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Roman K Thomas

Publications and source records attributed to Roman K Thomas.

At least 19 recordsLinked to original sources
PubMed2026

A targetable dependency on nonsense-mediated decay for cellular homeostasis and immune control in small cell lung cancer.

Small cell lung cancer (SCLC) is one of the most aggressive malignancies, characterized by rapid metastatic dissemination and poor overall survival. Despite harboring excessive alterations, expectedly resulting in immunogenic neoantigens, patients with SCLC remain largely refractory to immunotherapy. We found abundant frameshift mutations in SCLC, regarded as highly immunogenic, counterbalanced by a hyperactive nonsense-mediated decay (NMD) pathway, responsible for frameshift-mRNA degradation. NMD activity correlated with tumor mutational burden (TMB) across cancers, suggesting that SCLC and other TMBhigh cancers may depend on NMD to limit the accumulation of mutation-derived byproducts in order to maintain cellular homeostasis and evade immune recognition. In TMBhigh SCLC models, inhibition of NMD impaired cell proliferation and induced ER stress-dependent apoptosis due to the accumulation of misfolded proteins. Genetic and pharmacological NMD inhibition in vivo effectively controlled TMBhigh tumor growth without overt toxicity. By integrating genome and transcriptome sequencing with MHC-I immunopeptidomics and functional in vitro and in vivo assays, we identified that NMD inhibition boosted neoantigen expression and presentation by tumor cells and increased T cell recognition, thus enhancing overall tumor immunogenicity and further improving immunotherapy efficacy in vivo. Our work shows that SCLC - as a TMBhigh cancer - relies on NMD for survival and immune escape, uncovering a novel TMB-dependent tractable vulnerability for this devastating disease.

Humans↗
PubMed2025

Functional synapses between neurons and small cell lung cancer.

Small cell lung cancer (SCLC) is a highly aggressive type of lung cancer, characterized by rapid proliferation, early metastatic spread, frequent early relapse and a high mortality rate1-3. Recent evidence has suggested that innervation has an important role in the development and progression of several types of cancer4,5. Cancer-to-neuron synapses have been reported in gliomas6,7, but whether peripheral tumours can form such structures is unknown. Here we show that SCLC cells can form functional synapses and receive synaptic transmission. Using in vivo insertional mutagenesis screening in conjunction with cross-species genomic and transcriptomic validation, we identified neuronal, synaptic and glutamatergic signalling gene sets in mouse and human SCLC. Further experiments revealed the ability of SCLC cells to form synaptic structures with neurons in vitro and in vivo. Electrophysiology and optogenetic experiments confirmed that cancer cells can receive NMDA receptor- and GABAA receptor-mediated synaptic inputs. Fitting with a potential oncogenic role of neuron-SCLC interactions, we showed that SCLC cells derive a proliferation advantage when co-cultured with vagal sensory or cortical neurons. Moreover, inhibition of glutamate signalling had therapeutic efficacy in an autochthonous mouse model of SCLC. Therefore, following malignant transformation, SCLC cells seem to hijack synaptic signalling to promote tumour growth, thereby exposing a new route for therapeutic intervention.

Animals↗
PubMed2006

The major subtypes of human B-cell lymphomas lack mutations in BCL-2 family member BAD.

Members of the BCL-2 gene family are well known for their role in the pathogenesis of B-cell lymphomas in humans and in mouse models. A recent report that knockout mice deficient for the proapoptotic BCL-2 family member gene BAD frequently develop B-cell lymphomas prompted us to analyze a large collection of human B-cell lymphomas for inactivating mutations in the BAD gene. All 3 exons of the BAD gene were amplified and directly sequenced. The 81 lymphomas analyzed included 16 cases of B-cell chronic lymphocytic leukemia, 11 mantle-cell lymphomas, 10 follicular lymphomas, 7 MALT lymphomas, 8 Burkitt's lymphoma cell lines, 3 cell lines of multiple myeloma, 15 cases and 4 cell lines of diffuse large B-cell lymphoma and 7 Hodgkin's lymphoma lines. No mutations were found in any of the cases. We conclude that mutations in the BAD gene do not play a role in the pathogenesis of the major subtypes of human B-cell lymphomas.

Cell Line, Tumor↗
PubMed2006

Genomic approaches to lung cancer.

The last decade has seen remarkable success in clinical targeting of activated oncogenes in cancer. We have applied gene expression profiling, high-density single-nucleotide polymorphism arrays, and systematic resequencing of genes to identify novel oncogenes and signaling pathways in lung cancer that might represent therapeutic targets. Systematic resequencing of tyrosine kinase genes has led to the discovery of somatic mutations in the epidermal growth factor receptor (EGFR) gene in lung adenocarcinomas. These mutations range in frequency from 10% in Caucasian to 40% in East Asian patients. Lung cancer-derived EGFR mutations are oncogenic and are tightly associated with clinical response to the EGFR kinase inhibitors erlotinib and gefitinib. Furthermore, gene expression profiling has been shown to classify patients according to their clinical outcome, indicating that the application of this technique may help in guiding patient selection for therapy in the future. Finally, genome-wide analyses of copy number gains and losses were successfully applied to detect gene amplifications and deletions. Taken together, the application of genomics technologies has led to important discoveries with clinical implications in lung cancer that might help to improve clinical care for patients suffering from this highly fatal tumor.

ErbB Receptors↗
PubMed2006

Non-small-cell lung cancer and Ba/F3 transformed cells harboring the ERBB2 G776insV_G/C mutation are sensitive to the dual-specific epidermal growth factor receptor and ERBB2 inhibitor HKI-272.

Mutation-specific cancer therapy has shown promising clinical efficacy. In non-small-cell lung cancer (NSCLC), the presence of mutations in the epidermal growth factor receptor (EGFR) tyrosine kinase correlates with clinical response to small-molecule tyrosine kinase inhibitors. Here, we show that cells harboring the G776insV_G/C mutation in the related ERBB2 tyrosine kinase (also known as HER2 or Neu), present in a small percentage of NSCLCs, are sensitive to HKI-272, an irreversible dual-specific kinase inhibitor targeting both EGFR and ERBB2. In the ERBB2-mutant NCI-H1781 cell line, HKI-272 treatment inhibited proliferation by induction of G(1) arrest and apoptotic cell death. Furthermore, HKI-272 abrogated autophosphorylation of both ERBB2 and EGFR. Finally, Ba/F3 murine pro-B cells, engineered to express mutant ERBB2, became independent of interleukin-3 and sensitive to HKI-272. Thus, the subset of NSCLC patients with tumors carrying the ERBB2 G776insV_G/C mutation may benefit from treatment with HKI-272.

Carcinoma, Non-Small-Cell Lung↗
PubMed2006

Sensitive mutation detection in heterogeneous cancer specimens by massively parallel picoliter reactor sequencing.

The sensitivity of conventional DNA sequencing in tumor biopsies is limited by stromal contamination and by genetic heterogeneity within the cancer. Here, we show that microreactor-based pyrosequencing can detect rare cancer-associated sequence variations by independent and parallel sampling of multiple representatives of a given DNA fragment. This technology can thereby facilitate accurate molecular diagnosis of heterogeneous cancer specimens and enable patient selection for targeted cancer therapies.

Base Sequence↗
PubMed2006

Epidermal growth factor receptor variant III mutations in lung tumorigenesis and sensitivity to tyrosine kinase inhibitors.

The tyrosine kinase inhibitors gefitinib (Iressa) and erlotinib (Tarceva) have shown anti-tumor activity in the treatment of non-small cell lung cancer (NSCLC). Dramatic and durable responses have occurred in NSCLC tumors with mutations in the tyrosine kinase domain of the epidermal growth factor receptor (EGFR). In contrast, these inhibitors have shown limited efficacy in glioblastoma, where a distinct EGFR mutation, the variant III (vIII) in-frame deletion of exons 2-7, is commonly found. In this study, we determined that EGFRvIII mutation was present in 5% (3/56) of analyzed human lung squamous cell carcinoma (SCC) but was not present in human lung adenocarcinoma (0/123). We analyzed the role of the EGFRvIII mutation in lung tumorigenesis and its response to tyrosine kinase inhibition. Tissue-specific expression of EGFRvIII in the murine lung led to the development of NSCLC. Most importantly, these lung tumors depend on EGFRvIII expression for maintenance. Treatment with an irreversible EGFR inhibitor, HKI-272, dramatically reduced the size of these EGFRvIII-driven murine tumors in 1 week. Similarly, Ba/F3 cells transformed with the EGFRvIII mutant were relatively resistant to gefitinib and erlotinib in vitro but proved sensitive to HKI-272. These findings suggest a therapeutic strategy for cancers harboring the EGFRvIII mutation.

Animals↗
PubMed2006

Epidermal growth factor receptor activation in glioblastoma through novel missense mutations in the extracellular domain.

BACKGROUND: Protein tyrosine kinases are important regulators of cellular homeostasis with tightly controlled catalytic activity. Mutations in kinase-encoding genes can relieve the autoinhibitory constraints on kinase activity, can promote malignant transformation, and appear to be a major determinant of response to kinase inhibitor therapy. Missense mutations in the EGFR kinase domain, for example, have recently been identified in patients who showed clinical responses to EGFR kinase inhibitor therapy. METHODS AND FINDINGS: Encouraged by the promising clinical activity of epidermal growth factor receptor (EGFR) kinase inhibitors in treating glioblastoma in humans, we have sequenced the complete EGFR coding sequence in glioma tumor samples and cell lines. We identified novel missense mutations in the extracellular domain of EGFR in 13.6% (18/132) of glioblastomas and 12.5% (1/8) of glioblastoma cell lines. These EGFR mutations were associated with increased EGFR gene dosage and conferred anchorage-independent growth and tumorigenicity to NIH-3T3 cells. Cells transformed by expression of these EGFR mutants were sensitive to small-molecule EGFR kinase inhibitors. CONCLUSIONS: Our results suggest extracellular missense mutations as a novel mechanism for oncogenic EGFR activation and may help identify patients who can benefit from EGFR kinase inhibitors for treatment of glioblastoma.

Animals↗
PubMed2005

Inhibition of nuclear translocation of nuclear factor-kappaB despite lack of functional IkappaBalpha protein overcomes multiple defects in apoptosis signaling in human B-cell malignancies.

PURPOSE: Defective apoptosis signaling is a typical feature of classic Hodgkin's lymphoma, multiple myeloma, and activated B-cell-like diffuse large B-cell lymphoma. In these malignancies, the transcription factor nuclear factor-kappaB (NF-kappaB) is a critical mediator of apoptosis resistance and oncogenic growth, making it an attractive therapeutic target. Here, we sought to determine how to overcome apoptosis resistance experimentally in these malignancies by targeting NF-kappaB. EXPERIMENTAL DESIGN: We investigated the effect of different inhibitors of NF-kappaB on classic Hodgkin's lymphoma, multiple myeloma, and activated B-cell-like diffuse large B-cell lymphoma cell lines harboring different molecular defects in apoptosis signaling both quantitatively and qualitatively. RESULTS: The cyclopentenone prostaglandin, 15-deoxy-Delta12,14-prostaglandin J(2), a known inhibitor of NF-kappaB, induced caspase-dependent apoptosis; it restored mitochondrial apoptotic signaling by down-regulation of X-linked inhibitor of apoptosis protein and heat shock protein 27 and led to breakdown of the mitochondrial membrane potential and, finally, cleavage of caspase-3 irrespective of IkappaBalpha mutational status. Surprisingly, 15-deoxy-Delta12,14-prostaglandin J(2) and the IkappaB kinase inhibitor curcumin both reduced nuclear levels of p65 in cell lines lacking IkappaBalpha, suggesting that inhibition of nuclear translocation of NF-kappaB can occur in the absence of IkappaBalpha. Finally, a synthetic peptide that specifically abrogates the assembly of the IkappaB kinase complex killed IkappaBalpha-defective cells by induction of apoptosis, paralleled by reduction of nuclear NF-kappaB. CONCLUSIONS: These results show that molecular defects in apoptotic signaling, such as IkappaBalpha mutations, can be circumvented by targeting NF-kappaB through inhibition of the IkappaB kinase complex followed by induction of apoptosis in classic Hodgkin's lymphoma, multiple myeloma, and activated B-cell-like diffuse large B-cell lymphoma. Thus, targeting IkappaB kinases may represent an attractive therapeutic approach against these malignancies regardless of the mutational status of IkappaBalpha.

Active Transport, Cell Nucleus↗
PubMed2005

A transforming MET mutation discovered in non-small cell lung cancer using microarray-based resequencing.

We have designed resequencing microarrays to test the performance of this platform when interrogating a large number of exons (164 total) from genes associated with cancer. To evaluate false positive and negative rates, dideoxy sequencing was done for 335,420 bases interrogated by the arrays. From the array data, calls could be made for approximately 97.5% of the bases, and false positive rates were very low with only a single mutation reported from the array dataset for which the corresponding dideoxy trace had a clean wildtype sequence. For the nucleotide positions where array calls were made, false negative rates were 1.41% for heterozygous mutations. All the homozygous mutations were detected, but 8.11% were erroneously reported as heterozygous changes from the reference sequence by the array analysis software. In addition, 20 non-small cell lung cancer (NSCLC) samples were analyzed using the arrays, and both somatic and germline mutations were found. The most interesting findings were two MET mutations that have recently been implemented in NSCLC. Large scale MALDI-TOF genotyping indicated that one of these mutations (T1010I) might represent a true cancer-causing genotype, whereas the other (N375S) appears to be a common germline polymorphism.

Carcinoma, Non-Small-Cell Lung↗
PubMed2005

Patterned CpG methylation of silenced B cell gene promoters in classical Hodgkin lymphoma-derived and primary effusion lymphoma cell lines.

Hodgkin and Reed-Sternberg (HRS) cells of classical Hodgkin lymphoma (cHL) and primary effusion lymphoma (PEL) are derived from germinal center (GC) and post-GC B cells, respectively. Neither express many of the B cell genes or surface markers typically expressed by other GC-derived B cell lymphomas or normal B cells. This loss of B cell gene expression is not due to a lack of essential transcription factors, as studies have shown that the ectopic expression of missing transcription factors failed to reactivate endogenous target genes. These results implicate epigenetic mechanisms extinguishing B cell gene expression. Silenced endogenous B cell genes representing a surface receptor, B29 (Igbeta, CD79b), a signaling molecule, TCL1, and a transcription factor, Bob1 (OCA-B, OBF-1), were reactivated by 5-aza-2'-deoxycytidine, indicating that gene silencing in HRS and PEL cells is due to DNA methylation. Genomic bisulfite sequencing corroborated this prediction and revealed three distinct patterns of methylation for the silenced B29 and TCL1 promoters. These distinct patterns consisted of 5' promoter CpG methylation alone, 5' and 3' promoter CpG methylation sparing sites in the central cores, and complete CpG methylation throughout the promoter regions. The silenced Bob1 promoter showed one pattern of dense CpG methylation at essentially all sites. These consistent patterns predict that, although gene silencing in many HRS and PEL cells mimics appropriate gene silencing, in some cases of complete CpG methylation throughout entire promoters both the activation and targeting of methylation is abnormal.

B-Lymphocytes↗
PubMed2005

Reduced frequencies and suppressive function of CD4+CD25hi regulatory T cells in patients with chronic lymphocytic leukemia after therapy with fludarabine.

Globally suppressed T-cell function has been described in many patients with cancer to be a major hurdle for the development of clinically efficient cancer immunotherapy. Inhibition of antitumor immune responses has been mainly linked to inhibitory factors present in cancer patients. More recently, increased frequencies of CD4+CD25hi regulatory T cells (Treg cells) have been described as an additional mechanism reducing immunity. We assessed 73 patients with B-cell chronic lymphocytic leukemia (CLL) and 42 healthy controls and demonstrated significantly increased frequencies of cytotoxic T lymphocyte-associated protein 4 (CTLA4+)-, Forkhead box P3 (FOXP3+)-, glucocorticoid-induced tumor necrosis factor receptor-related protein (GITR+)-, CD62L+-, transforming growth factor beta1 (TGF-beta1+)-, interleukin 10 (IL-10+)-Treg cells in patients with CLL, with highest frequencies in untreated or progressing patients presenting with extended disease. Most surprisingly, in the majority of patients with CLL treated with fludarabine-containing therapy regimens the inhibitory function of Treg cells was decreased or even abrogated. In addition, frequencies of Treg cells were significantly decreased after therapy with fludarabine. In light of similar findings for cyclophosphamide the combination of fludarabine and cyclophosphamide might be further exploited in strategies reducing immunosuppression prior to cancer immunotherapy.

Adult↗
PubMed2005

From Hodgkin disease to Hodgkin lymphoma: biologic insights and therapeutic potential.

Reclassification of Hodgkin disease as Hodgkin lymphoma (HL) represents a milestone in the lymphoma field, awarding recent insights in the molecular biology of Hodgkin and Reed-Sternberg (H-RS) cells and their environment. This review summarizes antiapoptotic and proproliferative pathways involved in the pathogenesis of this disease with the ultimate goal of translating laboratory knowledge into clinical decision making. The focus is on potential targets and novel drugs, which are discussed in the context of the complex biology of HL. Considering that HL patients are more likely to die from acute and late treatment-related toxicities than from HL itself, the introduction of targeted, biologically based therapies for HL patients with palliative and eventually curative intention might be justified.

Antineoplastic Agents↗
PubMed2004

Part I: Hodgkin's lymphoma--molecular biology of Hodgkin and Reed-Sternberg cells.

Classic Hodgkin's lymphoma is characterised by Hodgkin and Reed-Sternberg cells and in most cases are derived from germinal-centre B cells. Despite progress in basic research showing the natural precursor cells of Hodgkin's lymphoma, most key questions still remain unanswered. Among these are the basic transforming events, the involvement of oncogenic viruses, the mechanisms enabling Hodgkin and Reed Sternberg cells to resist apoptosis in the germinal centre, and the molecular causes of their characteristic phenotype. Beyond the disclosure of these issues, the detection of changes in gene expression, gene mutations, and chromosomal imbalances specific of Hodgkin's lymphoma are central to recent research that may allow one a better understanding of the natural history of this type of lymphoma.

Apoptosis↗
PubMed2004

Part II: Hodgkin's lymphoma--diagnosis and treatment.

The outcome of patients with all stages of Hodgkin's lymphoma has improved dramatically over the past few decades. This is mainly due to the use of risk-adapted therapies using intensive polychemotherapeutic regimens in combination with other modalities. Patients with early favourable or unfavourable (intermediate) stage disease receive two or four cycles of chemotherapy, respectively, followed by involved-field radiotherapy (20-30Gy). Advanced stage Hodgkin's lymphoma is treated more aggressively using six to eight cycles of chemotherapy but the effectiveness of consolidative radiotherapy for patients who show a complete response after chemotherapy alone is still unknown. The main challenge in the near future will be the development of strategies that decrease late morbidity and mortality but retain the same efficacy of current regimens. In this paper we review current diagnostic techniques and management strategies used to treat Hodgkin's lymphoma, and the range of new modalities being used to improve long-term outcome and patient quality of life.

Antineoplastic Combined Chemotherapy Protocols↗
PubMed2004

Repeated clonal relapses in classical Hodgkin's lymphoma and the occurrence of a clonally unrelated diffuse large B cell non-Hodgkin lymphoma in the same patient.

Classical Hodgkin's lymphoma (cHL) and B-cell Non-Hodgkin Lymphoma (B-NHL) occasionally occur in the same patient. However, molecular studies that aim at determining the clonal relationship between both lymphomas are rare. In most instances, the lymphoma components appear to be derived from the same germinal center (GC) B cell precursor. We describe the molecular monitoring of repeated clonal relapses in a patient with cHL in whom diffuse large B cell NHL (DLBCL) developed concurrently. Intriguingly, both lymphomas were clonally unrelated. Thus, the derivation from a shared precursor likely is not a general rule in cHL and DLBCL arising in the same patient.

Adult↗
PubMed2004

Mutational analysis of the IkappaBalpha gene in activated B cell-like diffuse large B-cell lymphoma.

The lymphoma cells of the activated B cell-like (ABC-) subtype of diffuse large B-cell lymphoma (DLBCL) show constitutive activity of the transcription factor, nuclear factor kappaB (NFkappaB). We sought to determine whether mutations in the IkappaBalpha gene - the predominant inhibitor of NFkappaB - might play a role in the pathogenesis of ABC-DLBCL. All exons of the IkappaBalpha gene were directly sequenced from 10 cases of immunohistochemically classified ABC-DLBCL and from six non-ABC-DLBCL cases. Two novel polymorphisms were identified, based on their presence in tumour as well as non-tumour DNA of the respective patients: a duplication near the transcriptional start and a single nucleotide exchange in exon 1. A somatic missense mutation was identified in exon 3, in addition to a wild-type sequence in only one ABC-DLBCL case. Thus, also in this case no clonal biallelic inactivating mutation was present in the IkappaBalpha gene. We conclude that mutations in the IkappaBalpha gene do not play a dominant role in the pathogenesis of ABC-DLBCL.

DNA Mutational Analysis↗