmacotherapy often observed for older adults. Among individuals presenting to an Ontario FLS and classified as being at high risk for future fracture, our objective was to compare bone active medication initiation rates of patients 80 years and older with those 50-79 years old.

METHODS

In 39 FLS fracture clinics across Ontario, Canada, fracture prevention coordinators identified, assessed, and facilitated the referral of eligible patients for bone densitometry, fracture risk assessment, and implementation of pharmacotherapy in patients classified as high risk for future fracture. Variables assessed at baseline included age, sex, marital status, living location, fracture location, history of previous fracture, parent's history of hip fracture, history of falls, and fracture risk status. At 6 months, bone active medication initiation was assessed in patients classified as high risk for future fracture. The Chi-square test of independence was used to compare medication initiation rates between patients 80 + and those 50-79 years old.

RESULTS

Our sample size consisted of 808 patients aged 50-79 years and 346 aged 80 + years. After accounting for fracture risk status, there was no statistically significant difference in medication initiation rates of patients 50-79 and 80 + years old (76.9% versus 73.7%, p = 0.251).

CONCLUSION

A systematic approach to identifying patients at high risk for future fracture and tailoring treatment recommendations to these patients appeared to eliminate differences in treatment initiation rates based on older age.

Vibrio harveyi isolated from marine aquaculture species in eastern China and virulence to the large yellow croaker (Larimichthys crocea)

AIMS

Diseases of maricultured species caused by Vibrio harveyi are increasing in China and other regions. This study examined the genetic diversity, antimicrobial susceptibility, plasmid profiles and virulence potential of the V. harveyi isolated from marine organisms farmed in two provinces in eastern China between 2014 and 2019.

METHODS AND RESULTS

A total of 54 V. harveyi were obtained from seven marine species. Enterobacterial repetitive intergenic consensus (ERIC)-PCR fingerprinting revealed substantial genetic heterogeneity among the V. harveyi isolates. There was no significant correlation between ERIC-PCR genotypes and host origins or fish farms. All the isolates were resistant to amoxicillin and ampicillin, and 79·6% to kanamycin. We found that 61·1% of the V. harveyi isolates had plasmid(s) and there were 14 different plasmid profiles. Most isolates from fish hosts (76·5%) contained plasmids; however, 75% of isolates from nonfish hosts lacked plasmids. Experimental infection results showed that isolates with plasmid(s) were more virulent to large yellow croaker than isolates lacking plasmids (P < 0·05).

CONCLUSIONS

This study confirmed that V. harveyi isolates obtained from animals farmed in the coastal region of east China were genetically diverse. Our results suggest that the virulence of various V. harveyi strains to fish is associated with the plasmids they carry.

SIGNIFICANCE AND IMPACT OF THE STUDY

More than 50% of the V. harveyi isolates carried one to 11 plasmids. The plasmid-borne traits of V. harveyi strains might be important for host adaptation and virulence, but they were not associated with susceptibility to the tested antibiotics.

A graphical method for breaking logical loops based on multi-tree structure

Logical loops or circular logics, interpreted as circular supporting relations among systems, remain a longstanding challenge in the probabilistic safety assessment (PSA). Logical loops are commonly found in complex industrial systems. Due to the existence of the logical loops, the minimal cut sets cannot be directly obtained. In order to solve this problem, the logical loops should be broken properly. This paper proposes a graphical method based on multi-tree structure. By constructing the simplified multi-tree, logical loops both in linearly and non-linearly interrelated systems are solved. To illustrate this method, examples of linearly interrelated systems and non-linearly interrelated systems are given in this paper. As a supplement, this method is applied to the well-known complex logical loops in the nuclear power plant. It shows that this method is highly intuitive and efficient by means of graphs.

A graphical method for breaking logical loops based on multi-tree structure

Logical loops or circular logics, interpreted as circular supporting relations among systems, remain a longstanding challenge in the probabilistic safety assessment (PSA). Logical loops are commonly found in complex industrial systems. Due to the existence of the logical loops, the minimal cut sets cannot be directly obtained. In order to solve this problem, the logical loops should be broken properly. This paper proposes a graphical method based on multi-tree structure. By constructing the simplified multi-tree, logical loops both in linearly and non-linearly interrelated systems are solved. To illustrate this method, examples of linearly interrelated systems and non-linearly interrelated systems are given in this paper. As a supplement, this method is applied to the well-known complex logical loops in the nuclear power plant. It shows that this method is highly intuitive and efficient by means of graphs.

Pilot validation of blood-based biomarkers during pregnancy and postpartum in women with prior or current depression

Major depressive disorder (MDD) is more common in women than in men, and evidence of gender-related subtypes of depression is emerging. Previously identified blood-based transcriptomic biomarkers distinguished male and female subjects with MDD from those without the disorder. In the present pilot study, we investigated the performance of these biomarkers in pregnant and postpartum women with prior major depressive episodes, some of whom had current symptomatology. The symptom scores of 13 pregnant and 15 postpartum women were identified by the Inventory of Depressive Symptoms (IDS-SR-30) at the time of blood sampling. Blood levels of the 20 transcriptomic biomarkers and that of estrogen receptor 2 (ESR2), membrane progesterone receptor alpha and beta (mPRα, mPRβ) were measured. In pregnant women, transcript levels of ADCY3, ASAH1, ATP11C, CDR2, ESR2, FAM46A, mPRβ, NAGA, RAPH1, TLR7, and ZNF291/SCAPER showed significant association with IDS-SR-30 scores, of which ADCY3, FAM46A, RAPH1, and TLR7 were identified in previous studies for their diagnostic potential for major depression. ASAH1 and ATP11C were previously also identified as potential markers of treatment efficacy. In postpartum women, transcript levels of CAT, CD59, and RAPH1 demonstrated a trend of association with IDS-SR-30 scores. Transcript levels of ADCY3, ATP11C, FAM46A, RAPH1, and ZNF291/SCAPER correlated with ESR2 and mPRβ expressions in pregnant women, whereas these associations only existed for mPRβ in postpartum women. These results suggest that a blood biomarker panel can identify depression symptomatology in pregnant women and that expression of these biomarker genes are affected by estrogen and/or progesterone binding differently during pregnancy and postpartum.

Novel, abundant Drosha isoforms are deficient in miRNA processing in cancer cells

MicroRNAs (miRNAs) are a class of small noncoding RNAs about 22-nucleotide (nt) in length that collectively regulate more than 60% of coding genes. Aberrant miRNA expression is associated with numerous diseases, including cancer. miRNA biogenesis is licenced by the ribonuclease (RNase) III enzyme Drosha, the regulation of which is critical in determining miRNA levels. We and others have previously revealed that alternative splicing regulates the subcellular localization of Drosha. To further investigate the alternative splicing landscape of Drosha transcripts, we performed PacBio sequencing in different human cell lines. We identified two novel isoforms resulting from partial intron-retention in the region encoding the Drosha catalytic domain. One isoform (AS27a) generates a truncated protein that is unstable in cells. The other (AS32a) produces a full-length Drosha with a 14 amino acid insertion in the RIIID domain. By taking advantage of Drosha knockout cells in combination with a previously established reporter assay, we demonstrated that Drosha-AS32a lacks cleavage activity. Furthermore, neither Drosha-27a nor Drosha-32a were able to rescue miRNA expression in the Drosha knockout cells. Interestingly, both isoforms were abundantly detected in a wide range of cancer cell lines (up to 15% of all Drosha isoforms). Analysis of the RNA-seq data from over 1000 breast cancer patient samples revealed that the AS32a is relatively more abundant in tumours than in normal tissue, suggesting that AS32a may play a role in cancer development.

Transcervical dissection of metastatic suprahyoid retropharyngeal lymph nodes from papillary thyroid carcinoma through three anatomical barriers

Papillary thyroid carcinoma (PTC) rarely metastasizes to the suprahyoid retropharyngeal lymph nodes (SRPLNs). Studies on SRPLN metastasis from PTC and a description of the dissection of the SRPLNs via the transcervical approach are rare in the literature. In this study, the cases of six patients diagnosed with PTC with SRPLN metastasis, who underwent dissection of the SRPLNs between 2001 and 2017, were reviewed retrospectively. A transcervical approach was applied for exposure and dissection of the SRPLNs in all patients. All patients were successfully treated by transcervical resection of the metastatic SRPLNs. No patient needed a mandibulotomy or presented severe complications. The median duration of follow-up after dissection of the SRPLNs was 83 months. No recurrence of SRPLN metastasis was identified during follow-up, and none of the patients died of the disease. Surgery might be the best treatment for SRPLN metastasis from PTC. The transcervical route to the retropharyngeal space is through three anatomical barriers, including the submandibular gland, the posterior belly of the digastric muscle, and the blood vessels branching from the external carotid artery and internal jugular vein. Surgical removal of metastatic SRPLNs through the transcervical approach was safe and effective.

Impact of the extent of axillary surgery in patients with N2-3 disease in the de-escalation era: a propensity score-matched study

BACKGROUND

Reduction of surgeries in axillary has been proved feasible in breast cancer with negative and limited involved axillary lymph nodes. However, for women with a heavy axillary burden, the extent of dissection is still arguable.

PATIENTS AND METHODS

From a total of 7042 patients with breast cancer who underwent surgical treatments between 2008 and 2014, 692 (9.85%) patients with the axillary staging of N2-3M0 were classified into Level I-II dissection group and Level I-III dissection group. 203 pairs of patients were matched by the propensity score.

RESULTS

The positive rate of level-III lymph nodes is 62.4% in patients who underwent Level I-III dissection. There are 67 (22.1%) patients who experienced rise in staging from N2 to N3 due to level-III dissection. With a median follow-up of 62.4 months, no significant difference was observed in RFS (P = 0.897), MFS (P = 0.610) and OS (P = 0.755) between level I-II group and level I-III group. The same results were observed in the independent analysis of neoadjuvant and non-neoadjuvant subgroups. The binary regression model showed the positivity of level-III is only associated with involved lymph nodes in level-II.

CONCLUSION

Additional level-III dissection has a limited impact on survival but still valuable in an accurate stage. The reduction of surgeries in axillary should be treated with discretion in breast cancer patients with a heavy axillary burden.

AGO-bound mature miRNAs are oligouridylated by TUTs and subsequently degraded by DIS3L2

MicroRNAs (miRNAs) associated with Argonaute proteins (AGOs) regulate gene expression in mammals. miRNA 3' ends are subject to frequent sequence modifications, which have been proposed to affect miRNA stability. However, the underlying mechanism is not well understood. Here, by genetic and biochemical studies as well as deep sequencing analyses, we find that AGO mutations disrupting miRNA 3' binding are sufficient to trigger extensive miRNA 3' modifications in HEK293T cells and in cancer patients. Comparing these modifications in TUT4, TUT7 and DIS3L2 knockout cells, we find that TUT7 is more robust than TUT4 in oligouridylating mature miRNAs, which in turn leads to their degradation by the DIS3L2 exonuclease. Our findings indicate a decay machinery removing AGO-associated miRNAs with an exposed 3' end. A set of endogenous miRNAs including miR-7, miR-222 and miR-769 are targeted by this machinery presumably due to target-directed miRNA degradation.

0532 Cognitive Behavioral Therapy Delivered Via Telemedicine vs. Face-to-Face: Results from a Randomized Controlled Non-Inferiority Trial

Introduction

Telemedicine is increasingly an option for delivery of healthcare services, but its efficacy and acceptability for delivering CBT for insomnia has not been adequately tested. In a randomized controlled non-inferiority trial, we compared face-to-face and telemedicine delivery (via the AASM SleepTM platform) of CBT for insomnia for improving sleep and daytime functioning at post-treatment and 12-week follow-up.

Methods

Sixty-five adults with chronic insomnia (46 women, mean age 47.2 ± 16.3 years) were recruited primarily from insomnia clinics and screened for disqualifying sleep, medical, and mental health disorders. Eligible participants were randomized to 6 sessions of CBT for insomnia delivered face-to-face (n=32) or via AASM SleepTM (n=33). Participants completed self-report measures of insomnia (Insomnia Severity Index, ISI) and daytime functioning (fatigue, depression, anxiety, and overall functioning) at pre-treatment, post-treatment, and 12-week follow-up. The ISI was the primary non-inferiority outcome.

Results

Telemedicine was non-inferior to face-to-face delivery of CBT for insomnia, based on a non-inferiority margin of 4 points on the ISI (β = -0.07, 95% CI -2.28 to 2.14). Compared to pre-treatment, ISI scores improved significantly at post-treatment (β = -9.02, 95% CI -10.56 to -7.47) and at 12-week follow-up (β = -9.34, 95% CI -10.89 to -7.79). Similarly, daytime functioning measures improved from pre- to post-treatment, with sustained improvements at 12-week follow-up. Scores on the fatigue scale were lower in the telemedicine group at both post-treatment (F=4.64, df=1,119, p&lt;.03) and follow-up (F=5.79, df=1,119, p&lt;.02).

Conclusion

Insomnia and daytime functioning improve similarly whether CBT for insomnia is delivered via telemedicine or face-to-face. Telemedicine delivery of CBT for insomnia should be implemented more systematically to improve access to this evidence-based treatment.

Support

American Sleep Medicine Foundation Grant # 168-SR-17 (JT Arnedt, PhD)

0513 Comparison of Patient Satisfaction and Therapeutic Alliance for Telemedicine vs. Face-to-Face Delivered Cognitive Behavioral Therapy for Insomnia

Introduction

CBT for insomnia (CBTI) is effective but a barrier to its widespread use is the lack of evidence-based delivery modalities other than face-to-face. The perception and acceptability of telemedicine for the delivery of CBTI is unknown. We conducted a randomized controlled non-inferiority trial comparing face-to-face (F2F) and telemedicine (via AASM SleepTM) delivery of CBTI. We compared measures of patient satisfaction with treatment and the perception of the therapist’s warmth and skills between F2F and SleepTM.

Methods

Adults with insomnia were recruited from insomnia clinics and the community and screened for sleep, medical, and mental health disorders. Eligible participants were randomized to receive CBTI either via AASM SleepTM or F2F in 6 weekly sessions of 45-60 minutes each. Participants completed the Client Satisfaction Questionnaire (CSQ-8) and The Therapy Evaluation Questionnaire (TEQ) after completing treatment. The CSQ-8 score ranges from 8-32 with high scores indicating greater satisfaction. We also analyzed the two items on the TEQ that assess participants’ perception of therapist’s warmth and skills. Item scores ranged from 1-7, with higher scores indicating greater warmth and skills.

Results

Sixty-five adults with chronic insomnia were recruited primarily from insomnia clinics. Sixty-two participants (41 women, mean age 48.9 ± 15.4 years) completed all 6 sessions of CBTI via F2F (n=32) or via AASM SleepTM (n=30). Independent samples t-tests revealed no significant differences between conditions on patient satisfaction (SleepTM, 28.5 +/-4.2 vs F2F 29.9 +/-2.4, t(-1.5), p=.14), therapist warmth (SleepTM, 6.0 ±1.1 vs F2F, 6.4±0.95, t(-1.4), p=.16), or therapist skills (Sleep TM 6.4 ±1.0 vs F2F, 6.7±0.59, t(-1.5), p=.15).

Conclusion

Our findings suggest no differences in patient satisfaction, perception of therapist’s warmth, or confidence in therapist’s skills between telemedicine (via the AASM SleepTM) and F2F delivery of CBTI. Telemedicine-delivered CBTI should be implemented more widely.

Support

Research supported by American Sleep Medicine Foundation Grant # 168-SR-17 (JT Arnedt)

Singlet Pathway to the Ground State of Ultracold Polar Molecules

Starting from weakly bound Feshbach molecules, we demonstrate a two-photon pathway to the dipolar ground state of bi-alkali molecules that involves only singlet-to-singlet optical transitions. This pathway eliminates the search for a suitable intermediate state with sufficient singlet-triplet mixing and the exploration of its hyperfine structure, as is typical for pathways starting from triplet dominated Feshbach molecules. By selecting a Feshbach state with a stretched singlet hyperfine component and controlling the laser polarizations, we assure coupling to only single hyperfine components of the A^{1}Σ^{+} excited potential and the X^{1}Σ^{+} rovibrational ground state. In this way an ideal three level system is established, even if the hyperfine structure is not resolved. We demonstrate this pathway with ^{6}Li^{40}K molecules, and discuss its application to other important molecular species.

IsomiRs: Expanding the miRNA repression toolbox beyond the seed

MicroRNAs (miRNAs) are a class of small non-coding RNAs that play increasingly appreciated roles in gene regulation. In animals, miRNAs silence gene expression by binding to partially complementary sequences within target mRNAs. It is well-established that miRNAs recognize canonical target sites by base-pairing in the 5'region. However, the development of biochemical methods has identified many novel, non-canonical target sites, suggesting additional modes of miRNA-target association. Here, we review the current knowledge of miRNA-target recognition and how new evidence supports or challenges existing models. We also review the process by which microRNA isoforms achieve functional diversification via modulation of target recognition.

Validation of the BIOCHIP test for the diagnosis of bullous pemphigoid, pemphigus vulgaris and pemphigus foliaceus

BACKGROUND

The BIOCHIP is a novel multiplex indirect immunofluorescence technique used in the serological diagnosis of bullous pemphigoid and pemphigus. The BIOCHIP method combines the screening of autoantibodies and target antigen-specific substrates in a single miniature incubation field.

OBJECTIVE

To evaluate the diagnostic accuracy of the new immunofluorescence BIOCHIP multiplex tool in pemphigus and bullous pemphigoid.

METHODS

For the validation of the BIOCHIP, sera from patients with BP (n = 38), PF (n = 8) and pemphigus vulgaris (PV) (n = 23) were used. In addition, sera from disease control patients (n = 63) and healthy volunteers (n = 39) were used. The multiplex BIOCHIP and direct immunofluorescence (DIF) were performed for all BP, PF and PV patients. Additional indirect immunofluorescence (IIF) was performed on patients with BP, and ELISA was performed on patients with pemphigus.

RESULTS

The BIOCHIP mosaic showed a sensitivity of 86.8% and specificity of 85% for BP180 or BP230 being positive in BP. It demonstrated a sensitivity of 75% and specificity of 97.7% for Dsg1 in PF. The BIOCHIP was found to have a sensitivity of 60.9% and specificity of 73.6% for Dsg3 in PV.

CONCLUSION

The BIOCHIP mosaic-based immunofluorescence test is potentially a simple, time and effort saving test that can aid in the diagnosis and screening of BP, PV and PF. However, there is potential for interpretation bias and a learning curve that needs to be taken into consideration.

KSHV RNA-binding protein ORF57 inhibits P-body formation to promote viral multiplication by interaction with Ago2 and GW182

Cellular non-membranous RNA-granules, P-bodies (RNA processing bodies, PB) and stress granules (SG), are important components of the innate immune response to virus invasion. Mechanisms governing how a virus modulates PB formation remain elusive. Here, we report the important roles of GW182 and DDX6, but not Dicer, Ago2 and DCP1A, in PB formation, and that Kaposi's sarcoma-associated herpesvirus (KSHV) lytic infection reduces PB formation through several specific interactions with viral RNA-binding protein ORF57. The wild-type ORF57, but not its N-terminal dysfunctional mutant, inhibits PB formation by interacting with the N-terminal GW-domain of GW182 and the N-terminal domain of Ago2, two major components of PB. KSHV ORF57 also induces nuclear Ago2 speckles. Homologous HSV-1 ICP27, but not EBV EB2, shares this conserved inhibitory function with KSHV ORF57. By using time-lapse confocal microscopy of HeLa cells co-expressing GFP-tagged GW182, we demonstrated that viral ORF57 inhibits primarily the scaffolding of GW182 at the initial stage of PB formation. Consistently, KSHV-infected iSLK/Bac16 cells with reduced GW182 expression produced far fewer PB and SG, but 100-fold higher titer of infectious KSHV virions when compared to cells with normal GW182 expression. Altogether, our data provide the first evidence that a DNA virus evades host innate immunity by encoding an RNA-binding protein that promotes its replication by blocking PB formation.

3' Uridylation Confers miRNAs with Non-canonical Target Repertoires

Many microRNAs (miRNAs) exist alongside abundant miRNA isoforms (isomiRs), most of which arise from post-maturation sequence modifications such as 3' uridylation. However, the ways in which these sequence modifications affect miRNA function remain poorly understood. Here, using human miR-27a in cell lines as a model, we discovered that a nonfunctional target site unable to base-pair extensively with the miRNA seed sequence can regain function when an upstream adenosine is able to base-pair with a post-transcriptionally added uridine in the miR-27a tail. This tail-U-mediated repression (TUMR) is abolished in cells lacking the uridylation enzymes TUT4 and TUT7, indicating that uridylation alters miRNA function by modulating target recognition. We identified a set of non-canonical targets in human cells that are specifically regulated by uridylated miR-27a. We provide evidence that TUMR expands the targets of other endogenous miRNAs. Our study reveals a function of uridylated isomiRs in regulating non-canonical miRNA targets.

Etanercept reduces anxiety and depression in psoriasis patients, and sustained depression correlates with reduced therapeutic response to etanercept

BACKGROUND

The purpose of this study was to explore the correlation of anxiety and depression with therapeutic response to etanercept in psoriasis patients.

PATIENTS AND METHODS

One hundred and thirty-three patients with moderate-to-severe plaque psoriasis undergoing etanercept treatment were consecutively enrolled in this prospective cohort study, with all patients receiving etanercept treatment for 6 months. Psoriasis Area and Severity Index (PASI) score was evaluated at baseline (M0) and at month 1 (M1), M3 and M6 after treatment, and PASI 75/90 responses were calculated. The Hospital Anxiety and Depression Scale-Anxiety (HADS-A) score and the HADS-Depression (HADS-D) score were used to evaluate patients' anxiety and depression at M0, M1, M3 and M6. Sustained anxiety/depression were defined as HADS-A/D score≥8points both at M0 and M1.

RESULTS

Female gender and higher PASI score were associated with high risk of anxiety, while female gender, higher PASI score and longer disease duration were correlated with increased depression risk. After 6 months of etanercept treatment, 65.4% and 36.1% patients achieved PASI 75 and PASI 90 responses respectively, and both HADS-A and HADS-D scores were decreased. Most importantly, no correlation of baseline anxiety and depression with PASI 75 or PASI 90 response after 6 months of treatment was noted, while sustained depression, though not sustained anxiety, was observed to be correlated with decreased PASI 75 and PASI 90 responses.

CONCLUSIONS

Etanercept reduces anxiety and depression in psoriasis patients, and sustained depression correlates with reduced therapeutic response to etanercept.

Structural Differences between Pri-miRNA Paralogs Promote Alternative Drosha Cleavage and Expand Target Repertoires

MicroRNA (miRNA) processing begins with Drosha cleavage, the fidelity of which is critical for downstream processing and mature miRNA target specificity. To understand how pri-miRNA sequence and structure influence Drosha cleavage, we studied the maturation of three pri-miR-9 paralogs, which encode the same mature miRNA but differ in the surrounding scaffold. We show that pri-miR-9-1 has a unique Drosha cleavage profile due to its distorted and flexible stem structure. Cleavage of pri-miR-9-1, but not pri-miR-9-2 or pri-miR-9-3, generates an alternative miR-9 with a shifted seed sequence that expands the scope of its target RNAs. Analyses of low-grade glioma patient samples indicate that the alternative-miR-9 has a potential role in tumor progression. Furthermore, we provide evidence that distortion of pri-miRNA stems induced by asymmetric internal loops correlates with Drosha cleavage at non-canonical sites. Our studies reveal that pri-miRNA paralogs can have distinct functions via differential Drosha processing.

Human papillomavirus exposure and sexual behavior are significant risk factors for Barrett's dysplasia/esophageal adenocarcinoma

Given the comparable strains of high-risk human papillomavirus (HPV) present in a subset of Barrett's dysplasia and esophageal adenocarcinoma as in head and neck squamous cell carcinomas and the anatomical proximity of both lesions, we hypothesized that oral sex may increase the risk of Barrett's dysplasia/esophageal adenocarcinoma. Therefore, we compared the sexual behavior of patients with Barrett's dysplasia/esophageal adenocarcinoma and controls (hospital, reflux, and Barrett's metaplasia) to explore a plausible mechanism of viral transmission to the lower esophagus. A hospital-based case-control study involving 36 Barrett's dysplasia/esophageal adenocarcinoma subjects and 55 controls with known HPV DNA status and markers of transcriptional activity i.e p16INK4A and E6/E7 mRNA of the esophageal epithelium was conducted to evaluate differences in sexual history (if any). Barrett's dysplasia/esophageal adenocarcinoma patients were more likely than controls to be positive for HPV DNA (18 of 36, 50% vs. 6/55, 11%, p for trend <0.0001), be male (P = 0.001) and in a relationship (P = 0.02). Viral genotypes identified were HPV 16 (n = 14), 18 (n = 2), 11 (n = 1) and 6 (n = 1). HPV exposure conferred a significantly higher risk for Barrett's dysplasia/esophageal adenocarcinoma as compared with hospital/reflux/Barrett's metaplasia controls (OR = 6.8, 95% CI: 2.1-23.1, adjusted P = 0.002). On univariate analysis, ≥6 lifetime oral sex partners were significantly associated with dysplastic Barrett's esophagus and adenocarcinoma (OR, 4.0; 95% CI: 1.2-13.7, P = 0.046). After adjustment for confounders, HPV exposure and men with ≥2 lifetime sexual partners were at significant risk for Barrett's dysplasia/esophageal adenocarcinoma. If these initial findings can be confirmed in larger studies, it could lead to effective prevention strategies in combating some of the exponential increase in the incidence of esophageal adenocarcinoma in the West.

Clinical and echocardiographic predictors of embolism in infective endocarditis: systematic review and meta-analysis

OBJECTIVES

Prediction of embolic events (EEs) in infective endocarditis (IE) could inform clinical decisions, such as surgical timing. We conducted a systematic review to more precisely define associations between risk factors and EEs.

METHODS

We searched two bibliographic databases (1994-2018) for observational studies that reported EEs in IE patients and considered clinical, microbiological or echocardiographic risk factors. Studies that did not use Duke criteria or only investigated a subset of IE patients were excluded. Study quality was assessed using the Newcastle-Ottawa scale. A pooled risk ratio (RR) for each risk factor was estimated using random-effects models; statistical heterogeneity was estimated using I².

RESULTS

Of 3862 unique citations, 47 cohort studies (11 215 IE cases) were included; 54 risk factors were analysed in at least two studies, with nine studies reporting other individual factors. Most studies were of high methodological quality. Major predictors of EEs were intravenous drug use (RR 1.69, 95% CI 1.32-2.17; I² = 46%), Staphylococcus aureus infection (RR 1.64, 95% CI 1.45-1.86, I² = 32%), mitral valve vegetation (RR 1.24, 95% CI 1.11-1.37, I² = 30%), and vegetation size >10 mm (RR 1.87, 95% CI 1.57-2.21, I² = 48%). EE risk was also higher with human immunodeficiency virus, chronic liver disease, elevated C-reactive protein, Staphylococcus spp. infection, vegetation presence, and multiple, mobile or prosthetic mechanical valve vegetation, and lower with Streptococcus spp. infection. Most findings were unchanged in sensitivity analyses that removed studies with pulmonary EEs from the outcome.

CONCLUSIONS

Given the serious consequences of embolism, surgical evaluation may be considered in patients with these risk factors.

Lymphopenia is associated with late onset Pneumocystis jirovecii pneumonia in solid organ transplantation

BACKGROUND

Pneumocystis jirovecii pneumonia (PJP) affected 5%-15% of solid organ transplant (SOT) recipients prior to universal prophylaxis, classically with trimethoprim-sulfamethoxazole (TMP-SMX). Guidelines generally recommend 6-12 months of prophylaxis post-SOT, yet optimal duration and robust PJP risk stratification have not been established.

METHODS

A retrospective, single-center, case-control study of PJP among SOT recipients from January 1998 to December 2013 was conducted. Cases had positive PJ direct fluorescent antibody assay of respiratory specimens. Controls were matched 4:1 by nearest date of SOT. Univariate testing and multivariate logistic regressions were performed.

RESULTS

Fifteen cases were identified among 5505 SOT recipients (0.27% rate) and analyzed vs 60 controls. PJP occurred on average 6.1 years (range 0.9-13.8) post-SOT; no case was receiving PJP prophylaxis at diagnosis. Most were treated with reduced immunosuppression and TMP-SMX plus steroids (80%). Six patients (40%) required critical care; 3 (20%) died. There were no significant demographic differences, though cases tended to be older at SOT (54 vs 48 years, P = .1). In univariate analysis, prior viral infection was more common among cases (67% vs 37%, P = .08). Lower absolute lymphocyte count (ALC) at diagnosis date was strongly associated with PJP (400 vs 1230 × 10⁶  cells/μL, P < .001); odds of infection were high with ALC ≤ 500 × 10⁶ cells (OR 18.7, P < .01).

CONCLUSION

Pneumocystis jirovecii pneumonia is a rare, late complication of SOT with significant morbidity and mortality. Severe lymphopenia may be useful in identifying SOT recipients who warrant continued or reinstated PJP prophylaxis.

Abstract P3-07-08: Temozolomide as a targeted therapy strategy for triple negative breast cancer

BACKGROUND:

Approximately 15% of newly diagnosed breast cancers are classified as triple negative (TNBC). TNBCs are considered more aggressive and have a worse prognosis as no targeted therapies are currently available. These tumors are routinely treated with chemotherapy agents with only modest proven efficacy.

Temozolomide (TMZ) is an oral chemotherapy agent commonly used for the treatment of brain tumors and melanoma. TMZ is an alkylating agent, and its therapeutic benefit depends on its ability to alkylate/methylate DNA, most commonly at the N-7 or O-6 positions of guanine residues. This process leads to DNA damage and subsequently triggers cell death. Cells that express the enzyme O6-Methylguanine-DNA Methyltransferase (MGMT) are able to repair damage caused by TMZ. Tumors that lack expression of MGMT, owing to methylation of the gene promoter, demonstrate a better response to TMZ treatment as a result of synthetic lethality.

It was first reported in 2012 that TNBCs were more likely to be MGMT methylated, which was confirmed by another group that reported up to 64% of wild-type BRCA1 TNBC exhibited MGMT gene methylation. In 2013 it was found that basal-like breast cancers were more likely to be MGMT methylated and linked to larger tumor size. Together these findings suggest that a sub-population of TNBCs lack MGMT expression, due to promoter methylation.

Currently, TMZ is not a treatment option for breast cancers given the modest efficacy of TMZ noted in breast cancer clinical trials; however, most of these trials have focused on using this agent to either treat or prevent brain metastases, due to TMZs ability to cross the blood-brain barrier. Importantly, none of these trials investigated MGMT expression or specifically TNBC populations.

We hypothesize that TMZ may be a viable and efficacious treatment option for TNBCs that lack MGMT expression, due to promoter methylation.

METHODS:

We analyzed 12 archival specimens and 4 TNBC cell lines (HTB132, HTB26, HTB126 and HCC1806) for MGMT expression using a qRT-PCR clinical assay available from Calgary Laboratory Services. Additionally, we also looked at MGMT protein expression in the cell lines using Western Blot analysis to confirm the qRT-PCR results. Finally, we performed an in vitro assay with TNBC cell lines to determine cytotoxicity of TMZ.

RESULTS:

Analysis of the archival specimens found that 33% of samples analyzed had MGMT promoter methylation by qRT-PCR. Additionally, we found that HTB26 and HTB126 cell lines showed MGMT promoter methylation by qRT-pCR analysis. Western Blot analysis confirmed lack of MGMT expression in these two cell lines, and also identified another cell line (HCC1806) lacking MGMT protein that was classified as unmethylated by the qRT-PCR clinical assay. Moreover, our in vitro assay found that two cell lines (HTB26 and HCC1806) showed a noticeable response to treatment with TMZ. Interestingly, HTB126 did not show response to TMZ, suggesting that there may be another putative resistance pathway.

CONCLUSIONS:

Preliminary findings suggest that TMZ may be a viable targeted treatment option for TNBCs. Currently, we are investigating drug response using in vivo mouse models, as well as investigating synergistic combination therapy options.

Citation Format: Kornaga EN, Gratton K, Shi Q, Yang A, Nixon NA, Roldan Urgoiti G, Morris DG. Temozolomide as a targeted therapy strategy for triple negative breast cancer [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P3-07-08.

Occupational metal exposures, smoking and risk of diabetes and prediabetes

BACKGROUND

Metal exposure and tobacco smoking have been independently associated with diabetes, but no study has been conducted to investigate the interaction between them on the risk of diabetes.

AIMS

To investigate the effect of occupational exposure to metals, and potential effect modification by smoking, on the risk of diabetes and prediabetes in a cohort of Chinese male workers.

METHODS

We assessed metal exposure and tobacco smoking at baseline in the Jinchang Cohort of male workers. We used Poisson regression analyses to estimate the interaction between smoking and metal exposures based on occupations, which we grouped according to the measured urinary metal levels.

RESULTS

Among the 26008 study subjects, compared with non-smokers, the adjusted prevalence ratio (PR) for diabetes was 1.8 [95% confidence interval (CI) 1.3-2.4] for smokers of >40 pack-years. The adjusted PRs were 1.2 (95% CI 1.1-1.4) among mining/production workers and 2.7 (95% CI 2.4-3.0) among smelting/refining workers, both compared with office workers. There was significant effect modification under the additive model between smoking and metal exposure on the prevalence of diabetes (Pinteraction = 0.001), with an adjusted PR of 3.6 (95% CI 2.4-5.4) for those with >40 pack-years of smoking who had the highest metal exposures, whereas no significant interaction was observed for prediabetes.

CONCLUSIONS

Both exposure to metals and heavy smoking were associated with an increased prevalence of diabetes in this large cohort of male workers. There was also strong interaction between these two exposures in affecting diabetes risk that should be confirmed in future studies.

Use of Nested and Real-Time PCR for the Detection of Ceratocystis fagacearum in the Sapwood of Diseased Oak Species in Minnesota

Oak wilt caused by Ceratocystis fagacearum is a significant disease of Quercus spp. in the eastern United States. Early and accurate detection of the pathogen is particularly important when disease control is planned. Nested and real-time polymerase chain reaction (PCR) methods utilizing fungal DNA extracted from sapwood drill shavings of red, bur, and white oak at different stages of disease development were compared with culture-based detection from sapwood. The pathogen was detected in all (n = 3) actively wilting branches of each of nine red oak trees using all three methods. The lowest detection rate (33% of assayed branches; 6 of 8 trees) for actively wilting branches was found for white oak using isolation while nested PCR had a branch detection rate of 100% (8 of 8 trees) and real-time PCR of 87% (8 of 8 trees) for the same samples. For both bur and white oak, the pathogen was not detected by isolation in branches over 1 year after their death but was detected using both PCR methods. Only the PCR assays detected the fungus in sapwood samples underlying remnants of sporulation mats (n = 21; 90%, nested and 62%, real-time) on red oak. These PCR methods offer several significant improvements for laboratory-based detection methods of C. fagacearum.

Quantitative Characterization of the Exposure-Response Relationship for Cancer Immunotherapy: A Case Study of Nivolumab in Patients With Advanced Melanoma

To inform the benefit-risk assessment of nivolumab in patients with advanced melanoma, analyses of efficacy and safety exposure-response (E-R) relationships were conducted with data from patients with advanced melanoma enrolled in two clinical studies (phase I and phase III) who received nivolumab 0.1-10.0 mg/kg every 2 weeks. E-R efficacy analyses were performed by relating the nivolumab time-averaged concentration after the first dose (Cavg1 ) to two endpoints: RECIST objective response (OR) and overall survival (OS). E-R safety analyses characterized the relationship between nivolumab Cavg1 and the hazard of all-causality adverse events leading to discontinuation or death (AE-DC/D). Nivolumab exposure represented by Cavg1 was not a significant predictor of OR, OS, or the hazard of AE-DC/D. E-R efficacy and safety relationships were relatively flat over the exposure range.