Artificial intelligence-based analysis of tumor-infiltrating lymphocyte spatial distribution for colorectal cancer prognosis

BACKGROUND

Artificial intelligence (AI) technology represented by deep learning has made remarkable achievements in digital pathology, enhancing the accuracy and reliability of diagnosis and prognosis evaluation. The spatial distribution of CD3 + and CD8 + T cells within the tumor microenvironment has been demonstrated to have a significant impact on the prognosis of colorectal cancer (CRC). This study aimed to investigate CD3 CT (CD3 + T cells density in the core of the tumor [CT]) prognostic ability in patients with CRC by using AI technology.

METHODS

The study involved the enrollment of 492 patients from two distinct medical centers, with 358 patients assigned to the training cohort and an additional 134 patients allocated to the validation cohort. To facilitate tissue segmentation and T-cells quantification in whole-slide images (WSIs), a fully automated workflow based on deep learning was devised. Upon the completion of tissue segmentation and subsequent cell segmentation, a comprehensive analysis was conducted.

RESULTS

The evaluation of various positive T cell densities revealed comparable discriminatory ability between CD3 CT and CD3-CD8 (the combination of CD3 + and CD8 + T cells density within the CT and invasive margin) in predicting mortality (C-index in training cohort: 0.65 vs. 0.64; validation cohort: 0.69 vs. 0.69). The CD3 CT was confirmed as an independent prognostic factor, with high CD3 CT density associated with increased overall survival (OS) in the training cohort (hazard ratio [HR] = 0.22, 95% confidence interval [CI]: 0.12-0.38, P <0.001) and validation cohort (HR = 0.21, 95% CI: 0.05-0.92, P = 0.037).

CONCLUSIONS

We quantify the spatial distribution of CD3 + and CD8 + T cells within tissue regions in WSIs using AI technology. The CD3 CT confirmed as a stage-independent predictor for OS in CRC patients. Moreover, CD3 CT shows promise in simplifying the CD3-CD8 system and facilitating its practical application in clinical settings.

Thrombospondin 1 and Reelin act through Vldlr to regulate cardiac growth and repair

Adult mammalian cardiomyocytes have minimal cell cycle capacity, which leads to poor regeneration after cardiac injury such as myocardial infarction. Many positive regulators of cardiomyocyte cell cycle and cardioprotective signals have been identified, but extracellular signals that suppress cardiomyocyte proliferation are poorly understood. We profiled receptors enriched in postnatal cardiomyocytes, and found that very-low-density-lipoprotein receptor (Vldlr) inhibits neonatal cardiomyocyte cell cycle. Paradoxically, Reelin, the well-known Vldlr ligand, expressed in cardiac Schwann cells and lymphatic endothelial cells, promotes neonatal cardiomyocyte proliferation. Thrombospondin1 (TSP-1), another ligand of Vldlr highly expressed in adult heart, was then found to inhibit cardiomyocyte proliferation through Vldlr, and may contribute to Vldlr's overall repression on proliferation. Mechanistically, Rac1 and subsequent Yap phosphorylation and nucleus translocation mediate the regulation of the cardiomyocyte cell cycle by TSP-1/Reelin-Vldlr signaling. Importantly, Reln mutant neonatal mice displayed impaired cardiomyocyte proliferation and cardiac regeneration after apical resection, while cardiac-specific Thbs1 deletion and cardiomyocyte-specific Vldlr deletion promote cardiomyocyte proliferation and are cardioprotective after myocardial infarction. Our results identified a novel role of Vldlr in consolidating extracellular signals to regulate cardiomyocyte cell cycle activity and survival, and the overall suppressive TSP-1-Vldlr signal may contribute to the poor cardiac repair capacity of adult mammals.

Development of a SNP-based strain-identified method for Streptococcus thermophilus CICC 6038 and Lactobacillus delbrueckii ssp. bulgaricus CICC 6047 using pan-genomics analysis

The health benefits conferred by probiotics is specific to individual probiotic strains, highlighting the importance of identifying specific strains for research and production purposes. Streptococcus thermophilus CICC 6038 and Lactobacillus delbrueckii ssp. bulgaricus CICC 6047 are exceedingly valuable for commercial use with an excellent mixed-culture fermentation. To differentiate these 2 strains from other S. thermophilus and L. delbrueckii ssp. bulgaricus, a specific, sensitive, accurate, rapid, convenient, and cost-effective method is required. In this study, we conducted a pan-genome analysis of S. thermophilus and L. delbrueckii ssp. bulgaricus to identify species-specific core genes, along with strain-specific single-nucleotide polymorphisms (SNPs). These genes were used to develop suitable PCR primers, and the conformity of sequence length and unique SNPs was confirmed by sequencing for qualitative identification at the strain level. The results demonstrated that SNPs analysis of PCR products derived from these primers could distinguish CICC 6038 and CICC 6047 accurately and reproducibly from the other strains of S. thermophilus and L. delbrueckii ssp. bulgaricus, respectively. The strain-specific PCR method based on SNPs herein is universally applicable for probiotics identification. It offers valuable insights into identifying probiotics at the strain level that is fit-for-purpose in quality control and compliance assessment of commercial dairy products.

Identification and quantification of viable Lacticaseibacillus rhamnosus in probiotics using validated PMA-qPCR method

The identification and quantification of viable bacteria at the species/strain level in compound probiotic products is challenging now. Molecular biology methods, e.g., propidium monoazide (PMA) combination with qPCR, have gained prominence for targeted viable cell counts. This study endeavors to establish a robust PMA-qPCR method for viable Lacticaseibacillus rhamnosus detection and systematically validated key metrics encompassing relative trueness, accuracy, limit of quantification, linear, and range. The inclusivity and exclusivity notably underscored high specificity of the primers for L. rhamnosus, which allowed accurate identification of the target bacteria. Furthermore, the conditions employed for PMA treatment were fully verified by 24 different L. rhamnosus including type strain, commercial strains, etc., confirming its effective discrimination between live and dead bacteria. A standard curve constructed by type strain could apply to commercial strains to convert qPCR Cq values to viable cell numbers. The established PMA-qPCR method was applied to 46 samples including pure cultures, probiotics as food ingredients, and compound probiotic products. Noteworthy is the congruity observed between measured and theoretical values within a 95% confidence interval of the upper and lower limits of agreement, demonstrating the relative trueness of this method. Moreover, accurate results were obtained when viable L. rhamnosus ranging from 103 to 108 CFU/mL. The comprehensive appraisal of PMA-qPCR performances provides potential industrial applications of this new technology in quality control and supervision of probiotic products.

Effects of empagliflozin on progression of chronic kidney disease: a prespecified secondary analysis from the empa-kidney trial

BACKGROUND

Sodium-glucose co-transporter-2 (SGLT2) inhibitors reduce progression of chronic kidney disease and the risk of cardiovascular morbidity and mortality in a wide range of patients. However, their effects on kidney disease progression in some patients with chronic kidney disease are unclear because few clinical kidney outcomes occurred among such patients in the completed trials. In particular, some guidelines stratify their level of recommendation about who should be treated with SGLT2 inhibitors based on diabetes status and albuminuria. We aimed to assess the effects of empagliflozin on progression of chronic kidney disease both overall and among specific types of participants in the EMPA-KIDNEY trial.

METHODS

EMPA-KIDNEY, a randomised, controlled, phase 3 trial, was conducted at 241 centres in eight countries (Canada, China, Germany, Italy, Japan, Malaysia, the UK, and the USA), and included individuals aged 18 years or older with an estimated glomerular filtration rate (eGFR) of 20 to less than 45 mL/min per 1·73 m2, or with an eGFR of 45 to less than 90 mL/min per 1·73 m2 with a urinary albumin-to-creatinine ratio (uACR) of 200 mg/g or higher. We explored the effects of 10 mg oral empagliflozin once daily versus placebo on the annualised rate of change in estimated glomerular filtration rate (eGFR slope), a tertiary outcome. We studied the acute slope (from randomisation to 2 months) and chronic slope (from 2 months onwards) separately, using shared parameter models to estimate the latter. Analyses were done in all randomly assigned participants by intention to treat. EMPA-KIDNEY is registered at ClinicalTrials.gov, NCT03594110.

FINDINGS

Between May 15, 2019, and April 16, 2021, 6609 participants were randomly assigned and then followed up for a median of 2·0 years (IQR 1·5-2·4). Prespecified subgroups of eGFR included 2282 (34·5%) participants with an eGFR of less than 30 mL/min per 1·73 m2, 2928 (44·3%) with an eGFR of 30 to less than 45 mL/min per 1·73 m2, and 1399 (21·2%) with an eGFR 45 mL/min per 1·73 m2 or higher. Prespecified subgroups of uACR included 1328 (20·1%) with a uACR of less than 30 mg/g, 1864 (28·2%) with a uACR of 30 to 300 mg/g, and 3417 (51·7%) with a uACR of more than 300 mg/g. Overall, allocation to empagliflozin caused an acute 2·12 mL/min per 1·73 m2 (95% CI 1·83-2·41) reduction in eGFR, equivalent to a 6% (5-6) dip in the first 2 months. After this, it halved the chronic slope from -2·75 to -1·37 mL/min per 1·73 m2 per year (relative difference 50%, 95% CI 42-58). The absolute and relative benefits of empagliflozin on the magnitude of the chronic slope varied significantly depending on diabetes status and baseline levels of eGFR and uACR. In particular, the absolute difference in chronic slopes was lower in patients with lower baseline uACR, but because this group progressed more slowly than those with higher uACR, this translated to a larger relative difference in chronic slopes in this group (86% [36-136] reduction in the chronic slope among those with baseline uACR <30 mg/g compared with a 29% [19-38] reduction for those with baseline uACR ≥2000 mg/g; ptrend<0·0001).

INTERPRETATION

Empagliflozin slowed the rate of progression of chronic kidney disease among all types of participant in the EMPA-KIDNEY trial, including those with little albuminuria. Albuminuria alone should not be used to determine whether to treat with an SGLT2 inhibitor.

FUNDING

Boehringer Ingelheim and Eli Lilly.

Fermentation characteristics and postacidification of yogurt by Streptococcus thermophilus CICC 6038 and Lactobacillus delbrueckii ssp. bulgaricus CICC 6047 at optimal inoculum ratio

This study aimed to investigate the symbiosis between Streptococcus thermophilus CICC 6038 and Lactobacillus delbrueckii ssp. bulgaricus CICC 6047. In addition, the effect of their different inoculum ratios was determined, and comparison experiments of fermentation characteristics and storage stability of milk fermented by their monocultures and cocultures at optimal inoculum ratio were performed. We found the time to obtain pH 4.6 and ΔpH during storage varied among 6 inoculum ratios (1:1, 2:1, 10:1, 19:1, 50:1, 100:1). By the statistical model to evaluate the optimal ratio, the ratio of 19:1 was selected, which exhibited high acidification rate and low postacidification with pH values remaining between 4.2 and 4.4 after a 50-d storage. Among the 3 groups included in our analyses (i.e., the monocultures of S. thermophilus CICC 6038 [St] and Lb. bulgaricus CICC 6047 [Lb] and their cocultures [St+Lb] at 19:1), the coculture group showed higher acidification activity, improved rheological properties, richer typical volatile compounds, more desirable sensor quality after the fermentation process than the other 2 groups. However, the continuous accumulation of acetic acid during storage showed that acetic acid was more highly correlated with postacidification than d-lactic acid for the Lb group and St+Lb group. Our study emphasized the importance of selecting an appropriate bacterial consortium at the optimal inoculum ratio to achieve favorable fermentation performance and enhanced postacidification stability during storage.

Impact of primary kidney disease on the effects of empagliflozin in patients with chronic kidney disease: secondary analyses of the EMPA-KIDNEY trial

BACKGROUND

The EMPA-KIDNEY trial showed that empagliflozin reduced the risk of the primary composite outcome of kidney disease progression or cardiovascular death in patients with chronic kidney disease mainly through slowing progression. We aimed to assess how effects of empagliflozin might differ by primary kidney disease across its broad population.

METHODS

EMPA-KIDNEY, a randomised, controlled, phase 3 trial, was conducted at 241 centres in eight countries (Canada, China, Germany, Italy, Japan, Malaysia, the UK, and the USA). Patients were eligible if their estimated glomerular filtration rate (eGFR) was 20 to less than 45 mL/min per 1·73 m2, or 45 to less than 90 mL/min per 1·73 m2 with a urinary albumin-to-creatinine ratio (uACR) of 200 mg/g or higher at screening. They were randomly assigned (1:1) to 10 mg oral empagliflozin once daily or matching placebo. Effects on kidney disease progression (defined as a sustained ≥40% eGFR decline from randomisation, end-stage kidney disease, a sustained eGFR below 10 mL/min per 1·73 m2, or death from kidney failure) were assessed using prespecified Cox models, and eGFR slope analyses used shared parameter models. Subgroup comparisons were performed by including relevant interaction terms in models. EMPA-KIDNEY is registered with ClinicalTrials.gov, NCT03594110.

FINDINGS

Between May 15, 2019, and April 16, 2021, 6609 participants were randomly assigned and followed up for a median of 2·0 years (IQR 1·5-2·4). Prespecified subgroupings by primary kidney disease included 2057 (31·1%) participants with diabetic kidney disease, 1669 (25·3%) with glomerular disease, 1445 (21·9%) with hypertensive or renovascular disease, and 1438 (21·8%) with other or unknown causes. Kidney disease progression occurred in 384 (11·6%) of 3304 patients in the empagliflozin group and 504 (15·2%) of 3305 patients in the placebo group (hazard ratio 0·71 [95% CI 0·62-0·81]), with no evidence that the relative effect size varied significantly by primary kidney disease (pheterogeneity=0·62). The between-group difference in chronic eGFR slopes (ie, from 2 months to final follow-up) was 1·37 mL/min per 1·73 m2 per year (95% CI 1·16-1·59), representing a 50% (42-58) reduction in the rate of chronic eGFR decline. This relative effect of empagliflozin on chronic eGFR slope was similar in analyses by different primary kidney diseases, including in explorations by type of glomerular disease and diabetes (p values for heterogeneity all >0·1).

INTERPRETATION

In a broad range of patients with chronic kidney disease at risk of progression, including a wide range of non-diabetic causes of chronic kidney disease, empagliflozin reduced risk of kidney disease progression. Relative effect sizes were broadly similar irrespective of the cause of primary kidney disease, suggesting that SGLT2 inhibitors should be part of a standard of care to minimise risk of kidney failure in chronic kidney disease.

FUNDING

Boehringer Ingelheim, Eli Lilly, and UK Medical Research Council.

[Survival analysis of malignant tumors in cancer registration areas of Hubei province in China, 2013 to 2015]

Objective: To analyze the survival of newly diagnosed malignant tumors in cancer registration areas of Hubei Province from 2013 to 2015. Methods: From January 1, 2013 to December 31, 2015, all newly diagnosed malignant tumors were collected from cancer registration areas in Hubei Province, and patients were followed up using a combination of active and passive methods. Cancer survival was analyzed using the strs package in Stata software. Observed and expected survival were calculated using the life table and Ederer Ⅱ methods, and the difference in survival rate of patients with different sex, age, urban and rural areas and different cancer species was compared. Results: From 2013 to 2015, 83 987 new malignant tumors were diagnosed in cancer registration areas in Hubei Province, including 45 742 males (54.46%) and 38245 females (45.54%). The overall 5-year relative survival rate was 41.46%, 34.43% for men and 49.63% for women. With the increase of age, the observed survival rate and relative survival rate of patients of different genders showed a decreasing trend. The 5-year relative survival rate of patients with malignant tumors was 47.58% in urban areas and 26.58% in rural areas. The observed survival rate and relative survival rate in rural areas were significantly lower than those in urban areas. The overall 5-year relative survival rates for common malignancies were 20.61% for lung cancer, 15.36% for liver cancer, 22.89% for esophageal cancer, 34.92% for gastric cancer, and 54.87% for colorectal cancer. In addition, the 5-year relative survival rates of common malignant tumors in women were 78.65% for breast cancer and 52.55% for cervical cancer. Conclusions: In Hubei Province, the survival rate of malignant tumors is different among different genders, regions, age groups and cancer species. Prevention and treatment and health education should be strengthened for malignant tumor patients in rural areas and those with high incidence and low survival rate such as liver cancer and lung cancer, and relevant strategies should be formulated according to the gender and age distribution characteristics of different cancer species.

Artificial intelligence-assisted analysis for tumor-immune interaction within the invasive margin of colorectal cancer

BACKGROUND

In colorectal cancer (CRC), both tumor invasion and immunological analysis at the tumor invasive margin (IM) are significantly associated with patient prognosis, but have traditionally been reported independently. We propose a new scoring system, the TGP-I score, to assess the association and interactions between tumor growth pattern (TGP) and tumor infiltrating lymphocytes at the IM and to predict its prognostic validity for CRC patient stratification.

MATERIALS AND METHODS

The types of TGP were assessed in hematoxylin and eosin-stained whole-slide images. The CD3⁺ T-cells density at the IM was automatically quantified on immunohistochemical-stained slides using a deep learning method. A discovery (N = 347) and a validation (N = 132) cohorts were used to evaluate the prognostic value of the TGP-I score for overall survival.

RESULTS

The TGP-I score₃ (trichotomy) was an independent prognostic factor, with higher TGP-I score₃ associated with worse prognosis in the discovery (unadjusted hazard ratio [HR] for high vs. low 3.62, 95% confidence interval [CI] 2.22-5.90; p < 0.001) and validation cohort (unadjusted HR for high vs. low 5.79, 95% CI 1.84-18.20; p = 0.003). The relative contribution of each parameter to predicting survival was analyzed. The TGP-I score₃ had similar importance compared to tumor-node-metastasis staging (31.2% vs. 32.9%) and was stronger than other clinical parameters.

CONCLUSIONS

This automated workflow and the proposed TGP-I score could further provide accurate prognostic stratification and have potential value for supporting the clinical decision-making of stage I-III CRC patients.Key messagesA new scoring system, the TGP-I score, was proposed to assess the association and interactions of TGP and TILs at the tumor invasive margin.TGP-I score could be an independent predictor of prognosis for CRC patients, with higher scores being associated with worse survival.TGP-I score had similar importance compared to tumor-node-metastasis staging and was stronger than other clinical parameters.

An artificial intelligence-based ecological index for prognostic evaluation of colorectal cancer

BACKGROUND AND OBJECTIVE

In the tumor microenvironment (TME), the dynamic interaction between tumor cells and immune cells plays a critical role in predicting the prognosis of colorectal cancer. This study introduces a novel approach based on artificial intelligence (AI) and immunohistochemistry (IHC)-stained whole-slide images (WSIs) of colorectal cancer (CRC) patients to quantitatively assess the spatial associations between tumor cells and immune cells. To achieve this, we employ the Morisita-Horn ecological index (Mor-index), which allows for a comprehensive analysis of the spatial distribution patterns between tumor cells and immune cells within the TME.

MATERIALS AND METHODS

In this study, we employed a combination of deep learning technology and traditional computer segmentation methods to accurately segment the tumor nuclei, immune nuclei, and stroma nuclei within the tumor regions of IHC-stained WSIs. The Mor-index was used to assess the spatial association between tumor cells and immune cells in TME of CRC patients by obtaining the results of cell nuclei segmentation. A discovery cohort (N = 432) and validation cohort (N = 137) were used to evaluate the prognostic value of the Mor-index for overall survival (OS).

RESULTS

The efficacy of our method was demonstrated through experiments conducted on two datasets comprising a total of 569 patients. Compared to other studies, our method is not only superior to the QuPath tool but also produces better segmentation results with an accuracy of 0.85. Mor-index was quantified automatically by our method. Survival analysis indicated that the higher Mor-index correlated with better OS in the discovery cohorts (HR for high vs. low 0.49, 95% CI 0.27-0.77, P = 0.0014) and validation cohort (0.21, 0.10-0.46, < 0.0001).

CONCLUSION

This study provided a novel AI-based approach to segmenting various nuclei in the TME. The Mor-index can reflect the immune status of CRC patients and is associated with favorable survival. Thus, Mor-index can potentially make a significant role in aiding clinical prognosis and decision-making.

Development and validation of a scoring system incorporating tumor growth pattern and perineural invasion for risk stratification in colorectal cancer

Tumor growth pattern (TGP) and perineural invasion (PNI) at the invasive margin have been recognized as indicators of tumor invasiveness and prognostic events in colorectal cancer (CRC). This study aims to develop a scoring system incorporating TGP and PNI, and further investigate its prognostic significance for CRC risk stratification. A scoring system, termed tumor-invasion score, was established by summing TGP and PNI scores. The discovery cohort (N = 444) and the validation cohort (N = 339) were used to explore the prognostic significance of the tumor-invasion score. The endpoints of the event were disease-free survival (DFS) and overall survival (OS) which were analyzed by the Cox proportional hazard model. In the discovery cohort, Cox regression analysis showed that DFS and OS were inferior for score 4 group compared with score 1 group (DFS, hazard ratio (HR) 4.44, 95% confidence interval (CI) 2.49-7.92, p < 0.001; OS, 4.41, 2.37-8.19,p < 0.001). The validation cohort showed similar results (DFS, 4.73, 2.39-9.37, p < 0.001; OS, 5.52, 2.55-12.0, p < 0.001). The model combining tumor-invasion score and clinicopathologic information showed good discrimination performance than single predictors. TGP and PNI were associated with tumor invasiveness and survival in CRC. The tumor-invasion score generated by TGP and PNI scores served as an independent prognostic parameter of DFS and OS for CRC patients.

Desmoplastic Reaction Associates with Prognosis and Adjuvant Chemotherapy Response in Colorectal Cancer: A Multicenter Retrospective Study

Desmoplastic reaction (DR) is one of many tumor-host interactions and is associated with the overall survival (OS) of patients with colorectal cancer. However, the clinical significance of DR requires further study in large multicenter cohorts and its predictive value in adjuvant chemotherapy (ACT) response remains unclear. Here, a total of 2,225 patients with colorectal cancer from five independent institutions were divided into primary (N = 1,012 from two centers) and validation (N = 1,213 from three centers) cohorts. DR was classified as immature, middle, or mature depending on the presence of myxoid stroma and hyalinized collagen bundles at the invasive front of the primary tumor. OS among different subgroups were compared, and the correlations of DR type with tumor-infiltrating lymphocytes (TILs) within stroma, tumor stroma ratio (TSR), and Stroma AReactive Invasion Front Areas (SARIFA) were also analyzed. In the primary cohort, patients with mature DR had the highest 5-year survival rate. These findings were confirmed in validation cohort. In addition, for stage II colorectal cancer, patients classified as non-mature DR would benefit from ACT compared with surgery alone. Furthermore, immature and middle DR were more associated with high TSR, less distribution of TILs within stroma and positive SARIFA compared with mature. Taken together, these data suggest that DR is a robust-independent prognostic factor for patients with colorectal cancer. For patients with stage II colorectal cancer, non-mature DR could be a potential marker for recognizing high-risk patients who may benefit from ACT.

Significance

DR has the potential to identify patients with high-risk colorectal cancer and predict the efficacy of adjuvant chemotherapy in patients with stage II colorectal cancer. Our findings support reporting DR types as additional pathologic parameters in clinical practice for more precise risk stratification.

Necrosis score as a prognostic factor in stage I-III colorectal cancer: a retrospective multicenter study

BACKGROUND

Tumor necrosis results from failure to meet the requirement for rapid proliferation of tumor, related to unfavorable prognosis in colorectal cancer (CRC). However, previous studies used traditional microscopes to evaluate necrosis on slides, lacking a simultaneous phase and panoramic view for assessment. Therefore, we proposed a whole-slide images (WSIs)-based method to develop a necrosis score and validated its prognostic value in multicenter cohorts.

METHODS

Necrosis score was defined as the proportion of necrosis in the tumor area, semi-quantitatively classified into 3-level score groups by the cut-off of 10% and 30% on HE-stained WSIs. 768 patients from two centers were enrolled in this study, divided into a discovery (N = 445) and a validation (N = 323) cohort. The prognostic value of necrosis score was evaluated by Kaplan-Meier curves and the Cox model.

RESULT

Necrosis score was associated with overall survival, with hazard ratio for high vs. low in discovery and validation cohorts being 2.62 (95% confidence interval 1.59-4.32) and 2.51 (1.39-4.52), respectively. The 3-year disease free survival rates of necrosis-low, middle, and high were 83.6%, 80.2%, and 59.8% in discovery cohort, and 86.5%, 84.2%, and 66.5% in validation cohort. In necrosis middle plus high subgroup, there was a trend but no significant difference in overall survival between surgery alone and adjuvant chemotherapy group in stage II CRC (P = .075).

CONCLUSION

As a stable prognostic factor, high-level necrosis evaluated by the proposed method on WSIs was associated with unfavorable outcomes. Additionally, adjuvant chemotherapy provide survival benefits for patients with high necrosis in stage II CRC.

[Clinical and genetics characteristics of adult-onset cerebrotendinous xanthomatosis: analysis of a Chinese pedigree]

Objective: Clinical manifestations, imaging findings, pathologic features, and genetic mutations of Chinese adult patients with cerebrotendinous xanthomatosis (CTX) were analyzed in order to achieve a greater understanding of CTX that can improve early detection, diagnosis, and treatment. Methods: Clinical data including medical history, neurologic and auxiliary examinations, imaging findings, and genetic profile were collected for an adult patient with CTX admitted to the Sixth Medical Center of Chinese People's Liberation Army General Hospital in August 2020. Additionally, a systematic review of genetically diagnosed Chinese adult CTX cases reported in major databases in China and other countries was performed and age of onset, first symptoms, common signs and symptoms, pathologic findings, imaging changes, and gene mutations were analyzed. Results: The proband was a 39-year-old female with extensive, early-onset nervous system manifestations including cognitive dysfunction and ataxia. Systemic lesions included juvenile cataract and a tendon mass. Cranial magnetic resonance imaging revealed cerebral atrophy, symmetric white matter changes predominantly in the pyramidal tract, and lesions in the cerebellar dentate nucleus. A novel homozygous mutation in the sterol-27-hydroxylase (CYP27A1) gene (c.1477-2A>C) was identified. There were no family members with similar clinical presentation although some were carriers of the c.1477-2A>C mutation. The patient showed a good response to deoxycholic acid treatment. Totally there were 56 cases of adult CTX patients in China, mostly in East China (31/56, 55.4%), at a male-to-female ratio of 1.8 to 1. Multiple organs and tissues including nervous system, tendon, lens, lung, and skeletal muscle were affected in these cases. The most common neurologic manifestations were cognitive dysfunction (44/52, 84.6%) and ataxia (44/51, 86.3%). The cases were characterized by early onset, chronic progressive damage of multiple systems, long disease course, and delayed diagnosis, making the disease difficult to manage clinically and resulting in poor prognosis. The 2 most common genetic mutations in Chinese adult CTX patients were c.1263+1G>A and c.379C>T. Exon 2 of the CYP27A1 gene was identified as a mutation hot spot. Conclusions: Chinese adult patients with CTX have complex clinical characteristics, a long diagnostic cycle, and various CYP27A1 gene mutations. Early diagnosis and intervention can improve the prognosis of these patients.

Predictors of postoperative biochemical remission in lower Knosp grade growth hormone-secreting pituitary adenomas: a large single center study

PURPOSE

Growth hormone-secreting pituitary adenomas (GH-PAs) with a low Knosp grade are typically associated with a good postoperative biochemical remission (BR) rate. However, a proportion of patients do not achieve remission. In this study, we aimed to investigate predictive factors of postoperative remission for lower Knosp GH-PAs.

METHODS

In this retrospective study, we enrolled 140 patients who were diagnosed with lower Knosp (0-2) GH-PAs and received trans-sphenoidal surgery between December 2016 and June 2021 from the largest pituitary tumor surgery center in southern China. The univariate, binary Logistic regression, and receiver operating characteristic curve (ROC) analyses were employed to determine independent predictors and cutoff values of remission. The postoperative outcome was defined as remission using the 2010 consensus criteria of acromegaly.

RESULTS

One hundred and thirty six patients (97.1%) achieved gross total resection. The postoperative long-term BR was 68.6%. Empty sella, tumor maximum diameter and postoperative GH levels were independent factors predicting remission. ROC revealed that postoperative 24 h GH ≤ 1.3 ng/mL and  ≤ 1.23 ng/mL were valuable predictors for 3-month and long-term remission respectively, and that postoperative 3-month GH ≤ 1.6 ng/mL and tumor maximum diameter  ≤ 17 mm were predictors for delayed remission.

CONCLUSION

Early postoperative GH levels can be used as predictors of remission. However, BR was not associated with preoperative somatostatin analogs therapy or Knosp grade (0-2). For patients without residual tumor or recurrence and whose GH levels are slightly elevated within 1 year after surgery, adjuvant treatments may not be necessary.

[Evaluation of clinical safety and diagnostic efficacy of domestic liver-specific magnetic resonance contrast agent (gadoxetate disodium)]

Objective: To evaluate the clinical safety and diagnostic efficacy of domestic gadoxetate disodium (GdEOBDTPA). Methods: The imaging data from patients with space-occupying liver lesions who underwent GdEOBDTPA enhanced magnetic resonance examination at West China Hospital of Sichuan University between January 2020 and September 2020 were analyzed retrospectively. Clinical indicators were evaluated by the incidental condition of transient severe respiratory motion artifacts (TSM) in the arterial phase to assess the safety profile.The differences in quantitative and qualitative indicators for the risk factors of TSM in the arterial phase between the TSM group and the non-TSM group were compared by t-test and χ2 test. Observational indicators of the accuracy of diagnostic procedures: The 2018 version of the Liver Imaging Reporting and Data System (LI-RADS) was used to evaluate the main signs, auxiliary signs, and LR grades of lesions. Postoperative pathological findings were used as the gold standard for evaluating and diagnosing hepatocellular carcinoma (HCC). Simultaneously, the relative enhancement degree of the liver, the contrast between the lesion and the liver, and the cholangiography in the hepatobiliary phase were evaluated. The McNemar test was used to compare the differences in the diagnostic efficiency of physician 1 and physician 2 in the diagnosis of hepatocellular carcinoma according to the 2018 version of LI-RADS. Results: A total of 114 cases were included in this study. The incidence rate of TSM was 9.6% (11/114). Age [(53.8 ± 11.3) years vs. (55.4 ± 15.4) years, t = 0.465, P = 0.497], body weight [(65.8 ± 11.1) kg vs. (60.8 ± 7.6) kg, t = 1.468, P = 0.228], body mass index [(23.9 ± 3.1) kg/m(2) vs. (23.4 ± 3.0) kg/m(2), t = 0.171, P = 0.680], liver cirrhosis ratio (39 cases vs. 4 cases, χ (2) =1.776, P = 0.183), proportion of mild to moderate pleural effusion (32 cases vs. 4 cases, χ (2) = 0.000, P = 0.986), and proportion of mild to moderate ascites (47 cases vs. 5 cases χ (2) = 0.000, P = 0.991) had no statistically significant difference between the groups of non-TSM and TSM patients. According to the 2018 version of LI-RADS for the LR5 category, there was no statistically significant difference between the two physicians' HCC diagnoses in terms of sensitivity (91.4% vs.86.4%, χ (2) = 1.500, P = 0.219), specificity (72.7 % vs. 69.7%, χ (2) = 0.000, P = 1.000), positive predictive value (89.2% vs. 87.5%, χ (2) = 2.250, P = 0.125), negative predictive value (77.4% vs. 67.6%, χ (2) = 2.250, P = 0.125), and accuracy (86.0% vs. 81.6%, χ (2) = 0.131, P = 0.125). According to physicians 1 and 2 film review results, 91.2% (104/114) and 89.5% (102/114) of the contrast agent were discharged into the common bile duct or duodenum, respectively. In addition, 86.0% (98/114) of the patients had good liver enhancement, and 91.2% (104/114) of the lesions showed low signals relative to the liver background. Conclusion: Domestic gadoxetate disodium has a good clinical safety profile and diagnostic efficacy.

Kingella pumchi sp. nov., an organism isolated from human vertebral puncture tissue

A Gram-negative, non-motile rod and strictly aerobic bacterium, designated as 18B16333^T, was isolated from vertebral puncture tissue of a patient at Peking union medical college hospital in China. Growth occurred in NaCl concentrations of 0-1% (w/v) (optimum growth at 0% NaCl), at temperatures of 25-40 °C (optimum growth at 37 °C) and at pH 6.0-9.0 (optimum growth at pH 8.0). Diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine were the predominant polar lipids, and the major fatty acids were C_16:0, C_18:1 ω7c/C_18:1 ω6c and C_16:1 ω7c/C_16:1 ω6c. Phylogenetic analysis based on 16S rRNA gene sequence comparisons indicated that strain 18B16333^T was most closely related to Kingella potus CCUG 49773 ^T (97.3%, 16S rRNA gene sequence identity) and Neisseria bacilliformis CCUG 50858 ^T (96.8%). The ANI values between strain 18B16333^T and the type strains K. potus CCUG 49773 ^T, N. bacilliformis CCUG 50858 ^T, Kingella kingae CCUG 352 ^T and Neisseria gonorrhoeae CCUG 26876 ^T were 77.3%, 79.1%, 72.1% and 75.4%, respectively. The dDDH values between strain 18B16333^T and the four reference strains mentioned above were 24.8%, 26.9%, 24.2% and 20.7%. Further core gene analysis distinctively clustered strain 18B16333^T with four Kingella species but not with Neisseria species. Based on the phenotypic, chemotaxonomic, and phylogenetic properties, strain 18B16333^T represents a novel species of the genus Kingella, for which the name Kingella pumchi sp. nov. is proposed. The type strain is Kingella pumchi 18B16333^T (= CICC 24913 ^T = CCUG 75125 ^T).

Unfavourable intrauterine environment contributes to abnormal gut microbiome and metabolome in twins

OBJECTIVE

Fetal growth restriction (FGR) is a devastating pregnancy complication that increases the risk of perinatal mortality and morbidity. This study aims to determine the combined and relative effects of genetic and intrauterine environments on neonatal microbial communities and to explore selective FGR-induced gut microbiota disruption, metabolic profile disturbances and possible outcomes.

DESIGN

We profiled and compared the gut microbial colonisation of 150 pairs of twin neonates who were classified into four groups based on their chorionicity and discordance of fetal birth weight. Gut microbiota dysbiosis and faecal metabolic alterations were determined by 16S ribosomal RNA and metagenomic sequencing and metabolomics, and the long-term effects were explored by surveys of physical and neurocognitive development conducted after 2~3 years of follow-up.

RESULTS

Adverse intrauterine environmental factors related to selective FGR dominate genetics in their effects of elevating bacterial diversity and altering the composition of early-life gut microbiota, and this effect is positively related to the severity of selective FGR in twins. The influence of genetic factors on gut microbes diminishes in the context of selective FGR. Gut microbiota dysbiosis in twin neonates with selective FGR and faecal metabolic alterations features decreased abundances of Enterococcus and Acinetobacter and downregulated methionine and cysteine levels. Correlation analysis indicates that the faecal cysteine level in early life is positively correlated with the physical and neurocognitive development of infants.

CONCLUSION

Dysbiotic microbiota profiles and pronounced metabolic alterations are associated with selective FGR affected by adverse intrauterine environments, emphasising the possible effects of dysbiosis on long-term neurobehavioural development.

Artificial intelligence for quantifying Crohn's-like lymphoid reaction and tumor-infiltrating lymphocytes in colorectal cancer

Crohn's-like lymphoid reaction (CLR) and tumor-infiltrating lymphocytes (TILs) are crucial for the host antitumor immune response. We proposed an artificial intelligence (AI)-based model to quantify the density of TILs and CLR in immunohistochemical (IHC)-stained whole-slide images (WSIs) and further constructed the CLR-I (immune) score, a tissue level- and cell level-based immune factor, to predict the overall survival (OS) of patients with colorectal cancer (CRC). The TILs score and CLR score were obtained according to the related density. And the CLR-I score was calculated by summing two scores. The development (Hospital 1, N = 370) and validation (Hospital 2 & 3, N = 144) cohorts were used to evaluate the prognostic value of the CLR-I score. The C-index and integrated area under the curve were used to assess the discrimination ability. A higher CLR-I score was associated with a better prognosis, which was identified by multivariable analysis in the development (hazard ratio for score 3 vs score 0 = 0.22, 95% confidence interval 0.12-0.40, P < 0.001) and validation cohort (0.21, 0.05-0.78, P = 0.020). The AI-based CLR-I score outperforms the single predictor in predicting OS which is objective and more prone to be deployed in clinical practice.

Artificial intelligence for quantifying immune infiltrates interacting with stroma in colorectal cancer

Background

We proposed an artificial intelligence-based immune index, Deep-immune score, quantifying the infiltration of immune cells interacting with the tumor stroma in hematoxylin and eosin-stained whole-slide images of colorectal cancer.

Methods

A total of 1010 colorectal cancer patients from three centers were enrolled in this retrospective study, divided into a primary (N = 544) and a validation cohort (N = 466). We proposed the Deep-immune score, which reflected both tumor stroma proportion and the infiltration of immune cells in the stroma region. We further analyzed the correlation between the score and CD3⁺ T cells density in the stroma region using immunohistochemistry-stained whole-slide images. Survival analysis was performed using the Cox proportional hazard model, and the endpoint of the event was the overall survival.

Result

Patients were classified into 4-level score groups (score 1–4). A high Deep-immune score was associated with a high level of CD3⁺ T cells infiltration in the stroma region. In the primary cohort, survival analysis showed a significant difference in 5-year survival rates between score 4 and score 1 groups: 87.4% vs. 58.2% (Hazard ratio for score 4 vs. score 1 0.27, 95% confidence interval 0.15–0.48, P < 0.001). Similar trends were observed in the validation cohort (89.8% vs. 67.0%; 0.31, 0.15–0.62, < 0.001). Stratified analysis showed that the Deep-immune score could distinguish high-risk and low-risk patients in stage II colorectal cancer (P = 0.018).

Conclusion

The proposed Deep-immune score quantified by artificial intelligence can reflect the immune status of patients with colorectal cancer and is associate with favorable survival. This digital pathology-based finding might advocate change in risk stratification and consequent precision medicine.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12967-022-03666-3.

Saturn Anomalous Myriametric Radiation, a New Type of Saturn Radio Emission Revealed by Cassini

A new radio component namely Saturn Anomalous Myriametric Radiation (SAM) is reported. A total of 193 SAM events have been identified by using all the Cassini Saturn orbital data. SAM emissions are L-O mode radio emission and occasionally accompanied by a first harmonic in R-X mode. SAM's intensities decrease with increasing distance from Saturn, suggesting a source near Saturn. SAM has a typical central frequency near 13 kHz, a bandwidth greater than 8 kHz and usually drifts in frequency over time. SAM's duration can extend to near 11 hr and even longer. These features distinguish SAM from the regular narrowband emissions observed in the nearby frequency range, hence the name anomalous. The high occurrence rate of SAM after low frequency extensions of Saturn Kilometric Radiation and the SAM cases observed during compressions of Saturn's magnetosphere suggest a special connection to solar wind dynamics and magnetospheric conditions at Saturn.

Toripalimab (anti-PD-1) versus High-Dose Interferon-α2b as Adjuvant Therapy in Resected Mucosal Melanoma: A Phase II Randomized Trial

BACKGROUND

No standard of care for mucosal melanoma (MM) in the adjuvant setting has been established. Meanwhile, relapse-free survival (RFS) is only about five months after surgery alone. This phase II trial aimed to compare toripalimab vs. high-dose interferon-α2b (HDI) as an adjuvant therapy for resected MM.

PATIENTS AND METHODS

From July 2017 to May 2019, 145 patients with resected MM were randomized (1:1) to receive HDI (N = 72) or toripalimab (N = 73) for one year until disease relapse/distant metastasis, unacceptable toxicity, or withdrawal of consent. The primary endpoint was RFS. The secondary endpoints included distant metastasis-free survival (DMFS), overall survival (OS), and safety.

RESULTS

After a median follow-up of 26.3 months, the numbers of RFS, OS, and DMFS events were 51 vs. 46, 33 vs. 29, and 49 vs. 44 in the toripalimab arm and the HDI arm, respectively. The median RFS were 13.6 (95%CI: 8.31-19.02) months and 13.9 (95%CI: 8.28-19.61) months in the toripalimab arm and HDI arm, respectively. The DMFS was not significantly different between the two arms (HR: 1.00, 95%CI: 0.65-1.54). The median OS was 35.1 months (95%CI: 27.93-NR) in the toripalimab arm, with no significant difference in all-cause death (HR: 1.11, 95% CI: 0.66-1.84) for the two arms. The median sums of the patients' actual infusion doses were 3672 mg and 1054.5 MIU in the toripalimab arm and HDI arm, respectively. The incidence of treatment-emergent adverse events with a grade ≥ 3 was much higher in the HDI arm than in the toripalimab arm (87.5% vs. 27.4%).

CONCLUSION

Toripalimab showed a similar RFS and a more favorable safety profile than HDI, both better than historical data, suggesting that toripalimab might be the better treatment option. However, additional translational studies and better treatment regimens are still warranted to improve the clinical outcome of MM.

[Morvan syndrome with positive anti LGI1/CASPR2 antibodies in serum/cerebrospinal fluid:a case report and literature review]

To report a typical case of Morvan syndrome with positive anti-leucine rich glioma-inactivated 1(LGI1) and contactin-associated protein 2 (CASPR2) antibodies in serum and cerebrospinal fluid. A 39-years-old female initially presented weakness of extremeties. The main symptoms included paroxysmal limb pain, wheezing, itching, muscle twitching, epilepsy, hypomnesia, dysphoria, apathy, intractable insomnia, salivation and sweating. Tests of electrolytes found hypokalemia (2.7-3.1 mmol/L) and hyponatremia (130-136 mmol/L). Arterial blood gas analysis showed hypoxemia (oxygen saturation 50%-70%). Total thyroxine (TT4) was elevated to 207 nmol/L with positive thyroid peroxidase antibody (TPO-Ab) and thyroglobulin antibody (TG-Ab). LGI1and CASPR2 antibodies (CBA method) were positive in both serum and cerebrospinal fluid, and the remaining antibodies related to autoimmune encephalitis and paraneoplastic syndrome were negative. Head MRI was almost normal, while mild abnormalities were found in electroencephalogram. Electromyography showed slightly increased voltage of left quadriceps motor unit potential. After treated with corticosteroids, IVIG and mycophenolate mofetil, the patient completely improved. Cognitive function scores recovered from MoCA/MMSE (16/24) to MoCA/MMSE (26/29). Positivity of LGI1/CASPR2 antibodies both in serum/cerebrospinal fluid are rarely seen in patients with Morvan syndrome. Steroids and immunosuppressants are suggested for treatment as early as possible.

Genome-Based Analysis of Aspergillus niger Aggregate Species from China and Their Potential for Fumonisin B2 and Ochratoxin A Production

Based on entire genome sequencing, this study focused on the classification of Aspergillus niger aggregation species and investigated their potential for fumonisin B₂ (FB₂) and ochratoxin A (OTA) production. In the current study, 22 strains were used, namely 17 A. niger strains, four A. welwitschiae strains, and one A. lacticoffeatus (a synonym of A. niger) strain. Traditional multigene phylogenetic analysis, average nucleotide identity analysis (ANI), and the whole-genome single-nucleotide polymorphism (SNP) analyses were used to reconfirm the taxonomic status of A. niger, A. welwitschiae, and A. lacticoffeatus. The ability of A. niger to produce FB₂ and OTA on five culture substrates was determined, and the association between FB₂ and OTA gene clusters and toxin-producing abilities was explored. The results revealed that the ANI method could distinguish A. niger from A. welwitschiae, with an ANI value of < 98%. The SNP-based phylogenetic analysis suggested that A. niger and A. welwitschiae were two independent phylogenetic species. The ANI, SNP, and multigene phylogenetic analysis supported previous findings that A. lacticoffeatus was a synonymous species of A. niger. Aspergillus niger strains exhibited the varied potential of producing FB₂ and OTA on different culture media. The A. niger genome sequence analysis revealed no significant difference in fumonisin gene clusters between FB₂-nonproducing isolates and FB₂-producing isolates, and the integrity of the ochratoxin biosynthesis genes cluster was clearly associated with OTA production. In conclusion, gene sequencing can be useful in assessing A. niger's ability to produce OTA, but it cannot reliably predict its ability to produce FB₂.

Inoculum size of co-fermentative culture affects the sensory quality and volatile metabolome of fermented milk over storage

Lacticaseibacillus paracasei PC-01 is a probiotic candidate isolated from naturally fermented yak milk in Lhasa, Tibet, and it has been shown to possess excellent milk fermentation properties. This study used Lacticaseibacillus paracasei PC-01 as a co-fermentation strain to investigate the effect of inoculum size with a commercial starter in milk fermentation on the product flavor and profile of volatile metabolites over 28 d of cold storage. Lacticaseibacillus paracasei PC-01 was allowed to ferment in pasteurized milk with or without the commercial starter (YF-L904) at 42°C until the pH decreased to 4.5. The finished fermented milks were stored at 10°C for 28 d. Milk samples were taken at hour 0 (before fermentation) and then at d 1, 14, and 28 of cold storage. Different inoculum sizes of Lacticaseibacillus paracasei PC-01 had no significant effect on pH or titratable acidity during storage of fermented milk. Viable counts of strain PC-01 continued to increase during cold storage of the fermented milk. Generally, as storage of fermented milk proceeded, the overall sensory quality score decreased in all groups. However, the overall sensory scores of PC-01-M were generally higher than those of other groups, suggesting that a medium dose of Lacticaseibacillus paracasei PC-01 had the most obvious effect of slowing the decline in sensory quality of fermented milk during storage. Changes in sensory scores and consumer preferences were accompanied by increases in both the quantity and variety of key volatile metabolites in fermented milk during fermentation, post-ripening (d 1), and storage. Major differentially abundant metabolites, including acetaldehyde, methyl ketones, medium-chain and short-chain fatty acids, 2,3-butanedione, and acetoin, were enriched in fermented milks rated highly in the sensory evaluation. Our data confirmed that the inoculum size of co-fermentative culture affected the sensory quality and volatile metabolome of fermented milk over storage, and an optimal range of co-fermentative culture was titrated in this work.

Fbw7 Inhibits the Progression of Activated B-Cell Like Diffuse Large B-Cell Lymphoma by Targeting the Positive Feedback Loop of the LDHA/lactate/miR-223 Axis

Background

F-box and WD repeat domain-containing 7 (Fbw7) is well known as a tumor suppressor and ubiquitin ligase which targets a variety of oncogenic proteins for proteolysis. We previously reported that Fbw7 promotes apoptosis in diffuse large B-cell lymphoma (DLBCL) through Fbw7-mediated ubiquitination of Stat3. This study aimed to identify the mechanism of Fbw7-mediated aerobic glycolysis reprogramming in DLBCL.

Methods

Expression levels of Fbw7 and Lactate Dehydrogenase A (LDHA) in human DLBCL samples were evaluated by immunohistochemistry. Crosstalk between Fbw7 and LDHA signaling was analyzed by co-immunoprecipitation, ubiquitination assay, western blotting and mRNA quanlitative analyses. In vitro and in vivo experiments were used to assess the effect of the Fbw7-mediated LDHA/lactate/miR-223 axis on DLBCL cells growth.

Results

Fbw7 could interact with LDHA to trigger its ubiquitination and degradation. Inversely, lactate negatively regulated Fbw7 via trigging the expression of miR-223, which targeted Fbw7 3’-UTR to inhibit its expression. In vivo and in vitro experiments revealed that miR-223 promoted tumor growth and that the effects of miR-223 on tumor growth were primarily related to the inhibition of Fbw7-mediated LDHA’s ubiquitination.

Conclusions

We demonstrated that the ubiquitin-ligase Fbw7 played a key role in LDHA-related aerobic glycolysis reprogramming in DLBCL. Our study uncovers a negative functional loop consisting of a Fbw7-mediated LDHA/lactate/miR-223 axis, which may support the future ABC-DLBCL therapy by targeting LDHA-related inhibition.

Development and validation of a preoperative CT-based radiomic nomogram to predict pathology invasiveness in patients with a solitary pulmonary nodule: a machine learning approach, multicenter, diagnostic study

OBJECTIVES

To develop and validate a preoperative CT-based nomogram combined with radiomic and clinical-radiological signatures to distinguish preinvasive lesions from pulmonary invasive lesions.

METHODS

This was a retrospective, diagnostic study conducted from August 1, 2018, to May 1, 2020, at three centers. Patients with a solitary pulmonary nodule were enrolled in the GDPH center and were divided into two groups (7:3) randomly: development (n = 149) and internal validation (n = 54). The SYSMH center and the ZSLC Center formed an external validation cohort of 170 patients. The least absolute shrinkage and selection operator (LASSO) algorithm and logistic regression analysis were used to feature signatures and transform them into models.

RESULTS

The study comprised 373 individuals from three independent centers (female: 225/373, 60.3%; median [IQR] age, 57.0 [48.0-65.0] years). The AUCs for the combined radiomic signature selected from the nodular area and the perinodular area were 0.93, 0.91, and 0.90 in the three cohorts. The nomogram combining the clinical and combined radiomic signatures could accurately predict interstitial invasion in patients with a solitary pulmonary nodule (AUC, 0.94, 0.90, 0.92) in the three cohorts, respectively. The radiomic nomogram outperformed any clinical or radiomic signature in terms of clinical predictive abilities, according to a decision curve analysis and the Akaike information criteria.

CONCLUSIONS

This study demonstrated that a nomogram constructed by identified clinical-radiological signatures and combined radiomic signatures has the potential to precisely predict pathology invasiveness.

KEY POINTS

• The radiomic signature from the perinodular area has the potential to predict pathology invasiveness of the solitary pulmonary nodule. • The new radiomic nomogram was useful in clinical decision-making associated with personalized surgical intervention and therapeutic regimen selection in patients with early-stage non-small-cell lung cancer.

Preoperative CT-based peritumoral and tumoral radiomic features prediction for tumor spread through air spaces in clinical stage I lung adenocarcinoma

OBJECTIVES

This study aims to develop and evaluate preoperative CT-based peritumoral and tumoral radiomic features to predict tumor spread through air space (STAS) status in clinical stage I lung adenocarcinoma (LUAD).

MATERIALS AND METHODS

From June 2018 to December 2019, a retrospective diagnostic investigation was done. Patients with pathologically confirmed STAS status (N = 256) were eventually enrolled. The development cohort consisted of 191 patients (74.6%) chosen randomly in a 7:3 ratio, whereas the validation group consisted of 65 patients (25.4%). The performance of models was assessed using receiver operating characteristic analysis, accuracy, sensitivity, specificity, negative predictive values, and positive predictive values.

RESULTS

The STAS positive status was found in 85 (33.2%) of the 256 patients (female: 53.2%; median [IQR] age: 62.0, [53.0-79.0] years), while the STAS negative status was found in 171 patients (66.8%) (female:50.6%; median [IQR] age: 62.0, [53.0-87.0] years). The combined TRS and PRS-15 mm model had an AUC of 0.854 (95% CI, 0.799-0.909) in the development cohort and 0.870 (95% CI, 0.781-0.958) in the validation cohort, indicating that the tumor radiomic signature (TRS) model and different peritumoral radiomic signature (PRS) models were used to build the optimal gross radiomic signature (GRS) model. The radiomic nomogram achieves superior discriminatory performance than GRS and clinical and radiological signatures (CRS), with an AUC of 0.871 (95% CI, 0.820-0.922) in the development cohort and AUC of 0.869 (95% CI, 0.776-0.961) in the validation cohort. Based on the Akaike information criterion (AIC) and decision curve analysis (DCA), the radiomic nomogram provided greater clinical predictive capacity than clinical or any radiomic signatures alone.

CONCLUSION

In conclusion, we discovered that peritumoral characteristics were substantially related to STAS status. This study revealed the unit of radiomic signature and clinical signatures may have a better performance in STAS status.

Paenibacillus tianjinensis sp. nov., isolated from corridor air

A Gram-stain-positive, facultatively anaerobic, non-motile, endospore-forming and rod-shaped bacterium, occurring singly or in pairs, designated TB2019^T, was isolated from environmental monitoring samples of corridor air collected at the Tianjin Institute for Drug Control, Tianjin Province (PR China). The isolate was able to grow at 15-40 °C (optimum growth at 37 °C), pH 6.0-8.0 (pH 7.0) and in the presence of 0-2% (w/v) NaCl (0% NaCl). Comparison of 16S rRNA gene sequences indicated that TB2019^T was most closely related to Paenibacillus typhae CGMCC 1.11012^T (98.63%), Paenibacillus albidus Q4-3^T (98.19%), Paenibacillus borealis DSM 13188^T (97.55%), Paenibacillus helianthi P26E^T (97.33%) and Paenibacillus odorifer DSM 15391^T (97.19%). The digital DNA-DNA hybridization and the average nucleotide identity values between TB2019^T and the five type strains mentioned above ranged from 20.7 to 25.0% and 75.2 to 81.3%, respectively, and the genomic DNA G+C content was 49.52 mol%. The diagnostic cell-wall sugar was ribose, and the diagnostic amino acid was meso-diaminopimelic acid. The polar lipids of TB2019^T included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unidentified aminophospholipids and one unidentified phospholipid. MK-7 was the predominant menaquinone, and anteiso-C_15:0 (30.6%) was the major fatty acid. Based on the polyphasic taxonomic data, strain TB2019^T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus tianjinensis sp. nov. is proposed. The type strain is TB2019^T (=CICC 25065^T=JCM 34610^T).

A deep learning quantified stroma-immune score to predict survival of patients with stage II-III colorectal cancer

Background

Profound heterogeneity in prognosis has been observed in colorectal cancer (CRC) patients with intermediate levels of disease (stage II–III), advocating the identification of valuable biomarkers that could improve the prognostic stratification. This study aims to develop a deep learning-based pipeline for fully automatic quantification of immune infiltration within the stroma region on immunohistochemical (IHC) whole-slide images (WSIs) and further analyze its prognostic value in CRC.

Methods

Patients from two independent cohorts were divided into three groups: the development group (N = 200), the internal (N = 134), and the external validation group (N = 90). We trained a convolutional neural network for tissue classification of CD3 and CD8 stained WSIs. A scoring system, named stroma-immune score, was established by quantifying the density of CD3⁺ and CD8⁺ T-cells infiltration in the stroma region.

Results

Patients with higher stroma-immune scores had much longer survival. In the development group, 5-year survival rates of the low and high scores were 55.7% and 80.8% (hazard ratio [HR] for high vs. low 0.39, 95% confidence interval [CI] 0.24–0.63, P < 0.001). These results were confirmed in the internal and external validation groups with 5-year survival rates of low and high scores were 57.1% and 78.8%, 63.9% and 88.9%, respectively (internal: HR for high vs. low 0.49, 95% CI 0.28–0.88, P = 0.017; external: HR for high vs. low 0.35, 95% CI 0.15–0.83, P = 0.018). The combination of stroma-immune score and tumor-node-metastasis (TNM) stage showed better discrimination ability for survival prediction than using the TNM stage alone.

Conclusions

We proposed a stroma-immune score via a deep learning-based pipeline to quantify CD3⁺ and CD8⁺ T-cells densities within the stroma region on WSIs of CRC and further predict survival.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12935-021-02297-w.

The Crohn's-like lymphoid reaction density: a new artificial intelligence quantified prognostic immune index in colon cancer

BACKGROUND

The Crohn's-like lymphoid reaction (CLR) is manifested as peritumoral lymphocytes aggregation in colon cancer, which is a major component of the host immune response to cancer. However, the lack of a unified and objective CLR evaluation standard limits its clinical application. We, therefore, developed a deep learning model for the fully automated CLR density quantification on routine hematoxylin and eosin (HE)-stained whole-slide images (WSIs) and further investigated its prognostic validity for patient stratification.

METHODS

The CLR density was calculated by using a deep learning method on HE-stained WSIs. A training (N = 279) and a validation (N = 194) cohorts were used to evaluate the prognostic value of CLR density for overall survival (OS).

RESULT

The fully automated quantified CLR density was an independent prognostic factor, with high CLR density associated with increased OS in the discovery (HR 0.58, 95% CI 0.38-0.89, P = 0.012) and validation cohort (0.45, 0.23-0.88, 0.020). Integrating CLR density into a Cox model with other risk factors showed improved prognostic capability.

CONCLUSION

We developed a new immune indicator (CLR density) quantified by a deep learning method to evaluate the lymphocytes aggregation in colon cancer. The CLR density was demonstrated its predictive value for OS in two independent cohorts. This approach allows for the objective and standardized quantification while reducing pathologists' workload. Therefore, this fully automated standardized method of CLR evaluation had potential clinical value.

Significance of mitral L wave to predict late recurrence of atrial fibrillation after radiofrequency catheter ablation

Background

Mitral L wave, prominent mid-diastolic filling wave in echocardiographic examinations, is associated with severe left ventricular diastolic dysfunction, and that has been reported to predict recurrent atrial fibrillation (AF) after cardioversion. However, association between mitral L wave and the outcome of AF after radiofrequency catheter ablation (RFCA) has not been established.

Objective

The aim of this study is to evaluate the predictive value of mitral L wave on AF recurrence after RFCA.

Methods

250 patients including 164 paroxysmal AF (65.6%) and 86 non-paroxysmal AF (34.4%) who received RFCA in single center from January 2015 to December 2016 were enrolled consecutively. Echocardiographic examinations before RFCA were recorded, and the mitral L wave was defined as a distinct mid-diastolic flow velocity with a peak velocity ≥20 cm/s following the E wave. Systematic follow-up was conducted after RFCA. Univariate and multivariate analyses were carried out to determine the factors predicting late recurrence of AF (LRAF) which means AF recurrence after 3 months. Enrolled patients were divided into groups with the L wave (L-group; n=57) or without the L wave (NL-group; n=193) based on the findings of echocardiographic examinations.

Results

During a follow-up of 35.0±17.6 months, the ratio of LRAF in the L-group was significantly higher than that in the NL-group (32 (56.1%) vs. 41 (21.2%), Hazard ratio [HR]: 3.55, 95% confidence interval [CI]: 2.33 - 5.42, p&lt;0.001). Among the clinical factors, presence of mitral L wave, BNP value, non-paroxysmal AF and moderate-severe mitral regurgitation were related to LRAF. A multivariate analysis using a Cox proportional hazard model found that presence of mitral L wave (HR: 2.67, 95% CI: 1.30 - 5.48, p=0.007) was significantly associated with LRAF.

Conclusion

This study revealed that mitral L wave predicts late recurrence of AF after RFCA.

Funding Acknowledgement

Type of funding sources: None.

The forgotten role of food cultures

Fermentation is one of if not the oldest food processing technique, yet it is still an emerging field when it comes to its numerous mechanisms of action and potential applications. The effect of microbial activity on the taste, bioavailability and preservation of the nutrients and the different food matrices has been deciphered by the insights of molecular microbiology. Among those roles of fermentation in the food chain, biopreservation remains the one most debated. Presumably because it has been underestimated for quite a while, and only considered - based on a food safety and technological approach - from the toxicological and chemical perspective. Biopreservation is not considered as a traditional use, where it has been by design - but forgotten - as the initial goal of fermentation. The 'modern' use of biopreservation is also slightly different from the traditional use, due mainly to changes in cooling of food and other ways of preservation, Extending shelf life is considered to be one of the properties of food additives, classifying - from our perspective - biopreservation wrongly and forgetting the role of fermentation and food cultures. The present review will summarize the current approaches of fermentation as a way to preserve and protect the food, considering the different way in which food cultures and this application could help tackle food waste as an additional control measure to ensure the safety of the food.

Notoginsenoside R1 protects hypoxia-reoxygenation deprivation-induced injury by upregulation of miR-132 in H9c2 cells

BACKGROUND

Myocardial ischemia/reperfusion injury (IRI) is a common perioperative complication of heart and great vessels surgery, aggravating the original myocardial damage and seriously affecting the postoperative recovery of cardiac function. The aim of this study was to reveal the functional effects and potential mechanisms of notoginsenoside R1 (NG-R1) in myocardial cells injured by hypoxia-reoxygenation (H/R).

METHODS

The rat cardiomyocyte line H9c2 was subjected to H/R with or without NG-R1 treatment. The levels of miR-132 and HBEGF in the cell were altered by microRNA or short-hairpin RNA transfection. Cell viability, apoptosis, lactate dehydrogenase (LDH) and malondialdehyde (MDA) were monitored. Dual luciferin was used to detect the relationship between miR-132 and HBEGF.

RESULTS

NG-R1 (20 μM) had no impact on H9c2 cells, but cell viability was significantly reduced at 80 μM. NG-R1 (20 μM) protected H9c2 cells against H/R-induced cell damage, accompanied by increased cell viability, reduced cell apoptosis, and downregulation of LDH and MDA. Furthermore, the level of miR-132 was decreased in response to H/R exposure but then increased after NG-R1 treatment. When miR-132 was overexpressed, H/R-induced cell damage could be recovered. Downregulation of miR-132 limited the protective effect of NG-R1 on H/R damage. We also found that HBEGF was a direct target of miR-132. The expression of HBEGF was increased upon H/R damage, and this increase was reversed after NG-R1 treatment.

CONCLUSIONS

This study demonstrated that NG-R1 markedly protected H9c2 cells against H/R-induced damage via upregulation of miR-132 and downregulation of its target protein HBEGF.

Antidiuretic hormone inhibits osteogenic differentiation of dental follicle stem cells via V1a receptors and the PLC-IP3 pathway

OBJECTIVE

The aim of this study was to elucidate the molecular mechanism by which antidiuretic hormone (ADH) inhibited osteogenesis in dental follicle stem cells.

DESIGN

Rat dental follicle stem cells were cultured in osteogenic differentiation medium supplemented with ADH. Alkaline phosphatase enzyme activity, Alizarin Red S staining, MTT assay and RT-qPCR was used to examine ADH's impact on cell mineralization, viability, and osteogenic gene expression. Real-time calcium imaging analysis was performed to identify the ADH receptor and its mechanism of action.

RESULTS

ADH supplementation to the osteogenic differentiation medium inhibited cell mineralization without compromising cell viability and downregulated the expression of key osteogenic genes: DCN (Decorin), RUNX2 (Runt-related transcription factor 2) and BSP (Bone sialoprotein). Real-time calcium imaging analysis revealed that ADH (1-1000 nM) increased intracellular calcium in a concentration-dependent manner. Pretreatment of cells with V2255, a V1a receptor blocker, inhibited the calcium signals, but not with the V1b (Nelivaptan) or V2 (Tolvaptan). V2255 also reversed the inhibitory effect of ADH on osteogenesis. Furthermore, U73122, a Phospholipase C (PLC) inhibitor, 2-APB, an Inositol Triphosphate (IP₃) receptor blocker, and depletion of endoplasmic reticulum calcium stores abolished the calcium signals by ADH.

CONCLUSIONS

Our results demonstrated that ADH activates V1a receptors and the PLC-IP₃ pathway to stimulate intracellular calcium signals, which inhibits cell mineralization and osteogenic gene expression. These findings uncovered a novel function for ADH as a negative regulator of osteogenesis in dental follicle stem cells. The role of ADH in the pathogenesis of bone diseases remains to be determined.

Targeting cholesterol biosynthesis promotes anti-tumor immunity by inhibiting long noncoding RNA SNHG29-mediated YAP activation

Anti-tumor immunity through checkpoint inhibitors, specifically anti-programmed death 1 (PD-1)/programmed death ligand 1 (PD-L1) interaction, is a promising approach for cancer therapy. However, as early clinical trials indicate that colorectal cancers (CRCs) do not respond well to immune-checkpoint therapies, new effective immunotherapy approaches to CRC warrant further study. Simvastatin is an inhibitor of 3-hydroxy-3-methylglutaryl-coenzyme A (CoA) reductase (HMGCR), the rate-limiting enzyme of the mevalonate (MVA) pathway for the cholesterol biosynthesis. However, little is known about the functions of simvastatin in the regulation of immune checkpoints or long noncoding RNA (lncRNA)-mediated immunoregulation in cancer. Here, we found that simvastatin inhibited PD-L1 expression and promoted anti-tumor immunity via suppressing the expression of lncRNA SNHG29. Interestingly, SNHG29 interacted with YAP and inhibited phosphorylation and ubiquitination-mediated protein degradation of YAP, thereby facilitating downregulation of PD-L1 transcriptionally. Patient-derived tumor xenograft (PDX) models and the clinicopathological analysis in samples from CRC patients further supported the role of the lncRNA SNHG29-mediated PD-L1 signaling axis in tumor microenvironment reprogramming. Collectively, our study uncovers simvastatin as a potential therapeutic drug for immunotherapy in CRC, which suppresses lncRNA SNHG29-mediated YAP activation and promotes anti-tumor immunity by inhibiting PD-L1 expression.

Gas explosion-induced acute blast lung injury assessment and biomarker identification by a LC-MS-based serum metabolomics analysis

The objective of this study was to evaluate the histopathological effect of gas explosion on rats, and to explore the metabolic alterations associated with gas explosion-induced acute blast lung injury (ABLI) in real roadway environment using metabolomics analyses. All rats were exposed to the gas explosion source at different distance points (160 m and 240 m) except the control group. Respiratory function indexes were monitored and lung tissue analysis was performed to correlate histopathological effect to serum metabolomics. Their sera samples were collected to measure the metabolic alterations by ultra-performance liquid chromatography-mass spectrometry (UPLC-MS). HE staining in lung showed that the gas explosion caused obvious inflammatory pulmonary injury, which was consistent with respiratory function monitoring results and the serum metabolomics analysis results. The metabolomics identified 9 significantly metabolites different between the control- and ABLI rats. 2-aminoadipic acid, L-methionine, L-alanine, L-lysine, L-threonine, cholic acid and L-histidine were significantly increased in the exposed groups. Citric acid and aconitic acid were significantly decreased after exposure. Pathway analyses identified 8 perturbed metabolic pathways, which provided novel potential mechanisms for the gas explosion-induced ABLI. Therefore, metabolomics analysis identified both known and unknown alterations in circulating biomarkers, adding an integral mechanistic insight into the gas explosion-induced ABLI in real roadway environment.

Deep learning quantified mucus-tumor ratio predicting survival of patients with colorectal cancer using whole-slide images

BACKGROUND

In colorectal cancer (CRC), mucinous adenocarcinoma differs from other adenocarcinomas in gene-phenotype, morphology, and prognosis. However, mucinous components are present in a large number of adenocarcinomas, and the prognostic value of mucus proportion has not been investigated. Artificial intelligence provides a way to quantify mucus proportion on whole-slide images (WSIs) accurately. We aimed to quantify mucus proportion by deep learning and further investigate its prognostic value in two CRC patient cohorts.

METHODS

Deep learning was used to segment WSIs stained with hematoxylin and eosin. Mucus-tumor ratio (MTR) was defined as the proportion of mucinous component in the tumor area. A training cohort (N = 419) and a validation cohort (N = 315) were used to evaluate the prognostic value of MTR. Survival analysis was performed using the Cox proportional hazard model.

RESULT

Patients were stratified to mucus-low and mucus-high groups, with 24.1% as the threshold. In the training cohort, patients with mucus-high had unfavorable outcomes (hazard ratio for high vs. low 1.88, 95% confidence interval 1.18-2.99, P = 0.008), with 5-year overall survival rates of 54.8% and 73.7% in mucus-high and mucus-low groups, respectively. The results were confirmed in the validation cohort (2.09, 1.21-3.60, 0.008; 62.8% vs. 79.8%). The prognostic value of MTR was maintained in multivariate analysis for both cohorts.

CONCLUSION

The deep learning quantified MTR was an independent prognostic factor in CRC. With the advantages of advanced efficiency and high consistency, our method is suitable for clinical application and promotes precision medicine development.

Circadian Clock Disruption Suppresses PDL1+ Intraepithelial B Cells in Experimental Colitis and Colitis-Associated Colorectal Cancer

BACKGROUND & AIMS

The circadian clock is crucial for physiological homeostasis including gut homeostasis. Disorder of the circadian clock may contribute to many diseases including inflammatory bowel disease (IBD). However, the role and the mechanisms of circadian clock involvement in IBD still are unclear.

METHODS

Disorder of the circadian clock including chronic social jet lag and circadian clock gene deficiency mice (Bmal1-/-, and Per1-/-Per2-/-) were established. Dextran sulfate sodium (DSS) and/or azoxymethane were used to induce mouse models of colitis and its associated colorectal cancer. Flow cytometry, immunohistochemistry, immunofluorescence, Western blot, and reverse-transcription quantitative polymerase chain reaction were used to analyze the characteristics of immune cells and their related molecules.

RESULTS

Mice with disorders of the circadian clock including chronic social jet lag and circadian clock gene deficiency were susceptible to colitis. Functionally, regulatory B (Breg) cells highly expressing Programmed cell death 1 ligand 1 (PDL1) in intestinal intraepithelial lymphocytes (IELs) helped to alleviate the severity of colitis after DSS treatment and was dysregulated in DSS-treated Bmal1-/- mice. Notably, interleukin 33 in the intestinal microenvironment was key for Bmal1-regulated PDL1+ Breg cells and interleukin 33 was a target of Bmal1 transcriptionally. Dysregulated PDL1+ B cells induced cell death of activated CD4+ T cells in DSS-treated Bmal1-/- mice. Consequently, circadian clock disorder was characterized as decreased numbers of Breg+ PDL1+ cells in IELs and dysfunction of CD4+ T cells promoted colitis-associated colorectal cancer (CRC) in mice. In clinical samples from CRC patients, low expression of Bmal1 gene in paracancerous tissues and center area of tumor was associated closely with a poorer prognosis of CRC patients.

CONCLUSIONS

Our study uncovers the importance of the circadian clock regulating PDL1+ Breg+ cells of IELs in IBD and IBD-associated CRC.