Role of Tumor Molecular Profiling With FoundationOne®CDx in Advanced Solid Tumors: A Single-Centre Experience From Romania

Background In the field of precision oncology, comprehensive genomic profiling tests play a very important role by providing a complex understanding of the molecular characteristics of malignant tumors. Therefore, next-generation sequencing (NGS) has become a valuable tool in various aspects of cancer care from diagnosis and monitoring to treatment selection and personalized cancer treatment. Our aim was to evaluate the role of tumor molecular profiling in tailored treatment selection. Methods In our study, we conducted a retrospective analysis to assess the practicality of utilizing NGS testing in patients with metastatic solid tumors. The genomic testing was performed on blood or tissue samples from a fresh biopsy, less than six months old, and the expression of programmed death-ligand 1 was evaluated by immunohistochemistry. Results A total of 75 tests were performed on 66 patients between 2019 and 2022, with a success rate of 80%. The most common pathologies were gastro-intestinal tract cancer (26%), breast cancer (14%), non-small cell lung cancer (11%), and pancreatic cancer (11%). There were 9% liquid biopsies and 91% tissue biopsies. From all 66 patients tested, 55 had at least one genetic alteration. The most frequent genetic alteration found was TP53 (n=32) followed by KRAS (n=15) and BRCA1/2 (n=12) mutations. There were nine patients tested (14%) that presented a high tumor mutational burden, and only one patient presented high microsatellite instability. There were 37 patients (56%) with actionable alterations found from which 14 received matched therapy and four patients were enrolled in clinical trials. The NGS testing played a significant role in determining the next therapeutic strategy in 20 out of 66 patients (30.3%). Conclusion From all the patients included in our analysis, 83% had at least one mutation that is known to be of pathogenic significance but only 23% received treatment selected by the analysis of the tumor's genome, and only 6% were included in a clinical trial. This moderate success of personalized medicine using NGS testing highlights the importance of evaluating the factors that could lead to further improvement.

Streamlining Genetic Diagnosis With Long-Range Polymerase Chain Reaction (PCR)-Based Next-Generation Sequencing for Type I and Type II Collagenopathies

In the practice of clinical genetics, gene testing is usually guided by clinical diagnosis. When dealing with rare diseases, it is often necessary to create new test systems. The handling of a gene with a substantial number of exons poses a challenge both in sequential Sanger sequencing for each exon, and in the setup of capture probes to each exon for next-generation sequencing (NGS). We present very long amplicon sequencing (vLAS), an optimized long-range polymerase chain reaction (PCR)-based NGS method that overcomes this challenge. By utilizing approximately 20 Kb long PCR products and short-read NGS, vLAS is emerging as a highly adaptable and effective solution, especially for genes with numerous exons concentrated in a limited genomic region. Here, we demonstrate vLAS in the analysis of five patients with type I and two with type II collagenopathies. The integration of user-friendly NGS methods into genetic diagnosis enhances the practicality of clinical genetics.

Methodology for Isolation of miRNA From the Serum of Women Investigated for Pre-eclampsia

Background Pre-eclampsia remains a leading cause of maternal and foetal mortality with a poorly understood pathophysiology. It can lead to a range of clinical presentations, but proteinuria and hypertension are key components of the diagnosis. These signs arise due to disordered placental implantation due to poor trophoblastic invasion, resulting in placental oxidative stress due to hypoxia. Oxidative stress triggers the release of syncytiotrophoblast microvesicles (STMBs), of which placenta-derived exosomes may be a key component. The high specificity of exosomes for their cell of origin makes them ideal candidates as diagnostic biomarkers. We are particularly interested in the miRNAs (microRNAs) contained within these exosomes, as they may give us an insight into the genomic regulation within the pre-eclamptic placenta that leads to the disease state. The development of workflows for miRNA quantitation may enable us to identify novel biomarkers. Methods We extracted exosomes and purified total RNA from 23 serum samples using the Norgen Plasma/Serum Exosome Purification and RNA Isolation Midi Kit. We then used the bioanalyser to determine the concentration and quality of the RNA obtained. It uses rapid electrophoresis, requires minimal sample sizes, and can assess the quality of genetic material as small as 25 bases. Results We have successfully isolated RNA from these samples; however, the concentration of the total RNA was too low for downstream molecular analysis. We did gain insight into how to optimise and develop the workflow so that, with each attempt, the yield increased. Our greatest concentrations were obtained by combining serum samples from multiple patients, demonstrating that we needed a higher volume to optimise the yield. Future studies should aim to obtain samples specifically for use in this research so that we can process a larger volume of serum. Conclusions We have also noted that there is a positive correlation between the overall concentration of total RNA and a high sFlt-1/PlGF ratio. Preliminary analysis from Illumina identified with a high degree of confidence the presence of three miRNAs, namely, mir-498(46), mir-122(1), and mir-134(41). Further work is necessary to validate these findings and should focus on the possible future role of these miRNAs as biomarkers for the early diagnosis of pre-eclampsia.

A Rare Case of Therapy-Related B-cell Acute Lymphoblastic Leukemia Arising From Acute Myeloid Leukemia

Therapy-related acute lymphoblastic leukemia (t-ALL) is a rare potential complication of chemotherapy. We describe the case of a 47-year-old male patient who was originally diagnosed with t(8;21) positive acute myeloid leukemia (AML) in 2019, received chemotherapy, achieved remission, and was disease-free for the next two years. During a routine follow-up in 2022, he was found to have developed subclinical pancytopenia, and further studies indicated a diagnosis of pH-negative, near-tetraploid B-cell acute lymphoblastic leukemia (B-ALL) that was positive for a Tier 1 TP53 mutation, consistent with t-ALL. The patient had a prolonged treatment course complicated by social factors, such as the impact of both disease and treatment on his ability to work enough to make a living and live life with the quality he desired. The patient elected to pause treatment and resume it at a later date, after which, unfortunately, significant disease progression occurred and the patient died from complicating neutropenic sepsis and variceal bleeding. This case illustrates the challenges of managing social circumstances and patient goals in the setting of medically necessary but potentially harsh treatment courses. Given the aggressive nature of t-ALL and its overall poor prognosis, goals of care must be re-evaluated and discussed often to ensure alignment of therapy with a patient's wishes.

A New Era in Salivary Gland Carcinoma Treatment: A Case Report

Salivary gland cancers are rare and heterogenous malignancies which makes it hard to standardize treatments with good evidence levels. The localized disease approach is well established, with surgery to the primary site and adjuvant radiation therapy in patients with high-risk features. Treatment of advanced disease should be multidisciplinary. Local approaches, which include radiation therapy, surgery, and thermoablation, among others, have the potential to achieve durable disease control with low toxicity. Chemotherapy has shown disappointing results, so systemic treatment should be guided by actionable genetic alterations, which in salivary gland cancers rely on the histologic type. When directed molecular tests are not useful, a multigene panel should be performed. This case is a good example of how to integrate all these possible tretaments in clinical practice, including molecular testing and target treatment.

Comparative phylogenetic analysis and transcriptomic profiling of Dengue (DENV-3 genotype I) outbreak in 2021 in Bangladesh

Background

The next-generation sequencing (NGS) technology facilitates in-depth study of host-pathogen metatranscriptome. We, therefore, implicated phylodynamic and transcriptomic approaches through NGS technology to know/understand the dengue virus (DENV) origin and host response with dengue fever.

Methods

In this study, blood serum RNA was extracted from 21 dengue patients and 3 healthy individuals. Total transcriptomic data were analyzed for phylogenetic, phylodynamic, differential express gene (DEG), and gene ontology (GO) using respective bioinformatics tools.

Results

The viral genome sequence revealed dengue viral genome size ranges 10647 to 10707 nucleotide. Phylogenetic and phylodynamic analysis showed that the 2021 epidemic isolates were DENV-3 genotype-I and maintained as a new clade in compared to 2019 epidemic. Transcriptome analysis showed a total of 2686 genes were DEG in dengue patients compared to control with a q-value < 0.05. DESeq2 plot counts function of the top 24 genes with the smallest q-values of differential gene expression of RNA-seq data showed that 11 genes were upregulated, whereas 13 genes were downregulated. GO analysis showed a significant upregulation (p = < 0.001) in a process of multicellular organismal, nervous system, sensory perception of chemical stimulus, and G protein-coupled receptor signaling pathways in the dengue patients. However, there were a significant downregulation (p = < 0.001) of intracellular component, cellular anatomical entity, and protein-containing complex in dengue patients. Most importantly, there was a significant increase of a class of immunoregulatory proteins in dengue patients in compared to the controls, with increased GO of immune system process. In addition, upregulation of toll receptor (TLR) signaling pathways were found in dengue patients. These TLR pathways were particularly involved for the activation of innate system coupled with adaptive immune system that probably involved the rapid elimination of dengue virus infected cells. These differentially expressed genes could be further investigated for target based prophylactic interventions for dengue.

Conclusion

This is a first report describing DENV complete genomic features and differentially expressed genes in patients in Bangladesh. These genes may have diagnostic and therapeutic values for dengue infection. Continual genomic surveillance is required to further investigate the shift in dominant genotypes in relation to viral pathogenesis.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12985-023-02030-1.

A Case of HER2 Mutated Colorectal Cancer Treated Successfully With Fam-Trastuzumab Deruxtecan

Colorectal cancer is a malignant tumor arising from the inner lining of the colon or rectum and is the third most common cancer and the third leading cause of cancer-related deaths in the United States. Human epidermal growth factor receptor 2 (HER2) gene overexpressed or amplified colorectal cancer has shown treatment responses with HER2-directed therapies. We present a 78-year-old woman with metastatic colorectal cancer with a HER2 L726I mutation identified in tumor sequencing with amplification or overexpression of HER2. She had an excellent response to fam-trastuzumab deruxtecan. Our case is the first and most noteworthy case of a patient with metastatic colorectal cancer and a HER2 L726I mutation who achieved a remarkable clinical response to fam-trastuzumab deruxtecan.

Alveolar Soft Part Sarcoma of the Nasolabial Fold: A Case Report and Literature Review

Alveolar soft part sarcoma (ASPS) is a rare malignancy that is morphologically characterized by a distinctive nodular, organoid, or nested growth pattern in which the cells are separated by vascularized septa. The diagnosis is based on a combination of pathologic and immunohistochemical findings and the presence of an ASPSCR1-TFE3 gene fusion revealed by next-generation sequencing. ASPS most commonly occurs as a painless mass in the lower extremity, with likely involvement in the lungs if metastasis is present. Here we report a case of ASPS that exhibited the characteristic ASPSCR1-TFE3 gene fusion along with a reciprocal fusion of TFE3-ASPSCR1, which presented in the nasolabial fold of a 31-year-old female. An intraoral approach was utilized for complete surgical resection of the malignancy, resulting in continued remission after 11 months.

Congenital Infantile Myofibroma: The Importance of Molecular Diagnosis

Infantile myofibromatosis is an uncommon soft tissue neoplasm that may present at birth or in early infancy. Although rare, this neoplasm is one of the most common benign fibrous tumors of infancy. Even though these tumors do not spread, they can compress or damage nearby organs. There is not an established management protocol, but it is advisable to maintain periodic clinical and imagological control until stability. Watchful waiting is an option to consider in the absence of problematic symptoms and visceral involvement. We report a case of solitary infantile myofibromatosis, without visceral involvement. It showed an initial rapid growth, raising concern among medical doctors and motivating soft tissue biopsy, always recommended as the clinical picture deviates from the classic presentation. Histology interpretation is often challenging, making genetics and clinical evaluation essential to exclude and prevent the misdiagnosing of more aggressive lesions.

Ovarian Cancer With Breast Metastasis and Two Pathogenic Variants of BRCA1 Gene

Ovarian cancer is the second most common gynecologic cancer after uterine cancer in the United States. Ovarian cancer ranks sixth in cancer deaths among women, accounting for more deaths than other female reproductive system cancers. Breast metastasis in ovarian cancer is a rare presentation and predicts a poor prognosis and challenging management. Our case is a 42-year-old Chinese woman with high-grade serous ovarian carcinoma that presents with metastasis to the breast during the course of her illness. Genetic evaluation of the ovarian tumor showed two BRCA1 pathogenic variants. Germline pathogenic variant of c.2110_2111DelAA and a somatic variant of c.4071_4096+14del40. Our patient was offered different treatment regimens but showed progression of her disease. The low survival rate and high recurrence rate in ovarian cancer show that we still need to investigate our current approved treatments. Our report aims to shed light on the genetic evaluation of ovarian tumors and treatment options available in refractory cases of progressive ovarian cancer. Furthermore, we explain our investigational therapy regimen and the reasoning behind it.

The Prognostic Role of MYC Structural Variants Identified by NGS and FISH in Multiple Myeloma

PURPOSE

Structural variants (SV) of the MYC gene region are common in multiple myeloma and influence disease progression. However, the prognostic significance of different MYC SVs in multiple myeloma has not been clearly established.

EXPERIMENTAL DESIGN

We conducted a retrospective study of multiple myeloma comparing MYC SV subtypes identified by next-generation sequencing (NGS) and FISH to MYC expression and disease survival using 140 cases from Mayo Clinic and 658 cases from the MMRF CoMMpass study.

RESULTS

MYC SVs were found in 41% of cases and were classified into nine subtypes. A correlation between the presence of a MYC SV and increased MYC expression was identified. Among the nine MYC subtypes, the non-immunoglobulin (non-Ig) insertion subtype was independently associated with improved outcomes, while the Ig insertion subtype, specifically involving the IgL gene partner, was independently associated with poorer outcomes compared with other MYC SV subtypes. Although the FISH methodology failed to detect approximately 70% of all MYC SVs, those detected by FISH were associated with elevated MYC gene expression and poor outcomes suggesting a different pathogenic role for FISH-detected MYC subtypes compared with other MYC subtypes.

CONCLUSIONS

Understanding the impact of different MYC SVs on disease outcome is necessary for the reliable interpretation of MYC SVs in multiple myeloma. NGS approaches should be considered as a replacement technique for a more comprehensive evaluation of the multiple myeloma clone.

Detecting trisomy in products of conception from first-trimester spontaneous miscarriages by next-generation sequencing (NGS)

Miscarriage is the spontaneous loss of a clinically established intrauterine pregnancy before the fetus has reached viability. In order to compare the performance of traditional G banding karyotyping with next-generation sequencing (NGS) for detecting common trisomies in products of conception (POC). Chromosome abnormalities were detected by high-resolution G banding karyotyping and NGS. A total of 48 miscarriage samples, including 20 samples without karyotype result and 28 with karyotype results were selected and coded for analysis by NGS. The multiplex PCR analysis of maternal and miscarriage DNA for single nucleotide polymorphism (SNP) markers were used to simultaneously monitor maternal cell contamination (MCC), chromosomal status, and sex of the miscarriage tissue. NGS detection results of 21 chromosome abnormalities were consisted with that in karyotyping examination. These chromosome abnormalities samples included 9 chromosome 16 trisomies, 3 chromosome 22 trisomies, 2 chromosome 7 trisomies, 2 chromosome 18 trisomies, 1 chromosome 4 trisomies, one chromosome 10 trisomies, 1 chromosome 13 trisomies, 1 chromosome 15 trisomies and 1 sex chromosomal aneuploidies (45, X). Meanwhile, NGS analysis of seven chromosome normalities was adapted to the karyotyping examination. Therefore, NGS combined with multiplex PCR is an effective method to test trisomies in POC. The results mentioned above will contribute to a detailed understanding of the first-trimester spontaneous miscarriages.

Notch1 mutations are drivers of oral tumorigenesis

Disruption of NOTCH1 signaling was recently discovered in head and neck cancer. This study aims to evaluate NOTCH1 alterations in the progression of oral squamous cell carcinoma (OSCC) and compare the occurrence of these mutations in Chinese and Caucasian populations. We used a high-throughput PCR-based enrichment technology and next-generation sequencing (NGS) to sequence NOTCH1 in 144 samples collected in China. Forty-nine samples were normal oral mucosa from patients undergoing oral surgery, 45 were oral leukoplakia biopsies, and 50 were chemoradiation-naïve OSCC samples with 22 paired-normal tissues from the adjacent unaffected areas. NOTCH1 mutations were found in 54% of primary OSCC and 60% of premalignant lesions. Importantly, almost 60% of patients with leukoplakia with mutated NOTCH1 carried mutations that were also identified in OSCC, indicating an important role of these clonal events in the progression of early neoplasms. We then compared all known NOTCH1 mutations identified in Chinese patients with OSCC with those reported in Caucasians to date. Although we found obvious overlaps in critical regulatory NOTCH1 domains alterations and identified specific mutations shared by both groups, possible gain-of-function mutations were predominantly seen in Chinese population. Our findings demonstrate that premalignant lesions display NOTCH1 mutations at an early stage and are thus bona fide drivers of OSCC progression. Moreover, our results reveal that NOTCH1 promotes distinct tumorigenic mechanisms in patients from different ethnical populations.

Improving xylose utilization by recombinant Zymomonas mobilis strain 8b through adaptation using 2-deoxyglucose

BACKGROUND

Numerous attempts have been made to improve xylose utilization in Z. mobilis including adaptive approaches. However, no one has yet found a way to overcome the reduced xylose utilization observed in fermentations carried out in the presence of glucose as well as the inhibitory compounds found within pretreated and saccharified biomass. Our goal was to generate Z. mobilis strains that are more robust than the wildtype strain with increased productivity in fermenting the glucose and xylose present in PCS. Through adaptation in the presence of 2-deoxyglucose, we have generated Zymomonas mobilis strain #7, which is better suited to utilizing xylose in pretreated corn stover (PCS) fermentations in the presence of both glucose and model inhibitory compounds of acetate and furfural. Strain #7 over performed the parent strain 8b both on simultaneous saccharification and fermentation (SFF) of PCS and fermentation of saccharified PCS slurry. At 65% neutralized PCS liquor level, strain #7 used 86% of the xylose present in the liquor while strain 8b was not able to ferment the liquor under similar conditions. Similarly, under SSF process conditions with 20% total solids loading of PCS, strain #7 used more than 50% of the xylose present, while strain 8b did not utilize any xylose under this condition. We have further identified genetic alterations in strain #7 in relation to the parental strain 8b that may be responsible for these phenotypic enhancements.

RESULTS

We performed an extended lab-directed evolution of Z. mobilis strain 8b in the presence of acetate and a non-hydrolyzable glucose analogue 2-deoxyglucose. Following the adaptation, we identified and characterized numerous candidate strains and found a dramatic increase in xylose usage not only in shake flask, but also in a controlled PCS fermentation. We re-sequenced the genomes of evolved strains to identify genetic alterations responsible for these improved phenotypes, and identified two mutations that may be key to the improved xylose usage in these strains.

CONCLUSION

We have generated Z. mobilis strain #7, which can ferment xylose efficiently in the presence of toxins present in pretreated corn stover. Genetic alterations responsible for the improvement have been identified.

Genome-wide SNP calling using next generation sequencing data in tomato

The tomato (Solanum lycopersicum L.) is a model plant for genome research in Solanaceae, as well as for studying crop breeding. Genome-wide single nucleotide polymorphisms (SNPs) are a valuable resource in genetic research and breeding. However, to do discovery of genome-wide SNPs, most methods require expensive high-depth sequencing. Here, we describe a method for SNP calling using a modified version of SAMtools that improved its sensitivity. We analyzed 90 Gb of raw sequence data from next-generation sequencing of two resequencing and seven transcriptome data sets from several tomato accessions. Our study identified 4,812,432 non-redundant SNPs. Moreover, the workflow of SNP calling was improved by aligning the reference genome with its own raw data. Using this approach, 131,785 SNPs were discovered from transcriptome data of seven accessions. In addition, 4,680,647 SNPs were identified from the genome of S. pimpinellifolium, which are 60 times more than 71,637 of the PI212816 transcriptome. SNP distribution was compared between the whole genome and transcriptome of S. pimpinellifolium. Moreover, we surveyed the location of SNPs within genic and intergenic regions. Our results indicated that the sufficient genome-wide SNP markers and very sensitive SNP calling method allow for application of marker assisted breeding and genome-wide association studies.

Pyrosequencing-based transcriptome analysis of the asian rice gall midge reveals differential response during compatible and incompatible interaction

The Asian rice gall midge (Orseolia oryzae) is a major pest responsible for immense loss in rice productivity. Currently, very little knowledge exists with regard to this insect at the molecular level. The present study was initiated with the aim of developing molecular resources as well as identifying alterations at the transcriptome level in the gall midge maggots that are in a compatible (SH) or in an incompatible interaction (RH) with their rice host. Roche 454 pyrosequencing strategy was used to develop both transcriptomics and genomics resources that led to the identification of 79,028 and 85,395 EST sequences from gall midge biotype 4 (GMB4) maggots feeding on a susceptible and resistant rice variety, TN1 (SH) and Suraksha (RH), respectively. Comparative transcriptome analysis of the maggots in SH and RH revealed over-representation of transcripts from proteolysis and protein phosphorylation in maggots from RH. In contrast, over-representation of transcripts for translation, regulation of transcription and transcripts involved in electron transport chain were observed in maggots from SH. This investigation, besides unveiling various mechanisms underlying insect-plant interactions, will also lead to a better understanding of strategies adopted by insects in general, and the Asian rice gall midge in particular, to overcome host defense.

Genomics in eels--towards aquaculture and biology

Freshwater eels (genus Anguilla), especially the species inhabiting the temperate areas such as the European, American and Japanese eels, are important aquaculture species. Although artificial reproduction has been attempted since the 1930s and large numbers of studies have been conducted, it has not yet fully succeeded. Problems in eel artificial breeding are highly diverse, for instance, lack of basic information about reproduction in nature, no appropriate food for larvae, high mortality, and high individual variation in adults in response to maturation induction. Over the last decade, genomic data have been obtained for a variety of aquatic organisms. Recent technological advances in sequencing and computation now enable the accumulation of genomic information even for non-model species. The draft genome of the European eel Anguilla anguilla has been recently determined using Illumina technology and transcriptomic data based on next generation sequencing have been emerging. Extensive genomic information will facilitate many aspects of the artificial reproduction of eels. Here, we review the progress in genome-wide studies of eels, including additional analysis of the European eel genome data, and discuss future directions and implications of genomic data for aquaculture.

Construction of a high-density genetic map for grape using next generation restriction-site associated DNA sequencing

BACKGROUND

Genetic mapping and QTL detection are powerful methodologies in plant improvement and breeding. Construction of a high-density and high-quality genetic map would be of great benefit in the production of superior grapes to meet human demand. High throughput and low cost of the recently developed next generation sequencing (NGS) technology have resulted in its wide application in genome research. Sequencing restriction-site associated DNA (RAD) might be an efficient strategy to simplify genotyping. Combining NGS with RAD has proven to be powerful for single nucleotide polymorphism (SNP) marker development.

RESULTS

An F1 population of 100 individual plants was developed. In-silico digestion-site prediction was used to select an appropriate restriction enzyme for construction of a RAD sequencing library. Next generation RAD sequencing was applied to genotype the F1 population and its parents. Applying a cluster strategy for SNP modulation, a total of 1,814 high-quality SNP markers were developed: 1,121 of these were mapped to the female genetic map, 759 to the male map, and 1,646 to the integrated map. A comparison of the genetic maps to the published Vitis vinifera genome revealed both conservation and variations.

CONCLUSIONS

The applicability of next generation RAD sequencing for genotyping a grape F1 population was demonstrated, leading to the successful development of a genetic map with high density and quality using our designed SNP markers. Detailed analysis revealed that this newly developed genetic map can be used for a variety of genome investigations, such as QTL detection, sequence assembly and genome comparison.