P-288 COVID vaccination in women and IVF treatment outcomes

Study question

Does COVID-19 vaccination (mRNA or viral vector) in women affect outcomes following IVF treatment?

Summary answer

There was no difference in both pre-clinical and IVF clinical outcomes in women who received vaccination (1 or 2 doses) compared to those unvaccinated.

What is known already

The COVID-19 vaccination rollout has been unprecedented and commenced in the UK in December 2020.

Compared to the general population, pregnant women have higher risk of morbidity following COVID-19 infection. There is a drive by public health authorities for women of reproductive age to be vaccinated. However, there has been hesitancy in the uptake of vaccination amongst certain patient populations including those who are trying to conceive.

Emerging data has shown that follicular function is unaffected by COVID-19 vaccination, although this data is limited. IVF treatment is unique as we can evaluate both pre-clinical embryological outcomes and clinical outcomes.

Study design, size, duration

We conducted a retrospective analysis of 474 women undergoing IVF treatment between Jan and Dec 2021. COVID-19 vaccination status was recorded including: vaccination type, number of vaccine doses, and whether they had previously contracted COVID-19. We recorded pre-clinical and clinical outcomes: such as number of oocytes retrieved, fertilisation rate and clinical pregnancy.

Participants/materials, setting, methods

Women were categorised in the three cohorts- unvaccinated (Group 1), defined as the reference group, women who had first dose of COVID-19 vaccine (Group 2) and patients who had two doses of the vaccine (Group 3). Patients whose vaccination status were not known were excluded. Statistical analysis was performed through STATA software. Outcomes were modelled with multivariable logistic and negative binomial regressions and adjusted for the following confounders: age, BMI, parity and past COVID-19 infection.

Main results and the role of chance

Data from women was analysed, 22.6 % had completed 2 doses, 9.5 % had one vaccine and 9.7% were unvaccinated. Among these women 24.7% had previous COVID-19 infection prior to their IVF cycle.

The median number of oocytes retrieved for the entire cohort collected was 10.0 (inter-quartile range (IQR) 6.0, 14.0). There was no significant difference in the number of oocytes retrieved between women who had 1 vaccination dose, 2 doses compared to unvaccinated women (Incidence rate ratios (IRR) 1.18, 95% Confidence Interval (CI) [0.93,1.50] and 0.94, 95% CI [0.76,1.15] respectively).

There was no significance difference in the fertilisation rate between women who had one vaccination dose, 2 doses and unvaccinated women (IRR)1.02, 95% CI [0.83, 1.24] and 1.11 95% CI [0.93, 1.31] or failed fertiisation rates (Odds ratio (OR) 0.74, 95% CI [0.09, 6.09] and 0.71, 95% CI [0.12, 4.18].

With regards to clinical outcomes, 51.7% of the cohort had a positive urine pregnancy test. There was no significant difference in clinical pregnancy rate between women who had first vaccination dose and those who had both doses compared to unvaccinated women (OR 3.06, 95% CI [0.37, 3.68] & OR 1.7, 95% CI [ 0.64, 4.52] respectively).

Limitations, reasons for caution

This is a retrospective study and further accumulated data is warranted to validate the findings. Many patients at the time of analysis were still pregnant, hence we await live birth outcomes.

Wider implications of the findings

This is the first study to analyse the impact of COVID-19 vaccination on IVF outcomes. These initial findings are reassuring to patients and fertility clinicians on the safety of vaccination.

Trial registration number

not applicable

Multiomic analysis to reveal distinct molecular profiles of uterine and nonuterine leiomyosarcoma

11555

Background: Leiomyosarcoma (LMS) is a rare group of mesenchymal malignancies found in the uterus, retroperitoneum, skin, or other soft-tissue sites. Treatment for LMS is extrapolated from trials including both uterine (uLMS) and non-uLMS subtypes, although whether they respond similarly and have similar outcomes from treatment is not clear. We examined the molecular composition of LMS by site of origin to better inform future drug development and trial design. Methods: We reviewed 1115 specimens with LMS histology tested by Caris Life Sciences for targeted exome (NextSeq, 592 gene panel), whole exome, and whole transcriptome sequencing (NovaSeq). Specimens were stratified into uLMS, rpLMS (retroperitoneal), and otherLMS (non-uterine/retroperitoneal) subgroups based on tumor origin sites. Genomic data was analyzed for mutations, copy number aberrations, and fusions. RNA expression profiling included evaluation of individual genes and gene set enrichment analysis (GSEA). P-value adjustment performed by the Benjamini-Hochberg procedure. Results: The study cohort was comprised of 62.9% uLMS (n = 701), 14.9% rpLMS (n = 166) and 22.2% otherLMS (n = 248) specimens. Overall, LMS specimens most frequently harbored TP53 (64%, n = 612), ATRX (30%, n = 219), RB1 (22%, n = 156), and MED12 (16%, n = 94) mutations, with these genes accounting for 74.4% (n = 1044) of all observed pathogenic/likely pathogenic mutations. RB1 mutations were significantly less common in uLMS (15%) compared to rpLMS (30%, p < 0.05) and otherLMS (33%, p < 0.01), whereas MED12 mutations were almost exclusive to uLMS (22% vs 1% rpLMS, 3% otherLMS, p < 0.05). MAP2K4 copy number amplification were more common in rpLMS (22%, p < 0.001) and otherLMS (14%, p < 0.182) compared to uLMS (7%), with frequent co-amplification of nearby genes ( FLCN, GID4, SPECC1, GAS7, PER1, and AURKB) located at chr17p11-13. Actionable gene fusions involving ALK (2.1%, n = 11), FGFR1 (0.2%, n = 1), and NTRK1/2 (0.2%, n = 1 each) were rare overall, with similar prevalence across subtypes. Genomic alteration rates were not significantly different between rpLMS and otherLMS subtypes . RNA expression profiling identified significant upregulation of PI3K/AKT/mTOR, DDR, WNT/Beta-Catenin pathway genes in non-uLMS. GSEA indicated several immune-related gene sets were enriched in rpLMS and otherLMS compared to uLMS. Conclusions: Comprehensive molecular profiling suggests that LMS originating from the uterus represents a molecularly distinct disease compared to other primary sites of origin. We identified key genomic patterns which have potential for targeted therapy. These data provide insight for the framework of future clinical trials designed to separate uLMS from non-uLMS histologies, although further subdivision does not appear to be warranted.

Large scale multiomic analysis suggests mechanisms of resistance to immunotherapy in leiomyosarcoma

11512

Background: Leiomyosarcomas (LMS) have been reported to have immunohistochemical (IHC) and gene expression signatures suggestive of an immune-responsive tumor microenvironment. Despite this, immune checkpoint inhibitors have demonstrated minimal activity in LMS. We examined molecular profiles of LMS specimens from multiple institutions to explore mechanisms of immunotherapy (IO) resistance. Methods: LMS specimens (n = 1115), including 701 uterine (uLMS) and 414 soft tissue site (stLMS) samples, underwent next-generation sequencing (NGS) of DNA (592-gene panel or whole exome) and RNA (whole transcriptome, n = 537) at Caris Life Sciences (Phoenix, AZ). A threshold of 10 mut/Mb was used to identify high tumor mutational burden (TMB-H). IHC was performed for PD-L1 (SP142; 2+|5% positive). Deficient mismatch repair (dMMR)/high microsatellite instability (MSI-H) was tested by IHC and NGS, respectively. RNA expression was analyzed using Gene Set Enrichment Analysis and Microenvironment Cell Populations-counter, with results compared to melanoma (n = 1255) as a representative immunogenic tumor type. P-values were adjusted for multiple hypothesis testing. Results: TMB-H was observed in 3.8% (n = 41) of LMS specimens, with a median of 5 mut/Mb (IQR 3.3-6.7). dMMR/MSI-H was rarely detected (1.5%, n = 17), whereas 8.2% (n = 88) were positive for PD-L1 expression. uLMS and stLMS did not differ in TMB-H (3.4 vs 4.5%, p = 0.277), PD-L1 expression (8.6 vs 7.4%, p = 0.322), or dMMR/MSI-H (2.0 vs 0.7% p = 0.207). stLMS demonstrated upregulation of immune-related gene sets, including interferon γ (p = 0.035) and α (p = 0.033) response, inflammatory response (p = 0.038), interleukin-6/STAT3 signaling (p = 0.030), and TNFα signaling (p = 0.026) compared to uLMS. Immune cell infiltration was increased in stLMS over uLMS, most notably for CD8 T-cell and B-cell abundance ( > 2-fold increase, p < 0.0001). Compared to melanoma, all LMS had lower abundance of CD8 T cells, cytotoxic lymphocytes, and B-cells ( > 2-fold decrease, p < 0.0001). Fibroblasts were more prevalent in LMS relative to melanoma (3.2-fold increase, p < 0.0001). Interestingly, while higher CD8 T-cell infiltration was positively associated with dMMR/MSI-H among LMS specimens (p = 0.032), TMB-H and PD-L1 expression were associated with lower CD8 T-cell infiltration (p < 0.01). Conclusions: Only a small proportion of LMS are TMB-H or MSI-H, suggesting that the neoantigen burden in LMS may be insufficient to promote a robust anti-tumor response, even in the presence of PD-L1 positive tumor cells. Traditional predictive biomarkers of response to IO are unlikely to be useful in LMS. Furthermore, both uLMS and stLMS have an immune microenvironment characterized by a high fibroblast and low T cell abundance relative to melanoma. Future IO trials in LMS should focus on combination therapies that may reverse the observed T-cell exclusion/desmoplastic phenotype.

Randomized Trial Based on the Common-Sense Model of Self-regulation to Increase Child Dental Visits

INTRODUCTION

School screening and the note home (pinned to a backpack) informing parents/caregivers that their child needs to see a dentist have not been effective.

OBJECTIVES

The Family Access to a Dentist Study (FADS) evaluated the effectiveness of school interventions based on the common-sense model of self-regulation (CSM) among K-4 children needing restorative treatment.

METHODS

FADS was a multisite double-blind randomized controlled trial with 5 arms. FADS tested a CSM-driven referral letter and dental information guide (DIG) to move caregivers from inaccurate to accurate perceptions of dental caries. Six school districts from Ohio and Washington (14 schools) participated in school years 2015 to 2016 and 2016 to 2017. A total of 611 caregivers were randomized, and 86% (n = 597 children) completed the exit examination. The primary outcome was receipt of care based on a change in oral health status determined clinically within 1 school year.

RESULTS

In accordance with our primary aims, 5 arms were collapsed into 3: CSM letter and reduced CSM letter (combined), CSM letter + DIG and reduced CSM letter + reduced DIG (combined), and standard letter. Among all sites, 39.7% received restorative care (237 of 597). Combined analysis of sites revealed that the CSM referral letter (with and without the DIG) did not increase dental visits when compared with the standard letter. However, for combined sites (East Cleveland, Ohio; Washington), the CSM + DIG increased dental visits when compared with standard letter in univariate analysis (51.3% vs. 40.9%), indicating 1.6-times increased odds of a dental visit (95% CI, 0.97 to 2.58) after imputation and adjustment for covariates. The CSM + DIG group had 1.9-times increased odds (95% CI, 1.21 to 3.08) of care when compared the CSM letter alone.

CONCLUSION

A CSM-driven approach to informing caregivers of the chronic nature of caries with resources in an illustrative manner can increase the benefit of school oral health screening (ClinicalTrials.gov NCT02395120).

KNOWLEDGE TRANSFER STATEMENT

A school dental referral (note home) that tells a parent that the child has cavities has not been effective. In this trial, a referral based on the common-sense model of self-regulation increased follow-up care for children with restorative needs.

VITamin D and OmegA-3 TriaL (VITAL) bone health ancillary study: clinical factors associated with trabecular bone score in women and men

We investigated the association of clinical variables with TBS at baseline in the bone health sub-cohort of the VITamin D and OmegA-3 TriaL (VITAL). Lower TBS was associated with female sex, aging, BMI ≥ 25 kg/m², SSRI use, high alcohol intake, and presence of diabetes; there was a trend towards significance between lower TBS and history of fragility fractures.

INTRODUCTION

We investigated whether TBS differs by sex, race, body mass index (BMI), and other clinical variables.

METHODS

The VITamin D and OmegA-3 TriaL (VITAL) is determining effects of vitamin D₃ and/or omega-3 fatty acid (FA) supplements in reducing risks of cancer and cardiovascular disease. In the VITAL: Effects on Bone Structure/Architecture ancillary study, effects of these interventions on bone will be investigated. Here, we examine the associations of clinical risk factors with TBS assessments at baseline in the bone health sub-cohort, comprised of 672 participants (369 men and 303 women), mean (± SD) age 63.5 ± 6.0 years; BMI ≤ 37 kg/m², no bisphosphonates within 2 years or other bone active medications within 1 year.

RESULTS

TBS was greater in men than women (1.311 vs. 1.278, P < 0.001) and lower with elevated BMIs (P < 0.001), higher age (P = 0.004), diabetes (P = 0.008), SSRI use (P = 0.044), and high alcohol intake (P = 0.009). There was a trend for history of fragility fractures (P = 0.072), and lower TBS. TBS did not vary when analyzed by race, smoking, history of falls, and multivitamin or caffeine use.

CONCLUSIONS

Lower TBS was associated with female sex, aging, BMI ≥ 25 kg/m², SSRI use, alcohol use, and presence of diabetes; there was a trend between lower TBS and history of fragility fractures. TBS may be useful clinically to assess structural changes that may be associated with fractures among patients who are overweight or obese, those on SSRIs, or with diabetes. Ongoing follow-up studies will clarify the effects of supplemental vitamin D₃ and/or FA's on TBS and other bone health measures.

TRIAL REGISTRATION

NCT01747447.

Setting spatial conservation priorities despite incomplete data for characterizing metapopulations

Management of spatially structured species poses unique challenges. Despite a strong theoretical foundation, practitioners rarely have sufficient empirical data to evaluate how populations interact. Rather, assumptions about connectivity and source-sink dynamics are often based on incomplete, extrapolated, or modeled data, if such interactions are even considered at all. Therefore, it has been difficult to evaluate whether spatially structured species are meeting conservation goals. We evaluated how estimated metapopulation structure responded to estimates of population sizes and dispersal probabilities and to the set of populations included. We then compared outcomes of alternative management strategies that target conservation of metapopulation processes. We illustrated these concepts for Chinook salmon (Oncorhynchus tshawytscha) in the Snake River, USA. Our description of spatial structure for this metapopulation was consistent with previous characterizations. We found substantial differences in estimated metapopulation structure when we had incomplete information about all populations and when we used different sources of data (three empirical, two modeled) to estimate dispersal, whereas responses to population size estimates were more consistent. Together, these findings suggest that monitoring efforts should target all populations occasionally and populations that play key roles frequently and that multiple types of data should be collected when feasible. When empirical data are incomplete or of uneven quality, analyses using estimates produced from an ensemble of available datasets can help conservation planners and managers weigh near-term options. Doing so, we found trade-offs in connectivity and source dominance in metapopulation-level responses to alternative management strategies that suggest which types of approaches may be inherently less risky.

The effects of feeding history and environment on condition, body composition and growth of bluegills Lepomis macrochirus

Initial relative mass (W(R), low v. high) and energetic trajectory in time (starved v. fed) were experimentally manipulated in bluegill Lepomis macrochirus. Fed fish starting at low W(R) grew more and gained more W(R) than fed fish starting at high W(R). Similarly, starved fish starting at high W(R) lost more mass and W(R) than did starved fish starting at low W(R). Temporal changes in other variables did not consistently match that of W(R), but, by the end of the experiment, proximate composition showed a high correlation to W(R). Regression slopes of W(R) on proximate composition increased with time in the laboratory. Differences between wild and laboratory fish appeared to result from relaxation of environmental stress. When excess resources are available such that L. macrochirus grow, condition indices will increase, but individual response will depend on initial values and thus past environmental experience.

C-TAK1 regulates Ras signaling by phosphorylating the MAPK scaffold, KSR1

Kinase suppressor of Ras (KSR) is a conserved component of the Ras pathway that interacts directly with MEK and MAPK. Here we show that KSR1 translocates from the cytoplasm to the cell surface in response to growth factor treatment and that this process is regulated by Cdc25C-associated kinase 1 (C-TAK1). C-TAK1 constitutively associates with mammalian KSR1 and phosphorylates serine 392 to confer 14-3-3 binding and cytoplasmic sequestration of KSR1 in unstimulated cells. In response to signal activation, the phosphorylation state of S392 is reduced, allowing the KSR1 complex to colocalize with activated Ras and Raf-1 at the plasma membrane, thereby facilitating the phosphorylation reactions required for the activation of MEK and MAPK.

The potency and specificity of the interaction between the IA3 inhibitor and its target aspartic proteinase from Saccharomyces cerevisiae

The yeast IA3 polypeptide consists of only 68 residues, and the free inhibitor has little intrinsic secondary structure. IA3 showed subnanomolar potency toward its target, proteinase A from Saccharomyces cerevisiae, and did not inhibit any of a large number of aspartic proteinases with similar sequences/structures from a wide variety of other species. Systematic truncation and mutagenesis of the IA3 polypeptide revealed that the inhibitory activity is located in the N-terminal half of the sequence. Crystal structures of different forms of IA3 complexed with proteinase A showed that residues in the N-terminal half of the IA3 sequence became ordered and formed an almost perfect alpha-helix in the active site of the enzyme. This potent, specific interaction was directed primarily by hydrophobic interactions made by three key features in the inhibitory sequence. Whereas IA3 was cut as a substrate by the nontarget aspartic proteinases, it was not cleaved by proteinase A. The random coil IA3 polypeptide escapes cleavage by being stabilized in a helical conformation upon interaction with the active site of proteinase A. This results, paradoxically, in potent selective inhibition of the target enzyme.

Designing a quality assurance system for dietary data in a multicenter clinical trial: Women's Intervention Nutrition Study

Reliable dietary intake data are essential for determining outcomes in nutrition-related clinical trials. Nevertheless, systems for quality assurance of dietary intake data are often slighted in the design of such trials and not incorporated or monitored as the trials continue. The Women's Intervention Nutrition Study (WINS), a multicenter clinical trial investigating the effect of reduction of dietary fat intake together with adjuvant systemic therapy on recurrence rates in and survival of postmenopausal women with early stage, surgically treated, breast cancer, has developed a quality assurance system to minimize errors and to produce data that are complete and reliable. The system involves development of standardized procedures for data collection, a quality control program to evaluate the data collected, and continual monitoring and reevaluation. The WINS system is offered as a model for studies collecting dietary intake data, no matter how simple or complex the trial design.

Cutting costs without drawing blood

When looking for ways to cut costs, most managers reach for the head-count hatchet, and the markets usually roar with approval. But a company can almost always create far more sustainable value by rigorously evaluating the small-ticket capital items that often get rubber-stamped. Drawing on his experience as a consultant and providing numerous anecdotes, the author contends that those "little" requests often prove to be gold plated or unnecessary. A disciplined evaluation involves asking only eight questions and conducting postmortems--regular audits of units' capital spending. But the payoff is enormous. Because cutting the capital budget increases cash flow, the author argues that a permanent cut of just 15% in the planned level of capital spending could boost some companies' market capitalization by as much as 30%. The first three questions--Is this your investment to make? Does it really have to be new? How are our competitors meeting compliance needs?--are asked of operating managers as they assemble capital project requests. The next three are asked by senior managers of themselves and their colleagues as they examine proposals: Is the left hand duplicating investments made by the right? Are trade-offs between profit and capital spending well understood? Are there signs of budget massage? At the end of the review process, senior managers ask: Are we fully using shared assets? How fine-grained are our capacity measures? The author's suggestions for the postmortem include searching for systematic problems with whole classes of expenditures and making sure audit teams come up with specific recommendations for change.

Comparative evaluation of benzodiazepines for control of soman-induced seizures

This study evaluated the ability of six benzodiazepines to stop seizures produced by exposure to the nerve agent soman. Guinea pigs, previously prepared with electrodes to record electroencephalographic (EEG) activity, were pretreated with pyridostigmine (0.026 mg/kg, i.m.) 30 min before challenge with soman (56 microg/kg, s.c.) and then treated 1 min after soman exposure with atropine (2.0 mg/kg, i.m.) and pralidoxime chloride (2-PAM Cl; 25 mg/kg, i.m.). All animals developed seizures following this treatment. Benzodiazepines (avizafone, clonazepam, diazepam, loprazolam, lorazepam, and midazolam) were given i.m. 5 or 40 min after seizure onset. All benzodiazepines were effective in stopping soman-induced seizures, but there were marked differences between drugs in the rapidity of seizure control. The 50% effective dose (ED50) values and latencies for anticonvulsant effect for a given benzodiazepine were the same at the two times of treatment delay. Midazolam was the most potent and rapidly acting compound at both treatment times. Since rapid seizure control minimizes the chance of brain damage, use of midazolam as an anticonvulsant may lead to improved clinical outcome in the treatment of nerve agent seizures.

hMSH5: a human MutS homologue that forms a novel heterodimer with hMSH4 and is expressed during spermatogenesis

MutS homologues have been identified in nearly all organisms examined to date. They play essential roles in maintaining mitotic genetic fidelity and meiotic segregation fidelity. MutS homologues appear to function as a molecular switch that signals genomic manipulation events. Here we describe the identification of the human homologue of the Saccharomyces cerevisiae MSH5, which is known to participate in meiotic segregation fidelity and crossing-over. The human MSH5 (hMSH5) was localized to chromosome 6p22-21 and appears to play a role in meiosis because expression is induced during spermatogenesis between the late primary spermatocytes and the elongated spermatid phase. hMSH5 interacts specifically with hMSH4, confirming the generality of functional heterodimeric interactions in the eukaryotic MutS homologue, which also includes hMSH2-hMSH3 and hMSH2-hMSH6.

Synergistic activities of multiple phosphotyrosine residues mediate full signaling from the Drosophila Torso receptor tyrosine kinase

Here, we identify four tyrosine residues (Y644, Y698, Y767, and Y772) that become phosphorylated after activation of the Torso (Tor) receptor tyrosine kinase. Previously, we characterized phosphotyrosine sites (P-Y630 and P-Y918). Of the six P-Y sites identified, three (Y630, Y644, and Y698) are located in the kinase domain insert region, one (Y918) is located in the C-terminal tail region, and two (Y767 and Y772) are located in the activation loop of the kinase domain. To investigate the function of each P-Y residue in Tor signaling, we have generated transgenic Drosophila embryos expressing mutant Tor receptors containing either single or multiple tyrosine to phenylalanine substitutions. Single P-Y mutations were found to have either positive, negative, or no effect on the signaling activity of the receptor. Elimination of all P-Y sites within the kinase insert region resulted in the complete loss of receptor function, indicating that some combination of these sites is necessary for Tor signaling. Mutation of the C-terminal P-Y918 site revealed that this site is responsible for negative signaling or down-regulation of receptor activity. Mutation of the P-Y sites in the kinase domain activation loop demonstrated that these sites are essential for enzymatic activity. Our analysis provides a detailed in vivo example of the extent of cooperativity between P-Y residues in transducing the signal received by a receptor tyrosine kinase and in vivo data demonstrating the function of P-Y residues in the activation loop of the kinase domain.

Identification of constitutive and ras-inducible phosphorylation sites of KSR: implications for 14-3-3 binding, mitogen-activated protein kinase binding, and KSR overexpression

Genetic and biochemical studies have identified kinase suppressor of Ras (KSR) to be a conserved component of Ras-dependent signaling pathways. To better understand the role of KSR in signal transduction, we have initiated studies investigating the effect of phosphorylation and protein interactions on KSR function. Here, we report the identification of five in vivo phosphorylation sites of KSR. In serum-starved cells, KSR contains two constitutive sites of phosphorylation (Ser297 and Ser392), which mediate the binding of KSR to the 14-3-3 family of proteins. In the presence of activated Ras, KSR contains three additional sites of phosphorylation (Thr260, Thr274, and Ser443), all of which match the consensus motif (Px[S/T]P) for phosphorylation by mitogen-activated protein kinase (MAPK). Further, we find that treatment of cells with the MEK inhibitor PD98059 blocks phosphorylation of the Ras-inducible sites and that activated MAPK associates with KSR in a Ras-dependent manner. Together, these findings indicate that KSR is an in vivo substrate of MAPK. Mutation of the identified phosphorylation sites did not alter the ability of KSR to facilitate Ras signaling in Xenopus oocytes, suggesting that phosphorylation at these sites may serve other functional roles, such as regulating catalytic activity. Interestingly, during the course of this study, we found that the biological effect of KSR varied dramatically with the level of KSR protein expressed. In Xenopus oocytes, KSR functioned as a positive regulator of Ras signaling when expressed at low levels, whereas at high levels of expression, KSR blocked Ras-dependent signal transduction. Likewise, overexpression of Drosophila KSR blocked R7 photoreceptor formation in the Drosophila eye. Therefore, the biological function of KSR as a positive effector of Ras-dependent signaling appears to be dependent on maintaining KSR protein expression at low or near-physiological levels.

Drug-resistant HIV-1 proteases identify enzyme residues important for substrate selection and catalytic rate

A series of mutations, first identified in protease inhibitor-resistant HIV-1 viral isolates, were introduced into HIV-1 PR as individual substitutions. Mutants containing R8K, V32I, V82T, I84V, G48V/L90M, or V82T/I84V substitutions were analyzed for differences in substrate preference and catalytic efficiency using a set of single amino acid substituted HIV-1 CA-NCa cleavage site peptides. All mutants exhibited wild-type preference for large hydrophobic residues, especially Phe, in the P1' substrate position. Only the R8K and V32I mutants showed significant differences in subsite selection compared to wild-type enzyme. In a parallel study, the individual mutations R10K, L12V, I44V, A60M, I71V, and I108V were introduced into RSV PR. These amino acid positions are structurally equivalent to Arg8, Leu10, Val32, Met46, Ile54, and Ile84 in HIV-1 PR, respectively, which mutate in drug-resistance. The RSV R10K substitution significantly altered substrate specificity and catalytic rate, compared to wild-type, in a manner similar to that of the HIV-1 R8K mutant. Crystal structures of the RSV PR R10K, I44V, I71V, and Il08V mutant enzymes presented here indicate that each of these substitutions has little effect on the overall structure of the respective enzymes. Taken together, these data provide an explanation for the reported in vivo predilection for selection of large hydrophobic residues in the P1' substrate position of second locus mutations in the Gag polyprotein PR cleavage sites. The data also suggest that the selection of resistant enzymes is not simply limited to loss of binding to inhibitor but affects other steps in proteolysis.

Xenopus CRMP-2 is an early response gene to neural induction

A neural specific protein, CRMP-2 (for Collapsin Response Mediator Protein-2), is considered to mediate collapsin-induced growth cone collapse during neural development. We have isolated the Xenopus homologue of the CRMP-2 (XCRMP-2) cDNA and studied the expression of XCRMP-2 mRNA and protein during neural induction. Induction of XCRMP-2 mRNA and protein expression, like N-CAM, occurred at the midgastrula stage and increased through early neural developmental stages. Whole mount in situ hybridization demonstrated that expression of XCRMP-2 mRNA was localized in neural tissues such as the neural plate and tube at early stages, while its expression in the brain, spinal cord, and eyes was observed at later stages. Immunostaining of Xenopus embryos with the antibody against CRMP-2 also showed that the protein was specifically expressed in the neural tissues at early stages. XCRMP-2 expression was induced by neural inducers such as noggin and chordin which antagonize a neural inhibitor, BMP4. A dominant negative BMP receptor also induced XCRMP-2 expression, suggesting that transcription of XCRMP-2 gene was negatively regulated by the BMP4 signaling. These results indicate that expression of XCRMP-2 is an early response marking neural commitment, and that transcriptional control of XCRMP-2 gene, is one of the targets of BMP4 signaling.

Dual role of phosphatidylinositol-3,4,5-trisphosphate in the activation of protein kinase B

Protein kinase B (PKB) is a proto-oncogene that is activated in signaling pathways initiated by phosphoinositide 3-kinase. Chromatographic separation of brain cytosol revealed a kinase activity that phosphorylated and activated PKB only in the presence of phosphatidylinositol-3,4,5-trisphosphate [PtdIns(3,4,5)P3]. Phosphorylation occurred exclusively on threonine-308, a residue implicated in activation of PKB in vivo. PtdIns(3,4,5)P3 was determined to have a dual role: Its binding to the pleckstrin homology domain of PKB was required to allow phosphorylation by the upstream kinase and it directly activated the upstream kinase.

Bovine immunodeficiency virus tat gene: cloning of two distinct cDNAs and identification, characterization, and immunolocalization of the tat gene products

cDNAs encoding the bovine immunodeficiency virus (BIV) transactivator gene (tat) were cloned from virally infected cells and characterized. BIV expresses two distinct tat mRNAs composed of three exons that are derived by alternative splicing. The BIV tat mRNA splice variants encode Tat proteins of 103 (Tat103) and 108 (Tat108) amino acids. The Tat103 coding region is specified only by exon 2, while that of Tat108 is specified by a truncated exon 2 and the first 30 nt of exon 3. Thus, the first 98 amino acids of each Tat are identical, and have amino terminal, cysteine-rich, conserved core, basic, and carboxyl-terminal domains similar to Tats encoded by primate lentiviruses. BIV-infected bovine cells express a 14-kDa phosphorylated Tat protein identical in size to recombinant Tat expressed in bacteria. BIV Tat was shown to localize exclusively in the nucleoli of virally infected and Tat-expressing cells. Reporter gene assays indicated that Tat103 and Tat108 can strongly transactivate the BIV long terminal repeat (LTR) in virally permissive canine Cf2Th and nonpermissive HeLa and mouse NIH 3T3 cells, but not in permissive lapine EREp cells. However, an intact BIV tat gene is required for viral replication in both Cf2Th and EREp cells. Strong LTR activation by BIV Tat requires a TAR (transactivation responsive) element delimited by viral nt +1 to +31 and the Tat basic domain. BIV Tat strongly cross-transactivates the HIV-1 LTR in a TAR-dependent manner in Cf2Th, but not in EREp, HeLa, or NIH 3T3 cells. In contrast, strong, TAR-dependent cross-transactivation of the BIV LTR by HIV-1 Tat could not be demonstrated in any of these cell types. In Cf2Th cells Tat108 effects a moderately stronger transactivation of the BIV LTR than Tat103, indicative of a functional difference in BIV Tat proteins encoded by the mRNA splice variants. The present studies demonstrate that BIV Tat parallels the primate lentiviral Tats in structure and biochemistry but is not interchangeable with the latter.

Programming the Rous sarcoma virus protease to cleave new substrate sequences

The Rous sarcoma virus protease displays a high degree of specificity and catalyzes the cleavage of only a limited number of amino acid sequences. This specificity is governed by interactions between side chains of eight substrate amino acids and eight corresponding subsite pockets within the homodimeric enzyme. We have examined these complex interactions in order to learn how to introduce changes into the retroviral protease (PR) that direct it to cleave substrates. Mutant enzymes with altered substrate specificity and wild-type or greater catalytic rates have been constructed previously by substituting single key amino acids in each of the eight enzyme subsites with those residues found in structurally related positions of human immunodeficiency virus (HIV)-1 PR. These individual amino acid substitutions have now been combined into one enzyme, resulting in a highly active mutant Rous sarcoma virus (RSV) protease that displays many characteristics associated with the HIV-1 enzyme. The hybrid protease is capable of catalyzing the cleavage of a set of HIV-1 viral polyprotein substrates that are not recognized by the wild-type RSV enzyme. Additionally, the modified PR is inhibited completely by the HIV-1 PR-specific inhibitor KNI-272 at concentrations where wild-type RSV PR is unaffected. These results indicate that the major determinants that dictate RSV and HIV-1 PR substrate specificity have been identified. Since the viral protease is a homodimer, the rational design of enzymes with altered specificity also requires a thorough understanding of the importance of enzyme symmetry in substrate selection. We demonstrate here that the enzyme homodimer acts symmetrically in substrate selection with each enzyme subunit being capable of recognizing both halves of a peptide substrate equally.

Human immunodeficiency virus, type 1 protease substrate specificity is limited by interactions between substrate amino acids bound in adjacent enzyme subsites

The specificity of the retroviral protease is determined by the ability of substrate amino acid side chains to bind into eight individual subsites within the enzyme. Although the subsites are able to act somewhat independently in selection of amino acid side chains that fit into each pocket, significant interactions exist between individual subsites that substantially limit the number of cleavable amino acid sequences. The substrate peptide binds within the enzyme in an extended anti-parallel beta sheet conformation with substrate amino acid side chains adjacent in the linear sequence extending in opposite directions in the enzyme-substrate complex. From this geometry, we have defined both cis and trans steric interactions, which have been characterized by a steady state kinetic analysis of human immunodeficiency virus, type-1 protease using a series of peptide substrates that are derivatives of the avian leukosis/sarcoma virus nucleocapsid-protease cleavage site. These peptides contain both single and double amino acid substitutions in seven positions of the minimum length substrate required by the retroviral protease for specific and efficient cleavage. Steady state kinetic data from the single amino acid substituted peptides were used to predict effects on protease-catalyzed cleavage of corresponding double substituted peptide substrates. The calculated Gibbs' free energy changes were compared with actual experimental values in order to determine how the fit of a substrate amino acid in one subsite influences the fit of amino acids in adjacent subsites. Analysis of these data shows that substrate specificity is limited by steric interactions between pairs of enzyme subsites. Moreover, certain enzyme subsites are relatively tolerant of substitutions in the substrate and exert little effect on adjacent subsites, whereas others are more restrictive and have marked influence on adjacent cis and trans subsites.

Catalytic activity of the mouse guanine nucleotide exchanger mSOS is activated by Fyn tyrosine protein kinase and the T-cell antigen receptor in T cells

mSOS, a guanine nucleotide exchange factor, is a positive regulator of Ras. Fyn tyrosine protein kinase is a potential mediator in T-cell antigen receptor signal transduction in subsets of T cells. We investigated the functional and physical interaction between mSOS and Fyn in T-cell hybridoma cells. Stimulation of the T-cell antigen receptor induced the activation of guanine nucleotide exchange activity in mSOS immunoprecipitates. Overexpression of Fyn mutants with an activated kinase mutation and with a Src homology 2 deletion mutation resulted in a stimulation and suppression of the mSOS activity, respectively. The complex formations of Fyn-Shc, Shc-Grb2, and Grb2-mSOS were detected in the activated Fyn-transformed cells, whereas the SH2 deletion mutant of Fyn failed to form a complex with mSOS. Moreover, tyrosine phosphorylation of Shc was induced by the overexpression of the activated Fyn. These findings support the idea that Fyn activates the activity of mSOS bound to Grb2 through tyrosine phosphorylation of Shc. Unlike the current prevailing model, Fyn-induced activation of Ras might involve the stimulation of the catalytic guanine nucleotide exchange activity of mSOS.

Mutational analysis of the substrate binding pockets of the Rous sarcoma virus and human immunodeficiency virus-1 proteases

Mutations, designed by analysis of the crystal structures of Rous sarcoma virus (RSV) and human immunodeficiency virus type 1 (HIV-1) protease (PR), were introduced into the substrate binding pocket of RSV PR. The mutations substituted nonconserved residues of RSV PR, located within 10 A of the substrate, for those in structurally equivalent positions of HIV-1 PR. Changes in the activity of purified mutants were detected in vitro by following cleavage of synthetic peptides representing wild-type and modified RSV and HIV-1 gag and pol polyprotein cleavage sites. Substituting threonine for valine 104 (V104T), S107N, I44V, Q63M or deletion of residues 61-63 produced enzymes that were 2.5-7-fold more active than the wild type RSV PR. Substituting I42D, M73V, and A100L produced enzymes with lower activity, whereas a mutant that included both M73V and A100L was as active as wild type. Several substitutions altered the specificity for substrate. These include I42D and I44V, which contribute to the S2 and S2' subsites. These proteins exhibited HIV-1 PR specificity for P2- or P2'-modified peptide substrates but unchanged specificity with P4-, P3-, P1-, P1'-, and P3'-modified substrates. Changes in specificity in the S4 subsite were detected by deletion of residues 61-63. These results confirm the hypothesis that the subsites of the substrate binding pocket of the retroviral protease are capable of acting independently in the selection of substrate amino acids.

A Trk nerve growth factor (NGF) receptor point mutation affecting interaction with phospholipase C-gamma 1 abolishes NGF-promoted peripherin induction but not neurite outgrowth

We analyzed the function of Trk nerve growth factor (NGF) receptors containing a point mutation (Tyr-->Phe) in a major autophosphorylation site (Tyr-785). Tyr-785 is required for phospholipase C-gamma 1 to interact with Trk and to become tyrosine-phosphorylated in response to NGF. The altered receptors were transfected into a mutant subline of PC12 rat pheochromocytoma cells (designated PC12nnr5) that, unlike wild-type PC12 cells, lack expression of endogenous Trk and responsiveness to NGF. PC12nnr5 cells permanently transfected with Trk Y785F exhibit NGF-dependent autophosphorylation and normal NGF binding and internalization. Moreover, Trk Y785F mediates NGF-stimulated neurite outgrowth as well as a variety of additional responses including induction of immediate-early and late genes. However, in contrast to cells expressing wild-type Trk, cells expressing Trk Y785F lack NGF-promoted elevation of peripherin intermediate filament mRNA and protein. These observations indicate that phospholipase C-gamma 1 activation or other signaling pathways dependent on Tyr-785 autophosphorylation are selectively required for regulation of peripherin expression by NGF, but not for many other functional NGF responses. This supports the presence of multiple and separable signaling pathways in the NGF mechanism of action.

Locating essential Escherichia coli genes by using mini-Tn10 transposons: the pdxJ operon

The mini-Tn10 transposon (delta 16 delta 17Tn10) confers tetracycline resistance. When inserted between a gene and its promoter, it blocks transcription and prevents expression of that gene. Tetracycline in the medium induces divergent transcription of the tetA and tetR genes within the transposon, and this transcription extends beyond the transposon in both directions into the bacterial genes. If the mini-Tn10 inserts between an essential bacterial gene and its promoter, the insertion mutation can cause conditional growth which is dependent on the presence of tetracycline. Two essential genes in adjacent operons of Escherichia coli have been detected by screening for tetracycline dependence among tetracycline-resistant insertion mutants. These essential genes are the era gene in the rnc operon and the dpj gene in the adjacent pdxJ operon. The pdxJ operon has not been described previously. It consists of two genes, pdxJ and dpj. Whereas the dpj gene is essential for E. coli growth in all media tested, pdxJ is not essential. The pdxJ gene encodes a protein required in the biosynthesis of pyridoxine (vitamin B6).

Characterization of the secreted, native gp120 and gp160 of the human immunodeficiency virus type 1

We have previously shown that the cell line 6D5(451) chronically infected with the HIV-1 isolate HTLV-III(451), secretes the HIV-1 envelope glycoproteins gp120 and gp160 in the extracellular medium. The HTLV-III(451) gp120 and gp160 were purified by sequential affinity chromatographic steps using a monoclonal antibody to HIV-1 gp41 and an anti-HIV-1-positive human serum. Amino acid sequence analysis of gp120 and gp160 showed the loss of the signal peptide. Digestion of the purified gp120 and gp160 with endoglycosidases revealed that both proteins are heavily glycosylated and contain complex carbohydrates, in contrast to the intracellular form of gp160 which has been shown to contain mannose-rich immature sugars. Competitive binding analysis showed that while both gp120 and gp160 bind CD4, the affinity of gp160 was five times lower than that of gp120. Both gp120 and gp160 inhibited syncytia formation by HIV-1-infected cells when mixed with CD4+ cells. Furthermore, both gp120 and gp160 had strong mitogenic effects on the T cells from HIV-1-infected gibbons but not on cells from uninfected gibbons.

rev protein of human immunodeficiency virus type 1 affects the stability and transport of the viral mRNA

rev (trs/art) is an essential human immunodeficiency virus type 1 (HIV-1) regulatory protein. rev increases the levels of the gag- and env-producing mRNAs via a cis-acting element in the env region of HIV-1, named rev-responsive element. Our results show that rev increases the stability of the unspliced viral mRNA, while it does not affect the stability of the multiply spliced viral mRNAs that do not contain the rev-responsive element. The study of mutated proviral constructs producing mRNA that cannot be spliced revealed that the effect of rev on stability is independent of splicing. Our experiments also indicate that rev promotes the transport of the viral mRNA containing the rev-responsive element from the nucleus to the cytoplasm. The proposed functions of rev are consistent with its nuclear localization as shown by immunofluorescence. The selective effects of rev on the levels of the viral mRNA suggest a model for feedback regulation by rev leading to a steady state of viral expression.

Molecular and biochemical characterization of the human trk proto-oncogene

Molecular analysis of the human trk oncogene, a transforming gene isolated from a colon carcinoma biopsy, revealed the existence of a novel member of the tyrosine kinase gene family. This locus, which we now designate the trk proto-oncogene, codes for a protein of 790 amino acid residues that has several features characteristic of cell surface receptors. They include (i) a 32-amino-acid-long putative signal peptide, (ii) an amino-terminal moiety (residues 33 to 407) rich in consensus sites for N-glycosylation, (iii) a transmembrane domain, (iv) a kinase catalytic region highly related to that of other tyrosine kinases, and (v) a very short (15 residue) carboxy-terminal tail. Residues 1 to 392 were absent in the trk oncogene, as they were replaced by tropomyosin sequences. However, no other differences were found between the transforming and nontransforming trk alleles (residues 392 to 790), suggesting that no additional mutations are required to activate the transforming potential of this gene. The human trk proto-oncogene codes for a 140,000-dalton glycoprotein, designated gp140proto-trk. However, its primary translational product is a 110,000-dalton glycoprotein which becomes immediately glycosylated, presumably during its translocation into the endoplasmic reticulum. This molecule, designated gp110proto-trk, is further glycosylated to yield the mature form, gp140proto-trk. Both gp110proto-trk and gp140proto-trk proteins possess in vitro kinase activity specific for tyrosine residues. Finally, iodination of intact NIH 3T3 cells expressing trk proto-oncogene products indicated that only the mature form, gp140proto-trk, cross the plasma membrane, becoming exposed to the outside of the cell. These results indicate that the product of the human trk locus is a novel tyrosine kinase cell surface receptor for an as yet unknown ligand.

Function of c-mos proto-oncogene product in meiotic maturation in Xenopus oocytes

The c-mos proto-oncogene is expressed as a maternal mRNA in oocytes and early embryos of Xenopus laevis, but its translation product pp39mos is detectable only during progesterone-induced oocyte maturation. Microinjection of mos-specific antisense oligonucleotides into oocytes not only prevents expression of pp39mos, but also blocks germinal vesicle breakdown, indicating that it functions during reinitiation of meiotic division.

Identification and characterization of c-raf phosphoproteins in transformed murine cells

Protein products of the c-raf gene were detected and characterized in two transformed murine cells lines by immunoprecipitation analysis with raf-specific sera. Both proteins reacted with an antiserum directed to the carboxyl terminus of the c-raf coding region. The p48raf (Mr48,000) phosphoprotein was found in a cell line transformed by an LTR-activated c-raf gene (Mueller & Mueller, 1984). It was found to be phosphorylated on serine and threonine residues and became phosphorylated in immunoprecipitates when supplied with [gamma-32]ATP. In contrast, P74raf, which was detected into a spontaneously transformed 3T3 (R+/Cl 3) cell line and may represent the full-length gene product of c-raf, appeared to incorporate [32P]PO4 less efficiently in vivo and exhibited a barely detectable associated kinase activity in only half of the experiments. The p48raf is a transforming protein which, like P75gag-raf, lacks the amino-terminal region of the c-raf coding region. P74raf, which retains the amino-terminal region, differs from p48raf in its phosphorylation characteristics and may not be a transforming protein. These data are consistent with a model in which lack of amino-terminal sequences in the c-raf gene product p48raf may, in and of itself, suffice to make it a transforming protein.

Characterization of the TPR-MET oncogene p65 and the MET protooncogene p140 protein-tyrosine kinases

The proteins encoded by the human TPR-MET oncogene (p 65tpr-met) and the human MET protooncogene (p140met) have been identified. The p65tpr-met and p140met, as well as a truncated TPR-MET product expressed in Escherichia coli, p50met, are autophosphorylated in vitro on tyrosine residues. Using the immunocomplex kinase assay, p140met activity was detected in various human tumor epithelial cell lines. In vivo, p65tpr-met is phosphorylated on both serine and tyrosine residues, while p140met is phosphorylated on serine and threonine. p140met is labeled by cell-surface iodination procedures, suggesting that it is a receptor-like transmembrane protein-tyrosine kinase.

Mr 75,000 protein, a tumor marker in renal adenocarcinoma, reacting with antibodies to a synthetic peptide based on a cloned human endogenous retroviral nucleotide sequence

Using a rabbit antiserum to a synthetic undecapeptide deduced from a cloned human retroviral gag-gene-related DNA sequence, we found a specific immunohistochemical reaction in all of 42 tested renal cell adenocarcinomas (RCC), while none of 17 similarly tested Wilms' tumors and 65 carcinomas at other sites were positive. The RCC included two cases that presented with distant metastases. It had not been possible to establish the origin of these until immunohistochemical staining revealed this typical reaction. Subsequent renal angiography disclosed the primary. In immunoblotting the antiserum detected an Mr 75,000 protein in RCC tissue, and this reaction was blocked by the undecapeptide. The usefulness of this protein as a tumor marker for RCC is discussed.

Human placental syncytiotrophoblastic Mr 75,000 polypeptide defined by antibodies to a synthetic peptide based on a cloned human endogenous retroviral DNA sequence

Antibodies to a synthetic undecapeptide (NH2-Cys-Glu-Asn-Pro-Ser-Gln-Phe-Tyr-Glu-Arg-Leu-COOH), the sequence (except cysteine) of which was deduced from a previously reported cloned human retroviral gag-gene-related DNA sequence erv-1, were raised in rabbits. In immunohistochemical staining these antibodies reacted with normal human first-trimester placentas and with blighted ova and benign and malignant trophoblastic tumors (hydatidiform and destructive moles, choriocarcinomas) but not with any other normal embryonic or adult tissues tested. In all tissues the reactivity was mainly confined to cells with trophoblastic morphology. In immunoblotting the antibody detected an Mr 75,000 polypeptide in syncytiotrophoblasts isolated from first-trimester placentas and in three different lines of cultured choriocarcinoma cells. The undecapeptide blocked the reactivity of the antibody.

Human T-cell growth factor: partial amino acid sequence, cDNA cloning, and organization and expression in normal and leukemic cells

The partial amino acid sequences of human T-cell growth factors (TCGFs) isolated from normal peripheral blood lymphocytes and from a leukemia T-cell line (Jurkat) show that the amino-terminal sequences of the two proteins (15 residues) are identical. Oligonucleotides based on the published Jurkat TCGF DNA sequence were used to isolate six cDNA clones of TCGF mRNA from normal lymphocytes. The predicted amino acid sequence of normal lymphocyte TCGF was identical to the sequence of the Jurkat protein, showing that the differences in biochemical properties of the two proteins result from post-translational events. Amino acid and nucleotide sequence data suggest that TCGF is derived from a precursor polypeptide that is cleaved at the amino terminus but not at the carboxyl terminus. Hybridization of the cloned lymphocyte TCGF cDNA to cellular DNA and RNA strongly suggested that the TCGF gene is expressed as a single mRNA species from a single-copy gene. No differences in the organization of the TCGF gene in normal, leukemic, and human T-cell leukemia/lymphoma virus-infected cells was detected regardless of whether they produce TCGF or not.

Amino acid sequence homology of mammalian type C RNA virus major internal proteins

The NH2-terminal amino acid sequence of the major group-specific antigen, the major internal virion protein (p30; approximate molecular weight 30,000) of several mammalian type C RNA viruses was determined by the Edman degradation procedure using an automated protein sequenator. All of the proteins analyzed show a high degree of over-all sequence homology and also contain specific regions or single residues. All p30s begin with the sequence prolyl-leucylarginyl (Pro-Leu-Arg) and have an invariant, conserved region from residues 11 to 24. In this region only a single amino acid difference appears between the cat and mouse p30s. At position 17 alanine is found in the cat, and serine in all the mouse proteins. This homologous region starts at position 10 for RD-114 and baboon virus p30s, and at position 18 in the protein of the virus isolated from gibbon ape. The region extending from residue 4 to 10 shows considerable variability between p30s isolated from different mammalian species. Out of 24 residues compared, only a single amino acid difference was found between six different mouse p30s. At position 4, three have leucine, two have alanine, and one has serine. The comparative sequence data demonstrate that the viral p30s are products of related genes in the viruses from various mammalian species.

Feline leukemia and RD-114 virus group-specific proteins: comparison of amino terminal sequence

The major internal virion polypeptide from feline and RD-114 type C viruses has been subjected to amino terminal sequence analyses with the Beckman automated sequencer. These proteins, as well as their homologs in rat and mouse viruses, begin with the sequence prolylleucylarginyl (Pro-Leu-Arg). Virus RD-114 differs from conventional feline type C viruses that show about 80 percent relatedness based on calculation of the minimum number of base changes to give equivalent coding for the protein segments analyzed. In addition, insertion of a gap in the RD-114 sequence is necessary to maintain positional homology. The difference between RD-114 and feline leukemia virus appears as great as the difference between mouse type C viruses and either of these two viruses. Thus, even though current evidence suggests that RD-114 is of feline origin, the sequence differences between RD-114 and conventional feline virus group-specific proteins is well beyond that based on one or a few point mutations.