Recruitment of a SUMO isopeptidase to rDNA stabilizes silencing complexes by opposing SUMO targeted ubiquitin ligase activity.

Post-translational modification by SUMO (small ubiquitin-like modifier) plays important but still poorly understood regulatory roles in eukaryotic cells, including as a signal for ubiquitination by SUMO targeted ubiquitin ligases (STUbLs). Here, we delineate the molecular mechanisms for SUMO-dependent control of ribosomal DNA (rDNA) silencing through the opposing actions of a STUbL (Slx5:Slx8) and a SUMO isopeptidase (Ulp2). We identify a conserved region in the Ulp2 C terminus that mediates its specificity for rDNA-associated proteins and show that this region binds directly to the rDNA-associated protein Csm1. Two crystal structures show that Csm1 interacts with Ulp2 and one of its substrates, the rDNA silencing protein Tof2, through adjacent conserved interfaces in its C-terminal domain. Disrupting Csm1's interaction with either Ulp2 or Tof2 dramatically reduces rDNA silencing and causes a marked drop in Tof2 abundance, suggesting that Ulp2 promotes rDNA silencing by opposing STUbL-mediated degradation of silencing proteins. Tof2 abundance is rescued by deletion of the STUbL SLX5 or disruption of its SUMO-interacting motifs, confirming that Tof2 is targeted for degradation in a SUMO- and STUbL-dependent manner. Overall, our results demonstrate how the opposing actions of a localized SUMO isopeptidase and a STUbL regulate rDNA silencing by controlling the abundance of a key rDNA silencing protein, Tof2.

SUMO E3 ligase Mms21 prevents spontaneous DNA damage induced genome rearrangements.

Mms21, a subunit of the Smc5/6 complex, possesses an E3 ligase activity for the Small Ubiquitin-like MOdifier (SUMO). Here we show that the mms21-CH mutation, which inactivates Mms21 ligase activity, causes increased accumulation of gross chromosomal rearrangements (GCRs) selected in the dGCR assay. These dGCRs are formed by non-allelic homologous recombination between divergent DNA sequences mediated by Rad52-, Rrm3- and Pol32-dependent break-induced replication. Combining mms21-CH with sgs1Δ caused a synergistic increase in GCRs rates, indicating the distinct roles of Mms21 and Sgs1 in suppressing GCRs. The mms21-CH mutation also caused increased rates of accumulating uGCRs mediated by breakpoints in unique sequences as revealed by whole genome sequencing. Consistent with the accumulation of endogenous DNA lesions, mms21-CH mutants accumulate increased levels of spontaneous Rad52 and Ddc2 foci and had a hyper-activated DNA damage checkpoint. Together, these findings support that Mms21 prevents the accumulation of spontaneous DNA lesions that cause diverse GCRs.

Phosphorylation of the Synaptonemal Complex Protein Zip1 Regulates the Crossover/Noncrossover Decision during Yeast Meiosis.

Interhomolog crossovers promote proper chromosome segregation during meiosis and are formed by the regulated repair of programmed double-strand breaks. This regulation requires components of the synaptonemal complex (SC), a proteinaceous structure formed between homologous chromosomes. In yeast, SC formation requires the "ZMM" genes, which encode a functionally diverse set of proteins, including the transverse filament protein, Zip1. In wild-type meiosis, Zmm proteins promote the biased resolution of recombination intermediates into crossovers that are distributed throughout the genome by interference. In contrast, noncrossovers are formed primarily through synthesis-dependent strand annealing mediated by the Sgs1 helicase. This work identifies a conserved region on the C terminus of Zip1 (called Zip1 4S), whose phosphorylation is required for the ZMM pathway of crossover formation. Zip1 4S phosphorylation is promoted both by double-strand breaks (DSBs) and the meiosis-specific kinase, MEK1/MRE4, demonstrating a role for MEK1 in the regulation of interhomolog crossover formation, as well as interhomolog bias. Failure to phosphorylate Zip1 4S results in meiotic prophase arrest, specifically in the absence of SGS1. This gain of function meiotic arrest phenotype is suppressed by spo11Δ, suggesting that it is due to unrepaired breaks triggering the meiotic recombination checkpoint. Epistasis experiments combining deletions of individual ZMM genes with sgs1-md zip1-4A indicate that Zip1 4S phosphorylation functions prior to the other ZMMs. These results suggest that phosphorylation of Zip1 at DSBs commits those breaks to repair via the ZMM pathway and provides a mechanism by which the crossover/noncrossover decision can be dynamically regulated during yeast meiosis.

Molecular Circuitry of the SUMO (Small Ubiquitin-like Modifier) Pathway in Controlling Sumoylation Homeostasis and Suppressing Genome Rearrangements.

Small ubiquitin-like modifier (SUMO) E3 ligases are known to have a major role in preventing gross chromosomal rearrangements (GCRs); however, relatively little is known about the role of SUMO isopeptidases in genome maintenance and their role in controlling intracellular sumoylation homeostasis. Here we show the SUMO isopeptidase Ulp2 in Saccharomyces cerevisiae does not prevent the accumulation of GCRs, and interestingly, its loss causes subunit-specific changes of sumoylated minichromosome maintenance (MCM) helicase in addition to drastic accumulation of sumoylated nucleolar RENT and inner kinetochore complexes. In contrast, loss of Ulp1 or its mis-localization from the nuclear periphery causes substantial accumulations of GCRs and elevated sumoylation of most proteins except for Ulp2 targets. Interestingly, the E3 ligase Mms21, which has a major role in genome maintenance, preferentially controls the sumoylation of Mcm3 during DNA replication. These findings reveal distinct roles for Ulp1 and Ulp2 in controlling homeostasis of intracellular sumoylation and show that sumoylation of MCM is controlled in a subunit-specific and cell cycle dependent manner.

Phosphorylation of Sae2 Mediates Forkhead-associated (FHA) Domain-specific Interaction and Regulates Its DNA Repair Function.

Saccharomyces cerevisiae Sae2 and its ortholog CtIP in higher eukaryotes have a conserved role in the initial processing of DNA lesions and influencing their subsequent repair pathways. Sae2 is phosphorylated by the ATR/ATM family kinases Mec1 and Tel1 in response to DNA damage. Among the Mec1/Tel1 consensus phosphorylation sites of Sae2, we found that mutations of Thr-90 and Thr-279 of Sae2 into alanine caused a persistent Rad53 activation in response to a transient DNA damage, similar to the loss of Sae2. To gain insight into the function of this phosphorylation of Sae2, we performed a quantitative proteomics analysis to identify its associated proteins. We found that phosphorylation of Thr-90 of Sae2 mediates its interaction with Rad53, Dun1, Xrs2, Dma1, and Dma2, whereas Rad53 and Dun1 additionally interact with phosphorylated Thr-279 of Sae2. Mutations of the ligand-binding residues of Forkhead-associated (FHA) domains of Rad53, Dun1, Xrs2, Dma1, and Dma2 abolished their interactions with Sae2, revealing the involvement of FHA-specific interactions. Mutations of Thr-90 and Thr-279 of Sae2 caused a synergistic defect when combined with sgs1Δ and exo1Δ and elevated gross chromosomal rearrangements. Likewise, mutations of RAD53 and DUN1 caused a synthetic growth defect with sgs1Δ and elevated gross chromosomal rearrangements. These findings suggest that threonine-specific phosphorylation of Sae2 by Mec1 and Tel1 contributes to DNA repair and genome maintenance via its interactions with Rad53 and Dun1.

Applications of Machine Learning in Prognostication of mTBI: A Systematic Review.

OBJECTIVE: To review the literature regarding the current state and clinical applicability of machine learning (ML) models in prognosticating the outcomes of patients with mild traumatic brain injury (mTBI) in the early clinical presentation. DESIGN: Databases were searched for studies including ML and mTBI from inception to March 10, 2023. Included studies had a primary outcome of predicting post-mTBI prognosis or sequalae. The Prediction model study Risk of Bias for Predictive Models assessment tool (PROBAST) was used for assessing the risk of bias and applicability of included studies. RESULTS: Out of 1235 articles, 10 met the inclusion criteria, including data from 127,929 patients. The most frequently used modeling techniques were Support Vector Machine (SVM) and Artificial Neural Network (NN) and Area Under the Curve (AUC) ranged from 0.66-0.889. Despite promise, several limitations to studies exist such as low sample sizes, database restrictions, inconsistencies in patient presentation definitions and lack of comparison to traditional clinical judgment or tools. CONCLUSION: ML models show potential in early stage mTBI prognostication, but to achieve widespread adoption, future clinical studies prognosticating mTBI using ML need to reduce bias, provide clarity and consistency in defining patient populations targeted, and validate against established benchmarks.

Patient-specific rods in adult spinal deformity: a systematic review.

PURPOSE: The purpose of this review was to evaluate the effectiveness of patient-specific rods for adult spinal deformity. METHODS: A systematic review of the literature was performed through an electronic search of the PubMed, Scopus, and Web of Science databases. Human studies between 2012 and 2023 were included. Sample size, sagittal vertical axis (SVA), pelvic incidence-lumbar lordosis (PI-LL), pelvic tilt (PT), operation time, blood loss, follow-up duration, and complications were recorded for each study when available. RESULTS: Seven studies with a total of 304 adult spinal deformity patients of various etiologies were included. All studies reported SVA, and PT; two studies did not report PI-LL. Four studies reported planned radiographic outcomes. Two found a significant association between preoperative plan and postoperative outcome in all three outcomes. One found a significant association for PI-LL alone. The fourth found no significant associations. SVA improved in six of seven studies, PI-LL improved in all five, and three of seven studies found improved postoperative PT. Significance of these results varied greatly by study. CONCLUSION: Preliminary evidence suggests potential benefits of PSRs in achieving optimal spino-pelvic parameters in ASD surgery. Nevertheless, conclusions regarding the superiority of PSRs over traditional rods must be judiciously drawn, given the heterogeneity of patients and study methodologies, potential confounding variables, and the absence of robust randomized controlled trials. Future investigations should concentrate on enhancing preoperative planning, standardizing surgical methodologies, isolating specific patient subgroups, and head-to-head comparisons with traditional rods to fully elucidate the impact of PSRs in ASD surgery.

Using SILAC to Develop Quantitative Data-Independent Acquisition (DIA) Proteomic Methods.

Proteins are integral to biological systems and functions. Identifying and quantifying proteins can therefore offer systems-wide insights into protein-protein interactions, cellular signaling, and biological pathway activity. The use of quantitative proteomics has become a method of choice for identifying and quantifying proteins in complex matrices. Proteomics allows researchers to survey hundreds to thousands of proteins in a less biased manner than classical antibody-based protein capture strategies. Typically, discovery approaches have used data-dependent acquisition (DDA) methods, but this approach suffers from stochasticity that compromises quantitation. Recent developments in data-independent acquisition (DIA) proteomics workflows enable proteomic profiling of thousands of samples with increased peak picking consistency making it an excellent candidate for discovering and assessing biomarkers in clinical samples. However, quantitation of peptides from DIA datasets is computationally intensive, and guidelines on how to establish DIA methods are lacking. Method development and optimization require novel tools to visualize and filter DIA datasets appropriately. Here, a protocol and novel script workflow for the optimization of quantitative DIA methods using stable isotope labeling of amino acids in culture (SILAC) are presented. This protocol includes steps for cell growth and labeling, peptide digestion and preparation, and optimization of quantitative DIA methods. In addition, important steps for (1) computational analysis to identify and quantify peptides, (2) data visualizations to identify the linear abundance ranges for all peptides in the sample, and (3) descriptions of how to find high confidence quantitation abundance thresholds are described herein.

Development of a Formalized, Multifaceted Mentorship Program in Physical Medicine and Rehabilitation Residency Education.

ABSTRACT: Mentorship in medicine has long been a vital component to the training, development, and career advancement of physicians. Although optimal strategies for facilitating mentorship relationships are unknown, it is recognized that establishing a formalized mentorship program within residency training may augment mentor-mentee pairing, improve overall trainee experience, and enhance resident perception of strong mentoring relationships. A formalized mentorship program was successfully developed in a Canadian physical medicine and rehabilitation residency program, including innovations such as near-peer self-matching, a needs assessment survey, a speed dating event, formation of "link groups," and "fireside chats" with faculty members. This approach may serve as a guide for other medical education and residency programs seeking to implement a similar concept.

CRAF dimerization with ARAF regulates KRAS-driven tumor growth.

KRAS, which is mutated in ∼30% of all cancers, activates the RAF-MEK-ERK signaling cascade. CRAF is required for growth of KRAS mutant lung tumors, but the requirement for CRAF kinase activity is unknown. Here, we show that subsets of KRAS mutant tumors are dependent on CRAF for growth. Kinase-dead but not dimer-defective CRAF rescues growth inhibition, suggesting that dimerization but not kinase activity is required. Quantitative proteomics demonstrates increased levels of CRAF:ARAF dimers in KRAS mutant cells, and depletion of both CRAF and ARAF rescues the CRAF-loss phenotype. Mechanistically, CRAF depletion causes sustained ERK activation and induction of cell-cycle arrest, while treatment with low-dose MEK or ERK inhibitor rescues the CRAF-loss phenotype. Our studies highlight the role of CRAF in regulating MAPK signal intensity to promote tumorigenesis downstream of mutant KRAS and suggest that disrupting CRAF dimerization or degrading CRAF may have therapeutic benefit.

A proteome-wide analysis of kinase-substrate network in the DNA damage response.

The DNA damage checkpoint, consisting of an evolutionarily conserved protein kinase cascade, controls the DNA damage response in eukaryotes. Knowledge of the in vivo substrates of the checkpoint kinases is essential toward understanding their functions. Here we used quantitative mass spectrometry to identify 53 new and 34 previously known targets of Mec1/Tel1, Rad53, and Dun1 in Saccharomyces cerevisiae. Analysis of replication protein A (RPA)-associated proteins reveals extensive physical interactions between RPA-associated proteins and Mec1/Tel1-specific substrates. Among them, multiple subunits of the chromatin remodeling complexes including ISW1, ISW2, INO80, SWR1, RSC, and SWI/SNF are identified and they undergo DNA damage-induced phosphorylation by Mec1 and Tel1. Taken together, this study greatly expands the existing knowledge of the targets of DNA damage checkpoint kinases and provides insights into the role of RPA-associated chromatins in mediating Mec1 and Tel1 substrate phosphorylation in vivo.

Peripheral Neuropathy in the Lower Limbs of Individuals With Spinal Cord Injury or Disease: A Retrospective Study.

PURPOSE: This study investigated the frequency and types of peripheral neuropathy in the lower limbs of patients undergoing rehabilitation after traumatic spinal cord injury or spinal cord disease. METHODS: This study included consecutive patients with spinal cord injury/spinal cord disease who had electrophysiological assessments during their admission in a rehabilitation center from October 2015 to July 2019. Patients with traumatic spinal cord injury were compared with patients with nontraumatic spinal cord disease. RESULTS: There were 67 patients (52 male patients, 15 female patients; mean age = 56.5 yrs) of whom 36 patients had spinal cord injury and 31 patients had spinal cord disease. Most of the patients were middle-aged men with at least one preexisting medical comorbidity, who were mostly admitted for rehabilitation of cervical, incomplete spinal cord injury/spinal cord disease. Most patients (86.6%) had abnormal electrophysiological studies representing 5.57% of all admissions. A length-dependent polyneuropathy was diagnosed in 0.77% of all admissions (n = 8). The group of patients with spinal cord injury was comparable with the group of patients with spinal cord disease regarding the other baseline data, clinical, and electrophysiological findings. CONCLUSIONS: Diseases of the peripheral nervous system were similarly found among patients undergoing rehabilitation for either spinal cord injury or spinal cord disease. A length-dependent polyneuropathy was diagnosed in 0.77% of all admissions. Timely diagnosis and proper treatment of the cause of peripheral neuropathies in the lower limbs in these patients may potentially influence rehabilitation protocols and improve patient outcomes.

Functional mimicry revealed by the crystal structure of an eIF4A:RNA complex bound to the interfacial inhibitor, desmethyl pateamine A.

Interfacial inhibitors exert their biological effects through co-association with two macromolecules. The pateamine A (PatA) class of molecules function by stabilizing eukaryotic initiation factor (eIF) 4A RNA helicase onto RNA, resulting in translation initiation inhibition. Here, we present the crystal structure of an eIF4A1:RNA complex bound to an analog of the marine sponge-derived natural product PatA, C5-desmethyl PatA (DMPatA). One end of this small molecule wedges itself between two RNA bases while the other end is cradled by several protein residues. Strikingly, DMPatA interacts with the eIF4A1:RNA complex in an almost identical fashion as rocaglamide A (RocA), despite being completely unrelated from a structural standpoint. The structural data rationalize the ability of PatA analogs to target a wider range of RNA substrates compared to RocA. We define the molecular basis of how DMPatA is able to clamp eIF4A1 onto RNA, imparting potent inhibitory properties to this molecule.

Diagnostic accuracy and feasibility of depression screening in spinal cord injury: A systematic review.

Context: Individuals with spinal cord injury or disease (SCI/D) are at increased risk of depression, which is associated with poor short- and long-term outcomes. Accurate diagnosis is complicated by overlapping symptoms of both conditions, and a lack of consensus-derived guidelines specifying an appropriate depression screening tool. Objective: To conduct a systematic review to: (1) identify the diagnostic accuracy of established depression screening tools compared to clinical assessment; and, (2) to summarize factors that influence feasibility of clinical implementation among adults with SCI/D. Methods: A systematic search using MEDLINE, EMBASE, PsycINFO, CINAHL and the Cochrane databases using the terms spinal cord injury, depression or mood disorder, and screening or diagnosis identified 1254 initial results. Following duplicate screening, five articles assessing eight screening tools met the final inclusion and exclusion criteria. Measures of diagnostic accuracy and feasibility of implementation were extracted. The Quality Assessment Tool for Diagnostic Accuracy Studies 2 (QUADAS-2) was used to assess study quality. Results: The Patient Health Questionnaire-9 (PHQ-9) had the highest sensitivity (100%), and specificity (84%). The 2-item version, the PHQ-2, comprised the fewest questions, and six of the eight tools were available without cost. Utilizing the QUADAS-2 tool, risk of bias was rated as low or unclear risk for all studies; applicability of the results was rated as low concern. Conclusion: The PHQ-9 is an accurate and feasible tool for depression screening in the adult SCI/D population. Future studies should evaluate the implementation of screening tools and the impact of screening on access to mental health interventions.

The structure of mammalian ß-mannosidase provides insight into ß-mannosidosis and nystagmus.

ß-Mannosidase is a lysosomal enzyme from the glycosyl hydrolase family 2 that cleaves the single ß(1-4)-linked mannose at the nonreducing end of N-glycosylated proteins, and plays an important role in the polysaccharide degradation pathway. Mutations in the MANBA gene, which encodes the ß-mannosidase, can lead to the lysosomal storage disease ß-mannosidosis, as well as nystagmus, an eye condition characterized by involuntary eye movements. Here, we present the first structures of a mammalian ß-mannosidase in both the apo- and mannose-bound forms. The structure is similar to previously determined ß-mannosidase structures with regard to domain organization and fold, however, there are important differences that underlie substrate specificity between species. Additionally, in contrast to most other ligand-bound ß-mannosidases from bacterial and fungal sources where bound sugars were in a boat-like conformation, we find the mannose in the chair conformation. Evaluation of known disease mutations in the MANBA gene provides insight into their impact on disease phenotypes. Together, these results will be important for the design of therapeutics for treating diseases caused by ß-mannosidase deficiency. DATABASE: Structural data are available in the Protein Data Bank under the accession numbers 6DDT and 6DDU.

The ALS-FTD-linked gene product, C9orf72, regulates neuronal morphogenesis via autophagy.

Mutations in C9orf72 leading to hexanucleotide expansions are the most common genetic causes for amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). A phenotype resembling ALS and FTD is seen in transgenic mice overexpressing the hexanucleotide expansions, but is absent in C9orf72-deficient mice. Thus, the exact function of C9orf72 in neurons and how loss of C9orf72 may contribute to neuronal dysfunction remains to be clearly defined. Here, we showed that primary hippocampal neurons cultured from c9orf72 knockout mice have reduced dendritic arborization and spine density. Quantitative proteomic analysis identified C9orf72 as a component of the macroautophagy/autophagy initiation complex composed of ULK1-RB1CC1-ATG13-ATG101. The association was mediated through the direct interaction with ATG13 via the isoform-specific carboxyl-terminal DENN and dDENN domain of C9orf72. Furthermore, c9orf72 knockout neurons showed reduced LC3-II puncta accompanied by reduced ULK1 levels, suggesting that loss of C9orf72 impairs basal autophagy. Conversely, wild-type neurons treated with a ULK1 kinase inhibitor showed a dose-dependent reduction of dendritic arborization and spine density. Furthermore, expression of the long isoform of human C9orf72 that interacts with the ULK1 complex, but not the short isoform, rescues autophagy and the dendritic arborization phenotypes of c9orf72 knockout neurons. Taken together, our data suggests that C9orf72 has a cell-autonomous role in neuronal and dendritic morphogenesis through promotion of ULK1-mediated autophagy.

Directed network motifs in Alzheimer's disease and mild cognitive impairment.

Directed network motifs are the building blocks of complex networks, such as human brain networks, and capture deep connectivity information that is not contained in standard network measures. In this paper we present the first application of directed network motifs in vivo to human brain networks, utilizing recently developed directed progression networks which are built upon rates of cortical thickness changes between brain regions. This is in contrast to previous studies which have relied on simulations and in vitro analysis of non-human brains. We show that frequencies of specific directed network motifs can be used to distinguish between patients with Alzheimer's disease (AD) and normal control (NC) subjects. Especially interesting from a clinical standpoint, these motif frequencies can also distinguish between subjects with mild cognitive impairment who remained stable over three years (MCI) and those who converted to AD (CONV). Furthermore, we find that the entropy of the distribution of directed network motifs increased from MCI to CONV to AD, implying that the distribution of pathology is more structured in MCI but becomes less so as it progresses to CONV and further to AD. Thus, directed network motifs frequencies and distributional properties provide new insights into the progression of Alzheimer's disease as well as new imaging markers for distinguishing between normal controls, stable mild cognitive impairment, MCI converters and Alzheimer's disease.

Macrophage migration inhibitory factor as a chaperone inhibiting accumulation of misfolded SOD1.

Mutations in superoxide dismutase (SOD1) cause amyotrophic lateral sclerosis (ALS), a neurodegenerative disease characterized by loss of motor neurons and accompanied by accumulation of misfolded SOD1 onto the cytoplasmic faces of intracellular organelles, including mitochondria and the endoplasmic reticulum (ER). Using inhibition of misfolded SOD1 deposition onto mitochondria as an assay, a chaperone activity abundant in nonneuronal tissues is now purified and identified to be the multifunctional macrophage migration inhibitory factor (MIF), whose activities include an ATP-independent protein folding chaperone. Purified MIF is shown to directly inhibit mutant SOD1 misfolding. Elevating MIF in neuronal cells suppresses accumulation of misfolded SOD1 and its association with mitochondria and the ER and extends survival of mutant SOD1-expressing motor neurons. Accumulated MIF protein is identified to be low in motor neurons, implicating correspondingly low chaperone activity as a component of vulnerability to mutant SOD1 misfolding and supporting therapies to enhance intracellular MIF chaperone activity.