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Cells
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Transcriptome in Human Disease
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Transcriptome in Human Disease

A special issue of Cells (ISSN 2073-4409). This special issue belongs to the section "Cellular Pathology".

Deadline for manuscript submissions: closed (31 August 2023) | Viewed by 11361

Special Issue Editors

Dr. Chava Kimchi-Sarfaty

E-Mail Website
Guest Editor
US Food and Drug Administration, Hemostasis Branch, Rockville, MD, USA
Interests: human genetics; synonymous variations; therapeutics
Dr. Upendra Katneni

E-Mail Website
Co-Guest Editor
US Food and Drug Administration, Hemostasis Branch, Rockville, MD, USA
Interests: human genetics; synonymous variations; therapeutics

Special Issue Information

Dear Colleagues,

We invite you to contribute original research and review articles to a Special Issue of Cells highlighting the role of the transcriptome in human disease. Please note that the journal has a higher impact factor of 6.1.

Transcriptomic information can provide large-scale information about gene expression in specific biological contexts and may contribute towards a better understanding of disease progression and may aid in the design of improved therapeutics. This Special Issue will highlight research employing transcriptomic data to better understand human diseases such as cancer. Relevant topics include but are not limited to: reviews of publicly available transcriptomic databases; discussion of techniques and algorithms used to quantify transcriptomic expression levels; contributions of the non-coding transcriptome including miRNA, lncRNA and piRNA to disease; use of transcriptomic information in clinical practice; transcriptomics as biomarkers for disease risk, clinical outcome or treatment efficacy; transcriptomic dysregulation during embryogenesis.

We look forward to your contributions.

Dr. Chava Kimchi-Sarfaty
Dr. Upendra Katneni
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Cells is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • RNA-sequencing
  • transcriptome
  • pharmacogenomics
  • single-cell analysis
  • cancer

Published Papers (4 papers)

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Research

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16 pages, 6156 KiB  
Article
Transcriptomic Classification of Pituitary Neuroendocrine Tumors Causing Acromegaly
by Julia Rymuza, Paulina Kober, Natalia Rusetska, Beata J. Mossakowska, Maria Maksymowicz, Aleksandra Nyc, Szymon Baluszek, Grzegorz Zieliński, Jacek Kunicki and Mateusz Bujko
Cells 2022, 11(23), 3846; https://doi.org/10.3390/cells11233846 - 30 Nov 2022
Cited by 8 | Viewed by 1793
Abstract
Acromegaly results from growth hormone hypersecretion, predominantly caused by a somatotroph pituitary neuroendocrine tumor (PitNET). Acromegaly-causing tumors are histologically diverse. Our aim was to determine transcriptomic profiles of various somatotroph PitNETs and to evaluate clinical implication of differential gene expression. A total of [...] Read more.
Acromegaly results from growth hormone hypersecretion, predominantly caused by a somatotroph pituitary neuroendocrine tumor (PitNET). Acromegaly-causing tumors are histologically diverse. Our aim was to determine transcriptomic profiles of various somatotroph PitNETs and to evaluate clinical implication of differential gene expression. A total of 48 tumors were subjected to RNA sequencing, while expression of selected genes was assessed in 134 tumors with qRT-PCR. Whole-transcriptome analysis revealed three transcriptomic groups of somatotroph PitNETs. They differ in expression of numerous genes including those involved in growth hormone secretion and known prognostic genes. Transcriptomic subgroups can be distinguished by determining the expression of marker genes. Analysis of the entire cohort of patients confirmed differences between molecular subtypes of tumors. Transcriptomic group 1 includes ~20% of acromegaly patients with GNAS mutations-negative, mainly densely granulated tumors that co-express GIPR and NR5A1 (SF-1). SF-1 expression was verified with immunohistochemistry. Transcriptomic group 2 tumors are the most common (46%) and include mainly GNAS-mutated, densely granulated somatotroph and mixed PitNETs. They have a smaller size and express favorable prognosis-related genes. Transcriptomic group 3 includes predominantly sparsely granulated somatotroph PitNETs with low GNAS mutations frequency causing ~35% of acromegaly. Ghrelin signaling is implicated in their pathogenesis. They have an unfavorable gene expression profile and higher invasive growth rate. Full article
(This article belongs to the Special Issue Transcriptome in Human Disease)
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Review

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21 pages, 1365 KiB  
Review
Single-Cell Transcriptomics of Mtb/HIV Co-Infection
by Smita Kulkarni, Janice J. Endsley, Zhao Lai, Todd Bradley and Riti Sharan
Cells 2023, 12(18), 2295; https://doi.org/10.3390/cells12182295 - 17 Sep 2023
Viewed by 2541
Abstract
Tuberculosis (TB) and Human Immunodeficiency Virus (HIV) co-infection continues to pose a significant healthcare burden. HIV co-infection during TB predisposes the host to the reactivation of latent TB infection (LTBI), worsening disease conditions and mortality. There is a lack of biomarkers of LTBI [...] Read more.
Tuberculosis (TB) and Human Immunodeficiency Virus (HIV) co-infection continues to pose a significant healthcare burden. HIV co-infection during TB predisposes the host to the reactivation of latent TB infection (LTBI), worsening disease conditions and mortality. There is a lack of biomarkers of LTBI reactivation and/or immune-related transcriptional signatures to distinguish active TB from LTBI and predict TB reactivation upon HIV co-infection. Characterizing individual cells using next-generation sequencing-based technologies has facilitated novel biological discoveries about infectious diseases, including TB and HIV pathogenesis. Compared to the more conventional sequencing techniques that provide a bulk assessment, single-cell RNA sequencing (scRNA-seq) can reveal complex and new cell types and identify more high-resolution cellular heterogeneity. This review will summarize the progress made in defining the immune atlas of TB and HIV infections using scRNA-seq, including host-pathogen interactions, heterogeneity in HIV pathogenesis, and the animal models employed to model disease. This review will also address the tools needed to bridge the gap between disease outcomes in single infection vs. co-infection. Finally, it will elaborate on the translational benefits of single-cell sequencing in TB/HIV diagnosis in humans. Full article
(This article belongs to the Special Issue Transcriptome in Human Disease)
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24 pages, 1159 KiB  
Review
Aid or Antagonize: Nuclear Long Noncoding RNAs Regulate Host Responses and Outcomes of Viral Infections
by Viraj Kulkarni, Sahana Jayakumar, Mahesh Mohan and Smita Kulkarni
Cells 2023, 12(7), 987; https://doi.org/10.3390/cells12070987 - 23 Mar 2023
Cited by 5 | Viewed by 1901
Abstract
Long noncoding RNAs (lncRNAs) are transcripts measuring >200 bp in length and devoid of protein-coding potential. LncRNAs exceed the number of protein-coding mRNAs and regulate cellular, developmental, and immune pathways through diverse molecular mechanisms. In recent years, lncRNAs have emerged as epigenetic regulators [...] Read more.
Long noncoding RNAs (lncRNAs) are transcripts measuring >200 bp in length and devoid of protein-coding potential. LncRNAs exceed the number of protein-coding mRNAs and regulate cellular, developmental, and immune pathways through diverse molecular mechanisms. In recent years, lncRNAs have emerged as epigenetic regulators with prominent roles in health and disease. Many lncRNAs, either host or virus-encoded, have been implicated in critical cellular defense processes, such as cytokine and antiviral gene expression, the regulation of cell signaling pathways, and the activation of transcription factors. In addition, cellular and viral lncRNAs regulate virus gene expression. Viral infections and associated immune responses alter the expression of host lncRNAs regulating immune responses, host metabolism, and viral replication. The influence of lncRNAs on the pathogenesis and outcomes of viral infections is being widely explored because virus-induced lncRNAs can serve as diagnostic and therapeutic targets. Future studies should focus on thoroughly characterizing lncRNA expressions in virus-infected primary cells, investigating their role in disease prognosis, and developing biologically relevant animal or organoid models to determine their suitability for specific therapeutic targeting. Many cellular and viral lncRNAs localize in the nucleus and epigenetically modulate viral transcription, latency, and host responses to infection. In this review, we provide an overview of the role of nuclear lncRNAs in the pathogenesis and outcomes of viral infections, such as the Influenza A virus, Sendai Virus, Respiratory Syncytial Virus, Hepatitis C virus, Human Immunodeficiency Virus, and Herpes Simplex Virus. We also address significant advances and barriers in characterizing lncRNA function and explore the potential of lncRNAs as therapeutic targets. Full article
(This article belongs to the Special Issue Transcriptome in Human Disease)
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Other

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11 pages, 582 KiB  
Commentary
Tracing Translational Footprint by Ribo-Seq: Principle, Workflow, and Applications to Understand the Mechanism of Human Diseases
by Atefeh Bagheri, Artem Astafev, Tara Al-Hashimy and Peng Jiang
Cells 2022, 11(19), 2966; https://doi.org/10.3390/cells11192966 - 23 Sep 2022
Cited by 4 | Viewed by 4478
Abstract
RNA-seq has been widely used as a high-throughput method to characterize transcript dynamic changes in a broad context, such as development and diseases. However, whether RNA-seq-estimated transcriptional dynamics can be translated into protein level changes is largely unknown. Ribo-seq (Ribosome profiling) is an [...] Read more.
RNA-seq has been widely used as a high-throughput method to characterize transcript dynamic changes in a broad context, such as development and diseases. However, whether RNA-seq-estimated transcriptional dynamics can be translated into protein level changes is largely unknown. Ribo-seq (Ribosome profiling) is an emerging technology that allows for the investigation of the translational footprint via profiling ribosome-bounded mRNA fragments. Ribo-seq coupled with RNA-seq will allow us to understand the transcriptional and translational control of the fundamental biological process and human diseases. This review focuses on discussing the principle, workflow, and applications of Ribo-seq to study human diseases. Full article
(This article belongs to the Special Issue Transcriptome in Human Disease)
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