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Research Article

Microsatellite instability and early onset colorectal cancer in an emerging economy: A study in an Indonesian tertiary hospital.

[version 1; peer review: 3 approved with reservations]
PUBLISHED 06 Mar 2025
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Abstract

Background

Colorectal cancer (CRC) is one of the most common cancers globally, ranking 4th in men and 2nd in women. While once rare in Asian countries, the incidence of CRC has increased in these populations, likely due to risk factors such as a Western diet, smoking, sedentary lifestyles, and aging. In Indonesia, early-onset CRC (EOCRC) has risen alarmingly, with a previous study reporting an annual percentage change of 1.98% from 2009 to 2019. Several studies have linked EOCRC with Microsatellite Instability (MSI), which is gaining attention for its role in CRC diagnosis and treatment. This study aims to explore MSI status in Indonesian CRC patients to better understand its role in the rise of EOCRC and its potential in CRC screening.

Methods

Fixed formalin paraffin-embedded samples and corresponding clinical data were retrieved from 100 patients diagnosed with CRC between 2018 and 2020. DNA extraction was performed on the samples, and subsequent analysis utilized the N_lynch panel, real-time PCR, and HRM analysis. MSI status was determined based on the presence of two positive markers.

Results

As much as 12.4% of our subjects were MSI-H and 34% of the subjects were early onset cases. There is a significant difference of tumor location between MSI-H and MSS, in which larger percentage of MSI-H tumor was right-sided (33.3%) than left-sided (9.7%). No significant difference was found in terms of gender, age, onset, stage, and performance status. No significant difference between gender, tumor location, stage, MSI status, and performance status between early onset and late onset group.

Conclusion

There is a high rate of early onset CRC in Indonesia that is not caused by MSI but rather, possibly, by an undiscovered factor. Further study is needed to explore novel pathway that could explain this phenomenon.

Keywords

Colorectal cancer, early-onset, microsatellite instability, molecular profile, clinical implications.

Introduction

Colorectal cancer (CRC) is consistently among the top leading case of cancer in terms of incidence worldwide, ranking 4th in male and 2nd in female.1 Rising incidence of CRC possess significant burden of disease with projected increase of cases up to 3,154,674 cases by 2040.2 Although previously considered rare in Asian countries, it has been observed that there are an increased incidence of CRC cases in Asian populations, possibly due to exposure to risk factors such as western diet, smoking, lack of physical activity, and aging population.3 In Indonesia, number of CRC case has reached 12.4 cases per 100,000 individuals.1

Another alarming observation is rising number of early-onset CRC (EOCRC). One study based on CRC registry in USA reported annual increase of age-adjusted incidence rate of EOCRC by 1.3% in 1996 to 2016.3 Similar findings are also reported in Asia-Pacific region with increasing mortality rate especially in Southeast Asia.4 In Indonesia, previous study found annual percentage change of EOCRC reaching 1.98% from 2009 to 2019.5 Although the exact pathomechanism leading to EOCRC is not well understood, complex interplay between genetic predisposition and environmental factors is believed to play a big role.6

Many studies have explored the incidence of EOCRC and several reported its association with Microsatellite Instability (MSI).7,8 MSI, which is responsible for 20% of CRC cases, happens when there is a mutation in mismatch repair (MMR) genes.9 MSI has gained attention due to its implication in diagnosis and treatment of CRC. Guidelines recommend MSI testing in newly-diagnosed CRC to determine possibility of the case being hereditary and to determine prognosis.10,11 In addition, MSI testing also provides options for CRC treatment as Microsatellite Instability High (MSI-H) patients are candidate for treatment using Programmed Death-Ligand 1 (PDL-1) inhibitor therapy.12 MSI-H CRC tumors have distinct properties compared to Microsatellite Stable (MSS) counterpart, such as MSI-H mostly associated with right-sided tumor,13 mostly found in earlier stages,14 and have better prognosis.15 There are many ways to conduct MSI testing including immunochemistry, single-molecule molecular inversion probes, next generation sequencing, and fluorescent multiplex polymerase chain reaction and capillary electrophoresis.12

The cause of EOCRC rise and possible role of MSI in its patomechanism in Indonesia setting is still not well understood. In addition, there are not any recommendation for CRC MSI testing in Indonesia due to limited data of its significance. To author’s knowledge, there are currently only one study that provides insight of CRC MSI status in Indonesia but the data is limited to a single center.16 As Indonesia is a multiethnic and diverse country, more data of CRC MSI status from another center is needed to justify MSI testing in CRC diagnosis. This study aims to explore CRC MSI status in Indonesian patients to better understand role of MSI in EOCRC rise and role of MSI in CRC screening.

Methods

Ethical clearance

This study obtained approval from the Ethical Committee of the Faculty of Medicine, Universitas Indonesia, on June 23, 2022 (Protocol ID: KET-766/UN2.F1/ETIK/PPM.00.02/2022).

Patients and data collection

Patient data was collected from the medical archive of Ciptomangunkusumo Hospital, including sociodemographic information (age and sex), as well as pathology details such as tumor locations, histological grade, and TNM status. Patient data were collected from the medical archive of Ciptomangunkusumo Hospital between June 23, 2022, and included sociodemographic information (age and sex), as well as pathology details such as tumor locations, histological grade, and TNM status. Ethical approval for the study was obtained from the Ciptomangunkusumo Hospital ethics committee, and informed consent was provided by all participants prior to data collection.

DNA Extraction from Fixed Formalin Paraffin-Embedded (FFPE) samples

FFPE samples were obtained from the archive of the Department of Anatomical Pathology, Cipto Mangunkusumo Hospital, Jakarta. The samples were sliced into 1-2 slices with a thickness of 4-5 μm and placed into 1.5 ml centrifuge tubes. Genomic DNA extraction was performed using the QIAamp DNA FFPE tissue kit (Qiagen, USA) according to the manufacturer's protocol. The extracted DNA was quantified using a NanoDrop™ spectrophotometer (Thermo Scientific, Waltham, MA, USA).

MSI analysis using BioColoMelt-Dx panel MSI

Analysis was conducted using the BioColoMelt-Dx panel as previously described.16 Samples with adequate concentration and quality were adjusted to a concentration of 20 ng/μL for PCR application. The panel involved the detection of five mononucleotide microsatellite repeats, with separate reactions prepared for each marker. Each reaction consisted of nuclease-free water, PCR master mix, Evagreen dye, primers, and DNA template. The analysis was performed using a CFX-Connect real-time PCR instrument (Bio-Rad, Hercules, CA, USA) under specific temperature conditions. Melting analysis was subsequently conducted, and the data were analyzed using Precision Melt Analysis software (Bio-Rad, Hercules, CA, USA). MSI status was determined based on the presence of instability in at least two markers (≥40%).

HRM analysis

High-resolution melting analysis was performed by gradually increasing the temperature from 60 °C to 95 °C. The melting data were analyzed using Precision Melt AnalysisTM software (Bio-Rad, Hercules, CA, USA). MSI analysis classified samples as MSI if ≥2 markers (40%) showed instability, while samples without instability were classified as MSS tumors. Samples exhibiting MSI, BRAF mutation, and MLH1 promoter methylation were categorized as “Probable Lynch”.16 High-resolution melting analysis was conducted by gradually increasing the temperature from 60 °C to 95 °C, and the resulting data were analyzed using Precision Melt Analysis software (Bio-Rad, Hercules, CA, USA). Samples were classified as MSI if instability was observed in ≥2 markers (40%), while those without instability were categorized as MSS tumors. Samples showing MSI, a BRAF mutation, and MLH1 promoter methylation were identified as “Probable Lynch.”16

Results

Among 100 subjects with Colorectal Cancer (CRC) included in this study, 12 of them (12.4%) had Microsatellite Instability High (MSI-H) while the rest was found to be Microsatellite Stable (MSS). Among the samples, 34 (34%) of our CRC cases were early onset. Our study found a significant difference for location of tumor between MSI-H and MSS in which larger percentage of MSI-H tumor was right-sided (33.3%) than left-sided (9.7%). On the other hand, no significant difference was found in terms of gender and performance status between MSI-H and MSS. In our study, a decrease of MSI-H prevalence was found as the CRC stage increases (33.3%, 41.7% and 25.0% for stage II, III, and IV respectively) although the difference did not reach statistical significance.

Table 1. Subject characteristics.

Characteristics n = 100
Gender
 Male47 (47%)
 Female53 (53%)
Age 54.83 ± 14.70
Onset
 Early-Onset (< 50 years old)34 (34%)
 Late-Onset (≥ 50 years old)66 (66%)
BMI 121.98 (19.03-24.92)
Tumor Location (n = 83)
 Left-Sided 65 (78.3%)
 Right-Sided 18 (21.7%)
Stage (n = 87)
 I2 (2.3%)
 II15 (17.2%)
 III37 (42.5%)
 IV33 (37.9%)
MSI Status (n = 97)
 MSI212 (12.4%)
 MSS385 (87.6%)
PDL-1 4 (n = 93)
 Negative59 (63.4%)
 Positive34 (36.6%)
ECOG 51.00 (1.00-2.00)
Karnofsky Index 70.0 (60.0-100.0)

1 BMI: Body Mass Index.

2 MSI: Microsatellite Stable.

3 MSS: Microsatellite Stable.

4 PDL-1: Programmed Death Ligand -1.

5 ECOG: Eastern Cooperative Oncology Group.

Table 2. Subject characteristics based on onset of CRC.

CharacteristicsOnset p Value
Early Onset (< 50 years old, n = 34) Late Onset (≥ 50 years old, n = 66)
Gender
 Male17 (36.2%)30 (63.8%)0.68
 Female17 (32.1%)36 (67.9%)
BMI 1 (n = 87) 22.1 (18.0-26.6)22.6 (19.4-28.9)0.56
Tumor Location (n = 80)
 Left-Sided 21 (32.3%)44 (67.7%)1.00
 Right-Sided 6 (33.3%)12 (66.7%)
Stage (n = 87)
 I0 (0%)2 (3.4%)
 II5 (17.2%)10 (17.2%)
 III13 (44.8%)24 (41.4%)
 IV11 (37.9%)22 (37.9%)
MSI Status (n = 97)
 MSI27 (58.3%)5 (41.7%)0.10
 MSS326 (30.6%)59 (69.4%)
PDL-1 4 (n = 90)
 Negative21 (35.6%)38 (64.4%)0.82
 Positive11 (24.4%)23 (75.6%)
ECOG 5 Performance Status Scale (n = 80) 1.00 (1.00-2.00)0 (0.50-2.00)0.81
Karnofsky Index (n = 80) 80.0 (60.0-90.0)90.0 (60.0-100.0)1.00

1 BMI: Body Mass Index.

2 MSI: Microsatellite Stable.

3 MSS: Microsatellite Stable.

4 PDL-1: Programmed Death Ligand -1.

5 ECOG: Eastern Cooperative Oncology Group.

Table 3. Subject characteristics based on MSI status.

CharacteristicsMSI status p Value
MSI-H (n = 12) MSS (n = 85)
Tumor Location (n = 80)
 Left-Sided 6 (9.68%)56 (90.32%)0.023
 Right-Sided 6 (33.3%)12 (66.7%)
Stage (n = 87)
 I0 (0%)2 (100%)
 II4 (26.7%)11 (73.3%)
 III5 (14.29%)30 (85.71%)
 IV3 (9.09%)30 (90.1%)
PDL-1 1 (n = 90)
 Negative5 (9.09%)51 (90.1%)0.32
 Positive6 (17.6%)28 (82.4%)

1 PDL-1: Programmed Death Ligand-1.

Discussion

Early onset colorectal cancer has attracted attention of researchers and clinicians alike. Previous study found that as much as 41.4% of colorectal cancer cases in Indonesia are early onset.17 This result is in line with our study, in which we found that 34% of our subjects are categorized as early onset. This phenomenon begs the question on what causes early colorectal cancer cases in Indonesia and whether there are any therapies that can be done specifically to early CRC.

As the colon is a natural habitat for bacterial communities and contains around 100 trillion organisms, dysfunction of the microbiome may foster chronic inflammation and produce metabolites that are carcinogenic in nature. The high prevalence of early onset colorectal cancer may be attributed to the high prevalence of infectious diseases that occur in Indonesia.18

According to Dermawan et al. Typhoid fever is the 5th most prevalent disease in Indonesia in during 2020. There are emerging evidence that discuss the pathogenesis of colorectal cancer due to salmonella infection.19 Tumorigenesis is a multistep process that includes sustaining proliferative signaling, evasion of growth suppressors, resistance to apoptosis, replicative immortality, induction of angiogenesis and activation of invasion and metastasis.18

Microbes have been found to contribute to the development of tumors and may alter the microenvironment to be favorable for tumor growth. Salmonella infections may have varying outcomes which ranges from mild acute gastroenteritis to severe infections that are potentially fatal. Salmonella infections may also progress from acute to a chronic carrier state. Prolonged inflammation causes normal cells to develop dysplasia that could progress to cancer. A paper published by Jun Sun in 2022 found a significant increase in colorectal tumor incidence in mice inoculated with Salmonella in comparison to mice without bacterial infection.18

MSI has gained popularity as a marker to be evaluated after diagnosis of CRC.20 MSI-H tumors are known to have better prognosis at early stage21 and are target of PDL-1 inhibitor therapy.22 We have found several differences between our study and previous study that had been conducted in Indonesia. In our study, we found 12.4% of our subjects were MSI-H, whereas previous study found 19% of their subjects were MSI-H. In addition, in our study we found 21.2% of early onset subjects were MSI-H, whereas previous study reported as much as 30% of their early onset group were MSI-H.16 One of possible causes of this differences is the diversity of genetic profiles of the subjects.22 Cipto Mangunkusumo National General Hospital, where this study was conducted, is the national referral hospital of Indonesia and therefore its patients come from different regions with diverse ethnicity.

In this study, no significant differences were found in CRC stage, tumor location, gender, BMI, and MSI status between early and late onset colorectal cancer subjects. Previous studies have found MSI-H are mostly found in early onset colorectal cancer.8,23 Contrary to previous findings, we found that MSS dominate early colorectal cancer when compared to MSI. Indeed, our subjects were mostly at late stages which could explain the dominance of MSS due to shifting of nature of colorectal cancer from MSI to sporadic. In addition, there is a possibility of unique pathway of carcinogenesis, as stated in previous study by Susanti et al called “accelerated carcinogenesis” which may be investigated further in future studies.16

The location of CRC is significant in relation to the MSI status, in which the right side has a larger percentage than the left side (OR 0,21), CI 0,059-0,780). The trend in our study has found CRC in MSI-H patients are predominantly right sided (33.3%) than left-sided (9.7%). This is in line with a review by Gopal et al. in 2023 which described that CRC in MSI-H tends to be right-sided.13 This may be attributed to the distinct gene expression profiles of the right colon, including a higher rate of immune cell infiltration and different patterns of mucin production, which might influence tumor development and immune surveillance. The right colon’s gene expression profile often includes higher levels of genes associated with mismatch repair deficiencies, such as MLH1 and MSH2, which are crucial for maintaining genomic stability. When these genes are mutated or downregulated, it contributes to MSI, leading to a higher frequency of MSI CRCs in the right colon.24

Patients with MSI-H are also known to benefit from PDL-1 inhibitor therapy. MSI-H is associated with accumulation of neoantigens which causes accumulation of PDL-1, resulting in greater expression compared to its MSS counterpart.21 In our early onset subjects, most PDL-1 test showed negative result. This phenomenon may be due to our population that is dominated by late-stage CRC and therefore most likely dominated by sporadic CRC. However, when comparing between our MSI-H and MSS group, we found PDL-1 positive were mostly found in MSI group. This warrant clinicians to conduct PDL-1 examination in MSI-H patients that may benefit from PDL-1 inhibitor. This approach should be done for both early and late onset colorectal cancer. Despite our study having several limitations including limited number of subjects, markers examined, and lack of lymphocyte workups, our study has confirmed result of previous study which is the high number of early colorectal cancer cases with MSI-H in Indonesia. As most of the cases are MSS, further study should be considered to explore its multiomic aspects in order to find possible novel carcinogenesis pathways. Other key point that should be noted is that most of CRC cases found at our center were late stages due to delay in diagnosis, highlighting importance of early detection in Indonesia. In addition, lower age limit of detection should be considered for CRC screening in Indonesia due to high number of early onset CRC cases, as reflected on the result of this study. Because Indonesia still has limited data on CRC profile, we figure genetic workups as screening approach of CRC is still not viable to be conducted in Indonesia.

Ethical clearance

This study obtained approval from the Ethical Committee of the Faculty of Medicine, Universitas Indonesia (Protocol ID: KET-766/UN2.F1/ETIK/PPM.00.02/2022).

Data for microsatellite instability

Harvard Dataverse: Data for Microsatellite Instability, https://doi.org/10.7910/DVN/ONXE2E.25

Data are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).

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Abdullah M, Nursyirwan S, Rahadiani N et al. Microsatellite instability and early onset colorectal cancer in an emerging economy: A study in an Indonesian tertiary hospital.
[version 1; peer review: 3 approved with reservations]. F1000Research 2025, 14:273 (https://doi.org/10.12688/f1000research.155384.1)
NOTE: If applicable, it is important to ensure the information in square brackets after the title is included in all citations of this article.
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ApprovedThe paper is scientifically sound in its current form and only minor, if any, improvements are suggested
Approved with reservations A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.
Not approvedFundamental flaws in the paper seriously undermine the findings and conclusions
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Reviewer Report 12 Aug 2025
Reno Rudiman, Department of Surgery, School of Medicine, Universitas Padjadjaran, Bandung, Indonesia 
Approved with Reservations
VIEWS 1
The study tried to explore MSI status in Indonesian CRC patients, it is deemed relevant to the high incidence of CRC in the country population. 
The methods for data collection and laboratory analyses were clearly written, however there is ... Continue reading
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CITE
HOW TO CITE THIS REPORT
Rudiman R. Reviewer Report For: Microsatellite instability and early onset colorectal cancer in an emerging economy: A study in an Indonesian tertiary hospital.
[version 1; peer review: 3 approved with reservations]
. F1000Research 2025, 14:273 (https://doi.org/10.5256/f1000research.170557.r375999)
NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article.
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1
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Reviewer Report 03 Jul 2025
Nurul Syakima Ab Mutalib, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia 
Approved with Reservations
VIEWS 1
This research investigates the role of microsatellite instability (MSI) in early-onset colorectal cancer (EOCRC) within a cohort from a national referral hospital in Indonesia. The study analyzes 100 formalin-fixed paraffin-embedded (FFPE) colorectal cancer tissue samples collected between 2018 and ... Continue reading
CITE
CITE
HOW TO CITE THIS REPORT
Mutalib NSA. Reviewer Report For: Microsatellite instability and early onset colorectal cancer in an emerging economy: A study in an Indonesian tertiary hospital.
[version 1; peer review: 3 approved with reservations]
. F1000Research 2025, 14:273 (https://doi.org/10.5256/f1000research.170557.r393850)
NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article.
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Reviewer Report 14 Jun 2025
Hery Djagat Purnomo, Division of Gastroentero-Hepatology, Department of Internal Medicine, Dr Kariadi General Hospital, Medical Faculty, Diponegoro University, Semarang, Central Java, Indonesia 
Approved with Reservations
VIEWS 2
The introduction provides a strong background, citing up-to-date and relevant literature. The rationale for the study is clearly described, and the objectives are well aligned with the presented findings. The methodology, including patient selection, DNA extraction, MSI testing via BioColoMelt-Dx ... Continue reading
CITE
CITE
HOW TO CITE THIS REPORT
Purnomo HD. Reviewer Report For: Microsatellite instability and early onset colorectal cancer in an emerging economy: A study in an Indonesian tertiary hospital.
[version 1; peer review: 3 approved with reservations]
. F1000Research 2025, 14:273 (https://doi.org/10.5256/f1000research.170557.r375995)
NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article.

Comments on this article Comments (0)

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Alongside their report, reviewers assign a status to the article:
Approved - the paper is scientifically sound in its current form and only minor, if any, improvements are suggested
Approved with reservations - A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.
Not approved - fundamental flaws in the paper seriously undermine the findings and conclusions
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