bluuebunny/crossref_metadata_2025 huggingface dataset:
Phenotype testing, genome analysis, and metabolic interactions of three lactic acid bacteria strains existing as a consortium in a naturally fermented milk
Authors: Rodríguez Javier , Vázquez Lucía , Flórez Ana Belén , Mayo Baltasar
Published: September 2022

This work reports the characterization of three lactic acid bacteria (LAB) strains –Lactococcus lactis LA1, Lactococcus cremoris LA10, and Lactiplantibacillus plantarum LA30– existing as a stable consortium in a backslopping-inoculated, naturally fermented milk (NFM). This study aimed at uncovering the biochemical and genetic basis of the stability of the consortium and the cooperativity among the strains during milk fermentation. All three strains were subjected to phenotyping, covering the utilization of carbohydrates, enzyme activity, and antibiotic resistance. The strains were grown in milk individually, as well as in all possible combinations, and the resulting fermented product was analyzed for sugars, organic acids, and volatile compounds. Finally, the genomes of the three strains were sequenced and analyzed for genes associated with technological and safety properties. As expected, wide phenotypic diversity was seen between the strains. Lactococcus cremoris LA10 was the only strain to reach high cell densities and coagulate milk alone after incubation at 22°C for 24 h; congruently, it possessed a gene coding for a PrtP type II caseinolytic protease. Compared to any other fermentation, acetaldehyde concentrations were greater by a factor of six when all three strains grew together in milk, suggesting that its production might be the result of an interaction between them. Lactococcus lactis LA1, which carried a plasmid-encoded citQRP operon, was able to utilize milk citrate producing diacetyl and acetoin. No genes encoding virulence traits or pathogenicity factors were identified in any of the strains, and none produced biogenic amines from amino acid precursors, suggesting them to be safe. Lactiplantibacillus plantarum LA30 was susceptible to tetracycline, although it harbors a disrupted antibiotic resistance gene belonging to the tetM/tetW/tetO/tetS family. All three strains contained large numbers of pseudogenes, suggesting that they are well adapted (“domesticated”) to the milk environment. The consortium as a whole or its individual strains might have a use as a starter or as starter components for dairy fermentations. The study of simple consortia, such as that existing in this NFM, can help reveal how microorganisms interact with one another, and what influence they may have on the sensorial properties of fermented products.
Phylogeny, Evolution, and Transmission Dynamics of Canine and Feline Coronaviruses: A Retro-Prospective Study
Authors: Yang Hu , Peng Qianling , Lang Yifei , Du SenYan , Cao SanJie , Wu Rui , Zhao Qin , Huang Xiaobo , Wen Yiping , Lin Juchun , Zhao Shan , Yan Qigui
Published: September 2022

Canine coronavirus (CCoV) and feline coronavirus (FCoV) are endemic in companion animals. Due to their high mutation rates and tendencies of genome recombination, they pose potential threats to public health. The molecular characteristics and genetic variation of both CCoV and FCoV have been thoroughly studied, but their origin and evolutionary dynamics still require further assessment. In the present study, we applied a comprehensive approach and analyzed the S, M, and N genes of different CCoV/FCoV isolates. Discriminant analysis of principal components (DAPC) and phylogenetic analysis showed that the FCoV sequences from Chinese isolates were closely related to the FCoV clusters in Netherlands, while recombination analysis indicated that of S N-terminal domain (NTD) was the most susceptible region of mutation, and recombination of this region is an important cause of the emergence of new lineages. Natural selection showed that CCoV and FCoV subgenotypes were in selection constraints, and CCoV-IIb was in strong positive selection. Phylodynamics showed that the mean evolution rate of S1 genes of CCoV and FCoV was 1.281 × 10–3 and 1.244 × 10–3 subs/site/year, respectively, and the tMRCA of CCoV and FCoV was about 1901 and 1822, respectively. Taken together, our study centered on tracing the origin of CCoV/FCoV and provided ample insights into the phylogeny and evolution of canine and feline coronaviruses.
Proper irrigation amount for eggplant cultivation in a solar greenhouse improved plant growth, fruit quality and yield by influencing the soil microbial community and rhizosphere environment
Authors: Ji Tuo , Guo Xinyong , Wu Fengling , Wei Min , Li Jing , Ji Ping , Wang Ningxin , Yang Fengjuan
Published: September 2022

Water scarcity is a worldwide problem, and in order to obtain plenty of production, agricultural irrigation water accounts for a large portion. Many studies have shown that the interaction of root microorganisms and soil can promote crop growth. Developing ways to reduce irrigation to maintain soil fertility and ensure crop yield by regulating the root microenvironment is an important research goal. Here, we developed a reasonable irrigation plan for eggplant cultivation in a solar greenhouse. The maximum theoretical amount of water demand during eggplant planting obtained from a previous study was used as the control (CK), and the irrigation in the treatments was reduced by 10, 20 and 30% relative to this amount. The 10% irrigation reduction treatment (T1) significantly improved soil nutrients and increased soil catalase, urease and alkaline phosphatase activities (p < 0.05). Further analysis of rhizosphere microorganisms revealed the highest richness and diversity of the microbial community under the T1 treatment, with Bacilli as the most abundant bacteria and Aspergillaceae as the most abundant fungi and lower relative abundances of Chloroflexi and Acidobacteria (p < 0.05). Changes in microbial community structure under the influence of different irrigation treatments resulted in improvements in rhizosphere N cycling and nutrient catabolism. The plant–microbe interactions led to significant increases in eggplant plant height, root vigour, root surface area, leaf chlorophyll a, leaf net photosynthetic rate, water use efficiency, transpiration rate, and stomatal conductance under the T1 treatment compared to the CK treatment; soluble sugar, soluble protein and free amino acid contents in eggplant fruit increased by 10.8, 12.3 and 6.7%, respectively; and yield increased by 3.9%. Our research proved that the 10% irrigation reduction treatment (T1) could improve microbial community richness and fruit yield, which would improve irrigation efficiency and cost reduction in agriculture.
Requirements for MRN endonuclease processing of topoisomerase II-mediated DNA damage in mammalian cells
Authors: Sun Yilun , Soans Eroica , Mishina Margarita , Petricci Elena , Pommier Yves , Nitiss Karin C. , Nitiss John L.
Published: September 2022

During a normal topoisomerase II (TOP2) reaction, the enzyme forms a covalent enzyme DNA intermediate consisting of a 5′ phosphotyrosyl linkage between the enzyme and DNA. While the enzyme typically rejoins the transient breakage after strand passage, a variety of conditions including drugs targeting TOP2 can inhibit DNA resealing, leading to enzyme-mediated DNA damage. A critical aspect of the repair of TOP2-mediated damage is the removal of the TOP2 protein covalently bound to DNA. While proteolysis plays a role in repairing this damage, nucleolytic enzymes must remove the phosphotyrosyl-linked peptide bound to DNA. The MRN complex has been shown to participate in the removal of TOP2 protein from DNA following cellular treatment with TOP2 poisons. In this report we used an optimized ICE (In vivo Complex of Enzyme) assay to measure covalent TOP2/DNA complexes. In agreement with previous independent reports, we find that the absence or inhibition of the MRE11 endonuclease results in elevated levels of both TOP2α and TOP2β covalent complexes. We also examined levels of TOP2 covalent complexes in cells treated with the proteasome inhibitor MG132. Although MRE11 inhibition plus MG132 was not synergistic in etoposide-treated cells, ectopic overexpression of MRE11 resulted in removal of TOP2 even in the presence of MG132. We also found that VCP/p97 inhibition led to elevated TOP2 covalent complexes and prevented the removal of TOP2 covalent complexes by MRE11 overexpression. Our results demonstrate the existence of multiple pathways for proteolytic processing of TOP2 prior to nucleolytic processing, and that MRE11 can process TOP2 covalent complexes even when the proteasome is inhibited. The interactions between VCP/p97 and proteolytic processing of TOP2 covalent complexes merit additional investigation.
Potential Diffusion Tensor Imaging Biomarkers for Elucidating Intra-Individual Age-Related Changes in Cognitive Control and Processing Speed
Authors: Hsieh Shulan , Yang Meng-Heng
Published: September 2022

Cognitive aging, especially cognitive control, and processing speed aging have been well-documented in the literature. Most of the evidence was reported based on cross-sectional data, in which inter-individual age effects were shown. However, there have been some studies pointing out the possibility of overlooking intra-individual changes in cognitive aging. To systematically examine whether age-related differences and age-related changes might yield distinctive patterns, this study directly compared cognitive control function and processing speed between different cohorts versus follow-up changes across the adult lifespan. Moreover, considering that cognitive aging has been attributed to brain disconnection in white matter (WM) integrity, this study focused on WM integrity via acquiring diffusion-weighted imaging data with an MRI instrument that are further fitted to a diffusion tensor model (i.e., DTI) to detect water diffusion directionality (i.e., fractional anisotropy, FA; mean diffusivity, MD; radial diffusivity, RD; axial diffusivity, AxD). Following data preprocessing, 114 participants remained for further analyses in which they completed the two follow-up sessions (with a range of 1–2 years) containing a series of neuropsychology instruments and computerized cognitive control tasks. The results show that many significant correlations between age and cognitive control functions originally shown on cross-sectional data no longer exist on the longitudinal data. The current longitudinal data show that MD, RD, and AxD (especially in the association fibers of anterior thalamic radiation) are more strongly correlated to follow-up aging processes, suggesting that axonal/myelin damage is a more robust phenomenon for observing intra-individual aging processes. Moreover, processing speed appears to be the most prominent cognitive function to reflect DTI-related age (cross-sectional) and aging (longitudinal) effects. Finally, converging the results from regression analyses and mediation models, MD, RD, and AxD appear to be the representative DTI measures to reveal age-related changes in processing speed. To conclude, the current results provide new insights to which indicator of WM integrity and which type of cognitive changes are most representative (i.e., potentially to be neuroimaging biomarkers) to reflect intra-individual cognitive aging processes.
Cognitive and structural predictors of novel task learning, and contextual predictors of time series of daily task performance during the learning period
Authors: Smith Evan T. , Skolasinska Paulina , Qin Shuo , Sun Andrew , Fishwick Paul , Park Denise C. , Basak Chandramallika
Published: September 2022

Investigation into methods of addressing cognitive loss exhibited later in life is of paramount importance to the field of cognitive aging. The field continues to make significant strides in designing efficacious cognitive interventions to mitigate cognitive decline, and the very act of learning a demanding task has been implicated as a potential mechanism of augmenting cognition in both the field of cognitive intervention and studies of cognitive reserve. The present study examines individual-level predictors of complex skill learning and day-to-day performance on a gamified working memory updating task, the BirdWatch Game, intended for use as a cognitive intervention tool in older adults. A measure of verbal episodic memory and the volume of a brain region involved in verbal working memory and cognitive control (the left inferior frontal gyrus) were identified as predictors of learning rates on the BirdWatch Game. These two neuro-cognitive measures were more predictive of learning when considered in conjunction than when considered separately, indicating a complementary effect. Additionally, auto-regressive time series forecasting analyses were able to identify meaningful daily predictors (that is, mood, stress, busyness, and hours of sleep) of performance-over-time on the BirdWatch Game in 50% of cases, with the specific pattern of contextual influences on performance being highly idiosyncratic between participants. These results highlight the specific contribution of language processing and cognitive control abilities to the learning of the novel task examined in this study, as well as the variability of subject-level influences on task performance during task learning.
Effects of choline containing phospholipids on the neurovascular unit: A review
Authors: Roy Proshanta , Tomassoni Daniele , Nittari Giulio , Traini Enea , Amenta Francesco
Published: September 2022

The roles of choline and of choline-containing phospholipids (CCPLs) on the maintenance and progress of neurovascular unit (NVU) integrity are analyzed. NVU is composed of neurons, glial and vascular cells ensuring the correct homeostasis of the blood-brain barrier (BBB) and indirectly the function of the central nervous system. The CCPLs phosphatidylcholine (lecithin), cytidine 5′-diphosphocholine (CDP-choline), choline alphoscerate or α-glyceryl-phosphorylcholine (α-GPC) contribute to the modulation of the physiology of the NVU cells. A loss of CCPLs contributes to the development of neurodegenerative diseases such as Alzheimer’s disease, multiple sclerosis, Parkinson’s disease. Our study has characterized the cellular components of the NVU and has reviewed the effect of lecithin, of CDP-choline and α-GPC documented in preclinical studies and in limited clinical trials on these compounds. The interesting results obtained with some CCPLs, in particular with α-GPC, probably would justify reconsideration of the most promising molecules in larger attentively controlled studies. This can also contribute to better define the role of the NVU in the pathophysiology of brain disorders characterized by vascular impairment.
Neurosensory development of the four brainstem-projecting sensory systems and their integration in the telencephalon
Authors: Fritzsch Bernd , Elliott Karen L. , Yamoah Ebenezer N.
Published: September 2022

Somatosensory, taste, vestibular, and auditory information is first processed in the brainstem. From the brainstem, the respective information is relayed to specific regions within the cortex, where these inputs are further processed and integrated with other sensory systems to provide a comprehensive sensory experience. We provide the organization, genetics, and various neuronal connections of four sensory systems: trigeminal, taste, vestibular, and auditory systems. The development of trigeminal fibers is comparable to many sensory systems, for they project mostly contralaterally from the brainstem or spinal cord to the telencephalon. Taste bud information is primarily projected ipsilaterally through the thalamus to reach the insula. The vestibular fibers develop bilateral connections that eventually reach multiple areas of the cortex to provide a complex map. The auditory fibers project in a tonotopic contour to the auditory cortex. The spatial and tonotopic organization of trigeminal and auditory neuron projections are distinct from the taste and vestibular systems. The individual sensory projections within the cortex provide multi-sensory integration in the telencephalon that depends on context-dependent tertiary connections to integrate other cortical sensory systems across the four modalities.
Outcomes from the Northeast England cohort of autosomal dominant polycystic kidney disease (ADPKD) patients on tolvaptan
Authors: Gkekas Eleftherios , Tang Tsz Yau Tiffany , Green Alan , Davidson Han , Fraser Rachel , Sayer John A. , Srivastava Shalabh
Published: September 2022

Autosomal dominant polycystic kidney disease (ADPKD) is a cause of end-stage kidney disease (ESKD). The vasopressin V2-receptor antagonist tolvaptan has been shown within randomized clinical trials to slow down decline of kidney function in patients with ADPKD at risk of rapid progression. We performed a retrospective review of a Northeast England cohort of adult ADPKD patients who had been established on tolvaptan therapy to determine its efficacy in a real-world clinic setting. Other inclusion criteria involved a pre-treatment decline in greater than 2.5 ml/min/1.73m2/year based on readings for a 3 year period, and ability to tolerate and maintain tolvaptan treatment for at least 12 months. We calculated based on eGFR slopes, predicted time to reach ESKD with and without tolvaptan therapy. The cohort of patients included 21 from the Northeast of England. The mean rate of eGFR decline prior to treatment was -6.02 ml/min/1.73m2/year for the cohort. Following tolvaptan treatment, the average decline in eGFR was reduced to -2.47 ml/min/1.73m2/year, gaining a mean 8 years and 4 months delay to reach ESKD. The majority of patients (n=19) received and tolerated full dose tolvaptan (90 mg/30 mg). The real-life use of tolvaptan gave a dramatic improvement in eGFR slopes, much more than previously reported in clinical studies. These effects may be in part due to careful patient identification, selection and inclusion of patients who were able to tolerate tolvaptan therapy, excellent compliance with medication and a “tolvaptan clinic” effect where great personal care was given to these patients.
Transcranial alternating current stimulation combined with sound stimulation improves the cognitive function of patients with Alzheimer's disease: A case report and literature review
Authors: Liu Yang , Tang Can , Wei Kailun , Liu Di , Tang Keke , Chen Meilian , Xia Xuewei , Mao Zhiqi
Published: September 2022

Transcranial alternating current stimulation (tACS) is a relatively new non-invasive brain electrical stimulation method for the treatment of patients with Alzheimer's disease (AD), but it has poor offline effects. Therefore, we applied a new combined stimulation method to observe the offline effect on the cognitive function of patients with AD. Here, we describe the clinical results of a case in which tACS combined with sound stimulation was applied to treat moderate AD. The patient was a 73-year-old woman with a 2-year history of persistent cognitive deterioration despite the administration of Aricept and Sodium Oligomannate. Therefore, the patient received tACS combined with sound stimulation. Her cognitive scale scores improved after 15 sessions and continued to improve at 4 months of follow-up. Although the current report may provide a new alternative therapy for patients with AD, more clinical data are needed to support its efficacy.

Trial registration

Clinicaltrials.gov, NCT05251649.
Vertigoheel improves central vestibular compensation after unilateral peripheral vestibulopathy in rats
Authors: Hatat Bérénice , Boularand Romain , Bringuier Claire , Chanut Nicolas , Besnard Stéphane , Mueller Andrea M. , Weyer Kathrin , Seilheimer Bernd , Tighilet Brahim , Chabbert Christian
Published: September 2022

The aim of this study was to assess the effect of Vertigoheel on central vestibular compensation and cognitive deficits in rats subjected to peripheral vestibular loss. Young adult male Long Evans rats were subjected to bilateral vestibular insults through irreversible sequential ototoxic destructions of the vestibular sensory organs. Vestibular syndrome characteristics were monitored at several time points over days and weeks following the sequential insults, using a combination of behavioral assessment paradigms allowing appreciation of patterns of change in static and dynamic deficits, together with spatial navigation, learning, and memory processes. Vertigoheel administered intraperitoneally significantly improved maximum body velocity and not moving time relative to its vehicle control on days 2 and 3 and on day 2, respectively, after unilateral vestibular lesion (UVL). It also significantly improved postural control relative to its vehicle 1 day after UVL. Conversely, Vertigoheel did not display any significant effect vs. vehicle on the severity of the syndrome, nor on the time course of other examined parameters, such as distance moved, mean body velocity, meander, and rearing. Spatial cognition testing using Y- and T-maze and eight-radial arm maze did not show any statistically significant difference between Vertigoheel and vehicle groups. However, Vertigoheel potentially enhanced the speed of learning in sham animals. Evaluating Vertigoheel's effect on thigmotaxis during the open-field video tracking test revealed no significant difference between Vertigoheel and its vehicle control groups suggesting that Vertigoheel does not seem to induce sedative or anxiolytic effects that could negatively affect vestibular and memory function. Present observations reveal that Vertigoheel improves central vestibular compensation following the unilateral peripheral vestibular loss as demonstrated by improvement of specific symptoms.
Causal Association Between Tea Consumption and Bone Health: A Mendelian Randomization Study
Authors: Chen Song , Chen Tianlai , Chen Yibin , Huang Dianhua , Pan Yuancheng , Chen Shunyou
Published: September 2022

Background

Much observational research reported that tea consumption decreases the risk of osteoarthritis (OA), rheumatoid arthritis (RA), and osteoporosis (OP) which are the three major bone disorders. However, the observed correlation is inconclusive. To determine the causal relationship between genetically predicted tea intake and OA, RA, and OP, we performed a two-sample Mendelian randomization (MR) study based on large samples.

Methods

The European population’s genome-wide association meta-analysis (GWAS) dataset identified SNPs associated with tea consumption was obtained from Neale Lab’s analysis of UK Biobank data that comprised 349,376 participants of European ancestry. We extracted genetic data for knee OA (17,885 controls and 4,462 cases), hip OA (50,898 controls and 12,625 cases), and RA (43,923 controls and 14,361 cases) from the UK Biobank and OP cases (93083 controls and 1,175 cases) from FinnGen Data Freeze 2. A MR study was conducted to examine the effect of selected single nucleotide polymorphisms (SNPs) and OA, RA, and OP risk. Several sensitivity analyses were performed with weighted median and inverse-variance weighted methods for estimating the causal effects.

Results

In this MR study, the genetically predicted per one cup increase of tea consumption was not associated with knee OA (OR 1.11,95% CI: 0.79–1.55) using IVW with random effect. Genetic predisposition to tea consumption was not associated with hip OA (OR: 1.20, 95% CI: 0.84–1.71), RA (OR: 1.24 95% CI: 0.81–1.91), and OP (OR: 1.11, 95% CI: 0.89, 1.39). Following the sensitivity analysis, there was no potential pleiotropy.

Conclusion

According to our study, According to our study, there was no statistical power to confirm a causal relationship between tea consumption and the risk of knee OA, hip OA, RA, and OP.
Dietary meat mutagens intake and cancer risk: A systematic review and meta-analysis
Authors: Reng Qie , Zhu Ling Ling , Feng Li , Li Yong Jie , Zhu Yan Xing , Wang Ting Ting , Jiang Feng
Published: September 2022

Background

Clinical and preclinical studies suggested that certain mutagens occurring as a reaction of creatine, amino acids, and sugar during the high temperature of cooking meat are involved in the pathogenesis of human cancer. Here we conducted a systematic review and meta-analysis to examine whether meat mutagens [PhIP, MeIQx, DiMeIQx, total HCA, and B(a)P] present a risk factor for human cancer.

Methods

We searched the following databases for relevant articles published from inception to 10 Oct 2021 with no language restrictions: Pubmed, Embase, Cochrane Central Register of Controlled Trials (CENTRAL), Baidu Academic, Zhejiang Digital Library. Two independent researchers screened all titles and obtained eligible texts for further screening. Independent data extraction was conducted, and meta-analysis was carried out using random-effects models to calculate the risk ratio of the meat mutagens exposure.

Results

A total of 1,786,410 participants and 70,653 cancer cases were identified. Among these, there were 12 different types of cancer at various sites, i.e., breast, bladder, colorectal, colon, rectum, prostate, lung, Non-Hodgkin lymphoma, kidney, gastric, esophagus, pancreatic, hepatocellular carcinoma. Cancer risk was significantly increased by intake of PhIP (OR = 1.13;95% CI 1.07–1.21; p < 0.001), MeIQx (OR = 1.14; 95% CI: 1.07–1.21; p < 0.001), DiMeIQx (OR = 1.07; 95% CI: 1.01–1.13; p = 0.013), total HCA (OR = 1.20; 95% CI: 1.03–1.38; p = 0.016), and cancer risk was not significantly increased by intake of B(a)P (OR = 1.04; 95% CI: 0.98–1.10; p = 0.206).

Conclusion

Meat mutagens of PhIP, MeIQx, DiMeIQx, and total HCA have a positive association with the risk of cancer.

Systematic review registration

[www.crd.york.ac.uk/prospero], identifier [CRD42022148856].
Diagnostic accuracy and prognostic significance of Glypican-3 in hepatocellular carcinoma: A systematic review and meta-analysis
Authors: Jiang Donglei , Zhang Yingshi , Wang Yinuo , Xu Fu , Liang Jun , Wang Weining
Published: September 2022

Purpose

Glypican-3 (GPC-3) expression is abnormal in the occurrence and development of hepatocellular carcinoma (HCC). To explore whether GPC-3 has diagnostic accuracy and prognostic significance of HCC, we did a systematic review and meta-analysis.

Method

PubMed, Embase, Cochrane Library, and China National Knowledge Infrastructure were searched with keywords “GPC-3” and “HCC” and their MeSH terms from inception to July 2022. We applied the hierarchical summary receiver operating characteristic model and evaluated the diagnostic value of GPC-3 alone and combination, and the correlation between high and low GPC-3 expression on clinicopathological features and survival data in prognosis.

Results

Forty-one original publications with 6,305 participants were included, with 25 of them providing data for diagnostic value and 18 records were eligible for providing prognostic value of GPC-3. GPC-3 alone got good diagnostic value in patients with HCC when compared with healthy control and moderate diagnostic value when compared with patients with cirrhosis. In addition, combination of GPC-3 + AFP and GPC-3 + GP73 got great diagnostic value in HCC versus cirrhosis groups; the combination of GPC-3 can also improve the diagnostic accuracy of biomarkers. Moreover, we discovered that overexpression of GPC-3 was more likely found in HBV infection, late tumor stage, and microvascular invasion groups and causes shorter overall survival and disease free survival, which means poor prognosis.

Conclusion

GCP-3 could be used as a biomarker in HCC diagnosis and prognosis, especially in evaluated diagnostic value in combination with AFP or GP73, and in forecasting worse survival data of overexpression GPC-3

Systematic Review Registration

https://www.crd.york.ac.uk/PROSPERO/, identifier [CRD42022351566].
MET alterations in advanced pulmonary sarcomatoid carcinoma
Authors: Gong Chen , Xiong Huihua , Qin Kai , Wang Jianhua , Cheng Yi , Zhao Jing , Zhang Jing
Published: September 2022

Pulmonary sarcomatoid carcinoma (PSC) is a rare subset of NSCLC that accounts for about 0.5-1% of all primary lung carcinoma, and its malignant biological behavior is more aggressive than other pathological types of lung cancer. Recent studies have reported a variety of gene mutations associated with the occurrence, development and treatment of PSC, especially the mesenchymal-epithelial transition (MET) proto-oncogene alterations, including the exon 14 (METex14) skipping mutations as well as the amplification and overexpression of MET gene, which are associated with molecularly targeted therapy for PSC. METex14 skipping mutation is the most common and well-studied mutation type, occurring in about 22-31.8% of PSC patients, while the prevalence of MET amplification is reported as 4.8-13.6% and MET ovexpression is about 20.2%. Molecular pathology tests, including IHC and NGS, are valuable in determining the prognosis of patients with PSC and helping to determine the treatment. The existing clinical data have confirmed the efficacy of MET-TKI in PSC patients with MET alteration, among which the clinical study of Savolitinib has enrolled the largest proportion of PSC patients and achieved relatively good efficacy, but more clinical researches are still needed. The multi-disciplinary team may maximize the optimal treatment options for patients with the advanced PSC.
Liquid Biopsy-Driven Cetuximab Rechallenge Strategy in Molecularly Selected Metastatic Colorectal Cancer Patients
Authors: Mariani Stefano , Puzzoni Marco , Giampieri Riccardo , Ziranu Pina , Pusceddu Valeria , Donisi Clelia , Persano Mara , Pinna Giovanna , Cimbro Erika , Parrino Alissa , Spanu Dario , Pretta Andrea , Lai Eleonora , Liscia Nicole , Lupi Alessio , Giglio Enrica , Palomba Grazia , Casula Milena , Pisano Marina , Palmieri Giuseppe , Scartozzi Mario
Published: September 2022

Background

Rechallenge with EGFR inhibitors represents a promising strategy for patients with RAS wild type (WT) colorectal cancer (CRC) but definitive selection criteria are lacking. Recently, the RAS WT status on circulating tumor DNA (ct-DNA) emerged as a potential watershed for this strategy. Our study explored the liquid biopsy-driven cetuximab rechallenge in a RAS and BRAF WT selected population.

Methods

CRC patients with RAS and BRAF WT both on tumor tissue and on ct-DNA at baseline receiving rechallenge with cetuximab were eligible for our analysis. Ct-DNA was analyzed for RAS-BRAF mutations with pyro-sequencing and nucleotide sequencing assays. Real-time PCR and droplet digital PCR were performed to confirm the RAS-BRAF mutational status.

Results

A total of 26 patients were included in our analysis. In the global population, RR was 25.0%, median overall survival (mOS) was 5.0 months, and median progression-free survival (mPFS) was 3.5 months. Previous response to anti-EGFR was associated with improved mPFS (5.0 vs. 2.0 months, HR: 0.26, p = 0.048); anti-EGFR free interval > 14 months and anti-EGFR free interval > 16 months were associated with improved mPFS (respectively 7.0 vs. 3.0 months, HR: 0.27, p = 0.013 and not reached vs. 3.0 months, HR: 0.20, p = 0.002) and with improved mOS (respectively 13.0 vs. 5.0 months, HR: 0.27, p = 0.013 and 13.0 vs. 5.0 months, HR: 0.20, p = 0.002). Previous lines >2 were correlated with improved mPFS (4.0 vs. 1.0 month, HR: 0.05, p = 0.041) and with improved mOS (7.0 vs. 1.0 month, HR: 0.045, p = 0.034). In a multiple logistic regression model, only the anti-EGFR free interval was confirmed to be a significant predictor for mOS and mPFS.

Conclusions

Liquid biopsy-driven cetuximab rechallenge was confirmed to be effective. The clinical outcome was consistent with available results from phase II studies. In addition to the molecular selection through the analysis of ct-DNA for RAS, the long anti-EGFR free interval is confirmed as a prospective selection criterion for this therapeutic option.
Evolution of research trends in artificial intelligence for breast cancer diagnosis and prognosis over the past two decades: A bibliometric analysis
Authors: Syed Asif Hassan , Khan Tabrej
Published: September 2022

Objective

In recent years, among the available tools, the concurrent application of Artificial Intelligence (AI) has improved the diagnostic performance of breast cancer screening. In this context, the present study intends to provide a comprehensive overview of the evolution of AI for breast cancer diagnosis and prognosis research using bibliometric analysis.

Methodology

Therefore, in the present study, relevant peer-reviewed research articles published from 2000 to 2021 were downloaded from the Scopus and Web of Science (WOS) databases and later quantitatively analyzed and visualized using Bibliometrix (R package). Finally, open challenges areas were identified for future research work.

Results

The present study revealed that the number of literature studies published in AI for breast cancer detection and survival prediction has increased from 12 to 546 between the years 2000 to 2021. The United States of America (USA), the Republic of China, and India are the most productive publication-wise in this field. Furthermore, the USA leads in terms of the total citations; however, hungry and Holland take the lead positions in average citations per year. Wang J is the most productive author, and Zhan J is the most relevant author in this field. Stanford University in the USA is the most relevant affiliation by the number of published articles. The top 10 most relevant sources are Q1 journals with PLOS ONE and computer in Biology and Medicine are the leading journals in this field. The most trending topics related to our study, transfer learning and deep learning, were identified.

Conclusion

The present findings provide insight and research directions for policymakers and academic researchers for future collaboration and research in AI for breast cancer patients.
Pathological complete response in MMR-deficient/MSI-high and KRAS-mutant patient with locally advanced rectal cancer after neoadjuvant chemoradiation with immunotherapy: A case report
Authors: Zhang Mai , Yang Hua , Chen Ling , Du Kunli , Zhao Lina , Wei Lichun
Published: September 2022

To date, preoperative chemoradiation (CRT) is the standard of care for patients with locally advanced rectal cancer (LARC) regardless of status of mismatch repair. Immunotherapy showed promising results in the neoadjuvant treatment trials in patients with mismatch repair-deficient (dMMR) or high microsatellite instability (MSI-H) LARC. The efficacy of CRT plus programmed death 1 (PD-1) inhibitor in these patients with complex gene mutation remains unclear. Additionally, very few studies reported on whether such combination could induce abscopal effect. We report a case of dMMR and MSI-H LARC with KRAS mutation that achieved pathological complete response of primary lesion and liver metastases after neoadjuvant short-course radiotherapy followed by four cycles chemotherapy of XELOX plus PD-1 inhibitor tislelizumab and a subsequent total mesorectal excision. This case indicates that this combined treatment strategy has remarkable clinical response both in locoregional and distant diseases, which potentially leads to reduction in the risk of distant metastases and better locoregional control for this subgroup of population.
CDK7 is a prognostic biomarker for non-small cell lung cancer
Authors: Kuempers Christiane , Jagomast Tobias , Heidel Carsten , Paulsen Finn-Ole , Bohnet Sabine , Schierholz Stefanie , Dreyer Eva , Kirfel Jutta , Perner Sven
Published: September 2022

Aim

Non-small cell lung cancer (NSCLC) remains the leading cause of cancer-related death globally despite promising progress of personalized therapy approaches. Cyclin-dependent kinase 7 (CDK7) is a kinase involved in transcription, overexpressed in a broad spectrum of cancer types and found to be associated with an unfavourable prognosis. In this study, we aimed to investigate the protein expression of CDK7 in a large cohort of NSCLC incorporating adenocarcinomas (adNSCLC) and squamous cell carcinomas (sqNSCLC) and to correlate its expression with clinicopathological data.

Methods

We performed immunohistochemical staining of CDK7 on our cohort of NSCLC including 258 adNSCLC and 101 sqNSCLC and measured protein expression via a semi-automated read out. According to the median value of CDK7 the cohort was stratified in a CDK7 high and low expressing group, respectively, and results were correlated with clinico-pathological data.

Results

CDK7 was significantly higher expressed in sqNSCLC than in adNSCLC. In the group of sqNSCLC, CDK7 expression was significantly higher in sqNSCLC with lymph node metastases than in sqNSCLC with N0 stage. We found a significantly worse overall survival and disease-free survival for patients with CDK7 high expressing NSCLC.

Conclusion

Since a high CDK7 expression seems to be linked with a poor prognosis it might serve as a promising novel prognostic biomarker and its assessment could be implied in future routine diagnostic workup of NSCLC samples. Considering that CDK7 inhibitors are currently tested in several trials for advanced solid malignancies, it may also be a new target for future anti-cancer therapy.
Antitumor effects of Chinese herbal medicine compounds and their nano-formulations on regulating the immune system microenvironment
Authors: Sun Kexiang , Wu Linguangjin , Wang Shuyun , Deng Wanli
Published: September 2022

Traditional Chinese medicine (TCM), including herbal medicine, acupuncture and meditation, has a wide range of applications in China. In recent years, herbal compounding and active ingredients have been used to control tumor growth, reduce suffering, improve quality of life, and prolong the life span of cancer patients. To reduce side effects, herbal medicine can be used in conjunction with radiotherapy and chemotherapy or can be used as an adjuvant to strengthen the immune effect of anticancer vaccines. In particular, in the immunosuppressed tumor microenvironment, herbal medicine can have antitumor effects by stimulating the immune response. This paper reviews the advances in research on antitumor immunomodulation in Chinese herbal medicine, including the regulation of the innate immune system, which includes macrophages, MDSCs, and natural killer cells, and the adaptive immune system, which includes CD4+ T cells, CD8+ T cells, and regulatory T cells (Tregs), to influence tumor-associated inflammation. In addition, a combination of active ingredients of herbal medicine and modern nanotechnology alter the tumor immune microenvironment. In recent years, immunological antitumor therapy in TCM has been applied on a reasonably large scale both nationally and internationally, and there is potential for further clinical expansion. Investigation of immune modulation mechanisms in Chinese herbal medicine will provide novel perspectives of how herbal medicine controls tumor growth and metastasis, which will contribute to the evolution of tumor research.

Methodology

Experimental research between the years of 2012-2022, meta-analysis and reviews for the period 2002-2022 found on the Databases including PubMed, Embase, and the Cochrane database were used. The inclusion criteria were experimental research literature addressing the anti-tumor immunological effects of active ingredients and nanoparticles in Chinese herbal medicine. Exclusion criteria were articles that addressed Chinese herbal medicine and nano-formulations without discussing anti-tumor immunological effects in innate, adaptive immune cells, MDSCs, and nuclear factors.
Case report: Strategies for improving outcomes in patients with primary ovarian small-cell neuroendocrine carcinoma
Authors: Li YingYing , Wu Yueling , Zhang Ying , Li Xiaofang
Published: September 2022

Small-cell neuroendocrine carcinoma (SCNEC) of the ovary is a gynecological malignancy characterized by rapid progression and poor prognosis. SCNEC is divided into primary and metastatic tumor. Primary ovarian neuroendocrine cancer is extremely rare and has a low 5-year survival rate. This paper reports the clinical manifestations of a 58-year-old patient with primary ovarian Small-cell neuroendocrine carcinoma and the prognosis after surgical adjuvant chemotherapy. The prevailing literature on this carcinoma is also reviewed and summarized. Our analysis reveals that histopathological examination is the standard diagnostic tool for ovarian SCNEC. We also highlight the importance of comprehensive imaging evaluation, early pathological diagnosis and comprehensive aggressive treatment to the prognosis of patients.
Identification of cuproptosis-related patterns and construction of a scoring system for predicting prognosis, tumor microenvironment-infiltration characteristics, and immunotherapy efficacy in breast cancer
Authors: Li Wei , Zhang Xingda , Chen Yanbo , Pang Da
Published: September 2022

Background

Cuproptosis, a recently discovered refreshing form of cell death, is distinct from other known mechanisms. As copper participates in cell death, the induction of cancer cell death with copper ionophores may emerge as a new avenue for cancer treatment. However, the role of cuproptosis in tumor microenvironment (TME) cell infiltration remains unknown.

Methods

We systematically evaluated the cuproptosis patterns in The Cancer Genome Atlas (TCGA) database in breast cancer (BRCA) samples based on 10 cuproptosis-related genes (CRGs), and correlated these patterns with the prognosis and characteristics of TME cell infiltration. A principal component analysis algorithm was used to construct a cuproptosis score to quantify the cuproptosis pattern in individual tumors. Further, the relationships between the cuproptosis score and transcription background, clinical features, characteristics of TME cell infiltration, drug response, and efficacy of immunotherapy were assessed.

Results

Two distinct cuproptosis patterns with distinct prognoses were identified; their TME characteristics were found to be consistent with the immune-excluded and immune-inflamed phenotypes, respectively. The cuproptosis patterns in individual patients were evaluated using the cuproptosis score based on the cuproptosis phenotype-related genes, contributing to distinguishing biological processes, clinical outcome, immune cell infiltration, genetic variation, and drug response. Univariate and multivariate Cox regression analyses verified this score as an independent prognostic predictor in BRCA. A high cuproptosis score, characterized by immune activation, suggests an inflamed tumor and immune-inflamed phenotype with poor survival and a low cuproptosis score, characterized by immune suppression, indicates a non-inflamed tumor and immune-excluded phenotype with better survival. Significant differences were observed in the IC50 between the high and low cuproptosis score groups receiving chemotherapy and targeted therapy drugs. In the two immunotherapy cohorts, patients with a higher cuproptosis score experienced considerable therapeutic advantages and clinical benefits.

Conclusions

This study is the first to elucidate the prominent role of cuproptosis in the clinical outcome and the formation of TME diversity and complexity in BRCA. Estimating cuproptosis patterns in tumors could help predict the prognosis and characteristics of TME cell infiltration and guide more effective chemotherapeutic and immunotherapeutic strategies.
The oncogenic roles of JC polyomavirus in cancer
Authors: Zheng Hua-chuan , Xue Hang , Zhang Cong-yu
Published: September 2022

JC polyomavirus (JCPyV) belongs to the human polyomavirus family. Based on alternative splicing, the early region encodes the large and small T antigens, while the late region encodes the capsid structural proteins (VP1, VP2, and VP3) and the agnoprotein. The regulatory transcription factors for JCPyV include Sp1, TCF-4, DDX1, YB-1, LCP-1, Purα, GF-1, and NF-1. JCPyV enters tonsillar tissue through the intake of raw sewage, inhalation of air droplets, or parent-to-child transmission. It persists quiescently in lymphoid and renal tissues during latency. Both TGF-β1 and TNF-α stimulates JCPyV multiplication, while interferon-γ suppresses the process. The distinct distribution of caspid receptors (α-2, 6-linked sialic acid, non-sialylated glycosaminoglycans, and serotonin) determines the infection capabilities of JCPyV virions, and JCPyV entry is mediated by clathrin-mediated endocytosis. In permissive cells, JCPyV undergoes lytic proliferation and causes progressive multifocal leukoencephalopathy, while its DNA is inserted into genomic DNA and leads to carcinogenesis in non-permissive cells. T antigen targets p53, β-catenin, IRS, Rb, TGF-β1, PI3K/Akt and AMPK signal pathways in cancer cells. Intracranial injection of T antigen into animals results in neural tumors, and transgenic mice develop neural tumors, lens tumor, breast cancer, gastric, Vater’s, colorectal and pancreatic cancers, insulinoma, and hepatocellular carcinoma. Additionally, JCPyV DNA and its encoded products can be detected in the brain tissues of PML patients and brain, oral, esophageal, gastric, colorectal, breast, cervical, pancreatic, and hepatocellular cancer tissues. Therefore, JCPyV might represent an etiological risk factor for carcinogenesis and should be evaluated for early prevention, diagnosis, and treatment of cancers.
Mechanisms of FLASH effect
Authors: Lin Binwei , Huang Dan , Gao Feng , Yang Yiwei , Wu Dai , Zhang Yu , Feng Gang , Dai Tangzhi , Du Xiaobo
Published: September 2022

FLASH radiotherapy (FLASH-RT) is a novel radiotherapy technology defined as ultra-high dose rate (≥ 40 Gy/s) radiotherapy. The biological effects of FLASH-RT include two aspects: first, compared with conventional dose rate radiotherapy, FLASH-RT can reduce radiation-induced damage in healthy tissue, and second, FLASH-RT can retain antitumor effectiveness. Current research shows that mechanisms of the biological effects of FLASH-RT are related to oxygen. However, due to the short time of FLASH-RT, evidences related to the mechanisms are indirect, and the exact mechanisms of the biological effects of FLASH-RT are not completely clear and some are even contradictory. This review focuses on the mechanisms of the biological effects of FLASH-RT and proposes future research directions.