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\begin{document}

\title{Exploring the Theranostic roles of miRNA and Epigenetics in Autoimmune
Diseases - A Comprehensive Review}



\author[1]{Sagnik   Nag}%
\author[1]{Oishi Mitra}%
\author[1]{Garima  Tripathi}%
\author[1]{Souvik   Samanta}%
\author[1]{Bikramjit   Bhattacharya}%
\author[2]{Priti  Chandane}%
\author[3]{Sourav   Mohanto}%
\author[1]{Vino   Sundararajan}%
\author[4]{Sumira  Malik}%
\author[5]{Sarvesh   Rustagi}%
\author[6]{Suraj  Adhikari}%
\author[7]{Aroop Mohanty}%
\author[8]{Darwin A.  León‐Figueroa}%
\author[9]{Alfonso J.  Rodriguez-Morales}%
\author[10]{Joshuan Barboza}%
\author[11]{Ranjit Sah}%
\affil[1]{Vellore Institute of Technology}%
\affil[2]{University of Hyderabad}%
\affil[3]{Yenepoya (Deemed to be University)}%
\affil[4]{Amity University Jharkhand Campus}%
\affil[5]{Uttaranchal University}%
\affil[6]{Manipal College of Medical Sciences}%
\affil[7]{AIIMS Gorakhpur}%
\affil[8]{Universidad de San Martín de Porres Facultad de Medicina Humana}%
\affil[9]{Fundacion Universitaria Autonoma de las Americas}%
\affil[10]{Universidad César Vallejo}%
\affil[11]{Tribhuvan University}%


\vspace{-1em}



  
  \date{May 27, 2024}


\begingroup
\let\center\flushleft
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\maketitle
\endgroup





\selectlanguage{english}
\begin{abstract}
Autoimmune diseases (AD) are severe pathophysiological ailments that are
stimulated by an exaggerated immunogenic response towards self-antigens,
which can cause systemic or site-specific organ damage. An array of
complex genetic and epigenetic facets majorly contributes to the
progression of AD, thus providing significant insight into the
regulatory mechanism of microRNA (miRNA). miRNAs are short, non-coding
RNAs that have been identified as essential contributors to the
post-transcriptional regulation of host genome expression and as crucial
regulators of a myriad of biological processes such as immune
homeostasis, T helper cell differentiation, central and peripheral
tolerance, and immune cell development. Pertaining to the differential
expression of miRNA attributed in target tissues and cellular bodies of
innate and adaptive immunity, a paradigm of scientific expeditions
suggests an optimistic correlation between immunogenic dysfunction and
miRNA alterations. Therefore, it is not astonishing that dysregulations
in miRNA expression patterns are now recognized in a wide spectrum of
disorders, establishing themselves as potential biomarkers and
therapeutic targets. Owing to its theranostic potencies, miRNA targets
have been widely utilized in the development of biosensors and other
therapeutic molecules originating from the same. This article tends to
deliberate and conceptualize the brief pathogenesis and pertinent
epigenetic regulatory mechanism as well as miRNA networks majorly
affecting five different ADs namely Rheumatoid Arthritis (RA), Diabetes,
Multiple Sclerosis (MS), Systemic Lupus Erythematosus (SLE) and
Inflammatory Bowel Disorder (IBD) thereby providing novel theranostic
interventions.%
\end{abstract}%



\sloppy


\textbf{Exploring the Theranostic roles of miRNA and Epigenetics in
Autoimmune Diseases - A Comprehensive Review}

Sagnik Nag\textsuperscript{1+}, Oishi Mitra\textsuperscript{1+}, Garima
Tripathi\textsuperscript{1}, Souvik Samanta\textsuperscript{1},
Bikramjit Bhattacharya\textsuperscript{2}, Priti
Chandane\textsuperscript{3}, Sourav Mohanto\textsuperscript{4}, Vino
Sundararajan\textsuperscript{1}, Sumira Malik\textsuperscript{5,6,7},
Sarvesh Rustagi\textsuperscript{6}, Suraj Adhikari\textsuperscript{8},
Aroop Mohanty\textsuperscript{9}, Darwin A.
Le\selectlanguage{ngerman}ón\selectlanguage{english}-Figueroa\textsuperscript{10}, Alfonso J.
Rodriguez-Morales\textsuperscript{11,12,13}, Joshuan J.
Barboza\textsuperscript{14}, Ranjit Sah\textsuperscript{15,16,17*}

\textsuperscript{\textbf{1}} Department of Bio-Sciences, School of
Biosciences \& Technology, Vellore Institute of Technology (VIT),
Tiruvalam Road, Vellore, Tamil Nadu - 632014, India;
sagniknag234@gmail.com; oishi.mitra10@gmail.com;
ramatripathi17@gmail.com; SOUVIKSAMANTA43@gmail.com; svino@vit.ac.in

\textsuperscript{\textbf{2}} Department of Applied Microbiology, School
of Biosciences \& Technology, Vellore Institute of Technology (VIT),
Tiruvalam Road, Tamil Nadu - 632014, India;
bikramjitbhattacharya79@gmail.com

\textsuperscript{\textbf{3}} Department of Biochemistry, School of Life
Sciences, University of Hyderabad, Hyderabad, Telangana- 500046, India;
pritz.chandane285@gmail.com

\textsuperscript{4} Department of Pharmaceutics, Yenepoya Pharmacy
College \& Research Centre, Yenepoya (Deemed to be University),
Mangaluru, Karnataka-575018, India; mohanto111@gmail.com

\textsuperscript{5}Amity Institute of Biotechnology, Amity University
Jharkhand, Ranchi, Jharkhand, 834001, India; smalik@rnc.amity.edu

\textsuperscript{6}School of Applied and Life Sciences, Uttaranchal
University, 22 Dehradun, Uttarakhand, India;
sarveshrustagi@uttaranchaluniversity.ac.in

\textsuperscript{7}Guru Nanak College of Pharmaceutical Sciences,
Dehradun, Uttarakhand

\textsuperscript{8}Manipal College of Medical Sciences, Pokhara, Nepal.
Email: adhikarisuraj012@gmail.com

\textsuperscript{9}Department of Clinical Microbiology, All India
Institute of Medical Sciences, Gorakhpur, Uttar Pradesh, 273008, India;
aroopmohanty7785@yahoo.com

\textsuperscript{10}Facultad de Medicina Humana, Universidad de San
Martin de Porres, Chiclayo 15011, Peru. darwin\_leon@usmp.pe

\textsuperscript{11}Grupo de Investigacion Biomedicina, Faculty of
Medicine, Fundacion Universitaria Autonoma de las
Ame-ricas---Institucion Universitaria Vision de las Americas, Pereira
660003, Risaralda, Colombia; alfonso.rodriguez@uam.edu.co

\textsuperscript{12}Clinical Epidemiology and Biostatistics, School of
Medicine, Universidad Cientifica del Sur, Lima 4861, Peru

\textsuperscript{13}Gilbert and Rose-Marie Chagoury School of Medicine,
Lebanese American University, Beirut P.O. Box 36, Lebanon

\textsuperscript{14}Escuela de Medicina, Universidad Cesar Vallejo,
Trujillo 13007, Peru; jbarbozame@ucvvirtual.edu.pe

\textsuperscript{15}Department of Clinical Microbiology, Institute of
Medicine, Tribhuvan University Teaching Hospital, Kathmandu 44600,
Nepal; ranjitsah57@gmail.com

\textsuperscript{16}Department of Clinical Microbiology, DY Patil
Medical College, Hospital and Research Centre, DY Patil Vidyapeeth, Pune
411000, India

\textsuperscript{17}Department of Public Health Dentistry, Dr. D.Y.
Patil Dental College and Hospital, Dr. D.Y. Patil Vidyapeeth, Pune
411018, Maharashtra, India

\selectlanguage{english}\textbf{+} Equally contributing authors

*\textbf{Corresponding Author} : Dr. Ranjit Sah, Department of Clinical
Microbiology, Institute of Medicine, Tribhuvan University Teaching
Hospital. Email: ranjitsah57@gmail.com

\textbf{Data Availability Statement}

\textbf{Funding Statement}

\textbf{Conflict of Interest Disclosure --} \emph{The authors declare no
conflict of interest.}

\textbf{Permission to Reproduce material from other sources} \emph{--
Not applicable.}

\textbf{Author Contributions} - \emph{Conceptualization was conducted by
S.N. and O.M.; Writing---original draft preparation, investigation was
performed by S.N.; O.M.; G.T.; S.S.; B.B.; P.C.; S.M. (Sourav Mohanto);
and V.S.; Data curation, validation and formal analysis conducted by
S.N.; O.M.; S.M. (Sourav Mohanto); and V.S.; Writing---review and
editing was conducted by S.N.; O.M. and S.M. (Sumira Malik);
Visualization and validation was conducted by S.S.., S.R and S.N.;
Supervision and Project administration was conducted by S.M. (Sumira
Malik); V.S.; All authors have read and agreed to the published version
of the manuscript.}

\textbf{Abstract}

Autoimmune diseases (AD) are severe pathophysiological ailments that are
stimulated by an exaggerated immunogenic response towards self-antigens,
which can cause systemic or site-specific organ damage. An array of
complex genetic and epigenetic facets majorly contributes to the
progression of AD, thus providing significant insight into the
regulatory mechanism of microRNA (miRNA). miRNAs are short, non-coding
RNAs that have been identified as essential contributors to the
post-transcriptional regulation of host genome expression and as crucial
regulators of a myriad of biological processes such as immune
homeostasis, T helper cell differentiation, central and peripheral
tolerance, and immune cell development. Pertaining to the differential
expression of miRNA attributed in target tissues and cellular bodies of
innate and adaptive immunity, a paradigm of scientific expeditions
suggests an optimistic correlation between immunogenic dysfunction and
miRNA alterations. Therefore, it is not astonishing that dysregulations
in miRNA expression patterns are now recognized in a wide spectrum of
disorders, establishing themselves as potential biomarkers and
therapeutic targets. Owing to its theranostic potencies, miRNA targets
have been widely utilized in the development of biosensors and other
therapeutic molecules originating from the same. This article tends to
deliberate and conceptualize the brief pathogenesis and pertinent
epigenetic regulatory mechanism as well as miRNA networks majorly
affecting five different ADs namely Rheumatoid Arthritis (RA), Diabetes,
Multiple Sclerosis (MS), Systemic Lupus Erythematosus (SLE) and
Inflammatory Bowel Disorder (IBD) thereby providing novel theranostic
interventions.

\textbf{Keywords -} Autoimmune Diseases, miRNA, Epigenetic Regulation,
Diagnostics, Therapeutics

\textbf{Introduction}

Autoimmune diseases (ADs) are chronic and progressive ailments
designated by an exaggerated self-immunogenic response, accompanied by
the overproduction of self-antibodies leading to an overall systemic
dysfunction and abnormalities in cellular components. Depending on
various biological and physicochemical factors, ADs can bring damage to
a particular organ or other biological systems. The interaction of
environmental factors and genetic anomalies has a key role in showcasing
the pathological effects of ADs . The involvement of B cells in the
progression of ADs displays an array of different biological roles.
These biological roles mainly include the entrenched secretion of
self-antibodies; the presentation of self-antigens and arising
complementary interactions with T cells; the release of cytokines
involved in the inflammatory response; and the development of deranged
specialized microstructure named as germinal centers. With the help of
these cellular processes, autoimmune conditions that are often
categorized as antibody-mediated or as T cell-mediated, both are
considered to be controlled and affected by B cells . The maturation of
T-cells in the thymus is responsible for the elimination of a large
amount of auto-reactive T cells, but a bulk of T cells that have gained
maturity and are able to detect autoantigens can be observed in the
peripheral circulatory system of healthy people along with the people
suffering from AD. While they appear to be responsible for the
pathophysiology of a number of ADs in patients, these auto-reactive
cells are maintained in an unresponsive condition in healthy persons.
CD4+ CD25+ are considered to be T cells possessing a natural regulatory
mechanism and furthermore, it is a population of T cells that have been
recently discovered and is regarded to be predominantly responsible for
the modulation of the activity of these auto-reactive immune cells .
Recent studies suggest that in some types of autoimmunity, the
interaction between the environment and the host is influenced by
epigenetic alterations induced by various environmental factors,
including altered DNA methylation patterns. Due to environmental
factors, it may become difficult for certain cells to maintain
epigenetic homeostasis, which can result in loss of tolerance due to
abnormal expression of genes. These altered cells can subsequently
contribute to the onset of autoimmunity in those with a genetic
predisposition . Expression of genes and cellular processes are altered
by epigenetic changes, but the genomic sequence remains unaffected. The
key epigenetic processes include expression of non-coding RNA,
modification of amino termini of histone proteins by post-translational
alterations, and CpG DNA dinucleotides methylation and/or their
hydroxymethylation. Pathophysiology of ADs has been strongly connected
to disease responsible for triggering gene alterations or a combination
of genetic vulnerability, and epigenetic changes occurring due to the
involvement of various environmental factors. Thus, it is crucial to
understand how some ADs are caused by the concoction of genetic as well
as epigenetic pathways . A new family of noncoding RNA known as long
noncoding RNA (lncRNA) is essential for the control of both autoimmune
and immunological processes, whereas, on the other hand, endogenous
non-coding RNAs (ncRNAs) known as circular RNAs (circRNAs) showcases
itself as the crucial immune system gene modulators and is responsible
for the occurrence and progression of ADs . In addition to this, small,
conserved non-coding RNA molecules called miRNAs target the 3'
untranslated region (UTR) of particular messenger RNAs (mRNAs) and
either promote their destruction or suppress translation. Apoptosis,
differentiation, cell cycle, and immunological activities are the
biological processes that miRNA is known to control. According to recent
studies, miRNAs are essential for the regulatory mechanisms of
immunological processes and play a key role in preventing ADs . The
therapy of ADs has changed little over the past few decades due to
advancements in medicine, and the mechanisms behind many of these
diseases are still unknown. It's also important to understand how ADs
initiate, progress, and end. Owing to its unique regulatory properties
and pathogenic contributions, miRNA can legitimately serve as a
potential biomarker candidate to efficaciously diagnose the progression
of AD. Several daunting attempts were actualised to construct a
compendium of biosensors to detect sole pathogenic miRNA candidates
participating in AD pathophysiology. Due to the advent of advancing
progressions in the domain of material sciences and pharmaceutical
interventions, several miRNA encapsulating strategies have been
formulated to enhance site-directed specific drug delivery to curb a
number of ADs. Altered physiological microenvironment and physical
properties are some of the characteristic hallmarks of AD that demand
the application of stimuli-responsive drug delivery platforms to cater a
stimulus specific to the disease. Understanding the methods through
which miRNAs participate in these processes can therefore offer a new
window to advance our knowledge of ADs. This article tends to provide
insight into miRNA regulation and responsiveness towards the
complexities of immunological cascades associated with progressive ADs,
pertaining special emphasis on Rheumatoid arthritis (RA), Diabetes,
Multiple Sclerosis (MS), Systemic Lupus Erythematosus (SLE) and
Inflammatory bowel disorder (IBD), thereby providing optimistic
deliberations on novel theragnostic interventions concerning the same.
Along the same lines, it also heralds to showcase significant epigenetic
modulations for the above-mentioned ADs.

\textbf{Biogenesis of mi-RNA and its regulatory mechanism on ADs}

Small non-coding RNAs (19-21 nucleotides) called miRNAs majorly
influences the post-transcriptional regulation of gene expression by
either limiting messenger RNA (mRNA) translation or encouraging mRNA
degradation. miRNA was first identified in the year 1993 and it remains
conserved among a wide variety of species . miRNAs are the major
contributing factors in the pathophysiology of multiple diseases
including cancer, cardiovascular, metabolic and ADs . Animal miRNAs are
encoded as mono-cistronic (individual genes), poly-cistronic (cluster of
genes), or introns of host genes (intronic). Primary miRNA (pri-miRNA)
transcripts with hairpins and 5' and 3' flanking sequences are produced
by RNA polymerase II . As depicted in Figure 1, the processing is
carried out mainly by Drosha and Dicer, two members of the RNase III
family of enzymes , which work in complexes with dsRNA-binding proteins
(dsRBPs), such as DGCR8 and transactivation-responsive RNA-binding
protein (TRBP) in mammals, to catalyze the two steps of primary
precursor (pre-miRNA) processing in the canonical pathway . The
structural properties of individual pri-miRNA sequences influence the
effectiveness of pri-miRNA processing. Co-transcriptional processing of
pri-miRNAs results in a fast pool of 59-71-nt-long stem-loop pre-miRNAs.
Exportin-5, a member of the karyopherin protein family, exports nascent
pre-miRNAs to the cytoplasm in a GTP-dependent manner . Once in the
cytoplasm, the pre-miRNA is integrated into the RISC Loading Complex
(RLC), where it is processed into a 21-nt-long miRNA/miRNA* duplex by
the type III ribonuclease Dicer . Up to one-third of human mRNAs may be
miRNA targets, and miRNA-mediated gene regulation is essential for
normal physiological processes including the cell cycle,
differentiation, and death. miRNAs are essential for the control of
immunological processes and the avoidance of AD, as stated by the recent
research . There are various checkpoints that guarantee the deletion or
silencing of autoreactive T and B lymphocytes, which are produced
regularly and randomly throughout lymphomagenesis. But occasionally,
self-reactive lymphocytes manage to get past the checkpoints and
continue to live in peripheral lymphoid tissues. When these autoreactive
cells are triggered, they launch a vicious assault against self-tissues
that trigger ADs . miRNAs control autoimmunity by influencing the
formation, differentiation, and function of many cell types, including
innate immune cells (innate immunity), adaptive immune cells (adaptive
immunity), and local resident cells . Toll-like receptors (TLRs), C-type
lectin-like receptors (CLRs), nucleotide-binding oligomerization domain
(NOD)-like receptors, retinoic acid-inducible gene (RIG)-I-like
receptors (RLRs), are all expressed by host cells. These receptors are
capable of recognizing a wide range of pathogen-associated molecular
patterns (PAMPs) . These processes activate intracellular signaling
pathways, resulting in the release of proinflammatory cytokines,
chemokines, and interferons (IFNs) as well as the production of
co-stimulatory molecules. Several investigations have demonstrated that
miRNAs play critical roles in the biological processes of these adaptive
immune cells in autoimmunity, miRNAs also alter/regulate a particular
subgroup of T cells called regulatory T cells (Tregs) are essential for
regulating the immune response, which finally results in the upkeep of
self-tolerance and homeostasis . According to Husakova et al., (2016),
miRNAs have an impact on the development of CD8+ T cells, Th1 cells, Th2
cells, and Thymus by affecting the levels of miRNA-155, miRNA-147, and
miRNA-146a. The in-vivo application of the major miRNAs are already
known. The multi-modal applications of miRNA delves into the
conceptualization and understanding of various novel developmental
strategies for the treatment and prevention of ADs\selectlanguage{english}
\begin{figure}[H]
\begin{center}
\includegraphics[width=0.70\columnwidth]{figures/image1/image1}

\end{center}
\end{figure}

\textbf{Figure 1 -} \emph{Biogenesis of miRNA. Initial steps include the
formation of pre-miRNA followed by nuclear export and subsequent
cleavage to form matured miRNA and further the fate of the matured miRNA
is decided by the RISC complex attachment}

\textbf{miRNA in the progression of ADs}

miRNAs have always been considered as major contributors to the regular
immune system functioning, immunological tolerance pathways and
autoimmunity. Recent research from clinical investigations and animal
models indicates that miRNAs play a role in the etiology of various ADs.
A number of ADs in humans have a significant association between their
progression and the abnormal miRNA expression . In peripheral and
central lymphoid organs, miRNAs function at a number of checkpoints to
sustain immunological tolerance and combat ADs.\textbf{Figure 2 -}
\emph{Overview of role of miRNA involved in the disease pathogenesis,
biomarker detection and development of miRNA-based therapeutics for
different ADs}Latest evidence has now established specific miRNAs that
regulate the lineage specificity and effector potentials of T helper
subsets to promote immunological homeostasis .

\textbf{Table 1 -} \emph{Different ADs and their respective miRNAs
associated with disease pathogenesis}\selectlanguage{english}
\begin{longtable}[]{@{}lllll@{}}
\toprule
\begin{minipage}[t]{0.17\columnwidth}\raggedright\strut
\textbf{Autoimmune Disease}\strut
\end{minipage} & \begin{minipage}[t]{0.17\columnwidth}\raggedright\strut
\textbf{miRNA}\strut
\end{minipage} & \begin{minipage}[t]{0.17\columnwidth}\raggedright\strut
\textbf{Regulation}\strut
\end{minipage} & \begin{minipage}[t]{0.17\columnwidth}\raggedright\strut
\textbf{Mechanism}\strut
\end{minipage} & \begin{minipage}[t]{0.17\columnwidth}\raggedright\strut
\textbf{Reference}\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
Rheumatoid Arthritis\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
miRNA-126-3p, let-7d-5p, miRNA-431-3p, miRNA-221-3p, miRNA-24-3p,
miRNA-130a-3p, miRNA-339-5p, let-7i-5p, miRNA-486-5p\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
Upregulated\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
Promotes apoptosis and proinflammatory markers Anti-proliferative effect
and increases the apoptotic death of FLSs Maintains homeostasis and
associated with cartilage development pathways\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.17\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.17\columnwidth}\raggedright\strut
miRNA-320a, miRNA-132, miRNA-363, miRNA-498a, miRNA-124a, miRNA-140,
let-7a, miR-204-5p\strut
\end{minipage} & \begin{minipage}[t]{0.17\columnwidth}\raggedright\strut
Downregulated\strut
\end{minipage} & \begin{minipage}[t]{0.17\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.17\columnwidth}\raggedright\strut
\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
Diabetes\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
miRNA-375, miRNA-29a, miRNA-29b, miRNA-200, miRNA-7, miRNA-140-3p,
miRNA-574-3p, miRNA-139-5p, miRNA-106a, miRNA-17, miRNA-486-3p, miRNA16,
miRNA-222, miRNA-885-5p, miRNA-197\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
Upregulated\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
Malabsorption of glucose and insulin resistance Maintains glucose
homeostasis Beta cell differentiation and proliferation, regulates
apoptosis Controls glucose and lipid metabolism\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.17\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.17\columnwidth}\raggedright\strut
miRNA-155, miRNA-92a, miRNA-126, miRNA-34a, miRNA-214-3p
miRNA-27-3p\strut
\end{minipage} & \begin{minipage}[t]{0.17\columnwidth}\raggedright\strut
Downregulated\strut
\end{minipage} & \begin{minipage}[t]{0.17\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.17\columnwidth}\raggedright\strut
\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
Multiple Sclerosis\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
miRNA-155, miRNA-146a/b, miRNA-214, miRNA-23a, miRNA-219, miRNA-338,
miRNA-128, miRNA-27b, miRNA-340, miRNA-29b, miRNA-326, miRNA-301a,
miRNA-17-5p\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
Upregulated\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
miRNA expression altered in CNS lesions and in the immune system, which
effects gene expression and promotes the disease Contribute towards
Th-17 differentiation and polarization\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.17\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.17\columnwidth}\raggedright\strut
miRNA-219, miRNA-338, miRNA-23b, miRNA-25, miRNA-15a, miRNA-16-1
miRNA-17-92 cluster\strut
\end{minipage} & \begin{minipage}[t]{0.17\columnwidth}\raggedright\strut
Downregulated\strut
\end{minipage} & \begin{minipage}[t]{0.17\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.17\columnwidth}\raggedright\strut
\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
Systemic Lupus Erythematosus\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
miRNA-155, miRNA-15a, miRNA-124-3p, miRNA-377-3p, miRNA-21, miRNA-7,
miRNA-34a, miRNA-148a, miRNA-126,\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
Upregulated\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
Involved in Apoptotic pathway Triggers inflammation, exaggerated
immunogenic response and pathogenesis\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.17\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.17\columnwidth}\raggedright\strut
miRNA-17, miRNA-142-3p, miRNA-146a, miRNA-125b\strut
\end{minipage} & \begin{minipage}[t]{0.17\columnwidth}\raggedright\strut
Downregulated\strut
\end{minipage} & \begin{minipage}[t]{0.17\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.17\columnwidth}\raggedright\strut
\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
Inflammatory Bowel Disorder\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
miRNA-101, miRNA-515-5p, miRNA-623, miRNA-325, miRNA-876-5,
miRNA-1224-5p, miRNA-1226-5p, miRNA-1253, miRNA-455, miRNA-20a,
miRNA-17-5p, miRNA-424, miRNA-16-5p, miRNA-21-5p\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
Upregulated\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
Serve as biomarkers for disease diagnosis Enhances paracellular
permeability of the intestinal epithelium Boosts zonulin expression and
promotes epithelial permeability Reduces the expression of aquaporin 3,
resulting in a weakening of the intestinal barrier\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.17\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.17\columnwidth}\raggedright\strut
miRNA-24, miRNA-107, miRNA-10a, miRNA-223, miRNA-9, miRNA-21, miRNA-874,
miRNA-150, miRNA-125b, miRNA-17-92,\strut
\end{minipage} & \begin{minipage}[t]{0.17\columnwidth}\raggedright\strut
Downregulated\strut
\end{minipage} & \begin{minipage}[t]{0.17\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.17\columnwidth}\raggedright\strut
\strut
\end{minipage}\tabularnewline
\bottomrule
\end{longtable}

\textbf{3.1. Rheumatoid Arthritis} RA is a heterogeneous, enfeebling,
systemic AD. This chronic ailment pertaining to musculoskeletal pain,
prolonged morning stiffness, inflammatory alterations of the tissues of
synovial joints, cartilage and bones, often resulting in erosion of
bones and subsequently, complete destruction of joints, if not treated
on time . The internal extra-articular organs like skin, eyes, lungs,
heart, kidney, and blood vessels are also affected by this symmetrical
AD . People afflicted with RA range from 0.24\% to 1\% globally . It is
predominant in women compared to men and has increased prevalence in the
age group of 50-65 years . The emergence of non-communicable diseases
have become a leading cause of mortality worldwide and RA is one of
them. Both developed and low-middle income countries (LMIC) are severely
affected by these diseases . RA being a complex AD, the pathophysiology
is regulated by several inflammatory markers and immunogenic proteins. B
lymphocytes, T lymphocytes and macrophages predominantly contribute to
the progression of the disease . These autoreactive B cells induce the
secretion of cytokines like tumor necrosis factor-\selectlanguage{greek}α \selectlanguage{english}(TNF-\selectlanguage{greek}α\selectlanguage{english}),
interleukin-6 (IL-6), IL-12, IL-23, and IL-1\selectlanguage{greek}α \selectlanguage{english}in the diseased tissue.
Another cytokine, receptor activator of nuclear factor \selectlanguage{greek}κ\selectlanguage{english}B ligand (RANKL)
has been found to show enhanced production from memory B lymphocytes in
peripheral blood, synovial fluid and affected tissue of patients. This
cytokine is responsible for bone resorption as it binds to its receptor,
stimulates differentiation and activation of osteoclasts . B lymphocytes
are also responsible for the secretion of rheumatoid factors (RF) and
anti-citrullinated protein antibodies (ACPA) .\textbf{Figure 3 -}
\emph{Detailed immune regulation and miRNA networks involved in RA
proliferation. Illustrative representation of multifaceted roles of mast
cells secreting several proinflammatory interleukins like IL-6, IL-1 and
tumor necrosis factors leading to osteoclast maturation and subsequent
bone degradation}The activation of T lymphocytes are stimulated by both
B cells and macrophages. Synovial T cells have been reported to secrete
cytokines like, IL-15, IL-7, IL-13, IL-4, IL-2, basic fibroblast growth
factor, epidermal growth factor and these cytokines have a major
contribution in the etiology and pathogenesis of the ailment .
Macrophages, in the early stages of the disease, are known to stimulate
T cells and enhance the production of IL-1\selectlanguage{greek}α, \selectlanguage{english}IL-1\selectlanguage{greek}β, \selectlanguage{english}and Matrix
metalloproteinases (MMPs) . The inflammatory mediators secreted by the
autoreactive immune cells interact with neurons, and neuroglia and
result in neurogenic inflammation . RA patients are often broadly
classified into ACPA-positive and ACPA-negative. These two patient types
have very different pathophysiology, ACPA-positive being a more
clinically aggressive-phenotype. Citrullination is categorised as a
post-translational modification which results in the synthesis of a
polar (neutral) citrulline from a positively charged arginine and is
also aided by Ca2+-requiring enzyme peptidyl arginine-deiminase (PAD).
The genetic and epigenetic factors interact and trigger the production
of ACPA in diseased individuals. Environmental factors like smoking,
inhalation of nanosized silica or silica dust may trigger mucosal-TLRs
which activates Ca2+-dependent PADs and also antigen presenting cells
(APCs) like dendritic cells and B lymphocytes . miRNA-117-5p expression
is seen to be reduced in chronic RA. This miRNA specifically targets the
JAK-STAT pathway and downregulates the IL6 expression. Similarly,
several miRNAs acts as a biomarker and can be detected from the synovial
fluid or tissue in RA patients. miRNA-34a is regulated by NF-kB family
of cell signaling molecules, which are further activated by inflammatory
cytokine molecules . miRNA-29a acts as an anti-inflammatory marker in RA
fibroblast-like synoviocytes (RA-FLSs). The drop in miR-199a-3p
expression contributes to local hyperplasia. miRNA-375 in RA-FLSs
exhibits a positive effect on synovial pathogenesis that occurred as a
result of canonical Wnt signaling inactivation, thereby influencing the
progression of the disease and severity of the condition . Exosome
secreted miRNAs are important biomarkers and are vital targets for
developing therapies to treat RA. According to a study by Cunningham et
al. eight serum miRNAs viz., miRNA-126-3p, let-7d-5p, miRNA-431-3p,
miRNA-221-3p, miRNA-24-3p, miRNA-130a-3p, miRNA-339-5p, let-7i-5p are
found to have enhanced expression in RA afflicted individuals compared
to that of healthy people . Exosome derived miRNA-486-5p from synovial
tissue is associated with tumor initiation or suppression in a number of
cancers and also pulmonary fibrosis. miRNA-486-5p secreted from the
exosomes of RA Fibroblast-like synoviocytes (RA-FLS-Exo) has been
reported to promote osteoblast differentiation in RA patients by
decreasing the expression level of Tob1 gene and triggering the bone
morphogenetic protein (BMP)/Smad pathway . Fibroblast-like synoviocytes
are known to be responsible for cartilage destruction and maintenance
and progression of inflammation in RA patients. Mesenchymal stem cell
(MSC)-derived exosomes are evident to exhibit immunosuppressive effects
like suppressing B and T lymphocytes. miRNA-320a is found to have very
low expression levels in RA and is known to have anti-proliferative
effect and increases the apoptotic death of FLSs by downregulating
MAPK/ERK1/2 signaling pathway . There are
CD\textsuperscript{4+}CD\textsuperscript{25+}Foxp\textsuperscript{3+} T
cells also called regulatory T lymphocytes or Treg cells. These cells
are known to inhibit the autoimmune response found in RA. Patients
non-respondent to disease-modifying anti-rheumatic drugs (DMARDs, or
Methotrexate) are often treated with biological DMARDs or immunotherapy.
Increasing the number of Treg cells has demonstrated a reduction in the
pro-inflammatory responses. Stimulation of Treg cell-specific targeted
gene proliferation induced more and more production of Treg cell which
slowed the disease progression and proved itself to be an important
treatment for ADs .\textbf{3.2. Diabetes} Diabetes is a complicated and
persistent clinical condition requiring continuous biomedical support
and preventive measures which is just not concerned about glucose
management . Diabetes may be classified by three conditions namely, Type
1 Diabetes (T1D) and Ttype 2 Diabetes (T2D) and gestational diabetes .
T1D out of the above is concerned with an autoimmune abnormality wherein
the \selectlanguage{greek}β-\selectlanguage{english}cells producing Insulin in the pancreas are destroyed . Relative
insulin deficiency in T2D is predominantly impaired by \selectlanguage{greek}β-\selectlanguage{english}cell activity
of the pancreas and resistance to the action of insulin in specific
organs . The occurrence of diabetes in adults varying in the age group
of 21 to 80 over the world was predicted to shoot upto 10.6\% (536.7
million) in 2021 and 12.3\% (783.3 million) in 2045 . Small endogenous
miRNAs are predisposed to control cellular cycles, proliferation,
differentiation, and apoptosis by inhibiting the biogenic molecules that
control these processes, such as RNA transcripts, or by degrading mRNA .
According to various research groups, miRNA-375 was found to be
upregulated, impacting the beta cells that secrete insulin along with
other miRNA molecules such as miRNA-29a, miRNA-29b, miRNA-200, and
miRNA-7 . A cross-sectional nested, case-control based research study
was carried out by Barutta et al. to look at the differential expression
of miRNAs in the blood samples of patients suffering from T1D.. A
considerable upregulation of the miRNAs miRNA-140-3p, miRNA-574-3p,
miRNA-139-5p, miRNA-106a, miRNA-17, miRNA-486-3p, miRNA16, miRNA-222,
and miRNA-885-5p was found . Children with new-onset T1D were found to
have blood samples significantly overexpressed miRNA-197. It was also
claimed that miRNA-197 can accurately predict residual beta-cell
functioning . miRNA-155, miRNA-92a, and miRNA-126 were all noticeably
downregulated in the blood samples of T1D patients . Additionally,
diabetes is frequently characterized by endothelial homeostasis, which
is maintained by miRNA-126. Additionally, miRNA-126 regulates
endothelial inflammation in individuals with micro/macrovascular
problems related to diabetes, establishing a connection between these
issues and reduced levels of miRNA-126 . Patients suffering from T2D had
shown greater levels of miRNA-29a in their blood. It was determined that
miRNA-29a overexpression inhibits glucose absorption by stimulating
insulin, eventually leading to insulin resistance. Another study
involving plasma samples from T2D patients to look into the
dysregulation of miRNA-34a found that miRNA-34a was highly elevated and
connected to senescence or death in pancreatic cells with a decline in
SIRT1 activity. miRNA-130b was shown to be severely reduced in the blood
samples that were collected from the affected individuals along with
high urine albumin-to-creatinine ratios (UACR) in a research that
included 327 T2D patients with different levels of UACR . Additionally,
it was shown that blood levels of miRNA-130b had a bad correlation with
HbA1c and HIF1- levels. Furthermore, the serum miRNA-130b level was
closely correlated with insulin resistance and blood glucose levels in
T2DM. Evidences suggest that miRNA-214-3p and miRNA-27-3p might serve as
potential T2D biomarkers comes from reports of their downregulation in
whole-blood samples from T2D patients as well as in a population with
T2D risk factors . miRNA-26a in pancreatic beta cells has successfully
reduced Type 2 Diabetes by increasing peripheral insulin sensitivity and
maintaining beta cell activity . An alteration to the daily routine,
furthermore following a holistic diet, biomedical or surgical
therapeutic procedures, or considering a combination of these methods
can lead to diabetes remission. Lifestyle changes that affect daily
activities linked to nutrition and exercise have health impacts that go
well beyond those that are specifically relevant to diabetes
.\textbf{3.3. Multiple Sclerosis} MS is categorized as an
auto-immunogenic inflammatory disease inducing persistent demyelination
in the central nervous system (CNS). According to a study conducted
between September 2019 and March 2020, it was statistically estimated
that 2.8 million individuals across the globe suffer from MS
approximately 35.9 per 100,000 population . In younger individuals, MS
is the predominant contributor to atraumatic neurological impairment .
The fundamental clinical features of MS include several foci which are
found to be dispersed across the white matter which reverts back
throughout the illness's progression time and again . The etiological
factors that lead to the onset of MS include T-cell-mediated immune
responses that trigger cytokine release , alter the barrier permeability
between the brain and cerebrospinal fluid , axonal inflammation, gradual
demyelination and a rise in the pro-inflammatory miRNAs and its relevant
hallmarks. Macrophages, followed by CD8+ T-cells are significantly
observed in the influx, along with a lesser number of CD4+ T cells, B
cells, and plasma cells. Also, the lymphocytes that majorly contribute
to the progression of MS are Th1 and Th17 . Diverse genetic, epigenetic,
microbiological, and ecological variables aid the pathogenesis of MS.
miRNAs are quintessential epigenetic phenomena that regulate abnormal
cellular events during the prognosis of the disease. The key purpose of
miRNA is to monitor and control the translation of genes, either by
suppressing translation or by cleaving the target mRNA. In MS, miRNA
expression profiles are altered in CNS lesions as well as in the immune
system, which has significant implications on gene expression in the
array of cell types and ultimately promotes the disease . In the study
by Baulina et al., a range of miRNAs having altered expression during
the disease prognosis from varied sources were outlined that including
miRNA-155, miRNA-146a, miRNA-181c, miRNA-326, miRNA-346, miRNA-17,
miRNA-320a, miRNA-34a, miRNA-340, miRNA-132, and their target sequences
. Based on multiple data identified, miRNA-155 is regarded as the most
potent promoter of inflammation and is crucial for the pathophysiology
of the disease, by virtue of myeloid cell polarization to a
morphological and active pro-inflammatory type. Upregulation of
miRNA-155 has been detected in the cellular blood samples of individuals
affected by MS which may be a sign of a severe disease progression.
miRNA-155 modulates the MS risk genes PIK3R1 and PIK3CA which encodes
for proteins belonging to the phosphoinositide 3-kinase (PI3K) family.
Dysfunction of the PI3K family leads to oncogenesis, neurological and
immune disorders, and demyelination in MS . Dysregulation of
miRNA-3606-3p in patients of systemic sclerosis is a prominent biomarker
and can lead to the reduction of TGFBR2 expression . This can lead to
the severity of the diseased condition. However, an upsurge in miRNAs
like miRNA-126 and miRNA-139-5p in systemic sclerosis have found a
correlation to the inflammatory cytokines and signaling molecules like
IFN-B . With reference to a study on miRNAs to ascertain their
correlation with gadolinium-enhancing (Gd+) lesions for evaluating their
utility as MS activity biomarkers, it was observed that peripheral blood
mononuclear cells (PBMCs) of MS patients had overexpression of
miRNA-146a/b in comparison to the control. They hypothesized that this
elevation was particular to the critical stage of MS and contributed to
the proliferation of Th cells, which are effective in the aggravating
mechanisms that occur in the CNS of MS patients. First, activated T
cells traverse through the blood-brain barrier from the periphery into
the CNS. Cytotoxic CD8+ T cells can directly cause axonal damage, while
CD4+ T cells aid in retaining the CNS inflamed. Furthermore, regulatory
T cells (T reg), that sustain immune tolerance by inhibiting effector T
cells, carry out this control through the secretion of miRNA-based
exosomes, a route for gene silencing . miRNA-20a-5p and miRNA-20b-5p
were shown to be key regulators of 1,000 targeted genes according to
database analysis of miRNA-mRNA interactions 46, indicating that they
may be key players in MS pathogenesis . By analyzing the association of
the expression of miRNAs and its potential target genes, the involvement
of miRNAs in the disease prognosis has been established. Nevertheless,
the exact functioning of miRNA in the pathogenesis of MS is not well
identified. New medications and therapeutic modalities that effects
miRNAs will undoubtedly emerge with the development and use of new
advances in research, providing the groundwork for the eventual
eradication of different immunogenic disorders.\textbf{3.4. Systemic
lupus erythematosus} SLE is identified as a persistent inflammation
associated with auto-immunogenic ailment, caused by the progressive
decline of resistance to the self--antigens, stimulation of
dysfunctional immune T cells and B cells, synthesis of autoantibodies
(auto-Abs), and altered cytokine activity. Due to the advent of complex
molecular associations between epigenetic triggers, unbalanced hormone
levels, genetic susceptibility, epigenetic control, immune status, and
other unknown factors, SLE is strongly related to the downregulation of
the immunological responses both innate and adaptive . miRNAs are
significant regulators of ADs, where miRNA-146a and miRNA-155 are
demonstrated to be crucial in the pathogenesis of SLE. miRNA-146a was
found to be adversely correlated with the expression of the type I IFN
regulatory signaling system. The toll-like receptor (TLR)-myeloid
differentiation factor 88 (MyD88) pathway, which includes IRAK1 and
TRAF6, was proven to be a critical regulator of signaling pathways .
miRNA-155 is verified to upregulate the alteration of Treg phenotype in
MRL/lpr mice by modifying the CD62L expression . miRNA-17 is associated
with the production, division and activation of immune B cells, T helper
cells namely Th1, Th2, Th17 . In a study conducted by Kaga et al.,
miRNA-17 production was found to be more in the healthy control as
compared to that of the SLE patients and it was also observed that
miRNA-17 has an antagonistic relation with the interferon alpha mRNA
that may play a role in the etiology of the disease . miRNA-142-3p was
discovered to be considerably downregulated in SLE patients.
miRNA-142-3p, which is mostly produced in hematopoietic stem cells, has
been identified to be crucial for the immune response, particularly in
macrophages and Regulatory T cells . miRNA-20a downregulation was linked
to lupus nephritis and vascular thrombosis . miRNA-125a comprises the
inflammatory chemokine pathway. Recent studies have demonstrated that
miRNA-125a targets KLF13 in SLE, which results in increased production
of the inflammatory chemokine RANTES . miRNA-15a specifically has a
deleterious impact on the B-10 subpopulation, and miRNA-15a reduction
may help treat SLE . In a scientific study designed by Yan et al.,
miRNA-124-3p and miRNA-377-3p were highly expressed in PBMCs and serum
collected from patients affected by SLE in comparison to the healthy
controls . miRNA-21 is upregulated due to the hyperactivity of immune T
cells whereas miRNA-7 is related to the overproduction of B cells and
autoantibodies. miRNA-34a is responsible for the collapsing of the
immunological tolerance .\textbf{3.5. Inflammatory bowel disorder} The
term ''IBD'' corresponds to a group of relapsing, chronically
inflammatory gastrointestinal illnesses, notably Crohn's Disease and
Ulcerative Colitis . Over the past decade, as lifestyles and dietary
practices became more westernized, IBDs expanded around the world .
According to experimental data, excessive consumption of certain
macronutrients in the modern food habit triggers an inflammatory
response in colon by preying on innate immune sensors and disrupting the
metabolism of gut microbes. Even though incidence is stabilizing in
western nations, the burden is still significant since prevalence
exceeds 0.3\%. These findings underline the need for research into IBD
prevention and advances in healthcare systems to manage this difficult
and expensive condition . Immunometabolism regulates vulnerability to
intestinal inflammation, and the risk IBD genetically. This partially
influences metabolism and stress related signaling of innate immunity .
Some micro-RNAs, including miRNA-101, miRNA-515-5p, miRNA-623,
miRNA-325, miRNA-876-5p, miRNA-1224-5p, miRNA-1226-5p, and miRNA-1253,
have been found to invade bacterial membrane and subsequent regulate
gene transcription. This promotes bacterial proliferation and mobility,
which in turn affects the population and diversity of the gut
microorganisms . By reducing the over-expression of inflammatory
cytokine receptors like IL7R and IL17RA as well as signal proteins like
GP130, miRNA-31 reduced the inflammatory response in a mouse model of
Dextran Sodium Sulfate -induced colitisl, which Tian et al., 2019 found
to be hyper-expressed in tissues from patients suffering from IBD.
Another study using the DSS mouse model revealed that miRNA-155 binds to
SHIP-1 mRNA directly, resulting in a considerable drop in SHIP-1 levels,
which control cell membrane trafficking . The most often researched
miRNAs in relation to IBD appear to be miRNA-21, miRNA-155, and miRNA-31
. With links between miRNA-21 and IBD being reproduced in numerous
research and functional relevance being shown in mice models of IBD,
miRNA-21 is arguably considered to be prevalent in IBD. miRNA223
regulates innate immunity in intestinal inflammation . miRNA 214-3p and
miRNA 206 activate the NF-kB pathway and promote intestinal inflammation
. Some members of the regenerative gene (REG) family, I, including (REG
I\selectlanguage{greek}α, \selectlanguage{english}REG I\selectlanguage{greek}β \selectlanguage{english}and REG IV) are expressed in Crohn's disease and ulcerative
colitis and have a role in proliferative mucosal components in IBD.
Through the downregulation of miRNA-24, LPS caused REG IV expression in
human intestinal epithelial cells. Intestinal epithelial cells'
RAGE/TLR4 receptors controlled the LPS signal. Damaged intestinal cells
were replaced under IBD circumstances by intestinal cell growth. Since
REG IV is a growth factor for intestinal epithelial cells, it could help
to multiply intestinal cells to restore intestinal mucosa .

\textbf{Epigenetic networks underlying AD progression}

Epigenetic parameters have a great influence on cell signaling,
differentiation, gene expression and morphogenesis of cellular
development in an organism. Hence, they have an essential role to play
in the onset of a disorder and its related genetic background . There
are various epigenetic factors which are common in various disorders,
due to their long lasting effect on the nature and progression of the
genetic regulation in a diseased condition. The mechanisms like DNA
methylation and modification of histone proteins can contribute to the
pathogenesis of various ADs . These epigenetic parameters can correspond
to the initiation and prolongation of inflammation inADs. It has been
observed in various studies that miRNAs play a centric role as
epigenetic regulators and prevent the progress of inflammation . DNA
methylation is a process in which the methyl group is removed from the
methyl cytosine structures, which results in the loss of structural and
functional entities in various metabolic pathways. Ten-eleven
Translocation (TET) enzymes act as DNA methylases and take part in the
process of hypo or hyper methylation . Histone modifications act as
major epigenetic markers. They are involved in transcriptional
upregulation or downregulation, chromosomal compaction and DNA repair
techniques. One of the major histone modifying enzyme inhibitors, is
histone deacetylase inhibitor (HDACi) which is involved in the changes
that contribute to the growth and advancement of ADs . The interplay and
corresponding effects of the epigenetic regulation of miRNA is an area
of ongoing research. Epigenetic therapies is a new area of clinical
advancement that helps in the reversal of epigenetic alteration or
aberrations . Corresponding researches are being done in the line of the
development of epigenetic modifying drugs in conjugation with adjuvant
therapy. This can be used in T cell polarization and control of the
inflammatory processes.\textbf{4.1. Rheumatoid Arthritis}RA is a disease
caused by loss of autoimmunity, that encompasses synovial fluid
hyperplasia and inflammatory joint degradation . The inflammation in RA
is mediated by several factors like ACPAs which further result in
structural damage of the bone joints . The dynamic expression of the
diseased condition in the patients is due to the epigenetic regulation
of the genes directly associated with the immune system. The synovial
fibroblasts consist of a unique methylation pattern, which varies during
the course of gene progression and consequently affects its severity .
L1 (LINE) is hypomethylated and indirectly induces the surge of
cytokine, growth factors, receptor and inflammatory co factors . Local
hyperinflammation spike is noticed in the RA patients due to the
hypomethylation of the CpG islands associated with the IL6 promote gene.
This leads to the overexpression of IL6 and related proinflammatory
cytokines . Recent research has verified that epigenetically regulated
gene networks in the peripheral blood mononuclear cells consequently
result in the severity regulation of RA . The synovial cells modify
themselves in such a way that they start to show tolerance toward the
apoptosis. This in turn triggers the inflammatory cascades in the
pathogenesis pathway of RA development. This is majorly induced by the
histone modification and hypermethylation of the NFkB promoter gene .
The histone modifications like acetylation, methylation, citrullination,
phosphorylation and ubiquitination contribute to the changes in the
transcriptional factors, making the chromatin available for gene
expression. The different histones that take part in the RA pathogenesis
and histone modification are - H3K9, H3K14, H4K5, and H4K16 (for
acetylation), H2BK5, H3K4, H3K36, and H3K79 (for methylation), H3S10 and
H3S28, H4S1 (for phosphorylation) and H2BK120 (for ubiquitination) .
These developments can in turn be used as biomarkers and contribute to
the therapeutic application of this disease.\textbf{4.2.
Diabetes}Autoimmune dysfunction of pancreatic \selectlanguage{greek}β \selectlanguage{english}cells leads to the
development of type I diabetes. Its progression is monitored on a wider
scale as it is widely affected by the epigenetic regulation of the
various related genes . Glucose and insulin levels in the blood, affect
the degree of methylation. They regulate the homocysteine metabolism,
which further modulates the DNA methylation by DNMTs . These epigenetic
factors contribute in the glucose intolerance, due to the alteration in
the methionine metabolism. The immunogenic response is seen to be
related to the DNA methylation of several regulator genes. FOXP3
promoter region of the CD4+ is hypermethylated in the case of latent
autoimmune diabetes in adults (LADA) patients . The INS gene promoter in
diabetic patients is seen to be hypomethylated, which has consequently
culminated in the release of inflammatory cytokines like TNF-\selectlanguage{greek}β , \selectlanguage{english}IFN\selectlanguage{greek}γ,
\selectlanguage{english}IL6 and IL-1B . The histone modifications are mainly regulated by
histone-acetyltransferases (HATs) and histone-deacetylases (HDACs),
which regulate the process as transcription coactivators. RNA
modification and ncRNA regulation are also noticed in the aged group of
diabetic patients, which also attributes in cellular senescence and post
transcriptional modification . Miao et al have documented the histone
modification of H3K9Ac, H4K16Ac, H3K4me3, H3K9me2,3, H3K27me3 genes in
the diabetic pathway . As these genes are closely located to the DQB1
and DRB1 genes. This leads to a surge in the transcription process in
the monocytic cell line, thereby triggering the immunogenic pathway .
One of the most significant autoimmune markers of the progression type I
diabetic condition is the reduced expression of the H3 histone
acetylation that develops a consequent the expression of GAD
autoantibodies .\textbf{4.3. Sys}MS is a neurodegenerative, inflammatory
disease that results in physical and cognitive impairment. The
pathogenesis primarily roots from the self intolerance towards the
neuronal antigens. Most patients develop relapsing-remitting MS (RRMS)
and others develop primary progressive MS (PPMS). In case of PPMS, DNA
methylation of the primary epigenetic regulation that controls the
progression of MS. Studies are being conducted to identify and analyze
the differentially methylated CpG sites of CD4+ T lymphocytes genome .
The progression and mortality of the disease depends upon the
interaction and interplay of the genetic and environmental factors,
combined . The T cell exhibits autoreactivity that causes demyelination
which consequently leads to an inflammatory cascade in the central
nervous system. Studies have shown that the hypomethylation of promoter
region peptidyl arginine deaminase (PAD) -II contributes in the
citrullination of myelin basic protein (MBP) . This may lead to
irreversible molecular changes that can cause insatiable and chronic
inflammation. \emph{ATXN1} gene which encodes for polyglutamine protein
ataxin-1, which in turn protects the system from the demyelination
event. Studies have shown that in the event of hypomyelination of
\emph{ATXN1} gene, the pathogenetic mechanism scales up in the cellular
and molecular regulation of MS . Thelper (Th) 17 and T regulatory (Treg)
molecular balance has an important role to play in the progression and
dynamics of MS, due to their epigenetic dynamic nature. Histone
modification of forkhead Box P3 (FOXP3)- cell-type-specific regulatory
regions (CSRs) and RAR related orphan receptor C (RORC)-CSRs are
polarized Th17 cells are regulated by estrogen in pregnant women
suffering with MS, during their third trimester. A recent study shows
the correlation of epigenetics and disease progression via epigenomic
and transcriptomic profiling, where they have tried to compare
demyelinated MS lesions and normal-appearing white matter (NAWM).
Human-iPSC-derived oligodendrocytes were epigenetically edited to
understand the region-dependent hypermethylation of MBP which is
responsible for the myelination and axonal development . During the
pathogenesis of MS, antibodies are formed against different histone
proteins like H2b, H1, H3, H4, MBP, and DNA, that result in the
hydrolysis of H2A histone. This cross reactivity between the abzymes and
histone proteins can result in the aggravation of the disease condition
. Pedre et al. reported the increased expression of H3 histone
acetylation in chronic MS patients, which has also been seen as a side
effect to in turn increase the transcription pattern of the inhibitors
of oligodendrocytes and histone acetyltransferase (HAT) gene expression
in MS patients . The acetylation and deacetylation balance is hindered
during the early phase of MS progression, which can further modulate
that severity of the disease .\textbf{4.4. Systemic Lupus
Erythematosus}Autoantibodies and dysfunctional antigen presenting cells
are the classical characteristics of SLE. The pathogenetic pathway of
SLE is still a matter of debate, and has been seen to be largely
affected by the epigenetic and environmental regulation over the
patient's immune system . The large network in the immune system
contributes to lupus pathogenesis. Regulatory factor X (RFX) 1 acts as
an immune-suppressor and aggrevates the DNA methylation of the promoter
region of CD70 and CD11a . This promotes autoimmune response . According
to Hedrich et al, CpG-DNA methylation patterns are highly conserved and
close to the promoter region of IL7F. It is observed that the SLE
patients show low degree of methylation in the T- lymphocytes, as drawn
parallels with the study on healthy individuals . In other recent
findings, it has been seen that there is an increment in the levels of
5-hydroxymethylxytosine (5-hmC). This is due to the upregulation of ten
eleven translocation (TET)-2 and TET-3 factors, which are one of the
prominent DNA methylases and contribute in the enzymatic conversion of
5-methylcytosine (5-mc) into 5-hmC . In several SLE patients, DNA
hydroxymethylation pattern is observed in the signaling pathway genes,
which are then consequently related to the immune response genes and
factors like SOCS1, NRF2F6 and IL15RA. The methylation product - 5-hmC
and its aberrant regulation may contribute in the therapeutic
application of SLE . The Th17 cell maturation takes place through the
epigenetic modification if the transcriptional factors associated with
it, in the SLE patients. The STAT3 pathway plays a pathbreaking role in
the modification and modulation in T cell maturation and progression of
SLE pathogenesis . Histone modifications in the SLE is reported in the
form of trimethylation of histone H3 in H3K27me3, which contributes to
the increase of H3K27me3 in the CD4+ T cells of the SLE patients. This
trimethylation is made possible with the help of enhancer of zeste 2
polycomb repressive complex 2 subunit (Ezh2). The cumulative effect of
these histone modifications may lead to the t cell lineage development
in the SLE patients, which may attribute to the pathogenesis of the
disease . Recent research and studies have shown and possibility of 3D
genome alteration with respect to the progression of disease. The study
included testing the viability of cells when subjected to histone
modification of H3K27ac, H3K4me1, H3K4me3, SP11 knockdown and
transcription factor motif enhancement. These studies indicate the
indirect effect of epigenetic regulation over the genome structure and
function .\textbf{4.5. Inflammatory Bowel Disease}IBD is an autoimmune,
chronic, recurrent gastrointestinal disorder. Several factors like
environmental factors, gut microbiota, immune dysregulation contribute
to the advancement and cause of this disorder. Pathogenesis of this
disease can not be clearly elucidated as it can be manifested into
colorectal cancer, fistula development or stenosis syndrome . The IBD
has two twin forms- ulcerative colitis (UC) and Crohn's disease (CD).
IBD related genes undergo methylation and histone modification for
reshaping the disease progression . Mucosal methylation of HRAP2, FANCC,
GBGT1, DOK2 and TNFSF4 in the progressive IBD, may cause a significant
progression and severity of the disease . There are counter active
findings which are noticed in the case of CD patients where GBGT1,
IGFBP4, FAM10A4 genes are hypermethylated and in case of UC patients,
IFITM1 is hypomethylated. This helps us to regulate and differentiate
between the two subtypes. However, there is also the case of leukocyte
methylation in the CD sub type of IBD . At the molecular level, most
methylations occurring in the case of this disease, has a close
proximity to GWAS risk genes, like CARD9, CDH1, ICAM3 . According to a
group of British scientists, the region of the gut that is more prone to
DNA methylation of the intestinal region. Major histone modifications
are found to be abundant in the following histone proteins - H2BK5ac,
H3K36me1, H3K4me3, macroH2A and Rme2sym, in the case of CD patients, as
compared to the healthy people. These modifications can be consequently
analyzed with the presence of natural killer (NK) . This accounts for
the epigenetic biomarkers for the progressive and detectable approach of
IBD .

\textbf{Diagnostic Measures using miRNA as a Biomarker for AD}

Globally, AD affect nearly 8\% of the population, which include
approximately 80 disorders and exhibit several geo-epidemiological
variations; making it the fourth leading cause of mortality worldwide,
after cancer and heart disease . It has been found that women are 2.7
times more susceptible for developing AD as compared to men . Hence,
rapid and early diagnosis of AD is gaining prime importance in the light
of improving the quality of patients' lives . Traditionally, the
diagnosis of AD has been limited to the detection of autoantibodies in
patients' samples through western blotting, indirect immunofluorescence
and ELISA-based commercial assays . However, the pitfalls of such
techniques include expensive antibodies, longer incubation time, the
need for sophisticated instruments and complex procedures . Moreover,
the accuracy and sensitivity of these techniques is not upto the mark .
To overcome these limitations, a more sensitive and reliable technique
is needed for the diagnosis of AD. Recently, miRNAs have proven to be
effective non-invasive biomarkers for the diagnosis and prognosis of a
disease, to study its progression and analyse the drug responses
following treatment . This is because the abnormal miRNA expression
profile is strongly correlated with diseased states and research shows
that they are present in almost all biofluids . Despite the advent of
high-throughput technologies, the detection of miRNA comes with a number
of predicaments. Firstly, they are of short length
(\textasciitilde{}15-25 nt), making it difficult to develop a highly
specific probe. Secondly, distinct miRNAs harbour homologous sequences
which are prone to give false-positive results due to cross
hybridization . Conventional approaches detecting miRNA include
qRT-PCR,, northern blotting, enzymatic assays, oligonucleotide
microarrays, cloning and sequencing which come with several drawbacks
such as limited selectivity, low sensitivity, and ineffectiveness in
detecting extremely low miRNA concentrations in blood samples . All
these molecular techniques lack an integrated transducer element and are
amplification-based . In addition to being time-consuming and laborious,
these techniques do not take into account the susceptibility of miRNA to
degradation and hence give rise to bias, unreliable results .
Furthermore, these detection techniques do not encompass multiplexed
analysis, in vivo analysis, detecting circulating miRNAs and specificity
towards single-nucleotide, all of which are indispensable in clinical
settings . With the breakthrough of nanotechnology in medicine,
amplification-free biosensors have drawn considerable attention from the
academia as well as the industry . A biosensor is an integrated
analytical device consisting of mainly three components: (i) a
bio-recognition element such as enzymes, antibodies, DNA, RNA,
aptamers,etc. (ii) a transducer element which detects a biological
response and converts it into an electrical signal and (iii) a signal-
processing system that consists of an amplifier, a processor and a
display unit . This analytical device is highly effective in
quantitative or semi-quantitative detection of an analyte . It
incorporates the use of specific DNA probes which have complementary
sequence with target miRNA with highly adaptable transducer sensing
system . This enhances their multiplexing potential, allowing them to
provide rapid, label-free, extremely selective as well as sensitive
real-time detection of miRNA with respect to point-of-care (POC) aims
for clinical applications . On the basis of the type of signal
transducers used, biosensors for detecting miRNA are broadly classified
into optical and electrochemical biosensors . Optical biosensors are
highly effective in detecting biomarkers as they transduce the
absorbance or fluorescence signals of an optically-active reporter
linked to a nucleic acid probe when hybridized to the target miRNA .
This class of biosensors have a fairly simple and feasible design,
wherein the bio-recognition elements are immobilized on the surface of a
signal detection platform by either physical adsorption, covalent or
electrostatic bonding . The detection platforms are fabricated with
nanomaterials such as graphene oxide (GO), gold nanoparticles (AuNP),
and quantum dots (QD) . AuNPs are highly compatible with nucleic acids
as well as proteins, provide adequate surface area to volume ratio, have
excellent fluorophore quenching ability and exhibit good LSPR absorption
in the visible range . Surface Plasmon resonance (SPR) is another robust
and sophisticated optical method for fast and direct miRNA detection .
It measures the shifts in refractive index when an analyte forms a
complex on the surface of the electrode . Surface plasmon resonance
Imaging (SPRi) is a label free hybridization-based method and can
measure miRNA concentration for as low as 2 pM in less than 30 minutes .
Their limit of detection (LOD) is low as far as complex biological
samples are concerned . Several strategies are employed to enhance its
sensitivity such as the use of nanoparticles like AuNPs coupled with DNA
sandwich, GO--AuNPs hybrids, hybridization chain reaction method,
hairpin assembly, streptavidin-biotin approach, etc . Surface-enhanced
Raman scattering (SERS) is employable for rapid and accurate detection
of miRNA but is not suitable for medical diagnostics due to low
sensitivity . Another biosensing strategy under the optical methods is
fluorescence detection. Examples include Ag nano-cluster DNA probes, GO
with dye-labelled probes, carbon nanoparticles, magnetic beads, etc .
Polyaniline-gold (PANI-Au) nanomaterial and ruthenium (Ru)-based
electrochemiluminescence immunosensors have also been designed for label
free, highly sensitive quantification of miRNA . Overall, SPR-based
biosensors are commonly employed optical methods for diagnosis of AD due
to their high selectivity, high efficacy, affordability, and
reliability. However, biosensors working on the principle of
electrochemiluminescence demonstrate highest sensitivity .
Electrochemical biosensors are the most predominantly used sensors for
the diagnosis of AD . The transducer is a solid electrode which is
sensitive to changes in electrode properties caused by the hybridization
between the immobilized nucleotide probe and the complementary sequence
. In these, the transduction element is often Au, indium tin oxide,
glassy carbon, and graphite, the sensitivity of which is enhanced by
incorporation of a variety of nanoparticles, nanowires and enzymes . In
contrast to optical biosensors, electrochemical biosensors have simpler
electronic design, are inexpensive, and serve as excellent platforms for
point-of-care tests because of their easy-to-use miniaturized portable
integrated systems . This allows them to provide fast, accurate and
real-time quantification of analyte. These are further classified into
amperometric, impedimetric and voltammetric methods . The amperometric
and voltametric techniques measure changes in the current when a target
miRNA is hybridized to its complementary sequence; with the only
difference being that the current is measured at a fixed potential value
in amperometry, while the current is measured in a certain potential
ramp in voltammetry . Cyclic voltammetry (CV), linear sweep voltammetry
(LSV), differential pulse voltammetry (DPV) , and square wave
voltammetry (SWV) are different techniques under voltammetry . These are
further categorized as label-free biosensors if the redox reaction is
generated due to an electroactive nucleic acid base (adenine or guanine)
signals or enzymes such as duplex-specific nuclease; or as label-based
biosensors if the electrochemically active reporter species are
nanoparticles (Eg. Au,Ag, OsO\textsubscript{2}, or Ruthenium NPs) or
hybrid nanoparticles (Eg. GO--AuNPs, MoS\textsubscript{2} microcubes,
Au@NPFe2O3 nanocubes . Electrochemical impedance spectroscopy (EIS) is
another robust, label-free, and well-established technique for
quantification of miRNA . It is the most practical method to study
reaction mechanisms, biofunctionalization, nanostructure formation and
hybridization . EIS is more efficient and biocompatible as compared to
amperometric and voltammetric methods since it is less destructive and
more sensitive .\textbf{Figure 4} -- \emph{Illustrative depiction of
biosensor construction deploying miRNA signature molecules corresponding
to respective ADs using several biorecognition elements along with
assistive nanomaterials for eliciting robust signal amplification to
detect pathogenic miRNA indices.}Both optical and electrochemical
methods have their pros and cons in detecting miRNA with some giving a
much lower limit of detection and hence higher sensitivity than others .
However, selecting an optical or an electrochemical biosensor would
depend upon the experimental aim which would be different for research
and clinical purposes. In conclusion, biosensors offer unique advantages
over the use of traditional assays which makes them highly suitable POC
devices in the clinical diagnosis of AD . The incorporation of
nanoparticles in these biosensors have significantly brought down the
LOD to pM and fM range which is instrumental in the rapid and
early-stage diagnosis of AD. Further innovation is needed to develop in
vivo sensing platforms for AD . Table 2 lists down the different optical
and electrochemical techniques used for detecting miRNAs in RA,
Diabetes, MS, SLE and IBD, along with their references.\textbf{Table 2
-} \emph{Different techniques, their range and mechanism of detection of
miRNAs in different autoimmune diseases}\selectlanguage{english}
\begin{longtable}[]{@{}llllll@{}}
\toprule
\textbf{microRNA} & \textbf{Optical technique} & \textbf{Linear dynamic
range} & \textbf{Disease} & \textbf{Mechanism} &
\textbf{Reference}\tabularnewline
miRNA-21 & Fluorescence & 50 pM--1 nM & RA & Immobilized FAM-labelled
hairpin probes on AuNPs; amplification based on duplex-specific nuclease
&\tabularnewline
let-7a & Fluorescence & 10 fM--2 pM & RA & Helicase (RecQE) -assisted
hybridization chain reaction on graphene oxide (GO) platform
&\tabularnewline
miRNA-155 & Absorbance & 100 aM--100 fM & RA & DNA probe bound to
citrate-capped Au nanoparticles; target miRNA adsorbed on
polyethylenimine-capped AuNP surface &\tabularnewline
miRNA-15a & SPR (Surface Plasmon Resonance) & 5 fM--0.5 nM & RA &
Isolated Au islands on innovative chip installed on SPRi imager bordered
by hydrophobic fluoropolymer- CYTOP &\tabularnewline
miRNA-21, miRNA-155 & SPR (Surface Plasmon Resonance) & 10 aM--10 pM &
RA & SPR chip surface coated with antimonene nanosheets; amplification
due to interaction with AuNR-ssDNA &\tabularnewline
miRNA-155 & SERS (Surface Enhanced Raman Spectroscopy) & 1 fM--10 nM &
RA & SERS enhanced DSN amplification in DNA microcapsule using TB@CaCO3
blend &\tabularnewline
miRNA-21 & square wave voltammetry (SWV); electrochemical & 200 pM--1 fM
& T2DM & streptavidin-biotin interaction mediated deposition of AgNPs on
Au electrode &\tabularnewline
miRNA-155 & differential pulse voltammetry (DPV); electrochemical & 0.1
fM--1.0 nM & T2DM & Mo\textsubscript{2}C nanosheets depositied with
AuNPs based on catalytic hairpin assembly &\tabularnewline
miRNA-375 & square wave voltammetry (SWV); electrochemical & 10--30 fM &
T2DM & Immobilized miR-375 capture probe on Au electrode followed by
hybridization &\tabularnewline
miRNA-34a & electrochemical impedance spectroscopy (EIS) & 2--10 \selectlanguage{greek}µ\selectlanguage{english}g/mL &
T2DM & Immobilized ionic liquid (1-butyl-3-methylimidazolium
hexafluorophosphate) on activated pencil graphite electrodes
&\tabularnewline
miRNA-145 &
\vtop{\hbox{\strut Fluorescence}\hbox{\strut spectrophotometry}} & N/A &
MS & Hybridization chain reaction based formation of AgNCs in DNA
(highly fluorescent)/use of oligonucleotide hairpin probes
&\tabularnewline
miRNA- 23a, & & & & &\tabularnewline
\bottomrule
\end{longtable}

\selectlanguage{english}
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