bluuebunny/crossref_metadata_2025 huggingface dataset:
Indoline CD4-mimetic Compounds Mediate Potent and Broad HIV-1 Inhibition and Sensitization to Antibody-dependent Cellular Cytotoxicity
Authors: Fritschi Christopher , Anang Saumya , Gong Zhen , Mohammadi Mohammadjavad , Richard Jonathan , Bourassa Catherine , Severino Kenny T. , Richter Hannah , Yang Derek , Chen Hung-Ching , Chiu Ta-Jung , Seaman Michael , Madani Navid , Abrams Cameron , Finzi Andrés , Hendrickson Wayne A. , Sodroski Joseph , Smith Amos B.
Published: January 2023

Binding to the host cell receptors, CD4 and CCR5/CXCR4, triggers large-scale conformational changes in the human immunodeficiency virus (HIV-1) envelope glycoprotein (Env) trimer [(gp120/gp41)3] that promote virus entry into the cell. CD4-mimetic compounds (CD4mcs) comprise small organic molecules that bind in the highly conserved CD4-binding site of gp120 and prematurely induce inactivating Env conformational changes, including shedding of gp120 from the Env trimer. By inducing more “open,” antibody-susceptible Env conformations, CD4mcs also sensitize HIV-1 virions to neutralization by antibodies and infected cells to antibody-dependent cellular cytotoxicity (ADCC). Here, we report the design, synthesis and evaluation of novel CD4mcs based on an indoline scaffold. Compared with our current lead indane scaffold CD4mc, BNM-III-170, several indoline CD4mcs exhibit increased potency and breadth against HIV-1 variants from different geographic clades. Viruses that were selected for resistance to the lead indane CD4mc, BNM-III-170, are susceptible to inhibition by the indoline CD4mcs. The indoline CD4mcs also potently sensitize HIV-1-infected cells to ADCC mediated by plasma from HIV-1-infected individuals. Crystal structures indicate that the indoline CD4mcs gain potency compared to the indane CD4mcs through more favorable π-π overlap from the indoline pose and by making favorable contacts with the vestibule of the CD4-binding pocket on gp120. The rational design of indoline CD4mcs thus holds promise for further improvements in antiviral activity, potentially contributing to efforts to treat and prevent HIV-1 infection.
Inhibition of Type I PRMTs Reforms Muscle Stem Cell Identity Enhancing their Therapeutic Capacity
Authors: Dominici Claudia , Villarreal Oscar D. , Dort Junio , Heckel Emilie , Wang Yu Chang , Ragoussis Ioannis , Joyal Jean-Sebastien , Dumont Nicolas A. , Richard Stéphane
Published: January 2023

In skeletal muscle, muscle stem cells (MuSC) are the main cells responsible for regeneration upon injury. In diseased skeletal muscle, it would be therapeutically advantageous to replace defective MuSCs, or rejuvenate them with drugs to enhance their self-renewal and ensure long-term regenerative potential. One limitation of the replacement approach has been the inability to efficiently expand MuSCsex vivo,while maintaining their stemness and engraftment abilities. Herein, we show that inhibition of type I protein arginine methyltransferases (PRMTs) with MS023 increases the proliferative capacity ofex vivocultured MuSCs. Single cell RNA sequencing (scRNAseq) ofex vivocultured MuSCs revealed the emergence of subpopulations in MS023-treated cells which are defined by elevated Pax7 expression and markers of MuSC quiescence, both features of enhanced self-renewal. Furthermore, the scRNAseq identified MS023-specific subpopulations to be metabolically altered with upregulated glycolysis and oxidative phosphorylation (OxPhos). Transplantation of MuSCs treated with MS023 had a better ability to repopulate the MuSC niche and contributed efficiently to muscle regeneration following injury. Interestingly, the preclinical mouse model of Duchenne muscular dystrophy had increased grip strength with MS023 treatment. Our findings show that inhibition of type I PRMTs increased the proliferation capabilities of MuSCs with altered cellular metabolism, while maintaining their stem-like properties such as self-renewal and engraftment potential.
Tet-dependent 5-hydroxymethyl-Cytosine modification of mRNA regulates axon guidance genes inDrosophila
Authors: Singh Badri Nath , Tran Hiep , Kramer Joseph , Kirichenko Elmira , Changela Neha , Wang Fei , Feng Yaping , Kumar Dibyendu , Tu Min , Lan Jie , Bizet Martin , Fuks François , Steward Ruth
Published: January 2023

Modifications of mRNA, especially methylation of adenosine, have recently drawn much attention. The much rarer modification, 5-hydroxymethylation of cytosine (5hmC), is not well understood and is the subject of this study. Vertebrate Tet proteins are 5-methylcytosine (5mC) hydroxylases and catalyze the transition of 5mC to 5hmC in DNA. These enzymes have recently been shown to have the same function in messenger RNAs in both vertebrates and in Drosophila. TheTetgene is essential in Drosophila as Tet knock-out animals do not reach adulthood. We describe the identification of Tet-target genes in the embryo and larval brain by mapping one, Tet DNA-binding sites throughout the genome and two, the Tet-dependent 5hmrC modifications transcriptome-wide. 5hmrC modifications are distributed along the entire transcript, while Tet DNA-binding sites are preferentially located at the promoter where they overlap with histone H3K4me3 peaks. The identified mRNAs are preferentially involved in neuron and axon development and Tet knock-out led to a reduction of 5hmrC marks on specific mRNAs. Among the Tet-target genes were therobo2receptor and itsslitligand that function in axon guidance in Drosophila and in vertebrates.Tetknock-out embryos show overlapping phenotypes withrobo2and both Robo2 and Slit protein levels were markedly reduced in Tet KO larval brains. Our results establish a role for Tet-dependent 5hmrC in facilitating the translation of modified mRNAs primarily in cells of the nervous system.
Microbe-induced plant drought tolerance by ABA-mediated root morphogenesis and epigenetic reprogramming of gene expression
Authors: Alwutayd Khairiah M. , Rawat Anamika A. , Sheikh Arsheed H. , Almeida-Trapp Marilia , Veluchamy Alaguraj , Jalal Rewaa , Karampelias Michael , Froehlich Katja , Alzaed Waad , Tabassum Naheed , Schley Thayssa Rabelo , Schaeffner Anton R. , Daur Ihsanullah , Saad Maged M. , Hirt Heribert
Published: January 2023

The use of beneficial microbes to mitigate drought stress tolerance of plants is of great potential albeit little understood. We show here that a root endophytic desert bacterium,Pseudomonas argentinensissp. SA190, enhances drought stress tolerance in Arabidopsis. Transcriptome and genetic analysis demonstrate that SA190-induced root morphogenesis and gene expression is mediated via the plant abscisic acid (ABA) pathway. Moreover, we demonstrate that SA190 primes the promoters of target genes in an epigenetic manner which is ABA-dependent. Application of the SA190 priming technology on crops is demonstrated for alfalfa in field trials, showing enhanced performance under desert agriculture conditions. In summary, a single beneficial root bacterial strain can help to perform agriculture under drought and water limiting conditions.

Synopsis

Beneficial root endophytePseudomonas argentinensissp. SA190 confers drought tolerance in plants

SA190 modulates the expression of genes under drought stress in an ABA-dependent manner

SA190 primes genes via H3K4me3 histone mark enrichment

SA190 alters host plant physiology by improving the plant water status

SA190 enhances crop performance in open field conditions with limited irrigation
The impact of early life experiences and gut microbiota on neurobehavioral development among preterm infants: A longitudinal cohort study
Authors: Chen Jie , Li Hongfei , Zhao Tingting , Chen Kun , Chen Ming-Hui , Sun Zhe , Xu Wanli , Maas Kendra , Lester Barry , Cong Xiaomei
Published: January 2023

Objectives

To investigate the impact of early life experiences and gut microbiota on neurobehavioral development among preterm infants during neonatal intensive care unit (NICU) hospitalization.

Methods

Preterm infants were followed from the NICU admission until their 28thpostnatal day or until discharge. Daily stool samples, painful/stressful experiences, feeding patterns, and other clinical and demographic data were collected. Gut microbiota was profiled using 16S rRNA sequencing, and operational taxonomic units (OTUs) were selected to predict the neurobehaviors. The neurobehavioral development was assessed by the Neonatal Neurobehavioral Scale (NNNS) at 36 to 38 weeks of post-menstrual age (PMA). Fifty-five infants who had NNNS measurements were included in the sparse log-contrast regression analysis.

Results

Preterm infants who experienced high level of pain/stress during the NICU hospitalization that were associated with higher NNNS stress/abstinence scores. Eight operational taxonomic units (OTUs) were identified to be associated with of NNNS subscales after controlling demographic and clinical features, feeding patterns, and painful/stressful experiences. These OTUs, taxa belong to seven genera includingEnterobacteriaceae_unclassified, Escherichia-Shigella, Incertae_Sedis, Veillonella, Enterococcus, Clostridium_sensu_stricto_1, andStreptococcuswith five belonging toFirmicutesand two belonging toProteobacteriaphylum. The enriched abundance ofEnterobacteriaceae_unclassified(OTU17) andStreptococcus(OTU28) were consistently associated with less optimal neurobehavioral outcomes. The other six OTUs were also associated with infant neurobehavioral responses depending on days at NICU stay.

Conclusions

This study explored the dynamic impact of specific OTUs on neurobehavioral development among preterm infants after controlling for early life experiences, i.e., acute and chronic pain/stress, and feeding in the NICU.
Young, but not in the Dark - the Influence of Reduced Lighting on Gait Stability in Middle-aged adults
Authors: Naaman Tirtsa , Hayek Roee , Gutman Itai , Springer Shmuel
Published: January 2023

Background

The aim of this study was to investigate the effects of walking in reduced lighting with or without performing a secondary cognitive task on gait dynamics in middle-aged adults and to compare them with young and old adults.

Methods

Twenty young (age 28.8±4.1), 20 middle-aged (age 50.2±4.4), and 19 elderly (age 70.7±4.2) subjects participated in the study. Subjects walked on an instrumented treadmill at a self-determined pace under four conditions in randomized order: (1) walking in usual lighting (1000 lumens); (2) walking in near-darkness (5 lumens); (3) walking in usual lighting with a serial-7 subtraction dual-task; and (4) walking in near-darkness with a serial-7 subtraction dual-task. Variability in stride time and variability in the trajectory of the center of pressure in the sagittal and frontal planes (anterior/posterior and lateral variability) were measured. Repeated measures ANOVA and post hoc analysis were used to determine the effects of age, lighting conditions, and cognitive task on each gait outcome.

Results

Under usual lighting, stride time variability and anterior/posterior variability of the middle-aged subjects were similar to those of the young and lower than those of the old. The lateral variability of the middle-aged subjects was higher than that of young adults under both lighting conditions. Similar to the older adults, the middle-aged participants increased their stride time variability and anterior/posterior variability when walking in near-darkness, but they were the only ones to exhibit increased lateral variability in near-darkness. Young adult gait was not affected by lighting, and concurrent performance of a cognitive task while walking did not affect gait stability in all groups under any of the lighting conditions.

Conclusions

Gait stability decreases in middle age when walking in the dark. Recognition of functional deficits in middle age could promote appropriate interventions to optimize aging and reduce fall risk.
Flotillin-Associated rhodopsin (FArhodopsin), a widespread paralog of proteorhodopsin in aquatic bacteria with streamlined genomes
Authors: Haro-Moreno Jose M. , López-Pérez Mario , Alekseev Alexey , Podoliak Elizaveta , Kovalev Kirill , Gordeliy Valentin , Stepanauskas Ramunas , Rodriguez-Valera Francisco
Published: January 2023

Microbial rhodopsins are often found more than once in a single genome (paralogs) that often have different functions. We screened a large dataset of open ocean single-amplified genomes (SAGs) for co-occurrences of multiple rhodopsin genes. Many such cases were found among Pelagibacterales (SAR11), HIMB59 and the GammaproteobacteriaPseudothioglobusSAGs. These genomes always had abona fideproteorhodopsin and a separate cluster of genes containing a second rhodopsin associated with a predicted flotillin coding gene and have thus been named flotillin-associated rhodopsins (FArhodopsins). They are quite divergent from the other proteorhodopsin paralog and contain either DTT, DTL or DNI motives in their key functional amino acids. FArhodopsins are mainly associated with the lower layers of the epipelagic zone. All marine FArhodopsins had the retinal binding lysine, but we found their relatives in freshwater metagenomes that lack this key amino acid. Alfa-fold predictions of marine FArhodopsins indicate that their retinal pocket might be very reduced or absent, hinting that they are retinal-less (blind). Freshwater FArhodopsins were more diverse than marine FArhodopsins, but we could not determine if they are present as paralogs of other rhodopsins, due to the lack of SAGs or isolates. Although the function of FArhodopsins could not be established, their conserved genomic context indicated involvement in the formation of membrane microdomains. The conservation of FArhodopsins in diverse and globally abundant microorganisms suggests that they may be important in the adaptation to the twilight zone of aquatic environments.

IMPORTANCE

Rhodopsins have been shown to play a key role in the ecology of aquatic microbes. Here we describe a group of widespread rhodopsins in aquatic microbes associated with dim light conditions. Their characteristic genomic context found in both marine and freshwater environments indicates a novel potential involvement in membrane microstructure that could be important for the function of the co-existing proteorhodopsin proton pumps. The absence or reduction of the retinal binding pocket points to drastically different physiology. In addition to their ecological importance, novel rhodopsins have biotechnological potential in the nascent field of optogenetics.
Significance of Wastewater Surveillance in Detecting the Prevalence of SARS-CoV-2 Variants and Other Respiratory Viruses in the Community – A Multi-Site Evaluation
Authors: Khan Majid , Li Lin , Haak Laura , Payen Shannon Harger , Carine Madeline , Adhikari Kabita , Uppal Timsy , Hartley Paul D. , Vasquez-Gross Hans , Petereit Juli , Verma Subhash C. , Pagilla Krishna
Published: January 2023

Detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral genome in wastewater has proven to be useful for tracking the trends of virus prevalence within the community. The surveillance also provides precise and early detection of any new and circulating variants, which aids in response to viral outbreaks. Site-specific monitoring of SARS-CoV-2 variants provides valuable information on the prevalence of new or emerging variants in the community. We sequenced the genomic RNA of viruses present in the wastewater samples and analyzed for the prevalence of SARS-CoV-2 variants as well as other respiratory viruses for a period of one year to account for seasonal variations. The samples were collected from the Reno-Sparks metropolitan area on a weekly basis between November 2021 to November 2022. Samples were analyzed to detect the levels of SARS-CoV-2 genomic copies and variants identification. This study confirmed that wastewater monitoring of SARS-CoV-2 variants can be used for community surveillance and early detection of circulating variants and supports wastewater-based epidemiology (WBE) as a complement to clinical respiratory virus testing as a healthcare response effort. Our study showed the persistence of the SARS-CoV-2 virus throughout the year compared to a seasonal presence of other respiratory viruses, implicating SARS-CoV-2’s broad genetic diversity and strength to persist and infect susceptible hosts. Through secondary analysis, we further identified antimicrobial resistance (AMR) genes in the same wastewater samples and found WBE to be a feasible tool for community AMR detection and monitoring.

HIGHLIGHTS/KEY FINDINGS

WBE better represents regional virus prevalence under declining testing and clinical reporting rates.

SARS-CoV-2 virus was present throughout the year compared to a seasonal prevalence of other respiratory viral pathogens.

SARS-CoV-2 variant monitoring via WBE can provide insights into regionally co-circulating respiratory viruses, causing flu-like symptoms.

WBE-AMR gene monitoring is feasible and provides valuable insight into regional AMRs.

Our workflow enables the estimation of the relative proportion of different variants in any pooled samples.

GRAPHICAL ABSTRACT
Proteome Wide Association Studies of LRRK2 variants identify novel causal and druggable for Parkinson’s disease
Authors: Phillips Bridget , Western Daniel , Wang Lihua , Timsina Jigyasha , Sun Yichen , Gorijala Priyanka , Yang Chengran , Do Anh , Nykänen Niko-Petteri , Alvarez Ignacio , Aguilar Miquel , Pastor Pau , Morris John C. , Schindler Suzanne E. , Fagan Anne M. , Puerta Raquel , García-González Pablo , de Rojas Itziar , Marquié Marta , Boada Mercè , Ruiz Agustin , Perlmutter Joel S. ,   Dominantly Inherited Alzheimer Network (DIAN) Consortia, Ibanez Laura , Perrin Richard J. , Sung Yun Ju , Cruchaga Carlos
Published: January 2023

Common and rare variants in theLRRK2locus are associated with Parkinson’s disease (PD) risk, but the downstream effects of these variants on protein levels remains unknown. We performed comprehensive proteogenomic analyses using the largest aptamer-based CSF proteomics study to date (7,006 aptamers (6,138 unique proteins) in 3,107 individuals). We identified eleven independent SNPs in theLRRK2locus associated with the levels of 26 proteins as well as PD risk. Of these, only eleven proteins have been previously associated with PD risk (e.g., GRN or GPNMB). Proteome-wide association study (PWAS) analyses suggested that the levels of ten of those proteins were genetically correlated with PD risk and seven were validated in the PPMI cohort. Mendelian randomization analyses identified five proteins (GPNMB, GRN, HLA-DQA2, LCT, and CD68) causal for PD and nominate one more (ITGB2). These 26 proteins were enriched for microglia-specific proteins and trafficking pathways (both lysosome and intracellular). This study not only demonstrates that protein phenome-wide association studies (PheWAS) and trans-protein quantitative trail loci (pQTL) analyses are powerful for identifying novel protein interactions in an unbiased manner, but also thatLRRK2is linked with the regulation of PD-associated proteins that are enriched in microglial cells and specific lysosomal pathways.
Identification of differences in the magnitude and specificity of SARS-CoV-2 nucleocapsid antibody responses in naturally infected and vaccinated individuals
Authors: Pushpakumara Pradeep D. , Jeewandara Chandima , Bary Farha , Madushanka Deshan , Perera Lahiru , Aberathna Inoka Sepali , Nimasha Thashmi , Jayamali Jeewantha , Ranasinghe Thushali , Kuruppu Heshan , Danasekara Saubhagya , Wijewickrama Ananda , Ogg Graham S. , Malavige Gathsaurie Neelika
Published: January 2023

Background

As there are limited data on B cell epitopes for the nucleocapsid protein in SARS-CoV-2, we sought to identify the immunodominant regions within the N protein, recognized by patients with varying severity of natural infection with the Wuhan strain (WT), delta, omicron and in those who received the Sinopharm vaccines, which is an inactivated, whole virus vaccine.

Methods

Using overlapping peptides representing the N protein, with an in-house ELISA, we mapped the immunodominant regions within the N protein, in seronegative (n=30), WT infected (n=30), delta infected (n=30), omicron infected+vaccinated (n=20) and Sinopharm (BBIBP-CorV) vaccinees (n=30). We then investigated the sensitivity and specificity of these immunodominant regions and analysed their conservation with other SARS-CoV-2 variants of concern, seasonal human coronaviruses and bat Sarbecoviruses. We then investigated the kinetics of responses to these regions in those with varying severity of acute COVID-19.

Results

We identified four immunodominant regions aa 29-52, aa 155-178, aa 274 to 297 and aa 365 to 388, were highly conserved within SARS-CoV-2 and the bat coronaviruses. The magnitude of responses to these regions varied based on the infecting SARS-CoV-2 variants, with WT infected individuals predominantly recognizing aa155 to 178 regions, delta infected individuals and vaccinated+omicron infected individuals predominantly recognizing regions aa 29 to 52 and aa 274 to 294 regions. Sinopharm vaccinees recognized all four regions, with the magnitude of responses significantly lower than other groups. >80% of individuals gave responses above the positive cut-off threshold to many of the four regions, with some differences with individuals who were infected with different VoCs. These regions were found to be 100% specific, as none of the seronegative individuals gave any responses.

Conclusions

N-protein specific responses appear to be detectable in over 90% of those who were naturally infected or vaccinated with a whole virus inactivated vaccine, with responses mainly directed against four regions of the protein, which were highly conserved. As these regions were highly specific with high sensitivity, they have a potential to be used to develop diagnostic assays and to be used in development of vaccines.
Human CCR6+Th cells show both an extended stable gradient of Th17 activity and imprinted plasticity
Authors: Singh Satya P. , Parween Farhat , Edara Nithin , Zhang Hongwei H. , Chen Jinguo , Otaizo-Carrasquero Francisco , Cheng Debby , Oppenheim Nicole A. , Ransier Amy , Zhu Wenjun , Shamsaddini Amirhossein , Gardina Paul J. , Darko Samuel W. , Singh Tej Pratap , Douek Daniel C. , Myers Timothy G. , Farber Joshua M.
Published: January 2023

Th17 cells have been investigated in mice primarily for their contributions to autoimmune diseases. However, the pathways of differentiation of Th17 and related (type 17) cells and the structure of the type 17 memory population in humans are not well understood; such understanding is critical for manipulating these cellsin vivo. By exploiting differences in levels of surface CCR6, we found that human type 17 memory cells, including individual T cell clonotypes, form an elongated continuum of type 17 character along which cells can be driven by increasing RORγt. This continuum includes cells preserved within the memory pool with potentials that reflect the early preferential activation of multiple over single lineages. The CCR6+cells’ phenotypes and epigenomes are stable across cell divisions under homeostatic conditions. Nonetheless, activation in polarizing and non-polarizing conditions can yield additional functionalities, revealing, respectively, both environmentally induced and imprinted mechanisms that contribute differentially across the continuum to yield the unusual plasticity ascribed to type 17 cells.
A phosphorylation switch regulates RAB6 function during mitosis
Authors: Jimenez Ana Joaquina , Bousquet Hugo , Bardin Sabine , Perez Franck , Goud Bruno , Miserey Stéphanie
Published: January 2023

RAB GTPases are key regulators of membrane trafficking in eukaryotic cells. In addition to their role in interphase, several RAB proteins, including Golgi-associated RAB6, have mitotic functions. The aim of this study was to investigate how the interphasic and mitotic functions of RAB6 could be regulated. Since phosphorylation is a key regulatory process in mitosis, we looked for specific mitotic phosphorylation of RAB6 using a phospho-proteomic approach. We found that RAB6 is phosphorylated at position S52 by the mitotic kinase Pololike kinase 1 (Plk1) in mitosis. Phosphorylated RAB6 localizes at the spindle poles from prophase to anaphase. In metaphase, we observed RAB6A-positive structures containing Mad1 and Mad2 moving along the mitotic spindle via the dynein-dynactin complex. We provide evidence that phosphorylation impairs RAB6A binding to some of its known partners, including p150Gluedand Bicaudal-D2. In addition, the overexpression of RAB6A phospho-mutants lead to mitosis and cytokinesis defects. Our results suggest that a cycle of RAB6 phosphorylation/dephosphorylation is required for cell division.
The macrophage genetic cassette inr/dtor/pvf2 is a nutritional status checkpoint for developmental timing
Authors: Juarez-Carreño Sergio , Geissmann Frederic
Published: January 2023

A small number of signaling molecules, used reiteratively, control differentiation programs, but the mechanisms that adapt developmental timing to environmental cues are less understood. We report here that a macrophageinr/dtor/pvf2genetic cassette is a developmental timing checkpoint inDrosophila, which either licenses or delays biosynthesis of the steroid hormone in the endocrine gland and metamorphosis according to the larval nutritional status. Insulin-Receptor/dTor signaling in macrophages is required and sufficient for production of the PDGF/VEGF family growth factor Pvf2, which turns on transcription of the sterol biosynthesis Halloween genes in the prothoracic gland via its receptor Pvr. In response to a starvation event or genetic manipulation, low Pvf2 signal delays steroid biosynthesis until it becomes Pvr-independent, thereby prolonging larval growth before pupation. The significance of this developmental timing checkpoint for host fitness is illustrated by the observation that it regulates the size of the pupae and adult flies.

One sentence summary

A macrophage Inr/dtor/pvf2 cassette is a nutritional status checkpoint that controls developmental timing via steroid hormone biosynthesis in the endocrine gland.
Functional genomic analysis of adult and pediatric brain tumor isolates
Authors: Hoellerbauer Pia , Biery Matt C. , Arora Sonali , Rao Yiyun , Girard Emily J. , Mitchell Kelly , Dighe Pratiksha , Kufeld Megan , Kuppers Daniel A. , Herman Jacob A. , Holland Eric C. , Soroceanu Liliana , Vitanza Nicholas A. , Olson James M. , Pritchard Justin R. , Paddison Patrick J.
Published: January 2023

Background

Adult and pediatric tumors display stark differences in their mutation spectra and chromosome alterations. Here, we attempted to identify common and unique gene dependencies and their associated biomarkers among adult and pediatric tumor isolates using functional genetic lethal screens and computational modeling.

Methods

We performed CRISRP-Cas9 lethality screens in two adult glioblastoma (GBM) tumor isolates and five pediatric brain tumor isolates representing atypical teratoid rhabdoid tumors (ATRT), diffuse intrinsic pontine glioma, GBM, and medulloblastoma. We then integrated the screen results with machine learning-based gene-dependency models generated from data from >900 cancer cell lines.

Results

We found that >50% of candidate dependencies of 280 identified were shared between adult GBM tumors and individual pediatric tumor isolates. 68% of screen hits were found as nodes in our network models, along with shared and tumor-specific predictors of gene dependencies. We investigated network predictors associated with ADAR, EFR3A, FGFR1 (pediatric-specific), and SMARCC2 (ATRT-specific) gene dependency among our tumor isolates.

Conclusions

The results suggest that, despite harboring disparate genomic signatures, adult and pediatric tumor isolates share a preponderance of genetic dependences. Further, combining data from primary brain tumor lethality screens with large cancer cell line datasets produced valuable insights into biomarkers of gene dependency, even for rare cancers.

Importance of the Study

Our results demonstrate that large cancer cell lines data sets can be computationally mined to identify known and novel gene dependency relationships in adult and pediatric human brain tumor isolates. Gene dependency networks and lethality screen results represent a key resource for neuro-oncology and cancer research communities. We also highlight some of the challenges and limitations of this approach.
Harnessing antimicrobial peptide genes to expedite disease-resistant enhancement in aquaculture: Transgenesis and genome editing
Authors: Wang Jinhai , Cheng Yu
Published: January 2023

Numerous studies have demonstrated that genome editing and transgenesis by integrating vector-engineered antimicrobial peptide genes (AMGs) is effective to modulate the fish’s innate immune system. To generalize the knowledge of AMG application in aquaculture, here we recruited 540 data entries from a pool of empirical studies, which included 18 peer-reviewed publications and spanning 12 diseases. We systematically re-processed and re-analyzed these data by harnessing a cross-disease meta-analysis. On aggregate, AMG-genetic engineering aimed at enhancing disease resistance was shown to decrease the number of colony-forming units of bacteria, improve lysozyme activity, increase the post-infection survival rates, and alter the expression of AMGs and immune-related genes in aquatic animals. Furthermore, the AMG-pathogen combating activity was triggered within two hours after infection and lasted 48 hours, and the overexpression of AMGs was dominant in the spleen and skin, followed by the kidney and liver during this period. Typically, regardless of the type of AMGs, the synergistic expression of AMGs with IL, IKβ, TGFβ, C3b and TLR in AMG-integrated fish contributed to activating inflammatory/immune responses against pathogens. In addition, innovative CRISPR/Cas9-mediated systems enabling the site-directed knock-in of foreign genes at multiple loci were presented and prospected for disease-resistant enhancement in combination with other favorable fish-producing traits, including fast-growing, sterility, and enriched fatty acid. Altogether, our findings indicated that AMGs as transgenes have substantial potential to modulate the fish’s innate immune system and accelerate disease-resistant enhancement combined with genetic engineering.
Phenotypic subtyping via contrastive learning
Authors: Gorla Aditya , Sankararaman Sriram , Burchard Esteban , Flint Jonathan , Zaitlen Noah , Rahmani Elior
Published: January 2023

Defining and accounting for subphenotypic structure has the potential to increase statistical power and provide a deeper understanding of the heterogeneity in the molecular basis of complex disease. Existing phenotype subtyping methods primarily rely on clinically observed heterogeneity or metadata clustering. However, they generally tend to capture the dominant sources of variation in the data, which often originate from variation that is not descriptive of the mechanistic heterogeneity of the phenotype of interest; in fact, such dominant sources of variation, such as population structure or technical variation, are, in general, expected to be independent of subphenotypic structure. We instead aim to find a subspace with signal that is unique to a group of samples for which we believe that subphenotypic variation exists (e.g., cases of a disease). To that end, we introduce Phenotype Aware Components Analysis (PACA), a contrastive learning approach leveraging canonical correlation analysis to robustly capture weak sources of subphenotypic variation. In the context of disease, PACA learns a gradient of variation unique to cases in a given dataset, while leveraging control samples for accounting for variation and imbalances of biological and technical confounders between cases and controls. We evaluated PACA using an extensive simulation study, as well as on various subtyping tasks using genotypes, transcriptomics, and DNA methylation data. Our results provide multiple strong evidence that PACA allows us to robustly capture weak unknown variation of interest while being calibrated and well-powered, far superseding the performance of alternative methods. This renders PACA as a state-of-the-art tool for definingde novosubtypes that are more likely to reflect molecular heterogeneity, especially in challenging cases where the phenotypic heterogeneity may be masked by a myriad of strong unrelated effects in the data.

Code Availability

PACA is available as an open source R package on GitHub:https://github.com/Adigorla/PACA
ViralConsensus: A fast and memory-efficient tool for calling viral consensus genome sequences directly from read alignment data
Authors: Moshiri Niema
Published: January 2023

Motivation

In viral molecular epidemiology, reconstruction of consensus genomes from sequence data is critical for tracking mutations and variants of concern. However, as the number of samples that are sequenced grows rapidly, compute resources needed to reconstruct consensus genomes can become prohibitively large.

Results

ViralConsensus is a fast and memory-efficient tool for calling viral consensus genome sequences directly from read alignment data. ViralConsensus is orders of magnitude faster and more memory-efficient than existing methods. Further, unlike existing methods, ViralConsensus can pipe data directly from a read mapper via standard input and performs viral consensus calling on-the-fly, making it an ideal tool for viral sequencing pipelines.

Availability

ViralConsensus is freely available athttps://github.com/niemasd/ViralConsensusas an open-source software project.

Contact

niema@ucsd.edu

Supplementary information

Supplementary data are available online.
Caspase-4 dimerisation and D289 auto-processing elicits an interleukin-1β converting enzyme
Authors: Chan Amy H. , Vezyrgiannis Kassandra , Von Pein Jessica B. , Wang Xiaohui , Labzin Larisa I , Boucher Dave , Schroder Kate
Published: January 2023

The non-canonical inflammasome is a signalling complex critical for cell defence against cytosolic Gram-negative bacteria. A key step in the human non-canonical inflammasome pathway involves unleashing the proteolytic activity of caspase-4 within this complex. Caspase-4 induces inflammatory responses by cleaving gasdermin-D (GSDMD) to initiate pyroptosis, although the molecular mechanisms that activate caspase-4 and govern its capacity to cleave substrates are poorly defined. Caspase-11, the murine counterpart of caspase-4, acquires protease activity within the non-canonical inflammasome by forming a dimer that self-cleaves at D285 to directly cleave GSDMD. These cleavage events trigger signalling via the NLRP3-ASC-caspase-1 axis, leading to downstream cleavage of the pro-interleukin-1β (pro-IL-1β) cytokine precursor. Here, we show that caspase-4 first dimerises then self-cleaves at two sites – D270 and D289 – in the interdomain linker to acquire full proteolytic activity, cleave GSDMD and induce cell death. Surprisingly, caspase-4 dimerisation and self-cleavage at D289 generates a caspase-4 p34/p9 protease species that directly cleaves pro-IL-1β, resulting in its maturation and secretion independently of the NLRP3 inflammasome in primary human myeloid and epithelial cells. Our study thus elucidates the key molecular events that underpin signalling by the caspase-4 inflammasome, and identifies IL-1β as a natural substrate of caspase-4.
Graph Convolutional Learning of Multimodal Brain Connectome Data for Schizophrenia Classification
Authors: Ghosh Sanjay , Bhargava Eshan , Lin Chieh-Te , Nagarajan Srikantan S.
Published: January 2023

The long term goal of this work is to develop powerful tools for brain network analysis in order to study structural and functional connectivity abnormalities in psychiatric disorders like schizophrenia. Graph convolutional neural networks (GCNN) are quite effective for learning complex discriminate features in graph-structured data. Here, we explore the GCNN to learn the discriminating features in multimodal human brain connectomes for the purpose of schizophrenia disorder classification. In particular, we train and validate a network using both structural connectivity graphs obtained from diffusion tensor imaging data and functional connectivity from functional magnetic resonance imaging data.We compare the GCNN method with a support vector machine based classifier and other popular classification benchmarks. We demonstrate that the proposed graph convolution method has the best performance compared to existing benchmarks with F1 scores of 0.75 for schizophrenia classification. This demonstrates the potential of this approach for multimodal diagnosis and prognosis in mental health disorders.
Genomic evolution of non-small cell lung cancer patient-derived xenograft models
Authors: Hynds Robert E. , Huebner Ariana , Pearce David R. , Akarca Ayse U. , Moore David A. , Ward Sophia , Gowers Kate H.C. , Karasaki Takahiro , Hill Mark S. , Bakir Maise Al , Wilson Gareth A. , Pich Oriol , Sivakumar Monica , Aissa Assma Ben , Grönroos Eva , Chandrasekharan Deepak , Kolluri Krishna K. , Towns Rebecca , Wang Kaiwen , Cook Daniel E. , Bosshard-Carter Leticia , Naceur-Lombardelli Cristina , Rowan Andrew J. , Veeriah Selvaraju , Litchfield Kevin , Quezada Sergio A. , Janes Sam M. , Jamal-Hanjani Mariam , Marafioti Teresa ,   TRACERx Consortium, McGranahan Nicholas , Swanton Charles
Published: January 2023

Patient-derived xenograft (PDX) models of cancer, developed through injection of patient tumour cells into immunocompromised mice, have been widely adopted in preclinical studies, as well as in precision oncology approaches. However, the extent to which PDX models represent the underlying genetic diversity of a patient’s tumour and the extent of on-going genomic evolution in PDX models are incompletely understood, particularly in the context of heterogeneous cancers such as non-small cell lung cancer (NSCLC). To investigate the depiction of intratumour heterogeneity by PDX models, we derived 47 new subcutaneous multi-region PDX models from 22 patients with primary NSCLC enrolled in the clinical longitudinal cohort study TRACERx. By analysing whole exome sequencing data from primary tumours and PDX models, we find that PDX establishment creates a genomic bottleneck, with 76% of PDX models being derived from a single primary tumour subclone. Despite this, multiple primary tumour subclones were capable of PDX establishment in regional PDX models, indicating that PDX libraries derived from multiple tumour regions can capture intratumour heterogeneity. Acquisition of somatic mutations continued during PDX model expansion, and was associated with APOBEC- or mismatch repair deficiency-induced mutational signatures in a subset of models. Overall, while NSCLC PDX models retain truncal genomic alterations, the absence of subclonal heterogeneity representative of the primary tumour is a major limitation. Our results emphasise the importance of characterising and monitoring intratumour heterogeneity in the context of pre-clinical cancer studies.
The Cortical Representation of Language Timescales is Shared between Reading and Listening
Authors: Chen Catherine , Dupré la Tour Tom , Gallant Jack L. , Klein Dan , Deniz Fatma
Published: January 2023

Language comprehension involves integrating low-level sensory inputs into a hierarchy of increasingly high-level features. Prior work studied brain representations of different levels of the language hierarchy, but has not determined whether these brain representations are shared between written and spoken language. To address this issue, we analyzed fMRI BOLD data recorded while participants read and listened to the same narratives in each modality. Levels of the language hierarchy were operationalized astimescales, where each timescale refers to a set of spectral components of a language stimulus. Voxelwise encoding models were used to determine where different timescales are represented across the cerebral cortex, for each modality separately. These models reveal that between the two modalities timescale representations are organized similarly across the cortical surface. Our results suggest that, after low-level sensory processing, language integration proceeds similarly regardless of stimulus modality.
Ultra-fast genome-wide inference of pairwise coalescence times
Authors: Schweiger Regev , Durbin Richard
Published: January 2023

The pairwise sequentially Markovian coalescent (PSMC) algorithm and its extensions infer the coalescence time of two homologous chromosomes at each genomic position. This inference is utilized in reconstructing demographic histories, detecting selection signatures, genome-wide association studies, constructing ancestral recombination graphs and more. Inference of coalescence times between each pair of haplotypes in a large dataset is of great interest, as they may provide rich information about the population structure and history of the sample.

We introduce a new method,Gamma-SMC, which is>14 times faster than current methods. To obtain this speed up, we represent the posterior coalescence time distributions succinctly as a Gamma distribution with just two parameters; while in PSMC and its extensions, these are held as a vector over discrete intervals of time. Thus, Gamma-SMC has constant time complexity per site, without dependence on a number of discrete time states. Additionally, due to this continuous representation, our method is able to infer times spanning many orders of magnitude, and as such is robust to parameter misspecification. We describe how this approach works, illustrate its performance on simulated and real data, and use it to study recent positive selection in the 1000 Genomes Project dataset.
MYC enhancer invasion promotes prognostic cancer type-specific gene programs through an epigenetic switch
Authors: Jakobsen Simon T. , Jensen Rikke AM. , Ravnsborg Tina , Vaagenso Christian D. , Einarsson Hjorleifur , Madsen Maria S. , Andersson Robin , Jensen Ole N. , Siersbæk Rasmus
Published: January 2023

The transcription factor MYC is overexpressed in most cancers, where it drives multiple hallmarks of cancer progression. MYC is known to promote oncogenic transcription by binding to active promoters. In addition, MYC has also been shown to invade distal enhancers when expressed at oncogenic levels, but this enhancer binding has been proposed to have low gene-regulatory potential. Here, we demonstrate that MYC enhancer binding directly promotes cancer type-specific gene programs predictive of poor patient prognosis. MYC induces transcription of enhancer RNA through recruitment of RNAPII, rather than regulating RNAPII pause-release as is the case at promoters. This is mediated by MYC-induced H3K9 demethylation by KDM3A and acetylation by GCN5, leading to enhancer-specific BRD4 recruitment through its bromodomains, which facilitates RNAPII recruitment. Thus, we propose that MYC drives prognostic cancer type-specific gene programs by promoting RNAPII recruitment to enhancers through induction of an epigenetic switch.
Transcription factors mediating regulation of photosynthesis
Authors: Halpape Wiebke , Wulf Donat , Verwaaijen Bart , Stasche Anna Sophie , Zenker Sanja , Sielemann Janik , Tschikin Sebastian , Viehöver Prisca , Sommer Manuel , Weber Andreas P. M. , Delker Carolin , Eisenhut Marion , Bräutigam Andrea
Published: January 2023

Photosynthesis by which plants convert carbon dioxide to sugars using the energy of light is fundamental to life as it forms the basis of nearly all food chains. Surprisingly, our knowledge about its transcriptional regulation remains incomplete. Effort for its agricultural optimization have mostly focused on post-translational regulatory processes1–3but photosynthesis is regulated at the post-transcriptional4and the transcriptional level5. Stacked transcription factor mutations remain photosynthetically active5,6and additional transcription factors have been difficult to identify possibly due to redundancy6or lethality. Using a random forest decision tree-based machine learning approach for gene regulatory network calculation7we determined ranked candidate transcription factors and validated five out of five tested transcription factors as controlling photosynthesisin vivo. The detailed analyses of previously published and newly identified transcription factors suggest that photosynthesis is transcriptionally regulated in a partitioned, non-hierarchical, interlooped network.
APOBEC3F is the main source of editing identified during the 2022 outbreak of human monkeypox virus
Authors: Suspène Rodolphe , Raymond Kyle A. , Boutin Laetitia , Guillier Sophie , Lemoine Frédéric , Ferraris Olivier , Tournier Jean-Nicolas , Iseni Frédéric , Simon-Lorière Etienne , Vartanian Jean-Pierre
Published: January 2023

On May 6, 2022, a powerful outbreak of monkeypox virus (MPXV) had been reported outside of Africa, with many continuing new cases being reported around the world. Analysis of mutations among the two different lineages present in the 2021 and 2022 outbreaks revealed the presence of G->A mutations occurring in the 5’GpA context, indicative of APOBEC3 cytosine deaminase activity. By using a sensitive PCR (3D-PCR) method allowing differential amplification of AT-rich DNA, we demonstrate that G->A hypermutated MPXV genomes can be recovered experimentally from APOBEC3 transfection followed by MPXV infection. Here, among the 7 human APOBEC3 cytidine deaminases (A3A-A3C, A3DE, A3F-A3H), only APOBEC3F was capable of extensively deaminating cytidine residues in MPXV genomes. Hyperedited genomes were also recovered in ~42% of analyzed patients, indicating that editing is part of the natural cycle of MPXV infection. Moreover, we demonstrate that substantial repair of these mutations occurs. Upon selection, corrected G->A mutations escaping drift loss contribute to the MPXV evolution observed in the current epidemics. Thus, stochastic or transient overexpression ofAPOBEC3Fgene exposes the MPXV genome to a broad spectrum of mutations that may be modeling the mutational landscape after multiple cycles of viral replication.
To design or not to design? Comparison of beetle ultraconserved element probe set utility based on phylogenetic distance, breadth, and method of probe design
Authors: Gustafson Grey T. , Glynn Rachel D. , Short Andrew E. Z. , Tarasov Sergei , Gunter Nicole L.
Published: January 2023

Tailoring ultraconserved element (UCE) probe set design to focal taxa has been demonstrated to improve locus recovery and phylogenomic inference. However, beyond conducting expensivein vitrotesting, it remains unclear how best to determine whether an existing UCE probe set is likely to suffice for phylogenomic inference, or if tailored probe design will be desirable. Here we investigate the utility of eight different UCE probe sets for thein silicophylogenomic inference of scarabaeoid beetles. Probe sets tested differed in terms of (1) how phylogenetically distant from Scarabaeoidea taxa those used during probe design are, (2) breadth of phylogenetic inference probe set was designed for, and (3) method of probe design. As part of this study, two new UCE probe sets are produced for the beetle family Scarabaeidae and superfamily Hydrophiloidea. We find that, predictably, probe set utility decreases with increasing phylogenetic distance of design taxa from focal taxa, as well as with narrower breadth of phylogenetic inference probes were designed for. We also confirm previous findings regarding ways to optimize UCE probe design. Finally, we make suggestions regarding assessment of need forde novoprobe design and reinforce previous proposed methods for maximizing UCE probe design to improve phylogenomic inference.