[Risk factors of postoperative surgical site infection in colon cancer based on a single center database]

Objective: To explore the incidence and risk factors of postoperative surgical site infection (SSI) after colon cancer surgery. Methods: A retrospective case-control study was performed. Patients diagnosed with colon cancer who underwent radical surgery between January 2016 and May 2021 were included, and demographic characteristics, comorbidities, laboratory tests, surgical data and postoperative complications were extracted from the specialized prospective database at Department of General Surgery, Peking Union Medical College Hospital. Case exclusion criteria: (1) simultaneously multiple primary colon cancer; (2) segmental resection, subtotal colectomy, or total colectomy; (3) patients undergoing colostomy/ileostomy during the operation or in the state of colostomy/ileostomy before the operation; (4) patients receiving natural orifice specimen extraction surgery or transvaginal colon surgery; (5) patients with the history of colectomy; (6) emergency operation due to intestinal obstruction, perforation and acute bleeding; (7) intestinal diversion operation; (8) benign lesions confirmed by postoperative pathology; (9) patients not following the colorectal clinical pathway of our department for intestinal preparation and antibiotic application. Univariate analysis and multivariate analysis were used to determine the risk factors of SSI after colon cancer surgery. Results: A total of 1291 patients were enrolled in the study. 94.3% (1217/1291) of cases received laparoscopic surgery. The incidence of overall SSI was 5.3% (69/1291). According to tumor location, the incidence of SSI in the right colon, transverse colon, left colon and sigmoid colon was 8.6% (40/465), 5.2% (11/213), 7.1% (7/98) and 2.1% (11/515) respectively. According to resection range, the incidence of SSI after right hemicolectomy, transverse colectomy, left hemicolectomy and sigmoid colectomy was 8.2% (48/588), 4.5% (2/44), 4.8% (8 /167) and 2.2% (11/492) respectively. Univariate analysis showed that preoperative BUN≥7.14 mmol/L, tumor site, resection range, intestinal anastomotic approach, postoperative diarrhea, anastomotic leakage, postoperative pneumonia, and anastomotic technique were related to SSI (all P<0.05). Multivariate analysis revealed that anastomotic leakage (OR=22.074, 95%CI: 6.172-78.953, P<0.001), pneumonia (OR=4.100, 95%CI: 1.546-10.869, P=0.005), intracorporeal anastomosis (OR=5.288, 95%CI: 2.919-9.577,P<0.001) were independent risk factors of SSI. Subgroup analysis showed that in right hemicolectomy, the incidence of SSI in intracorporeal anastomosis was 19.8% (32/162), which was significantly higher than that in extracorporeal anastomosis (3.8%, 16/426, χ(2)=40.064, P<0.001). In transverse colectomy [5.0% (2/40) vs. 0, χ(2)=0.210, P=1.000], left hemicolectomy [5.4% (8/148) vs. 0, χ(2)=1.079, P=0.599] and sigmoid colectomy [2.1% (10/482) vs. 10.0% (1/10), χ(2)=2.815, P=0.204], no significant differences of SSI incidence were found between intracorporeal anastomosis and extracorporeal anastomosis (all P>0.05). Conclusions: The incidence of SSI increases with the resection range from sigmoid colectomy to right hemicolectomy. Intracorporeal anastomosis and postoperative anastomotic leakage are independent risk factors of SSI. Attentions should be paid to the possibility of postoperative pneumonia and actively effective treatment measures should be carried out.

A multi-dimensional integrative scoring framework for predicting functional variants in the human genome

Attempts to identify and prioritize functional DNA elements in coding and non-coding regions, particularly through use of in silico functional annotation data, continue to increase in popularity. However, specific functional roles can vary widely from one variant to another, making it challenging to summarize different aspects of variant function with a one-dimensional rating. Here we propose multi-dimensional annotation-class integrative estimation (MACIE), an unsupervised multivariate mixed-model framework capable of integrating annotations of diverse origin to assess multi-dimensional functional roles for both coding and non-coding variants. Unlike existing one-dimensional scoring methods, MACIE views variant functionality as a composite attribute encompassing multiple characteristics and estimates the joint posterior functional probabilities of each genomic position. This estimate offers more comprehensive and interpretable information in the presence of multiple aspects of functionality. Applied to a variety of independent coding and non-coding datasets, MACIE demonstrates powerful and robust performance in discriminating between functional and non-functional variants. We also show an application of MACIE to fine-mapping and heritability enrichment analysis by using the lipids GWAS summary statistics data from the European Network for Genetic and Genomic Epidemiology Consortium.

Perioperative nivolumab monotherapy versus nivolumab plus ipilimumab in resectable hepatocellular carcinoma: a randomised, open-label, phase 2 trial

BACKGROUND

Hepatocellular carcinoma has high recurrence rates after surgery; however, there are no approved standard-of-care neoadjuvant or adjuvant therapies. Immunotherapy has been shown to improve survival in advanced hepatocellular carcinoma; we therefore aimed to evaluate the safety and tolerability of perioperative immunotherapy in resectable hepatocellular carcinoma.

METHODS

In this single-centre, randomised, open-label, phase 2 trial, patients with resectable hepatocellular carcinoma were randomly assigned (1:1) to receive 240 mg of nivolumab intravenously every 2 weeks (for up to three doses before surgery at 6 weeks) followed in the adjuvant phase by 480 mg of nivolumab intravenously every 4 weeks for 2 years, or 240 mg of nivolumab intravenously every 2 weeks (for up to three doses before surgery) plus one dose of 1 mg/kg of ipilimumab intravenously concurrently with the first preoperative dose of nivolumab, followed in the adjuvant phase by 480 mg of nivolumab intravenously every 4 weeks for up to 2 years plus 1 mg/kg of ipilimumab intravenously every 6 weeks for up to four cycles. Patients were randomly assigned to the treatment groups by use of block randomisation with a random block size. The primary endpoint was the safety and tolerability of nivolumab with or without ipilimumab. Secondary endpoints were the proportion of patients with an overall response, time to progression, and progression-free survival. This trial is registered with ClinicalTrials.gov (NCT03222076) and is completed.

FINDINGS

Between Oct 30, 2017, and Dec 3, 2019, 30 patients were enrolled and 27 were randomly assigned: 13 to nivolumab and 14 to nivolumab plus ipilimumab. Grade 3-4 adverse events were higher with nivolumab plus ipilimumab (six [43%] of 14 patients) than with nivolumab alone (three [23%] of 13). The most common treatment-related adverse events of any grade were increased alanine aminotransferase (three [23%] of 13 patients on nivolumab vs seven [50%] of 14 patients on nivolumab plus ipilimumab) and increased aspartate aminotransferase (three [23%] vs seven [50%]). No patients in either group had their surgery delayed due to grade 3 or worse adverse events. Seven of 27 patients had surgical cancellations, but none was due to treatment-related adverse events. Estimated median progression-free survival was 9·4 months (95% CI 1·47-not estimable [NE]) with nivolumab and 19·53 months (2·33-NE) with nivolumab plus ipilimumab (hazard ratio [HR] 0·99, 95% CI 0·31-2·54); median time to progression was 9·4 months (95% CI 1·47-NE) in the nivolumab group and 19·53 months (2·33-NE) in the nivolumab plus ipilimumab group (HR 0·89, 95% CI 0·31-2·54). In an exploratory analysis, three (23%) of 13 patients had an overall response with nivolumab monotherapy, versus none with nivolumab plus ipilimumab. Three (33%) of nine patients had a major pathological response (ie, ≥70% necrosis in the resected tumour area) with nivolumab monotherapy compared with three (27%) of 11 with nivolumab plus ipilimumab.

INTERPRETATION

Perioperative nivolumab alone and nivolumab plus ipilimumab appears to be safe and feasible in patients with resectable hepatocellular carcinoma. Our findings support further studies of immunotherapy in the perioperative setting in hepatocellular carcinoma.

FUNDING

Bristol Myers Squibb and the US National Institutes of Health.

Efficacy and safety of HDL/apoA-1 mimetics on human and mice with atherosclerosis: a systematic review and meta-analysis

Funding Acknowledgements

Type of funding sources: Public grant(s) – National budget only. Main funding source(s): the National Natural Science Foundation of China

Background

Low high-density lipoprotein cholesterol (HDL-C) level as a residual risk factor of cardiovascular disease (CVD) is still causing concern, although using chemical drugs for raising HDL-C level failed. The effect of high-density lipoprotein/ apolipiproteinA-1(HDL/apoA-1) mimetics on atherosclerosis is controversial.

Aim

In this meta-analysis we analyzed the effect of high-density lipoprotein/ apolipiproteinA-1(HDL/apoA-1) mimetics on atherosclerotic lesion both in human and mice.

Methods

We systematically searched PubMed, Cochrane, Web of Science and EMBASE databases up to June 6, 2020 for eligible studies using wide search terms and included all the publications meet the including criteria. The methodological quality of the human studies was assessed using Review Manager (RevMan) software (version 5.3.). The methodological quality of the mice studies was assessed by using stair list. WMD(SMD) with 95% CI was used as a measure of the association between HDL/apoA-1 mimetics and plaque regression in human (in mice), after pooling data across trials in a random effect model. Sensitivity and subgroup analyses were used to explore sources of heterogeneity and the effect of potential confounders. STATA (version 14.0) was used to conduct all statistical analyses.

Results

We identified 15 randomized controlled trials in which 6 trails including 754 ACS (HDL/apoA-1 mimetics = 414, placebo = 340) patients used for efficacy analysis and all of 15 trails used for safety analysis and 17 controlled trials for animal study. The pooled results showed that the use of HDL/apoA-1 mimetics did not significant decreased the percent atheroma volume(p = 0.494) and total atheroma volume(p = 0.560) in patients with acute coronary syndrome (ACS). However, HDL/apoA-1 mimetics (or gene transfection) was significant associated with all of final percent lesion area, final lesion area and changes in lesion area (SMD, -1.75; 95% CI: -2.21∼-1.29, p = 0.000; SMD, -0.78; 95% CI: -1.18∼-0.38, p = 0.000; SMD: -2.06; 95% CI, -3.92∼-0.2, p = 0.03) in mice.

Conclusions

In human, HDL/apoA-1 mimetics cannot significantly improve atheroma volume in artery, although it is safe. However, in animal, the results suggest HDL/apoA-1 mimetics (or gene transfection) can decrease lesion area. So additional studies are needed to further investigate and explain the different efficacy of HDL/apoA-1 mimetic peptides between human and animal. Abstract Figure. Forest plots of human studies

Minimal residual disease assessment in colorectal cancer (MiRDA-C)

TPS236

Background: Detection of circulating tumor DNA (ctDNA) in the bloodstream is emerging as a novel marker for identifying of radiographically occult microscopic or minimal residual disease (MRD) in colorectal cancer (CRC) patients (pts) after curative intent treatments. Accumulating data suggest that ct-DNA defined MRD is a highly specific prognostic biomarker for future recurrences with a lead time of several months and prospective clinical trials are being conducted using ct-DNA defined MRD as an integral biomarker for improving risk stratification for adjuvant chemotherapy decision making. However, large scale, prospective data regarding kinetics of ctDNA-defined MRD with accurate pre-analytical methodology for plasma isolation and paired clinical data are limited. Methods: In this multi-center, prospective observational study, 1,000 pts with resectable CRC (stages II – IV) without other active malignancies undergoing therapy with curative intent will be enrolled any time from time of diagnosis up to start of adjuvant therapy (or ≤ 3 months post curative surgery, whichever is earlier). All therapeutic and surveillance visits decisions are at the discretion of the treating physicians. Serial biospecimens including blood (in Cell-Free DNA BCT tubes) to be processed to plasma and buffy coat in ≤ 2 days and formalin fixed tumor tissue will be collected at key time points until the time of radiographic recurrence or up to 5 years of surveillance. Blood draws will be at study entry, after each line of neoadjuvant therapy, post-surgery, during and after adjuvant therapy in addition to each surveillance visit. These blood draws will be coordinated with pts’ standard of care visits in order to minimize additional venipunctures. Relevant clinical data including demographics, cancer history, treatment details and outcomes, serum tumor markers and genomic data will be collected at each time point. Samples will be evaluated retrospectively with a primary objective of evaluating sensitivity and specificity of post-operative MRD for radiographic recurrences utilizing Guardant Health’s Reveal assay. Other key objectives include evaluating ctDNA kinetics with neoadjuvant and adjuvant therapies and to correlate with outcomes. The study is active, and enrollment is ongoing. Clinical trial information: NCT04739072.

Circulating tumor DNA dynamics on front-line chemotherapy with bevacizumab or cetuximab in metastatic colorectal cancer: A biomarker analysis for acquired genomic alterations in CALGB/SWOG 80405 (Alliance) randomized trial

193

Background: Enhanced understanding of the evolving clonal architecture under treatment stress is crucial to optimizing care and developing effective therapies in metastatic colorectal cancer (mCRC). Emergence of genomic alterations (GAs) [mutations (muts) and amplifications (amps)] in RAS, BRAF, EGFR, ERBB2, and MET have been recognized as key resistance mechanisms to anti-EGFR therapy in later lines in mCRC. Data regarding occurrence of these GAs under selective pressure in the first line setting is lacking. Methods: CALGB/SWOG 80405 was a randomized trial of bevacizumab (bev) vs cetuximab (cet) in first line mCRC. Patients (pts) with paired plasma samples (pre-treatment and post-progression) available for circulating tumor DNA (ctDNA) testing were included in this substudy. Sequencing of ctDNA was performed by Guardant360 assay in a CLIA-certified environment to detect GAs in 73 genes. RAS/BRAF status [mut vs. wild type (wt)] was based on clonal muts [pre-defined cutoff of relative MAF (rMAF) ≥ 25%] in ctDNA. Only samples with ≥1 GA were analyzed to minimize false negatives. The primary objective was to determine and compare prevalence of acquired GAs between study arms: bev (anti-VEGF) and cet (anti-EGFR). Descriptive statistics and Fisher’s exact test were used. Results: Baseline characteristics of ctDNA cohort were similar to the 80405 population. Among 133 randomized RAS/BRAF wt pts, 11 (15.3%) and 5 (8.2%) developed acquired GAs (OR 2.0, P = 0.29), in bev and cet arm, respectively. Key comparative data for pts with regard to acquired pathogenic GAs are shown in the table. Conclusions: In this randomized mCRC cohort, the ctDNA profile of acquired GAs with front line anti-EGFR chemotherapy appears to be strikingly distinct from that seen with later lines of therapy. Acquisition of GAs, classically associated with EGFR resistance in later line, was not only rare with upfront cet-chemotherapy but also comparable to bev-containing (anti-VEGF) regimen. The mechanisms of acquired resistance appear to differ when anti-EGFR therapy is administered in combination with highly active first line chemotherapy. Our findings have critical translational relevance to the timing and value of ctDNA-guided anti-EGFR rechallenge in mCRC pts, especially in those treated with anti-EGFR therapy upfront.[Table: see text]

Comparison of Clinical Efficacy and Urodynamic Changes Using Single-incision Slings (MiniArc® vs. Solyx™) for the Treatment of Female Stress Urinary Incontinence

Objective:

To compare the clinical efficacy and urodynamic parameter changes between the MiniArc and the Solyx sling for the treatment of female urodynamic stress incontinence (USI).

Materials and Methods:

One-hundred and thirty (MiniArc n = 79, BS-Solyx n = 51) patients were included in this study. Cough stress test (ST), pad test (PT), Incontinence Impact short form Questionnaire (IIQ-7), Urogenital Distress Inventory six-item questionnaire (UDI-6), Sexual Questionnaire-Short Form (PIS-Q), and urodynamic parametric changes were assessed to determine objective and subjective outcomes following the procedure. Objective cure was defined as negative ST and PT <2 g and subjective cure was defined as “No” to the answer of UDI-6 Question #3. Predictors of surgical failure were also determined.

Results:

All Solyx users, as opposed to 91.1% of MiniArc patients, obtained objective cure at postoperative 3 months (P = 0.042). No significant difference in subjective cure rates (93.7% vs. 90.2% at 3-months (P = 0.513); 89.9% vs. 80.4% at 1 year for Solyx and MiniArc patients, respectively (P = 0.126)) and improvement scores in UDI-6 and IIQ-7 were observed. The Solyx group incurred more de novo urgency (17.6% vs. 6.3% at 3 months (P = 0.042); 23.5% vs. 7.6% at 1 year (P = 0.01)). Both procedures yielded significant decrements in maximal urethral closure pressure (P < 0.001) and average flow rate (P = 0.015). The preoperative PT and sling type were strong predictors of surgical failure, where the Solyx tape reported lower odds (odds ratio = 0.174, P = 0.02) compared to the MiniArc sling.

Conclusion:

Single-incision mini-slings are safe and effective treatment for female USI. The Solyx SIS demonstrated superiority over the MiniArc in this study based on its higher objective cure rate and lower risk for surgical failure.

Moving beyond conventional stratified analysis to assess the treatment effect in a comparative oncology study

In a comparative oncology study with progression-free or overall survival as the endpoint, the primary or key secondary analysis is routinely stratified by patients' baseline characteristics when evaluating the treatment difference. The validity of a conventional strategy such as a stratified HR analysis depends on stringent model assumptions that are unlikely to be met in practice, especially in immunotherapy studies. Thus, the resulting summary is generally neither valid nor interpretable. This article discusses issues with conventional stratified analyses and presents alternatives using data from KEYNOTE-189, a recent immunotherapy trial for treating patients with metastatic, non-squamous, non-small-cell lung cancer.

Optical coherence tomography-defined vulnerable plaque characteristics in relation to functional severity of coronary stenoses stratified by quantitative flow ratio

Background

The functional severity and morphological features of epicardial lesions are both related to plaque vulnerability and adverse coronary events. However, their relationship remains controversial, especially in patients with non-ST-segment elevation acute coronary syndrome (NSTE-ACS).

Purpose

This study aimed to examine whether quantitative flow ratio (QFR), an angiography-based computation of fractional flow reserve, was associated with optical coherence tomography (OCT)-defined vulnerable plaques such as thin-cap fibroatheromas (TCFAs) in a board spectrum of population, including patients presenting stable angina and NSTE-ACS.

Methods

We identified patients who underwent OCT examinations from 2 prospective cohorts and then assessed interrogated vessels with QFR. Lesions were divided into tertiles: QFR-T1 (QFR &lt;0.85)&lt;qfr),&gt;, QFR-T2 (0.85 to 0.93) and QFR-T3 (QFR &gt;0.93).

Results

This post-hoc analysis included 83 lesions from 79 patients (mean age: 61.5±9.8 years, males: 58%). Patients with NSTE-ACS accounted for the majority of the population (67%). The median % diameter stenosis and median QFR value were 42% (36 to 49%) and 0.88 (0.83 to 0.95), respectively. The prevalence of OCT-TCFA was significantly higher in QFR-T1 (50%) than in QFR-T2 (14%) and QFR-T3 (19%) (p=0.003 and 0.018, respectively). Overall significant differences were observed among tertiles in maximum lipid arc, thinnest fibrous cap thickness (FCT), and minimal lumen area (MLA) (p=0.017, 0.040, and &lt;0.001, respectively). The Spearman's correlation analysis showed that QFR was significantly related to MLA (ρ = 0.537, p&lt;0.001), % area stenosis (ρ = –0.512, p&lt;0.001), maximum lipid arc (ρ = –0.360, p=0.002), lipid length (ρ = –0.242, p=0.038), lipid index (ρ = –0.333, p=0.004), and thinnest FCT (ρ = 0.315, p=0.006). In the multivariable analysis, QFR ≤0.80 remained as a significant determinant of TCFAs regardless of the presence of NSTE-ACS and the level of low-density lipoprotein cholesterol (adjusted odds ratio = 4.387, 95% confidence interval: 1.297 to 14.839, p=0.017). In addition, QFR demonstrated moderate predictive ability for OCT-TCFA (area under the curve = 0.72, 95% confidence interval: 0.58 to 0.86, p=0.003) with the best cutoff of ≤0.86 (sensitivity: 65%; specificity: 73%; negative predictive value: 85%; accuracy: 71%).

Conclusions

Lower QFR was related to OCT-TCFA and other vulnerable plaque characteristics in angiographically mild-to-intermediate stable lesions and culprit lesions from NSTE-ACS. The QFR might be a useful tool for ruling out high-risk, rupture-prone plaques without using any pressure wires or vasodilators.

Funding Acknowledgement

Type of funding sources: Foundation. Main funding source(s): The Jiangsu Provincial Key Research and Development Program Flow diagram of patient selectionOCT findings according to QFR tertiles

9p21 loss confers a cold tumor immune microenvironment and primary resistance to immune checkpoint therapy

Immune checkpoint therapy (ICT) provides substantial clinical benefits to cancer patients, but a large proportion of cancers do not respond to ICT. To date, the genomic underpinnings of primary resistance to ICT remain elusive. Here, we performed immunogenomic analysis of data from TCGA and clinical trials of anti-PD-1/PD-L1 therapy, with a particular focus on homozygous deletion of 9p21.3 (9p21 loss), one of the most frequent genomic defects occurring in ~13% of all cancers. We demonstrate that 9p21 loss confers "cold" tumor-immune phenotypes, characterized by reduced abundance of tumor-infiltrating leukocytes (TILs), particularly, T/B/NK cells, altered spatial TILs patterns, diminished immune cell trafficking/activation, decreased rate of PD-L1 positivity, along with activation of immunosuppressive signaling. Notably, patients with 9p21 loss exhibited significantly lower response rates to ICT and worse outcomes, which were corroborated in eight ICT trials of >1,000 patients. Further, 9p21 loss synergizes with PD-L1/TMB for patient stratification. A "response score" was derived by incorporating 9p21 loss, PD-L1 expression and TMB levels in pre-treatment tumors, which outperforms PD-L1, TMB, and their combination in identifying patients with high likelihood of achieving sustained response from otherwise non-responders. Moreover, we describe potential druggable targets in 9p21-loss tumors, which could be exploited to design rational therapeutic interventions.

Manganese promoted wheat straw decomposition by regulating microbial communities and enzyme activities

AIMS

This study investigated the dose-effect of manganese (Mn) addition on wheat straw (WS) decomposition, and explored the potential mechanisms of Mn involved in the acceleration of WS decomposition in regards to the soil microbial communities and enzyme activities.

METHODS AND RESULTS

A 180-day incubation experiment was performed to examine the decomposition of WS under four Mn levels, that is, 0, 0.25, 1 and 2 mg g^-1 . The effects of microbial communities and enzyme activities were evaluated using control (0 mg g^-1 ) and Mn (0.25 mg g^-1 ) treatments. Our results revealed that Mn (0.25 mg g^-1 ) addition significantly increased WS decomposition, and enhanced the release of carbon and nitrogen. Optimal Mn addition (0.25 mg g^-1 ) also caused significant increases in the activity of neutral xylanase (NEX), laccase (Lac), manganese peroxidase (MnP) and lignin peroxidase (LiP) within the incubation period. Mn (0.25 mg g^-1 ) addition also enriched some operational taxonomic units (OTUs) that, in turn, had the potential ability to decompose crop straw, such as secreting lignocellulolytic enzymes.

CONCLUSIONS

Mn (0.25 mg g^-1 ) could promote WS decomposition through enrichment of the microbial species involved in biomass decomposition, which enhanced the lignocellulose-degrading enzyme activity.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study provides evidence for Mn to promote WS biodegradation after Mn application, opening new windows to improve the utilization efficiency of crop residues.

[Artificial intelligence, radiomics and pathomics to predict response and survival of patients treated with radiations]

Artificial intelligence approaches in medicine are more and more used and are extremely promising due to the growing number of data produced and the variety of data they allow to exploit. Thus, the computational analysis of medical images in particular, radiological (radiomics), or anatomopathological (pathomics), has shown many very interesting results for the prediction of the prognosis and the response of cancer patients. Radiotherapy is a discipline that particularly benefits from these new approaches based on computer science and imaging. This review will present the main principles of an artificial intelligence approach and in particular machine learning, the principles of a radiomic and pathomic approach and the potential of their use for the prediction of the prognosis of patients treated with radiotherapy.

Natural history and prognostic factors for localised small bowel adenocarcinoma

Objective

Small bowel adenocarcinoma (SBA) is a rare malignancy with limited evidence regarding outcomes after curative resection of localised disease. We aimed to evaluate presentation and prognostic factors affecting overall survival (OS), relapse-free survival (RFS) and recurrence of SBA.

Methods

Consecutive patients with completely resected localised SBA (1979–2019) were retrospectively reviewed for presentation, patient and tumour characteristics, perioperative treatment, recurrence, outcomes, and prognostic factors.

Results

Among 257 total patients, median age was 58 years. Primary location was in the duodenum, jejunum and ileum in 52%, 29%, and 19% of patients, respectively. Median OS was 57.5 months and median follow-up was 40 months. In multivariate analysis, lymph node involvement, lymphovascular invasion, histologic grade and race were independent predictors of RFS, while race, stage and histologic grade were independent predictors of OS. No significant difference in OS or RFS was seen when evaluating the role of perioperative treatment. Median time to diagnosis from first medical evaluation was 31 days and did not change over time. Overall recurrence rate was 56%. Recurrence rate was higher in ileal (77%), than duodenal (54%) and jejunal (65%) SBA (p=0.01). Recurrence presented most commonly as distant metastasis (71%). Proficient mismatch repair was associated with decreased risk of locoregional recurrence (LR) but increased risk of distant recurrence (DR) when compared with deficient mismatch repair (dMMR) in univariate analysis.

Conclusions

Despite advances in diagnostic modalities, this study did not show any improvement in earlier diagnosis of SBA over the course of the past three decades. The predominant pattern of disease recurrence was distant across all SBA locations, but dMMR status demonstrated a robust predilection for LR as opposed to DR. Perioperative treatment did not improve outcomes; however, a lower stage disease was seen in patients that received neoadjuvant therapy, suggesting further exploration of this approach.

Immune Phenotype and Response to Neoadjuvant Therapy in Triple-Negative Breast Cancer

PURPOSE

Increasing tumor-infiltrating lymphocytes (TIL) is associated with higher rates of pathologic complete response (pCR) to neoadjuvant therapy (NAT) in patients with triple-negative breast cancer (TNBC). However, the presence of TILs does not consistently predict pCR, therefore, the current study was undertaken to more fully characterize the immune cell response and its association with pCR.

EXPERIMENTAL DESIGN

We obtained pretreatment core-needle biopsies from 105 patients with stage I-III TNBC enrolled in ARTEMIS (NCT02276443) who received NAT from Oct 22, 2015 through July 24, 2018. The tumor-immune microenvironment was comprehensively profiled by performing T-cell receptor (TCR) sequencing, programmed death-ligand 1 (PD-L1) IHC, multiplex immunofluorescence, and RNA sequencing on pretreatment tumor samples. The primary endpoint was pathologic response to NAT.

RESULTS

The pCR rate was 40% (42/105). Higher TCR clonality (median = 0.2 vs. 0.1, P = 0.03), PD-L1 positivity (OR: 2.91, P = 0.020), higher CD3⁺:CD68⁺ ratio (median = 14.70 vs. 8.20, P = 0.0128), and closer spatial proximity of T cells to tumor cells (median = 19.26 vs. 21.94 μm, P = 0.0169) were associated with pCR. In a multivariable model, closer spatial proximity of T cells to tumor cells and PD-L1 expression enhanced prediction of pCR when considered in conjunction with clinical stage.

CONCLUSIONS

In patients receiving NAT for TNBC, deep immune profiling through detailed phenotypic characterization and spatial analysis can improve prediction of pCR in patients receiving NAT for TNBC when considered with traditional clinical parameters.

CRISPR-Cas9 Ribonucleoprotein-Mediated Genomic Editing in Mature Primary Innate Immune Cells

CRISPR genome engineering has become a powerful tool to functionally investigate the complex mechanisms of immune system regulation. While decades of work have aimed to genetically reprogram innate immunity, the utility of current approaches is restricted by poor knockout efficiencies or limited specificity for mature cell lineages in vivo. Here, we describe an optimized strategy for non-viral CRISPR-Cas9 ribonucleoprotein (cRNP) genomic editing of mature primary mouse innate lymphocyte cells (ILCs) and myeloid lineage cells that results in an almost complete loss of single or double target gene expression from a single electroporation. Furthermore, we describe in vivo adoptive transfer mouse models that can be utilized to screen for gene function during viral infection using cRNP-edited naive natural killer (NK) cells and bone-marrow-derived conventional dendritic cell precursors (cDCPs). This resource will enhance target gene discovery and offer a specific and simplified approach to gene editing in the mouse innate immune system.

A novel clinical tool to estimate risk of false negative KRAS mutation in circulating tumor DNA testing

3594

Background: Recently, in metastatic colorectal cancer (mCRC), the detection of RAS mutations by circulating tumor (ct) DNA has recently emerged as a valid and non-invasive alternative approach, overall showing a high concordance with the standard tissue genotyping, giving information on response to EGFRi treatment and resistant mechanisms. However, RAS mutations may be missed due to low levels of any ctDNA in the blood (false-negative), and it has been difficult to distinguish this from patients without a RAS mutation in the tumor (true-negative). We propose a methodology that can be applied to multi-gene ctDNA testing panels to accurately distinguish true- and false-negative tests. Methods: 357 subjects with tissue and multi-panel ctDNA testing from MD Anderson (MDACC) were used as a training dataset and 295 subjects from Massachusetts General Hospital (MGH) dataset as the testing dataset. CtDNA panels contained between 65 and 70 genes, allowing evaluation of tumor ctDNA shedding from variant allele fraction (VAF) levels in the plasma from other genes (such as APC and TP53). Based on the relationship between KRAS and the VAFs of other gene, we established a Bayesian model providing a posterior probability of false negative in the ctDNA test, using thresholds of < 5% (low), 5-15% (medium), and > 15% (high). This model was validated on the MGH database. Results: Across both cohorts, 431 patients were ctDNA wild type for KRAS. Of those, 29 had tissue documenting a KRAS mutation for a false negative rate of 8%. The model provides the posterior probability that a KRAS mutation is indeed present in the tissue given the observed values of allele frequencies for other mutated genes in the plasma. In the validation cohort, a predicted low false negative had no false negatives (0/62, 95% CI 0%-5.8%), while a predicted medium false negative rate was associated with 3% false negative (1/32, 95% CI 0%-16%). In contrast, a high predicted false negative rate was associated with 5% false negative (5/100, 95% CI 1.6%-11%). The results demonstrate the ability of our tool to discriminate between subjects with true negative and false negatives, as a higher proportion of false negatives are observed at higher posterior probabilities. Conclusions: In conclusion, our approach provides increased confidence in KRAS ctDNA mutation testing in clinical practice, thereby facilitating the identification patients who will benefit from EGFR inhibition while reducing the risk of false negative tests. Extension of this methodology to NRAS and BRAF is possible, with clinical application enabled by a freely available online tool.

Rarity of acquired mutations (MTs) after first-line therapy with anti-EGFR therapy (EGFRi)

3514

Background: Colorectal cancers (CRC) lacking RAS MTs treated with EGFRi are thought to evolve by a repetitive process of genetic diversification and clonal evolution. Acquired MTs in KRAS, NRAS, BRAF, MAP2K1, and EGFR are known mechanisms of acquired resistance in the EGFRi refractory population. However, the prevalence of MTs in the first line (1L) setting is not well established as most experience with EGFRi has been beyond the 1L setting. Methods: We analyzed paired plasma samples from RAS/BRAF/EGFRWT mCRC patients (pts) enrolled in 3 large randomized phase 3 trials who had been treated with EGFRi and in whom paired baseline (BL) and time of progression (PRO) plasma samples had been collected for sequencing of ctDNA on a platform optimized for very low allele frequencies (Plasma Select-R™ and Resolution Bio™). Prevalence of MTs at BL and PRO from a 1L study (‘203; FOLFOX ± panitumumab) were compared with 2 studies in the third line setting (3L; ‘007; panitumumab + best supportive care [BSC] vs BSC; and 3L; ‘763; panitumumab vs. cetuximab), to assess the frequency of acquired resistance mutations via ctDNA analysis. Results: For pts with available paired plasma samples (n = 112 for ‘203; n = 89 for ‘007; n = 274 for ‘763), acquisition of at least one KRAS, NRAS, BRAF, MAP2K1, or EGFR MT was significantly less common in post-progression samples in the EGFR containing arms of the 1L ‘203 study compared to the 3L ‘763 and ‘007 studies (6.8% vs 50.4% vs 39.6%, respectively; p < 0.001). In the non EGFR containing arms of the ‘203 and ‘007 study, the rate of acquired MTs was 7.5% and 0%, respectively (p = 1). While this difference in the rate of acquired MTs between the EGFR and non EGFR containing arms was statistically significant for the 3L study (p < 0.001) it was not significant for the 1L study. Further, pts on both 3L studies treated with EGFRi who experienced CR, PR or SD acquired more MTs than those who had PD as best response (53.6% vs 33.3%, respectively; p < 0.001). This relationship was not significant in the 1L setting (7.7% vs 0%; p = 1). Subclonal MTs (rMAF < 25%) in KRAS, NRAS, EGFR, BRAF and MAP2K1 were present at BL in 129 pts (27%). Based on the hypothesis that EGFRi is selecting for rare existing mutated cells in the tumor, we would expect expansion of any preexisting subclones in the BL samples. However, in contrast to expectations, these subclones rarely expanded to become clonal at the time of progression (12.4%). Conclusions: In contrast to expectations, acquired KRAS, NRAS, BRAF, EGFR, or MAP2K1 MTs rarely develop after 1L therapy. While selective pressure appears to increase the frequency of acquired MTs in the 3L setting, preexisting subclonal MTs do not appear to be the dominant source of acquired MTs at progression, implying that there may also be a transient mutational process driving resistance rather than expansion of preexisting clones. These findings have significant implications for ongoing and planned EGFRi rechallenge studies.

Neoadjuvant atezolizumab (atezo) and nab-paclitaxel (nab-p) in patients (pts) with triple-negative breast cancer (TNBC) with suboptimal clinical response to doxorubicin and cyclophosphamide (AC)

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Background: Neoadjuvant anti-PD-(L)1 therapy confers an improvement in pathological complete response (pCR) rate in unselected TNBC. However, given the potential for long-term morbidity from immune related adverse events (irAE), it is important to optimize the risk-benefit ratio for the use of these novel agents in the curative neoadjuvant setting. Suboptimal clinical response to neoadjuvant therapy (NAT) by sonography is associated with low rates of pCR rate (2-5%, GeparTrio and Aberdeen trials). Here, we report the results of a single arm phase II study of atezo and nab-p as the second phase of NAT in pts with TNBC with suboptimal clinical response to AC (NCT02530489). Methods: Pts with stage I-III TNBC showing suboptimal response to 4 cycles of doxorubicin and cyclophosphamide (AC), defined as disease progression or a <80% reduction in tumor volume by sonography, were eligible. Pts received atezo (1200mg IV, Q3 weeks x 4), and nab-p (100mg/m2 IV, Q1 week, x 12) as the second phase of NAT before undergoing surgery followed by adjuvant atezo (1200mg IV, Q3 weeks, x 4 cycles). This single arm, two-stage Gehan-type study was designed to detect an improvement in pCR from 5% to 20% in order to deem the regimen worthy of further study in a large, randomized, phase II/III trial; success was defined as pCR in 8 out of 37 pts enrolled. In a subset of pts, sufficient baseline tumor tissue was available for stromal TIL assessment (n=29). Results: 34 pts were enrolled from 2/2016-12/2020. Among the 33 pts who have completed NAT, the pCR rate was 30% (10/33, 95% CI: 16-49%) and the pCR/RCB-I rate was 42% (14/33, 95% CI: 25-61%). Clinicopathological characteristics are described in the table below. Treatment-related adverse events (all grades) occurring in ≥ 20% of pts include fatigue (73%), anemia (55%), peripheral sensory neuropathy (55%), neutropenia (48%), rash (42%), ALT elevation (39%), AST elevation (33%), nausea (30%), anorexia (24%), diarrhea (21%), myalgia (21%). Discontinuation of atezo due to irAEs occurred in 4 pts (12%, nephritis [n=2]; adrenal insufficiency [n=1]; hepatitis [n=1]); 2 of these pts had pCR. Conclusions: This study met its primary endpoint, demonstrating a promising signal of activity in this high risk pt population (pCR=30% vs 5% in historical controls). The 12% discontinuation rate due to irAEs confirms that further evaluation of a strategy administering immunotherapy only to pts with high risk disease not responding to AC warrants further investigation. Exploratory genomic and immunological correlative studies are ongoing. Clinical trial information: NCT02530489. [Table: see text]

Implementation of a Novel Web-Based Lesion Selection Tool to Improve Acquisition of Tumor Biopsy Specimens

Introduction

For maximum utility of molecular characterization by next-generation sequencing (NGS) and better understanding of tumor microenvironment with immune correlates analysis, biopsy specimens must yield adequate tumor tissue, and sequential biopsy specimens should sample a consistent site. We developed a web-based lesion selection tool (LST) that enables management and tracking of the biopsy specimen collections.

Methods

Of 145 patients, the LST was used for 88 patients; the other 57 served as controls. We evaluated consistency of the lesion biopsied in longitudinal collections, number of cores obtained, and cores with adequate tumor cellularity for NGS. The Fisher exact test and Wilcoxon rank sum test were used to identify differences between the groups.

Results

The analysis included 30 of 88 (34%) patients in the LST group and 52 of 57 (91%) in the control group. The LST workflow ensured 100% consistency in the lesions biopsied compared with 75% in the control group in longitudinal collections and increased the proportion of patients in whom at least five cores were collected per biopsy.

Conclusions

The novel LST platform facilitates coordination, performance, and management of longitudinal biopsy specimens. Use of the LST enables sampling of the designated lesion consistently, which is likely to accurately inform us the effect of the treatment on tumor microenvironment and evolution of resistant pathways. Such studies are important translational component of any clinical trials and research as they guide the development of next line of therapy, which has significant effect on clinical utility. However, validation of this approach in a larger study is warranted.

Metastatic small bowel adenocarcinoma: role of metastasectomy and systemic chemotherapy

Background

Metastatic small bowel adenocarcinoma (SBA) has a poor prognosis. Due to its rarity, high-quality data are lacking to guide treatment. This retrospective analysis was conducted to help characterize the treatment options for patients with metastatic SBA while providing clinically meaningful prognostic information.

Patients and methods

In total, 437 patients who initially presented with or developed metastatic SBA between September 1977 and September 2019 were identified from the MD Anderson Tumor Registry. Clinical data were collected from review of the medical record. Overall response rates (ORR), time to progression (TTP), and overall survival (OS) were assessed across various treatments and treatment lines.

Results

The median OS from diagnosis of metastatic disease was 15.9 months [95% confidence interval (CI): 14.3-17.9]. Seventy-five patients (17.1%) underwent metastasectomy, which was associated with a median OS of 34.5 versus 17.1 months among patients who received chemotherapy alone (P < 0.001). Fluoropyrimidine plus platinum (n = 164) was the most common first-line chemotherapy, associated with an ORR of 59% and TTP of 8.1 months. Irinotecan with 5-FU (n = 101) was the most common second-line therapy associated with an ORR of 31% and TTP of 4.0 months. Twenty-two patients received immunotherapy; 5 of 6 patients with deficient mismatch repair (dMMR) responded, while 0 of 16 with proficient mismatch repair (pMMR) responded. Taxane-based chemotherapy was given to 34 patients with an ORR of 21% and a median TTP of 2.4 months. Among 11 patients who received anti-epidermal-growth-factor-receptor (EGFR) monotherapy, the best response was stable disease (SD) in 1 patient.

Conclusions

In well-selected patients with SBA, metastasectomy appears to be associated with improved OS. This improvement was seen across metastasectomy sites, including liver, lung and peritoneal. Anti-programmed cell death protein 1 (PD-1) based immunotherapy was active for dMMR SBA but not pMMR SBA. While taxane-based chemotherapy demonstrates therapeutic activity, the activity of anti-EGFR therapy was limited.

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Metastasectomy for well-selected metastatic SBA patients was associated with improved OS.

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Anti-PD1-based immunotherapy was active for dMMR SBA but not pMMR SBA.

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Taxane-based chemotherapy demonstrated clinical activity in refractory SBA.

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Anti-EGFR therapy demonstrated minimal activity in SBA.

Outcomes of changing systemic therapy in patients with relapsed breast cancer and 1 to 3 brain metastases

The development of brain metastases (BMs) in breast cancer (BC) patients remains a challenging complication. Current clinical practice guidelines recommend local treatment of BMs without changing systemic therapy (CST) in patients with stable extracranial disease. We retrospectively investigated the impact of CST (when applicable as per treating physician's discretion) following the diagnosis and management of oligometastatic (1-3) BMs in patients without extracranial metastases on the progression-free survival time (PFS), and overall survival (OS). Hazard ratios (HRs) were calculated using the Cox proportional hazard model. Among the 2645 patients with BC and BMs treated between 2002 and 2015, 74 were included for analysis. 40.5% of patients had HER2 + disease. Median time from diagnosis of BC to BMs was 17.6 months. 54%, 8%, and 38% of BMs were managed by radiation, craniotomy, or combination, respectively. Following the primary management of BMs, we observed that CST occurred in 26 (35.5%) patients, consisting of initiation of therapy in 13.5% and switching of ongoing adjuvant therapy in 22%. Median PFS was 6.6 months among patients who had CST compared to 7.1 months in those who did not (HR = 0.88 [0.52-1.47], p = 0.62). Median OS was 20.1 months among patients who had CST compared to 15.1 months in those who did not (HR = 0.68 [0.40-1.16], p = 0.16). Upon the successful local management of oligometastatic BMs in patients without extracranial disease, we did not find a significant difference in survival between patients who experienced a change in systemic therapy as compared to those who did not.

Contributions of epiphytic microbiota on the fermentation characteristics and microbial composition of ensiled six whole crop corn varieties

AIMS

The present study is aimed to reveal the variations in epiphytic microbial composition among six whole crop corn (WCC) varieties and their contributions on ensiling characteristics and microbial composition of WCC silage.

METHODS AND RESULTS

Six WCC varieties (JS06, YS23, BS20, JS39, JS40 and JS26) were ensiled for 90 days. All WCC varieties were well fermented with low pH value (<4·0) and high LA (73·6-124 g kg^-1 DM, dry matter) concentration. Of six varieties, JS40 had the highest LA (124 g kg^-1 DM) concentration, which was supported by highest relative abundance of Lactobacillus. Pantoea was the most dominant epiphytic bacteria in all fresh WCC varieties; however, the secondary dominant genera among six WCC were absolutely difference. Lactobacillus became predominant genus in 90-day silages except YS23. YS23 kept the more bacterial genus from fresh to 90-day silages than other silages, meanwhile Acinetobacter and Enterobacter were the dominant bacteria in YS23 silages.

CONCLUSIONS

Among six WCC varieties, JS40 silage had the highest LA. The variations in epiphytic microbiomes among fresh WCC affected terminal microbial community of 90-day silages. There were differences in fermentation characteristics among six WCC varieties, which might be partly attributed to variations in epiphytic microbiomes among fresh WCC.

SIGNIFICANCE AND IMPACT OF THE STUDY

The study not only enriches the research on microbial communities of plant phyllosphere but also provides theoretical basis for selecting WCC varieties and inoculants for the forage production.