Method of detecting conjunctival disease using ocular surface tissue, and aging biomarker

Patent metadata

Field	Value
Publication number	US-12365950-B2
Application number	US-201917252982-A
Country	US
Kind code	B2
Filing date	Jun 28, 2019
Priority date	Jun 29, 2018
Publication date	Jul 22, 2025
Grant date	Jul 22, 2025

Abstract

A method for detecting conjunctival diseases such as conjunctival MALT lymphoma, and an aging biomarker that serves as an indicator of the aging state of a subject are provided. The method for detecting conjunctival diseases comprises a step of comparing a microbial community structure of a microbiota in an ocular surface tissue specimen sampled from a healthy person with a microbial community structure of a microbiota in an ocular surface tissue specimen sampled from a subject to determine that the ocular surface tissue specimen of the subject has an indication of the conjunctival diseases. The aging biomarker a comprises bacterial species which belongs to the Corynebacteriaceae family or the Propionibacteriales family in an ocular surface tissue.

First claim

What is claimed is:

1. A method of detecting a conjunctival mucosa-associated lymphoid tissue lymphoma of a subject using microbiota of ocular surface tissue specimens from a healthy person and the subject, the method comprising:
(i) obtaining a first ocular surface tissue specimen from the healthy person and a second ocular surface tissue specimen from the subject,
(ii) performing a metagenomic analysis using a next-generation sequencer, on the first ocular surface tissue specimen and the second ocular surface tissue specimen so as to obtain sequence information of 16S rRNA genes of each bacterial species in each of the first ocular surface tissue specimen and the second ocular surface tissue specimen,
(iii) determining an abundance of a 16S rRNA gene of each of the bacterial species including at least one Delftia bacterial species in each of the first ocular surface tissue specimen and the second ocular surface tissue specimen by merging the sequence information of the 16S rRNA genes and taxonomically classifying merged sequences of each specimen so as to determine the bacterial species and the amount of each bacterial species contained in the first ocular surface tissue specimen and the second ocular surface tissue specimen; and calculating (a) an abundance ratio of each of the Delftia bacterial species present in the first ocular surface tissue specimen relative to all bacterial species present in the first ocular surface tissue specimen and (b) an abundance ratio of each of the Delftia bacterial species present in the second ocular surface tissue specimen relative to all bacterial species present in the second ocular surface tissue specimen,
(iv) comparing a first microbial community structure of a microbiota of the first ocular surface tissue specimen, which is the abundance ratio of the at least one Delftia bacterial species in the first ocular surface tissue specimen, with a second microbial community structure of a microbiota of the second ocular surface tissue specimen, which is the abundance ratio of the at least one Delftia bacterial species in the second ocular surface tissue specimen, and
(v) determining that the second ocular surface tissue specimen has an indication of the conjunctival mucosa-associated lymphoid tissue lymphoma
when the abundance ratio of the at least one Delftia bacterial species in the second microbial community structure is significantly higher than the abundance ratio of the at least one Delftia bacterial species in the first microbial community structure.

2. The method according to claim 1 ,
wherein the metagenomic analysis includes amplifying a part of the 16S rRNA genes of all bacterial species present in each of the first ocular surface tissue specimen and the second ocular surface tissue specimen to produce amplicons, sequencing the amplicons to obtain sequence reads, merging the sequence reads to obtain merged sequences, trimming the merged sequences to produce processed reads, clustering of the processed reads to obtain taxonomically classified reads.

3. The method according to claim 2 ,
wherein the abundance of the 16S rRNA gene of the at least one Delftia bacterial species is determined based on the abundance of the processed reads that correspond to the 16S IRNA gene of the at least one Delftia bacterial species present in the sequence information of 16S rRNA genes of the all bacterial species.

4. The method according to claim 2 ,
wherein the comparing comprises a linear discriminant analysis effect size analysis of the taxonomically classified reads.

5. The method according to claim 1 ,
wherein the subject on whom the method is practiced is a human who has been identified as having developed conjunctival mucosa-associated lymphoid tissue lymphoma, or as having a risk of developing conjunctival mucosa-associated lymphoid tissue lymphoma.

6. A method of detecting and treating a conjunctival mucosa-associated lymphoid tissue lymphoma of a subject, wherein the method comprises the method according to claim 1 , and
(vi) treating the conjunctival mucosa-associated lymphoid tissue lymphoma on the subject from which the second ocular surface tissue specimen, which has been determined to have an indication of the conjunctival mucosa-associated lymphoid tissue lymphoma, has been obtained.

7. The method according to claim 1 , further comprising:
measuring a pH of a tear fluid of the subject.

8. The method according to claim 1 , further comprising:
measuring an IgA concentration in a tear fluid of the subject.

Assignees

• Univ Osaka
• Otsuka Pharma Co Ltd

Inventors

• Nishida Kohji
• Hashida Noriyasu
• Iida Tetsuya
• Nakamura Shota
• Motooka Daisuke
• ASAO Kazunobu
• Ando Satoru

Classifications

• C12Q1/06

  Quantitative determination · CPC title

• C12Q1/6876

  Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes · CPC title

• C12Q1/6883

  for diseases caused by alterations of genetic material · CPC title

• C12Q1/689 Primary

  for bacteria · CPC title