Data-Independent Acquisition Mass Spectrometry Analysis of FFPE Rectal Cancer Samples Offers In-Depth Proteomics Characterization of the Response to Neoadjuvant Chemoradiotherapy.

Locally advanced rectal cancer (LARC) presents a challenge in identifying molecular markers linked to the response to neoadjuvant chemoradiotherapy (nCRT). This study aimed to utilize a sensitive proteomic method, data-independent mass spectrometry (DIA-MS), to extensively analyze the LARC proteome, seeking individuals with favorable initial responses suitable for a watch-and-wait approach. This research addresses the unmet need to understand the response to treatment, potentially guiding personalized strategies for LARC patients. Post-treatment assessment included MRI scans and proctoscopy. This research involved 97 LARC patients treated with intense chemoradiotherapy, comprising radiation and chemotherapy. Out of 97 LARC included in this study, we selected 20 samples with the most different responses to nCRT for proteome profiling (responders vs. non-responders). This proteomic approach shows extensive proteome coverage in LARC samples. The analysis identified a significant number of proteins compared to a prior study. A total of 915 proteins exhibited differential expression between the two groups, with certain signaling pathways associated with response mechanisms, while top candidates had good predictive potential. Proteins encoded by genes SMPDL3A, PCTP, LGMN, SYNJ2, NHLRC3, GLB1, and RAB43 showed high predictive potential of unfavorable treatment outcome, while RPA2, SARNP, PCBP2, SF3B2, HNRNPF, RBBP4, MAGOHB, DUT, ERG28, and BUB3 were good predictive biomarkers of favorable treatment outcome. The identified proteins and related biological processes provide promising insights that could enhance the management and care of LARC patients.

Young-Onset Colorectal Cancer in Serbia: Tertiary Cancer Center Experience.

Purpose: Early-onset colorectal cancer (CRC) is a growing problem. The aim of the study was to identify adolescent and young adult (AYA) patients with CRC in Serbia, treated in the single tertiary cancer center. Materials and Methods: This is a retrospective study that included only AYA patients (ages 18-39 years) with histologically confirmed CRC. In 11 year (2009-2019), 109 patients were identified from a single-institution database and their clinical variables and outcomes were analyzed. Results: The prevalence of a positive family history of CRC was 12.8%. Presenting symptoms were not different than traditional CRC. More than a quarter were diagnosed as an emergency. Left-sided tumors were diagnosed in 83.4% and mucinous tumors were recorded in one-third of the patients. Postoperatively patients mainly were in PS0-1 (97%). Patients presented as stages II (18.3%), III (47.7%), and IV (33.9%). The recurrence rate in local stages was 50%. Surgical treatment of localized metastatic disease was performed in almost half of the stage IV patients. Median disease-free survival for patients with the recurrent disease was 11.8 months. Median overall survival (OS) for the local and metastatic stage was 64.3 and 20.5 months, respectively. Survival analysis showed that performance status, bowel obstruction, N2 status, local invasions, disease stage, and surgery in stage IV had a statistically significant influence on OS. Conclusion: Serbian AYA CRC patients are of good general condition, with advanced left-sided tumors, common mucinous histology, and inverse histology features. Surgery in metastatic disease provided long-term survival. The outcome of the patient is influenced by a late diagnosis, inverse histological features, and treatment provided.

RResolver: efficient short-read repeat resolution within ABySS.

BACKGROUND: De novo genome assembly is essential to modern genomics studies. As it is not biased by a reference, it is also a useful method for studying genomes with high variation, such as cancer genomes. De novo short-read assemblers commonly use de Bruijn graphs, where nodes are sequences of equal length k, also known as k-mers. Edges in this graph are established between nodes that overlap by [Formula: see text] bases, and nodes along unambiguous walks in the graph are subsequently merged. The selection of k is influenced by multiple factors, and optimizing this value results in a trade-off between graph connectivity and sequence contiguity. Ideally, multiple k sizes should be used, so lower values can provide good connectivity in lesser covered regions and higher values can increase contiguity in well-covered regions. However, current approaches that use multiple k values do not address the scalability issues inherent to the assembly of large genomes. RESULTS: Here we present RResolver, a scalable algorithm that takes a short-read de Bruijn graph assembly with a starting k as input and uses a k value closer to that of the read length to resolve repeats. RResolver builds a Bloom filter of sequencing reads which is used to evaluate the assembly graph path support at branching points and removes paths with insufficient support. RResolver runs efficiently, taking only 26 min on average for an ABySS human assembly with 48 threads and 60 GiB memory. Across all experiments, compared to a baseline assembly, RResolver improves scaffold contiguity (NGA50) by up to 15% and reduces misassemblies by up to 12%. CONCLUSIONS: RResolver adds a missing component to scalable de Bruijn graph genome assembly. By improving the initial and fundamental graph traversal outcome, all downstream ABySS algorithms greatly benefit by working with a more accurate and less complex representation of the genome. The RResolver code is integrated into ABySS and is available at https://github.com/bcgsc/abyss/tree/master/RResolver .

Quality of life following two different techniques of an open ventral hernia repair for large hernias: a prospective randomized study.

BACKGROUND: We compare the health-related quality of life (QoL) of patients with incision hernias before and after surgery with two different techniques. METHODS: In this prospective randomized study, the study population consisted of all patients who underwent the first surgical incisional hernias repair during the 1-year study period. Patients who met the criteria for inclusion in the study were randomized into two groups: the first group consisted of patients operated by an open Rives sublay technique, and the second group included patients operated by a segregation component technique. The change in the quality of life before and 6 months after surgery was assessed using two general (Short form of SF-36 questionnaires and European Quality of Life Questionnaire-EQ-5D-3L), and three specific hernia questionnaires (Hernia Related Quality of Life Survey-HerQles, Eura HS Quality of Life Scale-EuraHS QoL, and Carolinas Comfort Scale-CCS). RESULTS: A total of 93 patients were included in the study. Patients operated on by the Rives technique had a better role physical score before surgery, according to the SF-36 tool, although this was not found after surgery. The postoperative QoL measured with each scale of all questionnaires was significantly better after surgery. Comparing two groups of patients after surgery, only the pain domain of the EuraHS Qol questionnaire was worse in patients operated by a segregation component technique. CONCLUSION: Both techniques improve the quality of life after surgery. Generic QoL questionnaires showed no difference in the quality of life compared to repair technique but specific hernia-related questionnaires showed differences.

Prognostic Factors for Post-Recurrence Survival in Stage II and III Colorectal Carcinoma Patients.

Background and objectives: This study aimed to evaluate prognostic factors for post-recurrence survival in local and locally advanced colorectal cancer patients. Materials and Methods: A total of 273 patients with stage III and high-risk stage II colorectal cancer were prospectively enrolled. All patients underwent operative treatment of the primary tumor and adjuvant fluorouracil-based chemotherapy. Results: Over the three-year period (2008-2010), a cohort of 273 patients with stage III and high-risk stage II colorectal cancer had been screened. During follow up, 105 (38.5%) patients had disease recurrence. Survival rates 1-, 3- and 5-year after recurrence were 53.9, 18.2 and 6.5%, respectively, and the median post-recurrence survival time was 13 months. Survival analysis showed that age at diagnosis (p < 0.01), gender (p < 0.05), elevated postoperative Ca19-9 (p < 0.01), tumor histology (adenocarcinoma vs. mucinous vs. signet ring tumors, p < 0.01) and tumor stage (II vs. III, p < 0.05) had a significant influence on post-recurrence survival. Recurrence interval and metastatic site were not related to survival following recurrence. Multivariate analysis showed that older age (HR 2.43), mucinous tumors (HR 1.51) and tumors expressing Ca19-9 at baseline (HR 3.51) were independently associated with survival following recurrence. Conclusions: Baseline patient and tumor characteristics largely predicted patient outcomes after disease recurrence. Recurrence intervals in local and locally advanced colorectal cancer were not found to be prognostic factors for post-recurrence survival. Older age, male gender, stage III and mucinous histology were poor prognostic factors after the disease had recurred. Stage II patients had remarkable post-recurrence survival compared to stage III patients.

Functional assessment of cancer therapy questionnaire for melanoma in the Serbian population: A factor analytic approach.

The aim of this study was to examine the psychometric properties of the Functional Assessment Cancer Therapy-Melanoma (FACT-M) questionnaire in the Serbian language. The FACT-M was translated into Serbian using the standard methodology after obtaining the licence from the Functional Assessment of Chronic Illness Therapy (FACIT) translation project team. This version of FACT-M was distributed to a cohort of consecutive patients with histologically confirmed high-risk skin melanoma treated at the tertiary referral center. To examine construct validity of the FACT-M in Serbian, we performed exploratory factor analysis (EFA) and confirmatory factor analysis (CFA). The FACT-General (FACT-G) did not fit the original 4-domain structure. Instead, we accepted a 7-domain structure which, aside from physical, emotional, social and functional well-being, had domains of 'friends' support', 'illness acceptance' and 'fear of death'. Melanoma scale (MS) and Melanoma surgery scale (MSS) did not fit the original one-dimensional structure. The MS was observed to have 4 domains: 'pain', 'skin problems', 'abdominal metastases' and 'other problems'. The MSS was observed to have 2 domains: 'having symptoms' and 'no symptoms'. It is suggested that the FACT-M questionnaire is analyzed using the newly extracted domains to examine quality of life of people with high-risk melanoma in Serbia.

Uptake of Human Papillomavirus Vaccine and Intention to Vaccinate among Healthy Pregnant Women in Serbia: A Cross-Sectional Study on Awareness, Knowledge, and Attitudes.

We aimed to assess awareness, knowledge, and attitudes of healthy pregnant women towards human papillomavirus (HPV), to estimate factors associated with a positive attitude towards HPV immunization and to assess the uptake of the vaccine among their children. A cross-sectional study was conducted at the University Clinic of Gynecology and Obstetrics, Belgrade, Serbia among pregnant women attending their regular gynecological check-ups at the 12th gestational week. Knowledge about HPV and HPV vaccine was assessed using a specifically designed 12-item and 5-item questionnaires. Out of total 265 included women, 79.3% had heard of HPV, and 37.5% knew that HPV vaccine exists. HPV vaccine knowledge score was associated with higher odds for a positive attitude towards vaccination of both female (OR = 4.10, 95% CI 1.50-11.29) and male (OR = 3.71, 95% CI 1.52-9.01) child. The number of children (OR = 1.32, 95% CI 1.04-1.67) and high vaccine knowledge score (OR = 1.64 95% CI 1.13-2.39) were independent predictors associated with willingness to vaccinate child against HPV. The gynecologist was the preferable point of reference for information seeking about the HPV vaccine. Despite relatively high HPV awareness and knowledge among pregnant women in Serbia, about one-third of them are HPV vaccine aware, and are willing to vaccinate their children against HPV.

A nationwide assessment of the burden of healthcare-associated infections and antimicrobial use among surgical patients: results from Serbian point prevalence survey, 2017.

BACKGROUND: As the only non-European Union (EU) country, Serbia participated in a second point prevalence survey of healthcare-associated infections (HAIs) and antimicrobial use (AMU) organized by the European Centre for Disease Prevention and Control (ECDC) in the EU countries. Here, we aimed to estimate the prevalence of HAI and AMU in patients who had recently undergone a surgery and to compare risk profile, HAI rates, and AMU among surgical patients and non-surgical patients. METHODS: A national PPS was performed in 65 Serbian acute-care hospitals, in November 2017. In this paper, the data of 61 hospitals for adult acute-care were analyzed. To ensure the comparability of study design we used the Serbian translation of ECDC case definitions and ECDC PPS protocol. The trained infection control staff, led by a hospital coordinator, reviewed medical records to identify HAI active at the time of the survey and AMU. Only inpatients admitted to the ward before 8 a.m. on the day if the survey were included. RESULTS: A total of 12,478 patients from 61 hospitals for adult acute-care were eligible for inclusion in this study. Significantly higher proportions of surgical patients were female, belonged to the 60-to-79 age group, and were less severely ill. Also, extrinsic factors (invasive devices, hospitalization at the ICU, and prior antibiotics therapy) were more frequent in surgical patients. Prevalence of HAIs was higher among surgical patients (261/3626; 7.2%) than among non-surgical patients (258/8852; 2.9%) (p < 0.0001). The highest prevalence of all HAIs was noted in patients who had kidney transplantation (4/11; 36.4%), while SSIs were the most prevalent among patients who had peripheral vascular bypass surgery (3/15; 20.0%). Non-surgical patients received treatment for community-acquired infections in significantly higher proportion (2664/8852; 64.3) (p < 0.001). Surgical prophylaxis for more than 1 day was applied in 71.4% of surgical patients. CONCLUSION: We have provided an insight into the burden of HAIs and AMU among Serbia acute-care hospitals, and highlighted several priority areas and targets for quality improvement.

Incidence and Risk Factors of 30-Day Surgical Site Infection after Primary Total Joint Arthroplasty in a Middle-Income Country: A Single-Center Experience.

The data about the incidence and risk factors for surgical site infections (SSIs) following total joint arthroplasty (TJA) in middle-income countries are still scant. The aim of this study was to assess the incidence and risk factors associated with 30-day SSIs following total hip arthroplasty (THA) and total knee arthroplasty (TKA). The study was conducted at the Clinic for Orthopedic Surgery and Traumatology, Clinical Center of Serbia (CCS) in Belgrade, from May 2016 to April 2018. All patients undergoing THA or TKA were followed throughout hospitalization until day 30 after discharge. Of the 1073 admitted patients, 459 had THA and 230 had TKA. The incidence rate of surgical site infections (SSIs) among the patients who underwent THA was 5.4%, which is 3.8 per 1000 postoperative patient-days, while the rate among those who had TKA was 4.8%, i.e., 3.4 per 1000 postoperative patient-days. Out of the 36 SSIs, 15 were deep and 21 were superficial incisional ones. Among the variables examined, the independent risk factors for SSIs after THA were the American Society of Anesthesiologists (ASA) score > 2 (RR = 3.17; 95% CI-1.26-8.02), smoking (RR = 3.14; 95% CI-1.26-7.82) and peripheral vascular disease (PVD) (RR = 6.09; 95% CI-2.35-15.77), and after TKA, only PVD (RR = 3.87; 95% CI-1.09-13.76) was the risk factor. Incidence rates of SSIs after arthroplasty are higher compared to reports from developed countries. Therefore, it is necessary to enhance infection prevention and control measures with strict control of modifiable risk factors.

Doppler ultrasonography combined with transient elastography improves the non-invasive assessment of fibrosis in patients with chronic liver diseases.

AIMS: Accurate clinical assessment of liver fibrosis is essential and the aim of our study was to compare and combine hemodynamic Doppler ultrasonography, liver stiffness by transient elastography, and non-invasive serum biomarkers with the degree of fibrosis confirmed by liver biopsy, and thereby to determine the value of combining non-invasive method in the prediction significant liver fibrosis. MATERIAL AND METHODS: We included 102 patients with chronic liver disease of various etiology. Each patient was evaluated using Doppler ultrasonography measurements of the velocity and flow pattern at portal trunk, hepatic and splenic artery, serum fibrosis biomarkers, and transient elastography. These parameters were then input into a multilayer perceptron artificial neural network with two hidden layers, and used to create models for predicting significant fibrosis. RESULTS: According to METAVIR score, clinically significant fibrosis (≥F2) was detected in 57.8% of patients. A model based only on Doppler parameters (hepatic artery diameter, hepatic artery systolic and diastolic velocity, splenic artery systolic velocity and splenic artery Resistance Index), predicted significant liver fibrosis with a sensitivity and specificity of75.0% and 60.0%. The addition of unrelated non-invasive tests improved the diagnostic accuracy of Doppler examination. The best model for prediction of significant fibrosis was obtained by combining Doppler parameters, non-invasive markers (APRI, ASPRI, and FIB-4) and transient elastography, with a sensitivity and specificity of 88.9% and 100%. CONCLUSION: Doppler parameters alone predict the presence of ≥F2 fibrosis with fair accuracy. Better prediction rates are achieved by combining Doppler variables with non-invasive markers and liver stiffness by transient elastography.

p21 does, but p53 does not predict pathological response to preoperative chemoradiotherapy in locally advanced rectal cancer.

PURPOSE: Preoperative chemoradiotherapy (CRT) is the standard treatment option in locally advanced rectal cancer. The tumor response is assessed through tumor and nodal downstaging and the tumor regression grade. Currently, there is no method to predict a tumor response to CRT. We aimed to evaluate whether p21 and p53 expressions could be a reliable predictors of pathological response to CRT. METHODS: Fifty patients with locally advanced rectal cancer were treated with preoperative radiotherapy combined with mitomycin C and capecitabine. p21 and p53 immumohistochemical staining was performed on pretreatment biopsies and the results were compared with tumor regression according to grading systems by Dworak (TRG grades) and by Wheeler (RCRG grades). RESULTS: Testing RCRG grades in relation to p21 expression showed statistically significant difference (p=0.021). RCRG 3 (poor response) was more frequent in the group of patients with low p21. According to Dworak, grade 4 (complete regression) was more frequent in the group of patients with positive p21 expression (p=0.032). Significant difference in p21 expression in grade 4 group compared with all other grade groups was also found (p=0.007). Patients with immune expression of p21 had significantly higher percentage of complete regression in comparison to the patients with low expression of p21. We haven't found any correlation between p53 expression and histopathological (HP) as well as regression grades. CONCLUSION: According to both grading systems, our results suggest that p53 expression does not, but p21 expression does predict pathological response to preoperative CRT.

Preoperative radiotherapy with capecitabine and mitomycin C in locally advanced rectal carcinoma.

PURPOSE: To evaluate the efficacy and safety of preoperative radiotherapy with capecitabine and mitomycin C in patients with locally advanced rectal cancer. METHODS: A prospective, open-label, non-randomized, phase II study was performed on 49 patients with locally advanced rectal cancer. Preoperative radiotherapy was conducted on linear accelerators (15 or 18 MV) with a tumor dose of 45 Gy in 25 fractions over 5 weeks, combined with mitomycin C 7 mg/m(2) on days 1 and 29 and oral capecitabine 825 mg/m(2) twice daily on days 1-35. Surgery was performed 5-6 weeks after the end of chemoradiation. The primary study endpoint was histopathological complete regression rate (pCR; Dworak grade 4). RESULTS: Disease stage at diagnosis was T3 in 34 patients (69%) and T4 in 15 patients (31%). Positive lymph nodes were diagnosed in 28 patients (57%). Toxicity (all grades) was documented in 35 patients (71%). Grade 3 toxicities were radiation dermatitis (25%), diarrhea (2%), neutropenia (2%), and granulocytopenia (2%). No patient experienced grade 4 toxicity. A pCR was seen in 8 (16%, 95% CI 9-29%) patients, a major response was noted in 24 (49%) patients and a minor response in 14 (29%) patients. R0 resection was performed in 46 patients (93.9%) and R1 in 3 patients (6.1%). Histopathological tumor downstaging was documented in 26 patients (53%). One-year disease-free survival was 93.3% and 1-year survival was 97.7%. CONCLUSION: Preoperative chemoradiation with capecitabine and mitomycin C appeared to be effective with low toxicity in patients with locally advanced rectal cancer.