Cluster-Partial Least Squares (c-PLS) regression analysis: Application to miRNA and metabolomic data

BACKGROUND

Biomedicine and biological research frequently involve analyzing large datasets generated by high-throughput technologies like genomics, transcriptomics, miRNomics, and metabolomics. Pathway analysis is a common computational approach used to understand the impact of experimental conditions, phenotypes, or interventions on biological pathways and networks. This involves statistical analysis of omic data to identify differentially expressed variables and mapping them onto predefined pathways. Analyzing such datasets often requires multivariate techniques to extract meaningful insights such as Partial Least Squares (PLS). Variable selection strategies like interval-PLS (iPLS) help improve understanding and predictive performance by identifying informative variables or intervals. However, iPLS is suboptimal to treat omic data such as metabolic or miRNA profiles, where features cannot be distributed along a continuous dimension describing their relationships as in e.g., vibrational or nuclear magnetic resonance spectroscopy.

RESULTS

This study introduces a novel variable selection approach called cluster PLS (c-PLS) that aims to assess the joint impact of variable groups selected based on biological characteristics (such as miRNA-regulated metabolic pathway or lipid classes) on the predictive performance of a multivariate model. The usefulness of c-PLS is shown using miRNomic and metabolomic datasets obtained from the analysis of 24 liver tissue biopsies collected in the frame of a clinical study of steatosis.

SIGNIFICANCE AND NOVELTY

Results obtained show that c-PLS enables analyzing the effect of biologically relevant variable clusters, facilitating the identification of biological processes associated with the independent variable, and the prioritization of the biological factors influencing model performance, thereby improving the understanding of the biological factors driving model predictions. While the strategy is tested for the evaluation of PLS models, it could be extended to other linear and non-linear multivariate models.

Comparing the direct assessment of steatosis in liver explants with mid- and near-infrared vibrational spectroscopy, prior to organ transplantation

A fast and accurate assessment of liver steatosis is crucial during liver transplantation surgery as it can negatively impact its success. Recent research has shown that near-infrared (NIR) and attenuated total reflectance-Fourier transform mid-infrared (ATR-FTIR) spectroscopy could be used as real-time quantitative tools to assess steatosis during abdominal surgery. Here, in the frame of a clinical study, we explore the performance of NIR and ATR-FTIR spectroscopy for the direct assessment of steatosis in liver tissues. Results show that both NIR and ATR-FTIR spectroscopy are able to quantify the % of steatosis with cross-validation errors of 1.4 and 1.6%, respectively. Furthermore, the two portable instruments used both provided results within seconds and can be placed inside an operating room evidencing the potential of IR spectroscopy for initial characterization of grafts in liver transplantation surgery. We also evaluated the complementarity of the spectral ranges through correlation spectroscopy.

Gut Microbiota and Plasma Bile Acids Associated with Non-Alcoholic Fatty Liver Disease Resolution in Bariatric Surgery Patients

Bariatric surgery (BS) has several benefits, including resolution of non-alcoholic fatty liver disease (NAFLD) in many patients. However, a significant percentage of patients do not experience improvement in fatty liver after BS, and more than 10% develop new or worsening NAFLD features. Therefore, a question that remains unanswered is why some patients experience resolved NAFLD after BS and others do not. In this study, we investigated the fecal microbiota and plasma bile acids associated with NAFLD resolution in twelve morbidly obese patients undergoing BS, of whom six resolved their steatosis one year after surgery and another six did not. Results indicate that the hallmark of the gut microbiota in responder patients is a greater abundance of Bacteroides, Akkermansia, and several species of the Clostridia class (genera: Blautia, Faecalibacterium, Roseburia, Butyricicoccusa, and Clostridium), along with a decreased abundance of Actinomycetes/Bifidobacterium and Faecalicatena. NAFLD resolution was also associated with a sustained increase in primary bile acids (particularly non-conjugated), which likely results from a reduction in bacterial gut species capable of generating secondary bile acids. We conclude that there are specific changes in gut microbiota and plasma bile acids that could contribute to resolving NAFLD in BS patients. The knowledge acquired can help to design interventions with prebiotics and/or probiotics to promote a gut microbiome that favors NAFLD resolution.

Higher Adherence to ERAS Society® Recommendations is Associated with Shorter Hospital Stay Without an Increase in Postoperative Complications or Readmissions in Bariatric Surgery: the Association Between Use of Enhanced Recovery After Surgery Protocols and Postoperative Complications after Bariatric Surgery (POWER 3) Multicenter Observational Study

PURPOSE

The effectiveness of enhanced recovery after surgery (ERAS) pathways in patients undergoing bariatric surgery remains unclear. Our objective was to determine the effect of the ERAS elements on patient outcomes following elective bariatric surgery.

MATERIALS AND METHODS

Prospective cohort study in adult patients undergoing elective bariatric surgery. Each participating center selected a single 3-month data collection period between October 2019 and September 2020. We assessed the 24 individual components of the ERAS pathways in all patients. We used a multivariable and multilevel logistic regression model to adjust for baseline risk factors, ERAS elements, and center differences RESULTS: We included 1419 patients. One hundred and fourteen patients (8%) developed postoperative complications. There were no differences in the incidence of overall postoperative complications between the self-designated ERAS and non-ERAS groups (54 (8.7%) vs. 60 (7.6%); OR, 1.14; 95% CI, 0.73-1.79; P = .56), neither for moderate-to-severe complications, readmissions, re-interventions, mortality, or hospital stay (2 [IQR 2-3] vs. 3 [IQR 2-4] days, 0.85; 95% CI, 0.62-1.17; P = .33) Adherence to the ERAS elements in the highest adherence quartile (Q1) was greater than 72.2%, while in the lowest adherence quartile (Q4) it was less than 55%. Patients with the highest adherence rates had shorter hospital stay (2 [IQR 2-3] vs. 3 [IQR 2-4] days, 1.54; 95% CI, 1.09-2.17; P = .015), while there were no differences in the other outcomes CONCLUSIONS: Higher adherence to ERAS Society® recommendations was associated with a shorter hospital stay without an increase in postoperative complications or readmissions.

TRIAL REGISTRATION

ClinicalTrials.gov Identifier: NCT03864861.

Simultaneous Complex Incisional Hernia Repair and Bariatric Surgery for Obese Patients: a Case Series of a Single-Center Early Experience

Purpose

Obesity is associated with recurrence of complex incisional hernia repair (CIHR). Bariatric procedure during CIHR can improve recurrence rates without increasing morbidity. This study aimed to describe our results after CIHR in patients with obesity, in which a simultaneous bariatric procedure was performed.

Materials and Methods

We performed a retrospective observational study including patients who underwent surgery between January 2014 and December 2018, with a complex incisional hernia (CIH) according to the Slater classification and body mass index (BMI) ≥35. CIHR was the main indication for surgery. We collected demographic data, comorbidities, CIH classification according to the European Hernia Society, type of bariatric procedure, postoperative morbidity using the Dindo-Clavien classification, and short-term results. Computed tomography (CT) is performed preoperatively.

Results

Ten patients were included in the study (7 women). The mean BMI was 43.63±4.91 kg/m². The size of the abdominal wall defect on CT was 8.86±3.93 cm. According to the European Hernia Society classification, all CIHs were W2 or higher. Prosthetic repair of the CIH was selected. Onlay, sublay, preperitoneal, and inlay mesh placement were performed twice each, as well as one modified component separation technique and one transversus abdominis release. Gastric leak after sleeve gastrectomy was the only major complication. Short-term outcomes included one recurrence, and % total weight loss was 24.04±8.03 after 1-year follow-up.

Conclusion

The association of bariatric procedures during CIHR seems to be feasible, safe, and could be an option for surgical treatment in selected patients.

Massive gastrointestinal pneumatosis in a patient with celiac disease and superior mesenteric artery syndrome

Pneumatosis intestinalis (PI) is a radiological finding representing the presence of gas in the bowell, independently of the cause or location. We present the case of a 55-year-old man who was admitted presenting two-week history of intense vomiting. The patient was previously diagnosed with superior mesenteric artery syndrome and celiac disease. Plain x-ray and TC showed gastric and intestinal pneumatosis with important retropneumoperitoneum. Due to clinical stability the patient was managed conservatively, with a favorable outcome.