Neurogenesis and gliogenesis continue in discrete regions of the adult mammalian brain. A fundamental question remains whether cell genesis occurs from distinct lineage-restricted progenitors or from ...self-renewing and multipotent neural stem cells in the adult brain. Here, we developed a genetic marking strategy for lineage tracing of individual, quiescent, and nestin-expressing radial glia-like (RGL) precursors in the adult mouse dentate gyrus. Clonal analysis identified multiple modes of RGL activation, including asymmetric and symmetric self-renewal. Long-term lineage tracing in vivo revealed a significant percentage of clones that contained RGL(s), neurons, and astrocytes, indicating capacity of individual RGLs for both self-renewal and multilineage differentiation. Furthermore, conditional
Pten deletion in RGLs initially promotes their activation and symmetric self-renewal but ultimately leads to terminal astrocytic differentiation and RGL depletion in the adult hippocampus. Our study identifies RGLs as self-renewing and multipotent neural stem cells and provides novel insights into in vivo properties of adult neural stem cells.
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► Individual adult radial glia-like cells self-renew and generate neurons and astrocytes ► Adult neural stem cells exhibit multiple modes of self-renewal in vivo ► Radial glia-like cells display heterogeneous behavior in the adult brain ► PTEN regulates quiescence, differentiation, and maintenance of adult neural stem cells
Human memory is thought to depend on a circuit of connected brain regions, but this hypothesis has not been directly tested. We derive a human memory circuit using 53 case reports of strokes causing ...amnesia and a map of the human connectome (n = 1000). This circuit is reproducible across discovery (n = 27) and replication (n = 26) cohorts and specific to lesions causing amnesia. Its hub is at the junction of the presubiculum and retrosplenial cortex. Connectivity with this single location defines a human brain circuit that incorporates > 95% of lesions causing amnesia. Lesion intersection with this circuit predicts memory scores in two independent datasets (N1 = 97, N2 = 176). This network aligns with neuroimaging correlates of episodic memory, abnormalities in Alzheimer's disease, and brain stimulation sites reported to enhance memory in humans.
Fragile X-associated tremor ataxia syndrome (FXTAS) results from a CGG repeat expansion in the 5′ UTR of FMR1. This repeat is thought to elicit toxicity as RNA, yet disease brains contain ...ubiquitin-positive neuronal inclusions, a pathologic hallmark of protein-mediated neurodegeneration. We explain this paradox by demonstrating that CGG repeats trigger repeat-associated non-AUG-initiated (RAN) translation of a cryptic polyglycine-containing protein, FMRpolyG. FMRpolyG accumulates in ubiquitin-positive inclusions in Drosophila, cell culture, mouse disease models, and FXTAS patient brains. CGG RAN translation occurs in at least two of three possible reading frames at repeat sizes ranging from normal (25) to pathogenic (90), but inclusion formation only occurs with expanded repeats. In Drosophila, CGG repeat toxicity is suppressed by eliminating RAN translation and enhanced by increased polyglycine protein production. These studies expand the growing list of nucleotide repeat disorders in which RAN translation occurs and provide evidence that RAN translation contributes to neurodegeneration.
•CGG repeats in the 5′ UTR of FMR1 elicit AUG-independent (RAN) translation•This produces an aggregation-prone polyglycine protein found in patients•CGG RAN translation explains pathologic differences in FXTAS mice•CGG RAN translation is critical for CGG repeat toxicity in fly disease models
CGG repeat expansions underlie the neurodegenerative disorder fragile X-associated tremor ataxia syndrome. Todd et al. describe how CGG repeats trigger non-AUG-initiated translation, producing a polyglycine protein that accumulates in FXTAS brains and contributes to toxicity in model systems.
The torpedo model of transcription termination asserts that the exonuclease Xrn2 attacks the 5′PO4-end exposed by nascent RNA cleavage and chases down the RNA polymerase. We tested this mechanism ...using a dominant-negative human Xrn2 mutant and found that it delayed termination genome-wide. Xrn2 nuclease inactivation caused strong termination defects downstream of most poly(A) sites and modest delays at some histone and U snRNA genes, suggesting that the torpedo mechanism is not limited to poly(A) site-dependent termination. A central untested feature of the torpedo model is that there is kinetic competition between the exonuclease and the pol II elongation complex. Using pol II rate mutants, we found that slow transcription robustly shifts termination upstream, and fast elongation extends the zone of termination further downstream. These results suggest that kinetic competition between elongating pol II and the Xrn2 exonuclease is integral to termination of transcription on most human genes.
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•Xrn2 exonuclease inactivation inhibits pol II transcription termination genome wide•Slow and fast transcription elongation shift termination upstream and downstream•Kinetic competition of Xrn2 and pol II appears to dictate where termination occurs•The torpedo model is validated as a general termination mechanism for RNA pol II
How are sites of transcription termination determined? Fong et al. show that where RNA polymerase II terminates downstream of polyadenylation sites is decided by a kinetic competition between the elongating polymerase and the RNA exonuclease Xrn2 that pursues it.
Relatlimab and nivolumab combination immunotherapy improves progression-free survival over nivolumab monotherapy in patients with unresectable advanced melanoma
. We investigated this regimen in ...patients with resectable clinical stage III or oligometastatic stage IV melanoma (NCT02519322). Patients received two neoadjuvant doses (nivolumab 480 mg and relatlimab 160 mg intravenously every 4 weeks) followed by surgery, and then ten doses of adjuvant combination therapy. The primary end point was pathologic complete response (pCR) rate
. The combination resulted in 57% pCR rate and 70% overall pathologic response rate among 30 patients treated. The radiographic response rate using Response Evaluation Criteria in Solid Tumors 1.1 was 57%. No grade 3-4 immune-related adverse events were observed in the neoadjuvant setting. The 1- and 2-year recurrence-free survival rate was 100% and 92% for patients with any pathologic response, compared to 88% and 55% for patients who did not have a pathologic response (P = 0.005). Increased immune cell infiltration at baseline, and decrease in M2 macrophages during treatment, were associated with pathologic response. Our results indicate that neoadjuvant relatlimab and nivolumab induces a high pCR rate. Safety during neoadjuvant therapy is favourable compared to other combination immunotherapy regimens. These data, in combination with the results of the RELATIVITY-047 trial
, provide further confirmation of the efficacy and safety of this new immunotherapy regimen.
Repeat expansions are responsible for over 40 monogenic disorders, and undoubtedly more pathogenic repeat expansions remain to be discovered. Existing methods for detecting repeat expansions in ...short-read sequencing data require predefined repeat catalogs. Recent discoveries emphasize the need for methods that do not require pre-specified candidate repeats. To address this need, we introduce ExpansionHunter Denovo, an efficient catalog-free method for genome-wide repeat expansion detection. Analysis of real and simulated data shows that our method can identify large expansions of 41 out of 44 pathogenic repeats, including nine recently reported non-reference repeat expansions not discoverable via existing methods.
AMP-activated protein kinase (AMPK) is a master sensor and regulator of cellular energy status. Upon metabolic stress, AMPK suppresses anabolic and promotes catabolic processes to regain energy ...homeostasis. Cancer cells can occasionally suppress the growth-restrictive AMPK pathway by mutation of an upstream regulatory kinase. Here, we describe a widespread mechanism to suppress AMPK through its ubiquitination and degradation by the cancer-specific MAGE-A3/6-TRIM28 ubiquitin ligase. MAGE-A3 and MAGE-A6 are highly similar proteins normally expressed only in the male germline but frequently re-activated in human cancers. MAGE-A3/6 are necessary for cancer cell viability and are sufficient to drive tumorigenic properties of non-cancerous cells. Screening for targets of MAGE-A3/6-TRIM28 revealed that it ubiquitinates and degrades AMPKα1. This leads to inhibition of autophagy, activation of mTOR signaling, and hypersensitization to AMPK agonists, such as metformin. These findings elucidate a germline mechanism commonly hijacked in cancer to suppress AMPK.
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•MAGE-A3/6 are normally testis restricted and aberrantly expressed in many cancers•MAGE-A3/6 are driver oncogenes competent to transform cells•MAGE-A3/6-TRIM28 ubiquitinates and degrades the AMPK tumor suppressor•MAGE-A3/6-TRIM28 suppresses autophagy and potentiates mTOR signaling
A cancer-specific E3 ubiquitin ligase ubiquitinates and degrades AMPK, resulting in downregulation of autophagy and increased mTOR signaling. This regulatory axis demonstrates how altered cellular metabolism can act as an oncogenic driver in cancer.
Motion‐activated cameras (“camera traps”) are increasingly used in ecological and management studies for remotely observing wildlife and are amongst the most powerful tools for wildlife research. ...However, studies involving camera traps result in millions of images that need to be analysed, typically by visually observing each image, in order to extract data that can be used in ecological analyses.
We trained machine learning models using convolutional neural networks with the ResNet‐18 architecture and 3,367,383 images to automatically classify wildlife species from camera trap images obtained from five states across the United States. We tested our model on an independent subset of images not seen during training from the United States and on an out‐of‐sample (or “out‐of‐distribution” in the machine learning literature) dataset of ungulate images from Canada. We also tested the ability of our model to distinguish empty images from those with animals in another out‐of‐sample dataset from Tanzania, containing a faunal community that was novel to the model.
The trained model classified approximately 2,000 images per minute on a laptop computer with 16 gigabytes of RAM. The trained model achieved 98% accuracy at identifying species in the United States, the highest accuracy of such a model to date. Out‐of‐sample validation from Canada achieved 82% accuracy and correctly identified 94% of images containing an animal in the dataset from Tanzania. We provide an r package (Machine Learning for Wildlife Image Classification) that allows the users to (a) use the trained model presented here and (b) train their own model using classified images of wildlife from their studies.
The use of machine learning to rapidly and accurately classify wildlife in camera trap images can facilitate non‐invasive sampling designs in ecological studies by reducing the burden of manually analysing images. Our r package makes these methods accessible to ecologists.
The main protease, M
(or 3CL
) in SARS-CoV-2 is a viable drug target because of its essential role in the cleavage of the virus polypeptide. Feline infectious peritonitis, a fatal coronavirus ...infection in cats, was successfully treated previously with a prodrug GC376, a dipeptide-based protease inhibitor. Here, we show the prodrug and its parent GC373, are effective inhibitors of the M
from both SARS-CoV and SARS-CoV-2 with IC
values in the nanomolar range. Crystal structures of SARS-CoV-2 M
with these inhibitors have a covalent modification of the nucleophilic Cys145. NMR analysis reveals that inhibition proceeds via reversible formation of a hemithioacetal. GC373 and GC376 are potent inhibitors of SARS-CoV-2 replication in cell culture. They are strong drug candidates for the treatment of human coronavirus infections because they have already been successful in animals. The work here lays the framework for their use in human trials for the treatment of COVID-19.
In February 2018, the United States enacted significant financial incentives for carbon capture, utilization, and storage (CCUS) that will make capture from the lowest-capture-cost sources ...economically viable. The largest existing low-capture-cost opportunity is from ethanol fermentation at biorefineries in the Midwest. An impediment to deployment of carbon capture at ethanol biorefineries is that most are not close to enhanced oil recovery (EOR) fields or other suitable geological formations in which the carbon dioxide could be stored. Therefore, we analyze the viability of a pipeline network to transport carbon dioxide from Midwest ethanol biorefineries to the Permian Basin in Texas, which has the greatest current carbon dioxide demand for EOR and large potential for expansion. We estimate capture and transport costs and perform economic analysis for networks under three pipeline financing scenarios representing different combinations of commercial and government finance. Without government finance, we find that a network earning commercial rates of return would not be viable. With 50% government financing for pipelines, 19 million tons of carbon dioxide per year could be captured and transported profitably. Thirty million tons per year could be captured with full government pipeline financing, which would double global anthropogenic carbon capture and increase the United States’ carbon dioxide EOR industry by 50%. Such a development would face challenges, including coordination between governments and industries, pressing timelines, and policy uncertainties, but is not unprecedented. This represents an opportunity to considerably increase CCUS in the near-term and develop long-term transport infrastructure facilitating future growth.
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