PTM-Mamba: A PTM-Aware Protein Language Model with Bidirectional Gated Mamba Blocks

Proteins serve as the workhorses of living organisms, orchestrating a wide array of vital functions. Post-translational modifications (PTMs) of their amino acids greatly influence the structural and functional diversity of different protein types and uphold proteostasis, allowing cells to swiftly respond to environmental changes and intricately regulate complex biological processes. To this point, efforts to model the complex features of proteins have involved the training of large and expressive protein language models (pLMs) such as ESM-2 and ProtT5, which accurately encode structural, functional, and physicochemical properties of input protein sequences. However, the over 200 million sequences that these pLMs were trained on merely scratch the surface of proteomic diversity, as they neither input nor account for the effects of PTMs. In this work, we fill this major gap in protein sequence modeling by introducing PTM tokens into the pLM training regime. We then leverage recent advancements in structured state space models (SSMs), specifically Mamba, which utilizes efficient hardware-aware primitives to overcome the quadratic time complexities of Transformers. After adding a comprehensive set of PTM tokens to the model vocabulary, we train bidirectional Mamba blocks whose outputs are fused with state-of-the-art ESM-2 embeddings via a novel gating mechanism. We demonstrate that our resultant PTM-aware pLM, PTM-Mamba , improves upon ESM-2's performance on various PTM-specific tasks. PTM-Mamba is the first and only pLM that can uniquely input and represent both wild-type and PTM sequences, motivating downstream modeling and design applications specific to post-translationally modified proteins. To facilitate PTM-aware protein language modeling applications, we have made our model available at: https://huggingface.co/ChatterjeeLab/PTM-Mamba .

Human-induced pluripotent stem cell-derived ovarian support cell co-culture improves oocyte maturation in vitro after abbreviated gonadotropin stimulation

STUDY QUESTION

Can in vitro maturation (IVM) and developmental competence of human oocytes be improved by co-culture with ovarian support cells (OSCs) derived from human-induced pluripotent stem cells (hiPSCs)?

SUMMARY ANSWER

OSC-IVM significantly improves the rates of metaphase II (MII) formation and euploid Day 5 or 6 blastocyst formation, when compared to a commercially available IVM system.

WHAT IS KNOWN ALREADY

IVM has historically shown highly variable performance in maturing oocytes and generating oocytes with strong developmental capacity, while limited studies have shown a positive benefit of primary granulosa cell co-culture for IVM. We recently reported the development of OSCs generated from hiPSCs that recapitulate dynamic ovarian function in vitro.

STUDY DESIGN, SIZE, DURATION

The study was designed as a basic science study, using randomized sibling oocyte specimen allocation. Using pilot study data, a prospective sample size of 20 donors or at least 65 oocytes per condition were used for subsequent experiments. A total of 67 oocyte donors were recruited to undergo abbreviated gonadotropin stimulation with or without hCG triggers and retrieved cumulus-oocyte complexes (COCs) were allocated between the OSC-IVM or control conditions (fetal-like OSC (FOSC)-IVM or media-only IVM) in three independent experimental design formats. The total study duration was 1 April 2022 to 1 July 2023.

PARTICIPANTS/MATERIALS, SETTING, METHODS

Oocyte donors between the ages of 19 and 37 years were recruited for retrieval after informed consent, with assessment of anti-Mullerian hormone, antral follicle count, age, BMI and ovarian pathology used for inclusion and exclusion criteria. In experiment 1, 27 oocyte donors were recruited, in experiment 2, 23 oocyte donors were recruited, and in experiment 3, 17 oocyte donors and 3 sperm donors were recruited. The OSC-IVM culture condition was composed of 100 000 OSCs in suspension culture with hCG, recombinant FSH, androstenedione, and doxycycline supplementation. IVM controls lacked OSCs and contained either the same supplementation, FSH and hCG only (a commercial IVM control), or FOSCs with the same supplementation (Media control). Experiment 1 compared OSC-IVM, FOSC-IVM, and a Media control, while experiments 2 and 3 compared OSC-IVM and a commercial IVM control. Primary endpoints in the first two experiments were the MII formation (i.e. maturation) rate and morphological quality assessment. In the third experiment, the fertilization and embryo formation rates were assessed with genetic testing for aneuploidy and epigenetic quality in blastocysts.

MAIN RESULTS AND THE ROLE OF CHANCE

We observed a statistically significant improvement (∼1.5×) in maturation outcomes for oocytes that underwent IVM with OSCs compared to control Media-IVM and FOSC-IVM in experiment 1. More specifically, the OSC-IVM group yielded a MII formation rate of 68% ± 6.83% SEM versus 46% ± 8.51% SEM in the Media control (P = 0.02592, unpaired t-test). FOSC-IVM yielded a 51% ± 9.23% SEM MII formation rate which did not significantly differ from the media control (P = 0.77 unpaired t-test). Additionally, OSC-IVM yielded a statistically significant ∼1.6× higher average MII formation rate at 68% ± 6.74% when compared to 43% ± 7.90% in the commercially available IVM control condition (P = 0.0349, paired t-test) in experiment 2. Oocyte morphological quality between OSC-IVM and the controls did not significantly differ. In experiment 3, OSC-IVM oocytes demonstrated a statistically significant improvement in Day 5 or 6 euploid blastocyst formation per COC compared to the commercial IVM control (25% ± 7.47% vs 11% ± 3.82%, P = 0.0349 logistic regression). Also in experiment 3, the OSC-treated oocytes generated blastocysts with similar global and germline differentially methylated region epigenetic profiles compared commercial IVM controls or blastocysts after either conventional ovarian stimulation.

LARGE SCALE DATA

N/A.

LIMITATIONS, REASONS FOR CAUTION

While the findings of this study are compelling, the cohort size remains limited and was powered on preliminary pilot studies, and the basic research nature of the study limits generalizability compared to randomized control trials. Additionally, use of hCG-triggered cycles results in a heterogenous oocyte cohort, and potential differences in the underlying maturation state of oocytes pre-IVM may limit or bias findings. Further research is needed to clarify and characterize the precise mechanism of action of the OSC-IVM system. Further research is also needed to establish whether these embryos are capable of implantation and further development, a key indication of their clinical utility.

WIDER IMPLICATIONS OF THE FINDINGS

Together, these findings demonstrate a novel approach to IVM with broad applicability to modern ART practice. The controls used in this study are in line with and have produced similar to findings to those in the literature, and the outcome of this study supports findings from previous co-culture studies that found benefits of primary granulosa cells on IVM outcomes. The OSC-IVM system shows promise as a highly flexible IVM approach that can complement a broad range of stimulation styles and patient populations. Particularly for patients who cannot or prefer not to undergo conventional gonadotropin stimulation, OSC-IVM may present a viable path for obtaining developmentally competent, mature oocytes.

STUDY FUNDING/COMPETING INTEREST(S)

A.D.N., A.B.F., A.G., B.P., C.A., C.C.K., F.B., G.R., K.S.P., K.W., M.M., P.C., S.P., and M.-J.F.-G. are shareholders in the for-profit biotechnology company Gameto Inc. P.R.J.F. declares paid consultancy for Gameto Inc. P.C. also declares paid consultancy for the Scientific Advisory Board for Gameto Inc. D.H.M. has received consulting services from Granata Bio, Sanford Fertility and Reproductive Medicine, Gameto, and Buffalo IVF, and travel support from the Upper Egypt Assisted Reproduction Society. C.C.K., S.P., M.M., A.G., B.P., K.S.P., G.R., and A.D.N. are listed on a patent covering the use of OSCs for IVM: U.S. Provisional Patent Application No. 63/492,210. Additionally, C.C.K. and K.W. are listed on three patents covering the use of OSCs for IVM: U.S. Patent Application No. 17/846,725, U.S Patent Application No. 17/846,845, and International Patent Application No.: PCT/US2023/026012. C.C.K., M.P.S., and P.C. additionally are listed on three patents for the transcription factor-directed production of granulosa-like cells from stem cells: International Patent Application No.: PCT/US2023/065140, U.S. Provisional Application No. 63/326,640, and U.S. Provisional Application No. 63/444,108. The remaining authors have no conflicts of interest to declare.

PepMLM: Target Sequence-Conditioned Generation of Peptide Binders via Masked Language Modeling

Target proteins that lack accessible binding pockets and conformational stability have posed increasing challenges for drug development. Induced proximity strategies, such as PROTACs and molecular glues, have thus gained attention as pharmacological alternatives, but still require small molecule docking at binding pockets for targeted protein degradation (TPD). The computational design of protein-based binders presents unique opportunities to access undruggable targets, but have often relied on stable 3D structures or predictions for effective binder generation. Recently, we have leveraged the expressive latent spaces of protein language models (pLMs) for the prioritization of peptide binders from sequence alone, which we have then fused to E3 ubiquitin ligase domains, creating a CRISPR-analogous TPD system for target proteins. However, our methods rely on training discriminator models for ranking heuristically or unconditionally-derived guide peptides for their target binding capability. In this work, we introduce PepMLM, a purely target sequence-conditioned de novo generator of linear peptide binders. By employing a novel masking strategy that uniquely positions cognate peptide sequences at the terminus of target protein sequences, PepMLM tasks the state-of-the-art ESM-2 pLM to fully reconstruct the binder region, achieving low perplexities matching or improving upon previously-validated peptide-protein sequence pairs. After successful in silico benchmarking with AlphaFold-Multimer, we experimentally verify PepMLM's efficacy via fusion of model-derived peptides to E3 ubiquitin ligase domains, demonstrating endogenous degradation of target substrates in cellular models. In total, PepMLM enables the generative design of candidate binders to any target protein, without the requirement of target structure, empowering downstream programmable proteome editing applications.

SaLT&PepPr is an interface-predicting language model for designing peptide-guided protein degraders

Protein-protein interactions (PPIs) are critical for biological processes and predicting the sites of these interactions is useful for both computational and experimental applications. We present a Structure-agnostic Language Transformer and Peptide Prioritization (SaLT&PepPr) pipeline to predict interaction interfaces from a protein sequence alone for the subsequent generation of peptidic binding motifs. Our model fine-tunes the ESM-2 protein language model (pLM) with a per-position prediction task to identify PPI sites using data from the PDB, and prioritizes motifs which are most likely to be involved within inter-chain binding. By only using amino acid sequence as input, our model is competitive with structural homology-based methods, but exhibits reduced performance compared with deep learning models that input both structural and sequence features. Inspired by our previous results using co-crystals to engineer target-binding "guide" peptides, we curate PPI databases to identify partners for subsequent peptide derivation. Fusing guide peptides to an E3 ubiquitin ligase domain, we demonstrate degradation of endogenous β-catenin, 4E-BP2, and TRIM8, and highlight the nanomolar binding affinity, low off-targeting propensity, and function-altering capability of our best-performing degraders in cancer cells. In total, our study suggests that prioritizing binders from natural interactions via pLMs can enable programmable protein targeting and modulation.

PAM-flexible genome editing with an engineered chimeric Cas9

CRISPR enzymes require a defined protospacer adjacent motif (PAM) flanking a guide RNA-programmed target site, limiting their sequence accessibility for robust genome editing applications. In this study, we recombine the PAM-interacting domain of SpRY, a broad-targeting Cas9 possessing an NRN > NYN (R = A or G, Y = C or T) PAM preference, with the N-terminus of Sc + +, a Cas9 with simultaneously broad, efficient, and accurate NNG editing capabilities, to generate a chimeric enzyme with highly flexible PAM preference: SpRYc. We demonstrate that SpRYc leverages properties of both enzymes to specifically edit diverse PAMs and disease-related loci for potential therapeutic applications. In total, the approaches to generate SpRYc, coupled with its robust flexibility, highlight the power of integrative protein design for Cas9 engineering and motivate downstream editing applications that require precise genomic positioning.

A General Assessment of India's Extremely Low Number of Transgender Cancer Patients

PURPOSE/OBJECTIVE(S)

Physiological transgender (TJ) is one of the most marginalized and oppressed community in the Indian subcontinent. The observable percentage of physiological transgender (TJ) cancer patients is extremely low. This concise report aims to assess the factors that contribute to the scarcity of transgender cancer patients.

MATERIALS/METHODS

The hospital database (2012-2021) of 2 centers in New Delhi (population 32 million) & 1 in Kolkata (15 million) were evaluated. In addition, 28 senior oncologists (ONC) and 17 trans women (TWs) completed a six-point questionnaire. ONC was asked how many TJ patients they had seen in their career, as well as histopathology/site. Furthermore, the data was extrapolated to account for all clinicians' cumulative years of experience. The questions for TWs were age and where they go if you have a disease or illness. And, do they know any TJ cancer patients?

RESULTS

India's last census (2011) revealed a half-million TJ population. TJ density must be at least 1 million to be comparable to the rest of the world. Hospital databases counted 10,486 patients, with no patient identified as TJ. A total of 37 TJ cancer patients were reported by 28 ONC with an average and collective years of their medical service of 23.1±4.1 and 646 years; distributed in 3 metropolis of 67 million (combined) population (Kolkata, New Delhi, and Mumbai). The average lifetime number of TJ cancer patients/oncologist was 1.3±1.1. Total 12 cases were head neck cancers, with 4 caused by human papillomavirus. The remaining 25 patients have 5 lung, 5 gynecological, 4 breast, 3 brain cancers, 2 soft tissue sarcomas, and 6 cases of unknown origin. The density of 5-year prevalent cancer cases in India is 0.2%, with an estimated 0.007% of TJ cancer patients. TW could not identify any cancer patients in their community.

CONCLUSION

Being transgender is a social taboo in this part of the world. Their legal rights and classification as the third gender are uncommon. TJs are denied access to standard education, mainstream occupations, and social respect. Although the exact number has never been determined, it is estimated that a large proportion (≈90%) of TJ people are forced to choose roadside begging and working as cheap sex workers. There is no clinical reason why TJs should have fewer cancer incidents, they should be more susceptible to cancer due to unhealthy living conditions, unprotected sex, lack of medical care, proper nutrition, and all other factors associated with their very low socioeconomic status. Nonetheless, it's difficult to find single TJ cancer patients in both public and private hospital OPD. They may be unable to access a traditional clinic due to social discrimination, financial constraints, or they may be unwilling to disclose their true sex. Even TJ's do not show up at free public clinics. The disclosure of true sex may be beneficial in obtaining better treatment, but the more prevalent reason is social unacceptability, which can be overcome through proper education and community economic growth.

Genome-wide profiling of prime editor off-target sites in vitro and in vivo using PE-tag

Prime editors have a broad range of potential research and clinical applications. However, methods to delineate their genome-wide editing activities have generally relied on indirect genome-wide editing assessments or the computational prediction of near-cognate sequences. Here we describe a genome-wide approach for the identification of potential prime editor off-target sites, which we call PE-tag. This method relies on the attachment or insertion of an amplification tag at sites of prime editor activity to allow their identification. PE-tag enables genome-wide profiling of off-target sites in vitro using extracted genomic DNA, in mammalian cell lines and in the adult mouse liver. PE-tag components can be delivered in a variety of formats for off-target site detection. Our studies are consistent with the high specificity previously described for prime editor systems, but we find that off-target editing rates are influenced by prime editing guide RNA design. PE-tag represents an accessible, rapid and sensitive approach for the genome-wide identification of prime editor activity and the evaluation of prime editor safety.

PAM-Flexible Genome Editing with an Engineered Chimeric Cas9

CRISPR enzymes require a defined protospacer adjacent motif (PAM) flanking a guide RNA-programmed target site, limiting their sequence accessibility for robust genome editing applications. In this study, we recombine the PAM-interacting domain of SpRY, a broad-targeting Cas9 possessing an NRN > NYN PAM preference, with the N-terminus of Sc++, a Cas9 with simultaneously broad, efficient, and accurate NNG editing capabilities, to generate a chimeric enzyme with highly flexible PAM preference: SpRYc. We demonstrate that SpRYc leverages properties of both enzymes to specifically edit diverse NNN PAMs and disease-related loci for potential therapeutic applications. In total, the unique approaches to generate SpRYc, coupled with its robust flexibility, highlight the power of integrative protein design for Cas9 engineering and motivate downstream editing applications that require precise genomic positioning.

Directed differentiation of human iPSCs to functional ovarian granulosa-like cells via transcription factor overexpression

An in vitro model of human ovarian follicles would greatly benefit the study of female reproduction. Ovarian development requires the combination of germ cells and several types of somatic cells. Among these, granulosa cells play a key role in follicle formation and support for oogenesis. Whereas efficient protocols exist for generating human primordial germ cell-like cells (hPGCLCs) from human induced pluripotent stem cells (hiPSCs), a method of generating granulosa cells has been elusive. Here, we report that simultaneous overexpression of two transcription factors (TFs) can direct the differentiation of hiPSCs to granulosa-like cells. We elucidate the regulatory effects of several granulosa-related TFs and establish that overexpression of NR5A1 and either RUNX1 or RUNX2 is sufficient to generate granulosa-like cells. Our granulosa-like cells have transcriptomes similar to human fetal ovarian cells and recapitulate key ovarian phenotypes including follicle formation and steroidogenesis. When aggregated with hPGCLCs, our cells form ovary-like organoids (ovaroids) and support hPGCLC development from the premigratory to the gonadal stage as measured by induction of DAZL expression. This model system will provide unique opportunities for studying human ovarian biology and may enable the development of therapies for female reproductive health.

Femtomolar detection of SARS-CoV-2 via peptide beacons integrated on a miniaturized TIRF microscope

The novel coronavirus SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) continues to pose a substantial global health threat. Along with vaccines and targeted therapeutics, there is a critical need for rapid diagnostic solutions. In this work, we use computational protein modeling tools to suggest molecular beacon architectures that function as conformational switches for high-sensitivity detection of the SARS-CoV-2 spike protein receptor binding domain (S-RBD). Integrating these beacons on a miniaturized total internal reflection fluorescence (mini-TIRF) microscope, we detect the S-RBD and pseudotyped SARS-CoV-2 with limits of detection in the femtomolar range. We envision that our designed mini-TIRF platform will serve as a robust platform for point-of-care diagnostics for SARS-CoV-2 and future emergent viral threats.

Expanding homogeneous culture of human primordial germ cell-like cells maintaining germline features without serum or feeder layers

In vitro expansion of human primordial germ cell-like cells (hPGCLCs), a pluripotent stem cell-derived PGC model, has proved challenging due to rapid loss of primordial germ cell (PGC)-like identity and limited cell survival/proliferation. Here, we describe long-term culture hPGCLCs (LTC-hPGCLCs), which actively proliferate in a serum-free, feeder-free condition without apparent limit as highly homogeneous diploid cell populations maintaining transcriptomic and epigenomic characteristics of hPGCLCs. Histone proteomics confirmed reduced H3K9me2 and increased H3K27me3 marks in LTC-hPGCLCs compared with induced pluripotent stem cells (iPSCs). LTC-hPGCLCs established from multiple human iPSC clones of both sexes were telomerase positive, senescence-free cells readily passaged with minimal cell death or deviation from the PGC-like identity. LTC-hPGCLCs are capable of differentiating to DAZL-positive M-spermatogonia-like cells in the xenogeneic reconstituted testis (xrTestis) organ culture milieu as well as efficiently producing fully pluripotent embryonic germ cell-like cells in the presence of stem cell factor and fibroblast growth factor 2. Thus, LTC-hPGCLCs provide convenient access to unlimited amounts of high-quality and homogeneous hPGCLCs.

CaSR expression in normal parathyroid and PHPT: new insights into pathogenesis from an autopsy-based study

PURPOSE

Calcium sensing receptor (CaSR), on the surface of normal parathyroid cells, is essential for maintaining serum calcium levels. The normal pattern of CaSR immunostaining remains undefined and is presumptively circumferential. Given the physiological variation in serum calcium, we postulated that CaSR expression could not be uniformly circumferential. Also, cytoplasmic expression has not been evaluated either in normal or pathological tissues. We studied normal parathyroid tissues derived from forensic autopsies and those rimming parathyroid adenomas for membranous and cytoplasmic CaSR immunoexpression. Results were compared with primary hyperparathyroidism (PHPT) to look for any pathogenetic implications.

MATERIALS AND METHODS

We evaluated 34 normal parathyroid tissues from 11 autopsies, 30 normal rims, 45 parathyroid adenoma, 10 hyperplasia, and 7 carcinoma cases. Membranous expression was categorized complete/incomplete and weak/moderate/strong; scored using Her2/Neu and Histo-scores; predominant pattern noted. Cytoplasmic expression was categorized negative/weak/moderate/strong; predominant intensity noted.

RESULTS

Normal autopsy-derived parathyroid tissues were Her2/Neu 3 + , but incomplete membranous staining predominated in 85%. Their immune-scores were significantly more than the cases (p <  < 0.05). The mean histo-score of normal rims was intermediate between the two (p <  < 0.05). Cytoplasmic expression was strong in all autopsy-derived tissues, weak/negative in hyperplasia (100%), moderate in 16% adenomas, and 43% carcinomas.

CONCLUSIONS

Normal autopsy-derived parathyroid tissues showed strong but predominantly incomplete membranous expression. Surface CaSR expression decreased in PHPT and is probably an early event in parathyroid adenoma, seen even in normal rims. Whether there is a defect in CaSR trafficking from the cytoplasm to the cell surface in adenoma and carcinoma needs further evaluation.

MegaGate: A toxin-less gateway molecular cloning tool

Gateway cloning employs the use of the ccdb toxin and has low colony numbers, making it difficult to apply at scale to clone libraries of cDNA vectors. In this protocol, we describe MegaGate, a toxin-less Gateway technology capable of robust cDNA library cloning that is efficient, cheap, and scalable. MegaGate eliminates the ccdb toxin used in Gateway recombinase cloning and instead utilizes meganuclease-mediated digestion to eliminate background vectors during cloning and is 99.8% efficient with high colony numbers. For complete details on the use and execution of this protocol, please refer to Kramme et al. (2021).

An integrated pipeline for mammalian genetic screening

With the recent advancements in genome editing, next-generation sequencing (NGS), and scalable cloning techniques, scientists can now conduct genetic screens at unprecedented levels of scale and precision. With such a multitude of technologies, there is a need for a simple yet comprehensive pipeline to enable systematic mammalian genetic screening. In this study, we develop unique algorithms for target identification and a toxin-less Gateway cloning tool, termed MegaGate, for library cloning which, when combined with existing genetic perturbation methods and NGS-coupled readouts, enable versatile engineering of relevant mammalian cell lines. Our integrated pipeline for sequencing-based target ascertainment and modular perturbation screening (STAMPScreen) can thus be utilized for a host of cell state engineering applications.

Targeted intracellular degradation of SARS-CoV-2 via computationally optimized peptide fusions

The COVID-19 pandemic, caused by the novel coronavirus SARS-CoV-2, has elicited a global health crisis of catastrophic proportions. With only a few vaccines approved for early or limited use, there is a critical need for effective antiviral strategies. In this study, we report a unique antiviral platform, through computational design of ACE2-derived peptides which both target the viral spike protein receptor binding domain (RBD) and recruit E3 ubiquitin ligases for subsequent intracellular degradation of SARS-CoV-2 in the proteasome. Our engineered peptide fusions demonstrate robust RBD degradation capabilities in human cells and are capable of inhibiting infection-competent viral production, thus prompting their further experimental characterization and therapeutic development.

Non-full-length Water-Soluble CXCR4QTY and CCR5QTY Chemokine Receptors: Implication for Overlooked Truncated but Functional Membrane Receptors

It was posited that functionalities of GPCRs require full-length sequences that are negated by residue deletions. Here we report that significantly truncated nfCCR5^QTY and nfCXCR4^QTY still bind native ligands. Receptor-ligand interactions were discovered from yeast 2-hybrid screening and confirmed by mating selection. Two nfCCR5^QTY (SZ218a, SZ190b) and two nfCXCR4^QTY (SZ158a, SZ146a) were expressed in E. coli. Synthesized receptors exhibited α-helical structures and bound respective ligands with reduced affinities. SZ190b and SZ158a were reconverted into non-QTY forms and expressed in HEK293T cells. Reconverted receptors localized on cell membranes and functioned as negative regulators for ligand-induced signaling when co-expressed with full-length receptors. CCR5-SZ190b individually can perform signaling at a reduced level with higher ligand concentration. Our findings provide insight into essential structural components for CCR5 and CXCR4 functionality, while raising the possibility that non-full-length receptors may be resulted from alternative splicing and that pseudo-genes in genomes may be present and functional in living organisms.

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Y2H screening reveals ligand interaction from truncated CXCR4 and CCR5 in QTY form

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Truncated CCR5^QTY and CXCR4^QTY can be produced in E. coli and bind native ligands

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Reconverted receptors localize on membranes and regulate cell signaling in HEK293

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Our finding indicates potential presence and function for truncated receptors

Publisher Correction: An engineered ScCas9 with broad PAM range and high specificity and activity

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

A Cas9 with PAM recognition for adenine dinucleotides

CRISPR-associated (Cas) DNA-endonucleases are remarkably effective tools for genome engineering, but have limited target ranges due to their protospacer adjacent motif (PAM) requirements. We demonstrate a critical expansion of the targetable sequence space for a type II-A CRISPR-associated enzyme through identification of the natural 5\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$^{\prime}$$\end{document}′-NAAN-3\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$^{\prime}$$\end{document}′ PAM preference of Streptococcus macacae Cas9 (SmacCas9). To achieve efficient editing activity, we graft the PAM-interacting domain of SmacCas9 to its well-established ortholog from Streptococcus pyogenes (SpyCas9), and further engineer an increased efficiency variant (iSpyMac) for robust genome editing activity. We establish that our hybrids can target all adenine dinucleotide PAM sequences and possess robust and accurate editing capabilities in human cells.

Protospacer adjacent motif (PAM) requirements limit the target range of CRISPR endonucleases. Here, the authors graft the 5\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$^{\prime}$$\end{document}′-NAAN-3\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$^{\prime}$$\end{document}′ PAM-interacting domain of SmacCas9 onto SpyCas9 to create adenine dinucleotide targeting chimeras.

Minimal PAM specificity of a highly similar SpCas9 ortholog

RNA-guided DNA endonucleases of the CRISPR-Cas system are widely used for genome engineering and thus have numerous applications in a wide variety of fields. CRISPR endonucleases, however, require a specific protospacer adjacent motif (PAM) flanking the target site, thus constraining their targetable sequence space. In this study, we demonstrate the natural PAM plasticity of a highly similar, yet previously uncharacterized, Cas9 from Streptococcus canis (ScCas9) through rational manipulation of distinguishing motif insertions. To this end, we report affinity to minimal 5'-NNG-3' PAM sequences and demonstrate the accurate editing capabilities of the ortholog in both bacterial and human cells. Last, we build an automated bioinformatics pipeline, the Search for PAMs by ALignment Of Targets (SPAMALOT), which further explores the microbial PAM diversity of otherwise overlooked Streptococcus Cas9 orthologs. Our results establish that ScCas9 can be used both as an alternative genome editing tool and as a functional platform to discover novel Streptococcus PAM specificities.

Elevated plasma ferritin in elderly individuals with high neocortical amyloid-β load

Ferritin, an iron storage and regulation protein, has been associated with Alzheimer's disease (AD); however, it has not been investigated in preclinical AD, detected by neocortical amyloid-β load (NAL), before cognitive impairment. Cross-sectional analyses were carried out for plasma and serum ferritin in participants in the Kerr Anglican Retirement Village Initiative in Aging Health cohort. Subjects were aged 65-90 years and were categorized into high and low NAL groups via positron emission tomography using a standard uptake value ratio cutoff=1.35. Ferritin was significantly elevated in participants with high NAL compared with those with low NAL, adjusted for covariates age, sex, apolipoprotein E ɛ4 carriage and levels of C-reactive protein (an inflammation marker). Ferritin was also observed to correlate positively with NAL. A receiver operating characteristic curve based on a logistic regression of the same covariates, the base model, distinguished high from low NAL (area under the curve (AUC)=0.766), but was outperformed when plasma ferritin was added to the base model (AUC=0.810), such that at 75% sensitivity, the specificity increased from 62 to 71% on adding ferritin to the base model, indicating that ferritin is a statistically significant additional predictor of NAL over and above the base model. However, ferritin's contribution alone is relatively minor compared with the base model. The current findings suggest that impaired iron mobilization is an early event in AD pathogenesis. Observations from the present study highlight ferritin's potential to contribute to a blood biomarker panel for preclinical AD.

The clinical utility of cycle of threshold value of GeneXpert MTB/RIF (CBNAAT) and its diagnostic accuracy in pulmonary and extra-pulmonary samples at a tertiary care center in India

BACKGROUND

There are knowledge gaps in the in-depth analysis of the most promising and robust diagnostic tool, GeneXpert MTB/RIF (CBNAAT). The cycle of threshold (CT) value of the CBNAAT test and its clinical implications has not been explored much.

AIMS AND OBJECTIVES

The study aimed at (a) estimating the diagnostic accuracy and incremental yield of Xpert MTB/RIF in various specimens (b) establishing the association between CT value category (high, medium, low, very low) and culture time-to-positivity (TTP).

METHODS

A total of 1000 samples, both pulmonary and extra-pulmonary were collected from presumptive TB cases in a large tertiary care hospital. Sensitivity and specificity of CBNAAT was calculated with culture as the gold standard. The association of CT value with culture TTP was also studied.

RESULTS

The overall sensitivity of CBNAAT was 88.5%, with bronchial washing specimen being the most sensitive (92.3%) and pleural fluid being the least (66.7%). In smear negative individuals, the sensitivity of CBNAAT was 80.9%. The additional yield of CBNAAT over smear microscopy was 10.9%. It was observed that as we move from high to very low CT category, culture positivity decreases significantly (p<0.001), whereas time taken for culture growth increases (p<0.001).

CONCLUSION

CBNAAT is a robust test for accurate diagnosis of tuberculosis both pulmonary and extra-pulmonary, smear negative as well, especially in resource-limited settings. The correlation between CT value and culture TTP has potential in predicting bacillary load, though further studies are required.

Association of Ambient Air Quality with Male's Pulmonary Function in Kolkata City, India

BACKGROUND

Kolkata is one of the polluted metropolitan cities in India where health effects of air pollution are raising serious concern.

OBJECTIVES

Purpose of the present study was to analyze association between levels of air pollutants and pulmonary function of adult males living in two different air pollutant zones of Kolkata.

METHODS

Air pollution data of two ambient air quality monitoring stations located at Rabindrabharati and Victoria Memorial was collected from West Bengal Pollution Control Board, Kolkata for the period from January to March 2012. Study was conducted on 200 males (17-22 yrs), subdivided into two groups from living within 3 km radius of that two monitoring stations. They were investigated for their spirometric lung functions following method and technique recommended by American Thoracic Society. Results were expressed as mean ± SD and independent samples T test was conducted to compare between groups.

RESULTS

PM10, SO2 concentrations were significantly higher in Rabindrabharati zone, whereas no significant differences were noted in NO2 and CO concentrations though values were higher at Rabindrabharati than Victoria Memorial. FVC, FEV1, FEF25-75%, MVV were significantly lower in males of Rabindrabharati zone.

CONCLUSION

Exposure to high air pollutant concentration might be associated with reduced pulmonary function in adult males.

PD-1 alters T-cell metabolic reprogramming by inhibiting glycolysis and promoting lipolysis and fatty acid oxidation

During activation, T cells undergo metabolic reprogramming, which imprints distinct functional fates. We determined that on PD-1 ligation, activated T cells are unable to engage in glycolysis or amino acid metabolism but have an increased rate of fatty acid β-oxidation (FAO). PD-1 promotes FAO of endogenous lipids by increasing expression of CPT1A, and inducing lipolysis as indicated by elevation of the lipase ATGL, the lipolysis marker glycerol and release of fatty acids. Conversely, CTLA-4 inhibits glycolysis without augmenting FAO, suggesting that CTLA-4 sustains the metabolic profile of non-activated cells. Because T cells utilize glycolysis during differentiation to effectors, our findings reveal a metabolic mechanism responsible for PD-1-mediated blockade of T-effector cell differentiation. The enhancement of FAO provides a mechanistic explanation for the longevity of T cells receiving PD-1 signals in patients with chronic infections and cancer, and for their capacity to be reinvigorated by PD-1 blockade.

Activation of T cells results in metabolic reprogramming to favour glycolysis. Here, Patsoukis et al. show that the surface receptor PD-1 inhibits glycolysis and increases the metabolism of lipids, providing a potential mechanism for the blockade of T effector functions but also for the longevity accompanying T cell exhaustion.

pH-dependent size and structural transition in P123 micelle induced gold nanoparticles

The transition of the structure and size of AuNPs at a pH value around 9.5, from slowly grown, well-faceted, large (≫19 nm), less uniform and near connected to fast grown, near symmetrical, small (<19 nm), more uniform and well-separated, is observed.

Malignant Leiomyoblastoma: An Incidental Diagnosis

DOI: http://www.dx.doi.org/10.3126/njog.v7i2.11147   Nepal Journal of Obstetrics and Gynaecology / Vol 7 / No. 2 / Issue 14 / July-Dec, 2012 / 55-56