bims-pideca 2022-12-18 papers

bims-pideca

Biomed News

on Class IA PI3K signalling in development and cancer

Issue of 2022–12–18
nineteen papers selected by
Ralitsa Radostinova Madsen, University College London

Role of Tumor Suppressor PTEN and Its Regulation in Malignant Transformation of Endometrium.
mTORC2 inhibition improves morphological effects of PTEN loss, but does not correct synaptic dysfunction or prevent seizures.
Binding of active Ras and its mutants to the Ras binding domain of PI-3-kinase: A quantitative approach to KD measurements.
Genome Editing of Pik3cd Impedes Abnormal Retinal Angiogenesis.
Delivery of Active AKT1 to Human Cells.
Endosomal lipid signaling reshapes the endoplasmic reticulum to control mitochondrial function.
Capivasertib Doubles PFS in Some Breast Cancers.
Efficient simultaneous double DNA knock-in in murine embryonic stem cells by CRISPR/Cas9 ribonucleoprotein-mediated circular plasmid targeting for generating gene-manipulated mice.
Correlated gene modules uncovered by high-precision single-cell transcriptomics.
An AAA-ATPase links mitochondrial division with DNA nucleoids.
Pharmacologic Inhibition of SHP2 Blocks Both PI3K and MEK Signaling in Low-epiregulin HNSCC via GAB1.
Insulin-like Growth Factor Binding Protein 3 Increases Mouse Preimplantation Embryo Cleavage Rate by Activation of IGF1R and EGFR Independent of IGF1 Signalling.
Engineered cell entry links receptor biology with single-cell genomics.
Upregulation of PIK3IP1 monitors the anti-cancer activity of PI3Kα inhibitors in gastric cancer cells.
Exploring functional protein covariation across single cells using nPOP.
Human genetic diversity alters off-target outcomes of therapeutic gene editing.
Generating colorblind-friendly scatter plots for single-cell data.
A Fast and Reliable Method to Generate Pure, Single Cell-derived Clones of Mammalian Cells.
MSstatsPTM: Statistical relative quantification of post-translational modifications in bottom-up mass spectrometry-based proteomics.

Biochemistry (Mosc). 2022 Nov;87(11): 1310-1326

Role of Tumor Suppressor PTEN and Its Regulation in Malignant Transformation of Endometrium.

Alina M Perevalova, Vyacheslav S Kobelev, Virab G Sisakyan, Lyudmila F Gulyaeva, Vladimir O Pustylnyak.

  Tumor-suppressive effects of PTEN are well-known, but modern evidence suggest that they are not limited to its ability to inhibit pro-oncogenic PI3K/AKT signaling pathway. Features of PTEN structure facilitate its interaction with substrates of different nature and display its activity in various ways both in the cytoplasm and in cell nuclei, which makes it possible to take a broader look at its ability to suppress tumor growth. The possible mechanisms of the loss of PTEN effects are also diverse - PTEN can be regulated at many levels, leading to change in the protein activity or its amount in the cell, while their significance for the development of malignant tumors has yet to be studied. Here we summarize the current data on the PTEN structure, its functions and changes in its regulatory mechanisms during malignant transformation of the cells, focusing on one of the most sensitive to the loss of PTEN types of malignant tumors - endometrial cancer.

Keywords:  PTEN; endometrial cancer; endometrial hyperplasia; gene regulation

DOI:  https://doi.org/10.1134/S0006297922110104
J Neurosci. 2022 Dec 16. pii: JN-RM-1354-22. [Epub ahead of print]

mTORC2 inhibition improves morphological effects of PTEN loss, but does not correct synaptic dysfunction or prevent seizures.

Erin R Cullen, Kamran Tariq, Amy N Shore, Bryan W Luikart, Matthew C Weston.

Hyperactivation of PI3K/PTEN-mTOR signaling during neural development is associated with focal cortical dysplasia (FCD), autism, and epilepsy. mTOR can signal through two major hubs, mTORC1 and mTORC2, both of which are hyperactive following PTEN loss of function (LOF). Here, we tested the hypothesis that genetic inactivation of the mTORC2 complex via deletion of Rictor is sufficient to rescue morphological and electrophysiological abnormalities in the dentate gyrus caused by PTEN loss, as well as generalized seizures. An established, early postnatal mouse model of PTEN loss in male and female mice showed spontaneous seizures that were not prevented by mTORC2 inactivation. This lack of rescue occurred despite the normalization or amelioration of many morphological and electrophysiological phenotypes. However, increased excitatory connectivity proximal to dentate gyrus granule neuron somas was not normalized by mTORC2 inactivation. Further studies demonstrated that, although mTORC2 inactivation largely rescued the dendritic arbor overgrowth caused by PTEN LOF, it increased synaptic strength and caused additional impairments of presynaptic function. These results suggest that a constrained increase in excitatory connectivity and co-occurring synaptic dysfunction is sufficient to generate seizures downstream of PTEN LOF, even in the absence of characteristic changes in morphological properties.SIGNIFICANCE STATEMENT:Homozygous deletion of the Pten gene in neuronal subpopulations in the mouse serves as a valuable model of epilepsy caused by mTOR hyperactivation. To better understand the physiological mechanisms downstream of Pten loss that cause epilepsy, as well as the therapeutic potential of targeted gene therapies, we tested whether genetic inactivation of the mTORC2 complex could improve the cellular, synaptic, and in vivo effects of Pten loss in the dentate gyrus. We found that mTORC2 inhibition improved or rescued all morphological effects of Pten loss in the dentate gyrus, but synaptic changes and seizures persisted. These data suggest that synaptic dysfunction can drive epilepsy caused by hyperactivation of PI3K/PTEN-mTOR, and that future therapies should focus on this mechanistic link.

DOI: https://doi.org/10.1523/JNEUROSCI.1354-22.2022
Anal Biochem. 2022 Dec 13. pii: S0003-2697(22)00479-1. [Epub ahead of print] 115019

Binding of active Ras and its mutants to the Ras binding domain of PI-3-kinase: A quantitative approach to KD measurements.

Ian Fleming, Jonathan P Hannan, George Hayden Swisher, Corey D Tesdahl, Justin G Martyr, Nicholas J Cordaro, Annette H Erbse, Joseph J Falke.

  Ras family GTPases (H/K/N-Ras) modulate numerous effectors, including the lipid kinase PI3K (phosphatidylinositol-3-kinase) that generates growth signal lipid PIP3 (phosphatidylinositol-3,4,5-triphosphate). Active GTP-Ras binds PI3K with high affinity, thereby stimulating PIP3 production. We hypothesize the affinity of this binding interaction could be significantly increased or decreased by Ras mutations at PI3K contact positions, with clinical implications since some Ras mutations at PI3K contact positions are disease-linked. To enable tests of this hypothesis, we have developed an approach combining UV spectral deconvolution, HPLC, and microscale thermophoresis to quantify the KD for binding. The approach measures the total Ras concentration, the fraction of Ras in the active state, and the affinity of active Ras binding to its docking site on PI3K Ras binding domain (RBD) in solution. The approach is illustrated by KD measurements for the binding of active H-Ras and representative mutants, each loaded with GTP or GMPPNP, to PI3Kγ RBD. The findings demonstrate that quantitation of the Ras activation state increases the precision of KD measurements, while also revealing that Ras mutations can increase (Q25L), decrease (D38E, Y40C), or have no effect (G13R) on PI3K binding affinity. Significant Ras affinity changes are predicted to alter PI3K regulation and PIP3 growth signals.

Keywords:  GMPPN; GMPPNP; GTP; HRas GTPase; Protein-nucleotide complex; Ras small G protein

DOI:  https://doi.org/10.1016/j.ab.2022.115019
Hum Gene Ther. 2022 Dec 14.

Genome Editing of Pik3cd Impedes Abnormal Retinal Angiogenesis.

Wenyi Wu, Gaoen Ma, Hui Qi, Lijun Dong, Fang Chen, Yun Wang, Xingxing Mao, Xiaoqing Guo, Jing Cui, Joanne Matsubara, Bart Vanhaesebroeck, Xiaohe Yan, Guoming Zhao, Shaochong Zhang, Hetian Lei.

Abnormal angiogenesis is associated with myriad human diseases including proliferative diabetic retinopathy. Signaling transduction via phosphoinositide 3-kinases (PI3Ks) plays a critical role in angiogenesis. Herein, we showed that p110δ, the catalytic subunit of PI3Kδ, was highly expressed in pathological retinal vascular endothelial cells (ECs) in a mouse model of oxygen-induced retinopathy (OIR) and in fibrovascular membranes from patients with proliferative diabetic retinopathy. To explore novel intervention with PI3Kδ expression, we developed a recombinant dual adeno-associated viral (rAAV) system for delivering CRISPR/Cas9 in which Streptococcus pyogenes (Sp) Cas9 expression was driven by an endothelial specific promoter of intercellular adhesion molecule 2 (pICAM2) to edit genomic Pik3cd, the gene encoding p110δ. We then demonstrated that infection of cultured mouse vascular endothelial cells with the dual rAAV1s of rAAV1-pICAM2-SpCas9 and rAAV1-SpGuide targeting genomic Pik3cd resulted in 80% DNA insertion/deletion in the locus of genomic Pik3cd and 70% depletion of p110δ expression. Furthermore, we showed that in the mouse model of OIR editing retinal Pik3cd with the dual rAAV1s resulted in not only a significant decrease in p110δ expression, and Akt activation, but also a dramatic reduction in pathological retinal angiogenesis. These findings reveal that Pik3cd editing is a novel approach to treating abnormal retinal angiogenesis.

DOI: https://doi.org/10.1089/hum.2022.079
Cells. 2022 Nov 29. pii: 3834. [Epub ahead of print]11(23):

Delivery of Active AKT1 to Human Cells.

Tarana Siddika, Nileeka Balasuriya, Mallory I Frederick, Peter Rozik, Ilka U Heinemann, Patrick O'Donoghue.

  Protein kinase B (AKT1) is a serine/threonine kinase and central transducer of cell survival pathways. Typical approaches to study AKT1 biology in cells rely on growth factor or insulin stimulation that activates AKT1 via phosphorylation at two key regulatory sites (Thr308, Ser473), yet cell stimulation also activates many other kinases. To produce cells with specific AKT1 activity, we developed a novel system to deliver active AKT1 to human cells. We recently established a method to produce AKT1 phospho-variants from Escherichia coli with programmed phosphorylation. Here, we fused AKT1 with an N-terminal cell penetrating peptide tag derived from the human immunodeficiency virus trans-activator of transcription (TAT) protein. The TAT-tag did not alter AKT1 kinase activity and was necessary and sufficient to rapidly deliver AKT1 protein variants that persisted in human cells for 24 h without the need to use transfection reagents. TAT-pAKT1T308 induced selective phosphorylation of the known AKT1 substrate GSK-3α, but not GSK-3β, and downstream stimulation of the AKT1 pathway as evidenced by phosphorylation of ribosomal protein S6 at Ser240/244. The data demonstrate efficient delivery of AKT1 with programmed phosphorylation to human cells, thus establishing a cell-based model system to investigate signaling that is dependent on AKT1 activity.

Keywords:  cell penetrating peptide; cellular signaling; kinase; phosphoinositide-dependent kinase (PDK1); protein kinase B (AKT1); recombinant protein; trans-activator of transcription (TAT)

DOI:  https://doi.org/10.3390/cells11233834
Science. 2022 Dec 16. 378(6625): eabq5209

Endosomal lipid signaling reshapes the endoplasmic reticulum to control mitochondrial function.

Wonyul Jang, Dmytro Puchkov, Paula Samsó, YongTian Liang, Michal Nadler-Holly, Stephan J Sigrist, Ulrich Kintscher, Fan Liu, Kamel Mamchaoui, Vincent Mouly, Volker Haucke.

Cells respond to fluctuating nutrient supply by adaptive changes in organelle dynamics and in metabolism. How such changes are orchestrated on a cell-wide scale is unknown. We show that endosomal signaling lipid turnover by MTM1, a phosphatidylinositol 3-phosphate [PI(3)P] 3-phosphatase mutated in X-linked centronuclear myopathy in humans, controls mitochondrial morphology and function by reshaping the endoplasmic reticulum (ER). Starvation-induced endosomal recruitment of MTM1 impairs PI(3)P-dependent contact formation between tubular ER membranes and early endosomes, resulting in the conversion of ER tubules into sheets, the inhibition of mitochondrial fission, and sustained oxidative metabolism. Our results unravel an important role for early endosomal lipid signaling in controlling ER shape and, thereby, mitochondrial form and function to enable cells to adapt to fluctuating nutrient environments.

DOI: https://doi.org/10.1126/science.abq5209
Cancer Discov. 2022 Dec 12. OF1

Capivasertib Doubles PFS in Some Breast Cancers.

In the phase III CAPItello-291 study, the combination of fulvestrant and capivasertib more than doubled progression-free survival compared with fulvestrant alone in patients with hormone receptor-positive, HER2-negative breast cancer who have developed resistance to aromatase inhibitors and CDK4/6 inhibitors. The AKT inhibitor could become a treatment option for these patients.

DOI: https://doi.org/10.1158/2159-8290.CD-NB2022-0078
Sci Rep. 2022 Dec 13. 12(1): 21558

Efficient simultaneous double DNA knock-in in murine embryonic stem cells by CRISPR/Cas9 ribonucleoprotein-mediated circular plasmid targeting for generating gene-manipulated mice.

Manabu Ozawa, Jumpei Taguchi, Kento Katsuma, Yu Ishikawa-Yamauchi, Mio Kikuchi, Reiko Sakamoto, Yasuhiro Yamada, Masahito Ikawa.

Gene targeting of embryonic stem (ES) cells followed by chimera production has been conventionally used for developing gene-manipulated mice. Although direct knock-in (KI) using murine zygote via CRISPR/Cas9-mediated genome editing has been reported, ES cell targeting still has merits, e.g., high throughput work can be performed in vitro. In this study, we first compared the KI efficiency of mouse ES cells with CRISPR/Cas9 expression vector and ribonucleoprotein (RNP), and confirmed that KI efficiency was significantly increased by using RNP. Using CRISPR/Cas9 RNP and circular plasmid with homologous arms as a targeting vector, knock-in within ES cell clones could be obtained efficiently without drug selection, thus potentially shortening the vector construction or cell culture period. Moreover, by incorporating a drug-resistant cassette into the targeting vectors, double DNA KI can be simultaneously achieved at high efficiency by a single electroporation. This technique will help to facilitate the production of genetically modified mouse models that are fundamental for exploring topics related to human and mammalian biology.

DOI: https://doi.org/10.1038/s41598-022-26107-z
Proc Natl Acad Sci U S A. 2022 Dec 20. 119(51): e2206938119

Correlated gene modules uncovered by high-precision single-cell transcriptomics.

Alec R Chapman, David F Lee, Wenting Cai, Wenping Ma, Xiang Li, Wenjie Sun, Xiaoliang Sunney Xie.

  Correlations in gene expression are used to infer functional and regulatory relationships between genes. However, correlations are often calculated across different cell types or perturbations, causing genes with unrelated functions to be correlated. Here, we demonstrate that correlated modules can be better captured by measuring correlations of steady-state gene expression fluctuations in single cells. We report a high-precision single-cell RNA-seq method called MALBAC-DT to measure the correlation between any pair of genes in a homogenous cell population. Using this method, we were able to identify numerous cell-type specific and functionally enriched correlated gene modules. We confirmed through knockdown that a module enriched for p53 signaling predicted p53 regulatory targets more accurately than a consensus of ChIP-seq studies and that steady-state correlations were predictive of transcriptome-wide response patterns to perturbations. This approach provides a powerful way to advance our functional understanding of the genome.

Keywords:  correlated gene modules; scRNA-seq; single cell; transcriptomics

DOI:  https://doi.org/10.1073/pnas.2206938119
Proc Natl Acad Sci U S A. 2022 Dec 20. 119(51): e2217949119

An AAA-ATPase links mitochondrial division with DNA nucleoids.

Nelson Yeung, Miho Iijima, Hiromi Sesaki.

DOI: https://doi.org/10.1073/pnas.2217949119
Cancer Res Commun. 2022 Sep;2(9): 1061-1074

Pharmacologic Inhibition of SHP2 Blocks Both PI3K and MEK Signaling in Low-epiregulin HNSCC via GAB1.

Richard Kurupi, Konstantinos V Floros, Sheeba Jacob, Ayesha T Chawla, Jinyang Cai, Bin Hu, Madhavi Puchalapalli, Colin M Coon, Rishabh Khatri, Giovanna Stein Crowther, Regina K Egan, Ellen Murchie, Patricia Greninger, Krista M Dalton, Maninderjit S Ghotra, Sosipatros A Boikos, Jennifer E Koblinski, Hisashi Harada, Yue Sun, Iain M Morgan, Devraj Basu, Mikhail G Dozmorov, Cyril H Benes, Anthony C Faber.

  Preclinical and clinical studies have evidenced that effective targeted therapy treatment against receptor tyrosine kinases (RTKs) in different solid tumor paradigms is predicated on simultaneous inhibition of both the PI3K and MEK intracellular signaling pathways. Indeed, re-activation of either pathway results in resistance to these therapies. Recently, oncogenic phosphatase SHP2 inhibitors have been developed with some now reaching clinical trials. To expand on possible indications for SHP099, we screened over 800 cancer cell lines covering over 25 subsets of cancer. We found HNSCC was the most sensitive adult subtype of cancer to SHP099. We found that, in addition to the MEK pathway, SHP2 inhibition blocks the PI3K pathway in sensitive HNSCC, resulting in downregulation of mTORC signaling and anti-tumor effects across several HNSCC mouse models, including an HPV+ patient-derived xenograft (PDX). Importantly, we found low levels of the RTK ligand epiregulin identified HNSCCs that were sensitive to SHP2 inhibitor, and, adding exogenous epiregulin mitigated SHP099 efficacy. Mechanistically, epiregulin maintained SHP2-GAB1 complexes in the presence of SHP2 inhibition, preventing downregulation of the MEK and PI3K pathways. We demonstrate HNSCCs were highly dependent on GAB1 for their survival and knockdown of GAB1 is sufficient to block the ability of epiregulin to rescue MEK and PI3K signaling. These data connect the sensitivity of HNSCC to SHP2 inhibitors and to a broad reliance on GAB1-SHP2, revealing an important and druggable signaling axis. Overall, SHP2 inhibitors are being heavily developed and may have activity in HNSCCs, and in particular those with low levels of epiregulin.

Keywords:  Epiregulin; Head and neck squamous cell carcinoma; SHP099; SHP2; Targeted therapy

DOI:  https://doi.org/10.1158/2767-9764.crc-21-0137
Cells. 2022 Nov 24. pii: 3762. [Epub ahead of print]11(23):

Insulin-like Growth Factor Binding Protein 3 Increases Mouse Preimplantation Embryo Cleavage Rate by Activation of IGF1R and EGFR Independent of IGF1 Signalling.

Charmaine J Green, Miriam Span, Monique H Rayhanna, Marisa Perera, Margot L Day.

  The viability of embryos cultured in vitro is poor compared to those that develop in vivo. The lack of maternally derived growth factors in vitro may contribute to this problem. Insulin-like growth factor binding protein 3 (IGFBP3) is one such growth factor that has been identified in the maternal reproductive system. This study examined the role of autocrine and exogenous IGFBP3 in mouse preimplantation embryos. Embryos expressed IGFBP3 across all stages of preimplantation development, and addition of exogenous IGFBP3 to embryo culture media increased the rate of development to the 2-, 4-, 5-, and 8-cell stages. Addition of inhibitors of the IGF1 and EGF receptors prevented this IGFBP3-mediated improvement in developmental rate, but the effect was not cumulative, indicating that both receptors are transactivated downstream of IGFBP3 as part of the same signalling pathway. Acute exposure to IGFBP3 increased phosphorylation of Akt and rps6 in 4-8 cell embryos, suggesting activation of the PI3-kinase/Akt pathway downstream of the IGF1 and EGFR receptors to promote cell proliferation and survival. In conclusion, addition of IGFBP3 to embryo culture media increases early cleavage rates independent of IGF1 signalling and therefore, IGFBP3 addition to IVF culture media should be considered.

Keywords:  insulin-like growth factor 1; insulin-like growth factor binding protein 3; mice; preimplantation embryo

DOI:  https://doi.org/10.3390/cells11233762
Cell. 2022 Dec 07. pii: S0092-8674(22)01460-X. [Epub ahead of print]

Engineered cell entry links receptor biology with single-cell genomics.

Bingfei Yu, Quanming Shi, Julia A Belk, Kathryn E Yost, Kevin R Parker, Rui Li, Betty B Liu, Huang Huang, Daniel Lingwood, William J Greenleaf, Mark M Davis, Ansuman T Satpathy, Howard Y Chang.

  Cells communicate with each other via receptor-ligand interactions. Here, we describe lentiviral-mediated cell entry by engineered receptor-ligand interaction (ENTER) to display ligand proteins, deliver payloads, and record receptor specificity. We optimize ENTER to decode interactions between T cell receptor (TCR)-MHC peptides, antibody-antigen, and other receptor-ligand pairs. A viral presentation strategy allows ENTER to capture interactions between B cell receptor and any antigen. We engineer ENTER to deliver genetic payloads to antigen-specific T or B cells to selectively modulate cellular behavior in mixed populations. Single-cell readout of ENTER by RNA sequencing (ENTER-seq) enables multiplexed enumeration of antigen specificities, TCR clonality, cell type, and states of individual T cells. ENTER-seq of CMV-seropositive patient blood samples reveals the viral epitopes that drive effector memory T cell differentiation and inter-clonal vs. intra-clonal phenotypic diversity targeting the same epitope. ENTER technology enables systematic discovery of receptor specificity, linkage to cell fates, and antigen-specific cargo delivery.

Keywords:  B cell receptor; T cell receptor; antigen specificity; ligand-receptor pairs; single-cell multiomics; targeted cargo delivery; viral display; virus-like particle

DOI:  https://doi.org/10.1016/j.cell.2022.11.016
Biochem Pharmacol. 2022 Dec 12. pii: S0006-2952(22)00475-0. [Epub ahead of print] 115380

Upregulation of PIK3IP1 monitors the anti-cancer activity of PI3Kα inhibitors in gastric cancer cells.

Xu-Bin Ma, Yang Wang, Ying-Jie Jia, Ya-Jie Liu, Ying-Qi Tian, Ying Liu, Gui-Qin Hou, Yi-Chao Xu, Hong-Min Liu.

  Gastric cancer remains one of the most malignant cancers in the world. The target-based drugs approved by FDA for gastric cancer treatment includes only three targets and benefit a small portion of gastric cancer patients. PIK3CA, a confirmed oncogene, mutates in 7-25% gastric cancer patients. PI3Kα inhibitor BYL719 has been approved for treating specific breast cancer. However, there is no comprehensive study about PI3Kα inhibitor in gastric cancer. In this study, we found pharmacological inhibition or knockdown of PI3Kα effectively inhibited the proliferation of partial gastric cancer cells. Then, we systematically explored the potential biomarkers for predicting or monitoring treatment response according to previous reports and found that basal expression of several receptor tyrosine kinases was related with the sensitivity of gastric cancer cells to BYL719. Next, RNA-seq technique was utilized and showed that BYL719 inhibited Myc targets V2 gene set in sensitive gastric cancer cells, and western blotting further verified that c-Myc was only inhibited in sensitive gastric cancer cells. More importantly, we firstly found BYL719 significantly elevated the expression of PIK3IP1 in sensitive gastric cancer cells, which was also observed in NCI-N87 cell derived xenograft mice models. Meanwhile, knockdown of PIK3IP1 partially rescued the cell growth inhibited by BYL719 in sensitive gastric cancer cells, suggesting the important role of PIK3IP1 in the antitumor activity of BYL719. In conclusion, our study provides biological evidence that PI3Kα is a promising target in specific gastric cancer and the elevation of PIK3IP1 could supply as a biomarker that monitoring treatment response.

Keywords:  BYL719; Drug sensitivity; Gastric cancer; PI3Kα; PIK3IP1

DOI:  https://doi.org/10.1016/j.bcp.2022.115380
Genome Biol. 2022 Dec 16. 23(1): 261

Exploring functional protein covariation across single cells using nPOP.

Andrew Leduc, R Gray Huffman, Joshua Cantlon, Saad Khan, Nikolai Slavov.

   BACKGROUND: Many biological processes, such as cell division cycle and drug resistance, are reflected in protein covariation across single cells. This covariation can be quantified and interpreted by single-cell mass spectrometry with sufficiently high throughput and accuracy.
RESULTS: Here, we describe nPOP, a method that enables simultaneous sample preparation of thousands of single cells, including lysing, digesting, and labeling individual cells in volumes of 8-20 nl. nPOP uses piezo acoustic dispensing to isolate individual cells in 300 pl volumes and performs all subsequent sample preparation steps in small droplets on a fluorocarbon-coated glass slide. Protein covariation analysis identifies cell cycle dynamics that are similar and dynamics that differ between cell types, even within subpopulations of melanoma cells delineated by markers for drug resistance priming. Melanoma cells expressing these markers accumulate in the G1 phase of the cell cycle, display distinct protein covariation across the cell cycle, accumulate glycogen, and have lower abundance of glycolytic enzymes. The non-primed melanoma cells exhibit gradients of protein abundance, suggesting transition states. Within this subpopulation, proteins functioning in oxidative phosphorylation covary with each other and inversely with proteins functioning in glycolysis. This protein covariation suggests divergent reliance on energy sources and its association with other biological functions. These results are validated by different mass spectrometry methods.
CONCLUSIONS: nPOP enables flexible, automated, and highly parallelized sample preparation for single-cell proteomics. This allows for quantifying protein covariation across thousands of single cells and revealing functionally concerted biological differences between closely related cell states. Support for nPOP is available at https://scp.slavovlab.net/nPOP .

Keywords:  Cell division cycle; Drug resistance; Protein covariation; Sample preparation; Single cell; Single-cell proteomics

DOI:  https://doi.org/10.1186/s13059-022-02817-5
Nat Genet. 2022 Dec 15.

Human genetic diversity alters off-target outcomes of therapeutic gene editing.

Samuele Cancellieri, Jing Zeng, Linda Yingqi Lin, Manuel Tognon, My Anh Nguyen, Jiecong Lin, Nicola Bombieri, Stacy A Maitland, Marioara-Felicia Ciuculescu, Varun Katta, Shengdar Q Tsai, Myriam Armant, Scot A Wolfe, Rosalba Giugno, Daniel E Bauer, Luca Pinello.

CRISPR gene editing holds great promise to modify DNA sequences in somatic cells to treat disease. However, standard computational and biochemical methods to predict off-target potential focus on reference genomes. We developed an efficient tool called CRISPRme that considers single-nucleotide polymorphism (SNP) and indel genetic variants to nominate and prioritize off-target sites. We tested the software with a BCL11A enhancer targeting guide RNA (gRNA) showing promise in clinical trials for sickle cell disease and β-thalassemia and found that the top candidate off-target is produced by an allele common in African-ancestry populations (MAF 4.5%) that introduces a protospacer adjacent motif (PAM) sequence. We validated that SpCas9 generates strictly allele-specific indels and pericentric inversions in CD34+ hematopoietic stem and progenitor cells (HSPCs), although high-fidelity Cas9 mitigates this off-target. This report illustrates how genetic variants should be considered as modifiers of gene editing outcomes. We expect that variant-aware off-target assessment will become integral to therapeutic genome editing evaluation and provide a powerful approach for comprehensive off-target nomination.

DOI: https://doi.org/10.1038/s41588-022-01257-y
Elife. 2022 Dec 16. pii: e82128. [Epub ahead of print]11

Generating colorblind-friendly scatter plots for single-cell data.

Tejas Guha, Elana J Fertig, Atul Deshpande.

  Reduced-dimension or spatial in situ scatter plots are widely employed in bioinformatics papers analyzing single-cell data to present phenomena or cell-conditions of interest in cell groups. When displaying these cell groups, color is frequently the only graphical cue used to differentiate them. However, as the complexity of the information presented in these visualizations increases, the usefulness of color as the only visual cue declines, especially for the sizable readership with color-vision deficiencies (CVDs). In this paper, we present scatterHatch, an R package that creates easily interpretable scatter plots by redundant coding of cell groups using colors as well as patterns. We give examples to demonstrate how the scatterHatch plots are more accessible than simple scatter plots when simulated for various types of CVDs.

Keywords:  genetics; genomics; none

DOI:  https://doi.org/10.7554/eLife.82128
Bio Protoc. 2022 Aug 20. pii: e4490. [Epub ahead of print]12(16):

A Fast and Reliable Method to Generate Pure, Single Cell-derived Clones of Mammalian Cells.

Zhe Han, Bindhu K Madhavan, Serap Kaymak, Peter Nawroth, Varun Kumar.

  Stable cell cloning is an essential aspect of biological research. All advanced genome editing tools rely heavily on stable, pure, single cell-derived clones of genetically engineered cells. For years, researchers have depended on single-cell dilutions seeded in 96- or 192-well plates, followed by microscopic exclusion of the wells seeded with more than or without a cell. This method is not just laborious, time-consuming, and uneconomical but also liable to unintentional error in identifying the wells seeded with a single cell. All these disadvantages may increase the time needed to generate a stable clone. Here, we report an easy-to-follow and straightforward method to conveniently create pure, stable clones in less than half the time traditionally required. Our approach utilizes cloning cylinders with non-toxic tissue-tek gel, commonly used for immobilizing tissues for sectioning, followed by trypsinization and screening of the genome-edited clones. Our approach uses minimal cell handling steps, thus decreasing the time invested in generating the pure clones effortlessly and economically. Graphical abstract: A schematic comparison showing the traditional dilution cloning and the method described here. Here, a well-separated colony (in the green box) must be preferred over the colonies not well separated (in the red box).

Keywords:   Cell culture ; Plasmid ; Stable mammalian cell clones ; Tissue-tek ; Transfection

DOI:  https://doi.org/10.21769/BioProtoc.4490
Mol Cell Proteomics. 2022 Dec 07. pii: S1535-9476(22)00285-7. [Epub ahead of print] 100477

MSstatsPTM: Statistical relative quantification of post-translational modifications in bottom-up mass spectrometry-based proteomics.

Devon Kohler, Tsung-Heng Tsai, Erik Verschueren, Ting Huang, Trent Hinkle, Lilian Phu, Meena Choi, Olga Vitek.

Liquid chromatography coupled with bottom up mass spectrometry (LC-MS/MS)-based proteomics is increasingly used to detect changes in post-translational modifications (PTMs) in samples from different conditions. Analysis of data from such experiments faces numerous statistical challenges. These include the low abundance of modified proteoforms, the small number of observed peptides that span modification sites, and confounding between changes in the abundance of PTM and the overall changes in the protein abundance. Therefore, statistical approaches for detecting differential PTM abundance must integrate all the available information pertaining to a PTM site, and consider all the relevant sources of confounding and variation. In this manuscript we propose such a statistical framework, which is versatile, accurate, and leads to reproducible results. The framework requires an experimental design, which quantifies, for each sample, both peptides with post-translational modifications and peptides from the same proteins with no modification sites. The proposed framework supports both label-free and tandem mass tag (TMT)-based LC-MS/MS acquisitions. The statistical methodology separately summarizes the abundances of peptides with and without the modification sites, by fitting separate linear mixed effects models appropriate for the experimental design. Next, model-based inferences regarding the PTM and the protein-level abundances are combined to account for the confounding between these two sources. Evaluations on computer simulations, a spike-in experiment with known ground truth, and three biological experiments with different organisms, modification types and data acquisition types demonstrate the improved fold change estimation and detection of differential PTM abundance, as compared to currently used approaches. The proposed framework is implemented in the free and open-source R/Bioconductor package MSstatsPTM.

DOI: https://doi.org/10.1016/j.mcpro.2022.100477