Association Between Preanalytical Factors and Tumor Mutational Burden Estimated by Next-Generation Sequencing-Based Multiplex Gene Panel Assay

BACKGROUND

Tumor mutational burden (TMB) measured via next-generation sequencing (NGS)-based gene panel is a promising biomarker for response to immune checkpoint inhibitors (ICIs) in solid tumors. However, little is known about the preanalytical factors that can affect the TMB score.

MATERIALS AND METHODS

Data of 199 patients with solid tumors who underwent multiplex NGS gene panel (OncoPrime), which was commercially provided by a Clinical Laboratory Improvement Amendments-licensed laboratory and covered 0.78 megabase (Mb) of capture size relevant to the TMB calculation, were reviewed. Associations between the TMB score and preanalytical factors, including sample DNA quality, sample type, sampling site, and storage period, were analyzed. Clinical outcomes of patients with a high TMB score (≥10 mutations per megabase) who received anti-programmed cell death protein 1 antibodies (n = 22) were also analyzed.

RESULTS

Low DNA library concentration (<5 nM), formalin-fixed paraffin-embedded tissue (FFPE), and the prolonged sample storage period (range, 0.9-58.1 months) correlated with a higher TMB score. After excluding low DNA library samples from the analysis, FFPE samples, but not the sample storage period, exhibited a marked correlation with a high TMB score. Of 22 patients with a high TMB score, we observed the partial response in 2 patients (9.1%).

CONCLUSION

Our results indicate that the TMB score estimated via NGS-based gene panel could be affected by the DNA library concentration and sample type. These factors could potentially increase the false-positive and/or artifactual variant calls. As each gene panel has its own pipeline for variant calling, it is unknown whether these factors have a significant effect in other platforms.

IMPLICATIONS FOR PRACTICE

A high tumor mutational burden score, as estimated via next-generation sequencing-based gene panel testing, should be carefully interpreted as it could be affected by the DNA library concentration and sample type.

Utility of ultrasound-guided liver tumor biopsy for next-generation sequencing-based clinical sequencing

AIM

Recent advances in next-generation sequencing (NGS) technologies allow for evaluation of genetic alterations in various cancer-related genes in daily clinical practice. Archival formalin-fixed paraffin-embedded (FFPE) tumor tissue is often used for NGS-based clinical sequencing assays; however, the success rate of NGS assays using archival FFPE tumor tissue is reported to be lower than that using fresh tumor tissue. We aimed to evaluate the feasibility and safety of ultrasound (US)-guided liver tumor biopsy for NGS-based multiplex gene assays.

METHODS

We compared the success rate of NGS assays between archival FFPE tumor tissues and US-guided liver tumor biopsy tissues, and summarized the treatment progress of the patients.

RESULTS

Next-generation sequencing assays using US-guided liver biopsy samples were successful in all patients (22/22), whereas the success rate with archival FFPE tumor tissue was 84.8% (151/178, P < 0.05). At least one potentially actionable genetic alteration was identified from the US-guided liver biopsy samples in 20 of 22 patients. Among the 18 patients with actionable genetic alterations targetable with drugs approved by the US Food and Drug Administration, eight initiated mutation-driven targeted therapies. Of these eight patients, four achieved partial response or stable disease for at least 4 months, and three were not assessable for response due to short exposure. There were no biopsy-related complications requiring additional treatment.

CONCLUSION

Our findings suggest that US-guided liver tumor biopsy is a useful and safe method for obtaining high-quality samples for NGS-based clinical sequencing. In cases with metastatic liver tumors, US-guided biopsy should be considered to provide accurate and optimal sequencing results for patients.

Combination of Mac-2 Binding Protein Glycosylation Isomer and Up-To-Seven Criteria as a Useful Predictor for Child-Pugh Grade Deterioration after Transarterial Chemoembolization for Hepatocellular Carcinoma

Transarterial chemoembolization (TACE) is the recommended first-line treatment for intermediate-stage hepatocellular carcinoma (HCC). In patients who became refractory to TACE, a treatment switch to tyrosine kinase inhibitors (TKIs) needs to be considered. However, TACE could worsen liver function, thereby narrowing the time window for a switch to TKIs because TKIs are recommended for patients with Child-Pugh grade A (CP-A). We investigated the factors associated with CP grade deterioration after TACE. Among patients who underwent TACE, 125 patients with CP-A were enrolled. The cumulative CP grade deterioration rates were 20.3%, 27.1%, and 41.4% at six months, one year, and two years, respectively. Multivariate analysis revealed that factors associated with CP grade deterioration included high Mac-2 binding protein glycosylation isomer (M2BPGi) levels (>2.00 cut-off index) and beyond the up-to-seven criteria. The cumulative CP grade deterioration rates of patients with high M2BPGi and beyond the up-to-seven criteria were 50.6% and 59.2% at six months and one year, respectively, which were significantly higher than for those in any other groups. The combination of M2BPGi and up-to-seven criteria could be a surrogate marker for predicting CP grade deterioration after TACE. In patients with intermediate-stage HCC, elevated M2BPGi levels, and beyond the up-to-seven criteria, an early treatment switch to TKIs should be considered to improve their prognosis.

Accelerated Progression of Hepatocellular Carcinoma during Immunosuppressive Therapy with Abatacept for Rheumatoid Arthritis

Abatacept, a cytotoxic T lymphocyte antigen-4 immunoglobulin recombinant fusion protein, is an immunosuppressive agent indicated for rheumatoid arthritis. Although no significant increase in malignancy has been reported in abatacept-treated patients, whether or not abatacept accelerates tumor progression in specific cancer types remains unclear. We herein report a 66-year-old woman who showed unusually rapid progression of hepatocellular carcinoma following abatacept therapy for rheumatoid arthritis. Abatacept was speculated to have accelerated her hepatocellular carcinoma progression in the setting of her preexisting risk factors: autoimmune hepatitis and long-term methotrexate use. We propose close tumor surveillance be performed during abatacept therapy, especially for high-risk patients.

Ultrasound-guided microfoam sclerotherapy with polidocanol for symptomatic giant hepatic cyst: Initial experience

AIM

In cases of symptomatic giant hepatic cysts, appropriate treatment is required to relieve symptoms. Ethanol, minocycline hydrochloride, and ethanolamine oleate have been conventionally used for ultrasound (US)-guided sclerotherapy. However, liquid sclerosing agents could mix with the residual fluid in the cyst and reduce their sclerotic effects. We carried out US-guided microfoam sclerotherapy using polidocanol for three patients and evaluated its efficacy and safety.

METHODS

Between May 2016 and March 2017, three female patients with symptomatic giant hepatic cysts were referred to our hospital. All of them were prospectively included in this study.

RESULTS

The maximum diameters of the hepatic cysts in the three patients were 92 × 89 × 86 mm, 155 × 119 × 140 mm, and 223 × 195 × 123 mm, respectively. Polidocanol microfoam was successfully administered through an 8.5-Fr pigtail catheter for all patients. One, two, and three microfoam sclerotherapy sessions were undertaken according to the initial cyst volume for cases 1, 2, and 3, respectively. The mean reduction rates of the cyst volume were 90.1% (85.5-98.9%) at 3 months, 96.3% (91.9-99.9%) at 6 months, and 99.5% (99.1-99.9%) at 9 months after treatment. No significant treatment-induced adverse effects were observed.

CONCLUSION

Ultrasound-guided microfoam sclerotherapy using polidocanol could be an effective and safe method for the treatment of symptomatic giant liver cysts.

Choledochoduodenal Fistula during Chemotherapy with Brentuximab Vedotin for Methotrexate-associated Lymphoproliferative Disorder

We herein report a patient with a history of rheumatoid arthritis treated with methotrexate, which caused methotrexate-associated lymphoproliferative disorder and obstructive jaundice due to an enlarged lymph node. The obstructive jaundice was treated with endoscopic biliary stenting. A histopathological examination revealed features of Hodgkin's lymphoma, and chemotherapy with brentuximab vedotin was administered. Cholangiography and duodenoscopy after four rounds of chemotherapy revealed a choledochoduodenal fistula that developed in response to chemotherapy. It should be noted that, in cases of lymphoma infiltrating the gastrointestinal wall, fistulae can occur because of rapid regression due to regimens comprising monoclonal antibodies, such as rituximab and brentuximab vedotin.

Novel approaches for molecular targeted therapy against hepatocellular carcinoma

Systemic chemotherapy using a multitargeted tyrosine kinase inhibitor is an established treatment for advanced-stage tumors in various organs. Comprehensive genomic analyses using next-generation sequencing technology revealed the intra- and intertumor heterogeneity of human hepatocellular carcinomas (HCCs), and provided evidence for the use of therapeutic agents effective against multiple targets in tumor cells. Recently, the efficacy and safety of a multitargeted tyrosine kinase inhibitor, lenvatinib, was confirmed by a randomized global phase III trial; thus, lenvatinib was approved as first-line therapy for HCC, providing a new therapeutic option for patients at an advanced stage. In this article, we introduce the application of molecular targeted therapy using lenvatinib and discuss future aspects of therapeutic options for advanced HCC.

Association of Mac-2-binding protein glycosylation isomer level with nutritional status in chronic liver disease

BACKGROUND AND AIM

Mac-2-binding protein glycosylation isomer (M2BPGi) was recently identified as a serum glycobiomarker for liver fibrosis. However, the relationship between M2BPGi and malnutrition in patients with chronic liver disease (CLD) is unknown. We aimed to evaluate whether M2BPGi could be a surrogate marker for malnutrition in patients with CLD.

METHODS

In total, 338 outpatients with CLD were enrolled (median age: 67 years). We evaluated the associations among liver fibrosis markers (M2BPGi, fibrosis-4 index, and aspartate aminotransferase-to-platelet count ratio index), Child-Pugh stages, and nutritional status markers.

RESULTS

The median value (range) of serum M2BPGi levels was 0.94 cut-off index (COI) (0.22-11.57) in chronic hepatitis and Child-Pugh A (n = 274), 4.775 COI (1.32-16.68) in Child-Pugh B (n = 46), and 11.37 COI (6.03-18.33) in Child-Pugh C (n = 18) (overall significance, P < 0.001). Serum M2BPGi levels showed a strong correlation with serum albumin concentration and controlling nutritional status score (rs  = -0.649, P < 0.001 and rs  = 0.671, P < 0.001, respectively). The correlations between M2BPGi and nutritional status markers were especially high in patients with hepatitis C virus infection and non-B non-C hepatitis and patients with hepatocellular carcinoma. Among the three fibrosis markers, M2BPGi yielded the highest area under the receiver operating characteristic curve (0.920) for predicting hypoalbuminemia at an optimal cut-off value of 2.41 (sensitivity, 87.3%; specificity, 87.6%; P < 0.001).

CONCLUSIONS

Serum M2BPGi levels are correlated with nutritional status markers in patients with CLD and could be a useful clinical marker of malnutrition.

Acute Anorectal Thrombophlebitis Caused by a Protein C Deficiency

A 46-year-old man visited the emergency department of our hospital with a 3-day history of anal pain, hemorrhaging, and a slight fever. He had previously been diagnosed with protein C deficiency and was prescribed dabigatran, a direct oral anticoagulant. Contrast-enhanced computed tomography showed severe rectal wall thickening with partial defect of enhancement. In addition, sigmoidoscopy revealed a dusky purplish swollen anorectal mucosa just above the dentate line. He was diagnosed with acute anorectal thrombophlebitis, and anticoagulant therapy with heparin was initiated. To our knowledge, this is the first case report of acute anorectal thrombophlebitis caused by protein C deficiency.

Utility of KRAS mutational analysis in the preoperative diagnosis of synchronous pancreatic cancer and intrahepatic cholangiocarcinoma: A case report

RATIONALE

It is often challenging to discriminate between intrahepatic cholangiocarcinoma (ICC) and metastatic liver tumors, especially when the hepatic tumor is small and of a mass-forming type.

PATIENT CONCERNS

We report a 69-year-old woman presented at our hospital with a small solid tumor in the head of the pancreas that was previously discovered during a medical checkup.

DIAGNOSES

The patient was diagnosed with synchronous pancreatic cancer and ICC.

INTERVENTIONS

The patient underwent clinical, histological, immunohistological, and KRAS mutational analysis.

OUTCOMES

Computed tomography revealed poorly enhanced small nodules in both the pancreatic head and liver. Biopsies of both nodules revealed adenocarcinoma; however, it was unclear whether the hepatic lesion was a metastasis of the pancreatic tumor or primary ICC. KRAS mutational analysis from FFPE biopsy samples revealed a discordance of mutation status between the tumors. Therefore, the patient was diagnosed with synchronous pancreatic cancer and ICC, whereupon she underwent hepatopancreatoduodenectomy.

LESSONS

KRAS mutational analysis of FFPE biopsy samples can be utilized for differentiating between ICC and metastatic liver tumor.

Proliferating EpCAM-Positive Ductal Cells in the Inflamed Liver Give Rise to Hepatocellular Carcinoma

Hepatocellular carcinoma (HCC) originates from regenerating liver cells with genetic alterations in chronically inflamed liver. Ductal cells and hepatocytes proliferate for liver regeneration, and proliferating ductal cells (PDC) derived from bile ductules have long been considered putative liver stem/progenitor cells and candidate cellular origins of HCC. The potential of PDC as tumor-originating cells, however, remains controversial in contrast to accumulating evidence that HCC originates from hepatocytes. Here, we demonstrate that PDCs expressing the established surface and cancer stem cell marker EpCAM give rise to HCC in inflamed liver. EpCAM-expressing PDCs were specifically labeled in newly developed Epcam^CreERT2 mice and traced in a chemically induced liver injury model. Stepwise accumulation of genetic alterations in EpCAM-positive cells was induced by the mutagenesis activity of activation-induced cytidine deaminase using conditional transgenic mice. Lineage-tracing experiments revealed that labeled PDC differentiated into cholangiocytes, but not into hepatocytes, in the chemically damaged liver. Nevertheless, EpCAM-positive PDC with genetic alterations gave rise to HCC after 8 months of chemical administration. PDC-derived HCC showed histologic characteristics of concomitant ductule-like structures resembling human cholangiolocellular carcinoma (CLC) and exhibited serial transitions from PDC-like CLC cells to hepatocyte-like HCC cells. The Wnt signaling pathway was specifically upregulated in the CLC components of PDC-derived HCC. Our findings provide direct experimental evidence that EpCAM-expressing PDC could be a cellular origin of HCC, suggesting the existence of stem/progenitor-derived hepatocarcinogenesis. Cancer Res; 77(22); 6131-43. ©2017 AACR.

Follicular lymphoma of the caecum resected endoscopically

Colorectal follicular lymphomas, primary or secondary, are rare. Magnifying endoscopy with narrow-band imaging is useful in the diagnosis of colorectal follicular lymphoma. In addition, immunohistochemistry is essential in differentiating follicular lymphoma cells from lymphoid follicle hyperplasia based on the presence of Bcl-2 expression. We herein report a rare case of follicular lymphoma of the caecum, presenting as a small polyp that was resected endoscopically.

Activation-Induced Cytidine Deaminase Contributes to Pancreatic Tumorigenesis by Inducing Tumor-Related Gene Mutations

Pancreatic ductal adenocarcinoma (PDAC) develops via an accumulation of various gene mutations. The mechanism underlying the mutations in PDAC development, however, is not fully understood. Recent insight into the close association between the mutation pattern of various cancers and specific mutagens led us to investigate the possible involvement of activation-induced cytidine deaminase (AID), a DNA editing enzyme, in pancreatic tumorigenesis. Our immunohistochemical findings revealed AID protein expression in human acinar ductal metaplasia, pancreatic intraepithelial neoplasia, and PDAC. Both the amount and intensity of the AID protein expression increased with the progression from precancerous to cancerous lesions in human PDAC tissues. To further assess the significance of ectopic epithelial AID expression in pancreatic tumorigenesis, we analyzed the phenotype of AID transgenic (AID Tg) mice. Consistent with our hypothesis that AID is involved in the mechanism of the mutations underlying pancreatic tumorigenesis, we found precancerous lesions developing in the pancreas of AID Tg mice. Using deep sequencing, we also detected Kras and c-Myc mutations in our analysis of the whole pancreas of AID Tg mice. In addition, Sanger sequencing confirmed the presence of Kras, c-Myc, and Smad4 mutations, with the typical mutational footprint of AID in precancerous lesions in AID Tg mice separated by laser capture microdissection. Taken together, our findings suggest that AID contributes to the development of pancreatic precancerous lesions by inducing tumor-related gene mutations. Our new mouse model without intentional manipulation of specific tumor-related genes provides a powerful system for analyzing the mutations involved in PDAC.

Leptin receptor somatic mutations are frequent in HCV-infected cirrhotic liver and associated with hepatocellular carcinoma

BACKGROUND & AIMS

Hepatocellular carcinoma develops in patients with chronic hepatitis or cirrhosis via a stepwise accumulation of various genetic alterations. To explore the genetic basis of development of hepatocellular carcinoma in hepatitis C virus (HCV)-associated chronic liver disease, we evaluated genetic variants that accumulate in nontumor cirrhotic liver.

METHODS

We determined the whole exome sequences of 7 tumors and background cirrhotic liver tissues from 4 patients with HCV infection. We then performed additional sequencing of selected exomes of mutated genes, identified by whole exome sequencing, and of representative tumor-related genes on samples from 22 cirrhotic livers with HCV infection. We performed in vitro and in vivo functional studies for one of the mutated genes.

RESULTS

Whole exome sequencing showed that somatic mutations accumulated in various genes in HCV-infected cirrhotic liver tissues. Among the identified genes, the leptin receptor gene (LEPR) was one of the most frequently mutated in tumor and nontumor cirrhotic liver tissue. Selected exome sequencing analyses detected LEPR mutations in 12 of 22 (54.5%) nontumorous cirrhotic livers. In vitro, 4 of 7 (57.1%) LEPR mutations found in cirrhotic livers reduced phosphorylation of STAT3 to inactivate LEPR-mediated signaling. Moreover, 40% of Lepr-deficient (C57BL/KsJ-db/db) mice developed liver tumors after administration of thioacetamide compared with none of the control mice.

CONCLUSIONS

Based on analysis of liver tissue samples from patients, somatic mutations accumulate in LEPR in cirrhotic liver with chronic HCV infection. These mutations could disrupt LEPR signaling and increase susceptibility to hepatocarcinogenesis.

Novel mouse models of hepatocarcinogenesis with stepwise accumulation of genetic alterations

Hepatocellular carcinoma (HCC) is one of the most common cancers worldwide. Various risk factors are involved in hepatocarcinogenesis. Among them, chronic inflammation, including chronic hepatitis and cirrhosis mainly caused by hepatitis B virus and/or hepatitis C virus infection, plays an important role in HCC development. On the other hand, comprehensive genetic analyses of HCC using whole genome and exome sequencing revealed that cancer cells possess a large number of somatic mutations, suggesting that a wide variety of genetic alterations and the resultant dysregulated molecular pathways contribute to the development of HCC. Activation-induced cytidine deaminase (AID) is a nucleotide-editing enzyme, and aberrant expression of AID induced by inflammatory responses contributes to hepatocarcinogenesis via the accumulation of genetic alterations in various tumor-related genes. Constitutive expression of AID in hepatocyte-lineage cells provides novel mouse models that recapitulate the tumorigenesis of human HCC through stepwise accumulation of genetic alterations.

Clinical characteristics of non-B non-C hepatocellular carcinoma: a single-center retrospective study

BACKGROUND/AIMS

To clarify risk factors and clinical features of both hepatitis B surface antigen and anti-HCV negative hepatocellular carcinoma (NBNC-HCC).

METHODS

HCC patients (n = 1,109) diagnosed at a single center were categorized based on the presence of serum hepatitis B surface antigen and HCVAb. Clinical characteristics of 127 NBNC-HCC patients were evaluated.

RESULTS

NBNC-HCC patients were stratified as those with alcoholic liver disease (ALD-HCC, n = 42) and alcohol-unrelated liver disease (non-ALD-HCC, n = 85). Compared with the ALD-HCC group, the non-ALD-HCC group had a higher prevalence of diabetes (p = 0.015), larger tumor size (p = 0.007), and higher tumor marker levels (p = 0.014). Liver function results were significantly worse in ALD-HCC than in non-ALD-HCC. Although the ALD-HCC group had a higher tendency toward recurrence than the non-ALD-HCC group, survival rates were similar between groups (p = 0.352).

CONCLUSION

Alcohol consumption was the most common etiologic factor for NBNC-HCC, and diabetes may be related to the development of HCC in non-ALD-HCC patients. Non-ALD-HCC tended to be diagnosed at a more advanced stage, whereas liver function was worse, and tumor recurrence rate was higher in ALD-HCC patients. Further examination of the risk factors and establishment of a precise surveillance system are necessary for early diagnosis and the development of curative therapies for NBNC-HCC.

Decrease in alpha-fetoprotein levels predicts reduced incidence of hepatocellular carcinoma in patients with hepatitis C virus infection receiving interferon therapy: a single center study

BACKGROUND

Increasing evidence suggests the efficacy of interferon therapy for hepatitis C in reducing the risk of hepatocellular carcinoma (HCC). The aim of this study was to identify predictive markers for the risk of HCC incidence in chronic hepatitis C patients receiving interferon therapy.

METHODS

A total of 382 patients were treated with standard interferon or pegylated interferon in combination with ribavirin for chronic hepatitis C in a single center and evaluated for variables predictive of HCC incidence.

RESULTS

Incidence rates of HCC after interferon therapy were 6.6% at 5 years and 13.4% at 8 years. Non-sustained virological response (non-SVR) to antiviral therapy was an independent predictor for incidence of HCC in the total study population. Among 197 non-SVR patients, independent predictive factors were an average alpha-fetoprotein (AFP) integration value ≥10 ng/mL and male gender. Even in patients whose AFP levels before interferon therapy were ≥10 ng/mL, reduction of average AFP integration value to <10 ng/mL by treatment was strongly associated with a reduced incidence of HCC. This was significant compared to patients with average AFP integration values of ≥10 ng/mL (P = 0.009).

CONCLUSIONS

Achieving sustained virological response (SVR) by interferon therapy reduces the incidence of HCC in hepatitis C patients treated with interferon. Among non-SVR patients, a decrease in the AFP integration value by interferon therapy closely correlates with reduced risk of HCC incidence after treatment.