Nuttapong Ngamphaiboon

Bridging the gap between clinicians and systems biologists: from network biology to translational biomedical research

With the wealth of data accumulated from completely sequenced genomes and other high-throughput experiments, global studies of biological systems, by simultaneously investigating multiple biological entities (e.g. genes, transcripts, proteins), has become a routine. Network representation is frequently used to capture the presence of these molecules as well as their relationship. Network biology has been widely used in molecular biology and genetics, where several network properties have been shown to be functionally important. Here, we discuss how such methodology can be useful to translational biomedical research, where scientists traditionally focus on one or a small set of genes, diseases, and drug candidates at any one time. We first give an overview of network representation frequently used in biology: what nodes and edges represent, and review its application in preclinical research to date. Using cancer as an example, we review how network biology can facilitate system-wide approaches to identify targeted small molecule inhibitors. These types of inhibitors have the potential to be more specific, resulting in high efficacy treatments with less side effects, compared to the conventional treatments such as chemotherapy. Global analysis may provide better insight into the overall picture of human diseases, as well as identify previously overlooked problems, leading to rapid advances in medicine. From the clinicians’ point of view, it is necessary to bridge the gap between theoretical network biology and practical biomedical research, in order to improve the diagnosis, prevention, and treatment of the world’s major diseases.

Safety and tolerability of docetaxel, cyclophosphamide, and trastuzumab compared to standard trastuzumab-based chemotherapy regimens for early-stage human epidermal growth factor receptor 2-positive breast cancer.

Purpose We evaluated the tolerability and cardiac safety of docetaxel, cyclophosphamide, and trastuzumab (TCyH) for the treatment of early-stage human epidermal growth factor receptor 2 (HER2)-positive breast cancer and compared to the standard trastuzumab-based chemotherapy regimens doxorubicin with cyclophosphamide followed by paclitaxel and trastuzumab (AC-TH) and docetaxel, carboplatin, and trastuzumab (TCaH). Methods We retrospectively reviewed early-stage, resectable, HER2-positive breast cancer patients treated with trastuzumab-based chemotherapy at a single comprehensive cancer center between 2004 and 2011. Patient characteristics, comorbidities, relative dose intensity (RDI) of each regimen, tolerability, and cardiac toxicity were evaluated. Results One hundred seventy-seven patients were included in the study (AC-TH, n=114; TCaH, n=39; TCyH, n=24). TCyH was solely administered in the adjuvant setting, whereas two-thirds of the AC-TH and TCaH groups were administered postoperatively. Patients treated with TCyH tended to have a more significant underlying cardiac history, higher Charlson comorbidity index, and were of an earlier stage. All patients treated with TCyH received granulocyte colony stimulating factor primary prophylaxis. No febrile neutropenia or grade ≥3 hematologic toxicity was observed in the TCyH group as compared to the AC-TH and TCaH groups. There were no significant differences in the rates of early termination, hospitalization, dose reduction, or RDI between the regimens. The symptomatic congestive heart failure rate between AC-TH, TCaH, and TCyH groups was not significantly different (4.4% vs. 2.6% vs. 8.3%, respectively, p=0.57). There was also no significant difference in the rate of early trastuzumab termination between patients treated with each regimen. Conclusion TCyH is well tolerated and should be investigated as an alternative adjuvant chemotherapy option for patients who are not candidates for standard trastuzumab-containing regimens. Larger clinical trials are necessary to support the wider use of TCyH as an adjuvant regimen.

Multi-Targeted Tyrosine Kinase Inhibitor-Induced Hyperammonemic Encephalopathy: a Report of Two Cases Using Pazopanib, Sunitinib, and Regorafenib

With the development of targeted therapies in the past decades, new side effects in relation to the mechanism of the therapies have surfaced. Several drugs were terminated in the early phases of clinical development due to unanticipated toxicities [1]. Currently in clinical practice, targeted therapies, such as tyrosine kinase inhibitors (TKIs), have becomewidely used for treatment of several malignancies. Physicians are now increasingly challenged to manage the undesired adverse effects to maximize the clinical benefits of these drugs for their patients. The common adverse effects of multi-targeted TKIs reported in clinical studies include hand-foot syndrome, diarrhea, hypertension, and metabolic and electrolyte imbalance [1]. These common toxicities were reported as a class effect of multi-targeted TKI, such as sorafenib, sunitinib, pazopanib, and regorafenib, due to the class-specific mechanism. However, other uncommon adverse effects are typically underreported before approval of these drugs. Therefore, physicians could potentially be faced with these uncommon toxicities in clinical practice. Neurological adverse effects are uncommonly reported in multi-targeted TKIs in their pivotal studies. In the CORRECT study, only one patient developed seizure after receiving regorafenib, an effect which was not observed in the GRID study [2, 3]. Similarly, neurological toxicities were rarely observed in the pivotal trials of other TKIs such as sorafenib, sunitinib, and pazopanib. Drug-induced hyperammonemic encephalopathy is one of the uncommon neurological adverse effects of multi-targeted TKI, which is rarely observed in clinical practice.We have two reported cases of metastatic gastrointestinal stromal tumor (GIST) patients who developed drug-induced hyperammonemic encephalopathy related to pazopanib, sunitinib, and regorafenib.

Emergence of Intrahepatic Cholangiocarcinoma: How High-Throughput Technologies Expedite the Solutions for a Rare Cancer Type

Intrahepatic cholangiocarcinoma (ICC) is the cancer of the intrahepatic bile ducts, and together with hepatocellular carcinoma (HCC), constitute the majority of primary liver cancers. ICC is a rare disorder as its overall incidence is < 1/100,000 in the United States and Europe. However, it shows much higher incidence in particular geographical regions, such as northeastern Thailand, where liver fluke infection is the most common risk factor of ICC. Since the early stages of ICC are often asymptomatic, the patients are usually diagnosed at advanced stages with no effective treatments available, leading to the high mortality rate. In addition, unclear genetic mechanisms, heterogeneous nature, and various etiologies complicate the development of new efficient treatments. Recently, a number of studies have employed high-throughput approaches, including next-generation sequencing and mass spectrometry, in order to understand ICC in different biological aspects. In general, the majority of recurrent genetic alterations identified in ICC are enriched in known tumor suppressor genes and oncogenes, such as mutations in TP53, KRAS, BAP1, ARID1A, IDH1, IDH2, and novel FGFR2 fusion genes. Yet, there are no major driver genes with immediate clinical solutions characterized. Interestingly, recent studies utilized multi-omics data to classify ICC into two main subgroups, one with immune response genes as the main driving factor, while another is enriched with driver mutations in the genes associated with epigenetic regulations, such as IDH1 and IDH2. The two subgroups also show different hypermethylation patterns in the promoter regions. Additionally, the immune response induced by host-pathogen interactions, i.e., liver fluke infection, may further stimulate tumor growth through alterations of the tumor microenvironment. For in-depth functional studies, although many ICC cell lines have been globally established, these homogeneous cell lines may not fully explain the highly heterogeneous genetic contents of this disorder. Therefore, the advent of patient-derived xenograft and 3D patient-derived organoids as new disease models together with the understanding of evolution and genetic alterations of tumor cells at the single-cell resolution will likely become the main focus to fill the current translational research gaps of ICC in the future.

Breast reconstruction in pregnancy: a case report of multidisciplinary team approach in immediate autologous flap reconstruction for pregnancy‐associated breast cancer

This report presents the results of immediate breast reconstruction with autologous flap in Pregnancy‐associated breast cancer (PABC). There was no obstetrics and surgical complications in our report. Immediate breast reconstruction can be performed in PABC after a careful selection. Multidisciplinary team approach is the key in managing these groups of patients.

Uncommon response of cisplatin and etoposide for treatment of advanced medullary thyroid carcinoma

Systemic treatment of Medullary thyroid carcinoma (MTC) is currently limited to the use of a tyrosine kinase inhibitor. Cytotoxic chemotherapy is not routinely recommended in the earlier lines of treatment due to the lack of efficacy. We describe a patient with locally advanced MTC who had an uncommon response to cisplatin and etoposide.

Abstract 5492: Functional characterization of human toll-like receptor 5 (TLR5) genetic variants

Toll-like Receptor 5 (TLR5) is a type 1 transmembrane receptor involved in the first line of defense against invading bacterial pathogens expressing flagellin. TLR5 is expressed on a wide variety of tumors and induction of TLR5 signaling exhibits anti-tumor activities via mobilization of innate and subsequent adaptive antitumor immune response. Entolimod, a pharmacologically optimized flagellin of Salmonella, is the first TLR5 agonist to enter clinical trials. This agent binds to TLR5 and activates NF-kB and other signaling pathways to elicit antitumor activity. The antitumor activity of entolimod has been shown to be dependent on the expression of functional TLR5 on tumors. Since TLR5 is genetically polymorphic, we hypothesized that variations in the gene would alter responses to therapy with entolimod. We therefore characterized genetic variants of TLR5. Expression constructs for nine naturally occurring human TLR5 variants namely Thr82Ile (Ile82): c.245C>T [rs764535]; Asn143Thr (Thr143): c.428A>C [rs5744167]; Arg149Cys (Cys149): c.445C>T [rs201906412]; Gln387Ter (Ter387 or 387*): c.1159C>T [rs147164861]; Arg392Ter (Ter392 or 392*): c.1174C>T [rs5744168]; Leu487Ile (487Ile): c.1459C>A [rs5744171]; Asn592Ser (Ser592): c.1775A>G [rs2072493]; Phe616Leu (Leu616): c.1846T>C [rs5744174] and Glu731Asp (Asp731): 2193A>T [rs148986834], were created from C-terminal FLAG-tagged wild type (WT) TLR5. All constructs together with a construct with no TLR5 insert (empty vector) were transfected in cos-1 cells. In vitro translation of the constructs in rabbit reticulocyte lysates (RRL) were also performed. Cos-1 cells transfected with constructs were also treated with flagellin and entolimod and with proteasome and autophagy inhibitors. Recombinant and synthesized proteins were examined by western blot analysis and NF-kB activity was measured using a Dual-Glo Luciferase Assay. The molecular weight of the recombinant proteins was approximately 100kD. There were variations in expression levels of immunoreactive proteins (10-80% of WT) and the NF-kB activity induced was lower or similar to WT. The Ile82 variant showed a significant reduction in levels of immunoreactive protein (10% of WT) which correlated with decreased NF-kB activity compared to WT, after stimulation. All proteins synthesized in RRL had similar molecular weight except Ter387 and Ter392 which expressed truncated proteins of approximately 40kD and had no NF-kB activity compared to the WT. The Ile82 protein was degraded primarily through the autophagy pathway. The mRNA and cytokine levels of the variant constructs will be reported. These results suggest that genetic variations in the TLR5 gene may be predictive of response to entolimod. This predictive biomarker will be explored in the ongoing phase I study of entolimod. Citation Format: Andrzej J. Wierzbicki, Araba A. Adjei, Nuttapong Ngamphaiboon, Thanyanan Reungwetwattana, Andrei V. Gudkov, Alex A. Adjei. Functional characterization of human toll-like receptor 5 (TLR5) genetic variants. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 5492. doi:10.1158/1538-7445.AM2015-5492