bluuebunny/crossref_metadata_2025 huggingface dataset:
In vivo kinetics of early, non-random methylome and transcriptome changes induced by DNA-hypomethylating treatment in primary AML blasts
Authors: Greve Gabriele , Andrieux Geoffroy , Schlosser Pascal , Blagitko-Dorfs Nadja , Rehman Usama-Ur , Ma Tobias , Pfeifer Dietmar , Heil Gerhard , Neubauer Andreas , Krauter Jürgen , Heuser Michael , Salih Helmut R. , Döhner Konstanze , Döhner Hartmut , Hackanson Björn , Boerries Melanie , Lübbert Michael
Published: April 2023

Despite routine use of DNA-hypomethylating agents (HMAs) in AML/MDS therapy, their mechanisms of action are not yet unraveled. Pleiotropic effects of HMAs include global methylome and transcriptome changes. We asked whether in blasts and T-cells from AML patients HMA-induced in vivo demethylation and remethylation occur randomly or non-randomly, and whether gene demethylation is associated with gene induction. Peripheral blood AML blasts from patients receiving decitabine (20 mg/m2 day 1–5) were serially isolated for methylome analyses (days 0, 8 and 15, n = 28) and methylome-plus-transcriptome analyses (days 0 and 8, n = 23), respectively. T-cells were isolated for methylome analyses (days 0 and 8; n = 16). We noted massive, non-random demethylation at day 8, which was variable between patients. In contrast, T-cells disclosed a thousand-fold lesser, random demethylation, indicating selectivity of the demethylation for the malignant blasts. The integrative analysis of DNA demethylation and transcript induction revealed 87 genes displaying a significant inverse correlation, e.g. the tumor suppressor gene IFI27, whose derepression was validated in two AML cell lines. These results support HMA-induced, non-random early in vivo demethylation events in AML blasts associated with gene induction. Larger patient cohorts are needed to determine whether a demethylation signature may be predictive for response to this treatment.
Genome-scale CRISPR screen reveals neddylation to contribute to cisplatin resistance of testicular germ cell tumours
Authors: Funke Kai , Einsfelder Ulf , Hansen Aylin , Arévalo Lena , Schneider Simon , Nettersheim Daniel , Stein Valentin , Schorle Hubert
Published: April 2023

Background

Type II testicular germ cell tumours (TGCT) are the most prevalent tumours in young men. Patients suffering from cisplatin-resistant TGCTs are facing very poor prognosis demanding novel therapeutic options. Neddylation is a known posttranslational modification mediating many important biological processes, including tumorigenesis. Overactivation of the neddylation pathway promotes carcinogenesis and tumour progression in various entities by inducing proteasomal degradation of tumour suppressors (e.g., p21, p27).

Methods

We used a genome-scale CRISPR/Cas9 activation screen to identify cisplatin resistance factors. TGCT cell lines were treated with the neddylation inhibitor (MLN4924)/cisplatin/combination and investigated for changes in viability (XTT assay), apoptosis/cell cycle (flow cytometry) as well as in the transcriptome (3’mRNA sequencing).

Results

NAE1overexpression was detected in cisplatin-resistant colonies from the CRISPR screen. Inhibition of neddylation using MLN4924 increased cisplatin cytotoxicity in TGCT cell lines and sensitised cisplatin-resistant cells towards cisplatin. Apoptosis, G2/M-phase cell cycle arrest, γH2A.X/P27 accumulation and mesoderm/endoderm differentiation were observed in TGCT cells, while fibroblast cells were unaffected.

Conclusions

We identified overactivation of neddylation as a factor for cisplatin resistance in TGCTs and highlighted the additive effect of NAE1 inhibition by MLN4924 in combination with cisplatin as a novel treatment option for TGCTs.
CMTR1 promotes colorectal cancer cell growth and immune evasion by transcriptionally regulating STAT3
Authors: You A-bin , Yang Hu , Lai Chun-ping , Lei Wen , Yang Lu , Lin Jia-lin , Liu Shun-cui , Ding Nan , Ye Feng
Published: April 2023

CMTR1, also called IFN-stimulated gene 95 kDa protein (ISG95), is elevated by viral infection in a variety of cells. However, the functions of CMTR1 in colorectal cancer (CRC), especially its roles in tumorigenesis and immune regulation, remain unclear. Here, we first identified CMTR1 as a novel oncogene in colorectal cancer. Based on The Cancer Genome Atlas (TCGA) database exploration and human tissue microarray (TMA) analysis, we found that CMTR1 expression was markedly higher in CRC tissues than in adjacent normal tissues. High CMTR1 expression was correlated with poor prognosis in CRC patients. Knockdown (KD) of CMTR1 significantly suppressed cell proliferation and tumorigenicity both in vitro and in vivo, whereas overexpression of CMTR1 resulted in the opposite effects. KEGG pathway analysis revealed differential enrichment in the JAK/STAT signaling pathway in colorectal cancer cells with CMTR1 KD. Mechanistically, suppression of CMTR1 expression inhibited RNAPII recruitment to the transcription start site (TSS) of STAT3 and suppressed STAT3 expression and activation. Furthermore, the efficacy of PD1 blockade immunotherapy was prominently enhanced in the presence of CMTR1 KD via increased infiltration of CD8 + T cells into the tumor microenvironment. Overall, it appears that CMTR1 plays a key role in regulating tumor cell proliferation and antitumor immunity.
Melatonin inhibits bladder tumorigenesis by suppressing PPARγ/ENO1-mediated glycolysis
Authors: Shen Dexin , Deng Zhao , Liu Wei , Zhou Fenfang , Fang Yayun , Shan Danni , Wang Gang , Qian Kaiyu , Yu Mengxue , Zhang Yi , Ju Lingao , Xiao Yu , Wang Xinghuan
Published: April 2023

Melatonin is a well-known natural hormone, which shows a potential anticancer effect in many human cancers. Bladder cancer (BLCA) is one of the most malignant human cancers in the world. Chemoresistance is an increasingly prominent phenomenon that presents an obstacle to the clinical treatment of BLCA. There is an urgent need to investigate novel drugs to improve the current clinical status. In our study, we comprehensively explored the inhibitory effect of melatonin on BLCA and found that it could suppress glycolysis process. Moreover, we discovered that ENO1, a glycolytic enzyme involved in the ninth step of glycolysis, was the downstream effector of melatonin and could be a predictive biomarker of BLCA. We also proved that enhanced glycolysis simulated by adding exogenous pyruvate could induce gemcitabine resistance, and melatonin treatment or silencing ofENO1could intensify the cytotoxic effect of gemcitabine on BLCA cells. Excessive accumulation of reactive oxygen species (ROS) mediated the inhibitory effect of melatonin on BLCA cells. Additionally, we uncovered that PPARγ was a novel upstream regulator of ENO1, which mediated the downregulation of ENO1 caused by melatonin. Our study offers a fresh perspective on the anticancer effect of melatonin and encourages further studies on clinical chemoresistance.
A novel tumour enhancer function of Insulin-like growth factor II mRNA-binding protein 3 in colorectal cancer
Authors: Di Fusco Davide , Di Grazia Antonio , Di Maggio Giulia , Segreto Maria Teresa , Iannucci Andrea , Maresca Claudia , De Stefano Alessandro , Sica Giuseppe , Stolfi Carmine , Monteleone Giovanni , Monteleone Ivan
Published: April 2023

CRC cells evolve a variety of strategies to limit or circumvent apoptosis cell death. RNA binding proteins (RBPs) regulate many of the molecular mechanisms that underlie the development of cancer. The insulin-like growth factor II mRNA-binding proteins (IMP) family are oncofoetal RBPs, consisting of IMP1, IMP2 and IMP3, which have an important role in RNA metabolism. IMP3 is highly expressed in colorectal cancer (CRC) tissue, where its expression often correlates with poor prognosis. However, the role of IMP3 in CRC is not fully understood. IMP3 expression was analysed using a public database and by Western blotting and immunohistochemistry in human colon samples derived from patients with sporadic CRC and healthy subjects. To address whether IMP3 controls cancer cell survival, we analysed cell death pathways in in vitro and in vivo experiments after IMP3 downregulation by siRNA or an antisense oligonucleotide. IMP3 was highly expressed in CRC samples compared to normal control tissues. The knockdown of IMP3 enhanced a caspase-independent cell death in CRC cell lines. Furthermore, the treatment of CRC cells with IMP3 siRNA did not alter the expression of GSDMD, GPX-4 and the activated form of RIP3, three key molecules that govern pyroptosis, ferroptosis and necroptosis, respectively. Abrogation of IMP3 in CRC significantly reduced Bcl-2 and Bcl-xL mRNA and was associated with an altered mitochondrial membrane potential that allowed the nuclear migration of the apoptosis-inducing factor (AIF). Moreover, specific immunoprecipitation experiments on CRC human cell lines indicated that IMP3 binds Bcl-2 and Bcl-xL mRNA, suggesting that IMP3 acts as a regulator of the intrinsic apoptotic pathway through the surveillance of anti-apoptotic Bcl mRNA metabolism. Finally, we showed that IMP3 block inhibited the growth of CRC cell lines in vivo after transplantation into immunodeficient mice. Altogether, these data support a novel role for IMP3 in controlling the intrinsic caspase-independent apoptotic pathway in CRC.
TIPE3 represses head and neck squamous cell carcinoma progression via triggering PGAM5 mediated mitochondria dysfunction
Authors: Chen Wei , Chen Xijuan , Wang Lixuan , Yang Rongchun , Zhang Weilin , Zhang Siyuan , Xia Juan , Cheng Bin , Wu Tong , Ren Xianyue
Published: April 2023

Mitochondria are essential organelles in balancing oxidative stress and cell death during cancer cell proliferation. Rapid tumor growth induces tremendous stress on mitochondria. The mammalian tumor necrosis factor-α-induced protein 8-likes (TIPEs) family plays critical roles in balancing cancer cell death and survival. Yet, the roles of TIPEs in HNSCC tumorigenesis and mitochondria stress maintenance is unclear. Based on an integrative analysis of public HNSCC datasets, we identified that the downregulation of TIPE3 via its promoter hypermethylation modification is the major event of TIPEs alterations during HNSCC tumorigenesis. Low expression levels of TIPE3 were correlated with high malignancy and poor clinical outcomes of HNSCC patients. Restoring TIPE3 represses HNSCC proliferation, migration, and invasion in vitro and in vivo, while silencing TIPE3 acted on an opposite way. Mechanistically, TIPE3 band to the PGAM5 and electron transport chain (ETC) complex. Restoring TIPE3 promoted PGAM5 recruiting BAX and dephosphorylating p-DRP1(Ser637), which triggered mitochondrial outer membrane permeabilization and fragmentation. Ultimately, TIPE3 induced ETC damage and oxygen consumption rate decrease, ROS accumulation, mitochondrial membrane potential depolarization, and cell apoptosis. Collectively, our work reveals that TIPE3 plays critical role in maintaining mitochondrial stress and cancer cell progression in HNSCC, which might be a potential therapeutic target for HNSCC patients.
Combination treatment with FAAH inhibitors/URB597 and ferroptosis inducers significantly decreases the growth and metastasis of renal cell carcinoma cells via the PI3K-AKT signaling pathway
Authors: Hao Junfeng , Chen Qiguang , Feng Yongmin , Jiang Qiyu , Sun Huiwei , Deng Botian , Huang Xin , Guan Jibin , Chen Qiuping , Liu Xincheng , Wang Yanjin , Cao Peng , Feng Fan , Li Xiaoyu
Published: April 2023

Ferroptosis, a nonapoptotic form of programmed cell death characterized by significant iron-dependent peroxidation of phospholipids, is regulated by cellular metabolism, redox homeostasis, and various cancer-related signaling pathways. Recently, considerable progress has been made in demonstrating the critical role of lipid metabolism in regulating ferroptosis, indicating the potential of combinational strategies for treating cancer in the future. In this study, we explored the combinational effects of lipid metabolism compounds and ferroptosis inducers on renal cell carcinoma (RCC) cells. We found potent synergy of the fatty acid amide hydrolase (FAAH) inhibitor URB597 with ferroptosis inducer (1S, 3R)-RSL3 (RSL3) in inhibiting the growth and metastasis of RCC cells both in vitro and in vivo via induction of G1 cell cycle arrest and promotion of the production of lipid peroxides, malondialdehyde (MDA), 4-hydroxynonenal (4-HNE), and cytosolic reactive oxygen species (ROS). In addition, inhibition of FAAH increased the sensitivity of RCC cells to ferroptosis. Genome-wide RNA sequencing indicated that the combination of URB597 and RSL3 has more significant effects on regulation of the expression of genes related to cell proliferation, the cell cycle, cell migration and invasion, and ferroptosis than either single agent alone. Moreover, we found that combinational treatment modulated the sensitivity of RCC cells to ferroptosis via the phosphatidylinositol 3 kinase (PI3K)-AKT signaling pathway. These data demonstrate that dual targeting of FAAH and ferroptosis could be a promising strategy for treating RCC.
Sphingomyelin 16:0 is a therapeutic target for neuronal death in acid sphingomyelinase deficiency
Authors: Gaudioso Ángel , Jiang Xuntian , Casas Josefina , Schuchman Edward H. , Ledesma María Dolores
Published: April 2023

Acid sphingomyelinase deficiency (ASMD) is a lysosomal storage disorder caused by mutations in the SMPD1 gene encoding for the acid sphingomyelinase (ASM). While intravenous infusion of recombinant ASM is an effective treatment for the peripheral disease, the neurological complications of ASMD remain unaddressed. It has been shown that aberrantly high level of total brain sphingomyelin (SM) is a key pathological event leading to neurodegeneration. Using mice lacking ASM (ASMko), which mimic the disease, we here demonstrate that among the SM species, SM16:0 shows the highest accumulation and toxicity in ASMko neurons. By targeting lysosomes, SM16:0 causes permeabilization and exocytosis of these organelles and induces oxidative stress and cell death. We also show that genetic silencing of Ceramide Synthase 5, which is involved in SM16:0 synthesis and overexpressed in the ASMko brain, prevents disease phenotypes in ASMko cultured neurons and mice. The levels of SM16:0 in plasma also show a strong correlation with those in brain that is higher than in liver, even at early stages of the disease. These results identify SM16:0 both as a novel therapeutic target and potential biomarker of brain pathology in ASMD.
Factor Xa cleaves SARS-CoV-2 spike protein to block viral entry and infection
Authors: Dong Wenjuan , Wang Jing , Tian Lei , Zhang Jianying , Settles Erik W. , Qin Chao , Steinken-Kollath Daniel R. , Itogawa Ashley N. , Celona Kimberly R. , Yi Jinhee , Bryant Mitchell , Mead Heather , Jaramillo Sierra A. , Lu Hongjia , Li Aimin , Zumwalt Ross E. , Dadwal Sanjeet , Feng Pinghui , Yuan Weiming , Whelan Sean P. J. , Keim Paul S. , Barker Bridget Marie , Caligiuri Michael A. , Yu Jianhua
Published: April 2023

Serine proteases (SP), including furin, trypsin, and TMPRSS2 cleave the SARS-CoV-2 spike (S) protein, enabling the virus to enter cells. Here, we show that factor (F) Xa, an SP involved in blood coagulation, is upregulated in COVID-19 patients. In contrast to other SPs, FXa exerts antiviral activity. Mechanistically, FXa cleaves S protein, preventing its binding to ACE2, and thus blocking viral entry and infection. However, FXa is less effective against variants carrying the D614G mutation common in all pandemic variants. The anticoagulant rivaroxaban, a direct FXa inhibitor, inhibits FXa-mediated S protein cleavage and facilitates viral entry, whereas the indirect FXa inhibitor fondaparinux does not. In the lethal SARS-CoV-2 K18-hACE2 model, FXa prolongs survival yet its combination with rivaroxaban but not fondaparinux abrogates that protection. These results identify both a previously unknown function for FXa and an associated antiviral host defense mechanism against SARS-CoV-2 and suggest caution in considering direct FXa inhibitors for preventing or treating thrombotic complications in COVID-19 patients.
MEK inhibition reduced vascular tumor growth and coagulopathy in a mouse model with hyperactive GNAQ
Authors: Schrenk Sandra , Bischoff Lindsay J. , Goines Jillian , Cai Yuqi , Vemaraju Shruti , Odaka Yoshinobu , Good Samantha R. , Palumbo Joseph S. , Szabo Sara , Reynaud Damien , Van Raamsdonk Catherine D. , Lang Richard A. , Boscolo Elisa
Published: April 2023

Activating non-inherited mutations in the guanine nucleotide-binding protein G(q) subunit alpha (GNAQ) gene family have been identified in childhood vascular tumors. Patients experience extensive disfigurement, chronic pain and severe complications including a potentially lethal coagulopathy termed Kasabach-Merritt phenomenon. Animal models for this class of vascular tumors do not exist. This has severely hindered the discovery of the molecular consequences ofGNAQmutations in the vasculature and, in turn, the preclinical development of effective targeted therapies. Here we report a mouse model expressing hyperactive mutantGNAQin endothelial cells. Mutant mice develop vascular and coagulopathy phenotypes similar to those seen in patients. Mechanistically, by transcriptomic analysis we demonstrate increased mitogen activated protein kinase signaling in the mutant endothelial cells. Targeting of this pathway with Trametinib suppresses the tumor growth by reducing vascular cell proliferation and permeability. Trametinib also prevents the development of coagulopathy and improves mouse survival.
PRMT3-mediated arginine methylation of IGF2BP1 promotes oxaliplatin resistance in liver cancer
Authors: Shi Yunxing , Niu Yi , Yuan Yichuan , Li Kai , Zhong Chengrui , Qiu Zhiyu , Li Keren , Lin Zhu , Yang Zhiwen , Zuo Dinglan , Qiu Jiliang , He Wei , Wang Chenwei , Liao Yadi , Wang Guocan , Yuan Yunfei , Li Binkui
Published: April 2023

Although oxaliplatin-based chemotherapy has been effective in the treatment of hepatocellular carcinoma (HCC), primary or acquired resistance to oxaliplatin remains a major challenge in the clinic. Through functional screening using CRISPR/Cas9 activation library, transcriptomic profiling of clinical samples, and functional validation in vitro and in vivo, we identify PRMT3 as a key driver of oxaliplatin resistance. Mechanistically, PRMT3-mediated oxaliplatin-resistance is in part dependent on the methylation of IGF2BP1 at R452, which is critical for the function of IGF2BP1 in stabilizing the mRNA of HEG1, an effector of PRMT3-IGF2BP1 axis. Also, PRMT3 overexpression may serve as a biomarker for oxaliplatin resistance in HCC patients. Collectively, our study defines the PRTM3-IGF2BP1-HEG1 axis as important regulators and therapeutic targets in oxaliplatin-resistance and suggests the potential to use PRMT3 expression level in pretreatment biopsy as a biomarker for oxaliplatin-resistance in HCC patients.
Nasopharyngeal carcinoma cells promote regulatory T cell development and suppressive activity via CD70-CD27 interaction
Authors: Gong Lanqi , Luo Jie , Zhang Yu , Yang Yuma , Li Shanshan , Fang Xiaona , Zhang Baifeng , Huang Jiao , Chow Larry Ka-Yue , Chung Dittman , Huang Jinlin , Huang Cuicui , Liu Qin , Bai Lu , Tiu Yuen Chak , Wu Pingan , Wang Yan , Tsao George Sai-Wah , Kwong Dora Lai-wan , Lee Anne Wing-Mui , Dai Wei , Guan Xin-Yuan
Published: April 2023

Despite the intense CD8+ T-cell infiltration in the tumor microenvironment of nasopharyngeal carcinoma, anti-PD-1 immunotherapy shows an unsatisfactory response rate in clinical trials, hindered by immunosuppressive signals. To understand how microenvironmental characteristics alter immune homeostasis and limit immunotherapy efficacy in nasopharyngeal carcinoma, here we establish a multi-center single-cell cohort based on public data, containing 357,206 cells from 50 patient samples. We reveal that nasopharyngeal carcinoma cells enhance development and suppressive activity of regulatory T cells via CD70-CD27 interaction. CD70 blocking reverts Treg-mediated suppression and thus reinvigorate CD8+ T-cell immunity. Anti-CD70+ anti-PD-1 therapy is evaluated in xenograft-derived organoids and humanized mice, exhibiting an improved tumor-killing efficacy. Mechanistically, CD70 knockout inhibits a collective lipid signaling network in CD4+ naïve and regulatory T cells involving mitochondrial integrity, cholesterol homeostasis, and fatty acid metabolism. Furthermore, ATAC-Seq delineates that CD70 is transcriptionally upregulated by NFKB2 via an Epstein-Barr virus-dependent epigenetic modification. Our findings identify CD70+ nasopharyngeal carcinoma cells as a metabolic switch that enforces the lipid-driven development, functional specialization and homeostasis of Tregs, leading to immune evasion. This study also demonstrates that CD70 blockade can act synergistically with anti-PD-1 treatment to reinvigorate T-cell immunity against nasopharyngeal carcinoma.
Targeting USP2 regulation of VPRBP-mediated degradation of p53 and PD-L1 for cancer therapy
Authors: Yi Jingjie , Tavana Omid , Li Huan , Wang Donglai , Baer Richard J. , Gu Wei
Published: April 2023

Since Mdm2 (Mouse double minute 2) inhibitors show serious toxicity in clinic studies, different approaches to achieve therapeutic reactivation of p53-mediated tumor suppression in cancers need to be explored. Here, we identify the USP2 (ubiquitin specific peptidase 2)-VPRBP (viral protein R binding protein) axis as an important pathway for p53 regulation. Like Mdm2, VPRBP is a potent repressor of p53 but VPRBP stability is controlled by USP2. Interestingly, the USP2-VPRBP axis also regulates PD-L1 (programmed death-ligand 1) expression. Strikingly, the combination of a small-molecule USP2 inhibitor and anti-PD1 monoclonal antibody leads to complete regression of the tumors expressing wild-type p53. In contrast to Mdm2, knockout of Usp2 in mice has no obvious effect in normal tissues. Moreover, no obvious toxicity is observed upon the USP2 inhibitor treatment in vivo as Mdm2-mediated regulation of p53 remains intact. Our study reveals a promising strategy for p53-based therapy by circumventing the toxicity issue.
A two-dimensional mid-infrared optoelectronic retina enabling simultaneous perception and encoding
Authors: Wang Fakun , Hu Fangchen , Dai Mingjin , Zhu Song , Sun Fangyuan , Duan Ruihuan , Wang Chongwu , Han Jiayue , Deng Wenjie , Chen Wenduo , Ye Ming , Han Song , Qiang Bo , Jin Yuhao , Chua Yunda , Chi Nan , Yu Shaohua , Nam Donguk , Chae Sang Hoon , Liu Zheng , Wang Qi Jie
Published: April 2023

Infrared machine vision system for object perception and recognition is becoming increasingly important in the Internet of Things era. However, the current system suffers from bulkiness and inefficiency as compared to the human retina with the intelligent and compact neural architecture. Here, we present a retina-inspired mid-infrared (MIR) optoelectronic device based on a two-dimensional (2D) heterostructure for simultaneous data perception and encoding. A single device can perceive the illumination intensity of a MIR stimulus signal, while encoding the intensity into a spike train based on a rate encoding algorithm for subsequent neuromorphic computing with the assistance of an all-optical excitation mechanism, a stochastic near-infrared (NIR) sampling terminal. The device features wide dynamic working range, high encoding precision, and flexible adaption ability to the MIR intensity. Moreover, an inference accuracy more than 96% to MIR MNIST data set encoded by the device is achieved using a trained spiking neural network (SNN).
Signalling inhibition by ponatinib disrupts productive alternative lengthening of telomeres (ALT)
Authors: Kusuma Frances Karla , Prabhu Aishvaryaa , Tieo Galen , Ahmed Syed Moiz , Dakle Pushkar , Yong Wai Khang , Pathak Elina , Madan Vikas , Jiang Yan Yi , Tam Wai Leong , Kappei Dennis , Dröge Peter , Koeffler H. Phillip , Jeitany Maya
Published: April 2023

Alternative lengthening of telomeres (ALT) supports telomere maintenance in 10–15% of cancers, thus representing a compelling target for therapy. By performing anti-cancer compound library screen on isogenic cell lines and using extrachromosomal telomeric C-circles, as a bona fide marker of ALT activity, we identify a receptor tyrosine kinase inhibitor ponatinib that deregulates ALT mechanisms, induces telomeric dysfunction, reduced ALT-associated telomere synthesis, and targets, in vivo, ALT-positive cells. Using RNA-sequencing and quantitative phosphoproteomic analyses, combined with C-circle level assessment, we find an ABL1-JNK-JUN signalling circuit to be inhibited by ponatinib and to have a role in suppressing telomeric C-circles. Furthermore, transcriptome and interactome analyses suggest a role of JUN in DNA damage repair. These results are corroborated by synergistic drug interactions between ponatinib and either DNA synthesis or repair inhibitors, such as triciribine. Taken together, we describe here a signalling pathway impacting ALT which can be targeted by a clinically approved drug.
Automated optimisation of solubility and conformational stability of antibodies and proteins
Authors: Rosace Angelo , Bennett Anja , Oeller Marc , Mortensen Mie M. , Sakhnini Laila , Lorenzen Nikolai , Poulsen Christian , Sormanni Pietro
Published: April 2023

Biologics, such as antibodies and enzymes, are crucial in research, biotechnology, diagnostics, and therapeutics. Often, biologics with suitable functionality are discovered, but their development is impeded by developability issues. Stability and solubility are key biophysical traits underpinning developability potential, as they determine aggregation, correlate with production yield and poly-specificity, and are essential to access parenteral and oral delivery. While advances for the optimisation of individual traits have been made, the co-optimization of multiple traits remains highly problematic and time-consuming, as mutations that improve one property often negatively impact others. In this work, we introduce a fully automated computational strategy for the simultaneous optimisation of conformational stability and solubility, which we experimentally validate on six antibodies, including two approved therapeutics. Our results on 42 designs demonstrate that the computational procedure is highly effective at improving developability potential, while not affecting antigen-binding. We make the method available as a webserver at www-cohsoftware.ch.cam.ac.uk.
Bactericidal synergism between phage endolysin Ply2660 and cathelicidin LL-37 against vancomycin-resistant Enterococcus faecalis biofilms
Authors: Zhang Huihui , Zhang Xinyuan , Liang Siyu , Wang Jing , Zhu Yao , Zhang Wanjiang , Liu Siguo , Schwarz Stefan , Xie Fang
Published: April 2023

Antibiotic resistance and the ability to form biofilms of Enterococcus faecalis have compromised the choice of therapeutic options, which triggered the search for new therapeutic strategies, such as the use of phage endolysins and antimicrobial peptides. However, few studies have addressed the synergistic relationship between these two promising options. Here, we investigated the combination of the phage endolysin Ply2660 and the antimicrobial peptide LL-37 to target drug-resistant biofilm-producing E. faecalis. In vitro bactericidal assays were used to demonstrate the efficacy of the Ply2660–LL-37 combination against E. faecalis. Larger reductions in viable cell counts were observed when Ply2660 and LL-37 were applied together than after individual treatment with either substance. Transmission electron microscopy revealed that the Ply2660–LL-37 combination could lead to severe cell lysis of E. faecalis. The mode of action of the Ply2660–LL-37 combination against E. faecalis was that Ply2660 degrades cell wall peptidoglycan, and subsequently, LL-37 destroys the cytoplasmic membrane. Furthermore, Ply2660 and LL-37 act synergistically to inhibit the biofilm formation of E. faecalis. The Ply2660–LL-37 combination also showed a synergistic effect for the treatment of established biofilm, as biofilm killing with this combination was superior to each substance alone. In a murine peritoneal septicemia model, the Ply2660–LL-37 combination distinctly suppressed the dissemination of E. faecalis isolates and attenuated organ injury, being more effective than each treatment alone. Altogether, our findings indicate that the combination of a phage endolysin and an antimicrobial peptide may be a potential antimicrobial strategy for combating E. faecalis.
Biological insights and novel biomarker discovery through deep learning approaches in breast cancer histopathology
Authors: Mandair Divneet , Reis-Filho Jorge S. , Ashworth Alan
Published: April 2023

Breast cancer remains a highly prevalent disease with considerable inter- and intra-tumoral heterogeneity complicating prognostication and treatment decisions. The utilization and depth of genomic, transcriptomic and proteomic data for cancer has exploded over recent times and the addition of spatial context to this information, by understanding the correlating morphologic and spatial patterns of cells in tissue samples, has created an exciting frontier of research, histo-genomics. At the same time, deep learning (DL), a class of machine learning algorithms employing artificial neural networks, has rapidly progressed in the last decade with a confluence of technical developments - including the advent of modern graphic processing units (GPU), allowing efficient implementation of increasingly complex architectures at scale; advances in the theoretical and practical design of network architectures; and access to larger datasets for training - all leading to sweeping advances in image classification and object detection. In this review, we examine recent developments in the application of DL in breast cancer histology with particular emphasis of those producing biologic insights or novel biomarkers, spanning the extraction of genomic information to the use of stroma to predict cancer recurrence, with the aim of suggesting avenues for further advancing this exciting field.
Exploring the genetic and genomic connection underlying neurodegeneration with brain iron accumulation and the risk for Parkinson’s disease
Authors: Alvarez Jerez Pilar , Alcantud Jose Luis , de los Reyes-Ramírez Lucia , Moore Anni , Ruz Clara , Vives Montero Francisco , Rodriguez-Losada Noela , Saini Prabhjyot , Gan-Or Ziv , Alvarado Chelsea X. , Makarious Mary B. , Billingsley Kimberley J. , Blauwendraat Cornelis , Noyce Alastair J. , Singleton Andrew B. , Duran Raquel , Bandres-Ciga Sara
Published: April 2023

Neurodegeneration with brain iron accumulation (NBIA) represents a group of neurodegenerative disorders characterized by abnormal iron accumulation in the brain. In Parkinson’s Disease (PD), iron accumulation is a cardinal feature of degenerating regions in the brain and seems to be a key player in mechanisms that precipitate cell death. The aim of this study was to explore the genetic and genomic connection between NBIA and PD. We screened for known and rare pathogenic mutations in autosomal dominant and recessive genes linked to NBIA in a total of 4481 PD cases and 10,253 controls from the Accelerating Medicines Partnership Parkinsons’ Disease Program and the UKBiobank. We examined whether a genetic burden of NBIA variants contributes to PD risk through single-gene, gene-set, and single-variant association analyses. In addition, we assessed publicly available expression quantitative trait loci (eQTL) data through Summary-based Mendelian Randomization and conducted transcriptomic analyses in blood of 1886 PD cases and 1285 controls. Out of 29 previously reported NBIA screened coding variants, four were associated with PD risk at a nominalpvalue < 0.05. No enrichment of heterozygous variants in NBIA-related genes risk was identified in PD cases versus controls. Burden analyses did not reveal a cumulative effect of rare NBIA genetic variation on PD risk. Transcriptomic analyses suggested thatDCAF17is differentially expressed in blood from PD cases and controls. Due to low mutation occurrence in the datasets and lack of replication, our analyses suggest that NBIA and PD may be separate molecular entities.
Monitoring the impact of climate extremes and COVID-19 on statewise sentiment alterations in water pollution complaints
Authors: Liu Anqi , Kam Jonghun , Kwon Sae Yun , Shao Wanyun
Published: April 2023

The COVID-19 pandemic and associated prevention policies can directly or indirectly alter the sentiment of individuals while registering water pollution complaints, but observational evidence remains limited. Here, we conducted a sentiment analysis on over 10,000 water pollution complaints from residents in Alabama, USA (2012–2021) to better understand how and to what extent COVID-19 has altered emotion (polarity score-based) and attitude (subjectivity) of water pollution complaints. We found that the 2017 state-wise drought significantly increased the percentage of negative water pollution complaints by +35%, with no significant alternation in attitude before the COVID-19 pandemic. Since COVID-19, the percentage of negative and subjective water pollution complaints significantly decreased and increased by −30 and +20%, respectively, and these sentiment alternations were maintained by 2021. This study provides a new direction for environmental governance and management, requiring a timely response to changes in the public’s emotions and attitudes during the next climate extremes and pandemics.
Dynamic antagonism between key repressive pathways maintains the placental epigenome
Authors: Weigert Raha , Hetzel Sara , Bailly Nina , Haggerty Chuck , Ilik Ibrahim A. , Yung Philip Yuk Kwong , Navarro Carmen , Bolondi Adriano , Kumar Abhishek Sampath , Anania Chiara , Brändl Björn , Meierhofer David , Lupiáñez Darío G. , Müller Franz-Josef , Aktas Tugce , Elsässer Simon J. , Kretzmer Helene , Smith Zachary D. , Meissner Alexander
Published: April 2023

DNA and Histone 3 Lysine 27 methylation typically function as repressive modifications and operate within distinct genomic compartments. In mammals, the majority of the genome is kept in a DNA methylated state, whereas the Polycomb repressive complexes regulate the unmethylated CpG-rich promoters of developmental genes. In contrast to this general framework, the extra-embryonic lineages display non-canonical, globally intermediate DNA methylation levels, including disruption of local Polycomb domains. Here, to better understand this unusual landscape’s molecular properties, we genetically and chemically perturbed major epigenetic pathways in mouse trophoblast stem cells. We find that the extra-embryonic epigenome reflects ongoing and dynamic de novo methyltransferase recruitment, which is continuously antagonized by Polycomb to maintain intermediate, locally disordered methylation. Despite its disorganized molecular appearance, our data point to a highly controlled equilibrium between counteracting repressors within extra-embryonic cells, one that can seemingly persist indefinitely without bistable features typically seen for embryonic forms of epigenetic regulation.
CD-CODE: crowdsourcing condensate database and encyclopedia
Authors: Rostam Nadia , Ghosh Soumyadeep , Chow Chi Fung Willis , Hadarovich Anna , Landerer Cedric , Ghosh Rajat , Moon HongKee , Hersemann Lena , Mitrea Diana M. , Klein Isaac A. , Hyman Anthony A. , Toth-Petroczy Agnes
Published: April 2023

The discovery of biomolecular condensates transformed our understanding of intracellular compartmentalization of molecules. To integrate interdisciplinary scientific knowledge about the function and composition of biomolecular condensates, we developed the crowdsourcing condensate database and encyclopedia (cd-code.org). CD-CODE is a community-editable platform, which includes a database of biomolecular condensates based on the literature, an encyclopedia of relevant scientific terms and a crowdsourcing web application. Our platform will accelerate the discovery and validation of biomolecular condensates, and facilitate efforts to understand their role in disease and as therapeutic targets.
Improving the sensitivity of in vivo CRISPR off-target detection with DISCOVER-Seq+
Authors: Zou Roger S. , Liu Yang , Gaido Oscar E. Reyes , Konig Maximilian F. , Mog Brian J. , Shen Leo L. , Aviles-Vazquez Franklin , Marin-Gonzalez Alberto , Ha Taekjip
Published: April 2023

Discovery of off-target CRISPR–Cas activity in patient-derived cells and animal models is crucial for genome editing applications, but currently exhibits low sensitivity. We demonstrate that inhibition of DNA-dependent protein kinase catalytic subunit accumulates the repair protein MRE11 at CRISPR–Cas-targeted sites, enabling high-sensitivity mapping of off-target sites to positions of MRE11 binding using chromatin immunoprecipitation followed by sequencing. This technique, termed DISCOVER-Seq+, discovered up to fivefold more CRISPR off-target sites in immortalized cell lines, primary human cells and mice compared with previous methods. We demonstrate applicability to ex vivo knock-in of a cancer-directed transgenic T cell receptor in primary human T cells and in vivo adenovirus knock-out of cardiovascular risk gene PCSK9 in mice. Thus, DISCOVER-Seq+ is, to our knowledge, the most sensitive method to-date for discovering off-target genome editing in vivo.
Characterizing uncertainty in Community Land Model version 5 hydrological applications in the United States
Authors: Yan Hongxiang , Sun Ning , Eldardiry Hisham , Thurber Travis B. , Reed Patrick M. , Malek Keyvan , Gupta Rohini , Kennedy Daniel , Swenson Sean C. , Wang Linying , Li Dan , Vernon Chris R. , Burleyson Casey D. , Rice Jennie S.
Published: April 2023

Land surface models such as the Community Land Model Version 5 (CLM5) are essential tools for simulating the behavior of the terrestrial system. Despite the extensive application of CLM5, limited attention has been paid to the underlying uncertainties associated with its hydrological parameters and how these uncertainties affect water resource applications. To address this long-standing issue, we use five meteorological datasets to conduct a comprehensive hydrological parameter uncertainty characterization of CLM5 over the hydroclimatic gradients of the conterminous United States. Key datasets produced from the uncertainty characterization experiment include: a benchmark dataset of CLM5 default hydrological performance, parameter sensitivities for 28 hydrological metrics, and large-ensemble outputs for CLM5 hydrological predictions. The presented datasets will assist CLM5 calibration and support broad applications, such as evaluating drought and flood vulnerabilities. The datasets can be used to identify the hydroclimatological conditions under which parametric uncertainties demonstrate substantial effects on hydrological predictions and clarify where further investigations are needed to understand how hydrological prediction uncertainties interact with other Earth system processes.
The Materials Provenance Store
Authors: Statt Michael J. , Rohr Brian A. , Guevarra Dan , Suram Santosh K. , Morrell Thomas E. , Gregoire John M.
Published: April 2023

We present a database resulting from high throughput experimentation, primarily on metal oxide solid state materials. The central relational database, the Materials Provenance Store (MPS), manages the metadata and experimental provenance from acquisition of raw materials, through synthesis, to a broad range of materials characterization techniques. Given the primary research goal of materials discovery of solar fuels materials, many of the characterization experiments involve electrochemistry, along with optical, structural, and compositional characterizations. The MPS is populated with all information required for executing common data queries, which typically do not involve direct query of raw data. The result is a database file that can be distributed to users so that they can independently execute queries and subsequently download the data of interest. We propose this strategy as an approach to manage the highly heterogeneous and distributed data that arises from materials science experiments, as demonstrated by the management of over 30 million experiments run on over 12 million samples in the present MPS release.
Contribution of serum lipids and cholesterol cellular metabolism in lung cancer development and progression
Authors: Hartmann Philipp , Trufa Denis I. , Hohenberger Katja , Tausche Patrick , Trump Sonja , Mittler Susanne , Geppert Carol I. , Rieker Ralf J. , Schieweck Oliver , Sirbu Horia , Hartmann Arndt , Finotto Susetta
Published: April 2023

Neoplasms of the lungs are the leading cause of cancer incidence and mortality worldwide. Although immunotherapy has increased the overall survival of patients with lung cancer, there is the need to improve this treatment. At this regard, blood lipid levels are thought to be linked to cancer risk and thus a preventive intervention through regulation of the nutrition of patients with lung cancer is gaining much attention. In this study, we therefore asked about the contribution of serum lipids and cholesterol cellular metabolism in lung cancer development and progression. We measured different serum lipids and analyzed cholesterol synthesis enzymes 3-hydroxy-3-methyl-glutaryl-CoA reductase (HMGCR) and acetyl-coenzyme A cholesterol acetyltransferase 1 (ACAT1) as well as the cholesterol cellular export protein ATP-binding cassette (ABC) A-1 mRNA by quantitative PCR (qPCR) in the control and tumoral regions of post-surgery lung tissues to analyze the accumulation of cholesterol in cancer cells in a cohort of patients with lung adenocarcinoma (LUAD). We found that triglycerides in serum directly correlated with the body mass index (BMI) in patients with LUAD. By contrast, we found that high-density lipoprotein (HDL) cholesterol inversely correlated with the BMI, C-reactive protein (CRP) and overall survival and total cholesterol inversely correlated with the tumor diameter, serum CRP and overall survival in these LUAD patients. Functionally, the role of cholesterol is indispensable for the growth and development of normal animal cells where it is tightly regulated. Excess of cellular cholesterol regulated by HMGCR is converted to cholesteryl esters by the enzyme ACAT1 and exported extracellularly by the cholesterol transporter ABCA1. Here we found HMGCR and ACAT1 upregulated and ABCA1 downregulated in the lung’s tumoral region of our LUAD cohort, indicating cholesterol dysregulated cellular export in lung tumor cells.
A global analysis of the effectiveness of policy responses to COVID-19
Authors: Agyapon-Ntra Kwadwo , McSharry Patrick E.
Published: April 2023

Governments implemented many non-pharmaceutical interventions (NPIs) to suppress the spread of COVID-19 with varying results. In this paper, country-level daily time series from Our World in Data facilitates a global analysis of the propagation of the virus, policy responses and human mobility patterns. High death counts and mortality ratios influence policy compliance levels. Evidence of long-term fatigue was found with compliance dropping from over 85% in the first half of 2020 to less than 40% at the start of 2021, driven by factors such as economic necessity and optimism coinciding with vaccine effectiveness. NPIs ranged from facial coverings to restrictions on mobility, and these are compared using an empirical assessment of their impact on the growth rate of case numbers. Masks are the most cost-effective NPI currently available, delivering four times more impact than school closures, and approximately double that of other mobility restrictions. Gathering restrictions were the second most effective. International travel controls and public information campaigns had negligible effects. Literacy rates and income support played key roles in maintaining compliance. A 10% increase in literacy rate was associated with a 3.2% increase in compliance, while income support of greater than half of previous earnings increased compliance by 4.8%.
Textile dual-band NFC-A4WP (13.56–6.78 MHz) combiner for wireless energy and data transmission for connected clothing
Authors: Garnier Baptiste , Mariage Philippe , Rault François , Cochrane Cédric , Koncar Vladan
Published: April 2023

An original fully textile combiner is proposed to power supply sensors close to a body with only one centralized source of energy like a smartphone, for instance. A solution is provided for taking into account the requirements of an industrial production process that need to minimize needle movements during an embroidery process. Moreover, the paper shows how to support several wireless power transmission standards that already exist, i.e. NFC and A4WP, or will exist to satisfy the tremendous needs of energy for distributed systems in the IoT domain. In this paper, a new textile-based flexible wireless system enabling communication and energy harvesting is proposed. Analytical, numerical, and experimental studies have been conducted to demonstrate that the structure has two resonant frequencies at 6.8 MHz and 13.6 MHz, which make it suitable for NFC and A4WP standards. Moreover, the losses caused by the system are 2.76 dB and 1.91 dB for A4WP and NFC, respectively. The results are successively presented to highlight the specificities of such textile multi-coils combiners. A method for gaining a resonant structure without any solid electronic component is explained.
Access, timeliness and retention for HIV testing under early infant diagnosis (EID) program, India
Authors: Kamble Suchit , Gawde Nilesh , Goel Noopur , Thorwat Mohan , Nikhare Kalyani , Bembalkar Shilpa , Kamble Sushmita , Brahme Radhika , Pawar Swapna , Sahoo Rakesh , Rana Manish , Singh Manishkumar , Mohiuddin Syed Ahmed , Hatnoor Shivappa , Narapureddy Bayapa Reddy , Saleem M. , Shekhawat Kirti , Verma Vinita , Kapoor Neha , Das Chinmoyee , Gangakhedkar Raman
Published: April 2023

Early Infant Diagnosis of HIV infection services are crucial for managing the perinatally acquired HIV infection. Assessing the performance of the EID services and its underlying determinants is important for the National AIDS Control Program, India. The objectives of this study were to find out access to HIV testing, the timeliness of the testing cascade, and the proportion of HIV exposed infants who are followed up to 18 months for a definitive diagnosis of HIV. The study design was a mixed method. A total of 11 states accounting for 80% of HIV-positive pregnant women were selected. Program records from a total of 62 Integrated counselling and testing centres (ICTCs) served as the source of information. The qualitative component included interviews of program managers at the state and district level, service providers at the ICTC level, and caregivers of HIV exposed infants. In the sampled 62 ICTCs, 78% of the HIV exposed infants had at least one HIV test. Of the infants who had HIV tests, 50% had at first sample collected by 8 weeks of age. The median turnaround time from sample collection to DNA PCR testing was 36 (IQR 19–70) days and that to next sample collection in case of detection of virus in the first sample was 66 (IQR 55–116) days. At 18 months of age, 544 (62%) HIV exposed infants were retained in the EID testing cascade. A total of 30 infants were diagnosed with HIV at a median age of 421 (IQR 149–650) days. More than three fourth of the HIV exposed infants had access to early infant diagnosis (EID) services. Both demand and supply-side factors contribute to access, timeliness and retention and there is a need to address these factors.
Access to germasiloxanes and alkynylgermanes mediated by earth-abundant species
Authors: Stachowiak-Dłużyńska Hanna , Kuciński Krzysztof , Broniarz Konstancja , Szafoni Ewelina , Gruszczyński Marcin , Lewandowski Dariusz , Consiglio Giuseppe , Hreczycho Grzegorz
Published: April 2023

The reactions between silanols or terminal acetylenes with alkynylgermanes have been accomplished using potassium bis(trimethylsilyl)amide as the catalyst. This strategy has provided an entry point into various organogermanes including germasiloxanes and alkynylgermanes. Remarkably, not only KHMDS but also simple bases such as KOH can serve as efficient catalysts in this process.