Pooled CRISPR screens with imaging on microraft arrays reveals stress granule-regulatory factors.

Genetic screens using pooled CRISPR-based approaches are scalable and inexpensive, but restricted to standard readouts, including survival, proliferation and sortable markers. However, many biologically relevant cell states involve cellular and subcellular changes that are only accessible by microscopic visualization, and are currently impossible to screen with pooled methods. Here we combine pooled CRISPR-Cas9 screening with microraft array technology and high-content imaging to screen image-based phenotypes (CRaft-ID; CRISPR-based microRaft followed by guide RNA identification). By isolating microrafts that contain genetic clones harboring individual guide RNAs (gRNA), we identify RNA-binding proteins (RBPs) that influence the formation of stress granules, the punctate protein-RNA assemblies that form during stress. To automate hit identification, we developed a machine-learning model trained on nuclear morphology to remove unhealthy cells or imaging artifacts. In doing so, we identified and validated previously uncharacterized RBPs that modulate stress granule abundance, highlighting the applicability of our approach to facilitate image-based pooled CRISPR screens.

Aberrant NOVA1 function disrupts alternative splicing in early stages of amyotrophic lateral sclerosis.

Amyotrophic lateral sclerosis (ALS) is a fatal disease characterized by aberrant alternative splicing (AS). Nuclear loss and cytoplasmic accumulation of the splicing factor TDP-43 in motor neurons (MN) are hallmarks of ALS at late stages of the disease. However, it is unknown if altered AS is present before TDP-43 pathology occurs. Here, we investigate altered AS and its origins in early stages of ALS using human induced pluripotent stem cell-derived motor neurons (MNs) from sporadic and familial ALS patients. We find high levels of the RNA-binding proteins NOVA1, NOVA2, and RBFOX2 in the insoluble protein fractions and observe that AS events in ALS-associated MNs are enriched for binding sites of these proteins. Our study points to an early disrupted function of NOVA1 that drives AS changes in a complex fashion, including events caused by a consistent loss of NOVA1 function. NOVA1 exhibits increased cytoplasmic protein levels in early stage MNs without TDP-43 pathology in ALS postmortem tissue. As nuclear TDP-43 protein level depletes, NOVA1 is reduced. Potential indications for a reduction of NOVA1 also came from mice over-expressing TDP-43 lacking its nuclear localization signal and iPSC-MN stressed with puromycin. This study highlights that additional RBP-RNA perturbations in ALS occur in parallel to TDP-43.

Glial cells maintain synapses by inhibiting an activity-dependent retrograde protease signal.

Glial cells regulate multiple aspects of synaptogenesis. In the absence of Schwann cells, a peripheral glial cell, motor neurons initially innervate muscle but then degenerate. Here, using a genetic approach, we show that neural activity-regulated negative factors produced by muscle drive neurodegeneration in Schwann cell-deficient mice. We find that thrombin, the hepatic serine protease central to the hemostatic coagulation cascade, is one such negative factor. Trancriptomic analysis shows that expression of the antithrombins serpin C1 and D1 is significantly reduced in Schwann cell-deficient mice. In the absence of peripheral neuromuscular activity, neurodegeneration is completely blocked, and expression of prothrombin in muscle is markedly reduced. In the absence of muscle-derived prothrombin, neurodegeneration is also markedly reduced. Together, these results suggest that Schwann cells regulate NMJs by opposing the effects of activity-regulated, muscle-derived negative factors and provide the first genetic evidence that thrombin plays a central role outside of the coagulation system.

LIN28 binds messenger RNAs at GGAGA motifs and regulates splicing factor abundance.

LIN28 is a conserved RNA-binding protein implicated in pluripotency, reprogramming, and oncogenesis. It was previously shown to act primarily by blocking let-7 microRNA (miRNA) biogenesis, but here we elucidate distinct roles of LIN28 regulation via its direct messenger RNA (mRNA) targets. Through crosslinking and immunoprecipitation coupled with high-throughput sequencing (CLIP-seq) in human embryonic stem cells and somatic cells expressing exogenous LIN28, we have defined discrete LIN28-binding sites in a quarter of human transcripts. These sites revealed that LIN28 binds to GGAGA sequences enriched within loop structures in mRNAs, reminiscent of its interaction with let-7 miRNA precursors. Among LIN28 mRNA targets, we found evidence for LIN28 autoregulation and also direct but differing effects on the protein abundance of splicing regulators in somatic and pluripotent stem cells. Splicing-sensitive microarrays demonstrated that exogenous LIN28 expression causes widespread downstream alternative splicing changes. These findings identify important regulatory functions of LIN28 via direct mRNA interactions.

Transcriptome-pathology correlation identifies interplay between TDP-43 and the expression of its kinase CK1E in sporadic ALS.

Sporadic amyotrophic lateral sclerosis (sALS) is the most common form of ALS, however, the molecular mechanisms underlying cellular damage and motor neuron degeneration remain elusive. To identify molecular signatures of sALS we performed genome-wide expression profiling in laser capture microdissection-enriched surviving motor neurons (MNs) from lumbar spinal cords of sALS patients with rostral onset and caudal progression. After correcting for immunological background, we discover a highly specific gene expression signature for sALS that is associated with phosphorylated TDP-43 (pTDP-43) pathology. Transcriptome-pathology correlation identified casein kinase 1ε (CSNK1E) mRNA as tightly correlated to levels of pTDP-43 in sALS patients. Enhanced crosslinking and immunoprecipitation in human sALS patient- and healthy control-derived frontal cortex, revealed that TDP-43 binds directly to and regulates the expression of CSNK1E mRNA. Additionally, we were able to show that pTDP-43 itself binds RNA. CK1E, the protein product of CSNK1E, in turn interacts with TDP-43 and promotes cytoplasmic accumulation of pTDP-43 in human stem-cell-derived MNs. Pathological TDP-43 phosphorylation is therefore, reciprocally regulated by CK1E activity and TDP-43 RNA binding. Our framework of transcriptome-pathology correlations identifies candidate genes with relevance to novel mechanisms of neurodegeneration.

Retropharyngeal Contralateral C7 Nerve Transfer to the Lower Trunk for Brachial Plexus Birth Injury: Technique and Results.

PURPOSE: Brachial plexus birth injuries with multiple nerve root avulsions present a particularly difficult reconstructive challenge because of the limited availability of donor nerves. The contralateral C7 has been described for brachial plexus reconstruction in adults but has not been well-studied in the pediatric population. We present our technique and results for retropharyngeal contralateral C7 nerve transfer to the lower trunk for brachial plexus birth injury. METHODS: We performed a retrospective review. Any child aged less than 2 years was included. Charts were analyzed for patient demographic data, operative variables, functional outcomes, complications, and length of follow-up. RESULTS: We had a total of 5 patients. Average nerve graft length was 3 cm. All patients had return of hand sensation to the ulnar nerve distribution as evidenced by a pinch test, unprompted use of the recipient limb without mirror movement, and an Active Movement Scale (AMS) of at least 2/7 for finger and thumb flexion; one patient had an AMS of 7/7 for finger and thumb flexion. Only one patient had return of ulnar intrinsic hand function with an AMS of 3/7. Two patients had temporary triceps weakness in the donor limb and one had clinically insignificant temporary phrenic nerve paresis. No complications were related to the retropharyngeal nerve dissection in any patient. Average follow-up was 3.3 years. CONCLUSIONS: The retropharyngeal contralateral C7 nerve transfer is a safe way to supply extra axons to the severely injured arm in brachial plexus birth injuries with no permanent donor limb deficits. Early functional recovery in these patients, with regard to hand function and sensation, is promising. TYPE OF STUDY/LEVEL OF EVIDENCE: Therapeutic V.

Reconstruction of the Isolated Columellar Defect: A Novel 2-Stage Technique and Review of the Literature.

The importance of the nasal complex cannot be overstated from a functional, social, and psychological perspective. The goal of reconstruction is to restore the trilaminar composition of the nose. This is accomplished by recreating the nasal lining and providing a cartilaginous framework to simultaneously support a patent airway and project the defining features to the overlying soft tissue. The columella is one of the smallest subunits of the nose, but the loss of this structure has important esthetic and structural implications. The ideal operation for an isolated defect of the columella remains elusive. The ideal reconstruction would match the pigmentation and texture of the surrounding nasal skin and provide a convex contour with underlying structural support. In addition, the donor site would not create a secondary deformity by disrupting normal anatomy. This report describes a novel 2-stage technique for reconstruction of the columella and reviews the current literature.

Management of the Acutely Burned Hand.

Despite contributing a small percentage to the total body surface area, hands are the most commonly burned body part and are involved in over 90% of severe burns. Although the mortality of isolated hand burns is negligible, morbidity can be substantial given our need for functioning hands when performing activities of daily living. The greatest challenges of treating hand burns are 2-fold. First, determining the depth of injury can be difficult even for the most experienced surgeon, but despite many diagnostic options, clinical examination remains the gold standard. Second, appropriate postoperative hand therapy is crucial and requires a multidisciplinary approach with an experienced burn surgeon, hand surgeon, and hand therapist. Ultimately, the goals of treatment should include preservation of function and aesthetics. In this review, we present an approach to the management of the acutely burned hand with discussion of both conservative and surgical options. Regardless of the initial treatment decision, subsequent care for this subset of patients should be aimed at preventing debilitating postburn scar contractures that can severely limit hand function and ultimately require reconstructive surgery.

Pediatric frontal sinus fractures: outcomes and treatment algorithm.

Pediatric frontal sinus fractures are a rare clinical entity. Owing to the large amount of force required to fracture the frontal sinus, it is often associated with severe intracranial and craniofacial injuries. The treatment of frontal sinus fractures is controversial, with many different established algorithms based mainly on the adult population. The authors present their experience with pediatric frontal sinus fractures; they also present a treatment algorithm. A retrospective review of the Cincinnati Children's Hospital Medical Center trauma database was performed. From 1998 to 2010, the authors identified patients between the ages of 0 and 18 with frontal sinus fractures and analyzed demographics, fracture pattern, associated injuries, methods of treatment, and complications. Descriptive statistics and univariate analyses were performed.A total of 39 patients were included in the study with a mean follow-up of 31.2 months. Fractures of the anterior and posterior table with displacement greater than one table width were significantly associated with higher hospital costs, higher velocity mechanism of injuries, lower Glasgow Coma Scale scores, nasofrontal outflow tract (NFOT) involvement, and cerebrospinal fluid leak. There were no differences in short- and long-term complications. Additionally, these patients were more likely to be treated surgically in the form of obliteration or cranialization.Patients without NFOT involvement can be managed with observation only. Patients with NFOT involvement or persistent cerebrospinal fluid leak should be treated with obliteration or cranialization, respectively, to reduce the risk of severe complications.

Thoracic outlet syndrome in the pediatric population: case series.

We present 4 patients, 4 months to 10 years of age, with thoracic outlet syndrome. All were referred to the brachial plexus clinic. Three patients were diagnosed with vascular thoracic outlet syndrome after clinical evaluation and diagnostic imaging. Three had a cervical rib and 1 had an anomalous first rib. All patients were treated surgically through a supraclavicular approach and had resolution of the symptoms. No postoperative complications were noted.

Global regulation of alternative splicing during myogenic differentiation.

Recent genome-wide analyses have elucidated the extent of alternative splicing (AS) in mammals, often focusing on comparisons of splice isoforms between differentiated tissues. However, regulated splicing changes are likely to be important in biological transitions such as cellular differentiation, or response to environmental stimuli. To assess the extent and significance of AS in myogenesis, we used splicing-sensitive microarray analysis of differentiating C2C12 myoblasts. We identified 95 AS events that undergo robust splicing transitions during C2C12 differentiation. More than half of the splicing transitions are conserved during differentiation of avian myoblasts, suggesting the products and timing of transitions are functionally significant. The majority of splicing transitions during C2C12 differentiation fall into four temporal patterns and were dependent on the myogenic program, suggesting that they are integral components of myogenic differentiation. Computational analyses revealed enrichment of many sequence motifs within the upstream and downstream intronic regions near the alternatively spliced regions corresponding to binding sites of splicing regulators. Western analyses demonstrated that several splicing regulators undergo dynamic changes in nuclear abundance during differentiation. These findings show that within a developmental context, AS is a highly regulated and conserved process, suggesting a major role for AS regulation in myogenic differentiation.

Discovery and functional interrogation of SARS-CoV-2 protein-RNA interactions.

The COVID-19 pandemic is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). The betacoronvirus has a positive sense RNA genome which encodes for several RNA binding proteins. Here, we use enhanced crosslinking and immunoprecipitation to investigate SARS-CoV-2 protein interactions with viral and host RNAs in authentic virus-infected cells. SARS-CoV-2 proteins, NSP8, NSP12, and nucleocapsid display distinct preferences to specific regions in the RNA viral genome, providing evidence for their shared and separate roles in replication, transcription, and viral packaging. SARS-CoV-2 proteins expressed in human lung epithelial cells bind to 4773 unique host coding RNAs. Nine SARS-CoV-2 proteins upregulate target gene expression, including NSP12 and ORF9c, whose RNA substrates are associated with pathways in protein N-linked glycosylation ER processing and mitochondrial processes. Furthermore, siRNA knockdown of host genes targeted by viral proteins in human lung organoid cells identify potential antiviral host targets across different SARS-CoV-2 variants. Conversely, NSP9 inhibits host gene expression by blocking mRNA export and dampens cytokine productions, including interleukin-1α/ß. Our viral protein-RNA interactome provides a catalog of potential therapeutic targets and offers insight into the etiology of COVID-19 as a safeguard against future pandemics.

Discovery and functional interrogation of SARS-CoV-2 protein-RNA interactions.

The COVID-19 pandemic is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). The betacoronvirus has a positive sense RNA genome which encodes for several RNA binding proteins. Here, we use enhanced crosslinking and immunoprecipitation to investigate SARS-CoV-2 protein interactions with viral and host RNAs in authentic virus-infected cells. SARS-CoV-2 proteins, NSP8, NSP12, and nucleocapsid display distinct preferences to specific regions in the RNA viral genome, providing evidence for their shared and separate roles in replication, transcription, and viral packaging. SARS-CoV-2 proteins expressed in human lung epithelial cells bind to 4773 unique host coding RNAs. Nine SARS-CoV-2 proteins upregulate target gene expression, including NSP12 and ORF9c, whose RNA substrates are associated with pathways in protein N-linked glycosylation ER processing and mitochondrial processes. Furthermore, siRNA knockdown of host genes targeted by viral proteins in human lung organoid cells identify potential antiviral host targets across different SARS-CoV-2 variants. Conversely, NSP9 inhibits host gene expression by blocking mRNA export and dampens cytokine productions, including interleukin-1α/ß. Our viral protein-RNA interactome provides a catalog of potential therapeutic targets and offers insight into the etiology of COVID-19 as a safeguard against future pandemics.

Huntington's disease mice and human brain tissue exhibit increased G3BP1 granules and TDP43 mislocalization.

Chronic cellular stress associated with neurodegenerative disease can result in the persistence of stress granule (SG) structures, membraneless organelles that form in response to cellular stress. In Huntington's disease (HD), chronic expression of mutant huntingtin generates various forms of cellular stress, including activation of the unfolded protein response and oxidative stress. However, it has yet to be determined whether SGs are a feature of HD neuropathology. We examined the miRNA composition of extracellular vesicles (EVs) present in the cerebrospinal fluid (CSF) of patients with HD and show that a subset of their target mRNAs were differentially expressed in the prefrontal cortex. Of these targets, SG components were enriched, including the SG-nucleating Ras GTPase-activating protein-binding protein 1 (G3BP1). We investigated localization and levels of G3BP1 and found a significant increase in the density of G3BP1-positive granules in the cortex and hippocampus of R6/2 transgenic mice and in the superior frontal cortex of the brains of patients with HD. Intriguingly, we also observed that the SG-associated TAR DNA-binding protein 43 (TDP43), a nuclear RNA/DNA binding protein, was mislocalized to the cytoplasm of G3BP1 granule-positive HD cortical neurons. These findings suggest that G3BP1 SG dynamics may play a role in the pathophysiology of HD.

An optimized 3D spoiled gradient recalled echo pulse sequence for hemorrhage assessment using inversion recovery and multiple echoes (3D SHINE) for carotid plaque imaging.

Intraplaque hemorrhage into the carotid atherosclerotic plaque has been shown to create instability and progression. We have developed an optimized 3D Spoiled Gradient recalled echo pulse sequence for Hemorrhage assessment using INversion recovery and multiple Echoes (3D SHINE) for carotid plaque imaging. The sequence was developed by incorporating multiecho acquisition to its clinically validated optimized single-echo counterpart 3D inversion recovery prepared fast spoiled gradient recalled sequence. With similar scan time (4 min), 3D spoiled gradient recalled echo pulse sequence for hemorrhage assessment using inversion recovery and multiple echoes maintained comparable high-resolution volumetric coverage, black-blood effect, contrast, signal-to-noise and contrast-to-noise ratios, and similar sensitivity and specificity in detecting whether intraplaque hemorrhage was present on an artery. The multiple echoes acquired with 3D SHINE allowed the estimation of intraplaque hemorrhage T*(2) and then the subsequent characterization of intraplaque hemorrhage (T*(2) for type I < 14 msec, and for type II > 14 msec). The type I intraplaque hemorrhage size estimated by 3D SHINE was significantly and positively correlated with the size estimated manually by an expert reviewer using the histology-validated multicontrast MRI technique (r = 0.836 ± 0.080, p < 0.001). With only one fast sequence, 3D SHINE can detect and characterize intraplaque hemorrhage that has previously required a multicontrast approach using a combination of black-blood T(1)-weighted, black-blood T(2)-weighted, and time-of-flight imaging techniques.

Conserved metabolite regulation of stress granule assembly via AdoMet.

Stress granules (SGs) are evolutionarily conserved condensates of ribonucleoproteins that assemble in response to metabolic stresses. Because aberrant SG formation is associated with amyotrophic lateral sclerosis (ALS), understanding the connection between metabolic activity and SG composition can provide therapeutic insights into neurodegeneration. Here, we identify 17 metabolic enzymes recruited to yeast SGs in response to physiological growth stress. Furthermore, the product of one of these enzymes, AdoMet, is a regulator of SG assembly and composition. Decreases in AdoMet levels increase SG formation, while chronic elevation of AdoMet produces SG remnants lacking proteins associated with the 5' end of transcripts. Interestingly, acute elevation of AdoMet blocks SG formation in yeast and motor neurons. Treatment of ALS-derived motor neurons with AdoMet also suppresses the formation of TDP-43-positive SGs, a hallmark of ALS. Together, these results argue that AdoMet is an evolutionarily conserved regulator of SG composition and assembly with therapeutic potential in neurodegeneration.

Untargeted mass spectrometry-based metabolomics approach unveils molecular changes in raw and processed foods and beverages.

In our daily lives, we consume foods that have been transported, stored, prepared, cooked, or otherwise processed by ourselves or others. Food storage and preparation have drastic effects on the chemical composition of foods. Untargeted mass spectrometry analysis of food samples has the potential to increase our chemical understanding of these processes by detecting a broad spectrum of chemicals. We performed a time-based analysis of the chemical changes in foods during common preparations, such as fermentation, brewing, and ripening, using untargeted mass spectrometry and molecular networking. The data analysis workflow presented implements an approach to study changes in food chemistry that can reveal global alterations in chemical profiles, identify changes in abundance, as well as identify specific chemicals and their transformation products. The data generated in this study are publicly available, enabling the replication and re-analysis of these data in isolation, and serve as a baseline dataset for future investigations.

Small-Molecule Modulation of TDP-43 Recruitment to Stress Granules Prevents Persistent TDP-43 Accumulation in ALS/FTD.

Stress granules (SGs) form during cellular stress and are implicated in neurodegenerative diseases such as amyotrophic lateral sclerosis and frontotemporal dementia (ALS/FTD). To yield insights into the role of SGs in pathophysiology, we performed a high-content screen to identify small molecules that alter SG properties in proliferative cells and human iPSC-derived motor neurons (iPS-MNs). One major class of active molecules contained extended planar aromatic moieties, suggesting a potential to intercalate in nucleic acids. Accordingly, we show that several hit compounds can prevent the RNA-dependent recruitment of the ALS-associated RNA-binding proteins (RBPs) TDP-43, FUS, and HNRNPA2B1 into SGs. We further demonstrate that transient SG formation contributes to persistent accumulation of TDP-43 into cytoplasmic puncta and that our hit compounds can reduce this accumulation in iPS-MNs from ALS patients. We propose that compounds with planar moieties represent a promising starting point to develop small-molecule therapeutics for treating ALS/FTD.

Linear phase-error correction for improved water and fat separation in dual-echo dixon techniques.

Large and spatially-linear phase errors along the frequency-encode direction may be induced by several common and hard-to-avoid system imperfections such as eddy currents. For data acquired in dual-echo Dixon techniques, the linear phase error can be more aggravated when compared to that acquired in a single echo and can pose challenges to a phase-correction algorithm necessary for successful Dixon processing. In this work, we propose a two-step process that first corrects the linear component of the phase errors with a modified Ahn-Cho algorithm (Ahn CB and Cho ZH, IEEE Trans. Med. Imaging 6:32, 1987) and then corrects the residual phase errors with a previously-developed region-growing algorithm (Ma J, Magn. Res. Med. 52:415, 2004). We demonstrate that successive application of the two-step process to data from a dual-echo Dixon technique provides a "1-2 punch" to the overall phase errors and can overcome local water and fat separation failures that are observed when the region-growing-based algorithm is applied alone.

Effects of refocusing flip angle modulation and view ordering in 3D fast spin echo.

Recent advances have reduced scan time in three-dimensional fast spin echo (3D-FSE) imaging, including very long echo trains through refocusing flip angle (FA) modulation and 2D-accelerated parallel imaging. This work describes a method to modulate refocusing FAs that produces sharp point spread functions (PSFs) from very long echo trains while exercising direct control over minimum, center-k-space, and maximum FAs in order to accommodate the presence of flow and motion, SNR requirements, and RF power limits. Additionally, a new method for ordering views to map signal modulation from the echo train into k(y)-k(z) space that enables nonrectangular k-space grids and autocalibrating 2D-accelerated parallel imaging is presented. With long echo trains and fewer echoes required to encode large matrices, large volumes with high in- and through-plane resolution matrices may be acquired with scan times of 3-6 min, as demonstrated for volumetric brain, knee, and kidney imaging.