TnpB homologues exapted from transposons are RNA-guided transcription factors.

Transposon-encoded tnpB and iscB genes encode RNA-guided DNA nucleases that promote their own selfish spread through targeted DNA cleavage and homologous recombination1-4. These widespread gene families were repeatedly domesticated over evolutionary timescales, leading to the emergence of diverse CRISPR-associated nucleases including Cas9 and Cas12 (refs. 5,6). We set out to test the hypothesis that TnpB nucleases may have also been repurposed for novel, unexpected functions other than CRISPR-Cas adaptive immunity. Here, using phylogenetics, structural predictions, comparative genomics and functional assays, we uncover multiple independent genesis events of programmable transcription factors, which we name TnpB-like nuclease-dead repressors (TldRs). These proteins use naturally occurring guide RNAs to specifically target conserved promoter regions of the genome, leading to potent gene repression in a mechanism akin to CRISPR interference technologies invented by humans7. Focusing on a TldR clade found broadly in Enterobacteriaceae, we discover that bacteriophages exploit the combined action of TldR and an adjacently encoded phage gene to alter the expression and composition of the host flagellar assembly, a transformation with the potential to impact motility8, phage susceptibility9, and host immunity10. Collectively, this work showcases the diverse molecular innovations that were enabled through repeated exaptation of transposon-encoded genes, and reveals the evolutionary trajectory of diverse RNA-guided transcription factors.

De novo gene synthesis by an antiviral reverse transcriptase.

Bacteria defend themselves from viral infection using diverse immune systems, many of which sense and target foreign nucleic acids. Defense-associated reverse transcriptase (DRT) systems provide an intriguing counterpoint to this immune strategy by instead leveraging DNA synthesis, but the identities and functions of their DNA products remain largely unknown. Here we show that DRT2 systems execute an unprecedented immunity mechanism that involves de novo gene synthesis via rolling-circle reverse transcription of a non-coding RNA (ncRNA). Unbiased profiling of RT-associated RNA and DNA ligands in DRT2-expressing cells revealed that reverse transcription generates concatenated cDNA repeats through programmed template jumping on the ncRNA. The presence of phage then triggers second-strand cDNA synthesis, leading to the production of long double-stranded DNA. Remarkably, this DNA product is efficiently transcribed, generating messenger RNAs that encode a stop codon-less, never-ending ORF (neo) whose translation causes potent growth arrest. Phylogenetic analyses and screening of diverse DRT2 homologs further revealed broad conservation of rolling-circle reverse transcription and Neo protein function. Our work highlights an elegant expansion of genome coding potential through RNA-templated gene creation, and challenges conventional paradigms of genetic information encoded along the one-dimensional axis of genomic DNA.

Loss of Pip4k2c confers liver-metastatic organotropism through insulin-dependent PI3K-AKT pathway activation.

Liver metastasis (LM) confers poor survival and therapy resistance across cancer types, but the mechanisms of liver-metastatic organotropism remain unknown. Here, through in vivo CRISPR-Cas9 screens, we found that Pip4k2c loss conferred LM but had no impact on lung metastasis or primary tumor growth. Pip4k2c-deficient cells were hypersensitized to insulin-mediated PI3K/AKT signaling and exploited the insulin-rich liver milieu for organ-specific metastasis. We observed concordant changes in PIP4K2C expression and distinct metabolic changes in 3,511 patient melanomas, including primary tumors, LMs and lung metastases. We found that systemic PI3K inhibition exacerbated LM burden in mice injected with Pip4k2c-deficient cancer cells through host-mediated increase in hepatic insulin levels; however, this circuit could be broken by concurrent administration of an SGLT2 inhibitor or feeding of a ketogenic diet. Thus, this work demonstrates a rare example of metastatic organotropism through co-optation of physiological metabolic cues and proposes therapeutic avenues to counteract these mechanisms.

Targeted DNA integration in human cells without double-strand breaks using CRISPR-associated transposases.

Conventional genome engineering with CRISPR-Cas9 creates double-strand breaks (DSBs) that lead to undesirable byproducts and reduce product purity. Here we report an approach for programmable integration of large DNA sequences in human cells that avoids the generation of DSBs by using Type I-F CRISPR-associated transposases (CASTs). We optimized DNA targeting by the QCascade complex through protein design and developed potent transcriptional activators by exploiting the multi-valent recruitment of the AAA+ ATPase TnsC to genomic sites targeted by QCascade. After initial detection of plasmid-based integration, we screened 15 additional CAST systems from a wide range of bacterial hosts, identified a homolog from Pseudoalteromonas that exhibits improved activity and further increased integration efficiencies. Finally, we discovered that bacterial ClpX enhances genomic integration by multiple orders of magnitude, likely by promoting active disassembly of the post-integration CAST complex, akin to its known role in Mu transposition. Our work highlights the ability to reconstitute complex, multi-component machineries in human cells and establishes a strong foundation to exploit CRISPR-associated transposases for eukaryotic genome engineering.

"Are They Listening, and Do They Find It Useful?"-Evaluation of Mid-Rotation Formative Subjective and Objective Feedback to Radiology Trainees.

BACKGROUND: Residents commonly receive only end-of-rotation evaluations and thus are often unaware of their progress during a rotation. In 2021, our neuroradiology section instituted mid-rotation feedback in which rotating residents received formative subjective and objective feedback. The purpose of this study was to describe our feedback method and to evaluate if residents found it helpful. METHODS: Radiology residents rotate 3-4 times on the neuroradiology service for 1-month blocks. At the midpoint of the rotation (2 weeks), 7-10 neuroradiology attendings discussed the rotating residents' subjective performance. One attending was tasked with facilitating this discussion and taking notes. Objective metrics were obtained from our dictation software. Compiled feedback was relayed to residents via email. A 16-question anonymous survey was sent to 39 radiology residents (R1-R4) to evaluate the perceived value of mid-rotation feedback. Odds ratios and 95% confidence intervals were computed using logistic regression. RESULTS: Sixty-nine percent (27/39) of residents responded to the survey; 92.6% (25/27) of residents reported receiving mid-rotation feedback in ≥50% of neuroradiology rotations; 92.3% (24/26) of residents found the subjective feedback helpful; 88.4% (23/26) of residents reported modifying their performance as suggested (100% R1-R2 vs 70% R3-R4; OR: 15.4 CI:1.26, >30.0);59.1% (13/22) of residents found the objective metrics helpful (75% R1-R2 vs 40% R3-R4; OR: 3.92 CI:0.74, 24.39) and 68.2% (15/22) stated they modified their performance based on these metrics (83.3% R1-R2 vs 50.0% R3-R4; OR:4.2 CI:0.73, 30.55); and 84.6% (22/26) of residents stated that mid-rotation subjective feedback and 45.5% (10/22) stated that mid-rotation objective feedback should be implemented in other sections. CONCLUSIONS: Majority of residents found mid-rotation feedback to be helpful in informing them about their progress and areas for improvement in the neuroradiology rotation, more so for subjective feedback than objective feedback. The majority of residents stated all rotations should provide mid-rotation subjective feedback.

Antagonistic conflict between transposon-encoded introns and guide RNAs.

TnpB nucleases represent the evolutionary precursors to CRISPR-Cas12 and are widespread in all domains of life, presumably due to the critical roles they play in transposon proliferation. IS605family TnpB homologs function in bacteria as programmable homing endonucleases by exploiting transposon-encoded guide RNAs to cleave vacant genomic sites, thereby driving transposon maintenance through DSB-stimulated homologous recombination. Whether this pathway is conserved in other genetic contexts, and in association with other transposases, is unknown. Here we uncover molecular mechanisms of transposition and RNA-guided DNA cleavage by IS607-family elements that, remarkably, also encode catalytic, self-splicing group I introns. After reconstituting and systematically investigating each of these biochemical activities for a candidate 'IStron' derived from Clostridium botulinum, we discovered sequence and structural features of the transposon-encoded RNA that satisfy molecular requirements of a group I intron and TnpB guide RNA, while still retaining the ability to be faithfully mobilized at the DNA level by the TnpA transposase. Strikingly, intron splicing was strongly repressed not only by TnpB, but also by the secondary structure of ωRNA alone, allowing the element to carefully control the relative levels of spliced products versus functional guide RNAs. Our results suggest that IStron transcripts have evolved a sensitive equilibrium to balance competing and mutually exclusive activities that promote transposon maintenance while limiting adverse fitness costs on the host. Collectively, this work explains how diverse enzymatic activities emerged during the selfish spread of IS607-family elements and highlights molecular innovation in the multi-functional utility of transposon-encoded noncoding RNAs.

Emergence of RNA-guided transcription factors via domestication of transposon-encoded TnpB nucleases.

Transposon-encoded tnpB genes encode RNA-guided DNA nucleases that promote their own selfish spread through targeted DNA cleavage and homologous recombination1-4. This widespread gene family was repeatedly domesticated over evolutionary timescales, leading to the emergence of diverse CRISPR-associated nucleases including Cas9 and Cas125,6. We set out to test the hypothesis that TnpB nucleases may have also been repurposed for novel, unexpected functions other than CRISPR-Cas. Here, using phylogenetics, structural predictions, comparative genomics, and functional assays, we uncover multiple instances of programmable transcription factors that we name TnpB-like nuclease-dead repressors (TldR). These proteins employ naturally occurring guide RNAs to specifically target conserved promoter regions of the genome, leading to potent gene repression in a mechanism akin to CRISPRi technologies invented by humans7. Focusing on a TldR clade found broadly in Enterobacteriaceae, we discover that bacteriophages exploit the combined action of TldR and an adjacently encoded phage gene to alter the expression and composition of the host flagellar assembly, a transformation with the potential to impact motility8, phage susceptibility9, and host immunity10. Collectively, this work showcases the diverse molecular innovations that were enabled through repeated exaptation of genes encoded by transposable elements, and reveals that RNA-guided transcription factors emerged long before the development of dCas9-based editors.

Genome editing with retroelements.

RNA-guided DNA writing enzymes offer promise for programmable gene insertion.

Transposon-encoded nucleases use guide RNAs to promote their selfish spread.

Insertion sequences are compact and pervasive transposable elements found in bacteria, which encode only the genes necessary for their mobilization and maintenance1. IS200- and IS605-family transposons undergo 'peel-and-paste' transposition catalysed by a TnpA transposase2, but they also encode diverse, TnpB- and IscB-family proteins that are evolutionarily related to the CRISPR-associated effectors Cas12 and Cas9, respectively3,4. Recent studies have demonstrated that TnpB and IscB function as RNA-guided DNA endonucleases5,6, but the broader biological role of this activity has remained enigmatic. Here we show that TnpB and IscB are essential to prevent permanent transposon loss as a consequence of the TnpA transposition mechanism. We selected a family of related insertion sequences from Geobacillus stearothermophilus that encode several TnpB and IscB orthologues, and showed that a single TnpA transposase was broadly active for transposon mobilization. The donor joints formed upon religation of transposon-flanking sequences were efficiently targeted for cleavage by RNA-guided TnpB and IscB nucleases, and co-expression of TnpB and TnpA led to substantially greater transposon retention relative to conditions in which TnpA was expressed alone. Notably, TnpA and TnpB also stimulated recombination frequencies, surpassing rates observed with TnpB alone. Collectively, this study reveals that RNA-guided DNA cleavage arose as a primal biochemical activity to bias the selfish inheritance and spread of transposable elements, which was later co-opted during the evolution of CRISPR-Cas adaptive immunity for antiviral defence.

A PSD-95 peptidomimetic mitigates neurological deficits in a mouse model of Angelman syndrome.

Angelman Syndrome (AS) is a severe cognitive disorder caused by loss of neuronal expression of the E3 ubiquitin ligase UBE3A. In an AS mouse model, we previously reported a deficit in brain-derived neurotrophic factor (BDNF) signaling, and set out to develop a therapeutic that would restore normal signaling. We demonstrate that CN2097, a peptidomimetic compound that binds postsynaptic density protein-95 (PSD-95), a TrkB associated scaffolding protein, mitigates deficits in PLC-CaMKII and PI3K/mTOR pathways to restore synaptic plasticity and learning. Administration of CN2097 facilitated long-term potentiation (LTP) and corrected paired-pulse ratio. As the BDNF-mTORC1 pathway is critical for inhibition of autophagy, we investigated whether autophagy was disrupted in AS mice. We found aberrantly high autophagic activity attributable to a concomitant decrease in mTORC1 signaling, resulting in decreased levels of synaptic proteins, including Synapsin-1 and Shank3. CN2097 increased mTORC1 activity to normalize autophagy and restore hippocampal synaptic protein levels. Importantly, treatment mitigated cognitive and motor dysfunction. These findings support the use of neurotrophic therapeutics as a valuable approach for treating AS pathology.

The retinal deep capillary plexus as a venous outflow system; insights from Sturge Weber Syndrome.

PURPOSE: To report on the venous abnormalities of a patient with Sturge-Weber syndrome (SWS). METHOD: Case report. PATIENT: A 29-year-old woman with a history of SWS since infancy was referred for evaluation of possible diffuse choroidal hemangioma. Multimodal imaging, including ultra-widefield fluorescein, indocyanine green, and optical coherence tomography-angiography (OCTA) were performed. RESULTS: Dilated fundus examination was remarkable for increased cupping of the optic disc in the right eye, venous tortuosity, and marked dilation of the choroidal vessels. Ultra-widefield fluorescein angiography confirmed marked venous tortuosity and dilation, as well as anastomoses of the retinal veins ipsilateral to the port wine stain. Indocyanine green angiography revealed marked engorgement of the vortex veins and choroidal vasculature. OCTA revealed dilated vascular channels in the deep capillary plexus (DCP) that were directly anastomosing to the superficial capillary plexus, but not the intermediate capillary plexus. Engorgement of the ampullae of the DCP vortex system was also observed. The normal contralateral eye was used as comparison for all imaging studies. CONCLUSION: These findings support the notion of generalized venous hypertension state in adult eyes with SWS and corroborate prior evidence that the deep capillary plexus acts as a venous outflow system.

Targeted DNA integration in human cells without double-strand breaks using CRISPR RNA-guided transposases.

Traditional genome-editing reagents such as CRISPR-Cas9 achieve targeted DNA modification by introducing double-strand breaks (DSBs), thereby stimulating localized DNA repair by endogenous cellular repair factors. While highly effective at generating heterogenous knockout mutations, this approach suffers from undesirable byproducts and an inability to control product purity. Here we develop a system in human cells for programmable, DSB-free DNA integration using Type I CRISPR-associated transposons (CASTs). To adapt our previously described CAST systems, we optimized DNA targeting by the QCascade complex through a comprehensive assessment of protein design, and we developed potent transcriptional activators by exploiting the multi-valent recruitment of the AAA+ ATPase, TnsC, to genomic sites targeted by QCascade. After initial detection of plasmid-based transposition, we screened 15 homologous CAST systems from a wide range of bacterial hosts, identified a CAST homolog from Pseudoalteromonas that exhibited improved activity, and increased integration efficiencies through parameter optimization. We further discovered that bacterial ClpX enhances genomic integration by multiple orders of magnitude, and we propose that this critical accessory factor functions to drive active disassembly of the post-transposition CAST complex, akin to its demonstrated role in Mu transposition. Our work highlights the ability to functionally reconstitute complex, multi-component machineries in human cells, and establishes a strong foundation to realize the full potential of CRISPR-associated transposons for human genome engineering.

The Use of Five-Strand Hamstring Autograft to Increase the Graft Size in Anterior Cruciate Ligament Reconstruction-A Prospective Cohort Study With Satisfactory Early Clinical Results.

Objectives: To report on the outcomes of using 5-strand hamstring autograft to increase the graft size for anterior cruciate ligament (ACL) reconstruction and to determine whether the clinical results are comparable to using conventional 4-strand graft. Methods: A prospective cohort study of patients with arthroscopic-assisted single-bundle ACL reconstruction using hamstring autograft from January 2019 to June 2021.The patients were prospectively recruited to undergo ACL reconstruction with either 5-strand hamstring graft (group A) or 4-strand hamstring graft (group B). Results: In total, 45 patients were included into the study. The mean diameter of the final graft was 8.9 ± 0.6 cm in the 5-strand group and 7.5 ± 0.8 cm in the 4-strand group (P < .001). Four-strand graft diameter measurements were taken intraoperatively in the 5-strand group before preparation of the 5-strand graft. The mean graft diameter of the 4-strand grafts was similar in both groups: 7.3 ± 0.3 mm in group A and 7.5 ± 0.8 mm in group B (P = .72). There was no statistically significant difference between the 2 groups of patients in terms of the Lysholm score, Knee Injury and Osteoarthritis Outcome Score (KOOS) Symptoms, KOOS Pain, KOOS Activities of Daily Living, KOOS Sports and KOOS Quality of Life scores. There were no postoperative complications of wound infection in both groups of patients. There was one case of graft rupture (4.8%) in the 4-strand group, which required revision reconstruction with patellar tendon graft 9 months postoperatively. There was no case of graft rupture in the 5-strand group (P = .29). Conclusions: The 5-strand hamstring graft technique provides a graft with significantly larger graft diameter than the quadrupled graft technique, with satisfactory short- to medium-term outcomes. The 5-strand graft is therefore a useful technique to increase the graft size when faced with the problem of small hamstring graft. Level of Evidence: Level II, prospective cohort study.

Endocardial ablation at the mitral valve vestibule and its surroundings for the treatment of arrhythmias linked to the greater cardiac vasculature.

BACKGROUND: The role of the epicardial vasculature in supraventricular and ventricular arrhythmias was described in clinical studies as well as its treatment by intravascular point ablation or alcohol injection. We report on a case series of patients with different arrhythmias linked to an epicardial site of origin with evidence supporting transmural extensions that were targeted for ablation with successful outcomes. METHODS: The records of patients who has catheter ablation for Supraventricular or Ventricular arrhythmias between 2015 and 2020 was searched for patients with (1) arrhythmias linked to the epicardial vasculature and (2) findings to support an endocardial connection to the epicardial vasculature by activation mapping, pace mapping, or differential pacing, and (3) were successfully ablated via an endocardial approach only. RESULTS: From the data searched, we identified five patients with the following arrhythmias left ventricular summit ectopy, peri-mitral atrial flutter, preexcitation with inducible atrioventricular reentry tachycardia (AVRT), and a concealed left side accessory pathway with inducible AVRT that were linked to the following vessels: Great Cardiac vein, persistent left superior vena cava, left coronary cusp, and left ventricular outflow tract. Endocardial connections were supported by a combination of electro anatomical activation mapping, pace-mapping, and differential pacing. Endocardial ablations performed in all patients were successful without complications. CONCLUSION: This report highlights a subset of patients with arrhythmias linked to the greater cardiac vascular system that can be safely and effectively ablated endocardially, given the limitations and possible complications of epicardial ablation within or in the proximity of the epicardial vasculature.

A genome-scale CRISPR screen reveals PRMT1 as a critical regulator of androgen receptor signaling in prostate cancer.

Androgen receptor (AR) signaling is the central driver of prostate cancer across disease states. While androgen deprivation therapy (ADT) is effective in the initial treatment of prostate cancer, resistance to ADT or to next-generation androgen pathway inhibitors invariably arises, most commonly through the re-activation of the AR axis. Thus, orthogonal approaches to inhibit AR signaling in advanced prostate cancer are essential. Here, via genome-scale CRISPR-Cas9 screening, we identify protein arginine methyltransferase 1 (PRMT1) as a critical mediator of AR expression and signaling. PRMT1 regulates the recruitment of AR to genomic target sites and the inhibition of PRMT1 impairs AR binding at lineage-specific enhancers, leading to decreased expression of key oncogenes, including AR itself. In addition, AR-driven prostate cancer cells are uniquely susceptible to combined AR and PRMT1 inhibition. Our findings implicate PRMT1 as a key regulator of AR output and provide a preclinical framework for co-targeting of AR and PRMT1 in advanced prostate cancer.

Integrative clinical and molecular characterization of translocation renal cell carcinoma.

Translocation renal cell carcinoma (tRCC) is a poorly characterized subtype of kidney cancer driven by MiT/TFE gene fusions. Here, we define the landmarks of tRCC through an integrative analysis of 152 patients with tRCC identified across genomic, clinical trial, and retrospective cohorts. Most tRCCs harbor few somatic alterations apart from MiT/TFE fusions and homozygous deletions at chromosome 9p21.3 (19.2% of cases). Transcriptionally, tRCCs display a heightened NRF2-driven antioxidant response that is associated with resistance to targeted therapies. Consistently, we find that outcomes for patients with tRCC treated with vascular endothelial growth factor receptor inhibitors (VEGFR-TKIs) are worse than those treated with immune checkpoint inhibitors (ICI). Using multiparametric immunofluorescence, we find that the tumors are infiltrated with CD8+ T cells, though the T cells harbor an exhaustion immunophenotype distinct from that of clear cell RCC. Our findings comprehensively define the clinical and molecular features of tRCC and may inspire new therapeutic hypotheses.

Supporting Equity and Inclusion of Deaf and Hard-of-Hearing Individuals in Professional Organizations.

Disability is an important and often overlooked component of diversity. Individuals with disabilities bring a rare perspective to science, technology, engineering, mathematics, and medicine (STEMM) because of their unique experiences approaching complex issues related to health and disability, navigating the healthcare system, creatively solving problems unfamiliar to many individuals without disabilities, managing time and resources that are limited by physical or mental constraints, and advocating for themselves and others in the disabled community. Yet, individuals with disabilities are underrepresented in STEMM. Professional organizations can address this underrepresentation by recruiting individuals with disabilities for leadership opportunities, easing financial burdens, providing equal access, fostering peer-mentor groups, and establishing a culture of equity and inclusion spanning all facets of diversity. We are a group of deaf and hard-of-hearing (D/HH) engineers, scientists, and clinicians, most of whom are active in clinical practice and/or auditory research. We have worked within our professional societies to improve access and inclusion for D/HH individuals and others with disabilities. We describe how different models of disability inform our understanding of disability as a form of diversity. We address heterogeneity within disabled communities, including intersectionality between disability and other forms of diversity. We highlight how the Association for Research in Otolaryngology has supported our efforts to reduce ableism and promote access and inclusion for D/HH individuals. We also discuss future directions and challenges. The tools and approaches discussed here can be applied by other professional organizations to include individuals with all forms of diversity in STEMM.

The use of antimicrobial photodynamic therapy in the successful management of a nonsurgical complex type II Dens Invaginatus.

Because of its complex root canal morphology, dens invaginatus (DI) is a developmental anomaly that represents an endodontic challenge to complete cleaning, shaping, and disinfecting the root canal system. The present case report describes the use of antimicrobial photodynamic therapy as an adjunctive treatment in the successful management of nonsurgical complex type II DI in a left maxillary lateral incisor with thin and fragile dentin walls associated with periradicular lesion.

Integrative molecular characterization of sarcomatoid and rhabdoid renal cell carcinoma.

Sarcomatoid and rhabdoid (S/R) renal cell carcinoma (RCC) are highly aggressive tumors with limited molecular and clinical characterization. Emerging evidence suggests immune checkpoint inhibitors (ICI) are particularly effective for these tumors, although the biological basis for this property is largely unknown. Here, we evaluate multiple clinical trial and real-world cohorts of S/R RCC to characterize their molecular features, clinical outcomes, and immunologic characteristics. We find that S/R RCC tumors harbor distinctive molecular features that may account for their aggressive behavior, including BAP1 mutations, CDKN2A deletions, and increased expression of MYC transcriptional programs. We show that these tumors are highly responsive to ICI and that they exhibit an immune-inflamed phenotype characterized by immune activation, increased cytotoxic immune infiltration, upregulation of antigen presentation machinery genes, and PD-L1 expression. Our findings build on prior work and shed light on the molecular drivers of aggressivity and responsiveness to ICI of S/R RCC.