Genetic alteration and mutation profiling of circulating cell-free tumor DNA (cfDNA) for diagnosis and targeted therapy of gastrointestinal stromal tumors

Amplification-free nucleic acids detection with next-generation CRISPR/dx systems

CRISPR-based diagnostics (CRISPR/Dx) have revolutionized the field of molecular diagnostics. It enables home self-test, field-deployable, and point-of-care testing (POCT). Despite the great potential of CRISPR/Dx in diagnoses of biologically complex diseases, preamplification of the template often is required for the sensitive detection of low-abundance nucleic acids. Various amplification-free CRISPR/Dx systems were recently developed to enhance signal detection at sufficient sensitivity. Broadly, these amplification-free CRISPR/Dx systems are classified into five groups depending on the signal enhancement strategies employed: CRISPR/Cas12a and/or CRISPR/Cas13a are integrated with: (1) other catalytic enzymes (Cas14a, Csm6, Argonaute, duplex-specific nuclease, nanozyme, or T7 exonuclease), (2) rational-designed oligonucleotides (multivalent aptamer, tetrahedral DNA framework, RNA G-quadruplexes, DNA roller machine, switchable-caged guide RNA, hybrid locked RNA/DNA probe, hybridized cascade probe, or "U" rich stem-loop RNA), (3) nanomaterials (nanophotonic structure, gold nanoparticle, micromotor, or microbeads), (4) electrochemical and piezoelectric plate biosensors (SERS nanoprobes, graphene field-effect transistor, redox probe, or primer exchange reaction), or (5) cutting-edge detection technology platforms (digital bioanalysis, droplet microfluidic, smartphone camera, or single nanoparticle counting). Herein, we critically discuss the advances, pitfalls and future perspectives for these amplification-free CRISPR/Dx systems in nucleic acids detection. The continued refinement of these CRISPR/Dx systems will pave the road for rapid, cost-effective, ultrasensitive, and ultraspecific on-site detection without resorting to target amplification, with the ultimate goal of establishing CRISPR/Dx as the paragon of diagnostics.

Comparison of endoscopic versus laparoscopic resection for gastric gastrointestinal stromal tumors: A preliminary meta-analysis

BACKGROUND AND AIM

For localized disease, complete surgical resection is regarded as the "gold standard" therapeutic modality. With the rapid development of endoscopic techniques, endoscopic resection (ESR) has been confirmed as an efficient and safe alternative for the treatment of gastrointestinal stromal tumors (GISTs) in the stomach. Nevertheless, the management of gastric GISTs remains poorly defined. The purpose of this study is to evaluate the security and effectiveness of ESR with laparoscopic resection (LAR) for gastric GISTs.

METHODS

A literature search of online databases was conducted to identify relevant comparative studies of ESR and LAR procedures for gastric GISTs published before April 10, 2020. The cumulative data analysis was also performed utilizing the software STATA.

RESULTS

In total, 10 studies involving 1165 patients met the inclusion criteria for analysis (651 for ESR and 514 for LAR). From the results of meta-analysis, patients who underwent ESR experienced decreased operative time (P = 0.000), less intraoperative blood loss (P = 0.002), earlier time to diet (P = 0.000), shorter hospital stay (P = 0.000), and lower total charges (P = 0.000) compared with LAR. Moreover, there were no significant differences between these two approaches concerning tumor rupture, conversion rate to other procedure, complete resection rate, postoperative complication rate, recurrence rate, and disease-free survival.

CONCLUSIONS

Endoscopic resection, as an effective alternative treatment strategy with satisfactory outcomes, is acceptable for selective patients with gastric GISTs compared with LAR. Further well-designed randomized controlled trials with large samples are warranted to corroborate our observations.

Radical excision versus local resection for primary rectal gastrointestinal stromal tumors. Cohort Study

BACKGROUND

Rectal gastrointestinal stromal tumor (GIST) is a rare digestive disease that originates in mesenchymal tissues and has malignant tendencies. At present, no standard treatment has been developed, and surgical approaches and the resection scope for rectal GISTs are controversial.

METHODS

The clinical, surgical, pathological and prognosis data of patients with primary rectal GIST in our center from January 2008 to January 2019 were retrospectively collected. The patients were divided into the radical excision (RE) and local resection (LR) groups.

RESULTS

A total of 537 GIST cases were collected, and 64 patients with primary rectal GIST were included in this study, including 25 cases in the RE group and 39 cases in the LR group. Tumor size (p = 0.013), distance from the anus (p = 0.038), National Institutes of Health (NIH) criteria (p = 0.001), preoperative adjuvant therapy (p = 0.016), postoperative adjuvant therapy (p = 0.028), blood loss (p = 0.048), operative time (p = 0.020) and the duration of hospitalization (p = 0.021) were statistically different between these 2 groups. The mean overall follow-up time was 46 months (range, 1-122 months). Disease recurrence was observed in 12 patients. No statistical differences were observed in 5-year disease-free survival (DFS) (93.3% vs 92.6%, p = 0.952) or overall survival (OS) (90.0% vs 91.6%, p = 0.832) between the RE group and the LR group.

CONCLUSION

Our study showed that LR has a similar prognosis to that of RE with respect to DFS and OS. For appropriate cases, LR has the advantages of a short operative time, less bleeding, and a quick recovery. Especially when combined with neoadjuvant therapy, LR can also achieve better perioperative efficacy. Therefore, LR is an effective method for resection of rectal GISTs and warrants clinical endorsement.

BRD4 promotes tumor progression and NF-κB/CCL2-dependent tumor-associated macrophage recruitment in GIST

The most commonly occurring sarcoma of the soft tissue is gastrointestinal stromal tumor (GIST). Treatment and prevention of the disease necessitate an understanding of the molecular mechanisms involved. However, the role of BRD4 in the progression of GIST is still unclear. While it is known there are abundant infiltrating tumor-associated macrophages (TAMs) in the tumor microenvironment, the exact role of these cells has yet to be studied. This work showed an upregulation of BRD4 in GIST that was associated with GIST prognosis. Through gain and loss of function studies, it was found that BRD4 promotes GIST growth and angiogenesis in vitro and in vivo. Mechanistically, BRD4 enhances CCL2 expression by activating the NF-κB signaling pathway. Furthermore, this CCL2 upregulation causes recruitment of macrophages into the tumor leading to tumor growth. A likely mechanism for interactions in the GIST microenvironment has been outlined by this work to show the role and potential use of BRD4 as a treatment target in GIST.

The correlation of clinicopathological features and prognosis in extranodal natural killer/T cell lymphoma: a report of 42 cases in the early stage

This study aimed to explore the clinicopathological features and prognostic correlation of extranodal natural killer (NK)/T cell lymphoma (ENKTCL) in the early stage, screen out the prognostic markers of ENKTCL, and to establish the molecular model of ENKTCL prognosis. A retrospective study was conducted in 88 patients from May 1999 to Dec 2013 in Chinese Academy of Medical Sciences Cancer Hospital, who were diagnosed with ENKTCL according to WHO lymphoid hematopoietic tumor classification (published in 2008). The clinical data and paraffin-embedded tissue blocks were collected. The expressions of CD56, MLH1, PDGFRA, VEGF, PD-L1, PD-1, CyclinD1, p53, and Ki-67 were detected by high-throughput tissue microarray and immunohistochemistry (IHC) staining. The relationship between nine protein expressions and the clinicopathological features and prognosis of patients with ENKTCL were analyzed. The survival time of the 42 patients with complete clinical and follow-up data was 0~153 months. The average survival time was 60.1 months. The survival rates of 1 year, 2 years, and 3 year were 85.7%, 78.6%, and 71.4%, respectively. Single factor survival analysis showed that the increase of serum lactate dehydrogenase (LDH ≥ 240UI/L) before treatment was associated with poor prognosis, and there was a significant difference in survival rate (P = 0.006). Different therapy methods were related with prognosis (P = 0.011); in specifically, radiotherapy alone had the best treatment effect, followed by concurrent chemoradiotherapy, and the worst was chemotherapy alone. But, multivariate statistics indicated that the LDH level and the treatment approach were not independent prognostic factors of ENKTCL. There was no statistical difference between epidemiological factors such as gender, age, and other clinicopathological factors including tumor location, B symptoms, β2-microglobulin levels before treatment, and prognosis. Survival analysis of single factor showed that the positive expression of PDGFRA and PD-L1 was, respectively, related to the poor prognosis of patients with ENKTCL (P = 0.040, 0.007). The patients with Ki-67 overexpression (≥ 50%) had a worse prognosis than those with lower expression (< 50%), and the difference of survival rate between the two groups has statistical significance (P = 0.038). The expression of CD56, MLH1, VEGF, PD-1, CyclinD1, and p53 has no effect on survival rate (P > 0.05). Multivariate survival analysis showed that the expression levels of PDGFRA, PD-L1, and Ki-67 were independent factors in the prognosis of patients with ENKTCL. And the positive expressions of these three proteins were risk factors for prognosis of patients with ENKTCL (PDGFRA: P = 0.045, HR = 8.265, 95% CI: 1.050-65.054; PD-L1: P = 0.005, HR = 9.369, 95% CI: 1.950-45.003; Ki-67: P = 0.023, HR = 3.545, 95% CI: 1.187-10.585). The elevation of serum lactate dehydrogenase (LDH ≥ 240UI/L) before treatment and the treatment approach were associated with poor prognosis, which could be used as adjunct indexes to the prognosis. However, they were not independent factors for the prognosis of patients with ENKTCL. The expressions of PDGFRA, PD-L1, and Ki-67 were independent factors in the prognosis of patients with ENKTCL and these three proteins were risk factors of prognosis. The above markers combined with clinical factors may establish the prognosis model of ENKTCL.

Advantage of Next-Generation Sequencing in Dynamic Monitoring of Circulating Tumor DNA over Droplet Digital PCR in Cetuximab Treated Colorectal Cancer Patients

Epidermal growth factor receptor (EGFR) blockade resistance is common in the treatment of RAS wide type colorectal cancer (CRC). During the treatment of cetuximab, acquired resistant genomic alterations always occurs earlier than disease progression observed by medical images. Identification of genomic alterations dynamically might have certain clinical significance. Because of the limitation of repeated tissue biopsy, liquid biopsy is increasingly recognized. Droplet digital polymerase chain reaction (ddPCR) is the main detection methods for circulating tumor DNA (ctDNA), however, the application of next-generation sequencing (NGS) for ctDNA detection becomes more and more popular. Here we develop a NGS-based ctDNA assay and evaluated its sensitivity and specificity while using ddPCR as control. These two technologies were both used for genomic alteration detection for the peripheral blood samples from cetuximab-treated colorectal cancer patients dynamically. Fifteen patients were enrolled in this study, including eight males and seven females. The sensitivity and specificity of our NGS assay were 87.5% and 100% respectively, and liner regression analysis comparing variant allele frequency (VAF) revealed high concordance between NGS and ddPCR (R2 = 0.98). NGS actually found more mutation information than ddPCR such as the additional dynamic changes of TP53 which were observed in the disease progression patients. Moreover, the variant allele fraction of TP53 was also found by NGS to be changed along with the clinical efficacy evaluation dynamically during the whole treatment process. In conclusion, our newly developed NGS-based ctDNA assay shows similar performance with ddPCR but have more advantages of its high throughput of multigenetic detection for the dynamic monitoring during the treatment of cetuximab in metastasis CRC patients.

Diagnosis and Treatment Monitoring of a Patient with Gastrointestinal Stromal Tumor by Next-Generation Sequencing and Droplet Digital Polymerase Chain Reaction Assay of a PDGFRA Mutation in Plasma-Derived Cell-Free Tumor DNA

In patients with a suspected malignancy, standard-of care management currently includes histopathologic examination and analysis of tumor-specific molecular abnormalities. Herein, we present a 77-year-old patient with an abdominal mass suspected to be a gastrointestinal stromal tumor (GIST) but without the possibility to collect a tumor biopsy. Cell-free DNA extracted from a blood sample was analyzed for the presence of mutations in GIST-specific genes using next generation sequencing. Furthermore, liquid biopsies were used to monitor the levels of mutant DNA copies during treatment with a tumor-specific mutation droplet digital PCR assay that correlated with the clinical and radiological response. Blood-based testing is a good alternative for biopsy-based testing. However, it should only be applied when biopsies are not available or possible to obtain because overall, in only 50%-85% of the cell-free plasma samples is the known tumor mutation detected.

Clinicopathological features and prognosis of 276 cases of primary small (≤ 2 cm) gastric gastrointestinal stromal tumors: a multicenter data review

BACKGROUND

Till present, there are still controversies over the epidemiology, pathological features, types of surgical treatment, and prognoses of primary small gastric GISTs (gGISTs).

METHODS

From January 1998 to January 2015, patients with primary small gGIST admitted from four high-volume medical centers of the Southern China were enrolled and their data were analyzed to evaluate their clinicopathological features, treatment and prognostic factors to provide evidence-based medical experience for clinical practice.

RESULTS

A total of 276 primary small gGIST cases over a period of 18 years were investigated and had a median age of 60 years (range 27-91 years old). Regarding the tumor sites, 24 (8.7%) cases were in the cardia of the stomach, 107 (38.8%) in the fundus, 117 (42.4%) in the gastric body, and 28 (10.1%) in the gastric antrum. Eleven patients (4.0%) underwent a preoperative biopsy. A total of 137 (49.6%), 75 (27.2%), and 64 (23.2%) patients underwent laparoscopic, open resection, and endoscopic resection, respectively. Sixty-four patients (23.2%) had local endoscopic resection, 172 (62.3%) had wedge resection, 7 (2.5%) had proximal gastrectomy, 19 (6.9%) had distal gastrectomy, and 14 (5.1%) had total gastrectomy. Mitotic counts were ≤ 5/50, (5-10)/50, and > 10/50 per HPF in 259 (93.8%), 7 (2.5%), and 10 (3.6%) cases, respectively. There were 259 cases (97.1%) of spindle cell type, 7 (2.5%) epithelial cell types and one case (0.4%) of mixed type. Immunohistochemistry showed 74.6% (206/276), 98.2% (271/276), and 97.4% (269/276) of the patients had co-expression of CD34+, CD117+, and DOG-1+, respectively. Thirty-nine patients underwent genetic testing (39/276, 14.1%). Three patients (1.1%) had positive resection margin. Five high-risk patients received follow-up treatment with imatinib with a median follow-up time of 38 months (range 3-156 months). The overall 1-, 3-, and 5-year overall survival rates were 100%, 99.6%, and 99.1%, respectively.

CONCLUSION

Though the incidence of primary small gGISTs increased per annum, the overall survival prognoses were high. Surgery or endoscopic resection was the primary mode of treatment. Pathological features of primary small gGISTs were similar to large gGISTs, and to achieve a timely surgical intervention, the identification of intermediate- and high-risk cases should be a future focus of study.

Evaluation of a novel liquid biopsy-based ColoScape assay for mutational analysis of colorectal neoplasia and triage of FIT+ patients: a pilot study

Circulating cell free tumour derived nucleic acids are becoming recognised as clinically significant and extremely useful biomarkers for detection of cancer and for monitoring the progression of targeted drug therapy and immunotherapy. Screening programmes for colorectal cancer in Europe use the Fetal Immunochemical Test (FIT) test as a primary screener. FIT+ patients are referred to immediate colonoscopy and the positive predictive value (PPV) is usually 25%. In this article, we report a study employing the ColoScape assay panel to detect mutations in the APC, KRAS, BRAF and CTNNB1 genes, in order to collect preliminary performance indicators and plan a future, larger population study. The assay was evaluated on 52 prospectively collected whole-blood samples obtained from FIT+ patients enrolled in the CRC screening programme of ASL NAPOLI 3 SUD, using colonoscopy as confirmation. The assay’s sensitivity for advanced adenomas was 53.8% and the specificity was 92.3%. The PPV was 70.0% and negative predicitive value (NPV) was 85.7%. Workflow optimisation is essential to maximise sensitivity. Of note, four of the six positive cases missed by ColoScape had a less than suboptimal DNA input (data not shown). Had they been ruled out as inadequate, sensitivity would have increased from 53.8% to 69%. However, as stated previously, this is not a clinical trial, but rather an initial, preliminary technical evaluation. In conclusion this study shows that ColoScape is a promising tool and further studies are warranted in order to validate its use for the triage of FIT+ patients.

Integration of traditional Chinese medicine and Western medicine in the era of precision medicine

Precision medicine has received growing recognition from clinicians, health systems, and the pharmaceutical industry, as well as patients and policymakers, which will leave a major impact on the practice of medicine. Interestingly, traditional Chinese medicine (TCM) provides personalized medical treatment based on the theory of TCM characterized by holistic concept and pattern differentiation. This, to some extent, is similar to the personalized medical treatment of precision medicine. In China, TCM as well as Western medicine (WM) plays an important role in healthcare. In this article, the authors summarized the influence of precision medicine on current medical directions, the advantages of TCM in disease treatment, further development of precision medicine and the strategies for integration of TCM and WM under this new treatment approach. In addition, the authors discuss the perspective of precise medical diagnosis and treatment, precise prevention, and the complementary advantages of the integration of TCM and WM. Finally, the authors give their perspectives on the challenges and opportunities presented by precision medicine, in the context of further research toward the integration of TCM and WM.

Circulating tumor DNA (ctDNA) in the era of personalized cancer therapy

The heterogeneity of tumor is considered as a major difficulty to victorious personalized cancer medicine. There is an extremeneed of consistent response evaluation for in vivo tumor heterogeneity anditscoupledconflict mechanisms. In this occasion researchers will be able to keep pace withpredictive, preventive, personalized, and Participatory (P4) medicine for cancer managements. In fact tumor heterogeneity is a central part of cancer evolution,soin order to progress in understanding of the dynamics within a tumor some diagnostic apparatus should be improved. Latest molecular techniques like Next generation Sequencing (NGS) and ultra-deep sequencing could disclose some clones within a liquid tumor biopsy which mainly responsible of treatment resistance. Circulating tumor DNA (ctDNA) as a main component of liquid biopsy is agifted biomarker for cancer mutation tracking as well as profiling. Personalized medicine facilitate learning regarding to genetic pools of tumor and their possible respond to treatment which could be much easier by using of ctDNA.With this information, cliniciansarelooking forward to find the best strategies for prevention, screening, and treatment in the way of precision medicine. Currently, numerous clinical efficacy of such informative improved treatment are in hand. Here we represent the review of plasma-derived ctDNA studies use in personalized cancer managements.

Advancements in microfluidic technologies for isolation and early detection of circulating cancer-related biomarkers

Isolation of circulating biomarkers using microfluidic devices for cancer diagnosis.

Prognostic role of tumor necrosis in patients undergoing curative resection for gastric gastrointestinal stromal tumor: a multicenter analysis of 740 cases in China

Tumor necrosis is associated with poor clinical outcomes in many malignancies. We aimed to determine whether tumor necrosis was an independent predictor of outcomes in gastric gastrointestinal stromal tumors (GISTs). We retrospectively analyzed data from 740 patients undergoing curative resection for gastric GIST at four centers between 2001 and 2015. Disease‐free survival (DFS) was estimated with the Kaplan–Meier method, and associations with prognosis were assessed with Cox regression models. Tumor necrosis was present in 122 cases (16.5%). The prevalence of tumor necrosis increased with higher risk‐stratification, including 0.7%, 7.4%, 17.3%, and 39.3% for very low‐, low‐, intermediate‐ and high‐risk tumors, respectively (P < 0.001). Tumor necrosis was associated with aggressive tumor biology, such as larger tumor size, higher mitotic index, tumor rupture, and presence of nuclear atypia (all P < 0.05). Multivariate analysis revealed that tumor necrosis was an independent predictor of unfavorable DFS (HR: 2.641; 95% CI: 1.359–5.131; P = 0.004). When stratified by the modified National Institutes of Health (NIH) classification, tumor necrosis still independently predicted DFS in high‐risk patients (P = 0.001) but not in non‐high‐risk patients (P = 0.349). The 5‐year DFS rate in high‐risk patients with and without tumor necrosis was 56.5% and 82.9%, respectively (P = 0.004). Notably, the prognostic significance of tumor necrosis was maintained when the patients were stratified by age, sex, tumor location, tumor size, and mitotic index (All P < 0.05). Tumor necrosis is a useful predictor of outcomes in gastric GIST, especially in high‐risk patients. Based on these results, we recommend that the current NIH classification should be further improved and expanded to include tumor necrosis as a valuable prognostic indicator.

Early Diagnosis of Breast Cancer

Early-stage cancer detection could reduce breast cancer death rates significantly in the long-term. The most critical point for best prognosis is to identify early-stage cancer cells. Investigators have studied many breast diagnostic approaches, including mammography, magnetic resonance imaging, ultrasound, computerized tomography, positron emission tomography and biopsy. However, these techniques have some limitations such as being expensive, time consuming and not suitable for young women. Developing a high-sensitive and rapid early-stage breast cancer diagnostic method is urgent. In recent years, investigators have paid their attention in the development of biosensors to detect breast cancer using different biomarkers. Apart from biosensors and biomarkers, microwave imaging techniques have also been intensely studied as a promising diagnostic tool for rapid and cost-effective early-stage breast cancer detection. This paper aims to provide an overview on recent important achievements in breast screening methods (particularly on microwave imaging) and breast biomarkers along with biosensors for rapidly diagnosing breast cancer.

eTumorType, An Algorithm of Discriminating Cancer Types for Circulating Tumor Cells or Cell-free DNAs in Blood

With the technology development on detecting circulating tumor cells (CTCs) and cell-free DNAs (cfDNAs) in blood, serum, and plasma, non-invasive diagnosis of cancer becomes promising. A few studies reported good correlations between signals from tumor tissues and CTCs or cfDNAs, making it possible to detect cancers using CTCs and cfDNAs. However, the detection cannot tell which cancer types the person has. To meet these challenges, we developed an algorithm, eTumorType, to identify cancer types based on copy number variations (CNVs) of the cancer founding clone. eTumorType integrates cancer hallmark concepts and a few computational techniques such as stochastic gradient boosting, voting, centroid, and leading patterns. eTumorType has been trained and validated on a large dataset including 18 common cancer types and 5327 tumor samples. eTumorType produced high accuracies (0.86-0.96) and high recall rates (0.79-0.92) for predicting colon, brain, prostate, and kidney cancers. In addition, relatively high accuracies (0.78-0.92) and recall rates (0.58-0.95) have also been achieved for predicting ovarian, breast luminal, lung, endometrial, stomach, head and neck, leukemia, and skin cancers. These results suggest that eTumorType could be used for non-invasive diagnosis to determine cancer types based on CNVs of CTCs and cfDNAs.