Pan-tumor validation of a NGS fraction-based MSI analysis as a predictor of response to Pembrolizumab.

Microsatellite instability high (MSI-H) and mismatch repair deficient (dMMR) tumor status have been demonstrated to predict patient response to immunotherapies. We developed and validated a next-generation sequencing (NGS)-based companion diagnostic (CDx) to detect MSI-H solid tumors via a comprehensive genomic profiling (CGP) assay, FoundationOne®CDx (F1CDx). To determine MSI status, F1CDx calculates the fraction of unstable microsatellite loci across >2000 loci using a fraction-based (FB) analysis.

The making and breaking of tRNAs by ribonucleases.

Ribonucleases (RNases) play important roles in supporting canonical and non-canonical roles of tRNAs by catalyzing the cleavage of the tRNA phosphodiester backbone. Here, we highlight how recent advances in cryo-electron microscopy (cryo-EM), protein structure prediction, reconstitution experiments, tRNA sequencing, and other studies have revealed new insight into the nucleases that process tRNA. This represents a very diverse group of nucleases that utilize distinct mechanisms to recognize and cleave tRNA during different stages of a tRNA's life cycle including biogenesis, fragmentation, surveillance, and decay.

New insights into RNA processing by the eukaryotic tRNA splicing endonuclease.

Through its role in intron cleavage, tRNA splicing endonuclease (TSEN) plays a critical function in the maturation of intron-containing pre-tRNAs. The catalytic mechanism and core requirement for this process is conserved between archaea and eukaryotes, but for decades, it has been known that eukaryotic TSENs have evolved additional modes of RNA recognition, which have remained poorly understood. Recent research identified new roles for eukaryotic TSEN, including processing or degradation of additional RNA substrates, and determined the first structures of pre-tRNA-bound human TSEN complexes.

Prioritizing Patient Safety and Minimizing Waste: Institutional Review of Cases and a Proposed Process for Designing a Surgical Pathology Gross-Only Examination Policy.

Objectives: Gross-only examination policies vary widely across pathology departments. Several studies-particularly a College of American Pathologists' Q-Probes study-have looked at the variations in gross-only policies, and even more studies have addressed the (in)appropriateness of certain specimen types for gross-only examination. Few, if any, studies have tackled the important task of how to revise and safely implement a new gross-only examination protocol, especially in collaboration with clinical colleagues.

Recent insights into the structure, function, and regulation of the eukaryotic transfer RNA splicing endonuclease complex.

The splicing of transfer RNA (tRNA) introns is a critical step of tRNA maturation, for intron-containing tRNAs. In eukaryotes, tRNA splicing is a multi-step process that relies on several RNA processing enzymes to facilitate intron removal and exon ligation. Splicing is initiated by the tRNA splicing endonuclease (TSEN) complex which catalyzes the excision of the intron through its two nuclease subunits.

Cryo-EM structures of the SARS-CoV-2 endoribonuclease Nsp15 reveal insight into nuclease specificity and dynamics.

Nsp15, a uridine specific endoribonuclease conserved across coronaviruses, processes viral RNA to evade detection by host defense systems. Crystal structures of Nsp15 from different coronaviruses have shown a common hexameric assembly, yet how the enzyme recognizes and processes RNA remains poorly understood. Here we report a series of cryo-EM reconstructions of SARS-CoV-2 Nsp15, in both apo and UTP-bound states.

Cryo-EM Structures of the SARS-CoV-2 Endoribonuclease Nsp15.

New therapeutics are urgently needed to inhibit SARS-CoV-2, the virus responsible for the on-going Covid-19 pandemic. Nsp15, a uridine-specific endoribonuclease found in all coronaviruses, processes viral RNA to evade detection by RNA-activated host defense systems, making it a promising drug target. Previous work with SARS-CoV-1 established that Nsp15 is active as a hexamer, yet how Nsp15 recognizes and processes viral RNA remains unknown.

Reconstitution of the human tRNA splicing endonuclease complex: insight into the regulation of pre-tRNA cleavage.

The splicing of tRNA introns is a critical step in pre-tRNA maturation. In archaea and eukaryotes, tRNA intron removal is catalyzed by the tRNA splicing endonuclease (TSEN) complex. Eukaryotic TSEN is comprised of four core subunits (TSEN54, TSEN2, TSEN34 and TSEN15).

Germline mutations of SMARCA4 in small cell carcinoma of the ovary, hypercalcemic type and in SMARCA4-deficient undifferentiated uterine sarcoma: Clinical features of a single family and comparison of large cohorts.

Objective: Small cell carcinoma of the ovary, hypercalcemic type (SCCOHT) and SMARCA4-deficient undifferentiated uterine sarcoma (SMARCA4-DUS) are rare and aggressive tumors, primarily affecting pre- and perimenopausal women. Inactivating SMARCA4 mutations are thought to be the driving molecular events in the majority of these tumors. Here, we report the clinical course of a family with germline SMARCA4 mutation and compare large cohorts of these rare tumor types.

We FRET so You Don't Have To: New Models of the Lipoprotein Lipase Dimer.

Lipoprotein lipase (LPL) is a dimeric enzyme that is responsible for clearing triglyceride-rich lipoproteins from the blood. Although LPL plays a key role in cardiovascular health, an experimentally derived three-dimensional structure has not been determined. Such a structure would aid in understanding mutations in LPL that cause familial LPL deficiency in patients and help in the development of therapeutic strategies to target LPL.

Biochemical Analysis of the Lipoprotein Lipase Truncation Variant, LPL, Reveals Increased Lipoprotein Uptake.

Lipoprotein lipase (LPL) is responsible for the hydrolysis of triglycerides from circulating lipoproteins. Whereas most identified mutations in the LPL gene are deleterious, one mutation, LPL, causes a gain of function. This mutation truncates two amino acids from LPL's C-terminus.

Modulation of the Activity of Mycobacterium tuberculosis LipY by Its PE Domain.

Mycobacterium tuberculosis harbors over 160 genes encoding PE/PPE proteins, several of which have roles in the pathogen's virulence. A number of PE/PPE proteins are secreted via Type VII secretion systems known as the ESX secretion systems. One PE protein, LipY, has a triglyceride lipase domain in addition to its PE domain.

Acute lymphoblastic leukemia with 4;11 translocation analyzed by a multi-modal strategy of conventional cytogenetics, FISH, morphology, flow cytometry and molecular genetics, and review of the literature.

We report a case of acute lymphoblastic leukemia (ALL) with a 4;11 translocation. Metaphase cells and interphase nuclei derived from a routine unstimulated culture of bone marrow were analyzed using a combined strategy of G-banding and fluorescent in situ hybridization (FISH) in addition to hematopathological analysis, flow cytometry, and molecular genetics. This multimodal approach enables a successful correlation of pathology and cytogenetics to support a comprehensive diagnosis of the patient.

Regulating environments to reduce obesity.

The marked increase in the prevalence of obesity appears to be attributable to environmental conditions that implicitly discourage physical activity while explicitly encouraging the consumption of greater quantities of energy-dense, low-nutrient foods. In the United States food environment, consumers are bombarded with advertising for unhealthy food, and receive inadequate nutritional information, especially at restaurants. In the US school environment children have access to sugary sodas and unhealthy a la carte foods in their cafeterias, at the same time getting inadequate physical activity and nutrition education.

MEK inhibition and phosphorylation of serine 4 on B23 are two coincident events in mitosis.

Previous studies have shown that activation of the Raf/MEK/ERK pathway is necessary for G2/M transition. However, as for the activation state of MEK in mitosis the conclusion is not consistent. Here we show that MEK is inhibited in mitosis.

Interaction between active Pak1 and Raf-1 is necessary for phosphorylation and activation of Raf-1.

Activation of Raf-1 is a complex process in which phosphorylation of Ser(338)-Tyr(341) is a critical step. Previous studies have shown that Pak1/2 is implicated in both Ras-dependent and -independent activation of Raf-1 by phosphorylating Raf Ser(338). The present study explores the structural basis of Raf-1 phosphorylation by Pak1.

Raf-1/MEK/MAPK pathway is necessary for the G2/M transition induced by nocodazole.

The dynamic balance between polymerization and depolymerization of microtubules is critical for cells to enter and exit mitosis, and drugs that disrupt this balance, such as taxol, colchicine, and nocodazole, arrest the cell cycle in mitosis. Although the Raf/MEK/MAPK pathway can be activated by these drugs, its role in mitosis has not been addressed. Here, we characterize activation of Raf/MEK/MAPK by nocodazole when mitosis is induced.

Substantial superiority of semiflexed (MTP) views in knee osteoarthritis: a comparative radiographic study, without fluoroscopy, of standing extended, semiflexed (MTP), and schuss views.

Objective: To improve the radiographic assessment of cartilage loss, as measured by joint space width (JSW) in patients with osteoarthritis (OA) of the knees required to detect the effect of structure modifying drugs in OA trials. This was achieved by determining which of 3 nonfluoroscopic radiographic views--standing extended, semiflexed, and schuss--produced the most accurate radioanatomic positioning of the joint and greater reproducibility in joint repositioning and JSW measurement.

Methods: Knees from 74 patients with OA of the knees who had medial tibiofemoral compartment JSW > or =2 mm in all views were studied.

Dysphoria in male alcoholics with a history of hallucinations.

This paper examines severity of depressive symptoms, as measured by the Beck Depression Inventory, in chronic alcoholics with and without a history of hallucinations. We found a) alcoholics entering alcohol treatment who have experienced hallucinations during detoxification report higher levels of subjective depression than alcoholics who have never experienced hallucinations, b) the level of subjective depression in alcoholics with a history of hallucinations remains higher at the end of inpatient alcohol treatment than in alcoholics without hallucinations, and c) hallucination is the important variable; alcoholics with blackouts, seizures, and delirium tremens, do not experience higher levels of depression during detoxification. The reporting of a significantly higher level of depressive symptoms by alcoholics with a history of experiencing hallucinations during withdrawal suggests that in some alcoholics, there exists a vulnerability for mood abnormalities which includes a predisposition toward other abnormal mental phenomena such as perceptual distortions.