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Neoplasms

Digestive System Disorders

Vaccine

Antibody drug conjugate (ADC)

Biological products

Disease domain score

A glimpse into the focused therapeutic areas

Technology Platform

Most used technologies in drug development

Targets

Most frequently developed targets

Disease Domain	Count

Neoplasms	5

Top 5 Drug Type	Count

Vaccine	2
Antibody drug conjugate (ADC)	2
Biological products	1

Top 5 Target	Count

MUC13(mucin 13, cell surface associated)	1
CEACAM5(Carcinoembryonic antigen related cell adhesion molecule 5)	1
ERK1(Extracellular-signal-regulated kinase1)	1

AbstractFormalin-fixed, paraffin-embedded (FFPE) tissue specimens are routinely used in pathological diagnosis. However, formalin induced artificial mutations make it challenging to accurately analyze next-generation sequencing data. Existing FFPE filtering tools tend to categorize all low-frequency variants as artifacts, making it difficult to identify true variants with low allele frequencies, compromising analysis of tumors with low tumor cell content. To address this issue, we developed DEEPOMICS FFPE, an AI model designed to distinguish true variants from artifacts. We gathered paired exome genome sequencing data from both fresh frozen and FFPE samples of 24 tumors from public sources. These data were used to train and validate the model, with a split of 70% for training and 30% for validation. The deep neural network model, comprising three hidden layers, was trained using input features derived from the outputs of the MuTect2 caller. We employed the SHapley Additive exPlanations algorithm to identify relevant features, and then fine-tuned them based on the training outcomes. We assessed the performance of the final DEEPOMICS FFPE model in comparison to existing models (MuTect filter, FFPolish, and SOBDetector) using well-defined test datasets. Our findings revealed 43 distinguishing characteristics for FFPE artifacts. Refining the quantification of these characteristics resulted in improved model performance. DEEPOMICS FFPE successfully filtered out 99.6% of artifacts while retaining 85.2% of true variants, achieving an F1-score of 87.8 in the validation dataset, surpassing the performance of existing tools. Furthermore, the model demonstrated consistent performance even for variants with low allele frequencies, exhibiting a specificity of 0.998, suggesting its capability to identify subclonal variants. Future enhancement of the model will include the ability to use other variant callers and analysis of whole genome sequencing data. This newly developed tool has potential applications in designing capture panels for personalized circulating tumor DNA assays and identifying candidate neoepitopes for personalized vaccine development. DEEPOMICS FFPE is freely accessible for research purposes on the web at http://deepomics.co.kr/ffpe.Citation Format: Dong-hyuk Heo, Inyoung Kim, Heejae Seo, Seong-Gwang Kim, Minji Kim, Jiin Park, Hongsil Park, Seungmo Kang, Juhee Kim, Soonmyung Paik, Seong-Eui Hong. Reducing artifactual somatic variant calls from formalin-fixed paraffin-embedded specimens by using DEEPOMICS FFPE, a bioinformatic approach based on deep neural networks [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2275.

24 Nov 2023·Science Advances

Partial in vivo reprogramming enables injury-free intestinal regeneration via autonomous Ptgs1 induction

Article

Author: Cha, Hyuk-Jin ; Kim, Somi ; Jung, Han-Sung ; Kim, Keun-Tae ; Lee, Seung-Yeon ; Koo, Bon-Kyoung ; Oh, Ji-Young ; Hong, Chang Pyo ; Kim, Jumee ; Jo, Beom-Ki ; Kim, Jong Kyoung ; Kwon, Eun-Ji ; Kim, Eun-Jung ; Adpaikar, Anish Ashok ; Roe, Jae-Seok ; Kim, Hwa-Ryeon

Tissue regeneration after injury involves the dedifferentiation of somatic cells, a natural adaptive reprogramming that leads to the emergence of injury-responsive cells with fetal-like characteristics. However, there is no direct evidence that adaptive reprogramming involves a shared molecular mechanism with direct cellular reprogramming. Here, we induced dedifferentiation of intestinal epithelial cells using OSKM (Oct4, Sox2, Klf4, and c-Myc) in vivo. The OSKM-induced forced dedifferentiation showed similar molecular features of intestinal regeneration, including a transition from homeostatic cell types to injury-responsive–like cell types. These injury-responsive–like cells, sharing gene signatures of revival stem cells and atrophy-induced villus epithelial cells, actively assisted tissue regeneration following damage. In contrast to normal intestinal regeneration involving Ptgs2 induction, the OSKM promotes autonomous production of prostaglandin E2 via epithelial Ptgs1 expression. These results indicate prostaglandin synthesis is a common mechanism for intestinal regeneration but involves a different enzyme when partial reprogramming is applied to the intestinal epithelium.

01 Sep 2023·Chemosphere

The effects of environmental Microplastic on wharf roach (Ligia exotica): A Multi-Omics approach

Article

Author: Shin, Dong-Min ; Bae, Myung Ae ; Jung, Jee-Hyun ; Han, Gi Myung ; Shim, Won Joon ; Jang, Mi ; Cho, Sung-Hee ; Cho, Youna ; Hong, Sang Hee ; Shin, Dongju ; Kim, Seong Soon ; Choi, Youmi ; Hong, Chang Pyo

This is the first report to evaluate the potential effects of microplastics (MPs) on wild wharf roaches (Ligia exotica) in a shoreline habitant. L. exotica is an important plastic detritus consumer in coastal area. A survey was conducted from May to June in the years 2019 and 2020 in two South Korean nearshore sites: Nae-do (as MPs-uncontaminated) and Maemul-do (as MPs-contaminated). MPs (>20 μm in size) were detected highly in gastrointestinal tracts of the L. exotica from Maemul-do, at an average level of 50.56 particles/individual. They were detected in much lower levels in the L. exotica from Nae-do. at an average rate of 1.00 particles/individual. The polymer type and shape were dominated by expanded polystyrene (EPS, 93%) and fragment (99.9%) in L. exotica from Maemul-do. Especially, Hexabromocyclododecanes, brominated flame retardants added to EPS, have been detected highly in L. exotica from Maemul-do (630.86 ± 587.21 ng/g l. w.) than those of Nae-do (detection limit: 10.5 ng/g l. w). Genome-wide transcriptome profiling revealed altered expression of genes associated with fatty acid metabolic processes, the innate-immune response-activating system and vesicle cytoskeletal trafficking in L. exotica from Maemul-do. The activation of the p53 signaling pathway (which is related to proteasome, ER regulation and cell morphogenesis) is likely to be involved in the EPS-uptake of wild L. exotica. Four neurosteroids were also detected in head tissue, and cortisol and progesterone concentrations differed significantly in L. exotica from Maemul-do. Our findings also suggest that resident plastic detritus consumer might be a useful indicator organism for evaluating pollution and potential effects of environmental microplastics.

100 Deals associated with Theragen Bio Co., Ltd.

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100 Translational Medicine associated with Theragen Bio Co., Ltd.

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Pipeline

Pipeline Snapshot as of 07 Nov 2024

The statistics for drugs in the Pipeline is the current organization and its subsidiaries are counted as organizations,Early Phase 1 is incorporated into Phase 1, Phase 1/2 is incorporated into phase 2, and phase 2/3 is incorporated into phase 3

Discovery

2

3

Preclinical

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Current Projects

Drug(Targets)	Indications	Global Highest Phase

TB-CV-01	Solid tumor More	Preclinical
TB-CV-02	Solid tumor More	Preclinical
TB-ADC-01 ( MUC13 )	Rectal Cancer More	Preclinical
TB-ADC-02 ( CEACAM5 )	Rectal Cancer More	Discovery
TB-SM-01 ( ERK1 )	Rectal Cancer More	Discovery