An Immune-Related Gene Prognostic Prediction Risk Model for Neoadjuvant Chemoradiotherapy in Rectal Cancer Using Artificial Intelligence

PURPOSE/OBJECTIVE(S)

To develop and validate an immune-related gene prognostic model (IRGPM) that can predict disease-free survival (DFS) in patients with locally advanced rectal cancer (LARC) who received neoadjuvant chemoradiotherapy and to clarify the immune characteristics of patients with different prognostic risks.

MATERIALS/METHODS

In this study, we obtained transcriptomic and clinical data from the Gene Expression Omnibus (GEO) database and rectal cancer database of West China Hospital. Genes in the RNA immune-oncology panel were extracted. Elastic net was used to identify the immune-related genes that significantly affected the DFS of patients. A prognostic risk model (IRGPM) for rectal cancer was constructed with the random forest method. The prognostic risk score was calculated by the model, and the patients were divided into high- and low-risk groups according to the median risk score. Immune characteristics were analyzed and compared between the high- and low-risk groups.

RESULTS

A total of 407 LARC samples were used in this study. A 20-gene signature was identified by elastic net and was found to be significantly correlated with DFS. The IRGPM was constructed on the basis of the 20 immune-related genes. Kaplan‒Meier survival analysis showed poorer 5-year DFS in the high-risk group than in the low-risk group, and the receiver operating characteristic (ROC) curve suggested good model prediction (areas under the curve (AUCs) of 0.87, 0.94, 0.95 at 1, 3, and 5 years, respectively). The model was validated in the GSE190826 cohort (AUCs of 0.79, 0.64, and 0.63 at 1, 3, and 5 years, respectively) and the cohort from our institution (AUCs of 0.64, 0.66, and 0. 64 at 1, 3, and 5 years, respectively). The differentially expressed genes between the high- and low-risk groups were enriched in cytokine‒cytokine receptor interactions. The patients in the low-risk group had higher immune scores than the patients in the high-risk group. Subsequently, we found that activated B cells, activated CD8 T cells, central memory CD8 T cells, macrophages, T follicular helper cells and type 2 helper cells were more abundant in the low-risk group. Moreover, we compared the expression of immune checkpoints and found that the low-risk group had a higher PDCD1 expression level.

CONCLUSION

The IRGPM, which was constructed based on the random forest and elastic net methods, is a promising method to distinguish DFS in LARC patients treated with a standard strategy. The low-risk group identified by IRGPM was characterized by the activation of adaptive immunity in tumor microenvironment.

Development and evaluation of machine learning models and nomogram for the prediction of severe acute pancreatitis

BACKGROUND AND AIM

Severe acute pancreatitis (SAP) in patients progresses rapidly and can cause multiple organ failures associated with high mortality. We aimed to train a machine learning (ML) model and establish a nomogram that could identify SAP, early in the course of acute pancreatitis (AP).

METHODS

In this retrospective study, 631 patients with AP were enrolled in the training cohort. For predicting SAP early, five supervised ML models were employed, such as random forest (RF), K-nearest neighbors (KNN), and naive Bayes (NB), which were evaluated by accuracy (ACC) and the areas under the receiver operating characteristic curve (AUC). The nomogram was established, and the predictive ability was assessed by the calibration curve and AUC. They were externally validated by an independent cohort of 109 patients with AP.

RESULTS

In the training cohort, the AUC of RF, KNN, and NB models were 0.969, 0.954, and 0.951, respectively, while the AUC of the Bedside Index for Severity in Acute Pancreatitis (BISAP), Ranson and Glasgow scores were only 0.796, 0.847, and 0.837, respectively. In the validation cohort, the RF model also showed the highest AUC, which was 0.961. The AUC for the nomogram was 0.888 and 0.955 in the training and validation cohort, respectively.

CONCLUSIONS

Our findings suggested that the RF model exhibited the best predictive performance, and the nomogram provided a visual scoring model for clinical practice. Our models may serve as practical tools for facilitating personalized treatment options and improving clinical outcomes through pre-treatment stratification of patients with AP.

Single-Cell Transcriptome Reveals the Metabolic and Clinical Features of a Highly Malignant Cell Subpopulation in Pancreatic Ductal Adenocarcinoma

Background: Pancreatic ductal adenocarcinoma (PDAC) is a malignant tumor with a high mortality rate. PDAC exhibits significant heterogeneity as well as alterations in metabolic pathways that are associated with its malignant progression. In this study, we explored the metabolic and clinical features of a highly malignant subgroup of PDAC based on single-cell transcriptome technology.

Methods: A highly malignant cell subpopulation was identified at single-cell resolution based on the expression of malignant genes. The metabolic landscape of different cell types was analyzed based on metabolic pathway gene sets. In vitro experiments to verify the biological functions of the marker genes were performed. PDAC patient subgroups with highly malignant cell subpopulations were distinguished according to five glycolytic marker genes. Five glycolytic highly malignant-related gene signatures were used to construct the glycolytic highly malignant-related genes signature (GHS) scores.

Results: This study identified a highly malignant tumor cell subpopulation from the single-cell RNA sequencing (scRNA-seq) data. The analysis of the metabolic pathway revealed that highly malignant cells had an abnormally active metabolism, and enhanced glycolysis was a major metabolic feature. Five glycolytic marker genes that accounted for the highly malignant cell subpopulations were identified, namely, EN O 1, LDHA, PKM, PGK1, and PGM1. An in vitro cell experiment showed that proliferation rates of PANC-1 and CFPAC-1 cell lines decreased after knockdown of these five genes. Patients with metabolic profiles of highly malignant cell subpopulations exhibit clinical features of higher mortality, higher mutational burden, and immune deserts. The GHS score evaluated using the five marker genes was an independent prognostic factor for patients with PDAC.

Conclusion: We revealed a subpopulation of highly malignant cells in PDAC with enhanced glycolysis as the main metabolic feature. We obtained five glycolytic marker gene signatures, which could be used to identify PDAC patient subgroups with highly malignant cell subpopulations, and proposed a GHS prognostic score.

POS0262 IDENTIFYING EROSIVE DISEASE FROM RADIOLOGY REPORTS OF VETERANS WITH INFLAMMATORY ARTHRITIS USING NATURAL LANGUAGE PROCESSING

Background:

The presence of erosive disease influences diagnosis, management, and prognosis in inflammatory arthritis (IA).Research of IA in large datasets is limited by a lack of methods for identifying erosions.

Objectives:

To develop methods for identifying articular erosions in radiology reports from veterans with IA.

Methods:

Included veterans had ≥2 ICD codes for ankylosing spondylitis (AS), psoriatic arthritis (PsA), or rheumatoid arthritis (RA) between 2005- 2019, in Veterans Affairs Corporate Data Warehouse. Chart review & annotation of radiology notes produced the reference standard, & identified erosion terms that informed classification rule development. A rule-based natural language processing (NLP) model was created & revised in training snippets. The NLP method was validated in an independent reference sample of IA patients at the snippet & patient levels

StepDescriptionNumber & example1 Radiology notesa.Select note titles potentially relevant to IAa. 35,141 notes titlesb.Extract notes with titles potentially related to IAb. 2,926,113 radiology notes2 Possible meaningful termsa.Compile list of root terms that may indicate erosiona. 11 root terms (i.e. ero*, pencil*cup, irreg*)b.Query radiology notes for root term variationsb. 1178 variations (i.e. erosion, erotic, erode)c.Select possible meaningful termsc. 179 possible terms (i.e. erosion, erode)3 Annotationa.Extract snippets^ containing possible meaningful termsa.5000 snippets from radiology notesb.Classify snippets according to: 1) Meaningful term, 2) Relevance to joint, 3) Attribution to IA, 4) Affirmationb.4068 classifications with 1017 snippets (in rounds of 50-417 snippets for NLP training & testing)4 Rule developmenta.Identify meaningful terms representing erosiona. 6 terms (pencil * cup, erosion, erosive, etc.)b.Exclude erosive processes irrelevant to joint(s)b. 28 irrelevant processes (i.e. gastric erosion)c. Exclude articular erosive processes not attributed to IAc. 5 non-IA processes IA (i.e. infection)d. Classify as affirmed/negated (erosion present/absent)d. 83 affirmation/negation rules5 NLP trainingDesign & revise NLP model until accuracy ≥90%6 rounds, 817 snippets (AS 417, RA 200, PsA 200)6 NLP testingTest NLP model200 snippets (AS 100, RA 50, PsA 50)7 Pt classificationa. Develop rules for classifying pts with discordant snippetsa. 5 rules developed in 368 ptsb. Build reference sample (pts classified as erosive or non-erosive via chart review)b. 30 IA pts (10 AS, 10 RA, 10 PsA)8 NLP validationValidate NLP model in reference sample at snippet level149 snippets (29 AS, 76 RA, 44 PsA)9 Method validationValidate methods (NLP+pt classification) at pt level30 IA pts (reference sample)

pt= patient. ^Snippets include text containing 30 words before & after meaningful terms

Results:

In 168,667 veterans with IA, the mean age was 63.1 & 90.3% were male. Method development involved radiology note & erosion term selection, rule development, NLP model building, & method validation. The NLP model accuracy was 94.6% at the snippet level & 90.0% at the patient level, for all IA patients.

Accuracy of methods.

Conclusion:

The methods accurately identify erosions from radiology reports of veterans with IA. They may facilitate a broad range of research involving cohort identification & disease severity stratification

References:

[1]Walsh JA, et al. J Rheumatol. 2020;47(1):42-49

Disclosure of Interests:

Gopi Penmetsa: None declared, Shaobo Pei: None declared, Brian Sauer Grant/research support from: I have been an investigator on research contracts supported by Abbvie., Jessica A. Walsh Consultant of: AbbVie, Amgen, Janssen, Lilly, Novartis, Pfizer, UCB, Grant/research support from: AbbVie, Merck, Pfizer, Bingjian Feng Grant/research support from: Bing-Jian Feng reports funding and sponsorship to his institution on his behalf from Pfizer Inc., Regeneron Genetics Center LLC, and Astra Zeneca (UK). The PERCH software, for which Bing-Jian Feng is the inventor, has been non-exclusively licensed to Ambry Genetics for clinical genetic testing services and research., Jodi Walker Shareholder of: Abbvie and mutual funds containing various pharmaceutical companies, Employee of: Abbvie, Kevin Douglas Shareholder of: employed by Abbvie, Employee of: employed by Abbvie, Jerry Clewell Shareholder of: Own Abbvie Shares and mutual funds that hold pharmaceutical and other health care stocks, Employee of: I am current Abbvie Inc employee and past employee of Eli Lilly co

Value of two-cycle docetaxel, cisplatin, and 5-fluorouracil induction chemotherapy in hypopharyngeal carcinoma

Various studies have investigated laryngeal function and survival after induction chemotherapy in hypopharyngeal carcinoma, but potential factors to help predict response rates after induction chemotherapy remain unknown. This retro- spective study evaluated which factors are related to an ineffective response to two-cycle docetaxel, cisplatin, and 5-fluoro- uracil (TPF) induction chemotherapy in hypopharyngeal carcinoma to determine potential candidates for this treatment in clinical practice. From Jan 2005 to Dec 2015, 81 patients diagnosed with hypopharyngeal squamous cell carcinoma based on a pathological examination were analyzed. They were administered two-cycle TPF induction chemotherapy, and magnetic resonance imaging was performed before and after induction chemotherapy. The mean survival time was 5.7 years (95% confidence interval, 5.1-6.2 years). The 1, 3, 5 and 6-year survival rates were 98.8%, 80.1%, 64.5%, and 54.2%, respectively. TPF induction chemotherapy was well tolerated; the main adverse effects resolved with symptomatic treatment. A response to TPF induction chemotherapy was associated with lymph node size, tumor grade, invasion region, T stage, and primary tumor. The following issues were significantly associated with an increasing non-response rate to two-cycle induction chemotherapy: increasing lymph node size, moderately differentiated squamous cell carcinoma, invasion of the esophagus along with the thyroid cartilage, and primary tumor in the piriform sinus. Lymph nodes of ≥2.15 cm, moderately differenti- ated tumor grade, or thyroid cartilage invasion were the best cutoff values for patients who did not respond to induction chemotherapy. However, the initial cancer site, cancer stage, and degree of cancer differentiation were not closely related to the efficacy of induction chemotherapy.

Chitosan containing azo-based Schiff bases: thermal, antibacterial and birefringence properties for bio-optical devices

Chitosan Azo derivatives show characteristic birefringence property.

The mitotic checkpoint kinase NEK2A regulates kinetochore microtubule attachment stability

Loss or gain of whole chromosome, the form of chromosome instability commonly associated with cancers is thought to arise from aberrant chromosome segregation during cell division. Chromosome segregation in mitosis is orchestrated by the interaction of kinetochores with spindle microtubules. Our studies show that NEK2A is a kinetochore-associated protein kinase essential for faithful chromosome segregation. However, it was unclear how NEK2A ensures accurate chromosome segregation in mitosis. Here we show that NEK2A-mediated Hec1 (highly expressed in cancer) phosphorylation is essential for faithful kinetochore microtubule attachments in mitosis. Using phospho-specific antibody, our studies show that NEK2A phosphorylates Hec1 at Ser165 during mitosis. Although such phosphorylation is not required for assembly of Hec1 to the kinetochore, expression of non-phosphorylatable mutant Hec1(S165) perturbed chromosome congression and resulted in a dramatic increase in microtubule attachment errors, including syntelic and monotelic attachments. Our in vitro reconstitution experiment demonstrated that Hec1 binds to microtubule in low affinity and phosphorylation by NEK2A, which prevents aberrant kinetochore-microtubule connections in vivo, increases the affinity of the Ndc80 complex for microtubules in vitro. Thus, our studies illustrate a novel regulatory mechanism in which NEK2A kinase operates a faithful chromosome attachment to spindle microtubule, which prevents chromosome instability during cell division.

Selective denervation and resection of cervical muscles in the treatment of spasmodic torticollis: long-term follow-up results in 207 cases

OBJECT

To report the outcome of patients with selective denervation and resection of cervical muscles for spasmodic torticollis.

METHODS

We reviewed 362 cases of surgically treated spasmodic torticollis. 207 patients were followed from 2 years to 29 years.

RESULTS

Total or marked relief of symptoms with preservation of normal of nearly normal movements has been obtained in 87.9%.

CONCLUSION

This procedure may be recommended if one to two years of conservative therapy does not offer satisfactory relief of symptoms.

Mutation of specific acidic residues of the CNF1 T domain into lysine alters cell membrane translocation of the toxin

The Rho-GTPases-activating toxin CNF1 (cytotoxic necrotizing factor 1) delivers its catalytic activity into the cytosol of eukaryotic cells by a low pH membrane translocation mechanism reminiscent of that used by diphtheria toxin (DT). As DT, CNF1 exhibits a translocation domain (T) containing two predicted hydrophobic helices (H1-2) (aa 350-412) separated by a short peptidic loop (CNF1-TL) (aa 373-386) with acidic residues. In the DT loop, the loss of charge of acidic amino acids, as a result of protonation at low pH, is a critical step in the transfer of the DT catalytic activity into the cytosol. To determine whether the CNF1 T domain operates similarly to the DT T domain, we mutated several ionizable amino acids of CNF1-TL to lysine. Single substitutions such as D373K or D379K strongly decreased the cytotoxic effect of CNF1 on HEp-2 cells, whereas the double substitution D373K/D379K induced a nearly complete loss of cytotoxic activity. These single or double substitutions did not modify the cell-binding, enzymatic or endocytic activities of the mutant toxins. Unlike the wild-type toxin, single- or double-substituted CNF1 molecules bound to the HEp-2 plasma membrane could not translocate their enzymatic activity directly into the cytosol following a low pH pulse.

[Wild plants used for the folk dietotherapy in Arhorchin Mongolians]

There are 13 species of native wild plants used for folk dietotherapy by Arhorchin Mongolians in Inner Mongolia. The local people have used those plants as vegetables, fruits and beverages to nourish body, cure scurvy, high blood pressure and 'xira-wusu' disease, repress 'hei' and maintain stomach.

[Yi nationality's sacred groves and biodiversity conservation in Chuxiong, Yunnan]

Sacred groves occur in many ethnic minority areas of Yunnan, China, which have ecologically multiplex functions and effects on biodiversity management and conservation at grassroots level. In this paper, an extensive field survey was carried out to evaluate the role of the sacred groves of the Yi nationality in Chuxiong of Yunnan. Three forest communities (sacred grove, common forest and natural reserve) under different management were sampled, and their plant species diversity was compared. The result shows that the total species, endemic species and Shannon-Wiener index in the sacred grove community were respectively 67, 17 and 2.96, higher than those in natural reserve (44.8 and 2.17) and common forest (34.4 and 2.39). The sacred groves of the Yi nationality in Chuxiong of Yunnan play an important role in local biodiversity conservation and management.

[Study on the epidemiological characteristics and strategy of surveillance in low endemic areas of malaria in Hubei]

Due to good programs on case finding and control, malaria has decreased to a low level in China. Hence, the existing surveillance program of undertaking blood smear from cases with fever finds very few positives in the millions of examinees. Previously, all blood slides were collected from clinically diagnosed cases of malaria (group 1), suspected malaria cases (group 2), fever of unknown reasons (group 3) or common cold (group 4) in low or moderate malaria endemic areas in Hubei Province. In low prevalence areas, the positive rates on slides were 0.6/10,000 and 0.1/10,000 in group 3 and group 4 while 95.38% of the confirmed malaria cases were from those having clinical malaria or suspected malaria. It is suggested that group 3 and group 4 be dropped from low prevalence areas to encourage greater efficiency in case detection in the clinical and the suspected malaria groups.

Surveillance for low-level malaria

Due to good detection and control, malaria has reached very low levels in China with the result that existing methods of surveillance, taking blood slides from all fever cases and those with a common cold, are finding very few malaria cases among the millions of persons examined. Passive case detection agents in areas of moderate and low endemicity in Hubei Province, China, were instructed to indicate on the form associated with each slide whether the patient was considered to be a clinical case of malaria (group 1), was thought to have malaria but did not have all the features (group 2), had fever alone and was not thought to be a case of malaria (group 3), or merely had a common cold (group 4). In the low endemic area (slide positivity rate 0.23%), only 5 cases in group 3 and 4 in group 2 were detected per 10,000 examinations. It is recommended that these categories be discontinued in malarious areas of low endemicity, to encourage greater efficiency in detecting cases in groups 1 and 2. In the moderately endemic area, with a slide positivity rate of 4.19%, all categories, including group 4, were considered valuable for detecting malaria cases.

Identification of a binding sequence for the 14-3-3 protein within the cytoplasmic domain of the adhesion receptor, platelet glycoprotein Ib alpha

The zeta-form 14-3-3 protein (14-3-3zeta) regulates protein kinases and interacts with several signaling molecules. We reported previously that a platelet adhesion receptor, glycoprotein (GP) Ib-IX, was associated with a 29-kDa protein with partial sequences identical to 14-3-3zeta. In this study, the interaction between GPIb-IX and recombinant 14-3-3zeta is reconstituted. Further, we show that the 14-3-3zeta binding site in GPIb is within a 15 residue sequence at the C terminus of GPIb-alpha, as indicated by antibody inhibition and direct binding of 14-3-3zeta to synthetic GPIb-alpha cytoplasmic domain peptides. The 14-3-3zeta binds to recombinant wild type GPIb-IX but not to the GPIb-alpha mutants lacking C-terminal 5 or more residues, suggesting that the C-terminal 5 residues of GPIb-alpha are critical. Similarity between the GPIb-alpha C-terminal sequence and the serine-rich regions of Raf and Bcr kinases suggests a possible serine-rich recognition motif for the 14-3-3 protein.

Analysis of impact of rigid projectiles on compound targets

We developed a model to simulate a person, with and without protective armor, being subjected to an impact of a high speed, rigid projectile. The complex nature of the head and chest are simulated in our layered, spaced, various thickness targets made of different materials. A rigid projectile-target interaction model is described. Target resistance force was obtained from a generalized Poncelet equation. Good agreement between observed and computed penetration phenomena was obtained.